title: SC_high

city: Wuxi

first: Yanfeng

last: Liu

state: Jiangsu

address: No.1800, Lihu Avenue

institute: Jiangnan University

data_processing:
Cutadapt is applied to find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
PANDASEQ is used to assemble paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases.
Genome_build: NCBI number:  AF330636.1
Supplementary_files_format_and_content: csv files include filtered sequences

molecule: other

source_name: Synthetic construct

extract_protocol:
After FACS-sorting and overnight regrowth in the same media used for growth, sorted fractions were miniprepped. PCR was used to verify that at least 10 plasmids were extracted per sorted cell; minipreps were PCR-amplified, further amplified with the addition of bin-specific barcodes, pooled, and amplified briefly again.
For each sample, >50ng purified PCR fragment was used for library preparation. These PCR products were treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dAtailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Adaptor-ligated DNA was then performed using DNA Clean Beads. A second PCR reaction was carried out with P5 and P7 primers carrying sequences which can anneal with flowcell to perform bridge PCR and index allowing for multiplexing. The final library product for sequencing were then purified by beads and was qualified.

value: wild type

tag: plasmid type

value: reporter gene with synthetic NCS

tag: expression level

value: high


title: Screening [AML3005.1.GEX]

status: Public on Oct 31 2023

type: SRA

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

library_source: transcriptomic single cell

data_processing:
Demultiplexing of raw reads using cellranger mkfastq
Alignment against GRCh38 and generation of count matrices using cellranger count
Assembly: GRCh38
Supplementary files format and content: count matrix, barcode list and feature list in csv file format

molecule: total RNA

organism: Homo sapiens

source_name: bone marrow

extract_protocol:
Ficoll-based extraction of bone marrow mononuclear cells and cryopreservation in FCS with 10% DMSO until analysis. Thawing in PBS supplemented with 10% FCS and 10% bovine DNase I, grade II. Bead-based dead cell removal with negative-selection strategy (Miltenyi). Resuspension in PBS with 0.04% ultra-pure BSA.
5' biased library construction according to manufacturer's specifications including T cell receptor sequencing and surface marker expression (CG000330, 10x Genomics).

tag: tissue

value: bone marrow

tag: treatment


title: SC_low

country: China

library_source: genomic

organism: Saccharomyces cerevisiae

tag: strain

tag: genotype

value: low


title: EOLN [AML3005.2.GEX]

value: decitabine


title: scATAC-seq from Naïve Lungs

city: Ithaca

first: Davide

last: Pisu

state: NY

address: 930 Campus Road

department: Microbiology and Immunology

institute: Cornell University

description: scATAC-seq nextGEM 1.1

library_source: genomic single cell

data_processing:
We utilized the ArchR software to perform integrative single-cell chromatin accessibility analysis. For the analysis we used the precompiled version of the mm10 genome in ArchR. Quality filtering parameters for data pre-processing included filtering out cells with TSS enrichment scores below 4 and less than 1000 unique fragments. As an additional step for quality control, we performed doublet identification and removal. Doublet scores were added to the Arrow files using the “addDoubletScores()” function with parameters knnMethod = UMAP, k =10 and LSIMethod = 1. Post doublet identification, cells suspected to be doublets were filtered using “filterDoublets()”, reducing the initial nuclei count from 9371 to 8493. Subsequently, dimensionality reduction has been performed using the Iterative Latent Semantic Indexing (LSI) on the insertion count matrix with the “addIterativeLSI()” function in ArchR for 4 iterations. Clustering was performed on the IterativeLSI dimensions using Seurat with a resolution of 0.7. UMAP embeddings were added with the addUMAP() function using parameters nNeighbors = 30, minDist = 0.5 and metric = cosine. The UMAP was plotted and color-coded by clusters.
To identify marker genes for each cluster, gene expression for marker genes was estimated from chromatin accessibility data by using gene scores. A gene score is considered as a prediction of how highly expressed a gene will be based on the accessibility of regulatory elements in the vicinity of the gene67. To create the gene scores, we used distance-weighted accessibility models as defined in ArchR and implemented in the function “addGeneScoreMatrix()”. Marker genes were then identified for each cluster using the Gene Score Matrix with a Wilcoxon test method. The markers for each cluster were filtered using an FDR <= 0.05 and Log2FC >= 0.58. Imputed weights were added using the function “addImputeWeights()” to visualize the marker genes e.g., "Mafb" and “Ly6a” on the UMAP. To visualize the local chromatin accessibility around specific genes on a per cluster basis, the “plotBrowserTrack” function was employed, considering 5,000 base pairs both upstream and downstream of the start of the genes of interest.
Single-cell timepoint RNA-seq data (scRNA-seq) was utilized for integration with ATAC-seq data. Unconstrained integration, a completely agnostic approach that takes all of the cells in the scATAC-seq experiment and attempt to align them to any of the cells in the scRNA-seq experiment, was used. The “addGeneIntegrationMatrix()” function was used to generate a gene integration matrix, which was named "GeneIntegrationMatrix". For visualization, a palette was derived from the scRNA-seq data's cell type categories. An embedding plot was generated using the “plotEmbedding()” function, colored by predicted cell groups to label and visualize the scATAC-seq clusters with the cell types predicted from our scRNA-seq dataset.
For TF analysis, the following steps were performed: 1) A reproducible peak set was determined using the “addReproduciblePeakSet()” function, with MACS2 as the peak caller. The “getMarkerFeatures()” function was employed to identify marker peaks unique to an individual cluster or a small group of clusters in an unsupervised fashion, using the above calculated peak matrix and accounting for biases such as TSS Enrichment and fragment counts. Significant marker peaks were determined with criteria set at FDR <= 0.05 & Log2FC >= 0.58. 2) To assess whether marker peaks or differential peaks were enriched for binding sites of specific transcription factors, we performed motif and feature enrichment analysis. We annotated the ArchR project with motif information using the “addMotifAnnotations()” function, employing the "cisbp" motif set. Analysis of enrichment of motifs within marker peaks was performed with the “peakAnnoEnrichment()” function, using the following criteria FDR <= 0.1 & Log2FC >= 0.5. The enriched transcription factor binding sites (TFBS) for each scATAC-seq cluster were then visualized in a ranked scatter plot.
Assembly: mm10
Supplementary files format and content: tab-delimited text file fragments.tsv.gz includes genomic locations of open chromatin and can be used as an input for the ArchR software
Supplementary files format and content: tab-delimited text file fragments.tsv.gz.tbi is the index for the location of genomic regions in the gragments.tsv.gz. Not needed for downstream analysis with ArchR

molecule: genomic DNA

organism: Mus musculus

source_name: lung

extract_protocol:
For nuclei isolation, sorted cells were centrifuged at 300 rcf for 5 minutes at 4°C and then resuspended in 150uL of PBS supplemented with 0.04% BSA. A 100µL aliquot of this cell suspension was transferred to a 0.2mL flat-cap tube, centrifuged again under the same conditions, and subsequently resuspended in 50uL of Lysis Buffer (containing 10mM Tris-HCL, 10mM NaCl, 3mM MgCl2, 0.1% Tween 20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin, and 1% BSA). This was incubated on ice for 4 minutes. Post-incubation, 50µL of Wash Buffer (comprising 10mM Tris-HCL, 10mM NaCl, 3mM MgCl2, 1% BSA, and 0.1% Tween 20) was added to the lysed cells. The nuclei suspension was then centrifuged at 500 rcf for 5 minutes at 4°C. The nuclei were washed with 45µL of a 1:20 dilution of the Nuclei Buffer (10x Genomics, PN-2000153/2000207) and centrifuged again using the same conditions. Finally, the isolated nuclei were resuspended in a volume of Diluted Nuclei Buffer to obtain a concentration ranging from 3080 to 7700 nuclei/µL. This was used as input for the 10X protocol (CG 000209 Rev D) targeting a recovery of 10,000 nuclei.
The transposition reaction and library construction were performed following the protocol from 10X (CG000209 REV D).
Sequencing was conducted on a NextSeq 500 with the parameters: Read 1N: 50 cycles, i7 index: 8 cycles, i5 index: 16 cycles, and Read 2N: 50 cycles.

value: lung

tag: cell line

value: In vivo Animal

tag: cell type

value: CD45+ cells

value: BL/6 mice

tag: timepoint

value: Naïve


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-C1

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: Mmul_10 (rheMac10), annotation: Ensembl release 104
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

organism: Macaca mulatta

extract_protocol:
Motor cortex of brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

treatment_protocol: For all snm3C-seq samples, in-situ 3C treatment was done during the nuclei preparation that allows capturing the chromatin conformation modality as described previously22. These steps were carried out using the Arima-3C BETA Kit (Arima Genomics). The nuclei were isolated and sorted into 384-well plates using previous methods21. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.

tag: brain region

value: Motor cortex

tag: gender

value: M


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-B2


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-C14


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-C2


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-C13


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-B14


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-D13


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-D1


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-B13


title: 24-month-old C57Bl/6 mouse 2

city: Jupiter

first: Christopher

middle: Lee

last: Haga

state: Florida

address: 130 Scripps Way, BldgA261A

department: Molecular Medicine

institute: UF Scripps Biomedical Research

library_source: transcriptomic

data_processing:
FASTQ files were quality checked with FASTQGroomer
CutAdapt was used to remove adapter sequences and short reads
Reads were mapped with HISAT2
Counts were calculated with featureCounts
Differential expression was carried out with the edgeR R package
Assembly: NCBI Build 37 mm9
Supplementary files format and content: csv file, raw counts from featureCounts

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
Whole bone marrow was isolated from C57Bl/6 mice.  Total RNA was extracted from 3-4 mice per group by Zymo RNA miniprep.
Poly-A mRNA was isolated by NEBNext poly(A) magnetic beads.  Library preparation was completed by the NEBNext Ulta II Directional RNA kit.

value: Bone marrow

tag: age

value: WT


title: Aorta, ATGL ECKO, scRNAseq

city: New Haven

first: Carlos

last: Fernandez-Hernando

address: 10 Amistad St

institute: Yale University

description: 10x Genomics

data_processing:
Sample demultiplexing, aligning reads to the mouse mm10 reference genome (University of California, Santa Cruz) with Software Tools for Academics and Researchers (STAR) and unique molecular identifier (UMI) processing were processed using CellRanger software (version 7.1.0, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole aorta

extract_protocol:
Aortic tissues were pre-digested with 1mg/mL Collagenase A (Roche, Cat No. 11088785103) for 7 min at 37 oC to remove the adventitia. Aortic tissues were then minced into 2-mm pieces and digested in DMEM (10% FBS) with 1.5 mg/mL Collagenase A and 0.5 mg/mL Elastase (Worthington, Cat No. LS006365) for 40 min at 37oC while shaking. The digested aortas were passed through a 40-mm filter to obtain single-cell suspensions. Total cell viability was obtained using live/dead viability dye eFluorTM 780 (Thermo Fisher Scientific, Cat No. 65-0865-14). Viable cells were sorted by a FACS Aria III (BD Biosciences) into 0.4% BSA/PBS
Sorted aortic cells were encapsulated into droplets and processed following manufacturer’s specification using 10X Genomics GemCode technology. Equal numbers of cells per sample were loaded on a 10X Genomics Chromium controller instrument to generate single-cell Gel Beads in emulsion (GEM) at the Yale Center for Genome Analysis. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM followed by complementary DNA (cDNA) generation using the Single-Cell 3’ Reagent Kits version 3.1 (10X Genomics). Libraries were sequenced on an Illumina Hiseq 4000 as 2 x 100 paired-end reads.

