title: ATAC-seq_T_B

description: Tumor tissue

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
After removal of the adaptor sequences, the reads were aligned to the hg38 human reference genome using the BWA-MEM software.
The model-based analysis of ChIPseq (MACS2 v2.1.2) was applied to call the ATAC-seq peak regions of each sample by using a bam file of uniquely mapped reads as the input, and the q-value cutoff for peak calling was 0.05. Peak annotation was performed by HOMER v4.9.1 function annotatePeaks.pl, which picks putative target genes that are located within ATAC-seq called peaks or contain the transcription start sites (TSSs) nearest to these peaks.
Motif analysis on peak regions was performed by HOMER v4.9.1 function findMotifsGenome.pl. Distribution of uniquely mapped reads resulting from ATAC-seq in a bigwig file across either peaks or gene body was analyzed using deeptools v3.2.1. To identify differential peaks between different stages of development, the ATAC-seq peaks of each sample were merged to generate a consensus set of unique peaks, among which the number of peaks was further counted for each sample using bedtools v2.25.0, and differential peaks were identified by DESeq2 (v1.16.0), with the thresholds of | log2FC| > 1 and p < 0.05.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
The first step is to extract the nucleus. After extraction, the cell counter is used to count and 50,000 nuclei are taken for next step. The Tn5 transposase carrying part of the joint incubated with 50,000 nuclei , cut, extracted DNA
The transposed DNA was purified with a MinElute Kit (Qiagen) and was used to generate the library via PCR amplification. All libraries were purified using a Qiagen MinElute PCR Purification Kit following the manufacturer’s instruction and were sequenced on an Illumina Novaseq 6000 platform.

value: pancreas


title: T6

status: Public on Jul 03 2024

type: SRA

city: Shanghai

first: Hailong

last: Ma

address: Zhizaoju Rd

country: China

institute: Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
Raw data (raw reads) were processed using Trimmomatic software. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2 software.
Raw read counts of each gene were obtained by htseq-count software.
Assembly: hg38
Supplementary files format and content: txt file contains raw counts of each gene

molecule: total RNA

organism: Homo sapiens

source_name: oral squamous cell carcinoma

extract_protocol:
extract protocol RNA was harvested using mirVanaTM miRNA ISOlation Kit (Ambion-1561).
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions

treatment_protocol: Tissue samples were collected from patients and snap frozen in liquid nitrogen within 30 min, then transfer to - 80 ℃ freezer for storage until RNA-seq detection

tag: tissue

value: oral squamous cell carcinoma


title: ATAC-seq_N_B

city: Jinan

first: Guoying

last: Dong

state: Shandong

address: Jinan lixia district Wenhua west road no. 44

department: Cheeloo College of Medicine

institute: Shandong University

description: Normal tissue

library_source: genomic

molecule: genomic DNA

source_name: pancreas


title: sgGal4 arm, day 14 time point, replicate 1, ribosome footprints

city: San Francisco

first: Albert

last: Xu

state: CA

address: 513 Parnassus Ave, HSW 640

department: Cell and Tissue Biology

country: USA

institute: University of California, San Francisco

description:
sgGal4_RP_rep1_d14
RP_counts.csv

data_processing:
library strategy: Ribosome profiling
Ribosome Profiling: Raw sequencing reads were converted from .fastq to .fasta using fastx-toolkit (v0.0.13), adapter sequences were trimmed using cutadapt (v3.4), and reads were collapsed by UMI using fastx-toolkit. Bowtie2 (v2.4.1) was used to filter out repeat RNAs (rRNA, snoRNA, miRNA). A custom Perl script was used to trim reads a second time and bbduk was used to directly remove contaminating reads mapping to the sgRNA. STAR aligner22 (v2.7.5a, GrCH38, Gencode v25) was used to align reads. RSubread was used to generate counts and the DESeq2 and Riborex packages were used for differential expression and differential translation analysis.
RNAseq: Raw sequencing reads were aligned to genome by STAR aligner (v2.7.5a, GrCH38, Gencode v25). RSubread was used to generate counts
Assembly: GrCh38, Gencode v25
Supplementary files format and content: RNA_counts.csv - counts generated by Rsubread of all the RNA samples
Supplementary files format and content: RP_counts.csv - counts generated by Rsubread of all the Ribosome Profiling samples

growth_protocol: K562 cells were grown in DMEM media supplemented with 10% Fetal Bovine Serum and 1% Pen/Strep/Glutamine

extract_protocol:
See protocol from Calviello et al 2021 (PMID: 33905506). Briefly, Direct-zol RNA Miniprep (Zymo Research) kits were used to isolate RNA from either cytosolic cell lysate (lysed in (20 mM Tris–HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2 1% (v/v) Triton X-100, 25 U/ml TurboDNase (Ambion)) or cycloheximide-fixed ribosomes (treated with RNAseI (ambion) and isolated from Illustra MicroSpin Columns S-400HR).
RNAseq libraries were prepared as per manufacturer's instructions using the NEBNext rRNA Depletion Kit V2 (NEB cat: E7400) and the NEBnext Ultra II Directional RNA Library Prep Kit (NEB cat: E7760). Ribosome Profiling libraries were prepared as previously described (PMID: 33905506). Briefly, purified RNA was ligated to 3' and 5' adapters, reverse transcribed, and PCR amplified.

treatment_protocol: 50ng/ml doxycycline to induce CRISPRi knockdown

tag: cell line

tag: cell type

value: immortalised myelogenous leukemia

tag: genotype

tag: molecule

value: ribosome protected footprints


title: T56


title: 26455-P, 7 months, rep5

city: Cleveland

first: Oliver

last: Wessely

state: OH

address: 9500 Euclid Avenue/NC10

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundation

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore!(v0.6.10) using the default parameters
Sequence reads were aligned to mouse genome (mm10) using Salmon (v1.10.1 )
Read count extraction using Salmon (Version 1.10.1)
Read count were normalized using the DESeq2 in R (Version 1.40.2)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including the normalized counts for each sample in a matrix table

organism: Mus musculus

source_name: kidney

extract_protocol:
miRNeasy Mini Kit (Qiagen,   74104)
TruSeq RNA Library Prep Kit (Illumina)

treatment_protocol: (i) Deoxycorticosterone acetate (DOCA) treatment: Four-month-old mice (n=9) were given two sequential subcutaneous DOCA pellet implants (50mg/pellet, 21-day release, Innnovative Research of America, Sarasota, FL) 3 weeks apart for a total of 6 weeks of sustained DOCA release. After 6 weeks, kidneys were extracted, and podocytes isolated by MACS using anti-Nephrin antibodies. (ii) High Fat Diet (HFD)-Induced Obesity Model: Four-month-old mice (n=11) were provided ad libitum HFD with 60 kcal% fat (D12492, Research Diets Inc, New Brunswick, NJ) for 12 weeks. At the end of 12 weeks, kidneys were extracted, and podocytes isolated by MACS using anti-Nephrin antibodies.

value: kidney

value: podocyte

value: wildtype

tag: treatment

value: untreated


title: T55


title: sgDDX3 arm, day 14 time point, replicate 1, ribosome footprints

description:
sgDDX3_RP_rep1_d14
RP_counts.csv


title: sgDDX3 arm, initial time point, replicate 1, ribosome footprints

description:
sgDDX3_RP_rep1_d0
RP_counts.csv


title: T57


title: KYSE510-EZH2 Cut&Tag-Seq

city: Los Angeles

first: Qian

last: Yang

address: 8700 Beverly Blvd

department: Department of Surgery

institute: CEDARS SINAI MEDICAL CENTER

data_processing:
Pair-end  reads were aligned to the hg19 reference genome using Bowtie. RNA-seq reads were trimmed for adaptor sequence, and then mapped to hg19 whole genome using STAR. For Cut&Tag-Seq, Bowtie2 was applied to do the alignment based on reference genome hg38.
Adaptors were removed using Trim galore software.
PCR duplicate reads were removed using Picard MarkDuplicates in Cut&Tag -Seq.
Blacklist regions were removed using ENCODE blacklist file in Cut&Tag -Seq.
SEACR peak calling package was applied to identify peaks with defalut parameters in Cut&Tag-Seq.
Assembly: hg38 for Cut&Tag and hg19 for RNA-Seq
Supplementary files format and content: gene expression matrix and bigwig files representing signal normalized to per million reads
Library strategy: Cut&Tag-seq

source_name: Esophageal Squamous Cell Carcinoma cell line

growth_protocol: KYSE510 cell line was cultured in RPMI-1640 (Corning, #10-040-CV) and FADU cell line was cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Corning, #10-013-CV). Both cell lines were supplemented with 10% of fetal bovine serum (FBS) (Omega, #FB-02), and 1% of penicillin/streptomycin (Thermofisher Scientific, #30-002-CI). Cell cultures were incubated in a 37°C incubator with 5% CO2

extract_protocol:
Total RNA was extracted by RNeasy Mini kit (QIAGEN #70106) according to the manufacturer’s instructions. DNA fragments were extracted by tagmentation reaction
Standard Illumina library preparation protocol

treatment_protocol: For RNA-Seq, KYSE510 cell line was transfected with two independent siRNA of either LAT1 or EZH2 using lipofectamine RNAiMAX (Thermofisher Scientific, 13778150) and incubated for 48 hours. Cut&Tag assay was performed according to the manufacturer’s protocols in KYSE510 and FADU cell line


title: T52


title: 26454-P, 7 months, rep4


title: sgGal4 control arm, final time point, replicate 1

data_processing:
Raw sequencing files were processed using the ScreenProcessing pipeline published in: PMID: 27661255
Supplementary files format and content: .counts: output from ScreenProcessing pipeline indicating raw number of each sgRNA for each sample
Supplementary files format and content: _librarytable.txt: output from ScreenProcessing pipeline with protospacer sequences for the genome-wide sgRNA library
Supplementary files format and content: _genetable.txt: output from ScreenProcessing pipeline with gene-level information on protospacer enrichment/depletion
Supplementary files format and content: _phenotypetable.txt: output from ScreenProcessing pipeline with protospacer-level enrichment/depletion calculations
Library strategy: CRISPR screen sequencing of sgRNA protospacer

extract_protocol:
As described in PMID: 27661255, Machery-Nagel NucleoSpin Blood XL kit was used to extract genomic DNA
Genomic DNA was digested with MfeI-HF, run on a 0.8% 1X TAE agarose gel, 400-650bp gel was excised and DNA was gel purified. NEBNext Ultra II Q5 master mix was used to add Illumina sample indexes and sequencing adapters. Target for PCR amplification was the sgRNA cassette used in the screen.

treatment_protocol: 50ng/ml doxycycline


title: ATAC-seq_T_A

description: Tumor tissue


title: Anti-DDX18 Hs766T-DDX18 cell-IgG-3

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
CUT&Tag-seq reads were aligned to the hg38 genome using BWA（0.7.13-r1126） . Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag-seq

source_name: pancrea

extract_protocol:
CUT&Tag assay was performed as described previously with modifications(Hatice et al., 2019 ). Briefly，100000 cells were washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail).
To amplify libraries, 21μL DNA was mixed with 2μL of a universal i5 and auniquely barcoded i7 primer. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. libraried clean-up was performed XP beads (Beckman Counter).

value: pancrea

value: cancer cell

value: DDX18 overexpressed

tag: antibody

value: anti-IgG


title: ATAC-seq_N_A

description: Normal tissue


title: T51


title: T53


title: sgGal4 control arm, final time point, replicate 2


title: 26452-P, 7 months, rep2


title: sgGal4 control arm, intial time point, replicate 1


title: 26106-P, 5.5 months with DOCA, rep9

value: DOCA


title: Anti-DDX18 Hs766T-DDX18 cell-IgG-2


title: T54


title: Anti-DDX18 Hs766T-DDX18 cell-3


title: T50


title: sgDDX3 arm, final time point, replicate 2


title: T5


title: 26105-P, 5.5 months with DOCA, rep8


title: 26451-P, 7 months, rep1


title: T49


title: sgGal4 control arm, initial time point, replicate 2


title: sgDDX3 arm, final time point, replicate 1


title: Anti-IgG Hs766T-DDX18 cell-IgG-1


title: 26104-P, 5.5 months with DOCA, rep7


title: sgDDX3 arm, initial time point, replicate 2


title: 26103-P, 5.5 months with DOCA, rep6


title: Anti-DDX18 Hs766T-DDX18 cell-1


title: T48


title: 26009-P, 5.5 months with DOCA, rep5


title: sgDDX3 arm, intial time point, replicate 1


title: T47


title: Anti-DDX18 Hs766T-con cell-3

value: control


title: 26007-P, 5.5 months with DOCA, rep3


title: APE99719

first: Xu

last: Pei

address: Jiangpu Road 1665

institute: Xinhua Hospita;

description: processed data(FPKM).txt

data_processing:
Solexa pipeline version 1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2
Fragments Per Kilobase of gene/transcript model per Million mapped fragments (FPKM) were cacluated with Ballgown
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

extract_protocol:
RNA was harvested using Trizol reagent. RiboZero Magnetic Gold  Kit (Human/Mouse/Rat) (Epicentre, an Illumina Company) and KAPA Stranded RNA-Seq Library Prep Kit (Illumina) 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: paired esophageal epithelial tissue

tag: tumor stage

value: II(AJCC 8th)


