title: C57BL/6J mice (no. 21), Restraint stress 14d(Stress-susceptible mice)

city: Seoul

first: Dong-Joo

last: Hwang

address: 1239, Yangjae-daero, Songpa-gu

department: Institute of Sport Science

country: South Korea

institute: Korea National Sport University

description: Library name: RS21

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Brain (ventral hippocampus)

growth_protocol: Naïve 8-week-old male C57BL/6J mice (Daehan Bio-Link, Chungbuk, Korea) were housed and acclimated to a controlled pathogen-free environment of animal facility at Korea National Sport University (KNSU) (12:12-h dark/ light cycle, 20°C ± 1°C, and 50% relative humidity) with ad libitum access to standard chow diet (SAFE R04-10, Aston Pharma, England) and distilled water.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: In brief, mice were individually placed in a ventilated 50 mL polyethylene tubes to induce immobilization for 2 hours daily, from 10 a.m. to 12 p.m. (during the light cycle). This process was repeated for 14 consecutive days. Following two weeks of chronic restraint stress, the mice subjected to a 4-week VWR exercise were housed in a home-cage equipped without (sedentary) or with a running wheel apparatus (Model: 0297-004M, Running Wheel for Mouse Home Cage, Columbus Instruments, OH, USA), allowing for voluntary access to exercise.

value: Brain (ventral hippocampus)

value: WT

value: Restraint stress


title: C2_33_Wk2

status: Public on Dec 04 2024

type: SRA

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

country: USA

institute: Case Western Reserve University

library_source: transcriptomic

data_processing:
Raw demultiplexed fastq paired end read files were trimmed of adapters and filtered using the program skewer to throw out any with an average phred quality score of less than 30 or a length of less than 10.
Trimmed reads were then aligned using the HISAT2 aligner to the Homo sapiens NCBI reference genome assembly version GRCh38 and sorted using SAMtools
Aligned reads were counted and assigned to gene meta-features using the program featureCounts as part of the Subread package.
Count files were imported into the R programming language and were assessed for quality control, normalized and analyzed utilizing the limma trend method.
Assembly: GRCh38
Supplementary files format and content: CSV file contains raw counts for each sample.
Supplementary files format and content: CSV file contains log2(n+3) TMM normalized counts per million for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

growth_protocol: in vivo

extract_protocol:
PBMC samples were thawed, pelleted, and lysed in 350 uL of RLT with beta-mercaptoethanol. RNA was isolated using the RNeasy Mini kit (Qiagen). RNA quality was assessed with the Fragment Analyzer (Agilent) and its Standard Sensitivity RNA kit.
Total RNA was normalized to 100 ng prior to random hexamer priming and libraries generated by the TruSeq Stranded Total RNA – Globin kit (Illumina). The resulting libraries were assessed on the Fragment Analyzer (Agilent) with the High Sense Large Fragment kit and quantified using a Qubit 3.0 fluorometer (Life Technologies)

tag: cell type

value: PBMC

tag: Sex

value: F

tag: batch

tag: donor

tag: timepoint

tag: vaccine response

value: R

tag: response status

value: HR


title: WT_Rep1_RPF

city: Saint Louis

first: Sofia

last: Origanti

state: MO

address: 3507 laclede avenue

institute: Saint Louis University

description:
rS01
Ribosome Profiling

library_source: other

data_processing:
FastQC (v0.12.1) was used to performed QC; fastq_quality_filter and fastx_collapser (FASTQX Toolkit 0.0.14) was used to perform seq collapse and the reads where less than 70% of bases with an accuracy for at least 99% were eleminated; Cutadapt (v4.6) was used to cut univerasl illumina Truseq adaptor; Perform STAR(v2.5.2b) mapping aligned to HG38(NCBI GCA_000001405.15); RibosomeProfilingqc (v1.12.0) was performed to obtain teh trascript tables; DESeq2 (v1.42.0) was used to performed DE analysis.
fastq_quality_filter and fastx_collapser (FASTQX Toolkit 0.0.14) was used to perform seq collapse and the reads where less than 70% of bases with an accuracy for at least 99% were eliminated
Cutadapt (v4.6) was used to cut universal illumina Truseq adaptor
Perform STAR(v2.5.2b) mapping aligned to HG38(NCBI GCA_000001405.15)
RibosomeProfilingqc (v1.12.0) was performed to obtain the transcript tables; DESeq2 (v1.42.0) was used to perform DE analysis.
Assembly: HG38(NCBI GCA_000001405.15)
Supplementary files format and content: RPFs_table_geneLevel.txt
Library strategy: Ribo-Seq

molecule: other

growth_protocol: The human colorectal carcinoma line (HCT116) was maintained in McCoy's 5A (modified) medium with 10% fetal bovine serum (FBS) and 100 units/mL penicillin and 100 mg/mL streptomycin (Gibco) (Penn/Strep). The generation of eIF6N106S/N106S homozygous mutant clones by CRISPR/Cas9 editing was as described in our previous study.

extract_protocol:
HCT116 cells of the indicated genotype were cultured to 60 to 70% cell density and were washed and scraped gently with ice cold PBS and snap frozen. Cells were then processed for Ribo-seq analysis at the RNA core at Case Western University. The appropriate volume of cell extract containing equal OD was treated with MNase, CaCl2 (5mM final concentration), and Turbo DNAse I and incubated at 25°C for 30 min; the digestion was stopped with SUPERase-inhibitor and placing on ice. The cell extract was then loaded onto a 15%-45% sucrose gradient to separate the polysomes by ultra-centrifugation at 41,000 RPM for 2 hours and 26 min at 4°C. The relevant fractions corresponding to the 80S monosome were collected and precipitated using ethanol and the RNA was isolated by phenol-chloroform extraction. The ribosome-protected fragments were then subjected to denaturing polyacrylamide-mediated gel electrophoresis and were gel-extracted based on size 25nt to 35nt. The RNA was precipitated and subjected to the RiboMinus Ribosomal RNA depletion kit (Ambion). The rRNA-depleted RNA footprints were then subjected to dephosphorylation.
Adapter ligation, reverse transcription and subsequent cDNA amplification was performed using the NEXT-Flex smRNA-Seq Kit v3 (Perkin Elmer)

tag: cell line

tag: genotype

value: Wt

tag: treatment


title: C2_29_Wk2


title: C2_66_Wk2

value: M


title: C57BL/6J mice (no. 19), Restraint stress 14d(Stress-susceptible mice)

description: Library name: RS19

organism: Mus musculus

tag: tissue


title: C57BL/6J mice (no. 18), Restraint stress 14d(Stress-susceptible mice)

description: Library name: RS18


title: C1_9_Wk2


title: Align-Unloaded-4_S4

city: Philadelphia

first: Katherine

last: Beigel

state: PA

address: 2716 South Street

department: Department of Biomedical and Health Informatics

institute: Children's Hospital of Philadelphia

description: S4 in rsem.merged.gene_counts.tsv

data_processing:
The RNA-seq pipeline nf-core/rnaseq (https://nf-co.re/rnaseq/3.10.1, v3.10.1) (reference genome: GRCh38, aligner: STAR (v2.7.10a), quantifier: RSEM (v1.3.1)) provided counts for 29,972 genes.
In R (v4.3.1), gene count data was filtered using the WGCNA (1.72-1) package; function goodSamplesGenes() was run with default parameters to remove genes with too many missing entries across samples, resulting in 20,410 remaining genes. Additional filtering removed genes with fewer than 50 counts across all samples. The remaining 14,892 genes were used to generate principal component analysis (PCA) plots and for differential expression analyses.
DESeq2 (v1.42.1) was used for differential gene expression analyses (Wald test method, BH procedure for FDR) between loaded versus unloaded samples (using the log2 fold change (LFC) shrinkage method).
Assembly: GRCh38
Supplementary files format and content: The processed data file rsem.merged.gene_counts.tsv is the matrix of gene-level raw counts across all samples from the nf-core/rnaseq pipeline output (for more information on this pipeline output, see: https://nf-co.re/rnaseq/3.10.1/docs/output#star-via-rsem).
Supplementary files format and content: The processed data file Mechanobio_Align-loaded_v_unloaded_DESeq2_Results_V1.csv is the DESeq2 differential expression results (with LFC shrinkage) comparing loaded HISMC samples to unloaded HISMC samples.

source_name: human intestinal smooth muscle

growth_protocol: 5x10^5 smooth muscle cells from human small intestine (cryopreserved at passage 1, ScienCell Research Laboratories, 2910) were plated on 10 cm tissue culture dishes coated with 0.1% gelatin (MilliporeSigma, G1890) (37oC, humidified incubator, 5% CO2) and cultured in . HISMC media (SMC medium (SMCM) (Sciencell, 1101), 2% FBS (fetal bovine serum, Sciencell, #0010), 1% Penicillin/Streptomycin (Sciencell, 0503), 1% smooth muscle cell growth supplement (Sciencell, 1152)). HISMC culture media was changed every other day. Cells were passaged a 90% confluence. After 1-2 passages, confluent HISMCs were cryopreserved in 90% fetal bovine serum (FBS)/10% dimethyl sulfoxide (DMSO) at 5x10 cells/mL. All experiments then used HISMCs at passage 3-5.

extract_protocol:
To isolate RNA from HISMCs on PCL scaffolds, each scaffold was minced in 500 μL TRizol (Ambion, 15596018) using sharp scissors and then vortexed for up to 15 minutes until dissolved. RNA was purified from cells lysed in TRIzol using the RNeasy Plus Mini kit (QIAGEN, 74134), with RNase Free DNase Set (QIAGEN, 79254) to remove residual DNA. RNA concentrations were measured by NanoDrop (ND-2000, Thermo Fisher Scientific).
Libraries were prepped using TruSeq total RNA sequencing kit (Illumina, 20020596; TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat) accoridng to manufacturer's protocols

treatment_protocol: Frozen HISMCs were thawed in a 37C water bath for 2-3 minutes, added to 10 mL of Iscove’s Modification of DMEM (Corning, 10-016-CM), and pelleted (270  g,  3  minutes). Aligned laminin-coated PCL scaffolds (30 mm x 5 mm) were seeded with 3500,000 HISMCs resuspended in 80 μL HISMC culture media. Seeded scaffolds were and maintained free-floating in HISMC culture media for 72 hours. “Loaded” scaffolds then experienced cyclic stretch (3% uniaxial stretch, 1 Hz) for 6 hours in HISMC culture media using a custom bioreactor while “unloaded” HISMC were maintained free-floating on scaffolds for 6 hours in fresh HISMC culture media. All cells were maintained at 37oC, 5% CO2 in a humidified incubator. Scaffolds were then cut in half. One half was dissolved in Trizol (Ambion, 15596018) for RNA extraction and the other half fixed in 4% paraformaldehyde for immunohistochemistry.