value: whole aorta

value: Vascular cells

value: ATGL ECKO

value: AAV8-PCSK9 + 4 week Western diet


title: naive non-activated ILC2

city: Vancouver

first: Wilf

last: Jefferies

country: Canada

institute: UBC

description:
Chromium Single Cell Controller (PN 110211)
10xGenomics

data_processing:
Preprocessing done by Cell Ranger v3.0.2
Gene expression analysis by Seurat V3
Assembly: GRCm38_90
Supplementary files format and content: tsv and mtx

source_name: Lung derived

extract_protocol:
ILC2s are enriched from lung tissues from mice, enriched with negative selection, followed by FACS with lineage and ILC2 specific markers.
Library construction performed based on manufacters instruction (Chromium Single Cell 3' Reagent Kits User Guide (v3.1)).

treatment_protocol: Activated samples are treated with IL33 and TSLP ex vivo for a week before sending off to sequencing. Non-activated samples are freshly isolated ILC2s.

value: Lung derived

value: innate lymphoid cells type 2

value: naive, non-activated


title: wk2 ta-activated ILC2

tag: time point

value: tumour carrying, activated


title: liver_CLP-2

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
reads were quality checked with fastqc and preprocessed in order to remove adapters with trimmomatic (v0.39)
reads were aligned to the mm10 reference genome with the BWA aligner (bwa mem) and read pairs that were not properly paired or mapping to the mitochondrial genome were excluded
ATAC-seq regions/peaks were called with genrich (0.6.1) operating it ATAC-seq mode (-j) and with the option to remove PCR duplicates set (-r)
in addition, bigwig coverage files were generated using python deeptools
Assembly: mm10
Supplementary files format and content: narrowPeak
Supplementary files format and content: bigwig

source_name: liver

extract_protocol:
nuclei were extracted from the liver tissues (Demonstrated Protocol-Nuclei Isolation from Mouse Brain Tissue for Single Cell ATAC Sequencing) and 100k nuclei were mixed with 2x reaction buffer and Tn5 Transposase in a total volume of 50 µL, and incubated for 30-45 min at 37°C. Transposed DNA was purified in 11 µL elution buffer according to the manufacturer’s protocol by using the Monarch PCR&DNA Cleanup kit (Biolabs)
Transposed DNA was purified in 11 µL elution buffer according to the manufacturer’s protocol by using the Monarch PCR&DNA Cleanup kit (Biolabs). Afterwards, transposed DNA was amplified according to published protocol and PCR primers95. Next, PCR-amplified DNA fragments between 150bp and 800bp were selected from the library by using SPRIselect beads (Beckman coulter) according to manufacturer’s instructions. The library quality was checked with the 2100 Bioanalyzer (Agilent) using the high sensitivity DNA kit (Agilent)

treatment_protocol: mice were subjected to SHAM or CLP surgery and livers are isolated 8h after the procedure and snap frozen in liquid nitrogen

value: liver

value: CLP


title: liver_SHAM-2

value: Sham


title: liver_CLP-3


title: liver_CLP-4


title: liver_SHAM-1


title: wk3 ta-non-activated ILC2

value: tumour carrying, non-activated


title: liver_SHAM-4


title: liver_CLP-1


title: liver_SHAM-3


title: Aorta, Control, scRNAseq

description: 10x Genomics

value: Control


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-A2

value: Motor cortex


title: 3-month-old C57Bl/6 mouse 2


title: 3-month-old C57Bl/6 mouse 1


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-B1

value: M


title: C2 [AML3003.3.GEX]

value: bone marrow

value: decitabine and ipilimumab


title: C4 [AML3001.4.GEX]


title: Screening [AML3003.1.GEX]


title: EOLN [AML3003.2.GEX]

value: decitabine


title: C7 [AML3003.4.GEX]


title: wk3 ta-activated ILC2

value: WT


title: wk2 ta-non-activated ILC2


title: EOLN [AML3001.2.GEX]


title: Screening [AML3001.1.GEX]


title: 24-month-old C57Bl/6 mouse 1

value: Bone marrow


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-A1


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-A14


title: M1_R2 (Multiome Gene Expression)

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: UCSD

description:
M1_R2_barcodes.tsv.gz
M1_R2_features.tsv.gz
M1_R2_matrix.mtx.gz

data_processing:
Raw sequencing was processed using cellranger-arc (10x Genomics), generating snRNA-seq UMI count matrices for intronic and exonic reads mapping in the sense direction of a gene.
Cells were filtered for low quality nuclei by requiring ≥1000 ATAC fragments and ≥500 genes detected per nuclei.
Genes were annotated with hg38 Gencode v33 for human, mm10 Gencode vM22 for mouse, ensembl release 104 (and Refseq GCF_003339765.1 for 10x multiome) for macaque, and GCA_009663435.2 for marmoset. To maximize the number of orthologous protein-coding quantified in macaque 10x multiome RNA data, we supplemented any missing protein coding genes in GCF_003339765.1 gtf with annotations present in Ensembl release 104.
Assembly: hg38 GRCh38
Assembly: mm10 GRCm38
Assembly: Mmul_10 (rheMac10)
Assembly: cj1700_1.1 (calJac4)
Supplementary files format and content: "barcode.tsv.gz" contains cell barcode information. "features.tsv.gz" consists of rows containing features (genes and peaks) and columns containing cell-associated barcodes. "matrix.mtx.gz" contains sparse feature-barcode matrix.   Files provided in tar archives.

source_name: primary motor cortex

extract_protocol:
[nuclei preparation protocol]  Brain tissue was pulverized using a mortar and pestle on dry ice and pre-chilled with liquid nitrogen. Pulverized brain tissue was resuspended in 1mL of chilled NIM-DP-L buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1X Protease Inhibitor (Pierce), 1U/μL Recombinant RNase inhibitor (Promega, PAN2515), and 0.1% Triton X-100). Tissue was Dounce homogenized with a loose pestle (5-10 strokes) followed by a tight pestle (15-25 strokes) or until solution was uniform. Nuclei were filtered using a 30μm CellTrics filter (Sysmex, 04-0042-2316) into a LoBind tube (Eppendorf, 22431021) and pelleted (1000 rcf, 10 min at 4˚C) (Eppendorf, 5920 R). Pellet was resuspended in 1 mL NIM-DP buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1x Protease Inhibitor, 1U/μL Recombinant RNase inhibitor) and pelleted (1000 rcf, 10 min at 4˚C). Pelleted nuclei were resuspended in 400uL 2μM 7-AAD (Invitrogen, A1310) in Sort Buffer (1mM EDTA, 1U/μL Recombinant RNase inhibitor, 1X Protease Inhibitor, 1% fatty acid-free BSA in PBS).
120,000 nuclei were sorted (Sony, SH800S) into a LoBind tube containing Collection Buffer (5U/uL Recombinant RNase inhibitor, 1X Protease Inhibitor, 5% fatty acid-free BSA in PBS). 5X Permeabilization Buffer (50mM Tris-HCl pH 7.4, 50mM NaCl, 15mM MgCl2, 0.05% Tween-20, 0.05% IGEPAL, 0.005% Digitonin, 5% fatty acid-free BSA in PBS, 5mM DTT, 1U/μL Recombinant RNase inhibitor, 5X Protease Inhibitor) was added for a final concentration of 1X. Nuclei were incubated on ice for 1 minute, then centrifuged (500 rcf, 5min at 4C). Supernatant was discarded and 650uL of Wash Buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1%.Tween-20, 1% fatty acid-free BSA in PBS, 1mM DTT, 1U/μL Recombinant RNase inhibitor, 1X Protease Inhibitor) was added without disturbing the pellet followed by centrifuging (500 rcf, 5 min at 4˚C). Supernatant was removed, and the pellet was resuspended in 7uL of 1X Nuclei Buffer (Nuclei Buffer (10x Genomics), 1mM DTT, 1 U/μL Recombinant RNase inhibitor). 1 μL of nuclei was diluted in 1X Nuclei Buffer, stained with Trypan Blue (Invitrogen, T10282) and counted. 16-20k nuclei were used for tagmentation reaction and controller loading and libraries were generated following manufacturer’s recommended protocol (https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression).
10x multiome ATAC-seq and RNA-seq libraries were paired-end sequenced on NextSeq 500 and NovaSeq 6000 to a depth of ~50,000 reads per cell for each modality.

value: primary motor cortex

tag: species

value: Macaque

tag: donor id

tag: Sex

tag: library type

value: 10x Genomics Multiome Gene Expression


title: M1_R2 (Multiome ATAC)

value: 10x Genomics Multiome ATAC


title: M1_Mac3 (Multiome Gene Expression)

description:
M1_mac3_barcodes.tsv.gz
M1_mac3_features.tsv.gz
M1_mac3_matrix.mtx.gz


title: M1_Mac3 (Multiome ATAC)


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-A13


title: M1_Dheni_neun (Multiome Gene Expression)

description:
NeuN+ sorted nuclei
M1_Dheni_neun_barcodes.tsv.gz
M1_Dheni_neun_features.tsv.gz
M1_Dheni_neun_matrix.mtx.gz


title: MC12

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
We used Salmon to quantify transcript-level expression and EdgeR to identify genes with significant differential expression between pairs of conditions based on replicated count data from bulk RNA-seq profiling. The normalized data were applied to R package GAGE for gene-set enrichment and pathway analysis. The p-values were corrected for multiple testing using FDR.
Assembly: mm8
Supplementary files format and content: FPKM normalized counts for each sample

source_name: pancreas tumor

growth_protocol: cell lines grown to 90% confluence

extract_protocol:
RNA was extracted using RNEasy kit from Qiagen.
poly A selection and library construction was completed at Azenta (Genewiz)

treatment_protocol: no treatment

value: pancreas tumor

value: Ink4a liver metastasis #36

value: FVB


title: MC10

value: Ink4a liver metastasis #35


title: MC7

value: Ink4a primary tumor #25


title: MC14

value: Ink4a liver metastasis #38


title: MC16

value: Ink4a liver metastasis #72


title: MC11

value: Ink4a primary tumor #36


title: MC13

value: Ink4a primary tumor #38


title: MC9

value: Ink4a primary tumor #35


title: EOLN [AML1008.2.GEX]

value: bone marrow

value: decitabine


title: C4 [AML1008.4.GEX]

value: decitabine and ipilimumab


title: EOLN [AML1002.2.GEX]


title: MC15

value: Ink4a primary tumor #72


title: Screening [AML1008.1.GEX]


title: C4 [AML1002.4.GEX]


title: EOT [AML1008.5.GEX]

value: end of treatment


title: C1 [AML1008.3.GEX]


title: KD-3

city: Shanghai

first: Chenbo

last: Ding

state: None Selected

address: 280 Chongqing South Rd

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Visualizations using volcano-plots and heatmaps were produced with R. Gene Ontology
Enrichment analysis of biological process was performed by Reactome signaling pathway analysis based on differentially expressed genes
The statistical analysis and data visualization were achieved by R (3.6.0)
Assembly: mm10
Supplementary files format and content: Table-delimited text file includes raw counts for each sample
Supplementary files format and content: Table-delimited text file includes RPKM vaules for each sample

source_name: Organoid

extract_protocol:
Total RNAs were isolated by RNeasy Micro Kit (QIAGEN, cat. 74034) following the manufacturer’s protocol
mRNA for RNA-seq analysis was purified using polyA+ selection
RNA-seq libraries were constructed by Yale Center for Genome Analysis (YCGA) using SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian (Clontech)

value: Organoid

value: Primary cell

value: Intestinal epithelial cells

value: KO

value: Dox


title: Screening [AML1002.1.GEX]


title: EOT [AML1026.4.GEX]


title: MC8

value: pancreas tumor

value: Ink4a liver metastasis #25

value: FVB


title: M1_Dheni_neun (Multiome ATAC)

value: primary motor cortex

value: Macaque

value: M

value: 10x Genomics Multiome ATAC


title: HPC-2 16wk rep #2

city: Lund

first: Maroulio

last: Pertesi

address: Sölvegatan 19

country: Sweden

institute: Lund University

data_processing:
Low quality bases and Illumina adapters were trimmed using Trimmomatic (v0.36)
Trimmed reads were aligned to the mouse reference genome (GRCm38/mm10) using HISAT2 (v2.0.5)
Duplicated reads were marked and filtered out using Picard MarkDuplicates tool (v8.25) (http://broadinstitute.github.io/picard/)
Fragments aligned to the mouse genes (Ensembl GRCm38.91) were quantified using the featureCounts tool
Assembly: mouse reference genome (GRCm38/mm10)
Supplementary files format and content: tab-delimited text file contains raw counts for each sample (as a matrix table)

growth_protocol: mice were housed in ventilated racks with free access to autoclaved food and water

extract_protocol:
Spine, femurs, tibia, and iliac bones were crushed in PBS+2% FBS. Bone marrow was enriched for cKit, followed by FACS sort of live LSK SLAM (CD3e-, B220-, GR-1-, CD11b-, TER119-, cKIT+, SCA-1+, CD48-, CD150+) HSCs into sterile PBS+RNAse inhibitor and snap freezed at -80 degrees.
cDNA syntesis and amplification were done using SMART-Seq v4 (Takara), followed by library preparation using Nextera XT DNA library prep kit (Illumina).