title: 26008-P, 5.5 months with DOCA, rep4


title: Anti-IgG Hs766T-con cell-IgG-3


title: AE99719

description: processed data(FPKM).txt

value: esophageal squamous cell carcinoma


title: T45


title: Anti-DDX18 Hs766T-DDX18 cell-2


title: T46


title: 26453-P, 7 months, rep3


title: Anti- DDX18 Hs766T-con cell-2


title: T44


title: 26006-P, 5.5 months with DOCA, rep2


title: 26005-P, 5.5 months with DOCA, rep1


title: T43


title: 26470-P, 5.5 months, rep10


title: APE94929

description: processed data(FPKM).txt


title: Anti-DDX18 Hs766T-con cell-1


title: T42


title: no DDX3 transgene with sgDDX3 Nuclear RNAseq replicate 2

data_processing:
RNAseq: Raw sequencing reads were aligned to genome by STAR aligner (v2.7.5a, ENSEMBL GrCh38, NCBI RefSeq GCF_000001405.40) and STAR was used to generate counts.
Assembly: ENSEMBL GrCh38, NCBI RefSeq GCF_000001405.40
Supplementary files format and content: "SAMPLENAME_ReadsPerGene.out.tab": counts generated by STAR of reads per gene for each sample

molecule: nuclear RNA

extract_protocol:
Approximately 5-10 million cells were washed and resuspended in PBS and 10% of cells were resuspended in RIPA buffer for the total fraction. The remaining 90% was pelleted and resuspended in 200ul cytoplasm lysis buffer (10mM Tris-HCl pH 7.0, 150mM NaCl, 0.15% NP-40) and incubated on ice for 5 minutes. Lysate was then layered on top of 450uL sucrose buffer (25% sucrose, 10mM Tris-HCl, 150mM NaCl) and centrifuged at 13,000 RPM at 4°C for 10 minutes to pellet nuclei. The top (cytoplasm) fraction was isolated. Nuclei were resuspended in 400uL nuclei wash buffer (1x PBS with 1mM EDTA, 0.1% Triton-X) and centrifuged at 3,500 RPM at 4°C for 1 minute. To isolate the nuclear fraction, the washed nuclei were resuspended in 125uL RIPA buffer, then to 100ul lysate 1ul of Proteinase K (Thermo Fisher cat: EO0491) was added, and incubated at 50C for 10 min. RNA was isolated from nuclear and cytoplasmic fractions with the Quick-RNA Microprep kit (Zymo cat: R1051).
RNAseq libraries were prepared as per manufacturer’s instructions using the NEBNext rRNA Depletion Kit V2 (NEB cat: E7400) and the NEBnext Ultra II Directional RNA Library Prep Kit (NEB cat: E7760).

value: immortalized myelogenous leukemia


title: 26469-P, 5.5 months, rep9


title: T41

value: oral squamous cell carcinoma


title: 26468-P, 5.5 months, rep8


title: APE97040

description: processed data(FPKM).txt


title: Anti-IgG Hs766T-con cell-IgG-2


title: APE88722

description: processed data(FPKM).txt


title: 26467-P, 5.5 months, rep7


title: no DDX3 transgene with sgDDX3 Cytoplasmic RNAseq replicate 2

molecule: cytoplasmic RNA


title: T40


title: AE97040

description: processed data(FPKM).txt


title: 26465-P, 5.5 months, rep5


title: no DDX3 transgene with sgDDX3 Cytoplasmic RNAseq replicate 1


title: 26466-P, 5.5 months, rep6


title: PIF4ox pistil grown at nAT - replicate 4

city: Brno

first: Helene

middle: S.

last: Robert

address: Kamenice 5

country: Czech Republic

institute: CEITEC Masaryk University

description:
S35SPIF4_NC4
unfertilized pistils (stage 11-12) from 35S::PIF4 plants grown at nAT (21/18) after the start of flowering

data_processing:
Clean reads were generated by removing adaptor sequences and low-quality reads using fqtools.
The reads were mapped to the Arabidopsis genome using Araport11 (TAIR10, http://www.arabidopsis .org/).
FeatureCounts was used to determine read count for each gene in each sample. The FPKM values were calculated to provide a measure of gene expression levels in each sample.
Assembly: Araport11 (TAIR10, http://www.arabidopsis .org/)
Supplementary files format and content: gene_count
Supplementary files format and content: gene_fpkm

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: pistils

growth_protocol: Plants were grown in a Fytoscope growth chamber (FS WI, Plant Systems Instruments (PSI), Czech Republic) under growth conditions with a longday regime (16 h light and 8 h dark), LED illumination with an intensity of 150 umol.m-2.s-1, and 35% 45% humidity.

extract_protocol:
Gynoecium samples from flowers at stages 11 and 12 (before anthesis) were collected from wild type, phyb and 35S::PIF4 plants grown at nAT and hAT. Total RNA was extracted from 100 mg of ovules using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's protocol. RNA isolates were treated with rDNAse Macherey Nagel) to remove traces of contaminant DNA and purified using a RNeasy MinElute Cleanup Kit (Qiagen).
mRNAseq libraries were constructed by Novogene, starting with 100 ng of high-quality RNA per sample. mRNA purification was performed using oligo(dT) attached magnetic beads, followed by fragmentation and first-strand cDNA synthesis. Second strand cDNA synthesis, end repair, adapter ligation, and size selection were performed. PCR enrichment yielded in the final cDNA library.

treatment_protocol: For normal conditions (nAT), the temperature was set at 21oC during the day and 18oC at night. For high ambient temperature conditions (hAT), the temperature wat set at 28oC during the day and 24oC at night. Plants were grown at nAT until flowering is induced and moved to hAT.

value: pistils


title: T4


title: AE88722

description: processed data(FPKM).txt


title: Anti-IgG Hs766T-con cell-IgG-1


title: 26464-P, 5.5 months, rep4


title: PIF4ox pistil grown at nAT - replicate 3

description:
S35SPIF4_NC3
unfertilized pistils (stage 11-12) from 35S::PIF4 plants grown at nAT (21/18) after the start of flowering


title: PIF4ox pistil grown at nAT - replicate 2

description:
S35SPIF4_NC2
unfertilized pistils (stage 11-12) from 35S::PIF4 plants grown at nAT (21/18) after the start of flowering


title: T38


title: AE94929

description: processed data(FPKM).txt


title: uninfected Nuclear RNAseq replicate 1

value: uninfected


title: no DDX3 transgene with sgDDX3 Nuclear RNAseq replicate 1


title: T37


title: PIF4ox pistil grown at nAT - replicate 1

description:
S35SPIF4_NC1
unfertilized pistils (stage 11-12) from 35S::PIF4 plants grown at nAT (21/18) after the start of flowering


title: uninfected Cytoplasmic RNAseq replicate 2


title: T36


title: 26463-P, 5.5 months, rep3

value: kidney


title: 26462-P, 5.5 months, rep2

value: podocyte


title: PIF4ox pistil grown at hAT - replicate 4

description:
S35SPIF4_HT4
unfertilized pistils (stage 11-12) from 35S::PIF4 plants grown at hAT (28/24) after the start of flowering


title: T35


title: T39


title: 26461-P, 5.5 months, rep1

value: wildtype


title: PIF4ox pistil grown at hAT - replicate 3

description:
S35SPIF4_HT3
unfertilized pistils (stage 11-12) from 35S::PIF4 plants grown at hAT (28/24) after the start of flowering


title: PIF4ox pistil grown at hAT - replicate 2

description:
S35SPIF4_HT2
unfertilized pistils (stage 11-12) from 35S::PIF4 plants grown at hAT (28/24) after the start of flowering


title: uninfected Nuclear RNAseq replicate 2


title: sgNUP160 Nuclear RNAseq replicate 1


title: neutrophils of peripheral blood, AD, scRNA-seq

first: Xiaolin

last: Zhang

state: Shanghai

address: Humin Road 3210

institute: Shanghai Mental Health Center

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Preprocessing of the data was done using the 10X Genomics Cell Ranger software version 5.0.0 in default mode.
Assembly: mm10
Supplementary files format and content: Cell Ranger (barcodes.tsv, features.tsv, matrix.mtx)

source_name: blood

extract_protocol:
Neutrophils were enriched using EasySepTM Mouse Neutrophil Enrichment Kit (STEMCELL, 19762) according to the manufacturer’s instruction.
Reverse transcription and library preparation were performed using the 10X Genomics Single-Cell v3.0 kit following the 10X Genomics protocol.

value: blood

value: neutrophil


title: neutrophils of peripheral blood, WT, scRNA-seq

description: 10X Genomics

value: WT


title: PIF4ox pistil grown at hAT - replicate 1

description:
S35SPIF4_HT1
unfertilized pistils (stage 11-12) from 35S::PIF4 plants grown at hAT (28/24) after the start of flowering


title: T33


title: sgNUP160 Cytoplasmic RNAseq replicate 2


title: phyb pistil grown at nAT - replicate 4

description:
phyb_NC4
unfertilized pistils (stage 11-12) from phyb-9 plants grown at nAT (21/18) after the start of flowering


title: T32


title: sgNUP160 Cytoplasmic RNAseq replicate 1


title: 28-2_lentivirus containing the miR-200c/141 cluster + lentivirus containing the miR-200b/200a/429 cluster_2D culture 3

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

country: Canada

institute: University of Guelph

description:
PE150
O282200f3
28-2 cells infected with a lentivirus containing the miR-200c/141 cluster + a lentivirus containing the miR-200b/200a/429 cluster and grown as 2D culture, sample 3

data_processing:
adapters removed, reads containing N>10% removed, Qscore<=5 removed by Novogene
data was provided by Novogene as .fq.gz files
data was analyzed using Genialis software and the standard RNA-seq pipeling
Assembly: GRCm39_ens109
Supplementary files format and content: xlsx file containing featurecounts data

source_name: murine ovarian cancer cell 28-2

growth_protocol: All cells were maintained in DMEM media (GIBCO, Burlington, ON) supplemented with 10% FBS, 2% glutamine, 1% sodium pyruvate, 1% 4-(2-hydroxyethyl)-1-piper- azineethanesulfonic acid (HEPES), and 1% antibiotic/antimycotic. ID8EV cells were cultured with 30ug/ml puromycin, ID8-200f cells were cultured with 40ug/ml puromycin + 50ug/ml hygromycin, 28-2EV cells were cultured with 30ug/ml puromycin and 28-2-200f cells were cultured with 1000ug/ml hygromycin + 60ug/ml puromycin. Antibiotics were obtained from InvivoGen, San Diego, CA).

extract_protocol:
Total RNA was extracted using the miRVana miRNA extraction kit from Thermo Fisher Scientific
libraries were created by Novogene using Illumina kits

treatment_protocol: ID8 or 28-2 cells were infected with lentiviral particles containing the pLV[Exp]-EGFP:T2A:Puro-EF1A>mCherry (vector ID: VB160109-10005, VectorBuilder Inc., Chicago, IL, USA). ID8-200f and 28-2-200f cells were created by infecting ID8 or 28-2 cells with lentiviral particles containing pLV[Exp]-mCherry:T2A:Hygro-CMV>[Ex_miR200c-141] and lentiviral particles containing pLenti 4.1 Ex_miR200b-200a-429

value: murine ovarian cancer cell 28-2

value: overexpress miR-200c/141 and miR-200b/200a/429 cluster

value: lentivirus with miR-200c/141 + lentivirus with miR-200b/200a/429


title: T31


title: 28-2_lentivirus containing the miR-200c/141 cluster + lentivirus containing the miR-200b/200a/429 cluster_2D culture 2

description:
PE150
O282200f2
28-2 cells infected with a lentivirus containing the miR-200c/141 cluster + a lentivirus containing the miR-200b/200a/429 cluster and grown as 2D culture, sample 2


title: phyb pistil grown at nAT - replicate 3

description:
phyb_NC3
unfertilized pistils (stage 11-12) from phyb-9 plants grown at nAT (21/18) after the start of flowering


title: sgGal4 Nuclear RNAseq replicate 2


title: T30


title: 28-2_lentivirus containing the miR-200c/141 cluster + lentivirus containing the miR-200b/200a/429 cluster_2D culture 1

description:
PE150
O282200f1
28-2 cells infected with a lentivirus containing the miR-200c/141 cluster + a lentivirus containing the miR-200b/200a/429 cluster and grown as 2D culture, sample 1


title: sgGal4 Nuclear RNAseq replicate 1


title: phyb pistil grown at nAT - replicate 2

description:
phyb_NC2
unfertilized pistils (stage 11-12) from phyb-9 plants grown at nAT (21/18) after the start of flowering


title: uninfected Cytoplasmic RNAseq replicate 1


title: 28-2_control lentivirus and grown as 2D culture 3

description:
PE150
O282EV3
28-2 cells infected with control lentivirus and grown as 2D culture, sample 3

value: control

value: control lentivirus


title: phyb pistil grown at nAT - replicate 1

description:
phyb_NC1
unfertilized pistils (stage 11-12) from phyb-9 plants grown at nAT (21/18) after the start of flowering


title: T3


title: sgNUP160 Nuclear RNAseq replicate 2


title: T34


title: sgGal4 Cytoplasmic RNAseq replicate 2


title: T29


title: 28-2_control lentivirus and grown as 2D culture 2

description:
PE150
O282EV2
28-2 cells infected with control lentivirus and grown as 2D culture, sample 2


title: phyb pistil grown at hAT - replicate 4

description:
phyb_HT4
unfertilized pistils (stage 11-12) from phyb-9 plants grown at hAT (28/24) after the start of flowering


title: sgGal4 Cytoplasmic RNAseq replicate 1


title: T28


title: phyb pistil grown at hAT - replicate 3

description:
phyb_HT3
unfertilized pistils (stage 11-12) from phyb-9 plants grown at hAT (28/24) after the start of flowering


title: 28-2_control lentivirus and grown as 2D culture 1

description:
PE150
O282EV1
28-2 cells infected with control lentivirus and grown as 2D culture, sample 1


title: sgDDX3 Nuclear RNAseq replicate 2


title: T27


title: phyb pistil grown at hAT - replicate 2

description:
phyb_HT2
unfertilized pistils (stage 11-12) from phyb-9 plants grown at hAT (28/24) after the start of flowering