value: human intestinal smooth muscle

value: 5x105 smooth muscle cells from human small intestine (cryopreserved at passage 1, ScienCell Research Laboratories, 2910)

value: human intestinal smooth muscle cells (HISMC)

value: seeded on electrospun aligned poly-ε-caprolactone nano-fibrous scaffolds, no strecthing (unloaded) in culture for 6 hours


title: C1_7_BL

value: BL


title: C57BL/6J mice (no. 12), Stress-susceptible mice, Voluntary wheel running 14d(Effective response to VWR)

description: Library name: RES12

value: Restraint stress & Voluntary wheel running


title: Align-Unloaded-2_S2

description: S2 in rsem.merged.gene_counts.tsv


title: C1_46_Wk2

value: LR


title: C1_43_Wk2

value: NR


title: C57BL/6J mice (no. 10), Stress-susceptible mice, Voluntary wheel running 14d(Effective response to VWR)

description: Library name: RES10

value: Brain (ventral hippocampus)


title: C1_42_Wk2


title: C1_41_Wk2


title: C1_40_Wk2


title: C57BL/6J mice (no. 9), Stress-susceptible mice, Voluntary wheel running 14d(Effective response to VWR)

description: Library name: RES9

value: WT


title: C1_34_Wk2


title: C57BL/6J mice (no. 20), Stress-susceptible mice, Voluntary wheel running 14d(Ineffective response to VWR)

description: Library name: RER20


title: Align-Loaded-3percent-1hz-3_S11

description: S11 in rsem.merged.gene_counts.tsv

value: seeded on electrospun aligned poly-ε-caprolactone nano-fibrous scaffolds, subjected to uniaxial 3% cyclic stretch at 1 Hz (loaded) in culture for 6 hours


title: Align-Unloaded-1_S1

description: S1 in rsem.merged.gene_counts.tsv


title: C2_83_Wk2

value: PBMC


title: Align-Unloaded-3_S3

description: S3 in rsem.merged.gene_counts.tsv


title: C57BL/6J mice (no. 19), Stress-susceptible mice, Voluntary wheel running 14d(Ineffective response to VWR)

description: Library name: RER19


title: C1_37_Wk2

value: F


title: C1_36_Wk2


title: Align-Loaded-3percent-1hz-2_S10

description: S10 in rsem.merged.gene_counts.tsv


title: C1_31_Wk2


title: C1_32_Wk2


title: C57BL/6J mice (no. 12)

description: Library name: C12


title: C1_30_Wk2

value: R


title: Align-Loaded-3percent-1hz-1_S9

description: S9 in rsem.merged.gene_counts.tsv


title: C57BL/6J mice (no. 6), Stress-susceptible mice, Voluntary wheel running 14d(Ineffective response to VWR)

description: Library name: RER6


title: Mes clone 31 treated

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

country: France

institute: Cancer Research Centre of Lyon

library_source: transcriptomic single cell

data_processing:
Cell Ranger version 7.1.0
Assembly: GRCh38-2020-A
Supplementary files format and content: H5 (Hierarchical Data Format 5) count matrices. Genes as rows, cells as columns

molecule: polyA RNA

source_name: breast

extract_protocol:
10x Genomics 3' v3 protocol
10x Genomics 3' v3 kit
UMI-based scRNA-seq

treatment_protocol: Doxorubicin

value: breast

value: human mammary epithelial cells (hMEC)

value: hMEC + shTP53-HRASG12V-hTERT

tag: population

value: InB

tag: clone

value: clone 31

value: Doxorubicin


title: C1_44_Wk2

value: M


title: C1_29_Wk2

value: HR


title: C1_27_Wk2


title: C57BL/6J mice (no. 2)

description: Library name: C2


title: Align-Loaded-3percent-1hz-4_S12

description: S12 in rsem.merged.gene_counts.tsv

value: human intestinal smooth muscle

value: 5x105 smooth muscle cells from human small intestine (cryopreserved at passage 1, ScienCell Research Laboratories, 2910)

value: human intestinal smooth muscle cells (HISMC)


title: C1_26_Wk2

value: NR


title: Mes clone 7 treated

value: clone 7


title: Mes clone 7 untreated


title: C1_23_Wk2

value: LR


title: C1_24_Wk2

value: PBMC


title: C1_35_Wk2


title: left ventricle, MI, 7d, input rep 3

city: shanghai

first: Shan

last: Kou

address: No.393 Middle Huaxia Road

department: Life Science and Technology

country: China

institute: ShanghaiTech University

library_source: genomic

data_processing:
Raw reads were processed to generate high-quality clean reads by removing sequencing adapters, short reads (length < 35 bp), and low-quality reads using Fastp (v0.23.2).
Bowtie 2 was used to map the clean reads to the mouse genome (assembly GRCm38).
Duplicate reads were subsequently eliminated using Picard MarkDuplicates.
The MACS peak-finding algorithm was used for ChIP and input peak detection, and the p-value cutoff was set as 0.01.
The ChIPseeker R package was used to annotate the features of genes overlapping with ChIP peaks.
Assembly: GRCm38
Supplementary files format and content: PW1-binding peaks of ChIP-seq

molecule: genomic DNA

source_name: heart

extract_protocol:
Minced tissue was homogenized using a mechanical tissue homogenizer, then cross-linked with 1% formaldehyde for 10 min at room temperature and then quenched with 125 mM glycine.
ChIP and input DNA fragments were end-repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module followed by adaptor ligation with the NEBNext Ultra Ligation Module. The DNA libraries were amplified for 15 cycles and sequenced using Illumina Hi-Seq with paired-end 2x150 as the sequencing mode.

treatment_protocol: MI 7d

value: heart

value: wild type

value: MI 7d


title: C1_22_Wk2

value: F


title: C1_20_Wk2


title: C1_19_Wk2

value: R


title: left ventricle, MI, 7d, ChIP rep 2


title: C1_16_Wk2


title: Mes clone 14 untreated

value: breast

value: human mammary epithelial cells (hMEC)

value: hMEC + shTP53-HRASG12V-hTERT

value: Mes

value: clone 14


title: C1_15_Wk2

value: HR


title: Mes clone 2 treated

value: clone 2

value: Doxorubicin


title: C1_10_Wk2

value: NR


title: Mes clone 2 untreated


title: left ventricle, MI, 7d, ChIP rep 1


title: C1_13_Wk2

value: M


title: C57BL/6J mice (no. 8)

description: Library name: C8

value: Brain (ventral hippocampus)

value: WT


title: C1_8_Wk2

value: PBMC


title: left ventricle, MI, 7d, input rep 1

value: heart

value: wild type


title: Mes clone 31 untreated

value: InB

value: clone 31


title: Epi clone 2 treated

value: breast

value: Epi


title: C1_6_Wk2

value: R

value: LR


title: C1_7_Wk2

value: F


title: Mes clone 14 treated

value: human mammary epithelial cells (hMEC)

value: hMEC + shTP53-HRASG12V-hTERT

value: Mes

value: clone 14


title: B cells, B220+, CSP_HAuMT_Set2, CSP

city: Boston

first: Duane

middle: R.

last: Wesemann

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine, Division of Allergy and Clinical Immunology

institute: Brigham and Women's Hospital

description:
Library name: WL-54-CSP
10x Genomics

data_processing:
CellRanger count and vdj to process raw fastq files into a set of seven files per each sample: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, all_contig.fasta, filtered_contig.fasta, all_contig_annotations.csv, filtered_contig_annotations.csv v8.0.1
Assembly: GRCm39-2024-A
Supplementary files format and content: CellRanger count output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger vdj output files: all_contig.fasta, filtered_contig.fasta, all_contig_annotations.csv, filtered_contig_annotations.csv

molecule: protein

source_name: Spleen / mLN / PPs

extract_protocol:
Single cells after sorting were encapsulated in Gel beads in Emulsion (GEM) using the 10X Controller with a Chromium Next GEM Single Cell 5' Kit v3, Chromium Single Cell Mouse BCR Amplification Kit, and Chromium 5’ Feature Barcode Kit.
library preparation using Chromium GEM-X Single Cell 5' Reagent Kits v3 (10X Genomics) according to the manufacturer’s protocol. Briefly, after gel-beads in emulsion (GEMs) generation, RT-PCR, cDNA amplification, fragmentation, end repair, A-tailing and sample indexing were performed.
CITE-seq

value: Spleen / mLN / PPs

value: B cell

value: HA-uMT


title: B cells, B220+, BCR_HAuMT_Set2, BCR

description:
Library name: WL-55-BCR
10x Genomics


title: Epi clone 1 treated

value: clone 1

value: Doxorubicin


title: B cells, B220+, BCR_B18383_Set2, BCR

description:
Library name: WL-53-BCR
10x Genomics


title: B cells, B220+, CSP_B18383_Set2, CSP

description:
Library name: WL-52-CSP
10x Genomics


title: Epi clone 1 untreated


title: B cells, B220+, CSP_HAuMT_Set1, CSP

description:
Library name: WL-48-CSP
10x Genomics


title: Bulk_RNAseq_Telo_GFPCells_Rep1

city: Ithaca

first: Tudorita

last: Tumbar

state: NY

address: 526 Campus Rd

department: Molecular biology and genetics

institute: Cornell University

data_processing:
Exon specific counts matrix was generated using featureCounts function from Rsubread (v2.14.2) followed by RPKM normalization for comparisons with nascent RNA-seq data.
Assembly: mm39
Supplementary files format and content: Sample specific exon counts matrix as a txt file.

source_name: Skin

growth_protocol: Dorsal skin of Polr2bf/f-GFP; K14-Cre mice were collected at postnatal day (PD)21.

extract_protocol:
A small piece of skin tissue was flash frozen (for RNA isolation from the whole skin tissue) and rest of the skin tissue was enzymatically digested using collagenase-trypsin method. After preparing the single cell suspension, dead cells were stained with Propidium Iodide (PI). Live GFP+ keratinocytes were FACS-purified and directly collected in TRIzol LS
Total RNAs were isolated following the manufacturer’s protocol with the following additions: after the first phase separation, additional chloroform extraction step of the aqueous layer in Phase-lock Gel heavy tubes (Quanta Biosciences); addition of 1ul Glycoblue (ThermoFisher) immediately prior to isopropanol precipitation; two washes of the RNA pellet with 75% ethanol. Quality of each sample was confirmed by measuring RNA concentration using Qubit RNA HS kit (ThermoFisher) and by determining RNA integrity with Fragment Analyzer (Agilent). Ribosomal RNA was subtracted by hybridization from total RNA samples using the NEBNext rRNA Depletion Kit (New England Biolabs). TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs) and libraries were  sequenced on a NovaSeq with 2x150bp paired-end settings.