treatment_protocol: cells isolated from mice transplanted with 8000 LSK (CD3e-, B220-, GR-1-, CD11b-, TER119-, cKIT+, SCA-1+) 3, 4, 5, 6, 8, 10, 13, 16 weeks earlier into lethally irradiated (900cGy) recipients

tag: developmental stage

value: Mouse age 8-12 weeks


title: HPC-2 10wk rep #2

value: cells isolated from mice transplanted with 8000 LSK (CD3e-, B220-, GR-1-, CD11b-, TER119-, cKIT+, SCA-1+) 3, 4, 5, 6, 8, 10, 13, 16 weeks earlier into lethally irradiated (900cGy) recipients


title: HPC-2 10wk rep #3


title: HPC-2 13wk rep #2


title: HPC-2 16wk rep #3


title: HPC-2 10wk rep #1


title: HPC-2 13wk rep #1


title: EOLN [AML1026.2.GEX]

value: bone marrow

value: decitabine


title: C1 [AML1026.3.GEX]

value: decitabine and ipilimumab


title: M1_Dheni (Multiome ATAC)

description:
M1_Dheni_barcodes.tsv.gz
M1_Dheni_features.tsv.gz
M1_Dheni_matrix.mtx.gz


title: HPC-2 13wk rep #3


title: HPC-2 16wk rep #1


title: HPC-2 8wk rep #3


title: Screening [AML1026.1.GEX]


title: H3i, YPGal, RNA-seq biol rep2

city: Pathumthani

first: Peerapat

last: Khamwachirapithak

address: Phahonyothin Road, Khlong Luang

country: Thailand

institute: Thammasat University

data_processing:
FastQC
Reads were align to Saccer3 genome using the Hisat2
Sorting and indexing using Samtools
Duplication was removed by Picard tools
Raw read counts were normalized by DEseq2
Assembly: Saccer3
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Cell pellet

growth_protocol: Cells were cultured in YPGal medium at 30°C and 230 rpm before H3-shutoff experiment. The H3 inducible shut-off strain (i.e., “DGS200.1” or  “H3i”) from the YEF473A strain by knocking out the HHT1 gene (encoding H3), and replacing the native promoter of the HHT2 gene (the other H3-encoding gene) with an inducible Gal1 promoter.

extract_protocol:
RNA was extracted by MagMax96 total RNA isolation kit (AM1830, Invitrogen) for the first and second replicates. Trizol reagent (15596026, Invitrogen) was used in extraction with glass beads for the third replicate.
Librarires of the first and second replicates were prepared using the Illumina TruSeq Stranded mRNA Library Prep. For the third replicate, the TruSeq Stranded mRNA LT sample prep kit was used for library construction.

treatment_protocol: Switching media from YPGal to YPD

value: Cell pellet

value: Yeast cell

value: YPGal


title: M1_Dheni (Multiome Gene Expression)

value: 10x Genomics Multiome Gene Expression


title: KC-2

value: Organoid

value: Primary cell

value: Intestinal epithelial cells

value: KO

value: DMSO


title: KD-1

value: Dox


title: KC-3


title: H3i, YPD, RNA-seq biol rep2

value: YPD


title: KD-2


title: WT, YPD, RNA-seq biol rep2

value: WT


title: KC-1


title: WT, YPGal, RNA-seq biol rep2


title: WD-2


title: sma3e491_CeMbio_3

city: Berkeley

first: Michael

last: Shapira

state: California

address: Valley Life Sciences Building

department: Integrative Biology

institute: University of California, Berkeley

data_processing:
FASTQ files were checked for their quality and preprocessed (e.g. adapter trimming, filtering) using fastp (Chen et al. 2018; https://doi.org/10.1093/bioinformatics/bty560).
Kallisto (version 0.46.1) was applied for transcript quantification (Bray et al. 2016; https://doi.org/10.1038/nbt.3519).
Genome_build: Caenorhabditis_elegans.WBcel235.cdna.all.fa.gz
Supplementary_files_format_and_content: Kallisto output as .tsv file per sample with transcript (target_id), length, effective length (eff_length), estimated counts (est_counts), and transcripts per million (tpm)

organism: Caenorhabditis elegans

source_name: whole population

growth_protocol: Worm strains (dbl-1(nk3), sma-3(e491), ctIs40 [dbl-1(+) + sur-5::GFP], and N2) were synchronized by bleaching and grown  from L1 larval stage to gravid adults (24 h post L4) at 25 °C on either CeMbio or OP50 plates.

extract_protocol:
Gravid adults were rinsed off the plates with M9 + 0.025% Triton, washed 5x to get rid of offspring, mixed with TRIzol reagent (Invitrogen), and snap-frozen in liquid nitrogen. After breaking open the worms by 5-7 thaw-freeze cycles total RNA was isolated using the NucleoSpin miRNA extraction kit, protocol 5.2 (Macherey-Nagel).
RNA sequencing libraries were prepared from total RNA according to standard Illumina protocols using the TruSeq RNA Library Kit v2, with indexed adaptors for multiplex sequencing, and submitted for 100 bp paired-end sequencing on a NovaSeq 6000.

treatment_protocol: NGM plates were seed with either 10x OP50 or 10x CeMbio. For the OP50 plates, a culture of OP50 in LB was grown at 37 °C over night, concentrated 10x in its own supernatant, and 200 µl was used for inoculation. For the CeMbio plates, every bacterial strain was grown individually in LB at 28 °C for 2 nights, adjusted to the lowest OD in their own supernatant, mixed in equal volumes, concentrated 10x, and 200 µl was used for inoculation. Plates were prepared freshly only few days before adding the worms, incubated for one over night at room temperature after inoculation, and stored at 4 °C until used.

tag: worm strain

value: 1 d adults (24 h post L4)

tag: bacterial treatment

value: CeMbio

tag: biological replicate


title: WD-1

tag: tissue

tag: treatment


title: WC-1

tag: cell line

tag: genotype


title: dbl1oex_CeMbio_3


title: RNA trunk Noto E9.5

city: Berlin

first: Frederic

last: Koch

address: Ihnestraße 63-73

department: Developmental Genetics

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: R2 fastq files contain the UMIs of the Ovation SoLo RNA-Seq kit used

data_processing:
Prior to mapping, the first 5 nucleotides of the forward and reverse reads were trimmed using fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/index.html) according to manufacturer’s instructions (NuGEN). The resulting reads were mapped to chromosomes 1-19, X, Y and M of the mouse mm10 genome using TopHat2 (v2.1.1) and bowtie (v1.2.2) and the RefSeq annotation in gtf format (UCSC), providing the options ‘--no-coverage-search --no-mixed --no-discordant -g1 --mate-inner-dist 250 --mate-std-dev 100 --library-type fr-secondstrand’. Read duplications resulting from the PCR amplification of the library were removed using the NuDup deduplication script provided by NuGEN (http://nugentechnologies.github.io/nudup/). Wiggle files were generated with BEDTools version 2.23.0, converted to bigwig format and visualized in the Integrated Genome Browser. FPKM values were calculated using Cufflinks (v2.2.1) with options ‘-u --no-effective-length-correction -b’.
Assembly: mm10
Supplementary files format and content: *.bw: tag denisty files of ChIP data in bigWig format
Supplementary files format and content: *.narrowPeak: peak files for ChIP-Seq tracks used in analysis obtained by MACS
Supplementary files format and content: RNA_FPKM.txt: normalized per gene abundance measurements (FPKM) for RNA-Seq samples obtained by Cuffdiff

source_name: FACS sorted T+/Noto+/Foxa2+ from trunk tissues of TS16 embryos obtained by tetraploid complementation assays

growth_protocol: ES cell lines were cultured according to standard conditions. Cells were maintained on gelatinized plates and mitotically inactive primary mouse embryo fibroblasts with standard ESC medium, refreshed daily, containing 15% FCS and 1000 U/ml leukemia inhibitory factor. ES cells were used to generate embryos via the tetraploid complementation assay.

extract_protocol:
Total RNA from approximately 200-20000 cells was isolated using the RNeasy Micro kit (Qiagen) and genomic DNA was digested on column with the addition of an extra 1ul of RNase-free DNase I (Roche) to ensure complete digestion.
Sequencing libraries were prepared using the Ovation SoLo RNA-Seq system (NuGen) according to manufacturer’s recommendations, starting at step A.9 with 12 µl purified DNA. After each amplification step, libraries were quantified with the Qubit the High Sensibility DNA assay (Thermo Fisher 12102). Library size was validated using DNA High Sensitivity Bioanalyzer chips (Agilent 5067-4626).

value: genetically modified F1G4 (C57BL/6N x SV129) mES cells

tag: cell type

value: notochord

value: T::H2B-Venus (BAC), Noto::H2B-mCherry (BAC), Foxa2::H2B-mTurquoise (BAC)

value: In order to obtain single cell suspensions from embryo tissue for FACS sorting, 10ul of 5% BSA in PBS was added to the pooled samples and 100ul of ice-cold 0.05% trypsin was added. A homogenous suspension was achieved by slow pipetting and the reaction was stopped with the addition of 200ul of 5% BSA in PBS. Before cell sorting on a FACS Aria II (Becton Dickinson), the cell suspension was filtered through a 35µm mesh. Cells were sorted directly into Eppendorf tubes containing 350µl RLT buffer (Qiagen) and 3.5ul b-mercaptoethanol.