title: phyb pistil grown at hAT - replicate 1

description:
phyb_HT1
unfertilized pistils (stage 11-12) from phyb-9 plants grown at hAT (28/24) after the start of flowering


title: T26


title: Col-0 pistil grown at nAT - replicate 4

description:
COL_NC4
unfertilized pistils (stage 11-12)  from Col-0 plants grown at nAT (21/18) after the start of flowering

value: wild-type


title: T25


title: ID8_lentivirus containing the miR-200c/141 cluster + lentivirus containing the miR-200b/200a/429 cluster_2D culture 1

description:
PE150
ID8-200f1
ID8 cells infected with a lentivirus containing the miR-200c/141 cluster + a lentivirus containing the miR-200b/200a/429 cluster and grown as 2D culture, sample 1

source_name: murine ovarian cancer cell ID8

value: murine ovarian cancer cell ID8


title: sgDDX3 Nuclear RNAseq replicate 1

value: immortalized myelogenous leukemia


title: Col-0 pistil grown at nAT - replicate 3

description:
COL_NC3
unfertilized pistils (stage 11-12)  from Col-0 plants grown at nAT (21/18) after the start of flowering


title: sgDDX3 Cytoplasmic RNAseq replicate 2


title: ID8_control lentivirus and grown as 2D culture 3

description:
PE150
ID8EV3
ID8 cells infected with control lentivirus and grown as 2D culture, sample 3


title: sgCNOT1 Nuclear RNAseq replicate 2


title: T24

value: oral squamous cell carcinoma


title: Col-0 pistil grown at nAT - replicate 2

description:
COL_NC2
unfertilized pistils (stage 11-12)  from Col-0 plants grown at nAT (21/18) after the start of flowering

value: pistils


title: T23


title: sgDDX3 Cytoplasmic RNAseq replicate 1


title: T22


title: sgCNOT1 Nuclear RNAseq replicate 1


title: Col-0 pistil grown at nAT - replicate 1

description:
COL_NC1
unfertilized pistils (stage 11-12)  from Col-0 plants grown at nAT (21/18) after the start of flowering


title: sgCNOT1 Cytoplasmic RNAseq replicate 2


title: ID8_lentivirus containing the miR-200c/141 cluster + lentivirus containing the miR-200b/200a/429 cluster_2D culture 3

description:
PE150
ID8-200f3
ID8 cells infected with a lentivirus containing the miR-200c/141 cluster + a lentivirus containing the miR-200b/200a/429 cluster and grown as 2D culture, sample 3


title: ID8_control lentivirus and grown as 2D culture 1

description:
PE150
ID8EV1
ID8 cells infected with control lentivirus and grown as 2D culture, sample 1


title: T20


title: sgCNOT1 Cytoplasmic RNAseq replicate 1


title: Col-0 pistil grown at hAT - replicate 4

description:
COL_HT4
unfertilized pistils (stage 11-12) from Col-0 plants grown at hAT (28/24) after the start of flowering


title: Sorted FBs TAC Il1b-KO_Rep3

first: Angelo

last: Pelonero

address: 1650 Owens Street

department: Cardiovascular Disease Institute

institute: Gladstone Institutes (UCSF)

description: Single-cell RNAseq in the mEFSK-positive cardiac fibroblasts with or without Il1b deletion in Cx3cr1-positive cells

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with intronic reads kept with the Cellranger Suite v5 from 10X genomics
Additional filtering, quality control and doublet removal was performed using Seurat v3
Assembly: mm10
Supplementary files format and content: Cellranger count normalized gene-cellbarcode expression matrix w/ accompanying cell and feature information in tsv format

source_name: heart

extract_protocol:
Isolation from mouse hearts were performed using two methodologies: to isolate non-cardiomyocytes (non-CM) cells from the ventricles using Langendorff perfusion (#1) and to isolate all nuclei from the ventricles using a Langendorff-free protocol (#2). For #1, after a proper level of anesthesia was induced, a thoracotomy was performed and the mouse heart was isolated, cannulated, and perfused with perfusion buffer (120.4 mM NaCl, 14.7 mM KCl, 0.6 mM KH2PO4, 0.6 mM Na2HPO4, 1.2 mM MgSO4, 10 mM Na-HEPES, 4.6 mM NaHCO3, 30 mM taurine, 10 mM 2,3-butanedione monoxime, and 5.5 mM glucose, pH 7.0) in a Langendorff perfusion system (Radnoti 120108EZ) for 5-10 minutes at 37°C. The cannulated heart was then digested with digestion buffer (perfusion buffer with 300 units/mL collagenase II (Worthington Biochemical) and 50 μM CaCl2) for approximately 10 min at 37°C. At the end of digestion, the atria and great vessels were removed and the ventricular tissue was transferred and gently teased into small pieces in stop buffer (perfusion buffer with 10% fetal bovine serum) at 37°C. After gently pipetting, the cell suspension was passed through a 250 μM strainer in a 50ml conical centrifuge tube and centrifuged at 30xg for 3 minutes at room temperature (RT). The supernatant, which contained most of the non-cardiomyocytes (non-CMs), was divided from the pellet (which contained the CM fraction). The non-CM fraction was centrifuged again at 30xg for 3 minutes at RT and the supernatant retained. The supernatant was filtered with a cell strainer (70 μm) and centrifuged at 400xg for 3 minutes at RT for eliminating debris. The non-CM pellet was resuspended in 1mL cold PBS 0.5% BSA. Cells were counted with trypan blue using a hemocytometer and 15k cells were used for subsequent 10X Genomics Chromium single-cell RNAseq preparation. For single cell ATAC, 500k isolated and purified non-CMs were resuspended in 100uL lysis buffer (Tris-HCl 10mM pH 7.4, NaCl 10mM, MgCl2 3mM, Tween-20 0.1%, P40 0.1%, Digitonin 0.01%, BSA 1% in nuclease-free water), pipetted 10 times, and kept on ice for 5 minutes. Nuclei were washed with 1mL 1X PBS with 1% BSA and centrifuged for 5 minutes at 4 °C. The nuclei pellet was resuspended in 1mL 1X PBS with 1% BSA and filtered with a 10uM strainer (pluriSelect #43-50010-00). Nuclei were counted after DAPI staining using a hemocytometer and 10k non-CM nuclei were used for subsequent 10X Genomics Chromium single-cell ATAC-seq preparation. finally centrifuged at 400xg for 3 minutes in stop buffer at RT and the supernatant was discarded. For #2, after the mouse heart was isolated it was rinsed in a sterile 10cm petri dish containing 1X PBS on ice to remove excess blood and transferred to a 10cm petri dish containing 2ml of ice cold lysis buffer (320 mM sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 2 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8.0, 0.20% triton X-100) and minced into very small pieces. The minced heart tissue in 2ml of lysis buffer was transferred to a “Type A” dounce homogenizer and subjected to 50 strokes. This solution was subsequently transferred to a “Type B” dounce homogenizer and subjected to 3 strokes. The solution was serially passed through 100 μM and 70 μM strainers and then centrifuged at 1,000xg at 4 °C for 8 minutes. The nuclear pellet was resuspended in nuclei resuspension buffer (430 mM sucrose, 70 mM KCl, 2 mM MgCl2, 10 mM Tris-HCl ph 7.2, EGTA 5 mM, 10% glycerol). Nuclei were counted after DAPI staining using a hemocytometer and 15,000 nuclei were used for subsequent 10X Genomics Chromium single-nuclei RNAseq and 10,000 nuclei were used for ATAC-seq.
For sc/snRNA-seq library preparation, cells or nuclei were loaded onto the 10X Genomics Chromium instrument according to manufacturer’s protocols (Chip G, PN-1000120). All experiments were conducted with version 3.1 NEXT GEM reagents (PN-1000121), using 9 cycles of cDNA amplification for the GEM kit (PN-1000123) and 9 cycles of library amplification for library kit (PN-1000157). Each sample was indexed with a unique sample primer (Single Index Kit T Set A, PN-000213).

value: Sorted cardiac fibroblasts

value: heart

tag: strain

tag: age

value: 3-5 months


title: Sorted FBs TAC WT _Rep3


title: ID8_lentivirus containing the miR-200c/141 cluster + lentivirus containing the miR-200b/200a/429 cluster_2D culture 2

description:
PE150
ID8-200f2
ID8 cells infected with a lentivirus containing the miR-200c/141 cluster + a lentivirus containing the miR-200b/200a/429 cluster and grown as 2D culture, sample 2


title: Col-0 pistil grown at hAT - replicate 3

description:
COL_HT3
unfertilized pistils (stage 11-12) from Col-0 plants grown at hAT (28/24) after the start of flowering


title: DDX3 WT Nuclear RNAseq replicate 2

value: DDX3 WT


title: T2


title: Col-0 pistil grown at hAT - replicate 2

description:
COL_HT2
unfertilized pistils (stage 11-12) from Col-0 plants grown at hAT (28/24) after the start of flowering


title: DDX3 WT Nuclear RNAseq replicate 1


title: ID8_control lentivirus and grown as 2D culture 2

description:
PE150
ID8EV2
ID8 cells infected with control lentivirus and grown as 2D culture, sample 2


title: T19


title: Col-0 pistil grown at hAT - replicate 1

description:
COL_HT1
unfertilized pistils (stage 11-12) from Col-0 plants grown at hAT (28/24) after the start of flowering


title: Sorted FBs TAC Il1b-KO_Rep2


title: DDX3 WT Cytoplasmic RNAseq replicate 2


title: DDX3 WT Cytoplasmic RNAseq replicate 1


title: Sorted FBs TAC WT _Rep1


title: T18


title: adbp-1 mutant L4 stage biol rep 2

city: Haifa

first: Ayelet

last: Lamm

address: Technion st

department: Biology

country: Israel

institute: Technion

data_processing:
The quality of RNA-seq reads was estimated by FastQC.
reads were processed and aligned to the C. elegans WS220 reference genome. The expression levels for each gene were evaluated by read counts. DESeq2 package in R  was used to identify differentially expressed genes.
Assembly: ws220
Supplementary files format and content: DEseq2 results based on normalized read counts; excel

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: All strains were raised at 20°C on enriched NGM with OP50 as food.

extract_protocol:
RNA was extracted by using Direct-zol RNA MiniPrep Plus (ZYMO). The RNA was treated with TURBO DNAse (Ambion).
Illumina TruSeq® RNA Sample Preparation kit.

value: whole worm

tag: Stage

value: L4 stage

value: adbp-1(qj1) II


title: T21


title: DDX3 T532M Nuclear RNAseq replicate 2

value: DDX3 T532M


title: T16


title: adbp-1 mutant L4 stage biol rep 1


title: DDX3 T532M Nuclear RNAseq replicate 1


title: T15


title: KO_rep2

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

description: 10x Genomics

data_processing:
Cellranger version 6.1.1 used with mm10 genome to align and count reads and generate filtered_feature_bc_matrix with default settings
filtered_feature_bc_matrix imported with R 4.1.2 and Seurat 4.1.1
Seurat SCTransform + CCA used to normalize and integrate datasets
PCA dimension reduction
UMAP visualization, louvain community clusters
Assembly: mm10
Supplementary files format and content: Seurat Objects in R data format. Read into R using the command readRDS(). Contains log normalized counts in "RNA" assay.

source_name: ocular immune cells

extract_protocol:
At 3 days following injury, mice were perfused with ice-cold saline solution, and eyes (n=16 WT eyes and n=16 Itgam-/-) were harvested and kept on ice. For two replicates per genotype, 8 eyes were used per sample. Eyes were cut open to collect vitreous humor in a 1.5 ml tube, and in a separate tube, retinas were collected. Retinas were subsequently digested in collagenase (1mg/ml) at 37°C for 30 min and manually triturated with a wide-bore pipette tip to generate a single-cell suspension. To block gene transcription, actinomycin D was added to the digestion solution. Cells from vitreous were pelleted by centrifugation at 500g and combined with retinal cells. To enrich for immune cells, cells were run over an anti-CD45+ magnetic beads column (Miltenyi, 130-052-301). Cells were eluted and counted with a hemocytometer.
The Chromium Next GEM Single Cell 3’ Reagent kit v3.1 (Dual Index) was used. Barcoding and library preparation was performed following the manufacturer’s protocols. Briefly, to generate single-cell gel-bead-in-emulsion (GEMs) solution, approximately 15,000 cells, in a final volume of 43 µl, were loaded on a Next GEM Chip G (10x Genomics) and processed with the 10x Genomics Chromium Controller

treatment_protocol: retro-orbital optic nerve crush combined with intro-ocular injection of particulate beta-glucan

value: ocular immune cells

value: Itgam-/-

value: 3 days post optic nerve crush plus intra-ocular injection of particulate beta-glucan

tag: developmental stage

value: adult


title: adbp-1 mutant embryo stage biol rep 3

value: embryo stage


title: DDX3 T532M Cytoplasmic RNAseq replicate 2


title: adbp-1 mutant embryo stage biol rep 2


title: T14


title: KO_rep1

description: 10x Genomics


title: WT_rep1

description: 10x Genomics

value: WT


title: DDX3 T532M Cytoplasmic RNAseq replicate 1

value: immortalized myelogenous leukemia


title: T13

value: oral squamous cell carcinoma


title: adbp-1 mutant embryo stage biol rep 1


title: T17


title: adbp-1 mutant L4 stage biol rep 3


title: PBMC_rep2

description: 10x Genomics

source_name: PBMC

value: PBMC

value: naive mice


title: DDX3 R534S Nuclear RNAseq replicate 1

value: DDX3 R534S


title: Lung Epithelium, ALI, rep3

city: Rotterdam

first: Bernard

middle: Setiawan

last: Stikker

state: South Holland

address: Dr Molewaterplein 40

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus MC

data_processing:
Reads were aligned to the hg38 build of the human reference genome using HISAT2.
H3K4Me2-enriched regions were identified using HOMER’s findPeaks command (-region -size 1000 -minDist 2500)
Called peaks were merged using HOMER's mergePeaks command
Assembly: hg38
Supplementary files format and content: bedGraph.gz files to visualize in UCSC Genome Browser

source_name: Bronchial brush

growth_protocol: Lymphocytes were cultured using RPMI 1640 (Gibco), 10% fetal calf serum (HyClone), 55 uM 2-mercaptoethanol (Sigma-Aldrich), 2 mM L-alanyl-L-glutamine (GlutaMAX, Gibco), 1 mM sodium pyruvate (Gibco), 0.1 mM nonessential amino acids (Gibco), 1% pen/strep (Gibco), 10 mM Hepes (Gibco) at 37 °C, 5% CO2. The primary bronchial epithelial cells were cultured at air-liquid interface conditions as previously described (Burgess et al., 2021; PMID: 32907887).  For mast cell culture, we refer to PMID:32112426. Neutrophils and Eosinophils were FACS sorted from PBMCs and directly lysed for ChIPmentation assays.