value: Skin

value: Keratinocytes

value: Polr2b.fl.fl.GFP; K14Cre

tag: time


title: Anagen_Polr2b.fl.fl.GFP_ShhCreERT2_GFP_Rep2

data_processing:
PReCIS-seq reads were first trimmed with fastp (v0.23.2), then mapped to the mouse rDNA using bowtie2 (v2.4.4) to deplete nascent rRNA. The rRNA-depleted reads were then mapped to the mm39 reference genome using STAR (v2.7.10b) and UMI duplicate reads were removed using umi_tools (v 1.1.2). The de-duplicated BAM files were then converted to CPM-normalized bigWig files using samtools and visualized using Integrated Genome Viewer (IGV). Promoter-proximal and gene body counts were obtained using the BRGenomics package in R and are provided as supplementary data files.
Assembly: mm39
Supplementary files format and content: Strand specific bigWig files
Library strategy: PRO-seq

growth_protocol: For PReCIS-seq on mouse skin tissues, whole dorsal skin was collected at postnatal day PD21 and PD24 for Polr2bf/f-GFP; K14-Cre mice and PD35 for Polr2bf/f-GFP; Shh-CreERT2 mice that were tamoxifen injected at PD27. For PRO-seq on isolated keratinocytes, keratinocytes were isolated from back skin of PD0.5 mice and prepped for PRO-seq. For PRO-seq on cultured samples, keratinocytes were cultured in vitro in low calcium (0.05 mM) containing E-media and then processed for PRO-seq.

extract_protocol:
For mouse skin samples, samples were flash-frozen in liquid N2, followed by dry pulverization of frozen tissue through a cell crusher and douncing. Chromatin was isolated using NUN buffer and fragmented with DNase I, and nascent RNA was biotin-labeled through a run-on reaction. Cell-type-specific nascent RNAs were enriched through GFP pull-down and library preparation steps were then followed as previously described for PRO-seq assay. All input samples were processed without GFP pull-down that served as controls for cell-type specific nascent RNA enrichment.
Nascent RNA libraries were generated using the PRO-seq protocol.

value: Epithelial

value: Polr2b.fl.fl.GFP; ShhCreERT2


title: Anagen_Polr2b.fl.fl.GFP_ShhCreERT2_GFP_Rep1


title: left ventricle, MI, 7d, input rep 2

value: heart

value: wild type

value: MI 7d


title: B cells, B220+, BCR_HAuMT_Set1, BCR

description:
Library name: WL-49-BCR
10x Genomics


title: EMT+ clone 3 treated

value: breast

value: human mammary epithelial cells (hMEC)

value: hMEC + murine ZEB1 + HRAS G12V

value: EMT+

value: clone 3


title: B cells, B220+, BCR_B18383_Set1, BCR

description:
Library name: WL-47-BCR
10x Genomics

value: Spleen / mLN / PPs

value: B cell


title: Anagen_Polr2b.fl.fl.GFP_ShhCreERT2_Input_Rep2

value: All cells in skin


title: B cells, B220+, CSP_B18383_Set1, CSP

description:
Library name: WL-46-CSP
10x Genomics


title: EMT+ clone 3 untreated


title: Anagen_Polr2b.fl.fl.GFP_ShhCreERT2_Input_Rep1


title: Bulk_RNAseq_Telo_GFPCells_Rep2


title: Epi clone 2 untreated

value: hMEC + shTP53-HRASG12V-hTERT

value: Epi

value: clone 2


title: snMultiome sequencing, liver, maternal obese, GEX

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str, 31

department: LIMES

country: Germany

institute: University of Bonn

description: Library name: wtHFDCDCDm_RNA

data_processing:
Multiome files were demultiplexed - the resulting files where further processed using cellranger-arc count with the cellranger provided reference 'refdata-cellranger-arc-mm10-2020-A-2.0.0'
Assembly: mm10
Supplementary files format and content: CellRanger output files: [Merged]_filtered_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files: [Merged]_atac_fragements.tsv.gz; [Merged]_atac_fragements.tsv.gz.tbi - Fragements and Index files

molecule: nuclear RNA

source_name: liver

growth_protocol: 3-4 weeks old mice were fed either control or high-fat diet (CD / HFD) for 8 weeks. Offspring were weaned by CD-fed mothers and fed CD diet. Mice used for experiment were ascrificed at week 11-13.

extract_protocol:
Nuclei were isolated from ~50 mg of flash-frozen adult liver tissue for simultaneous single-nucleus RNA sequencing (snRNA-seq) and single-nucleus ATAC sequencing (snATAC-seq) using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (10x Genomics, Cat# 1000283). For more details please see linked manuscript
During the reverse transcription (RT) reaction, cDNA tagging was achieved with 16-nucleotide barcodes and 10-nucleotide molecular identifiers. The pre-amplified product was split into two aliquots: 40 μl for ATAC library construction and 35 μl for further cDNA amplification. For snRNA-seq library preparation, 25% of the total cDNA was used to generate gene expression (GEX) libraries. Libraries were prepared and sequenced according to the manufacturer’s protocols: snATAC libraries used the 10x Genomics Single Index N Set, and snRNA-seq libraries used the Dual Index TT Set A.  For more details please see linked manuscript

value: liver

tag: library type

value: mRNA

value: wt

tag: age

value: Adult

tag: maternal diet

value: HFDCD

tag: offspring diet

value: CD

tag: condition

value: HFDCDCD

tag: merged

value: wtHFDCDCD


title: snMultiome sequencing, liver, maternal obese, ATAC

description:
Library name: wtHFDCDCDm_ATAC
single nucleus ATAC-Seq (rather than ATAC-seq)

value: ATAC


title: snMultiome sequencing, liver, maternal lean, GEX

description: Library name: wtCDCDCDm_RNA

value: CDCD

value: CDCDCD

value: wtCDCDCD


title: snMultiome sequencing, liver, maternal lean, ATAC

description:
Library name: wtCDCDCDm_ATAC
single nucleus ATAC-Seq (rather than ATAC-seq)

value: CDD


title: EMT+ clone 2 treated

value: breast

value: human mammary epithelial cells (hMEC)

tag: cell type

value: hMEC + murine ZEB1 + HRAS G12V

value: EMT+

value: Doxorubicin


title: MT 2-7 C

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

data_processing:
FASTQ files were aligned to mouse genome build mm10 using STAR (Dobin et al., 2013) (version 2.7.9a).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 2.0.3) and Ensembl annotation build 100 (uniquely aligned proper pairs, same strand).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Variance-stabilizing transformation (VST) was accomplished using the varianceStabilizingTransformation function in the DESeq2 R package (version 1.32.0) (Love et al., 2014).
All analyses were performed using the R environment for statistical computing (version 4.1.2).
Assembly: mm10
Supplementary files format and content: counts.txt: 55450 x 18 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: 55450 x 18 matrix of variance-stabilizing-transformed (VST) expression values

growth_protocol: C2C12 myoblast cells were cultured in growth medium consisting of Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), and 1% 100X penicillin-streptomycin L-glutamine (P/S/G). Myoblasts were transfected with PEI and two of the Meg3 promoter-specific CRISPR-Cas9/gRNA constructs or the pX458 vector alone and 72 h later EGFP positive cells selected by FACS. A population of 3000 - 10000 EGFP positive cells was collected at the end of each sort and grown. A population of cells transfection of the pX458 transfected cells was obtained for use as a control in experiments. The EGFP positive cell populations were serial diluted in growth medium to a concentration of one cell per well in a 96 well plate and grown up. Prior to differentiation, C2C12 myoblasts were grown in growth medium to confluence. To induce differentiation, the media was changed to differentiation media consisting of DMEM, 2% horse serum, and 1% P/S/G.

extract_protocol: RNA was isolated from C2C12 cells using TRIzol reagent (Invitrogen) followed by phenol-chloroform extraction, precipitated with 100% isopropanol, and washed with 70% ethanol. RNA pellets were air-dried and resuspended in RNase-free water. RNA samples corresponding to myoblasts and myotubes (day 3 of differentiation) were submitted to the Boston University Microarray and Sequencing Resource Core in triplicate for library prep and Illumina sequencing.

treatment_protocol: Pairs of guide RNAs were designed to target regions of the Meg3 proximal regulatory region for deletion using in silico design tools provided through MIT (https://crispr.mit.edu) and the Broad Institute (https://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design). DNA was isolated from the CRISPR-edited clonal C2C12 cells and PCR genotyping was then used to confirm the presence of CRISPR-Cas9 deletions by using the primers flanking the region of the Meg3 promoter that was targeted for deletion.

value: myotube

value: Dlk1-Dio3 knockout


title: EMT+ clone 2 untreated

value: clone 2


title: Anagen_Polr2b.fl.fl.GFP_K14Cre_GFP_Rep1

value: Skin

value: Keratinocytes

value: Polr2b.fl.fl.GFP; K14Cre


title: MT 2-7 A


title: Anagen_Polr2b.fl.fl.GFP_K14Cre_GFP_Rep2


title: Anagen_Polr2b.fl.fl.GFP_K14Cre_Input_Rep2

value: All cells in skin


title: MT 2-4 B

value: Dlk1-Dio3 overexpressor


title: MT 2-4 A


title: EMT- clone 4 untreated

value: hMEC + HRAS G12V

value: EMT-

value: clone 4


title: Anagen_Polr2b.fl.fl.GFP_K14Cre_Input_Rep1


title: MT px C

value: control


title: EMT- clone 2 treated

value: breast


title: Telogen_Polr2b.fl.fl.GFP_K14Cre_GFP_Rep2


title: MT px B


title: EMT- clone 2 untreated

value: human mammary epithelial cells (hMEC)


title: Telogen_Polr2b.fl.fl.GFP_K14Cre_GFP_Rep1


title: H2087_LCC_Tb_7d_2

city: New York

first: Zhenghan

last: Wang

address: 417 East 68th St

department: CBG

institute: Memorial Sloan Kettering Cancer Centerr

data_processing:
Multiplexed sequencing libraries were run on a Hiseq2500 platform and more than 30-40 million raw paired-end reads were generated for each sample. For data analysis, reads pairs in FASTQ format (50bp/50bp) were assessed for quality using FastQC v0.11.5 and mapped to human genome hg19 with STAR2.5.2b using standard settings for paired reads. Uniquely mapped reads were assigned to annotated genes with HTSeq v0.6.1p1 with default settings. Read counts were normalized by library size, and differential gene expression analysis based on a negative binomial distribution was performed using DESeq2 v3.4. Gene set enrichment analysis (GSEA) was performed using previously curated gene sets.
Assembly: hg19
Supplementary files format and content: Excel

extract_protocol:
RNA was extracted from cells using the RNeasy Mini Kit (Qiagen, Cat #: 74106).
Total RNA purified from cells was quantified by Ribogreen and quality assessed by Agilent BioAnalyzer. 500 ng of RNA with integrity number (RIN) > 9.5 from each sample was used for library construction with TruSeq RNA Sample Prep Kit v2 (Illumina) according to manufacturer’s instructions

value: Lung adenocarcinoma cells

value: dormant metastatic derivative

value: TGF-β for 7 days


title: MB 2-7 C

value: myoblast


title: H2087_LCC_Tb_7d_1


title: Telogen_Polr2b.fl.fl.GFP_K14Cre_Input_Rep2


title: DU145/tet-XISTshRNA_DOX+ Rep3

first: Atrayee

last: Bhattacharya

address: 450 Bookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Assembly: hg38
Supplementary files format and content: .CSV counts file
Supplementary files format and content: .CSV deseq file

source_name: prostate

growth_protocol: DU145 cells (American Type Culture Collection (ATCC), Manassas, VA, USA) were cultured in RPMI1640 medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS; GEMINI Bio-Products, West Sacramento, CA, USA).