title: dbl1nk3_CeMbio_3


title: RNA trunk Noto E8.5

source_name: FACS sorted T+/Noto+/Foxa2+ from trunk tissues of TS12 embryos obtained by tetraploid complementation assays


title: HPC-2 5wk rep #3

tag: strain

value: Mouse age 8-12 weeks

value: cells isolated from mice transplanted with 8000 LSK (CD3e-, B220-, GR-1-, CD11b-, TER119-, cKIT+, SCA-1+) 3, 4, 5, 6, 8, 10, 13, 16 weeks earlier into lethally irradiated (900cGy) recipients


title: HPC-2 6wk rep #1


title: HPC-2 6wk rep #3


title: HPC-2 5wk rep #2


title: HPC-2 6wk rep #2


title: HPC-2 8wk rep #1


title: HPC-2 8wk rep #2


title: sma3e491_OP50_3


title: N2_CeMbio_3


title: WC-2


title: RNA NotoP E9.5

source_name: FACS sorted Noto+/T+/Foxa2+ from caudal ends of TS16 embryos obtained by tetraploid complementation assays

value: notochord progenitors


title: RNA NotoP E8.5

source_name: FACS sorted Noto+/T+/Foxa2+ from caudal ends of TS12 embryos obtained by tetraploid complementation assays


title: dbl1oex_OP50_3


title: N2_OP50_3


title: EOLN [AML1022.2.GEX]

value: bone marrow

value: decitabine


title: HPC-2 4wk rep #3


title: HPC-2 4wk rep #1


title: dlb1nk3_OP50_3


title: HPC-2 4wk rep #2


title: HPC-2 5wk rep #1


title: HPC-2 3wk rep #3


title: EOLN [AML1012.2.GEX]


title: dbl1oex_CeMbio_2


title: Screening [AML1022.1.GEX]


title: Screening [AML1012.1.GEX]


title: C2 [AML1012.3.GEX]

value: decitabine and ipilimumab


title: Screening [AML1016.1.GEX]


title: C2 [AML1016.2.GEX]


title: EOT [AML1012.4.GEX]

value: end of treatment


title: HPC-2 3wk rep #2


title: RNA MP E9.5

source_name: FACS sorted T+/Noto-/Foxa2- from caudal ends of TS16 embryos obtained by tetraploid complementation assays

value: mesodermal progenitors


title: RNA MP E8.5

source_name: FACS sorted T+/Noto-/Foxa2- from caudal ends of TS12 embryos obtained by tetraploid complementation assays


title: C10 [AML1010.5.GEX]

source_name: bone marrow


title: C4 [AML1010.4.GEX]


title: HPC-2 3wk rep #1

value: untreated


title: sma3e491_CeMbio_2


title: C1 [AML1010.3.GEX]


title: G2021_115_16

city: Grand Forks

first: Kai

last: Guo

state: ND

address: 1301 N Columbia Rd Stop 9037

institute: University of North Dakota

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then processed using the Hisat2 sequence alignment programs. Reads were mapped to the mm10 genome reference to identify transcripts.
Count value were calculated by featureCount
Normalized by DESeq2 with rlogTransformed
Assembly: mm10
Supplementary files format and content: tab-delimited text files include rlogTransformed values for each Sample ...

source_name: Primary Epithelial cell

extract_protocol:
Epithelial cell  frozen on dry ice, and DNA/RNA was harvested using Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA and RNA quantity was assessed using a Qubit fluorometer, and the quality was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS‐122‐2001, RS‐122‐2002; Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary Epithelial cell

value: IAV

tag: time

value: Day 7


title: EOLN [AML1010.2.GEX]


title: HPC-2 Steady state rep #7


title: G2021_115_15


title: N2_CeMbio_2

tag: age

value: 1 d adults (24 h post L4)

value: CeMbio


title: Screening [AML1010.1.GEX]


title: dbl1nk3_CeMbio_2


title: G2021_115_14


title: dbl1oex_OP50_2


title: G2021_115_13


title: G2021_115_12


title: sma3e491_OP50_2


title: HPC-2 Steady state rep #6


title: HPC-2 Steady state rep #3


title: HPC-2 Steady state rep #5


title: N2_OP50_2


title: G2021_115_11


title: HPC-2 Steady state rep #4


title: HPC-2 Steady state rep #2


title: dlb1nk3_OP50_2


title: G2021_115_7


title: EOLN [AML1006.2.GEX]


title: C2 [AML1019.5.GEX]


title: HPC-2 Steady state rep #1


title: dbl1oex_CeMbio_1


title: EOLN [AML1019.2.GEX]


title: G2021_115_6


title: Screening [AML1019.1.GEX]


title: HPC-1 16wk rep #3


title: sma3e491_CeMbio_1


title: G2021_115_5


title: EOT [AML1007.5.GEX]


title: HPC-1 16wk rep #2


title: Between C1 and C2 [AML1019.4.GEX]


title: C4 [AML1007.4.GEX]


title: N2_CeMbio_1


title: C1 [AML1019.3.GEX]


title: dbl1nk3_CeMbio_1


title: EOLN [AML1007.2.GEX]


title: sma3e491_OP50_1


title: dbl1oex_OP50_1


title: N2_OP50_1


title: C1 [AML1007.3.GEX]


title: RNA-seq_BMDM_Brg1Si_DexLPS_rep4

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

data_processing:
Gene level quantification was performed with Salmon version 1.4.0 (https://combine-lab.github.io/salmon/). Settings:  -libType A, -gcBias, -biasSpeedSamp 5. Gene annotations were obtained from Genecode (M25, GRCm38, mm10). (https://www.gencodegenes.org/) release M25 (GRCm38.p6).
Gene count normalization and differential expression analysis was performed with DESeq2 (doi: 10.1186/s13059-014-0550-8) version 1.32.0 (R version 4.1.0) after import of gene-level estimates with tximport version 1.20.0 (doi: 10.12688/f1000research.7563.1) in R.
For gene annotation Ensembl Transcript Ids were mapped to mgi_symbol using the Bioconductor package biomaRt (doi:10.1093/bioinformatics/bti525) version 2.48.2 and information from Ensembl (GRCm38.p6)
Genome_build: GRCm38.p6 (mm10)
Supplementary_files_format_and_content: .txt containingg the DESeq-normalized count data and DESeq log2-fold changes and statistics for all comparisons

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow from male wild type mice was flushed with RPMI (Thermo Scientific) into Falcon tubes. Erythrocytes were removed with AKC lycis. Afterwards, the cells were purified via a Ficoll gradient ( GE Healthcare, 17-5442-02) and incubated with macxrophage differentiation medium (DMEM (4.5g/l glucose,Sigma ), 30% supernatant of L929 cells, 20% FBS and 1% Pen/Strep) for 7 days in non-cell culture treated plates. Differentiated macrophages were dissociated with Versene (Gibco) and gene silencing was performed using the RNAimax kit (Invitrogen) based on the manufacturer's instructions in serum free conditions (macrophage -SFM medium, Thermo-Scientific, 12065074). For gene silencing 50nM sicontrol (Dharmacon, D-001206-14) or siBRG1 (Dharmacon, M-041135-01-0005 ) were applied to the cells.

extract_protocol:
RNA was extracted with the Rneasy mini kit (Qiagen).The quality of RNA was determined by the Agillent 2100 Bioanalyzer with the 6000 RNA nano reagents (Agillent Technologies)
Library preparation and rRNA depletion was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacture's manual. 500 ng RNA were used as input for each sample.

treatment_protocol: In the last 6 hours of the gene silencing cells were treated with 0.1% EtoH and 0.1% D-PBS (vehicle), 0.1% EtoH and 100ng/ml LPS (LPS) or 1µM Dex and 100ng/ml LPS (LPS+Dex).

value: bone marrow-derived macrophages

value: 6h 1uM Dex and 100ng/ml LPS

tag: sirna

value: 48h BRG1 siRNA

value: male


title: Screening [AML1007.1.GEX]


title: shP2_3

city: Dalian

first: jinxin

last: lu

state: Liaoning

address: lvshunkou district lvshun south goad west sector No.9

institute: Dalian Medical University

data_processing:
The RNA-seq data were mapped to the reference genome hg38 using the software Hisat2 v2.0.5 based on the default parameters.
The expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) estimated each gene expression levels by featureCounts (v1.5.0-p3).
Assembly: Homo Sapiens(GRCh38/hg38)

growth_protocol: MDA-MB-231 cells were cultured in Leibovitz's L-15 Medium (Gibco) supplemented with 10% FBS, at 37°C incubator without CO2.

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
Libraries were prepared according to the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s recommendations.

value: breast cancer stem cell

value: shP4 konckdown


title: RNA-seq_BMDM_Brg1Si_DexLPS_rep3


title: dlb1nk3_OP50_1


title: C1 [AML1022.3.GEX]

first: Livius

last: Penter

institute: Dana-Farber Cancer Institute

data_processing:
Demultiplexing of raw reads using cellranger mkfastq
Alignment against GRCh38 and generation of count matrices using cellranger count
Assembly: GRCh38
Supplementary files format and content: count matrix, barcode list and feature list in csv file format

extract_protocol:
Ficoll-based extraction of bone marrow mononuclear cells and cryopreservation in FCS with 10% DMSO until analysis. Thawing in PBS supplemented with 10% FCS and 10% bovine DNase I, grade II. Bead-based dead cell removal with negative-selection strategy (Miltenyi). Resuspension in PBS with 0.04% ultra-pure BSA.
5' biased library construction according to manufacturer's specifications including T cell receptor sequencing and surface marker expression (CG000330, 10x Genomics).

value: bone marrow


title: shP2_2

value: shP3 konckdown


title: X83.CTRL2, CTRL unexposed

city: Leuven

first: Felix

last: De Bie

address: Herestraat 49

department: Development and Regeneration

institute: KU Leuven

data_processing:
Trimmed reads (Trimmomatic v.0.36.) were mapped on the Rabbit reference genome (OryCun2.0) using STAR aligner v.2.5.2b.
RNA-seq analysis: DESeq2
Assembly: OryCun2.0
Supplementary files format and content: csv files contain count values for each sample

organism: Oryctolagus cuniculus

source_name: Lung

extract_protocol: RNeasy mini kit (Qiagen) according to manufacturors protocol

value: Lung

value: Placebo


title: shP2_1

value: shP2 konckdown


title: RNA-seq_BMDM_Brg1Si_DexLPS_rep2


title: RNA-seq_BMDM_Brg1Si_DexLPS_rep1


title: shP1_3

value: shP1 konckdown


title: HPC-1 16wk rep #1

value: Mouse age 8-12 weeks

value: cells isolated from mice transplanted with 8000 LSK (CD3e-, B220-, GR-1-, CD11b-, TER119-, cKIT+, SCA-1+) 3, 4, 5, 6, 8, 10, 13, 16 weeks earlier into lethally irradiated (900cGy) recipients


title: HPC-1 10wk rep #1


title: HPC-1 13wk rep #1


title: HPC-1 13wk rep #3


title: HPC-1 10wk rep #3


title: HPC-1 13wk rep #2


title: G2021_115_3

value: Primary Epithelial cell

value: PBS

value: Day 7


title: G2021_115_4


title: G2021_115_2


title: X81.CDH2, CDH exposed

value: Treprostinil


title: HPC-1 10k rep #2


title: X81.CDH3, CDH exposed


title: G2021_115_1


title: shP1_1


title: shP1_2


title: X81.CDH1, CDH exposed


title: ctrl_3

value: WT


title: RNA-seq_BMDM_Brg1Si_LPS_rep2

value: bone marrow-derived macrophages

value: 6h 0.1% EtoH and 100ng/ml LPS

value: 48h BRG1 siRNA


title: RNA-seq_BMDM_Brg1Si_LPS_rep1

value: male


title: RNA-seq_BMDM_Brg1Si_LPS_rep3


title: HPC-1 8wk rep #2


title: HPC-1 8wk rep #3


title: HPC-1 6wk rep #3


title: HPC-1 8wk rep #1


title: X56.CDH1, CDH unexposed


title: RNA-seq_BMDM_Brg1Si_veh_rep3

value: 6h 0.1% EtoH and 0.1% D-PBS


title: X83.CTRL1, CTRL unexposed


title: HPC-1 6wk rep #2


title: X61.CDH2, CDH unexposed


title: X61.CDH1, CDH unexposed


title: HPC-1 6wk rep #1


title: RNA-seq_BMDM_Brg1Si_veh_rep2


title: HPC-1 5wk rep #3


title: Brainstem at 11 weeks of gestation

city: XiaMen

first: chao

last: tu

state: FuJian

address: JiMei street,668

department: Center for precision medicine

institute: HuaQiao university

description: 10x Genomics

data_processing:
Aligned and quantified using the Cell Ranger Single-Cell Software Suite (v.3.0.1, 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: gzip files and raw count matrix files

source_name: brainstem

extract_protocol:
Human fetal brainstem tissue was dissected and digested to prepare single cell suspensions.
Using chromium next GEM single cell 3’ GEM protocol (Library &Gel Bead Kit v3.1, 16 rxns PN-1000121)

value: brainstem

tag: gestational age

value: 11 weeks


title: ctrl_1

value: breast cancer stem cell


title: Brainstem at 9 weeks of gestation

description: 10x Genomics

value: 9 weeks


title: ctrl_2


title: TMD436, shTONSL Clone3, rep2 (RNA-seq)