extract_protocol:
Cells were crosslinked using 1% formaldehyde. Cells were lysed and chromatin was sonicated using a Biorupter Pico (Diagenode).
H3K4Me2-marked chromatin was immunoprecipitated using 1 µL of antiH3K4Me2 antibody (ab32356, Abcam). Chromatin-antibody complexes were immobilized on magnetic beads and subjected to tagmentation. Eluted DNA was purified using MinElute spin columns (Qiagen) and amplified for 8-12 cycles using barcoded sequencing primers as per standard ATAC-Seq protocol. Libraries were purified using dual (0.5x-2.0x) SPRI Ampure XP beads (Beckman Coulter) and sequenced on a Illumina HiSeq2500 (Illumina) running a single-read 50 bp protocol.

value: Bronchial brush

value: Lung Epithelium

tag: chip antibody

value: H3K4me2 (ab32356, Abcam)


title: DDX3 R534S Nuclear RNAseq replicate 2


title: T12


title: T10


title: PBMC_rep1

description: 10x Genomics


title: SNCA_IL10

city: Milan

first: Edoardo

middle: Niccolò

last: Bellini

state: Lombardia

address: Via Olgettina 58

department: Neuroscience

country: Italy

institute: San Raffaele Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v 6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The normalization, scaling, dimensionality reduction clusterization steps were perfromed using Seurat V
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
Nigral tissues were dissociated using Adult Brain Dissociation Kit and OctoMACS Separator (both from Miltenyi Biotec) following manufacturer’s instructions. Collected cells were stained by Zombie Aqua Fixable Viability Kit (Biolegend) to label dead cells. Cells were sorted using a FACSAria Fusion sorter (BD) excluding cells labeled with anti-O4, anti-PSA-NCAM and anti-ACSA2 antibodies and selecting hematopoietic cells stained by anti-CD45 antibody. Cells were collected in PBS 0.04% BSA to be processed for sequencing.
After cell counting, cells deriving from the 4 different animals for each experimental condition were pulled together and nuclei were extracted following 10x Genomics protocol for Nuclei Isolation from Embryonic Mouse Brain Single Cell RNA-seq. A total of 1 million cells for each experimental condition were used as a starting point for nuclei extraction. After nuclei counting single cell libraries were prepared using Chromium Next Gene Expression Reagent Bundle (10x Genomics, cod. FC51000285).  For each experimental group a unique RNA-seq library was obtained and sequenced on a Nova-seq6000 platform at San Raffaele hospital omics facility

treatment_protocol: Five mice per group were injected bilaterally in the Substantia Nigra with 1,5uL of LV Mock ("WT" group), LV SNCA WT ("SNCA" group), LV IL10 ("IL10" group) or both LV SNCA WT and LV IL10 ("SNCA_IL10" group). After 5 weeks mice were perfused with PBS and the nigrostriatal tissue collected to be processed.

value: brain

value: 5 weeks old


title: DDX3 R534S Cytoplasmic RNAseq replicate 2


title: Lung Epithelium, ALI, rep2


title: Lung Epithelium, ALI, rep1


title: T1


title: DDX3 R534S Cytoplasmic RNAseq replicate 1


title: Mast cell, non-stimulated 0h, rep2

source_name: Mast cell (precursor-derived)

value: Mast cell (precursor-derived)


title: IL10

description: 10x Genomics


title: DDX3-R376C Nuclear RNAseq replicate 2


title: SNCA

description: 10x Genomics


title: Mast cell, non-stimulated 0h, rep1


title: DDX3-R376C Nuclear RNAseq replicate 1


title: N9

source_name: paracancerous tissues

value: paracancerous tissues


title: WT

description: 10x Genomics


title: DDX3-R376C Cytoplasmic RNAseq replicate 1


title: N7


title: T11

source_name: oral squamous cell carcinoma


title: Eosinophil, resting, rep2

source_name: Eosinophil

value: Eosinophil


title: Eosinophil, resting, rep3


title: scRNA-Seq TAC_antiIL1B_Ab2

first: Michael

last: Alexanian

institute: Gladstone Institutes

description:
TAC_antiIL1B_Ab2
Single-cell RNAseq in non-cardiomyocytes in the adult mouse heart with our without antibody-mediated IL1B neutralization

source_name: Heart Tissue (ventricles)

extract_protocol:
Isolation from mouse hearts were performed using two methodologies: to isolate non-cardiomyocytes (non-CM) cells from the ventricles using Langendorff perfusion (#1) and to isolate all nuclei from the ventricles using a Langendorff-free protocol (#2). For #1, after a proper level of anesthesia was induced, a thoracotomy was performed and the mouse heart was isolated, cannulated, and perfused with perfusion buffer (120.4 mM NaCl, 14.7 mM KCl, 0.6 mM KH2PO4, 0.6 mM Na2HPO4, 1.2 mM MgSO4, 10 mM Na-HEPES, 4.6 mM NaHCO3, 30 mM taurine, 10 mM 2,3-butanedione monoxime, and 5.5 mM glucose, pH 7.0) in a Langendorff perfusion system (Radnoti 120108EZ) for 5-10 minutes at 37°C. The cannulated heart was then digested with digestion buffer (perfusion buffer with 300 units/mL collagenase II (Worthington Biochemical) and 50 μM CaCl2) for approximately 10 min at 37°C. At the end of digestion, the atria and great vessels were removed and the ventricular tissue was transferred and gently teased into small pieces in stop buffer (perfusion buffer with 10% fetal bovine serum) at 37°C. After gently pipetting, the cell suspension was passed through a 250 μM strainer in a 50ml conical centrifuge tube and centrifuged at 30xg for 3 minutes at room temperature (RT). The supernatant, which contained most of the non-cardiomyocytes (non-CMs), was divided from the pellet (which contained the CM fraction). The non-CM fraction was centrifuged again at 30xg for 3 minutes at RT and the supernatant retained. The supernatant was filtered with a cell strainer (70 μm) and centrifuged at 400xg for 3 minutes at RT for eliminating debris. The non-CM pellet was resuspended in 1mL cold PBS 0.5% BSA. Cells were counted with trypan blue using a hemocytometer and 15k cells were used for subsequent 10X Genomics Chromium single-cell RNAseq preparation. For single cell ATAC, 500k isolated and purified non-CMs were resuspended in 100uL lysis buffer (Tris-HCl 10mM pH 7.4, NaCl 10mM, MgCl2 3mM, Tween-20 0.1%, P40 0.1%, Digitonin 0.01%, BSA 1% in nuclease-free water), pipetted 10 times, and kept on ice for 5 minutes. Nuclei were washed with 1mL 1X PBS with 1% BSA and centrifuged for 5 minutes at 4 °C. The nuclei pellet was resuspended in 1mL 1X PBS with 1% BSA and filtered with a 10uM strainer (pluriSelect #43-50010-00). Nuclei were counted after DAPI staining using a hemocytometer and 10k non-CM nuclei were used for subsequent 10X Genomics Chromium single-cell ATAC-seq preparation. finally centrifuged at 400xg for 3 minutes in stop buffer at RT and the supernatant was discarded. For #2, after the mouse heart was isolated it was rinsed in a sterile 10cm petri dish containing 1X PBS on ice to remove excess blood and transferred to a 10cm petri dish containing 2ml of ice cold lysis buffer (320 mM sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 2 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8.0, 0.20% triton X-100) and minced into very small pieces. The minced heart tissue in 2ml of lysis buffer was transferred to a “Type A” dounce homogenizer and subjected to 50 strokes. This solution was subsequently transferred to a “Type B” dounce homogenizer and subjected to 3 strokes. The solution was serially passed through 100 μM and 70 μM strainers and then centrifuged at 1,000xg at 4 °C for 8 minutes. The nuclear pellet was resuspended in nuclei resuspension buffer (430 mM sucrose, 70 mM KCl, 2 mM MgCl2, 10 mM Tris-HCl ph 7.2, EGTA 5 mM, 10% glycerol). Nuclei were counted after DAPI staining using a hemocytometer and 15,000 nuclei were used for subsequent 10X Genomics Chromium single-nuclei RNAseq and 10,000 nuclei were used for ATAC-seq.
For sc/snRNA-seq library preparation, cells or nuclei were loaded onto the 10X Genomics Chromium instrument according to manufacturer’s protocols (Chip G, PN-1000120). All experiments were conducted with version 3.1 NEXT GEM reagents (PN-1000121), using 9 cycles of cDNA amplification for the GEM kit (PN-1000123) and 9 cycles of library amplification for library kit (PN-1000157). Each sample was indexed with a unique sample primer (Single Index Kit T Set A, PN-000213).
Single Cell or Nuclei RNA-seq

value: non-cardiomyocyte  cells

value: Heart Tissue (ventricles)

value: 3-5 months


title: Eosinophil, resting, rep1


title: scRNA-Seq TAC_IgG_Ab2

description:
TAC_IgG_Ab2
Single-cell RNAseq in non-cardiomyocytes in the adult mouse heart with our without antibody-mediated IL1B neutralization


title: N69

extract_protocol:
extract protocol RNA was harvested using mirVanaTM miRNA ISOlation Kit (Ambion-1561).
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions


title: N68


title: DDX3-R351W Nuclear RNAseq replicate 2


title: DDX3-R351W Nuclear RNAseq replicate 1


title: scRNA-Seq TAC_antiIL1B_Ab1

description:
TAC_antiIL1B_Ab1
Single-cell RNAseq in non-cardiomyocytes in the adult mouse heart with our without antibody-mediated IL1B neutralization


title: N67


title: N8


title: Neutrophil, resting, rep3

source_name: Neutrophil

value: Neutrophil


title: scRNA-Seq TAC_IgG_Ab1

description:
TAC_IgG_Ab1
Single-cell RNAseq in non-cardiomyocytes in the adult mouse heart with our without antibody-mediated IL1B neutralization


title: DDX3-R351W Cytoplasmic RNAseq replicate 2

value: immortalized myelogenous leukemia


title: Neutrophil, resting, rep2


title: scRNA-Seq TAC_BRD4KO_rep2

description:
TAC_BRD4KO_rep2
Single-nuclei RNAseq in cardiac ventricles with or without Brd4 deletion in Cx3cr1-positive cells

value: Nuclei from all heart tissue


title: Sorted FBs TAC WT _Rep2

value: Sorted cardiac fibroblasts

value: heart


title: DDX3-R351W Cytoplasmic RNAseq replicate 1


title: N66


title: N65


title: Neutrophil, resting, rep1


title: WT_rep2

description: 10x Genomics

value: ocular immune cells

value: WT

value: 3 days post optic nerve crush plus intra-ocular injection of particulate beta-glucan

value: adult


title: DDX3-R326H Nuclear RNAseq replicate 2


title: scRNA-Seq TAC_BRD4KO_rep1

description:
TAC_BRD4KO_rep1
Single-nuclei RNAseq in cardiac ventricles with or without Brd4 deletion in Cx3cr1-positive cells


title: CD19+ Bcell,memory,rep2

source_name: Memory B cell

value: Memory B cell

value: H3K4me2 (ab32356, Abcam)


title: DDX3-R326H Cytoplasmic RNAseq replicate 2


title: N64


title: CD19+ Bcell,memory,rep3


title: N63


title: DDX3-R326H Cytoplasmic RNAseq replicate 1


title: scRNA-Seq CD45pos_TAC_BRD4KO_rep2

description:
CD45pos_TAC_BRD4KO_rep2
Single-cell RNAseq in the CD45-positive cardiac cells with or without Brd4 deletion in Cx3cr1-positive cells

value: CD45 sorted cells


title: CD19+ Bcell,memory,rep1


title: DDX3-R326H Nuclear RNAseq replicate 1


title: N62

value: paracancerous tissues


title: scRNA-Seq TAC_WT_2

description:
TAC_WT_2
Single-nuclei RNAseq in cardiac ventricles with or without Brd4 deletion in Cx3cr1-positive cells


title: CD19+ Bcell,naive,rep3

source_name: Naive B cell

value: Naive B cell


title: DDX3-G325E Nuclear RNAseq replicate 2


title: N61


title: N60


title: scRNA-Seq TAC_WT_rep1

description:
TAC_WT_rep1
Single-nuclei RNAseq in cardiac ventricles with or without Brd4 deletion in Cx3cr1-positive cells


title: scRNA-Seq CD45pos_TAC_WT_rep2

description:
CD45pos_TAC_WT_rep2
Single-cell RNAseq in the CD45-positive cardiac cells with or without Brd4 deletion in Cx3cr1-positive cells