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: RNA Seq in DU145 prostate cancer cell line with tet-XIST shRNA (from GenePharma (Shanghai, China)) silencing. Transduced cells were selected for growth in 1-2 g/ml puromycin or 100 g/ml geneticin. For inducible gene silencing, cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline (DOX; Millipore Sigma).

value: prostate

value: Prostate Cancer

value: DOX


title: MB 2-7 B

value: Dlk1-Dio3 knockout


title: MT 2-7 B

value: myotube


title: EMT- clone 4 treated

value: Doxorubicin


title: H2087_LCC_Tb_3d_2

value: TGF-β for 3 days


title: DU145/tet-XISTshRNA_DOX+ Rep2


title: C1_25_Wk2

value: PBMC

tag: Sex

value: F

tag: batch

tag: donor

tag: timepoint

value: NR


title: MB 2-7 A

tag: cell line

tag: genotype


title: Telogen_Polr2b.fl.fl.GFP_K14Cre_Input_Rep1

tag: tissue

value: Skin

value: All cells in skin

value: Polr2b.fl.fl.GFP; K14Cre


title: DU145/tet-XISTshRNA_DOX+ Rep1

tag: treatment


title: H2087_LCC_Tb_3d_1

value: Lung adenocarcinoma cells


title: Optimization_Polr2b.fl.fl.GFP_K14Cre_GFP_Rep2

value: Keratinocytes


title: MB 2-4 C

value: Dlk1-Dio3 overexpressor


title: DU145/tet-XISTshRNA_DOX- Rep3

value: DMSO


title: C1_38_Wk2

value: M

tag: vaccine response

tag: response status


title: MT 2-4 C


title: MB 2-4 B

value: myoblast


title: Optimization_Polr2b.fl.fl.GFP_K14Cre_GFP_Rep1

tag: time


title: DU145/tet-XISTshRNA_DOX- Rep2

value: prostate

value: Prostate Cancer


title: Optimization_Polr2b.fl.fl.GFP_K14Cre_PolII_Rep2


title: MB 2-4 A


title: DU145/tet-XISTshRNA_DOX- Rep1


title: Optimization_Polr2b.fl.fl.GFP_K14Cre_PolII_Rep1


title: THP-1 cells, acetylated, NELFE, 2

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
Basecalls were performed using bcl2fastq.
ChIP-seq experiment were aligned to UCSC human genome (hg19) using bowtie 1.0.1.
Duplicated reads were removed with Picard tools 2.3.0.
bigWig files were generated using HOMER 4.11.1. Read count for bigwig was normalized using spike-in control for H2BK120ac and NELFE ChIP-seq. Read count for bigwig was normalized to 10 million reads for Pol2 ChIP-seq
Peaks were called using HOMER 4.11.1  findPeaks.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Cell were fixed with 1% formaldehyde for 15 min. After quenching and cell lysis, chromatin was sonicated using BioRaptor II (BM Equipment Co.).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit. 10 ng of DNA was used as starting material for Input and ChIP samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Tapestation.

value: monocytic leukemia

value: WT

tag: chip antibody

value: NELFE (proteintech, 10705-1-AP)

value: catalyst and acetyl donor, 45 min


title: siLDHBE_r3

city: Bern

first: Liang

last: Zhao

address: Murtenstrasse 24

country: Switzerland

institute: DBMR

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: DEResults.xlsx

source_name: lung

growth_protocol: cells were maintained in RPMI-1640 suppleemented with 10% FBS and incubated in humidited atmosphere with 5% CO2 at 37 degree.

extract_protocol: Total RNA was isolated and purified using RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: cells were first transfected with siRNA against non-targeted control or LDHB for 48 hours and then treated with Erastin for another 20 hours.

value: lung

value: siLDHB

value: Erastin

value: 20 hours


title: MB px C

value: control


title: Optimization_Polr2b.fl.fl.GFP_K14Cre_Input_Rep2

value: Skin

value: All cells in skin

value: Polr2b.fl.fl.GFP; K14Cre


title: siLDHBE_r2


title: MB px B


title: THP-1 cells, control, NELFE, 2

value: mutant catalyst and acetyl donor, 45 min


title: Optimization_Polr2b.fl.fl.GFP_K14Cre_Input_Rep1


title: MB px A


title: CD45+ cells isolated from MyC-CaP HSPC, developed through PBS treatment, for library 2 CITE-seq

city: San Francisco

first: Aram

last: Lyu

state: CA

address: 513 Parnassus Avenue, HSE 301

institute: University of California San Francisco

description:
The processed data includes both scRNAseq and CITEseq.
PCPBS2_barcodes.tsv.gz
PCPBS2_features.tsv.gz
PCPBS2_matrix.mtx.gz

data_processing:
CellRanger v5 count was run on mouse scRNAseq and CITEseq libraries from the same sample to generate a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz. CellRanger v3 count was run on patient scRNAseq to generate a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.
Assembly: GRCm38, GRCh38, mouse_reference_CITEseq.csv
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
For patients, viably cryopreserved tumor tissue samples were digested in RPMI containing Collagenase I & II (0.1 mg/ml, Thermo Fisher Scientific) and DNase I (Thermo Fisher Scientific), minced, and then subjected to 1-hour digestion using the gentleMACS system (Miltenyi Biotec). Live cell isolation was performed using MACS LS columns (Miltenyi Biotec). The 10x Genomics Chromium Controller was utilized to generate GEM bead emulsions using the Single Cell 5′ Library & Gel Bead Kit (10x Genomics). For mice, a cohort of FVB/NJ mice bearing MyC-CaP were injected s.c. with either degarelix (n = 3) or PBS (n = 3), as described above. HSPC or CRPC tissues were harvested upon reaching a tumor volume > 350 mm3. Tumors were sequentially digested 3 times with 12 ml of a cocktail of 2 mg/ml (w/v) Collagenase Type IV and 100 Kunitz U/ml DNase I (both from Sigma-Aldrich) for 12 minutes per digest. All single-cell suspensions were filtered using 70 μm filters (Fisher Scientific) and subjected to red blood cell lysis using ACK Lysing Buffer (Quality Biological). For the cell surface protein staining, cells were incubated with CD45.1-Brilliant Violet 510 (A20) for 30 minutes at 4°C. After immunostaining, cells were washed twice in FWB and resuspended in FWB containing 1 μg/ml propidium iodide for viability assessment. Cells were then sorted into CD45+ and CD45- populations using BD FACSAria (BD Biosciences). Each population was transferred into separate 75 mm flow cytometry tubes, centrifuged for 5 minutes at 250 g at 4˚C, and the supernatant was discarded. After staining with the hashtag (2, 4, and 6 (M1/42, 30-F11)) and TotalSeq-C surface (CD11c (N418), CD163 (S15049I), F4/80 (BM8), and Ly-6G (1A8)) antibodies, cell viability and count were reassessed. The 10x Genomics Chromium Controller was utilized to generate GEM bead emulsions using the Single Cell 5′ Library & Gel Bead Kit (10x Genomics) according to the manufacturer's protocol.
After generating GEM bead emulsions, we performed the synthesis and amplification of cDNA, followed by library preparation steps using 10x Genomics kits according to the manufacturer's protocol.

value: CD45+ cells

value: FVB/NJ injected with MyC-CaP

value: PBS

tag: library type

value: ADT


title: THP-1 cells, acetylated, H2BK120ac, 2

value: monocytic leukemia


title: H2087_LCC_SB_2

value: Lung adenocarcinoma cells

value: dormant metastatic derivative

value: SB505124 for 3 days


title: THP-1 cells, control, H2BK120ac, 2

value: WT


title: H2087_LCC_SB_1


title: siLDHBE_r1

value: lung

value: siLDHB


title: CD45+ cells isolated from MyC-CaP HSPC, developed through PBS treatment, for library 1 CITE-seq

description:
The processed data includes both scRNAseq and CITEseq.
PCPBS1_barcodes.tsv.gz
PCPBS1_features.tsv.gz
PCPBS1_matrix.mtx.gz

value: prostate


title: siCTR_E_r2

value: siCTRL

value: Erastin

value: 20 hours


title: PCIF1 KO 5' SLAM-seq 6 h rep1

first: Ben

middle: R

last: Hawley

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

data_processing:
Reads with the 5' UMI and linker sequence were identified and UMI placed in FASTQ headers. Remaining 5' and 3' adaptor sequences trimmed using cutadapt. Reads aligned to GRCh38 using STAR and demultiplexed using UMI tools. 5' end of demultiplexed aligned reads were assigned as TSS.
For SLAM-seq reads, C to T transitions in the sense direction were identifed using samtools mpileup and converted to a transition rate using custom scripts. Half-life per TSS isoform calculated by first-order decay kinetics.
For polysome reads, mean ribosome load (MRL) for each TSS isoform was calculated.
Genome_build: GRCh38
Supplementary_files_format_and_content: Half-lives and Rsq values of lm fit for each TSS isoform
Supplementary_files_format_and_content: Mean ribosome load values for each TSS isoform
Supplementary_files_format_and_content: HEK293T_MRL.txt: Translational efficiency
Supplementary_files_format_and_content: MRL_change_PCIF1KO.txt: differential analysis
Supplementary_files_format_and_content: TSS_halflives.txt: Half-lives
Supplementary_files_format_and_content: WT_KO_halflife.txt: differential analysis

growth_protocol: HEK293T cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Polysome samples were prepared by lysis in polysome lysis buffer. Following fractionation, RNA was extracted from sucrose by the addition of 50 mM EDTA and an equal volume TRIZOL LS, and homogenised for 20 minutes at 50°C with frequent mixing. For 5'UTR-SLAM-seq, 4SU-containing RNAs were directly extracted by a standard TRIZOL protocol.
ReCappable-seq

value: PCIF1 knockout


title: THP-1 cells, acetylated, Pol2, 2

value: Pol2 (Active Motif, 91151)

value: catalyst and acetyl donor, 45 min


title: CD45+ cells isolated from MyC-CaP CRPC, developed through degarelix treatment (ADT), for library 2 CITEseq

description:
The processed data includes both scRNAseq and CITEseq.
PCADT2_barcodes.tsv.gz
PCADT2_features.tsv.gz
PCADT2_matrix.mtx.gz

value: CD45+ cells

value: FVB/NJ injected with MyC-CaP

value: degarelix (androgen-deprivation therapy (ADT))


title: PCIF1 KO 5' SLAM-seq 2 h rep1


title: THP-1 cells, control, Pol2, 2

value: monocytic leukemia

value: mutant catalyst and acetyl donor, 45 min


title: PCIF1 KO 5' SLAM-seq 0 h rep1


title: siLDHB_r2

value: DMSO


title: THP-1 cells, acetylated, NELFE, 1

value: NELFE (proteintech, 10705-1-AP)