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

data_processing:
The sequence data were mapped to the human reference genome hg38 with STAR-2.5.2b
FeatureCounts (subread-1.5.1) was used to quantify gene expression (parameters applied: "“-s 2 –p –Q 10")
Differential expression analysis was performed using edgeR
Assembly: hg38
Supplementary files format and content: Excel table including FPKMs, raw counts, log2 fold change, p-values and FDR

source_name: Breast

growth_protocol: MEM +10%FBS+ antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: QIAGEN, RNeasy mini kit, Cat No.71406. 1ug of total RNA was used for the construction of sequencing libraries.

value: Breast

value: Cancer cells

value: TONSL knockdown

value: shTONSL Clone3


title: Brainstem at 12 weeks of gestation

description: 10x Genomics

value: 12 weeks


title: TMD436, shTONSL Clone3, rep1 (RNA-seq)


title: RNA-seq_BMDM_ctrlSi_LPS_rep1

value: 48h control siRNA


title: TMD436, shTONSL Clone2, rep3 (RNA-seq)

value: shTONSL Clone2


title: RNA-seq_BMDM_ctrlSi_DexLPS_rep3

value: 6h 1uM Dex and 100ng/ml LPS


title: RNA-seq_BMDM_ctrlSi_LPS_rep2

value: bone marrow-derived macrophages


title: RNA-seq_BMDM_Brg1Si_veh_rep1


title: RNA-seq_BMDM_ctrlSi_DexLPS_rep1


title: RNA-seq_BMDM_ctrlSi_DexLPS_rep2


title: TMD436, shTONSL Clone3, rep3 (RNA-seq)


title: RNA-seq_BMDM_ctrlSi_LPS_rep3

value: 6h 0.1% EtoH and 100ng/ml LPS


title: RNA-seq_BMDM_ctrlSi_DexLPS_rep4


title: TMD436, shTONSL Clone2, rep2 (RNA-seq)


title: RNA-seq_BMDM_ctrlSi_veh_rep3


title: CTRL-miRNAs

type: RNA

city: Columbia

first: Narendra

middle: P

last: Singh

state: South Carolina

address: 6439 Garners Ferry Road,

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina

description: Male mice were treated with vehicle, the latter consisting of an equal amount of DMSO in corn oil, On day 3, testes were harvested and single cell suspensions were prepared. miRNA arrays were performed using total RNAs including microRNA and using Affymetrix microarray platform

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
More than 1.5 fold increase or decrease

label: biotin

source_name: Testes

label_protocol: Purified miRNA samples isolated from testes and ovaries harvested from mice 72h post-exposure to TCDD were labeled using the Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kit using the manufacturer's specifications for 100 format miRNA 4.0 arrays. GeneChip™ Hybridization, Wash, and Stain kit was used in conjunction with the Affymetrix® Hybridization Oven and Affymetrix® Fluidics Station on the 450 protocol to prepare Affymetrix® GeneChip® miRNA 4.0 arrays. Prepared arrays were then analyzed using the GeneChip™ Scanner 3000 7G (All products in this section are sourced from ThermoFisher Scientific, Waltham, MA, USA 02451).  Microarray intensity was quantified, and differential expression was analyzed using Applied Biosystems Transcription Analysis Console (TAC) 4.0 software. Expression data were analyzed using Ingenuity Pathway Analysis (IPA) and miRNA targets were determined using the current target prediction database miRDB (Chen and Wang, 2020), and target prediction algorithm, MirTarget (Liu and Wang, 2019) as well as web-based TargetScan.

growth_protocol: Both ovaries and testes cells were cultured in complete medium for 6 hrs at 37C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Both Male and female Mice were  either treated with TCDD (10µg/kg body weight) or Vehicle, the latter consisting of an equal amount of DMSO in corn oil, On day 3, ovaries and testes were harvested and single cell suspensions were prepared. miRNA arrays were performed using total RNAs including microRNA and using Affymetrix microarray platform

value: Testes cells


title: Ovaries-TCDD-miRNAs

description: Female mice were treated with TCDD (t 10µg/kg body weight). On day 3, ovaries and testes were harvested and single cell suspensions were prepared. miRNA arrays were performed using total RNAs including microRNA and using Affymetrix microarray platform

source_name: Ovaries

value: Ovaries cells


title: TCDD-miRNAs

description: Male mice were treated with TCDD (10µg/kg body weight). On day 3, testes were harvested and single cell suspensions were prepared. miRNA arrays were performed using total RNAs including microRNA and using Affymetrix microarray platform


title: HFD_3

city: Lübeck

first: Henriette

last: Kirchner

address: Ratzeburger Allee 160

department: Institute for Human Genetics

institute: University of Lübeck

description: microRNA expression from pre-diabetic murine liver

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Data analysis was performed with the Transcriptome Analysis Console software (version 4.0.2.5) with the analysis type 'Expression (Gene)'. As summarization method 'RMA+DABG (Mouse Only)' was used for signal normalization. A probe set was considered expressed if at least 50% of the detection above background (DABG) values were below the DABG threshold.

source_name: liver sample, HFD, 24 weeks

label_protocol: Affymetrix standard protocol

extract_protocol: RNA was isolated from snap-frozen liver using the miRNeasy mini kit (Qiagen, Germany) according to the manufacturer’s instructions.

treatment_protocol: Mice were maintained on a 12-h light-dark cycle with free access to water and 58% high fat diet (HFD) (Research Diets, D12331) for 24 weeks. All mice were fasted for 4 hours at the start of the light phase before being sacrificed by cervical dislocation for organ withdrawal.

value: liver

tag: gender

value: male

tag: condition

value: HFD

tag: duration

value: 24 weeks


title: Ovaries-Vehicle-miRNAs

description: Female mice were treated with vehicle, the latter consisting of an equal amount of DMSO in corn oil, On day 3, ovaries were harvested and single cell suspensions were prepared. miRNA arrays were performed using total RNAs including microRNA and using Affymetrix microarray platform


title: RNA-seq_BMDM_ctrlSi_veh_rep2

value: 6h 0.1% EtoH and 0.1% D-PBS

tag: Sex


title: TMD436, shTONSL Clone2, rep1 (RNA-seq)

value: Breast


title: HFD_6


title: HFD_4


title: HPC-1 Steady state rep #8

tag: developmental stage

value: Mouse age 8-12 weeks

value: untreated


title: HPC-1 4wk rep #3

value: cells isolated from mice transplanted with 8000 LSK (CD3e-, B220-, GR-1-, CD11b-, TER119-, cKIT+, SCA-1+) 3, 4, 5, 6, 8, 10, 13, 16 weeks earlier into lethally irradiated (900cGy) recipients


title: HPC-1 5wk rep #2


title: HPC-1 3wk rep #3


title: HPC-1 3wk rep #2


title: HPC-1 5wk rep #1


title: HPC-1 3wk rep #1


title: HPC-1 4wk rep #1


title: HPC-1 4wk rep #2


title: HFD_2


title: HPC-1 Steady state rep #7


title: TMD436, shTONSL Clone1, rep3 (RNA-seq)

value: Cancer cells

value: TONSL knockdown

value: shTONSL Clone1


title: RNA-seq_BMDM_ctrlSi_veh_rep1

value: 48h control siRNA


title: HPC-1 Steady state rep #6


title: TMD436, shTONSL Clone1, rep2 (RNA-seq)


title: LV3_EC_ATAC

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

institute: Sun Yat-sen University

data_processing:
Ror RNAseq data, alignment to the Ensembl reference genome mm9 was performed using the Tophat and bowtie2. Alignment files were sorted using SAMtools v.1.10.2. Count tables were generated using HTSeq-0.6.1.
ATAC-seq data were aligned using Bowtie2 and removed PCR duplicates using Picard. We called Peaks using MACS2. Peaks from the biological replicates were merged using Samtools and Bedtools.
For scRNAseq, the Cell Ranger Software (version 1.2.0) was used to perform the first preprocessing step. ‘cellranger count’ was used to performing read filtering, alignment, and count matrix generation from fastq files per sample. The reads were aligned to the mm10 (refdata-gex-mm10-2020-A) reference genome provided by 10xGenomics. The gene-barcode matrix was generated using only confidently mapped reads with valid barcodes and unique molecular identifiers
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: txt file include count and peak signal for each sample;txt file  include  barcode and gene count.

source_name: Endothelial cells

extract_protocol:
Mice were deeply anaesthetized and perfused transcardially with 20 ml of ice-cold phosphate buffered saline (PBS). After perfusion, whole brain, lung and liver were immersed in ice-cold PBS, which were minced with a razor blade and disaggregated in Type IV collagenase (400 U/ml, Worthington,Lakewood, NJ), Dispase (1.2 U/ml, Worthington, Lakewood, NJ) and DNase I (32 U/ml, Worthington, Lakewood, NJ) in 6 mL 1× PBS with Ca2+ and Mg2+ (GIBCO) at 37 °C for 60 min, with gentle trituration every 10 min. After adequate disaggregation, 1 ml of FBS was added to the disaggregation reaction then the disaggregated cells were washed with 1× ice-cold PBS and filtered through a 40-μm mesh. After centrifugation at 400g for 5 min, cell pellets were resuspended in 10 ml 20% BSA and centrifuged at 1,000 g at 4 °C for 25 min to remove the myelin (only for brain).   The pellets were then resuspended in 1× PBS/3% FBS/0.1% NaN3/2 mM EDTA and blocked with rat anti-mouse CD16/32 (Mouse BD Fc Block, BD Pharmingen) for 10 min on ice. Endothelial cells were labeled with PE-Cyanine7 rat anti-mouse CD31 (cat. # 25-0311-82, eBiosciences, CA), and pericytes were labeled with APC rat anti-mouse PDGFRβ (cat. #17-1402-82, eBiosciences, CA). PE rat anti-mouse CD45 (cat. #516087, BD Pharmingen, CA) and 7-AAD (Invitrogen) were added to exclude hematopoietic lineage cells and dead cells. Staining was done for 1 h at 4 °C. Cells were washed and PE-cyanine7-CD31+/APC-PDGFRβ−/PE-CD45−/7-AAD− cells were sorted into EGM-2/MV medium (cat. #CC3202, Clontech, Mountain View, CA) with an Aria III sorter (BD). ECs were centrifuged at 2,000 g at 4 °C for 10 min and resuspended in Trizol (Life Technologies) or extraction buffer for RNA , DNA, protein extraction.
RNAseq:RNA-seq was performed as we previously reported (PMID:28288111). The RNA-seq data were generated from EC cells after FACS purification. Each RNA-seq analysis was conducted on three biological replicates. ECs total RNA was extracted using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). In brief, mRNA was first enriched from total RNA by poly-A. Oligo-dT-directed reverse transcription generated complementary DNAs corresponding to the 3′end of poly-A transcripts; the complementary DNA was amplified by PCR using the Ovation 3′-DGE System kit (NuGen Technologies, San Carlos, CA). Amplified cDNA was sheared using a Covaris ultrasonicator and then libraries were prepared using the Ovation SP + Ultralow DR Multiplex System (NuGen Technologies, San Carlos, CA). Deep sequencing was then performed on the Illumina Hiseq-2500 platform (Illumina, Hayward, CA) in single-end 50 bp format.  ATAC-seq:Briefly, ECs were lysed in cold lysis buffer (10 mM Tris-HCl, Ph7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal) and tagmentation performed using Illumina Nextera DNA kit (FC-121-1030) for 30 min at 37 °C on a shaking thermomixer. Tagmented DNA was purified using Qiagen MinElute kit (Cat no. 28004) and amplified using NEB Next High-Fidelity 2X PCR Mast Mix (Cat no. M0543S) for 11 cycles as follows: 72 °C, 5 min; 98 °C, 30 s; 98 °C, 10 s; 63 °C, 30 s; 72 °C, 1 min. Library preparation was complete after further clean up using Qiagen PCR MinElute kit (Cat no. 28004) and Beckman Coulter XP AMPpure beads (A63880). Tagmentation size was assessed using Agilent 2100 Bioanalyser. Libraries were quantified with Qubit 2.0 (Life Technologies) and sequenced using paired-end 150 bp reads on the Illumina HiSeq4000 platform at XX. Three biological replicates were used for analysis.scRNAseq:Single-cell RNA-seq libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kit 3.1(10X Genomics, US). Briefly, Brain ECs (1~2 x105) were isolated by FCAS from young, middle and aged mice (n=2 each group). Single-cell suspension at a density of 500-1000 cells/µL in FACS buffer was added to 10X Genomics GefmCode Single-cell instrument that generateed single-cell Gel Bead-In-EMlusion (GEMs). RNA transcripts from single cells were uniquely barcoded (16 nt) and reverse-transcribed within droplets. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. All libraries were quantified by using High Sensitivity DNA assay Kit (Agilent, US). All single-cell libraries were sequenced on a Novaseq 6000 system (Illumina, US).