title: DDX3-G325E Nuclear RNAseq replicate 1


title: CD19+ Bcell,naive,rep2


title: CD19+ Bcell,naive,rep1


title: N6


title: scRNA-Seq CD45pos_TAC_WT_rep1

description:
CD45pos_TAC_WT_rep1
Single-cell RNAseq in the CD45-positive cardiac cells with or without Brd4 deletion in Cx3cr1-positive cells


title: scRNA-Seq CD45+ Sham

description:
CD45+ Sham
Single-cell RNAseq in the CD45-positive cardiac cells with or without Brd4 deletion in Cx3cr1-positive cells


title: DDX3-G325E Cytoplasmic RNAseq replicate 2


title: N59


title: CD8+ Tcell, memory, rep3

source_name: Memory CD8+ T cell

value: Memory CD8+ T cell


title: DDX3-G325E Cytoplasmic RNAseq replicate 1


title: CD8+ Tcell, memory, rep2


title: K562_nuclear_ZFC3H1_60min_rep2_dox

city: Boston

first: Brendan

middle: Michael

last: Smalec

state: MA

address: 77 Avenue Louis Pasteur, Rm 356

department: Genetics

institute: Harvard Medical School

description:
ZFC3H1_60_nuc_rep2_dox
K562_dox_ZFC3H1_nuc_rep2_exons.tsv
K562_dox_ZFC3H1_nuc_rep2_introns.tsv
K562_dox_ZFC3H1_nuc_rep2_protein_coding.tsv
K562_dox_ZFC3H1_nuc_rep2_retained_introns.tsv
K562_dox_ZFC3H1_nuc_rep2_retained_introns_with_exons.tsv
K562_dox_ZFC3H1_nuc_rep2_unspliced_junctions.tsv

data_processing:
Read trimming with cutadapt v2.5 (see Churchman lab github for complete steps)
Alignment with STAR v2.7.0a (see Churchman lab github for complete steps)
Conversion to .cit format with GRAND-SLAM v2.0.5d (see Churchman lab github for complete steps)
Estimation of fraction new RNA with GRAND-SLAM v2.0.5d (see Churchman lab github for complete steps)
Assembly: K562 data: hg38; NIH-3T3 data: mm10
Supplementary files format and content: .tsv files containing fraction new RNA estimates from GRAND-SLAM

extract_protocol:
RNA was extracted from subcellular fractions with Trizol LS according to the manufacturer's protocol.
2.5ug purified RNA was subjected to TimeLapse chemistry (Schofield et al., 2018) and then 1ug was used for library preparation with the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara) according to the manufacturer's protocol.

value: ZFC3H1 shRNA + doxycycline

tag: time


title: N58

data_processing:
Raw data (raw reads) were processed using Trimmomatic software. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2 software.
Raw read counts of each gene were obtained by htseq-count software.
Assembly: hg38
Supplementary files format and content: txt file contains raw counts of each gene


title: CD8+ Tcell, memory, rep1


title: scRNA-Seq TAC_JQ1_rep3

description:
TAC_JQ1_rep3
Single-cell RNAseq in non-cardiomyocytes in the adult mouse heart with our without BET inhibitio JQ1

value: non-cardiomyocyte  cells

value: Heart Tissue (ventricles)

value: 3-5 months


title: K562_nuclear_ZFC3H1_60min_rep1_dox

description:
ZFC3H1_60_nuc_rep1_dox
K562_dox_ZFC3H1_nuc_rep1_exons.tsv
K562_dox_ZFC3H1_nuc_rep1_introns.tsv
K562_dox_ZFC3H1_nuc_rep1_protein_coding.tsv
K562_dox_ZFC3H1_nuc_rep1_retained_introns.tsv
K562_dox_ZFC3H1_nuc_rep1_retained_introns_with_exons.tsv
K562_dox_ZFC3H1_nuc_rep1_unspliced_junctions.tsv


title: scRNA-Seq TAC_JQ1_rep2

description:
TAC_JQ1_rep2
Single-cell RNAseq in non-cardiomyocytes in the adult mouse heart with our without BET inhibitio JQ1


title: CD8+ Tcell, naive, rep3

source_name: Naive CD8+ T cell

value: Naive CD8+ T cell


title: N57


title: scRNA-Seq CD45pos_TAC_BRD4KO_rep1

description:
CD45pos_TAC_BRD4KO_rep1
Single-cell RNAseq in the CD45-positive cardiac cells with or without Brd4 deletion in Cx3cr1-positive cells


title: scRNA-Seq TAC_JQ1_rep1

description:
TAC_JQ1_rep1
Single-cell RNAseq in non-cardiomyocytes in the adult mouse heart with our without BET inhibitio JQ1


title: CD8+ Tcell, naive, rep2


title: K562_total_ZFC3H1_60min_rep2_dox

description:
ZFC3H1_60_tot_rep2_dox
K562_dox_ZFC3H1_tot_rep2_exons.tsv
K562_dox_ZFC3H1_tot_rep2_introns.tsv
K562_dox_ZFC3H1_tot_rep2_protein_coding.tsv
K562_dox_ZFC3H1_tot_rep2_retained_introns.tsv
K562_dox_ZFC3H1_tot_rep2_retained_introns_with_exons.tsv
K562_dox_ZFC3H1_tot_rep2_unspliced_junctions.tsv


title: K562_total_ZFC3H1_60min_rep1_dox

description:
ZFC3H1_60_tot_rep1_dox
K562_dox_ZFC3H1_tot_rep1_exons.tsv
K562_dox_ZFC3H1_tot_rep1_introns.tsv
K562_dox_ZFC3H1_tot_rep1_protein_coding.tsv
K562_dox_ZFC3H1_tot_rep1_retained_introns.tsv
K562_dox_ZFC3H1_tot_rep1_retained_introns_with_exons.tsv
K562_dox_ZFC3H1_tot_rep1_unspliced_junctions.tsv


title: N55


title: N54


title: Mtb infected PBMCs

city: beijing

first: lu

last: z

state: - 选择 -

address: beijing

institute: institution of microbology

description: The PBMCs from healthy volunteer's blood  were seeded in 100-mm dishes at 1  10^7 cells/dish then infected with Mtb at a multiplicity of infection (MOI) of 5. After 2 hours, the media were discarded. Cells were washed for three times with 1  PBS to exclude noninternalized bacteria, and were  incubated with the fresh DMEM medium for additional 10 hours.

data_processing:
Basecalls were performed using bcl2fastq v.217 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score >30. using Trimmomatic v0.33, discarding reads left with <20bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. only uniquely mapping reads  with at most two mismatches were retained.
Binding sites were identified using MACS1.4 with a chromatin input library as the control data set. MACS assigns every candidate peak an enrichment P value, and those below a user-defined threshold P value (default 10−5) are reported as the final peaks. The ratio between the ChIP-seq tag count and λlocal is reported as the fold enrichment.

source_name: Blood

extract_protocol:
Cells were seeded in 100-mm dishes at 1 × 107 cells/dish then cross-linked with 1% formaldehyde for 10 minutes at room temperature, and quenched for 5 minutes with 0.125 M glycine. Afterward, cells were collected and lysed in 1% SDS lysis buffer supplemented with protease inhibitors cocktail, sonicated with a 1/8-inch probe (5 seconds on/10 seconds off, 30 cycles, 25% of maxi power) by sonicator (Branson 550) to obtain genomic DNA fragments with an average size of 150–500 bp. ChIP was performed following the protocol provided by Millipore ChIP Assay kit (Millipore, Cat# 17-409) according to the manufacturer’s introduction.
ChIP-seq libraries were prepared using the KAPA HtP Library Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Blood

value: Human PBMCs

value: Mycobacterium tuberculosis (Mtb) infected


title: CD8+ Tcell, naive, rep1


title: scRNA-Seq TAC_rep2

description:
TAC_rep2
Single-cell RNAseq in non-cardiomyocytes in the adult mouse heart with our without BET inhibitio JQ1


title: K562_total_ZFC3H1_0min_rep1_dox

description:
ZFC3H1_0_tot_rep1_dox
K562_dox_ZFC3H1_tot_rep1_exons.tsv
K562_dox_ZFC3H1_tot_rep1_introns.tsv
K562_dox_ZFC3H1_tot_rep1_protein_coding.tsv
K562_dox_ZFC3H1_tot_rep1_retained_introns.tsv
K562_dox_ZFC3H1_tot_rep1_retained_introns_with_exons.tsv
K562_dox_ZFC3H1_tot_rep1_unspliced_junctions.tsv


title: K562_total_ZFC3H1_0min_rep2_dox

description:
ZFC3H1_0_tot_rep2_dox
K562_dox_ZFC3H1_tot_rep2_exons.tsv
K562_dox_ZFC3H1_tot_rep2_introns.tsv
K562_dox_ZFC3H1_tot_rep2_protein_coding.tsv
K562_dox_ZFC3H1_tot_rep2_retained_introns.tsv
K562_dox_ZFC3H1_tot_rep2_retained_introns_with_exons.tsv
K562_dox_ZFC3H1_tot_rep2_unspliced_junctions.tsv


title: Sorted FBs TAC Il1b-KO_Rep1

description: Single-cell RNAseq in the mEFSK-positive cardiac fibroblasts with or without Il1b deletion in Cx3cr1-positive cells

source_name: heart

value: Sorted cardiac fibroblasts

value: heart


title: Uninfected PBMCs

description: The PBMCs from healthy volunteer's blood  were seeded in 100-mm dishes at 1  10^7 cells/dish and then  incubated with the fresh DMEM medium for 12 hours.

value: No Treatment


title: N53

first: Hailong

last: Ma

institute: Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine


title: scRNA-Seq Sham_rep3

description:
Sham_rep3
Single-cell RNAseq in non-cardiomyocytes in the adult mouse heart with our without BET inhibitio JQ1


title: K562_nuclear_PABPN1_60min_rep2_dox

description:
PABPN1_60_nuc_rep2_dox
K562_dox_PABPN1_nuc_rep2_exons.tsv
K562_dox_PABPN1_nuc_rep2_introns.tsv
K562_dox_PABPN1_nuc_rep2_protein_coding.tsv
K562_dox_PABPN1_nuc_rep2_retained_introns.tsv
K562_dox_PABPN1_nuc_rep2_retained_introns_with_exons.tsv
K562_dox_PABPN1_nuc_rep2_unspliced_junctions.tsv

value: PABPN1 shRNA + doxycycline


title: scRNA-Seq TAC_rep3

description:
TAC_rep3
Single-cell RNAseq in non-cardiomyocytes in the adult mouse heart with our without BET inhibitio JQ1


title: scRNA-Seq Sham_rep2

description:
Sham_rep2
Single-cell RNAseq in non-cardiomyocytes in the adult mouse heart with our without BET inhibitio JQ1


title: N56


title: NRVMs, si-RNA Dsp biol rep5

city: Chicago,

first: Daniel

last: Selgrade

state: IL

address: 303 E. Superior Street

institute: Northwestern University

data_processing:
Raw reads were trimmed with trimmomatic (v0.36) and aligned to the human (hg19)  or rat (rn6) genome using STAR with default settings.
Uniquely aligned reads were assigned to genes using htseq-count.
Raw counts were normalized with EdgeR and used to identify differentially expressed genes.
Assembly: rn6
Assembly: hg19
Supplementary files format and content: tab-delimited text file contains CPM for each sample as well as log fold change, logCPM, likelihood ratio, p-value and FDR p-value for each gene.

organism: Rattus norvegicus

source_name: NRVM

growth_protocol: NRVCMs were cultured in M199 medium (Lonza) supplemented with 1% penicillin/streptomycin, heat-inactivated horse serum (Gibco), 15 µM vitamin B12 (Sigma-Aldrich), and 100 µM bromodeoxyuridine (Sigma-Aldrich). EHTs were cultured in  Dulbecco’s Modified Eagle’s Medium (DMEM) low glucose (Sigma, Cat#D5546), 10% horse serum (heat inactivated, New Zealand origin, Gibco, Cat#26050088), 1% Penicillin/Streptomycin (Thermo, Cat#15070063), and 0.1% human insulin (10 mg/mL, Sigma Cat#19278).

extract_protocol:
RNA was isolated using TRIzol™ Reagent (ThermoFisher Scientific). RNA isolation was performed with the Aurum Total RNA Mini Kit (Biorad) according to manufacturer specifications.
RNA libraries for RNA-Seq were prepared using TruSeq Stranded mRNA (Illumina) according to manufacturer's protocols.

treatment_protocol: For siRNA knockdown, constructs were cloned into the pAd/cytomegalovirus (CMV)/V5-DEST vector (Invitrogen) and used to generate virus using the ViraPower Adenoviral Expression System (Invitrogen).

value: NRVM

value: Dsp knockdown

value: siRNA


title: NRVMs, si-RNA Dsp biol rep4


title: N50

address: Zhizaoju Rd

value: paracancerous tissues


title: scRNA-Seq Sham_rep1

description:
Sham_rep1
Single-cell RNAseq in non-cardiomyocytes in the adult mouse heart with our without BET inhibitio JQ1


title: K562_total_PABPN1_60min_rep2_dox

description:
PABPN1_60_tot_rep2_dox
K562_dox_PABPN1_tot_rep2_exons.tsv
K562_dox_PABPN1_tot_rep2_introns.tsv
K562_dox_PABPN1_tot_rep2_protein_coding.tsv
K562_dox_PABPN1_tot_rep2_retained_introns.tsv
K562_dox_PABPN1_tot_rep2_retained_introns_with_exons.tsv
K562_dox_PABPN1_tot_rep2_unspliced_junctions.tsv


title: K562_total_PABPN1_60min_rep1_dox

description:
PABPN1_60_tot_rep1_dox
K562_dox_PABPN1_tot_rep1_exons.tsv
K562_dox_PABPN1_tot_rep1_introns.tsv
K562_dox_PABPN1_tot_rep1_protein_coding.tsv
K562_dox_PABPN1_tot_rep1_retained_introns.tsv
K562_dox_PABPN1_tot_rep1_retained_introns_with_exons.tsv
K562_dox_PABPN1_tot_rep1_unspliced_junctions.tsv


title: scATAC-Seq CD45pos_TAC_BRD4KO_rep2

description:
CD45pos_TAC_BRD4KO_rep2
Single-cell ATAC-seq in CD45-positive cardiac cells  with or without Brd4 deletion in Cx3cr1-positive cells