title: CD45+ cells isolated from MyC-CaP HSPC, developed through PBS treatment, for library 2 scRNA-seq

value: PBS

value: mRNA


title: WT 5' SLAM-seq 12 h rep1

value: wild-type


title: PCIF1 KO 5' SLAM-seq 12 h rep1


title: siLDHB_r1

value: lung

value: siLDHB


title: THP-1 cells, acetylated, H2BK120ac, 1

value: WT


title: WT 5' SLAM-seq 2 h rep1


title: CD45+ cells isolated from MyC-CaP HSPC, developed through PBS treatment, for library 1 scRNA-seq

value: prostate


title: THP-1 cells, control, H2BK120ac, 1


title: siCTRL_r3

value: siCTRL

value: 20 hours


title: siCTRL_r2


title: siCTR_E_r1

value: Erastin


title: THP-1 cells, acetylated, Pol2, 1

value: Pol2 (Active Motif, 91151)

value: catalyst and acetyl donor, 45 min


title: siCTRL_r1


title: CD45+ cells isolated from MyC-CaP CRPC, developed through degarelix treatment (ADT), for library 2 scRNA-seq

value: CD45+ cells

value: FVB/NJ injected with MyC-CaP

value: degarelix (androgen-deprivation therapy (ADT))


title: pancreatic islets, NCD_3

city: Nanjing

first: Chen

last: Liu

address: 101 Longmian Avenue

institute: Nanjing Medical University

data_processing:
Reads were produced from the library preparations using an Illumina platform after the clusters were created. BioMarker Technologies handled (Beijing, China) all the sequencing and data-processing procedures. Differentially expressed genes were considered significant with an p ≤ 0.05 and an absolute value of log2 (fold change) >0.5.
Assembly: mus_musculus_Ensembl_97
Supplementary files format and content: Processed_data_Readcout_TPM.txt

source_name: pancreatic islets

extract_protocol:
Total RNA from islets of NCD and HFD mice was isolated using the RNeasy mini kit (Qiagen), following the protocol for total RNA isolation. RNA integrity and concentration were assessed using an RNA Nano 6000 Assay Kit for the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA), according to the manufacturer’s instructions.
Following the guidelines stipulated by the manufacturer, sequenced libraries were constructed with the NEBNext Ultra small RNA Sample Library Prep Kit for Illumina (NEB, USA). Index codes were added to attribute sequences to each sample. The index-coded samples were clustered with the assistance of a cBot Cluster Generation System equipped with a TruSeq PE Cluster Kitv3-cBot-HS (Illumia) following the directions stipulated by the manufacturer.

value: pancreatic islets

value: primary islets

value: NCD-fed


title: CD45+ cells isolated from MyC-CaP CRPC, developed through degarelix treatment (ADT), for library 1 scRNA-seq

description:
The processed data includes both scRNAseq and CITEseq.
PCADT1_barcodes.tsv.gz
PCADT1_features.tsv.gz
PCADT1_matrix.mtx.gz

value: mRNA


title: THP-1 cells, control, Pol2, 1

value: monocytic leukemia

value: mutant catalyst and acetyl donor, 45 min


title: pancreatic islets, NCD_2


title: HBL1-MUT31

city: Vancouver BC

first: Christian

last: Steidl

state: British Columbia

address: 675, West 10th Ave

department: Department of Lymphoid Cancer Research

country: Canada

institute: BC Cancer

description:
HBL1_Counts.txt
F40854

data_processing:
Reads were aligned to the GRCh37 reference using the STAR aligner (v2.5.3a_modified) which also generated per-gene count data with HTSeq-Count.
Raw counts were read into R (v4.1.0), and only genes with a total count ≥ 10 across all samples were retained (22,723 genes).
Differential expression was performed between all PRAME wild-type clones (SU-DHL-4, Karpas422 and HBL-1) and all PRAME deleted clones (heterozygous and homozygous) with DESeq2 (v1.18.1).
GSEA Preranked (v4.1.0) was used to examine specific pathways between the two types with the p-value as the ranking feature.
Genome_build: GRCh37
Supplementary_files_format_and_content: SUDHL4_Counts.txt, Karpas422_Counts.txt, HBL1_Counts.txt

source_name: Cell line

extract_protocol: RNAseq was performed on an Illumina HiSeq 2500 (paired-end 75bp reads).

tag: pathology

value: Diffuse Large B-cell Lymphoma (Activated B-cell-like)

tag: prame mutational status

value: MUT

tag: prame allele status

value: Homozygous


title: THP-1 cells, acetylated, 45 min, 2

data_processing:
Basecalls were performed using bcl2fastq.
Sequenced reads from RNA-seq experiments were aligned by using HISAT2 v2.1.0.
FPKM was calculated using cufflinks v2.2.1
Assembly: hg19
Supplementary files format and content: fpkm_tracking

extract_protocol:
RNA was harvested using NucleoSpin RNA and reverse transcribed using SuperScript III First-Strand Synthesis System for RT-PCR (Invitrogen).
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

tag: cell type

value: WT

value: catalyst and acetyl donor

value: 45 min


title: HBL1-CON2

description:
HBL1_Counts.txt
F40853


title: pancreatic islets, NCD_1


title: THP-1 cells, control, 45 min, 2

value: mutant catalyst and acetyl donor


title: pancreatic islets, HFD_3

value: HFD-fed


title: WT 5' SLAM-seq 0 h rep1

value: wild-type


title: THP-1 cells, acetylated, 4 h, 2

value: 4 h


title: WT 5' SLAM-seq 6 h rep1


title: THP-1 cells, control, NELFE, 1

value: NELFE (proteintech, 10705-1-AP)


title: HBL1-MUT13

description:
HBL1_Counts.txt
F40852


title: pancreatic islets, HFD_2

value: pancreatic islets


title: THP-1 cells, control, 4 h, 2


title: pancreatic islets, HFD_1

value: primary islets


title: THP-1 cells, acetylated, 45 min, 1


title: HBL1-MUT14

description:
HBL1_Counts.txt
F40850


title: THP-1 cells, control, 45 min, 1


title: XYP-001, scRNAseq

city: Hangzhou

first: Yicheng

last: Xie

address: 3333 Binsheng Rd

institute: Children’s Hospital Zhejiang University School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: barcodes.tsv; genes.tsv; matrix.mtx.

extract_protocol:
Lung tissues were obtained from the control and asthma groups.The tissues were dissociated into single cells in dissociation solution.Single cell suspensions were loaded to 10× Chromium (10× Genomics, USA) to capture more than 3,000 single cells for the Single-cell 3′ Library using Gel Bead Kit V3 (1000075, 10× Genomics, USA) according to the manufacturer’s instructions. The following cDNA amplification and library construction steps were performed according to the manufacturer’s recommendation. Sequencing was performed on the NovaSeq6000 sequencer (Illumina, USA) with a minimum depth of 60,000~90,000 reads per cell and 150 bp (PE150) paired-end reads performed by LC-Bio Technology Co., Ltd (China).
RNA: 3' transcriptome sequencing, cDNA fragmentation, end filling, adding A, connection connector, Index PCR.

tag: Sex

value: female

value: lung


title: Karpas422_PRAME_2-16_2

description:
Karpas422_Counts.txt
A93529

value: Diffuse Large B-cell Lymphoma (Germinal Centre B-cell-like)

value: Mutant


title: HBL1-WT

description:
HBL1_Counts.txt
F40849

value: Diffuse Large B-cell Lymphoma (Activated B-cell-like)


title: Model, scRNAseq

description: 10x Genomics

value: Model


title: Karpas422_PRAME_2-16_1

description:
Karpas422_Counts.txt
A93528

value: Homozygous


title: 12_month_old_PABPN1A17/+4

city: Leiden

first: Vered

last: Raz

address: Einthovenweg

department: Human genetics

country: Netherlands

institute: LUMC

data_processing:
For the demultiplexing the pooled samples we used the well barcode from the oligodT primer using Ultraplex
mouse reads in FASTQ format are first filtered using Cutadapt (version 2.10) to remove all of the remaining adapter sequences. Then, the reads were aligned to the Ensembltranscriptomeversion 104 using STAR (version 2.7.5a) including UMI-based deduplication using UMI-Tools (version 1.1.1) to generate transcriptome-based alignment in binary alignment map (BAM) format so that we could visualize using the Integrative Genomics Viewer (IGV).
HTSeq Count is part of the HTSeq Python package used to generate count tables
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples
Supplementary files format and content: tab-delimited text files include filtered-out low-expressed genes and with LCPM values for each Sample

source_name: tongue

extract_protocol:
RNA isolation was carried out from 40 cryosections taken from the tongue median region, N=4 wild type and N=4 A17/+ female mice. Cryosections were collected in a MagNA lyser green beads tubes (Roche, 3358941001), and tissue was homogenized in QIAzol lysis reagent (Qiagen, 79306) using the MagNA 406 Lyser. Subsequently, total RNA was isolated with the miRNeasy Mini Kit (217004, Qiagen) using the manufacturer’s protocol. DNA was removed using RNAse-free DNAse set (Qiagen, 79254) using the manufacturer’s protocol. RNA integrity was assessed with the Agilent 2100 Bioanalyzer using Eukaryote Total RNA Nano chips according to the manufacturer’s protocol (Agilent 415 BioAnalyzer, 824.070.709)
The generation of cDNA for the RNA-seq data was carried out with the mcSCRB-seq protocol, with the following modifications to the workflow: instead of single cells, we used 1–100ng isolated total RNA, 7.5% PEG8000 was replaced with 0.5% polyvinylpyrrolidone, and the oligo-dT primer was replaced with the SCIFI_LIG384_001 primer. All samples were barcoded during reverse transcription using a well barcode. Illumina paired-end sequencing of the library was done on a NovaSeq 6000 using paired-end 150-bp sequencing and v1.5 chemistry. After sequencing, read 1 will contain the cDNA information and read 2 will contain only the unique molecular identifier

value: tongue


title: Karpas422_PRAME_2-3_2

description:
Karpas422_Counts.txt
A93527

value: Heterozygous


title: 12_month_old_PABPN1A17/+3


title: shDDX50-4 biorep4 kc211226

city: Stanford

first: Douglas

last: Porter

address: 269 Campus Drive

department: Dermatology

institute: Stanford

data_processing:
Salmon (v.1.10) was used to quantify gene abundances using only “basic” tagged Gencode v.39 transcripts. Quantifications analyzed with DESeq2 (v.1.38.3), with apeGLM shrinkage.
Assembly: hg38
Supplementary files format and content: VST quantification by DESeq2.

source_name: Primary keratinocytes

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500). Cells were induced to differentiate by the addition of 1.2 mM calcium for 3 days at full confluence. Biological replicates were performed in all cases using primary cells from at least 2 independent, unrelated donors.