value: Endothelial cells

value: 2-4 months


title: LV2_EC_ATAC


title: HFD_5


title: TMD436, PLKO, rep3 (RNA-seq)

value: WT

value: shControl


title: TMD436, shTONSL Clone1, rep1 (RNA-seq)


title: LV1_EC_ATAC

value: liver


title: HPC-1 Steady state rep #5


title: HPC-1 Steady state rep #4


title: LG4_EC_ATAC

value: lung


title: TMD436, PLKO, rep2 (RNA-seq)


title: HFD_1

value: male

value: HFD


title: Liver_obese_T2D T2D70

description:
Liver_obese_T2D
noncoding RNA expression from diabetic and non-diabetic liver of human obese subjects

hyb_protocol: After preparation of the hybridization cocktail using additionaly 3 nM control oligo B2  and hybridiztion controls (GeneChip Hybridization Control Kit, Applied Biosystems), 21.5 µl biotin-labeld sample were injected into one GeneChip miRNA 4.0 Array, multi-species (Applied Biosystems) per sample. Hybridization was performed for 18 h at 48 °C and 60 rpm. Arrays were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChip miRNA 4.0 Array, multi-species were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data analysis was performed with the Transcriptome Analysis Console software (version 4.0.2.15) with the analysis type 'Expression (Gene)'. As summarization method 'RMA+DABG (Human Only)' was used for signal normalization. ANOVA method 'ebayes' was used for comparison. A probe set was considered expressed if at least 50% of the detection above background (DABG) values were below the DABG threshold.

source_name: liver biopsy of an obese human subject with type-2-dabetes

label_protocol: Biotinylated RNA was prepared according to the FlashTag Biotin HSR RNA Labeling Kit (Applied Biosystems, USA) from 500 ng total RNA.

extract_protocol: RNA was isolated from snap-frozen liver using the miRNeasy mini kit (Qiagen, Germany) according to the manufacturer’s instructions blinded.

tag: bmi

value: m


title: Liver_obese_ND ND88

description:
Liver_obese_ND
noncoding RNA expression from diabetic and non-diabetic liver of human obese subjects

source_name: liver biopsy of an non-diabetic obese human subject

value: non-diabetic

value: w


title: HPC-1 Steady state rep #3

value: Mouse age 8-12 weeks

value: untreated


title: HPC-1 Steady state rep #2


title: LG3_EC_ATAC


title: TMD436, PLKO, rep1 (RNA-seq)

value: Breast

value: Cancer cells


title: LG2_EC_ATAC


title: Primary breast epithelial cells, rep3 (RNA-seq)

data_processing:
The sequence data were mapped to the human reference genome hg38 with STAR-2.5.2b
FeatureCounts (subread-1.5.1) was used to quantify gene expression (parameters applied: "“-s 2 –p –Q 10")
Differential expression analysis was performed using edgeR
RNA-seq
Assembly: hg38
Supplementary files format and content: Excel table including FPKMs, raw counts, log2 fold change, p-values and FDR

extract_protocol: To be updated.

value: Primary breast epithelial cells

value: Female


title: TONSL overexpressing Primary breast epithelial cells, rep2 (RNA-seq)

value: TONSL overexpression


title: Primary breast epithelial cells, rep2 (RNA-seq)


title: TONSL overexpressing Primary breast epithelial cells, rep1 (RNA-seq)


title: TONSL overexpressing Primary breast epithelial cells, rep3 (RNA-seq)


title: HPC-1 Steady state rep #1


title: Primary breast epithelial cells, rep1 (RNA-seq)


title: HSC 16wk rep #3

source_name: HSC

value: HSC

value: cells isolated from mice transplanted with 8000 LSK (CD3e-, B220-, GR-1-, CD11b-, TER119-, cKIT+, SCA-1+) 3, 4, 5, 6, 8, 10, 13, 16 weeks earlier into lethally irradiated (900cGy) recipients


title: Primary breast epithelial cells, rep3 (ATAC-seq)

data_processing:
Integration of RNA-seq data with ATAC-seq data and motif enrichment analyses were performed as described previously (Oncogene 40:1332-1346)
To correlate chromatin accessibility with gene expression changes, promoter and enhancer regions were analyzed separately. Promoters and enhancers with open or closed configuration in primary and TONSL overexpressing cells were aligned with gene expression data of the same by gene symbols. Genes with open/close promoter/enhancer chromatin and up/down gene expression were selected by a relative relaxed filter p-value < 0.05 for ATAC-seq data to capture the minimally altered TONSL-responsive sites and FDR < 0.05 for RNA-seq data to capture TONSL-responsive genes. A more stringent filter FDR < 0.05 was used in both RNA-seq and ATAC-seq data to determine TONSL-responsive genes with more convincing TONSL-dependent changes in chromatin accessibility.
Assembly: hg38
Supplementary files format and content: Excel table including peak annotation, log2 fold change, and FDR

growth_protocol: Primary cells were maintained in media prep described in PMID: 30992305 in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.

value: WT


title: BR3_EC_ATAC

value: brain

value: Endothelial cells

value: 2-4 months


title: BR4_EC_ATAC


title: BR1_EC_ATAC


title: LG1_EC_ATAC

value: lung


title: BR2_EC_ATAC


title: TONSL overexpressing Primary breast epithelial cells, rep3 (ATAC-seq)


title: HSC 13wk rep #1

data_processing:
Low quality bases and Illumina adapters were trimmed using Trimmomatic (v0.36)
Trimmed reads were aligned to the mouse reference genome (GRCm38/mm10) using HISAT2 (v2.0.5)
Duplicated reads were marked and filtered out using Picard MarkDuplicates tool (v8.25) (http://broadinstitute.github.io/picard/)
Fragments aligned to the mouse genes (Ensembl GRCm38.91) were quantified using the featureCounts tool
Assembly: mouse reference genome (GRCm38/mm10)
Supplementary files format and content: tab-delimited text file contains raw counts for each sample (as a matrix table)

extract_protocol:
Spine, femurs, tibia, and iliac bones were crushed in PBS+2% FBS. Bone marrow was enriched for cKit, followed by FACS sort of live LSK SLAM (CD3e-, B220-, GR-1-, CD11b-, TER119-, cKIT+, SCA-1+, CD48-, CD150+) HSCs into sterile PBS+RNAse inhibitor and snap freezed at -80 degrees.
cDNA syntesis and amplification were done using SMART-Seq v4 (Takara), followed by library preparation using Nextera XT DNA library prep kit (Illumina).


title: HSC 13wk rep #2


title: HSC 16wk rep #1


title: HSC 13wk rep #3


title: HSC 16wk rep #2


title: HSC 10wk rep #3


title: TONSL overexpressing Primary breast epithelial cells, rep2 (ATAC-seq)


title: HSC 10k rep #2


title: Liver_obese_T2D T2D84

value: liver


title: Primary breast epithelial cells, rep2 (ATAC-seq)


title: Liver_obese_ND ND75

value: non-diabetic


title: Liver_obese_T2D T2D87

value: w


title: T2_DAPI 1

city: Vienna

first: Ruben

last: Gutzat

state: Vienna

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute GmbH

description: 400 nuclei

data_processing:
data were processed with the nextflow pipeline (https://nf-co.re/rnaseq/3.12.0)
Output Salmon count table was used for differential gene expression analysis using DESeq2
Assembly: Tair10
Supplementary files format and content: The table contains: first column is gene ID, the next columns are Log2FoldChange, pvalue and p.adj value of pairwise comparison and the following columns are descriptions of genes and transposons

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: Shoot apices

growth_protocol: Plants were grown on soil in short-day growth conditions (8h light/16h dark) for 21 days, then transfer to long-day (16h light / 8h dark) growth condition for 2 days.

extract_protocol:
All steps were done on ice, and with the RNase inhibitors. 300 apices were dissected and immersed in 3% glyoxal. The samples were vacuumed for 10 min twice and washed with Galbraith buffer. Next, the samples were grounded by Bioruptor  for 1 min and debris was filtered. The mixture was subjected to centrifugation at 2000g for 3 min at 4oC and resuspended by Galbraith buffer with 5 µg/mL DAPI  prior to Florescence-activated nuclei sorting.
Smart-seq3 single cell strategy

tag: ecotype

value: Transgenes pCLV::H2BmCherry and pAGO9::GFP-AGO9 in Col-0 ecotype

tag: developmental age

value: 21-day-old grown in short-day (8h light / 16h dark), then transferred to long-day (16h light / 8h dark) for 2 days

value: stem cells


title: TONSL overexpressing Primary breast epithelial cells, rep1 (ATAC-seq)

tag: tissue

value: Breast

tag: treatment


title: T2_DAPI 2

description: 400 nuclei


title: T2_DAPI 3

description: 400 nuclei


title: T2_GFP 4

description: 200 nuclei


title: T2_GFP 3

description: 200 nuclei


title: T2_DAPI 4

description: 400 nuclei


title: T2_GFP 2

description: 200 nuclei


title: HSC 8wk rep #3

value: Mouse age 8-12 weeks


title: HSC 8wk rep #2


title: HSC 10wk rep #1


title: CRC59

city: shanghai

first: Kong

last: Cheng

address: 270 Dong 'an Road

institute: fudan university shanghai cancer center

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh37_genome_ensembl_v73
Supplementary files format and content: RPKM values for each Sample

source_name: Tumor tissue

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Tumor tissue

value: snap-frozen tissues


title: HSC 8wk rep #1

value: HSC


title: CRC58


title: Primary breast epithelial cells, rep1 (ATAC-seq)

value: Primary breast epithelial cells

tag: genotype

value: Female


title: HSC 6wk rep #2

tag: cell type

value: cells isolated from mice transplanted with 8000 LSK (CD3e-, B220-, GR-1-, CD11b-, TER119-, cKIT+, SCA-1+) 3, 4, 5, 6, 8, 10, 13, 16 weeks earlier into lethally irradiated (900cGy) recipients