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger-Atac Suite v2 from 10X genomics
Additional filtering, quality control and doublet removal was performed using ArchR v1.0.1
Assembly: mm10
Supplementary files format and content: Cellranger-atac fragments fileș în tsv format

extract_protocol:
Isolation from mouse hearts were performed using two methodologies: to isolate non-cardiomyocytes (non-CM) cells from the ventricles using Langendorff perfusion (#1) and to isolate all nuclei from the ventricles using a Langendorff-free protocol (#2). For #1, after a proper level of anesthesia was induced, a thoracotomy was performed and the mouse heart was isolated, cannulated, and perfused with perfusion buffer (120.4 mM NaCl, 14.7 mM KCl, 0.6 mM KH2PO4, 0.6 mM Na2HPO4, 1.2 mM MgSO4, 10 mM Na-HEPES, 4.6 mM NaHCO3, 30 mM taurine, 10 mM 2,3-butanedione monoxime, and 5.5 mM glucose, pH 7.0) in a Langendorff perfusion system (Radnoti 120108EZ) for 5-10 minutes at 37°C. The cannulated heart was then digested with digestion buffer (perfusion buffer with 300 units/mL collagenase II (Worthington Biochemical) and 50 μM CaCl2) for approximately 10 min at 37°C. At the end of digestion, the atria and great vessels were removed and the ventricular tissue was transferred and gently teased into small pieces in stop buffer (perfusion buffer with 10% fetal bovine serum) at 37°C. After gently pipetting, the cell suspension was passed through a 250 μM strainer in a 50ml conical centrifuge tube and centrifuged at 30xg for 3 minutes at room temperature (RT). The supernatant, which contained most of the non-cardiomyocytes (non-CMs), was divided from the pellet (which contained the CM fraction). The non-CM fraction was centrifuged again at 30xg for 3 minutes at RT and the supernatant retained. The supernatant was filtered with a cell strainer (70 μm) and centrifuged at 400xg for 3 minutes at RT for eliminating debris. The non-CM pellet was resuspended in 1mL cold PBS 0.5% BSA. Cells were counted with trypan blue using a hemocytometer and 15k cells were used for subsequent 10X Genomics Chromium single-cell RNAseq preparation. For single cell ATAC, 500k isolated and purified non-CMs were resuspended in 100uL lysis buffer (Tris-HCl 10mM pH 7.4, NaCl 10mM, MgCl2 3mM, Tween-20 0.1%, P40 0.1%, Digitonin 0.01%, BSA 1% in nuclease-free water), pipetted 10 times, and kept on ice for 5 minutes. Nuclei were washed with 1mL 1X PBS with 1% BSA and centrifuged for 5 minutes at 4 °C. The nuclei pellet was resuspended in 1mL 1X PBS with 1% BSA and filtered with a 10uM strainer (pluriSelect #43-50010-00). Nuclei were counted after DAPI staining using a hemocytometer and 10k non-CM nuclei were used for subsequent 10X Genomics Chromium single-cell ATAC-seq preparation. finally centrifuged at 400xg for 3 minutes in stop buffer at RT and the supernatant was discarded. For #2, after the mouse heart was isolated it was rinsed in a sterile 10cm petri dish containing 1X PBS on ice to remove excess blood and transferred to a 10cm petri dish containing 2ml of ice cold lysis buffer (320 mM sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 2 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8.0, 0.20% triton X-100) and minced into very small pieces. The minced heart tissue in 2ml of lysis buffer was transferred to a “Type A” dounce homogenizer and subjected to 50 strokes. This solution was subsequently transferred to a “Type B” dounce homogenizer and subjected to 3 strokes. The solution was serially passed through 100 μM and 70 μM strainers and then centrifuged at 1,000xg at 4 °C for 8 minutes. The nuclear pellet was resuspended in nuclei resuspension buffer (430 mM sucrose, 70 mM KCl, 2 mM MgCl2, 10 mM Tris-HCl ph 7.2, EGTA 5 mM, 10% glycerol). Nuclei were counted after DAPI staining using a hemocytometer and 15,000 nuclei were used for subsequent 10X Genomics Chromium single-nuclei RNAseq and 10,000 nuclei were used for ATAC-seq.
For scATAC-seq library preparation, nuclei were first transposed with Tn5 enzyme (PN-2000138) and then loaded onto the Chromium instrument (Chip H, PN-1000161) using the version 1.1 NEXT GEM reagents (PN-1000175). Library preparation proceeded with 12 cycles each of GEM barcoding and library amplification. Each sample was indexed with a unique sample primer (Single Index Plate N Set A, PN-3000427). For both scRNA-seq and scATAC-seq, samples were pooled separately into respective libraries and sequenced on an Illumina NextSeq 500 (Illumina, software 4.0.2) and/or a lane of a Novaseq S4 (Illumina, software v1.5), according to manufacturer’s guidelines for sc/snRNA-seq and scATAC-seq, respectively.

value: CD45 sorted cells


title: NRVMs, si-RNA Jup biol rep6

value: Jup knockdown


title: K562_total_PABPN1_0min_rep2_dox

description:
PABPN1_0_tot_rep2_dox
K562_dox_PABPN1_tot_rep2_exons.tsv
K562_dox_PABPN1_tot_rep2_introns.tsv
K562_dox_PABPN1_tot_rep2_protein_coding.tsv
K562_dox_PABPN1_tot_rep2_retained_introns.tsv
K562_dox_PABPN1_tot_rep2_retained_introns_with_exons.tsv
K562_dox_PABPN1_tot_rep2_unspliced_junctions.tsv


title: N5


title: scATAC-Seq CD45pos_TAC_BRD4KO_rep1

description:
CD45pos_TAC_BRD4KO_rep1
Single-cell ATAC-seq in CD45-positive cardiac cells  with or without Brd4 deletion in Cx3cr1-positive cells


title: scRNA-Seq TAC_rep1

description:
TAC_rep1
Single-cell RNAseq in non-cardiomyocytes in the adult mouse heart with our without BET inhibitio JQ1

value: non-cardiomyocyte  cells


title: N52


title: N48


title: K562_total_PABPN1_0min_rep1_dox

description:
PABPN1_0_tot_rep1_dox
K562_dox_PABPN1_tot_rep1_exons.tsv
K562_dox_PABPN1_tot_rep1_introns.tsv
K562_dox_PABPN1_tot_rep1_protein_coding.tsv
K562_dox_PABPN1_tot_rep1_retained_introns.tsv
K562_dox_PABPN1_tot_rep1_retained_introns_with_exons.tsv
K562_dox_PABPN1_tot_rep1_unspliced_junctions.tsv


title: scATAC-Seq CD45pos_TAC_WT_rep2

description:
CD45pos_TAC_WT_rep2
Single-cell ATAC-seq in CD45-positive cardiac cells  with or without Brd4 deletion in Cx3cr1-positive cells

value: Heart Tissue (ventricles)


title: N49


title: NRVMs, si-RNA Jup biol rep5


title: NRVMs, si-RNA Dsp biol rep6


title: scATAC-Seq CD45pos_TAC_WT_rep1

description:
CD45pos_TAC_WT_rep1
Single-cell ATAC-seq in CD45-positive cardiac cells  with or without Brd4 deletion in Cx3cr1-positive cells

value: 3-5 months


title: K562_nuclear_EXOSC10_60min_rep2_dox

description:
EXOSC10_60_nuc_rep2_dox
K562_dox_EXOSC10_nuc_rep2_exons.tsv
K562_dox_EXOSC10_nuc_rep2_introns.tsv
K562_dox_EXOSC10_nuc_rep2_protein_coding.tsv
K562_dox_EXOSC10_nuc_rep2_retained_introns.tsv
K562_dox_EXOSC10_nuc_rep2_retained_introns_with_exons.tsv
K562_dox_EXOSC10_nuc_rep2_unspliced_junctions.tsv

value: EXOSC10 shRNA + doxycycline


title: N51


title: NRVMs, si-RNA Jup biol rep4


title: N47


title: K562_nuclear_PABPN1_60min_rep1_dox

description:
PABPN1_60_nuc_rep1_dox
K562_dox_PABPN1_nuc_rep1_exons.tsv
K562_dox_PABPN1_nuc_rep1_introns.tsv
K562_dox_PABPN1_nuc_rep1_protein_coding.tsv
K562_dox_PABPN1_nuc_rep1_retained_introns.tsv
K562_dox_PABPN1_nuc_rep1_retained_introns_with_exons.tsv
K562_dox_PABPN1_nuc_rep1_unspliced_junctions.tsv


title: K562_nuclear_EXOSC10_60min_rep1_dox

description:
EXOSC10_60_nuc_rep1_dox
K562_dox_EXOSC10_nuc_rep1_exons.tsv
K562_dox_EXOSC10_nuc_rep1_introns.tsv
K562_dox_EXOSC10_nuc_rep1_protein_coding.tsv
K562_dox_EXOSC10_nuc_rep1_retained_introns.tsv
K562_dox_EXOSC10_nuc_rep1_retained_introns_with_exons.tsv
K562_dox_EXOSC10_nuc_rep1_unspliced_junctions.tsv


title: scATAC-Seq CD45pos_Sham

description:
CD45pos_Sham
Single-cell ATAC-seq in CD45-positive cardiac cells  with or without Brd4 deletion in Cx3cr1-positive cells


title: K562_total_EXOSC10_60min_rep2_dox

description:
EXOSC10_60_tot_rep2_dox
K562_dox_EXOSC10_tot_rep2_exons.tsv
K562_dox_EXOSC10_tot_rep2_introns.tsv
K562_dox_EXOSC10_tot_rep2_protein_coding.tsv
K562_dox_EXOSC10_tot_rep2_retained_introns.tsv
K562_dox_EXOSC10_tot_rep2_retained_introns_with_exons.tsv
K562_dox_EXOSC10_tot_rep2_unspliced_junctions.tsv


title: NRVMs, si-RNA Pkp2 biol rep4

value: Pkp2 knockdown


title: N45


title: NRVMs, si-RNA Pkp2 biol rep5


title: K562_total_EXOSC10_60min_rep1_dox

description:
EXOSC10_60_tot_rep1_dox
K562_dox_EXOSC10_tot_rep1_exons.tsv
K562_dox_EXOSC10_tot_rep1_introns.tsv
K562_dox_EXOSC10_tot_rep1_protein_coding.tsv
K562_dox_EXOSC10_tot_rep1_retained_introns.tsv
K562_dox_EXOSC10_tot_rep1_retained_introns_with_exons.tsv
K562_dox_EXOSC10_tot_rep1_unspliced_junctions.tsv


title: scATAC-Seq TAC_BRD4KO_rep1

description:
TAC_BRD4KO_rep1
Single-cell ATAC-seq in cardiac ventricles with or without Brd4 deletion in Cx3cr1-positive cells

value: Nuclei from all heart tissue


title: NRVMs, si-RNA scramble biol rep6

value: WT scramble siRNA


title: K562_total_EXOSC10_0min_rep2_dox

description:
EXOSC10_0_tot_rep2_dox
K562_dox_EXOSC10_tot_rep2_exons.tsv
K562_dox_EXOSC10_tot_rep2_introns.tsv
K562_dox_EXOSC10_tot_rep2_protein_coding.tsv
K562_dox_EXOSC10_tot_rep2_retained_introns.tsv
K562_dox_EXOSC10_tot_rep2_retained_introns_with_exons.tsv
K562_dox_EXOSC10_tot_rep2_unspliced_junctions.tsv


title: N44


title: N43


title: NRVMs, si-RNA scramble biol rep5


title: scATAC-Seq TAC_WT_rep2

description:
TAC_WT_rep2
Single-cell ATAC-seq in cardiac ventricles with or without Brd4 deletion in Cx3cr1-positive cells


title: N42


title: K562_total_EXOSC10_0min_rep1_dox

description:
EXOSC10_0_tot_rep1_dox
K562_dox_EXOSC10_tot_rep1_exons.tsv
K562_dox_EXOSC10_tot_rep1_introns.tsv
K562_dox_EXOSC10_tot_rep1_protein_coding.tsv
K562_dox_EXOSC10_tot_rep1_retained_introns.tsv
K562_dox_EXOSC10_tot_rep1_retained_introns_with_exons.tsv
K562_dox_EXOSC10_tot_rep1_unspliced_junctions.tsv


title: NRVMs, si-RNA scramble biol rep4


title: K562_nuclear_DIS3_60min_rep2_dox

description:
DIS3_60_nuc_rep2_dox
K562_dox_DIS3_nuc_rep2_exons.tsv
K562_dox_DIS3_nuc_rep2_introns.tsv
K562_dox_DIS3_nuc_rep2_protein_coding.tsv
K562_dox_DIS3_nuc_rep2_retained_introns.tsv
K562_dox_DIS3_nuc_rep2_retained_introns_with_exons.tsv
K562_dox_DIS3_nuc_rep2_unspliced_junctions.tsv