extract_protocol:
Total RNA was extracted using the RNeasy Plus kit (QIAGEN, 74136), followed by poly(A) enrichment and library preparation using the NEB Ultra II (non-directional) kit (E6111).
NEB Ultra II (non-directional) kit (E6111)

value: Primary keratinocytes

tag: replicate

value: Biological replicate 4

value: shRNA against DDX50, #4


title: 12_month_old_PABPN1A17/+2


title: shControl biorep4 kc211226

value: Control shRNA


title: Karpas422_PRAME_1-4_2

description:
Karpas422_Counts.txt
A93525


title: 12_month_old_PABPN1A17/+1


title: shDDX50-3 biorep2 kc211226

value: Biological replicate 2

value: shRNA against DDX50, #3


title: Karpas422_single_3_1

description:
Karpas422_Counts.txt
A93522

value: WT


title: 12_month_old_WT4


title: Karpas422_single_3_2

description:
Karpas422_Counts.txt
A93523


title: shControl biorep3 kc211226

value: Biological replicate 3


title: Karpas422_PRAME_1-4_1

description:
Karpas422_Counts.txt
A93524


title: 12_month_old_WT2


title: left ventricle, MI, 7d, ChIP rep 3

data_processing:
Raw reads were processed to generate high-quality clean reads by removing sequencing adapters, short reads (length < 35 bp), and low-quality reads using Fastp (v0.23.2).
Bowtie 2 was used to map the clean reads to the mouse genome (assembly GRCm38).
Duplicate reads were subsequently eliminated using Picard MarkDuplicates.
The MACS peak-finding algorithm was used for ChIP and input peak detection, and the p-value cutoff was set as 0.01.
The ChIPseeker R package was used to annotate the features of genes overlapping with ChIP peaks.
Assembly: GRCm38
Supplementary files format and content: PW1-binding peaks of ChIP-seq

extract_protocol:
Minced tissue was homogenized using a mechanical tissue homogenizer, then cross-linked with 1% formaldehyde for 10 min at room temperature and then quenched with 125 mM glycine.
ChIP and input DNA fragments were end-repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module followed by adaptor ligation with the NEBNext Ultra Ligation Module. The DNA libraries were amplified for 15 cycles and sequenced using Illumina Hi-Seq with paired-end 2x150 as the sequencing mode.

value: heart

value: wild type

value: MI 7d


title: 12_month_old_WT3


title: shDDX50-4 biorep3 kc211226


title: Karpas422_single_1_2

description:
Karpas422_Counts.txt
A93521

value: Diffuse Large B-cell Lymphoma (Germinal Centre B-cell-like)


title: THP-1 cells, control, 4 h, 1

value: monocytic leukemia

value: mutant catalyst and acetyl donor

value: 4 h


title: THP-1 cells, acetylated, 4 h, 1

value: catalyst and acetyl donor


title: shControl biorep2 kc211226


title: 12_month_old_WT1

value: tongue


title: Karpas422_single_1_1

description:
Karpas422_Counts.txt
A93520


title: Prostate, Tissue, Treated, 3

first: Panagiotis

last: Chouvardas

institute: University of Bern

description:
Treated_3
Tis.Processed.txt

data_processing:
library strategy: bulk RNA Barcoding and sequencing (BRB-seq)
Read trimming, alignment, and quantification steps were performed by Alithea Genomics using STARsolo v2.7.9a and the GRCm38.103 (mouse) reference genome.
Utilizing the parameters “--soloUMIdedup NoDedup 1MM_Directional”, and “--quantMode GeneCounts” 52, we generated raw and UMI-deduplicated count matrices, opting for non-deduplicated counts for subsequent analyses.
Assembly: GRCm38.103
Supplementary files format and content: Org.Processed.txt = UMI count matrix of organoid samples
Supplementary files format and content: Tis.Processed.txt = UMI count matrix of tissue samples

source_name: Prostate

extract_protocol:
RNA was extracted from snap-frozen tissues and organoids by homogenization in Tripure Isolation Reagent (Sigma). Only RNA samples having between >200 ng and 1000 ng and with an RNA integrity number >6 were used.
Samples were sent to Alithea Genomics SA (Lausanne, Switzerland) for library preparation and sequencing using highly (prostate tissue) or extraction-free (organoids) multiplexed 3’-end bulk RNA barcoding and sequencing (MERCURIUSTM BRB-seq service 50). The generation of bulk RNA Barcoding and sequencing (BRB-seq) libraries was performed using the MERCURIUSTM BRB-seq (prostate tissue) or DRUG-seq (organoids) library preparation kit for Illumina and following the manufacturer’s manual (Alithea Genomics, #10813 (prostate tissue); #10841 (organoids)). All libraries were sequenced on Illumina Novaseq 6000.

value: Prostate

value: NPKC


title: shDDX50-3 biorep1 kc211226

value: Primary keratinocytes

value: Biological replicate 1


title: Karpas422_wt_bulk_2

description:
Karpas422_Counts.txt
A93519


title: shDDX50-1 biorep2 kc211226

value: Biological replicate 2

value: shRNA against DDX50, #1


title: Prostate, Tissue, Treated, 2

description:
Treated_2
Tis.Processed.txt


title: Control, Bio Replicate 3, scRNAseq

city: Houston

first: Cynthia

last: Reinhart-King

state: TX

address: 6100 Main Street

department: Biomedical Engineering

institute: Rice University

description:
Library name: Sample 5
custom inDrops

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the inDrops method [https://github.com/indrops/indrops].
Assembly: Mus musculus GRCm38 [ENSEMBL release 85]
Supplementary files format and content: Comma-separated values files

source_name: mammary tumor

extract_protocol:
Fresh tumors were isolated in a sterile biosafety cabinet and placed in ice cold HBSS during transit from mouse facility to laboratory. Tumors were rinsed several times in ice cold HBSS and minced with sterile scalpels. Minced tumor was then enzymatically digested using the Human Tumor Dissociation Kit from Milytenyi Biotec (130-095-929). Post-enzymatic digestion, cells were passed through 100µm and 70 µm strainers (Miltenyi Biotec 130-110-916) to remove debris and undigested fragments. Cell suspensions then underwent several brief rounds of washing in 1X PBS with 3mM EDTA and an incubation in TrypLE (ThermoFisher Scientific 12604013) for 10 min to break apart cell clusters. Cells were suspended in PBS without EDTA and diluted to a concentration of 150k cells/ml for encapsulation.
(1CellBio) with an in vitro transcription library preparation protocol (Klein et al., 2015). As per Klein et al., the CEL-Seq work flow is summarized: 1) RT, 2) ExoI, 3) SPRI purification (SPRIP), 4) SSS, 5) SPRIP, 6) T7 in vitro transcription linear Amplification, 7) SPRIP, 8) RNA Fragmentation, 9) SPRIP, 10) primer ligation, 11) RT, 12) library enrichment PCR.

treatment_protocol: Mice were treated with control or BAPN in drinking water once per week starting at week 6 until endpoint.

value: mammary tumor

value: MMTV-PyMT positive

value: Control

tag: batch


title: Control, Bio Replicate 2, scRNAseq

description:
Library name: Sample 3
custom inDrops


title: Prostate, Tissue, Treated, 1

description:
Treated_1
Tis.Processed.txt


title: shControl biorep1 kc211226

value: Control shRNA


title: Prostate, Tissue, Untreated, 4

description:
Untreated_4
Tis.Processed.txt


title: shDDX50-1 biorep1 kc211226


title: BAPN, Bio Replicate 2, scRNAseq

description:
Library name: Sample 4
custom inDrops

value: BAPN


title: SUDHL-4_PRAME_A2-10_2

description:
SUDHL4_Counts.txt
A93517

value: Diffuse Large B-cell Lymphoma (Germinal Centre B-cell-like)

value: Mutant

value: Homozygous


title: Karpas422_wt_bulk_1

description:
Karpas422_Counts.txt
A93518

value: WT


title: Karpas422_PRAME_2-3_1

description:
Karpas422_Counts.txt
A93526

value: Heterozygous


title: STAU1 shDDX50-1 3

data_processing:
STAR (Love et al., 2014) (v. 2.7) was used to map raw, paired-end, fastq files to the rDNA locus, then to a genome of repetitive elements, then to the genome. Custom scripts were used for read processing (https://github.com/dfporter/easyclip-snakemake). Reads were assigned to genes, separating exons and introns, using HTSeq (v. 0.13.5).
Assembly: hg38
Supplementary files format and content: Text file of read counts per million reads mapping to the indicated elements.
Library strategy: CLIP-seq

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500). Cells were induced to differentiate by the addition of 1.2 mM calcium for 3 days at full confluence. Cells with low glucose and the corresponding normal glucose condition were maintained in glucose-free DMEM (Gibco, #11966025) supplied with SFM supplement (rEGF: Gibco, #10450-013; BPE: 13028-014), 1X Sodium Pyruvate (Gibco, 11360070) and a final concentration of 0.5 g/L (“low” glucose, Gibco, A2494001) or 4.5 g/L glucose (“normal” glucose) with adding 1.2 mM calcium during differentiation for 3 days. All the “low” and “normal” conditions indicated referred to day 3 differentiated cells if not specified.

extract_protocol:
Cells were lysed by lysis buffer and sonication, followed by immunopurification of the protein of interest, according to the easyCLIP protocol (https://doi.org/https://doi.org/10.1002/cpz1.659).
Libraries were constructed with the easyCLIP protocol (https://doi.org/10.1038/s41467-021-21623-4 and https://doi.org/https://doi.org/10.1002/cpz1.659).


title: BAPN, Bio Replicate 1, scRNAseq

description:
Library name: Sample 2
custom inDrops


title: SUDHL-4_PRAME_A2-10_1

description:
SUDHL4_Counts.txt
A93516


title: STAU1 shDDX50-4 3

value: shRNA against DDX50, #4


title: Prostate, Tissue, Untreated, 2

description:
Untreated_2
Tis.Processed.txt

value: Prostate


title: SUDHL-4_PRAME_A2-9_2

description:
SUDHL4_Counts.txt
A93515


title: Prostate, Tissue, Untreated, 3

description:
Untreated_3
Tis.Processed.txt

value: NPKC


title: STAU1 shControl 3

value: Primary keratinocytes


title: SUDHL-4_PRAME_A2-9_1

description:
SUDHL4_Counts.txt
A93514


title: C1_28_Wk2

city: Cleveland

first: Mark

last: Cameron

address: 10900 Euclid Ave

institute: Case Western Reserve University

data_processing:
Raw demultiplexed fastq paired end read files were trimmed of adapters and filtered using the program skewer to throw out any with an average phred quality score of less than 30 or a length of less than 10.
Trimmed reads were then aligned using the HISAT2 aligner to the Homo sapiens NCBI reference genome assembly version GRCh38 and sorted using SAMtools
Aligned reads were counted and assigned to gene meta-features using the program featureCounts as part of the Subread package.
Count files were imported into the R programming language and were assessed for quality control, normalized and analyzed utilizing the limma trend method.
Assembly: GRCh38
Supplementary files format and content: CSV file contains raw counts for each sample.
Supplementary files format and content: CSV file contains log2(n+3) TMM normalized counts per million for each sample.