title: HSC 6wk rep #1

tag: strain


title: CRC57


title: CRC56


title: CRC55


title: Liver_obese_T2D T2D97


title: Liver_obese_ND ND94


title: HSC 6wk rep #3


title: Liver_obese_ND ND57


title: Liver_obese_T2D T2D91


title: Liver_obese_ND ND9


title: HSC 5wk rep #3


title: CRC54


title: Liver_obese_ND ND45


title: Liver_obese_T2D T2D15


title: Liver_obese_ND ND18

value: m


title: CRC53


title: Liver_obese_ND ND102


title: Liver_obese_ND ND38


title: HSC 5wk rep #1


title: Liver_obese_T2D T2D56


title: Liver_obese_T2D T2D12


title: Liver_obese_T2D T2D11


title: T2_RFP 3

description: 200 nuclei


title: T2_RFP 1

description: 200 nuclei


title: T2_RFP 2

description: 200 nuclei


title: T2_RFP 4

description: 200 nuclei


title: Liver_obese_ND ND14


title: T2_RFP_GFP 1

description: 200 nuclei


title: T2_GFP 1

description: 200 nuclei


title: Liver_obese_ND ND7


title: HSC 4wk rep #3


title: Liver_obese_T2D T2D92


title: Liver_obese_ND ND96


title: CRC52


title: T1_DAPI 6

description: 400 nuclei

value: 21-day-old grown in short-day (8h light / 16h dark)


title: HSC 5wk rep #2


title: Liver_obese_ND ND40


title: HSC 4wk rep #2


title: T2_RFP_GFP 2

description: 200 nuclei


title: CRC51


title: HSC 4wk rep #1


title: CRC50


title: Liver_obese_T2D T2D20


title: HSC 3wk rep #3


title: CRC47


title: CRC48


title: CRC46


title: HSC 3wk rep #1


title: HSC 3wk rep #2


title: CRC45


title: T1_DAPI 5

description: 400 nuclei


title: T1_DAPI 4

description: 400 nuclei


title: HSC Steady state rep #8

value: untreated


title: T1_DAPI 3

description: 400 nuclei


title: T1_DAPI 1

description: 400 nuclei


title: HSC Steady state rep #7


title: HSC Steady state rep #6


title: T1_DAPI 2

description: 400 nuclei


title: T1_GFP 4

description: 200 nuclei


title: CRC49


title: T1_GFP 6

description: 200 nuclei


title: CRC43


title: HSC Steady state rep #5


title: T1_GFP 3

description: 200 nuclei


title: HSC Steady state rep #4


title: Liver_obese_T2D T2D98

value: liver


title: CRC42


title: CRC41


title: Liver_obese_ND ND36

value: non-diabetic


title: T1_GFP 2

description: 200 nuclei


title: Liver_obese_ND ND33

value: w


title: HSC Steady state rep #3


title: Liver_obese_ND ND34


title: CRC40


title: T1_GFP 1

description: 200 nuclei

value: Transgenes pCLV::H2BmCherry and pAGO9::GFP-AGO9 in Col-0 ecotype


title: HSC Steady state rep #2


title: T1_RFP 6

description: 200 nuclei


title: CRC44


title: Liver_obese_T2D T2D105


title: Liver_obese_ND ND106


title: Liver_obese_ND ND37


title: Liver_obese_T2D T2D35


title: T1_GFP 5

description: 200 nuclei


title: CRC39


title: Liver_obese_ND ND60


title: Liver_obese_T2D T2D16


title: Liver_obese_ND ND31


title: HSC Steady state rep #1


title: Liver_obese_T2D T2D43


title: CRC38


title: T1_RFP 5

description: 200 nuclei


title: T1_RFP 4

description: 200 nuclei


title: ChIP T NotoPdiff

data_processing:
Prior to mapping, the forward and reverse reads were trimmed to 50bp using fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Reads were mapped to chromosomes 1-19, X, Y and M of the mouse mm10 genome using bowtie version 1.3.1, providing the options ‘ -y -m 1 -S  -I 100 -X 500’. The mapping information of the paired-end reads was used to elongate each fragment to its original size using a custom pearl script, with the result stored as a BED file. Reads were then sorted and deduplicated such that only one fragment with the same starting and end position was retained. For visualization, wiggle files were generated with BEDTools version 2.23.0, converted to bigwig format and visualized in the Integrated Genome Browser. Peak detection was performed using MACS version 3.0.0b1 (https://github.com/macs3-project/MACS) using the elongated and deduplicated bed files as inputs and setting a q-value cutoff of 0.1.
Assembly: mm10
Supplementary files format and content: *.bw: tag denisty files of ChIP data in bigWig format
Supplementary files format and content: *.narrowPeak: peak files for ChIP-Seq tracks used in analysis obtained by MACS
Supplementary files format and content: RNA_FPKM.txt: normalized per gene abundance measurements (FPKM) for RNA-Seq samples obtained by Cuffdiff

source_name: in vitro differentiated cell cultures

growth_protocol: To initiate NotoP differentiation, ESCs were removed from feeders by dissociation using 0.05% trypsin and then plated onto tissue culture plates for four short successive periods (25’, 20’, 15’, 10’) to remove feeders. To induce differentiation, a protocol slightly modified from Gouti et al. was used. In short, cells were plated on CellBINDSurface dishes precoated with 0.1% gelatin at a density of 1 x 104 cells per cm2 in a medium consisting of ‘N2B27’ medium, supplemented with 10 ng/ml bFGF for 3 days (d1-d3). From d2-d4 µM CHIR99021 was added to the medium. For induction of Foxa2 expression, 1ng/ml doxycycline was applied from d2-d4.

extract_protocol:
For sonication, complete protease inhibitors without EDTA (Roche) at 1x final concentration was added to all lysis buffers (LB) prior to use. Each pellet was resuspended in LB1 (50mM Hepes pH7.5, 140mM NaCl, 1mM EDTA pH8, 10% glycerol, 0.75% NP-40, 0.25% triton X-100) and rotated at 4°C for 20 minutes. The cell suspension was homogenized using a douncer with a tight pestle with 3x 15 strokes, with short resting times on ice in between. The chromatin was pelleted by centrifugation at 1400g and 4°C for 5 minutes and resuspended in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 10mM Tris pH 8) per cell pellet. After 10 minutes rotation at 4°C, the centrifugation step was repeated and each pellet was resuspended in 1.5ml LB3 (1mM EDTA pH8, 0.5mM EGTA, 10mM Tris pH8, 100mM NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine), transferred to 15ml Falcon tubes and sonicated using a W-450D Digital Sonifier (Branson) sonicator for 14 cycles of 10s on/50s off in a 4°C coldroom with tubes chilled in ice water. After sonication, 150ul of triton X-100 was added per tube, transferred to two 1.5ml Eppendorf tubes and debris was pelleted by centrifugation at 20,000g and 4°C for 10 minutes. The solubilized chromatin was then pooled and mixed thoroughly. After taking 50ul as an input control, the chromatin was distributed into 1.5ml aliquots, snap frozen and stored at -80C until use. For ChIP, 25ul of protein-coated Dynal beads (Life Technologies) were washed 3x using 1ml of blocking solution (PBS containing 0.5% BSA), resuspended in 500ml of blocking solution together with approximately 2.5ug antibody and rotated overnight at 4C. The antibodies used were a goat polyclonal anti-T (R&D, AF2085) and a rabbit polyclonal anti-Foxa2 (Diagenode, 2683-6041). The next day, three further washes using 1ml blocking buffer were performed and the beads were resuspended in 100ml blocking buffer. Chromatin equivalent to approximately 2x10^6 cells was added and rotated overnight at 4C. The following day, washing steps (8 and 9 washes for Foxa2 and T respectively) were performed using 1ml RIPA buffer (50mM Hepes pH7.6, 500mM LiCl, 1mM EDTA pH8, 1% NP-40, 0.7% Na-Deoxycholate) containing 1x complete protease inhibitors without EDTA and finally once with 1ml of TEN (10mM Tris pH8, 1mM EDTA pH8, 50mM NaCl). The immunoprecipates were eluted in two subsequent steps using 100ml of 1x elution buffer (50mM Tris pH8, 10mM EDTA pH8, 1% SDS) and incubation at 65C while shaking for 10 minutes each. The eluates were combined and incubated overnight (13h-15h) at 65C under agitation. The next day, 200ml of TE were added to dilute the SDS of the elution and the ChIPs were purified with two subsequent phenol:chloroform:isoamylalcohol (25:24:1, pH8) isolations and a MinElute (Qiagen) purification.
ChIP-Seq sequencing libraries were generated using the TrueSeq ChIP-Seq kit (Ilumina) following the manufacturer’s instructions with minor modifications. After adapter ligation, 0.95x of AMPure XP beads (Beckman Coulter A63880) were used for a single purification and the DNA was eluted using 15 µl of resuspension buffer (RSB, Illumina). After the addition of 1 µl primer mix (25 mM each, Primer 1: 5’-AATGATACGGCGACCACCGA*G-3’; Primer2: 5’- CAAGCAGAAGACGGCATACGA*G-3’) and 15µl 2x Kapa HiFi HotStart Ready Mix (Kapa Biosystems), amplification was performed for 45 s at 98°C, 5 cycles of [15 seconds at 98°C, 30 s at 63°C and 30 s at 72°C] and a final 1 min incubation at 72°C. The PCR products were purified using 0.95x of beads and eluted using 21 µl of RSB. Libraries were directly amplified for additional 13 cycles and purified using AMPure XP beads. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS bioanalyzer chips (Agilent 5067-4626).

value: in vitro differentiated cell cultures

tag: cell line

value: genetically modified F1G4 (C57BL/6N x SV129) mES cells

value: in vitro generated notochord progenitor-like cells

value: TRE::Foxa2-IRES-EGFP (Rosa26 locus); T::H2B-mCherry-T2A-irTA (BAC); Noto::H2B-mTurquoise (BAC)

value: Crosslinking was performed directly on differentiating cells in growth medium with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 50mM Hepes pH7.8) for 10 minutes at room temperature, with the dishes placed on a shaker. The crosslinking reaction was quenched with the addition of 1/10th volume of 2.5M glycine and 5 minutes incubation. Dishes were placed on ice or in a 4°C cold room and washed twice with cold PBS. Cells were scraped and washed off using cold PBS, containing 0.05% Triton X-100 to break the surface tension. Cells were pooled in aliquots of ~30-50x10^6 in Eppendorf tubes, snap frozen and stored at -80°C until sonication.


title: CRC37

value: Tumor tissue

value: snap-frozen tissues


title: ChIP H3K9me2 NotoPdiff

data_processing:
Prior to mapping, the forward and reverse reads were trimmed to 50bp using fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Reads were mapped to chromosomes 1-19, X, Y and M of the mouse mm10 genome using bowtie version 1.3.1, providing the options ‘ -y -m 1 -S  -I 100 -X 500’. The mapping information of the paired-end reads was used to elongate each fragment to its original size using a custom pearl script, with the result stored as a BED file. Reads were then sorted and deduplicated such that only one fragment with the same starting and end position was retained. For visualization, wiggle files were generated with BEDTools version 2.23.0, converted to bigwig format and visualized in the Integrated Genome Browser.
Assembly: mm10
Supplementary files format and content: *.bw: tag denisty files of ChIP data in bigWig format
Supplementary files format and content: *.narrowPeak: peak files for ChIP-Seq tracks used in analysis obtained by MACS
Supplementary files format and content: RNA_FPKM.txt: normalized per gene abundance measurements (FPKM) for RNA-Seq samples obtained by Cuffdiff

source_name: FACS sorted Noto+/T+ cells from in vitro differentiated cultures

extract_protocol:
Cells were processed using the iDeal ChIP-Seq kit (Diagenode) according to manufacturer’s instructions. Approximately 200,000 cells were used per ChIP with the following antibodies: anti-H3K4me1 (pAb-194-050, Diagenode), anti-H3K4me3 (ab8580, Abcam), anti-H3K27ac (ab4729, Abcam) and anti-H3K9me2 (A90-0042, Diagenode).
ChIP-Seq sequencing libraries were generated using the TrueSeq ChIP-Seq kit (Ilumina) following the manufacturer’s instructions with minor modifications. After adapter ligation, 0.95x of AMPure XP beads (Beckman Coulter A63880) were used for a single purification and the DNA was eluted using 15 µl of resuspension buffer (RSB, Illumina). After the addition of 1 µl primer mix (25 mM each, Primer 1: 5’-AATGATACGGCGACCACCGA*G-3’; Primer2: 5’- CAAGCAGAAGACGGCATACGA*G-3’) and 15µl 2x Kapa HiFi HotStart Ready Mix (Kapa Biosystems), amplification was performed for 45 s at 98°C, 5 cycles of [15 seconds at 98°C, 30 s at 63°C and 30 s at 72°C] and a final 1 min incubation at 72°C. The PCR products were purified using 0.95x of beads and eluted using 21 µl of RSB. Libraries were directly amplified for additional 13 cycles and purified using AMPure XP beads. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS bioanalyzer chips (Agilent 5067-4626).