value: DIS3 shRNA + doxycyline


title: N41


title: NRVMs, si-RNA Pkp2 biol rep6


title: 3T3_chromatin_WT_120min_rep2

description:
S5-chr
3T3_chromatin_WT_rep2.tsv


title: K562_nuclear_DIS3_60min_rep1_dox

description:
DIS3_60_nuc_rep1_dox
K562_dox_DIS3_nuc_rep1_exons.tsv
K562_dox_DIS3_nuc_rep1_introns.tsv
K562_dox_DIS3_nuc_rep1_protein_coding.tsv
K562_dox_DIS3_nuc_rep1_retained_introns.tsv
K562_dox_DIS3_nuc_rep1_retained_introns_with_exons.tsv
K562_dox_DIS3_nuc_rep1_unspliced_junctions.tsv


title: NRVMs, si-RNA Dsp biol rep2


title: K562_total_DIS3_60min_rep2_dox

description:
DIS3_60_tot_rep2_dox
K562_dox_DIS3_tot_rep2_exons.tsv
K562_dox_DIS3_tot_rep2_introns.tsv
K562_dox_DIS3_tot_rep2_protein_coding.tsv
K562_dox_DIS3_tot_rep2_retained_introns.tsv
K562_dox_DIS3_tot_rep2_retained_introns_with_exons.tsv
K562_dox_DIS3_tot_rep2_unspliced_junctions.tsv


title: 3T3_chromatin_WT_60min_rep2

description:
S4-chr
3T3_chromatin_WT_rep2.tsv


title: N4


title: N46


title: N40


title: 3T3_chromatin_WT_30min_rep2

description:
S3-chr
3T3_chromatin_WT_rep2.tsv


title: scATAC-Seq TAC_BRD4KO_rep2

description:
TAC_BRD4KO_rep2
Single-cell ATAC-seq in cardiac ventricles with or without Brd4 deletion in Cx3cr1-positive cells


title: NRVMs, si-RNA Dsp biol rep1


title: 3T3_chromatin_WT_15min_rep2

description:
S2-chr
3T3_chromatin_WT_rep2.tsv


title: K562_total_DIS3_60min_rep1_dox

description:
DIS3_60_tot_rep1_dox
K562_dox_DIS3_tot_rep1_exons.tsv
K562_dox_DIS3_tot_rep1_introns.tsv
K562_dox_DIS3_tot_rep1_protein_coding.tsv
K562_dox_DIS3_tot_rep1_retained_introns.tsv
K562_dox_DIS3_tot_rep1_retained_introns_with_exons.tsv
K562_dox_DIS3_tot_rep1_unspliced_junctions.tsv


title: 3T3_chromatin_WT_0min_rep2

description:
S1-chr
3T3_chromatin_WT_rep2.tsv


title: NRVMs, si-RNA Jup biol rep3


title: N38


title: NRVMs, si-RNA Dsp biol rep3


title: scATAC-Seq TAC_WT_rep1

description:
TAC_WT_rep1
Single-cell ATAC-seq in cardiac ventricles with or without Brd4 deletion in Cx3cr1-positive cells


title: N39


title: K562_total_DIS3_0min_rep1_dox

description:
DIS3_0_tot_rep1_dox
K562_dox_DIS3_tot_rep1_exons.tsv
K562_dox_DIS3_tot_rep1_introns.tsv
K562_dox_DIS3_tot_rep1_protein_coding.tsv
K562_dox_DIS3_tot_rep1_retained_introns.tsv
K562_dox_DIS3_tot_rep1_retained_introns_with_exons.tsv
K562_dox_DIS3_tot_rep1_unspliced_junctions.tsv


title: N37


title: NRVMs, si-RNA Jup biol rep2


title: NRVMs, si-RNA Jup biol rep1


title: NRVMs, si-RNA Pkp2 biol rep3


title: K562_nuclear_scramble_60min_rep2_dox

description:
scramble_60_nuc_rep2_dox
K562_dox_scramble_nuc_rep2_exons.tsv
K562_dox_scramble_nuc_rep2_introns.tsv
K562_dox_scramble_nuc_rep2_protein_coding.tsv
K562_dox_scramble_nuc_rep2_retained_introns.tsv
K562_dox_scramble_nuc_rep2_retained_introns_with_exons.tsv
K562_dox_scramble_nuc_rep2_unspliced_junctions.tsv

value: scramble shRNA + doxycycline


title: N35


title: 3T3_chromatin_WT_60min_rep1

description:
R4-chr
3T3_chromatin_WT_rep1.tsv


title: N34


title: K562_total_scramble_60min_rep2_dox

description:
scramble_60_tot_rep2_dox
K562_dox_scramble_tot_rep2_exons.tsv
K562_dox_scramble_tot_rep2_introns.tsv
K562_dox_scramble_tot_rep2_protein_coding.tsv
K562_dox_scramble_tot_rep2_retained_introns.tsv
K562_dox_scramble_tot_rep2_retained_introns_with_exons.tsv
K562_dox_scramble_tot_rep2_unspliced_junctions.tsv


title: K562_nuclear_scramble_60min_rep1_dox

description:
scramble_60_nuc_rep1_dox
K562_dox_scramble_nuc_rep1_exons.tsv
K562_dox_scramble_nuc_rep1_introns.tsv
K562_dox_scramble_nuc_rep1_protein_coding.tsv
K562_dox_scramble_nuc_rep1_retained_introns.tsv
K562_dox_scramble_nuc_rep1_retained_introns_with_exons.tsv
K562_dox_scramble_nuc_rep1_unspliced_junctions.tsv


title: 3T3_chromatin_WT_15min_rep1

description:
R2-chr
3T3_chromatin_WT_rep1.tsv


title: NRVMs, si-RNA Pkp2 biol rep1


title: NRVMs, si-RNA Pkp2 biol rep2


title: K562_total_scramble_60min_rep1_dox

description:
scramble_60_tot_rep1_dox
K562_dox_scramble_tot_rep1_exons.tsv
K562_dox_scramble_tot_rep1_introns.tsv
K562_dox_scramble_tot_rep1_protein_coding.tsv
K562_dox_scramble_tot_rep1_retained_introns.tsv
K562_dox_scramble_tot_rep1_retained_introns_with_exons.tsv
K562_dox_scramble_tot_rep1_unspliced_junctions.tsv


title: K562_total_DIS3_0min_rep2_dox

description:
DIS3_0_tot_rep2_dox
K562_dox_DIS3_tot_rep2_exons.tsv
K562_dox_DIS3_tot_rep2_introns.tsv
K562_dox_DIS3_tot_rep2_protein_coding.tsv
K562_dox_DIS3_tot_rep2_retained_introns.tsv
K562_dox_DIS3_tot_rep2_retained_introns_with_exons.tsv
K562_dox_DIS3_tot_rep2_unspliced_junctions.tsv


title: 3T3_chromatin_WT_0min_rep1

description:
R1-chr
3T3_chromatin_WT_rep1.tsv


title: NRVMs, si-RNA scramble biol rep3


title: K562_total_scramble_0min_rep2_dox

description:
scramble_0_tot_rep2_dox
K562_dox_scramble_tot_rep2_exons.tsv
K562_dox_scramble_tot_rep2_introns.tsv
K562_dox_scramble_tot_rep2_protein_coding.tsv
K562_dox_scramble_tot_rep2_retained_introns.tsv
K562_dox_scramble_tot_rep2_retained_introns_with_exons.tsv
K562_dox_scramble_tot_rep2_unspliced_junctions.tsv


title: 3T3_total_WT_120min_rep2

description:
H5-tot
3T3_total_WT_rep2.tsv


title: N32


title: NRVMs, si-RNA scramble biol rep2


title: 3T3_chromatin_WT_120min_rep1

description:
R5-chr
3T3_chromatin_WT_rep1.tsv


title: N36


title: 3T3_chromatin_WT_30min_rep1

description:
R3-chr
3T3_chromatin_WT_rep1.tsv


title: N31


title: 3T3_total_WT_30min_rep2

description:
H3-tot
3T3_total_WT_rep2.tsv


title: 3T3_total_WT_60min_rep2

description:
H4-tot
3T3_total_WT_rep2.tsv


title: N30


title: K562_cytoplasm_PABPC4_60min_rep2

description:
PABPC4_60_cyto_rep2
K562_PABPC4_cyto_rep2.tsv

value: PABPC4 shRNA


title: 3T3_total_WT_15min_rep2

description:
H2-tot
3T3_total_WT_rep2.tsv


title: N3


title: N33


title: K562_nuclear_PABPC4_60min_rep2

description:
PABPC4_60_nuc_rep2
K562_PABPC4_nuc_rep2.tsv


title: N29


title: 3T3_total_WT_0min_rep2

description:
H1-tot
3T3_total_WT_rep2.tsv


title: N28


title: K562_nuclear_PABPC4_60min_rep1

description:
PABPC4_60_nuc_rep1
K562_PABPC4_nuc_rep1.tsv


title: 3T3_polysome_WT_120min_rep2

description:
H5-poly
3T3_polysome_WT_rep2.tsv


title: N27


title: K562_chromatin_PABPC4_60min_rep2

description:
PABPC4_60_chr_rep2
K562_PABPC4_cyto_rep2.tsv


title: 3T3_polysome_WT_60min_rep2

description:
H4-poly
3T3_polysome_WT_rep2.tsv


title: K562_total_scramble_0min_rep1_dox

description:
scramble_0_tot_rep1_dox
K562_dox_scramble_tot_rep1_exons.tsv
K562_dox_scramble_tot_rep1_introns.tsv
K562_dox_scramble_tot_rep1_protein_coding.tsv
K562_dox_scramble_tot_rep1_retained_introns.tsv
K562_dox_scramble_tot_rep1_retained_introns_with_exons.tsv
K562_dox_scramble_tot_rep1_unspliced_junctions.tsv


title: N26


title: NRVMs, si-RNA scramble biol rep1


title: 3T3_polysome_WT_30min_rep2

description:
H3-poly
3T3_polysome_WT_rep2.tsv


title: K562_total_PABPC4_60min_rep2

description:
PABPC4_60_tot_rep2
K562_PABPC4_total_rep2.tsv


title: K562_cytoplasm_PABPC4_60min_rep1

description:
PABPC4_60_cyto_rep1
K562_PABPC4_cyto_rep1.tsv


title: N25


title: N24


title: Pituitary, group E, fish 240

type: RNA

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent G2565BA DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Pituitary

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon post smolts were kept in tanks with brackish water within a flow-through system, with an average salinity of 20 ± 0.4 ppt and mean temperature of 12.1 ± 0.2°C

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

treatment_protocol: Various light treatments were explored, including continuous exposure (Group A), increasing exposure (Group B), and decreasing exposure (Groups C, D and E) were investigated on growth and sexual maturation, sampling was performed after 18 weeks to assess gonadal growth and blood steroid hormone levels. All groups were provided with the same feed, except for Group E, which received a low-fat diet.