extract_protocol:
PBMC samples were thawed, pelleted, and lysed in 350 uL of RLT with beta-mercaptoethanol. RNA was isolated using the RNeasy Mini kit (Qiagen). RNA quality was assessed with the Fragment Analyzer (Agilent) and its Standard Sensitivity RNA kit.
Total RNA was normalized to 100 ng prior to random hexamer priming and libraries generated by the TruSeq Stranded Total RNA – Globin kit (Illumina). The resulting libraries were assessed on the Fragment Analyzer (Agilent) with the High Sense Large Fragment kit and quantified using a Qubit 3.0 fluorometer (Life Technologies)

value: PBMC

value: F

tag: donor

tag: timepoint

value: R

value: HR


title: Prostate, Tissue, Untreated, 1

description:
Untreated_1
Tis.Processed.txt

tag: genotype


title: Skin_Polr2b.fl.fl.GFP_K14Cre_GFP_Rep2

first: Tudorita

last: Tumbar

institute: Cornell University

data_processing:
ChIP-seq reads were first trimmed with cutadapt (v1.18), then mapped to the mouse reference genome mm10 with Bowtie2 (v2.3.5). The BAM files were then converted to RPM normalized bigWig format and visualized using Integrated Genome Viewer (IGV). The correlation analysis was performed using plotCorrelation from deepTools (v3.5.5). Heatmap and profile plots of read signal across genes were generated using the plotHeatmap and plotProfile functions from deepTools.
Assembly: mm10
Supplementary files format and content: Sample specific bigwig files.

growth_protocol: The V6.5 mESCs were grown to ~70% confluence without irradiated feeders in standard mouse ES cell medium containing LIF for atleast two passages before using them for  the experiment. For ChIP-seq on mouse skin tissues, whole dorsal skin from Polr2bf/f-GFP or Polr2bf/f-GFP; K14-Cre mice were collected at postnatal day PD24.

extract_protocol:
Samples were flash-frozen in liquid N2, followed by dry pulverization of frozen tissue through a cell crusher. Samples were cross-linked with 1% formaldehyde, quenched with 125 mM glycine, and washed with ice cold PBS with protease inhibitors (ThermoFisher, A32965). After pelleting, samples were resuspended in ice-cold swelling buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP40, 5 mM NaF, 2 mM Na2VO4, 1 mM PMSF, 1X PIC) and dounced with both tight and loose pestle for 20 times on ice, followed by filtering through a 70 µm filter. After centrifugation (1,000xg 10 min 4°C), samples were resuspended in sonication buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1 % Na-Deoxycholate, 0.1% SDS, 5mM NaF, 2 mM Na2VO4, 1mM PMSF, 1X PIC) and fragmented using Bioruptor at high setting for 30 second ON + 30 second OFF pulses for a total of 30 minutes.
DNA libraries were constructed by Tn5 tagmentation. Briefly, primer A 5′-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3’ or primer B 5′-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-3′ was annealed to Tn5-rev oligo 5′-[phos]CTGTCTCTTATACACATCT-3′. Transposons were assembled using Tn5 and primers A and B in DF buffer (100 mM HEPES, pH 7.2, 200 mM NaCl, 0.2 mM EDTA, 2 mM DTT, 0.2% Triton X-100, 20% glycerol). Tagmented DNA was PCR amplified and purified with AMpure XP beads (Beckman Coulter, A63880) and quality checked by running on 6% Native PAGE gels and Fragment Analyzer. The ChIP DNA libraries were sequenced with Illumina NextSeq500, 2x37 bp

tag: tissue

value: Skin

value: Keratinocytes

value: Polr2b.fl.fl.GFP; K14Cre


title: STAU1 shDDX50-4 2

tag: treatment


title: SUDHL-4_PRAME_A2-6_2

description:
SUDHL4_Counts.txt
A93513

tag: cell line


title: Prostate, Organoid, NPC, 3

description:
NPC_Exp20_22_p1
Org.Processed.txt

data_processing:
library strategy: Digital RNA with pertUrbation of Genes (DRUG)-seq
Read trimming, alignment, and quantification steps were performed by Alithea Genomics using STARsolo v2.7.9a and the GRCm38.103 (mouse) reference genome.
Utilizing the parameters “--soloUMIdedup NoDedup 1MM_Directional”, and “--quantMode GeneCounts” 52, we generated raw and UMI-deduplicated count matrices, opting for non-deduplicated counts for subsequent analyses.
Assembly: GRCm38.103
Supplementary files format and content: Org.Processed.txt = UMI count matrix of organoid samples
Supplementary files format and content: Tis.Processed.txt = UMI count matrix of tissue samples

value: NPC


title: Skin_Polr2b.fl.fl.GFP_K14Cre_PolII_Rep2

value: All cells in skin


title: Skin_Polr2b.fl.fl.GFP_K14Cre_GFP_Rep1


title: Prostate, Organoid, NPKC, 4

description:
NPKC_Exp2_21_p5
Org.Processed.txt


title: STAU1 shDDX50-1 2

value: shRNA against DDX50, #1


title: SUDHL-4_single_6_2

description:
SUDHL4_Counts.txt
A93511

value: Diffuse Large B-cell Lymphoma (Germinal Centre B-cell-like)


title: Control, Bio Replicate 1, scRNAseq

description:
Library name: Sample 1
custom inDrops

value: mammary tumor

value: MMTV-PyMT positive

value: Control


title: SUDHL-4_single_6_1

description:
SUDHL4_Counts.txt
A93510

value: WT


title: Prostate, Organoid, NC, 2

description:
NC_Exp19_22_p2
Org.Processed.txt

value: Prostate

value: NC


title: STAU1 shDDX50-1 1

value: Primary keratinocytes


title: Skin_Polr2b.fl.fl.GFP_K14Cre_IgG_Rep2


title: Skin_Polr2b.fl.fl.GFP_K14Cre_PolII_Rep1


title: STAU1 shDDX50-4 1

value: shRNA against DDX50, #4


title: SUDHL-4_single_5_2

description:
SUDHL4_Counts.txt
A93509


title: Prostate, Organoid, NPK, 3

description:
NPK_Exp53_22_p0
Org.Processed.txt

value: NPK


title: Skin_Polr2b.fl.fl.GFP_K14Cre_IgG_Rep1


title: STAU1 shControl 1

value: Control shRNA


title: STAU1 shControl 2


title: Prostate, Organoid, NC, 1

description:
NC_Exp43_22_p4
Org.Processed.txt


title: Skin_Polr2b.fl.fl.GFP_K14Cre_Input_Rep2

value: Skin


title: HA STAU1 H gluc 3

value: Lentiviral integration of HA-tagged STAU1


title: Prostate, Organoid, NC, 3

description:
NC_Exp37_22_p1
Org.Processed.txt


title: Prostate, Organoid, NPK, 2

description:
NPK_Exp10_21_p4
Org.Processed.txt


title: SUDHL-4_PRAME_A2-6_1

description:
SUDHL4_Counts.txt
A93512

value: Mutant

value: Heterozygous


title: SUDHL-4_wt_bulk_1

description:
SUDHL4_Counts.txt
A93506


title: Skin_Polr2b.fl.fl.GFP_GFP_Rep2

value: Keratinocytes


title: HA STAU1 H gluc 2


title: Skin_Polr2b.fl.fl.GFP_GFP_Rep1


title: Prostate, Organoid, NPK, 1

description:
NPK_Exp22_22_p4
Org.Processed.txt


title: SUDHL-4_wt_bulk_2

description:
SUDHL4_Counts.txt
A93507


title: HA STAU1 L gluc 3


title: Prostate, Organoid, NP, 2

description:
NP_Exp10_19_p5
Org.Processed.txt

value: NP


title: HA STAU1 H gluc 1


title: Skin_Polr2b.fl.fl.GFP_K14Cre_Input_Rep1

value: All cells in skin

value: Polr2b.fl.fl.GFP; K14Cre


title: P60 wild-type replicate4

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

institute: IBS/KAIST

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.2) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.26.0).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

growth_protocol: A targeting vector for the mouse Dyrk1a-Ile48LysfsX2 mutation was introduced to C57BL/6J embryonic stem cells by homologous recombination. Targeted embryonic stem cells were injected into BALB/c blastocysts to generate chimeric mice, which were then crossed with C57BL/6J mice to generate F1 progeny. Heterozygote mice were crossed with protamine-Flp mice to remove the neomycin cassette. Mice were bred and maintained at the mouse facility of Korea Advanced Institute of Science and Technology (KAIST) according to the Animal Research Requirements of KAIST, and all procedures were approved by the Committee of Animal Research at KAIST (KA2022-063-v1). Animals were fed ad libitum and housed under a 12-h light/dark cycle (light phase from 01:00 am to 13:00 pm). Mice were weaned at postnatal day 21 (P21), and mixed-genotype littermates of the same gender were housed together until experiments.

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

tag: strain

value: wildtype

tag: age


title: Skin_Polr2b.fl.fl.GFP_PolII_Rep2

address: 526 Campus Rd

tag: time


title: HA STAU1 L gluc 2


title: SUDHL-4_single_5_1

description:
SUDHL4_Counts.txt
A93508

value: Diffuse Large B-cell Lymphoma (Germinal Centre B-cell-like)

value: WT


title: P60 wild-type replicate3


title: Prostate, Organoid, NPKC, 3

description:
NPKC_Exp34_22_p0
Org.Processed.txt

value: Prostate

value: NPKC


title: Prostate, Organoid, NP, 3

description:
NP_Exp4_20_p5
Org.Processed.txt


title: Skin_Polr2b.fl.fl.GFP_PolII_Rep1


title: P60 wild-type replicate2


title: Skin_Polr2b.fl.fl.GFP_IgG_Rep2


title: P60 wild-type replicate5


title: HA STAU1 Prog 3

value: Primary keratinocytes


title: Prostate, Organoid, NP, 1

description:
NP_Exp6_22_p4
Org.Processed.txt


title: Prostate, Organoid, N, 3

description:
N_Exp15_20_p2
Org.Processed.txt

value: N


title: Prostate, Organoid, NPKC, 2

description:
NPKC_Exp36_22_p0
Org.Processed.txt


title: P60 knockin replicate5

value: Knockin


title: Skin_Polr2b.fl.fl.GFP_IgG_Rep1

value: Skin


title: Skin_Polr2b.fl.fl.GFP_Input_Rep2


title: HA STAU1 Prog 1

value: Lentiviral integration of HA-tagged STAU1


title: Skin_Polr2b.fl.fl.GFP_Input_Rep1


title: Prostate, Organoid, NPC, 2

description:
NPC_Exp12_21_p1
Org.Processed.txt

value: NPC


title: P60 knockin replicate4


title: shSTAU1-3 4h biorep2 stability STAU1

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500). Human skin keratinocyte cells were induced to differentiate by the addition of 1.2 mM calcium for 3 days at full confluence in the 50/50 media. Biological replicates were performed in all cases using primary cells from at least 2 independent, unrelated donors.