value: Cells were washed 2x PBS and dissociated by trypsinization at 37°C for 10min. Trypsin/EDTA was quenched using a double volume of 5%BSA/PBS, resuspended and kept on ice until further procedure. All samples were immediately filtered (35µm mesh) and sorted on a FACS Aria II (Becton Dickinson) flow cytometer. Cells were sorted into PBS 5% BSA in BSA coated glass tubes. After sorting, cells were pelleted by centrifugation, transferred to 1.5 ml low binding tubes and washed in PBS containing  0.05% Triton X-100 to break the surface tension.  Crosslinking was performed by adding 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 50mM Hepes pH7.8) to cells resuspended in 500µl PBS for 10 minutes at room temperature with agitation. The crosslinking reaction was quenched with the addition of 1/10th volume of 2.5M glycine and 5 minutes incubation. Pellets were washed twice using cold PBS, containing 0.05% Triton X-100 to break the surface tension. Cells were pooled in aliquots of ~0.6x106 in Eppendorf tubes, snap frozen and stored at -80°C until sonication.


title: T1_RFP 3

description: 200 nuclei

value: stem cells


title: LNCaP_Veh

city: San Antonio

first: Zhijie

middle: Jason

last: Liu

state: TEXAS

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: Universality of Texas Health Science Center at San Antonio

description: vehicle control sample

data_processing:
Basecalls performed using Illuminal CASAVA software.
GRO-seq reads were aligned to human genome (hg19) using bowtie with “--best --strata –m 1 –v 2” parameters. Duplicated reads were eliminated for subsequent analysis.
To balance the clonal amplification bias and total useful reads, only at most three reads was allowed for each unique genomic position.
edgeR 3.16.5 was used to call the differential eRNAs.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: prostate cancer cells

growth_protocol: LNCaP obtained from ATCC were cultured in RPMI1640 media supplemented with 10% FBS in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
Cells were subjected to nuclear run-on for 5 minutes at 30°C with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing.
We followed a previous published protocol (Ingolia et al., 2009 Science; Wang et al., 2011 Nature). Briefly, the run-on RNA were first added with a polyA tracts by RNA polyA polymerase. This polyA tail enables the run-on RNA to be reverse transcribed into single strand cDNA by Reverse Transcriptase. The cDNA was circularized by CircLigase (Epicentre) and re-linearized by APE I, subsequently subjected to PCR amplification and deep sequencing.

treatment_protocol: To test the role of AR condensation on enhancer assembly and gene expression, we used 1,6 hexanediol (1,6 HD) to chemically disrupt phase separation in cells. Before experiment, the LNCaP cells were hormone-stripped in phenol red-free RPMI1640 medium plus 5% charcoal-treated FBS for 3 days, followed by three different treatments for 2 hours: 1. ethanol as vehicle control; 2. 100 nM DHT as hormone stimulation sample; 3. 100 nM DHT plus 2.5% 1,6 HD as condensation disruption condition.

value: LNCaP

value: Veh:stripping 3 days, ethanol


title: CRC36


title: T1_RFP 1

description: 200 nuclei

value: 21-day-old grown in short-day (8h light / 16h dark)


title: CRC34


title: CRC35


title: T1_RFP 2

description: 200 nuclei


title: T1_RFP_GFP 6

description: 200 nuclei


title: CRC33


title: CRC32


title: CRC31


title: CRC30


title: ChIP H3K4me3 NotoPdiff

value: FACS sorted Noto+/T+ cells from in vitro differentiated cultures


title: ChIP H3K9me2 MPdiff

source_name: FACS sorted T+/Noto- cells from in vitro differentiated cultures

value: in vitro generated mesoderm progenitor cells


title: CRC29


title: T1_RFP_GFP 4

description: 200 nuclei


title: T1_RFP_GFP 3

description: 200 nuclei


title: T1_RFP_GFP 2

description: 200 nuclei


title: LNCaP_DHT

description: hormone stimulation sample

value: DHT:stripping 3 days, DHT 100nM 2hr


title: LNCaP_PQ69_shAR_Dox

description: experimental sample with endogenous AR knockdown and with BLRP AR-pQ69 overexpression

data_processing:
Basecalls performed using Illuminal CASAVA software.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v1.1.2 with only uniquely mapped reads retained.
Peaks were called using MACS2 with q-value less than 1e-5. The peaks overlapped with the blacklist regions downloaded from UCSC were removed
Assembly: hg19
Supplementary files format and content: bigWig file

growth_protocol: The established BLRP-tagged Tet-On inducible stable lines were established from LNCaP cell line (ATCC) and their growing were maintained at RPMI1640 medium with G418 (300 μg/ml), hygromycin (100ug/ml) and puromycin (0.3 μg/ml) for stable selection. All cell lines were cultured in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with streptavidin magnet beads pull-down.
The extracted ChIP DNA was ligated to specific adaptors using KAPA LTP Library Preparation Kit (KK8230) or KAPA Hyper Prep Kit (KK8504), according to the manufacturer’s instructions.

treatment_protocol: To perform Biotin ChIP experiments through Biotin-streptavidin pull-down, we used the BLRP-tagged Tet-On inducible LNCaP stable lines that can in vivo biotinylate BLRP-tagged proteins. For each line, we have prepared two different cell samples for biotin ChIP: the control one was transduced with control shRNA and not treated with doxycycline; the experimental sample was transduced with AR shRNA TRCN0000003718 and treated by 2 μg/ml doxycycline for 24 hours. Both cell samples were hormone-stripped in phenol red-free RPMI1640 medium plus 5% charcoal-treated FBS for 3 days, followed by treatment with 100 nM DHT for 2 hours before collection for biotin ChIP experiments.

tag: transfection

value: LNCaP stable cell line with pBirA (G418), pRetro-TetR (Hygromycin), and pRetro-BLRP-AR-pQ69 (puromycin) (AR cDNA is shAR3718-Resistant)

value: AR-PQ69:shAR3718, +DOX (2ug/ml 1d), stripped 3 days, DHT 100nM 2hr

tag: chip antibody

value: Biotin-ChIP using Streptavidin Magnetic beads (Solulink)


title: T1_RFP_GFP 5

description: 200 nuclei

value: Transgenes pCLV::H2BmCherry and pAGO9::GFP-AGO9 in Col-0 ecotype


title: CRC28


title: T1_RFP_GFP 1

description: 200 nuclei


title: LNCaP_dIDR_shAR_Dox

description: experimental sample with endogenous AR knockdown and with BLRP AR-dIDR overexpression

value: LNCaP stable cell line with pBirA (G418), pRetro-TetR (Hygromycin), and pRetro-BLRP-AR-dIDR (puromycin) (AR cDNA is shAR3718-Resistant)

value: AR-dIDR:shAR3718, +DOX (2ug/ml 1d), stripped 3 days, DHT 100nM 2hr


title: Liver_obese_T2D T2D51

value: liver

tag: age

value: m


title: LNCaP_16HD

description: condensation disruption sample

value: DHT+1,6HD:stripping 3 days, DHT 100nM + 2.5% 1,6 HD  2hr


title: LNCaP_PQ69_shCtrl_noDOX

description: negative control without endogenous AR knockdown and without BLRP AR-pQ69 overexpression

value: AR-PQ69:shCTL, No DOX, stripped 3 days, DHT 100nM 2hr


title: AngII+Si-NAT10_RNA_3

city: Nanjing

first: Chuanxi

last: Yang

state: China

address: 300 Guangzhou Road, 210029, Nanjing, PR China

department: Department of Cardiology

institute: School of Medicine, Southeast University

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For acRIP-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
For acRIP-seq: The m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”. Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
For Ribo-seq: The reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using bowtie2 software, remaining reads were used to align to reference genome and transcriptome (Ensembl Version 91) using hisat23 and bowtie2 software separately.
For Ribo-seq:ORF identification was performed using Price5 software.  Read counts were calculated using featureCounts6 software.  Raw counts were further normalized as RPKM values using fpkm function in DESeq27 package.
Assembly: mm10 and hg38
Supplementary files format and content: mRNA-seq_9 mouse_All.count.txt
Supplementary files format and content: Ribo-seq_9 mouse_All.count.txt
Supplementary files format and content: 12hsa_acRIP-seq_input.count.txt
Supplementary files format and content: 12mmu_acRIP-seq_input.count.txt

source_name: heart ventricular tissue

extract_protocol:
For acRIP-seq: Briefly, the concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852).   Total RNA was fragmented into 100-200 nt RNA fragments using ZnCl2.   Subsequently, the purified RNA was incubated with anti-ac4c polyclonal antibody  for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments.   The ac4c-enriched RNA was eluted from the beads in RLT buffer supplied in RNeasy Mini Kit (QIAGEN, 74106).   The RNA-seq library was prepared by NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, E7775).  For Ribo-seq:tissue were pulverized manually under liquid nitrogen and treated by ice-cold PBS containing 100 μg/mL cycloheximide.     Ribosome profiling was performed using Epi™ Ribosome Profiling Kit (Epibiotek, R1814).     Subsquently, RPFs (ribosome-protected RNA fragments) was extracted using RNA clean&ConcentratorTM-5 kit (ZYMO, R1016).     EpiTM RiboRNA Depletion Kit  (Epibiotek, R1805) was used for rRNA depletion.     Sequencing libraries were constructed using QIAseq miRNA Library kit (QIAGEN, 1103679).
RNA libraries were prepared for sequencing using standard Illumina protocols
acRIP-seq; Ribo-seq; RNA-seq

treatment_protocol: Silencing and inhibiting NAT10

value: heart ventricular tissue


title: H3i, YPD, RNA-seq biol rep1

first: Peerapat

last: Khamwachirapithak

institute: Thammasat University

data_processing:
FastQC
Reads were align to Saccer3 genome using the Hisat2
Sorting and indexing using Samtools
Duplication was removed by Picard tools
Raw read counts were normalized by DEseq2
Assembly: Saccer3
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Cell pellet

extract_protocol:
RNA was extracted by MagMax96 total RNA isolation kit (AM1830, Invitrogen) for the first and second replicates. Trizol reagent (15596026, Invitrogen) was used in extraction with glass beads for the third replicate.
Librarires of the first and second replicates were prepared using the Illumina TruSeq Stranded mRNA Library Prep. For the third replicate, the TruSeq Stranded mRNA LT sample prep kit was used for library construction.

value: Cell pellet

value: Yeast cell

value: YPD


title: LNCaP_WT_shAR_Dox

description: experimental sample with endogenous AR knockdown and with BLRP AR-WT overexpression

value: LNCaP

value: LNCaP stable cell line with pBirA (G418), pRetro-TetR (Hygromycin), and pRetro-BLRP-AR-WT (puromycin) (AR cDNA is shAR3718-Resistant)

value: AR-WT:shAR3718, +DOX (2ug/ml 1d), stripped 3 days, DHT 100nM 2hr