tag: developmental stage of testis

value: Stage I

value: Pituitary

tag: group

value: group E

tag: FISH id

value: fish 240


title: 3T3_polysome_WT_15min_rep2

description:
H2-poly
3T3_polysome_WT_rep2.tsv


title: Pituitary, group E, fish 233

tag: tissue

value: fish 233


title: Pituitary, group E, fish 226

value: fish 226


title: K562_total_PABPC4_0min_rep2

description:
PABPC4_0_tot_rep2
K562_PABPC4_total_rep2.tsv

tag: cell line


title: N22

value: paracancerous tissues


title: K562_total_PABPC4_0min_rep1

description:
PABPC4_0_tot_rep1
K562_PABPC4_total_rep1.tsv


title: Pituitary, group E, fish 236

value: fish 236


title: 3T3_cytoplasm_WT_120min_rep2

description:
H5-cyto
3T3_cytoplasm_WT_rep2.tsv


title: 3T3_polysome_WT_0min_rep2

description:
H1-poly
3T3_polysome_WT_rep2.tsv


title: 3T3_cytoplasm_WT_60min_rep2

description:
H4-cyto
3T3_cytoplasm_WT_rep2.tsv


title: Pituitary, group D, fish 255

value: group D

value: fish 255


title: N23


title: Pituitary, group E, fish 221

value: fish 221


title: Pituitary, group D, fish 198

value: fish 198


title: K562_chromatin_PABPC4_60min_rep1

description:
PABPC4_60_chr_rep1
K562_PABPC4_cyto_rep1.tsv


title: K562_cytoplasm_DDX3X_60min_rep2

description:
DDX3X_60_cyto_rep2
K562_DDX3X_cyto_rep2.tsv

value: DDX3X shRNA


title: N21


title: Pituitary, group D, fish 193

value: fish 193


title: 3T3_cytoplasm_WT_30min_rep2

description:
H3-cyto
3T3_cytoplasm_WT_rep2.tsv


title: N20


title: K562_nuclear_DDX3X_60min_rep2

description:
DDX3X_60_nuc_rep2
K562_DDX3X_nuc_rep2.tsv


title: 3T3_cytoplasm_WT_15min_rep2

description:
H2-cyto
3T3_cytoplasm_WT_rep2.tsv


title: Pituitary, group D, fish 180

value: fish 180


title: K562_nuclear_DDX3X_60min_rep1

description:
DDX3X_60_nuc_rep1
K562_DDX3X_nuc_rep1.tsv


title: K562_cytoplasm_DDX3X_60min_rep1

description:
DDX3X_60_cyto_rep1
K562_DDX3X_cyto_rep1.tsv


title: N19


title: N2


title: Pituitary, group D, fish 176

value: fish 176


title: 3T3_nuclear_WT_120min_rep2

description:
H5-nuc
3T3_nuclear_WT_rep2.tsv


title: Pituitary, group B, fish 211

value: Stage IV

value: group B

value: fish 211


title: Pituitary, group B, fish 213

value: Stage III

value: Pituitary

value: fish 213


title: N18


title: K562_chromatin_DDX3X_60min_rep2

description:
DDX3X_60_chr_rep2
K562_DDX3X_chromatin_rep2.tsv


title: 3T3_nuclear_WT_60min_rep2

description:
H4-nuc
3T3_nuclear_WT_rep2.tsv


title: N17


title: K562_chromatin_DDX3X_60min_rep1

description:
DDX3X_60_chr_rep1
K562_DDX3X_chromatin_rep1.tsv


title: Pituitary, group B, fish 203

value: Stage I

value: fish 203


title: 3T3_nuclear_WT_15min_rep2

description:
H2-nuc
3T3_nuclear_WT_rep2.tsv


title: N16

value: paracancerous tissues


title: K562_total_DDX3X_60min_rep2

description:
DDX3X_60_tot_rep2
K562_DDX3X_total_rep2.tsv


title: N15


title: K562_total_DDX3X_60min_rep1

description:
DDX3X_60_tot_rep1
K562_DDX3X_total_rep1.tsv


title: 3T3_nuclear_WT_0min_rep2

description:
H1-nuc
3T3_nuclear_WT_rep2.tsv


title: 3T3_cytoplasm_WT_0min_rep2

description:
H1-cyto
3T3_cytoplasm_WT_rep2.tsv


title: Pituitary, group B, fish 160

value: fish 160


title: Pituitary, group B, fish 202

value: Stage V

value: fish 202


title: K562_total_DDX3X_0min_rep2

description:
DDX3X_0_tot_rep2
K562_DDX3X_total_rep2.tsv


title: Pituitary, group A, fish 250

value: group A

value: fish 250


title: N14


title: K562_total_DDX3X_0min_rep1

description:
DDX3X_0_tot_rep1
K562_DDX3X_total_rep1.tsv

value: DDX3X shRNA


title: 3T3_total_WT_120min_rep1

description:
G5-tot
3T3_total_WT_rep1.tsv


title: N13


title: 3T3_total_WT_60min_rep1

description:
G4-tot
3T3_total_WT_rep1.tsv


title: 3T3_total_WT_30min_rep1

description:
G3-tot
3T3_total_WT_rep1.tsv


title: Pituitary, group A, fish 245

value: fish 245


title: Pituitary, group A, fish 190

value: fish 190


title: N12


title: K562_cytoplasm_scramble_60min_rep2

description:
scramble_60_cyto_rep2
K562_cytoplasm_scramble_rep2.tsv

value: scramble shRNA


title: Pituitary, group A, fish 188

value: fish 188


title: N11


title: 3T3_nuclear_WT_30min_rep2

description:
H3-nuc
3T3_nuclear_WT_rep2.tsv


title: K562_cytoplasm_scramble_60min_rep1

description:
scramble_60_cyto_rep1
K562_cytoplasm_scramble_rep1.tsv


title: N10


title: 3T3_total_WT_15min_rep1

description:
G2-tot
3T3_total_WT_rep1.tsv


title: 3T3_total_WT_0min_rep1

description:
G1-tot
3T3_total_WT_rep1.tsv


title: Pituitary, group A, fish 184

value: Stage IV

value: fish 184


title: K562_nuclear_scramble_60min_rep1

description:
scramble_60_nuc_rep1
K562_nuclear_scramble_rep1.tsv


title: N1


title: K562_nuclear_scramble_60min_rep2

description:
scramble_60_nuc_rep2
K562_nuclear_scramble_rep2.tsv


title: 3T3_polysome_WT_120min_rep1

description:
G5-poly
3T3_polysome_WT_rep1.tsv


title: K562_chromatin_scramble_60min_rep2

description:
scramble_60_chr_rep2
K562_chromatin_scramble_rep2.tsv


title: MAST4-KD ARD cells rep3

city: chengdu

first: Yushan

last: Cui

address: Guo Xue Xiang #37 Chengdu, Sichuan Province,  P.R.China

department: Department of Hematology

institute: West China Hospital, Sichuan University

data_processing:
Illumina Bcl2fastq (v2.17.1.14) software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Cutadapt (V1.9.1), then aligned to whole genome via software Hisat2 (v2.0.1).
FPKM (Fragments Per Kilo bases per Million reads) to estimate gene expression levels was performed by HTSeq (v0.6.1)  and differential expression analysis used the DESeq2 Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: ARD MM cell lines

growth_protocol: CTR-KD and MAST4-KD ARD MM cells were cultured in RPMI1640 medium containing 10% fetal bovine serum and 100 U penicillin / 0.1 mg/ml streptomycin.

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)
Next generation sequencing library preparations were constructed  using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (Vazyme, Cat No. NR603, China)

treatment_protocol: CTR-KD and MAST4-KD ARD MM cell lines were established by infecting lentivirus carrying CTR or MAST4 shRNA

tag: cell type

value: Human MM cell line ARD


title: 3T3_polysome_WT_30min_rep1

description:
G3-poly
3T3_polysome_WT_rep1.tsv


title: MAST4-KD ARD cells rep2

tag: genotype


title: Testis, group E, fish 236

source_name: Testis

value: Testis

value: group E

value: fish 236


title: K562_total_scramble_60min_rep2

description:
scramble_60_tot_rep2
K562_total_scramble_rep2.tsv


title: 3T3_polysome_WT_15min_rep1

description:
G2-poly
3T3_polysome_WT_rep1.tsv


title: Testis, group E, fish 233

value: Stage I

value: fish 233


title: MAST4-KD ARD cells rep1


title: CTR-KD ARD  cells rep3

value: CTR-KD


title: Testis, group E, fish 240

value: fish 240


title: K562_total_scramble_60min_rep1

description:
scramble_60_tot_rep1
K562_total_scramble_rep1.tsv


title: K562_total_scramble_0min_rep2

description:
scramble_0_tot_rep2
K562_total_scramble_rep2.tsv


title: 3T3_polysome_WT_0min_rep1

description:
G1-poly
3T3_polysome_WT_rep1.tsv


title: Testis, group E, fish 226


title: Testis, group E, fish 221

value: fish 221


title: CTR-KD ARD  cells rep2


title: 3T3_cytoplasm_WT_120min_rep1

description:
G5-cyto
3T3_cytoplasm_WT_rep1.tsv


title: K562_total_scramble_0min_rep1

description:
scramble_0_tot_rep1
K562_total_scramble_rep1.tsv


title: 3T3_cytoplasm_WT_60min_rep1

description:
G4-cyto
3T3_cytoplasm_WT_rep1.tsv


title: CTR-KD ARD  cells rep1


title: K562_chromatin_WT_120min_rep2

description:
U5-chr
K562_chromatin_WT_rep2.tsv


title: 3T3_polysome_WT_60min_rep1

description:
G4-poly
3T3_polysome_WT_rep1.tsv


title: K562_chromatin_scramble_60min_rep1

description:
scramble_60_chr_rep1
K562_chromatin_scramble_rep1.tsv


title: Testis, group D, fish 193

value: group D

value: fish 193


title: KO_12dpa

first: Jessica

middle: A

last: Lehoczky

address: 60 Fenwood Rd.

department: Orthopedic Surgery

institute: Brigham and Women's Hospital

data_processing:
Base-calling and raw read files generated with Illumina platform
10x Genomics Cell Ranger software v7.1.0 was used to convert raw BCL files to FASTQ files, align read to mouse mm10-2020-A transcriptome, filter low quality cells, and count barcodes and unique molecular identifiers (UMIs)
Assembly: mm10-2020-A
Supplementary files format and content: cellranger output files: matrix.mtx, features.tsv, and barcodes.tsv

source_name: digit tip blastema

extract_protocol:
Digit tip blastemas were manually dissected followed by trypsin and collagenase I enzymatic digestion. Red blood cells were lysed with ACK lysis buffer. Dissociated single cells were washed, filtered and resuspended in 0.4% BSA in PBS then FACS sorted with 1ug/mL propidium iodide. Live cells were collected and adjusted to concentration of 1000 cells/uL for single cell RNAseq library construction.
All samples used the 10x Chromium transcriptomics platform (10x Genomics) implemented by the Brigham and Women's Hospital Single Cell Genomics Core. 10x Chromium Single Cell 3' v3 chemistry was used per manufacturer's protocol.

value: digit tip blastema

value: homozygous Mest knock-out

tag: Sex

value: male and female

value: 8 weeks old


title: 3T3_cytoplasm_WT_30min_rep1

description:
G3-cyto
3T3_cytoplasm_WT_rep1.tsv

tag: treatment


title: 3T3_cytoplasm_WT_15min_rep1

description:
G2-cyto
3T3_cytoplasm_WT_rep1.tsv


title: K562_total_PABPC4_60min_rep1

description:
PABPC4_60_tot_rep1
K562_PABPC4_total_rep1.tsv

value: PABPC4 shRNA


title: WT_12dpa

value: homozygous Mest wild-type


title: K562_chromatin_WT_30min_rep2

description:
U3-chr
K562_chromatin_WT_rep2.tsv


title: 28dpa

data_processing:
Base-calling and raw read files generated with Illumina platform
10x Genomics Cell Ranger software v3.0.2 was used to convert raw BCL files to FASTQ files, align read to mouse mm10 transcriptome, filter low quality cells, and count barcodes and unique molecular identifiers (UMIs)
Assembly: mm10
Supplementary files format and content: cellranger output files: matrix.mtx, feautres.tsv, and barcodes.tsv

source_name: digit tip

extract_protocol:
Tissue was manually dissected followed by trypsin and collagenase I enzymatic digestion. Ref blood cells were lysed with ACK lysis buffer. Dissocaited single cells were washed, filtered and resuspended in 0.4% BSA in PBS and adjusted to concentration of 1000 cells/uL for single cell RNAseq library construction.
All samples used the 10x Chromium transcriptomics platform (10x Genomics) implemented by the Brigham and Women's Hospital Single Cell Genomics Core. The 12dpa library was made with the 10x Chromium Single Cell 3' v2 chemistry, and all other libraries (11dpa, 14dpa, 17dpa, 28dpa, and unamputated) were made with the 10x Chromium Single Cell 3' v3 chemistry as per manufacturer's protocol.

value: digit tip

value: FVB/NJ

value: wildtype

value: male

value: 6 weeks old


title: 3T3_cytoplasm_WT_0min_rep1

description:
G1-cyto
3T3_cytoplasm_WT_rep1.tsv


title: Testis, group D, fish 176

value: Stage I

value: Testis

value: fish 176


title: Testis, group D, fish 180

value: fish 180


title: Testis, group D, fish 255

value: group D

value: fish 255


title: 3T3_nuclear_WT_120min_rep1

description:
G5-nuc
3T3_nuclear_WT_rep1.tsv


title: K562_chromatin_WT_15min_rep2

description:
U2-chr
K562_chromatin_WT_rep2.tsv


title: K562_chromatin_WT_0min_rep2

description:
U1-chr
K562_chromatin_WT_rep2.tsv


title: rIAPP427

first: Montgomery

last: Blencowe

address: 610 Charles E Young Drive East

institute: UCLA

data_processing:
Illumina’s NextSeq 500 platform was used to generate 75 bp, paired-end reads (260 ± 6M reads per sample).
Short reads were aligned to the mouse reference genome build GRCm38 (mm10) using the STAR aligner
The HT-Seq package 25260700 was used to count the number of fragments aligned to known exonic regions.
Assembly: mm10
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

source_name: Islet

growth_protocol: We used control wild-type FVB mice, beta cell specific human-IAPP expressing mice, and beta cell specific rodent-IAPP expressing mice bred at UCLA. Animals were maintained on a 12-h day/night cycle with Harlan Teklad Rodent Diet 8604 and water ad libitum.

extract_protocol:
RNA was extracted from islet samples (165±6 islets per mouse) were using the RNeasy Mini Kit (Qiagen). RNA integrity was confirmed using the Agilent Bioanalyzer 2100 (RIN score range: 8.4–9.5)
RNA-seq libraries were prepared using the TruSeq with Ribo-Zero treatment (Illumina, San Diego, CA, USA) to deplete rRNA.

value: Islet

tag: strain background

value: FVB

value: rIAPP


title: rIAPP421


title: 3T3_nuclear_WT_60min_rep1

description:
G4-nuc
3T3_nuclear_WT_rep1.tsv


title: Testis, group B, fish 211

value: Stage IV

value: group B

value: fish 211


title: K562_total_WT_120min_rep2

description:
U5-tot
K562_total_WT_rep2.tsv


title: 3T3_nuclear_WT_30min_rep1

description:
G3-nuc
3T3_nuclear_WT_rep1.tsv


title: K562_total_WT_60min_rep2

description:
U4-tot
K562_total_WT_rep2.tsv


title: Testis, group B, fish 203

value: fish 203


title: rIAPP419


title: Testis, group D, fish 198

value: fish 198


title: Testis, group B, fish 202

value: Stage V

value: fish 202


title: rIAPP420


title: 3T3_nuclear_WT_15min_rep1

description:
G2-nuc
3T3_nuclear_WT_rep1.tsv


title: Testis, group B, fish 160

value: fish 160


title: Testis, group B, fish 213

value: Stage III

value: fish 213


title: rIAPP413


title: 3T3_nuclear_WT_0min_rep1

description:
G1-nuc
3T3_nuclear_WT_rep1.tsv


title: K562_total_WT_15min_rep2

description:
U2-tot
K562_total_WT_rep2.tsv


title: K562_total_WT_30min_rep2

description:
U3-tot
K562_total_WT_rep2.tsv


title: Testis, group A, fish 250

value: Stage I

value: Testis

value: group A

value: fish 250


title: rIAPP412

value: Islet


title: Testis, group A, fish 245

value: fish 245


title: K562_total_WT_0min_rep2

description:
U1-tot
K562_total_WT_rep2.tsv


title: hIAPP430

value: FVB

value: hIAPP