treatment_protocol: For actinomycin D treatment, differentiated keratinocytes were treated with 5 µg/mL actinomycin D (~4 µM) or DMSO for the indicated time before harvesting the cells.

value: Biological replicate 2

value: shSTAU1 #3, 4h after actinomycin treatment


title: P60 knockin replicate3


title: Prostate, Organoid, N, 2

description:
N_Exp18_22_p4
Org.Processed.txt


title: mESC_Polr2b.fl.fl.GFP_Ef1aCre_GFP_Rep2

source_name: Embryo

value: Embryo

value: ESCs

value: Polr2b.fl.fl.GFP; Ef1aCre


title: shSTAU1-3 0h biorep2 stability STAU1

value: shSTAU1 #3


title: Prostate, Organoid, NPKC, 1

description:
NPKC_Exp47_22_p0
Org.Processed.txt


title: P60 wild-type replicate1

value: Brain

value: wildtype


title: mESC_Polr2b.fl.fl.GFP_Ef1aCre_GFP_Rep1


title: P60 knockin replicate2


title: P60 knockin replicate1


title: Prostate, Organoid, NPC, 1

description:
NPC_Exp19_20_p4
Org.Processed.txt


title: HA STAU1 Prog 2


title: shSTAU1-2 4h biorep2 stability STAU1

value: shSTAU1 #2, 4h after actinomycin treatment


title: shSTAU1-2 0h biorep2 stability STAU1

value: shSTAU1 #2


title: mESC_Polr2b.fl.fl.GFP_Ef1aCre_PolII_Rep2


title: P21 wild-type replicate6


title: shSTAU1-1 4h biorep2 stability STAU1

value: shSTAU1 #1, 4h after actinomycin treatment


title: HBL1-CON1

description:
HBL1_Counts.txt
F40851

value: Diffuse Large B-cell Lymphoma (Activated B-cell-like)

value: WT


title: P21 wild-type replicate5


title: mESC_Polr2b.fl.fl.GFP_PolII_Rep2


title: mouse inner ear organoid, day 21, rep2

first: Alan

last: Cheng

address: 240 Pasteur Drive

institute: Stanford University

data_processing:
Cell Ranger - 6.0.0
Seurat - 4.3.0
Assembly: mm10
Supplementary files format and content: Files containing the cell barcodes and detected features for each sample are provided in .tsv format. A filtered matrix file containing the number of detected UMIs for each feature and barcode is also provided in .mtx format (filtered to contain only cell-associated barcodes).

source_name: inner ear organoid

growth_protocol: Inner ear organoids were generated as described in Hartman et al., 2018, with minor modifications. Briefly, Fbxo2-VHC mouse embryonic stem cells were resuspended in ectodermal differentiation medium and plated into 96-well U-bottom suspension (Nulcon Sphera, Thermo Fisher) plates at a concentration of 3,000 cells per well. At day in vitro (DIV) 1, the media was supplemented with 2% matrigel (Corning). On DIV3, organoids were exposed to 10ng/mL BMP4 (Reprocell) to induce BMP signaling and 1μM RepSox (Selleckchem) to repress TGFß signaling. On DIV4, developing organoids were further exposed to 50ng/mL FGF2 (Peprotech) to induce FGF signaling and 1μM LDN193189 (Reprocell) to repress BMP signaling. On DIV8, organoids were washed with 1x PBS and transferred to maturation media containing 1% matrigel and 3μM CHIR99021 (Selleckchem) to induce Wnt signaling. After DIV10, half media changes were performed every 2 days up until the last time point at DIV21.

extract_protocol:
For DIV3 and DIV4 time points, organoids were washed once in 1X PBS, incubated in Accutase dissociation reagent for 3 minutes at 37°C, and dissociated by manual trituration with a P200 pipette tip. This step was repeated twice. DIV8, DIV16 and DIV21 organoids were first incubated for 20 minutes in 0.5mg/mL Thermolysin at 37°C before incubation in Accutase for 3 minutes. Organoids were then mechanically dissociated using a 23G blunt ended needle connected to a sterile 1mL syringe, returned to the incubator for an additional 3 minutes, and dissociated a second time. Cells from all time points were then collected in 1mL 1X PBS, spun down at 4°C at 400xg for 10 minutes, and resuspended in 400μL of DMEM/F12+10%FBS. Cell clumps were removed by filtering through a 35μm strainer cap. Cells were then placed on ice and brought immediately to the Stanford Functional Genomics Core for 10X Genomics scRNA-seq capture and sequencing.
10X Genomics Single Cell 3' v3

value: inner ear organoid

value: 21 days in vitro


title: shSTAU1-1 0h biorep2 stability STAU1

value: Primary keratinocytes

value: shSTAU1 #1


title: P21 wild-type replicate4


title: mouse inner ear organoid, day 21, rep1


title: shControl 4h biorep2 stability STAU1

value: Biological replicate 2

value: Control shRNA, 4h after actinomycin treatment


title: mESC_Polr2b.fl.fl.GFP_PolII_Rep1

value: Embryo


title: P21 wild-type replicate3


title: mESC_Polr2b.fl.fl.GFP_Input_Rep2

value: ESCs


title: shControl 0h biorep2 stability STAU1

value: Control shRNA


title: P21 wild-type replicate2


title: mouse inner ear organoid, day 16, rep2

value: 16 days in vitro


title: mESC_Polr2b.fl.fl.GFP_Input_Rep1


title: shSTAU1-3 4h biorep1 stability STAU1

value: Biological replicate 1

value: shSTAU1 #3, 4h after actinomycin treatment


title: mouse inner ear organoid, day 16, rep1


title: Prostate, Organoid, N, 1

description:
N__Exp16_22_p0
Org.Processed.txt

value: Prostate

value: N


title: PROseq_Cultured_Undiff_keratinocytes_Rep2

data_processing:
PReCIS-seq reads were first trimmed with fastp (v0.23.2), then mapped to the mouse rDNA using bowtie2 (v2.4.4) to deplete nascent rRNA. The rRNA-depleted reads were then mapped to the mm39 reference genome using STAR (v2.7.10b) and UMI duplicate reads were removed using umi_tools (v 1.1.2). The de-duplicated BAM files were then converted to CPM-normalized bigWig files using samtools and visualized using Integrated Genome Viewer (IGV). Promoter-proximal and gene body counts were obtained using the BRGenomics package in R and are provided as supplementary data files.
Assembly: mm39
Supplementary files format and content: Strand specific bigWig files
Library strategy: PRO-seq

extract_protocol:
For mouse skin samples, samples were flash-frozen in liquid N2, followed by dry pulverization of frozen tissue through a cell crusher and douncing. Chromatin was isolated using NUN buffer and fragmented with DNase I, and nascent RNA was biotin-labeled through a run-on reaction. Cell-type-specific nascent RNAs were enriched through GFP pull-down and library preparation steps were then followed as previously described for PRO-seq assay. All input samples were processed without GFP pull-down that served as controls for cell-type specific nascent RNA enrichment.
Nascent RNA libraries were generated using the PRO-seq protocol.

value: Skin

value: Keratinocytes

value: Newborn


title: P21 wild-type replicate1

value: Brain

value: wildtype


title: P21 knockin replicate4

value: Knockin


title: mESC_Polr2b.fl.fl.GFP_Ef1aCre_PolII_Rep1

value: Polr2b.fl.fl.GFP; Ef1aCre


title: shSTAU1-3 0h biorep1 stability STAU1

value: Primary keratinocytes

value: shSTAU1 #3


title: PROseq_Cultured_Undiff_keratinocytes_Rep1

value: WT


title: mouse inner ear organoid, day 8, rep2

value: inner ear organoid

value: 8 days in vitro


title: MT px A

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

institute: Boston University

data_processing:
FASTQ files were aligned to mouse genome build mm10 using STAR (Dobin et al., 2013) (version 2.7.9a).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 2.0.3) and Ensembl annotation build 100 (uniquely aligned proper pairs, same strand).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Variance-stabilizing transformation (VST) was accomplished using the varianceStabilizingTransformation function in the DESeq2 R package (version 1.32.0) (Love et al., 2014).
All analyses were performed using the R environment for statistical computing (version 4.1.2).
Assembly: mm10
Supplementary files format and content: counts.txt: 55450 x 18 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: 55450 x 18 matrix of variance-stabilizing-transformed (VST) expression values

extract_protocol: RNA was isolated from C2C12 cells using TRIzol reagent (Invitrogen) followed by phenol-chloroform extraction, precipitated with 100% isopropanol, and washed with 70% ethanol. RNA pellets were air-dried and resuspended in RNase-free water. RNA samples corresponding to myoblasts and myotubes (day 3 of differentiation) were submitted to the Boston University Microarray and Sequencing Resource Core in triplicate for library prep and Illumina sequencing.

value: myotube

value: control


title: P21 knockin replicate2


title: P21 knockin replicate3


title: mouse inner ear organoid, day 11, rep1

value: 11 days in vitro


title: CD45+ cells isolated from MyC-CaP CRPC, developed through degarelix treatment (ADT), for library 1 CITEseq

data_processing:
CellRanger v5 count was run on mouse scRNAseq and CITEseq libraries from the same sample to generate a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz. CellRanger v3 count was run on patient scRNAseq to generate a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.
Assembly: GRCm38, GRCh38, mouse_reference_CITEseq.csv
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
For patients, viably cryopreserved tumor tissue samples were digested in RPMI containing Collagenase I & II (0.1 mg/ml, Thermo Fisher Scientific) and DNase I (Thermo Fisher Scientific), minced, and then subjected to 1-hour digestion using the gentleMACS system (Miltenyi Biotec). Live cell isolation was performed using MACS LS columns (Miltenyi Biotec). The 10x Genomics Chromium Controller was utilized to generate GEM bead emulsions using the Single Cell 5′ Library & Gel Bead Kit (10x Genomics). For mice, a cohort of FVB/NJ mice bearing MyC-CaP were injected s.c. with either degarelix (n = 3) or PBS (n = 3), as described above. HSPC or CRPC tissues were harvested upon reaching a tumor volume > 350 mm3. Tumors were sequentially digested 3 times with 12 ml of a cocktail of 2 mg/ml (w/v) Collagenase Type IV and 100 Kunitz U/ml DNase I (both from Sigma-Aldrich) for 12 minutes per digest. All single-cell suspensions were filtered using 70 μm filters (Fisher Scientific) and subjected to red blood cell lysis using ACK Lysing Buffer (Quality Biological). For the cell surface protein staining, cells were incubated with CD45.1-Brilliant Violet 510 (A20) for 30 minutes at 4°C. After immunostaining, cells were washed twice in FWB and resuspended in FWB containing 1 μg/ml propidium iodide for viability assessment. Cells were then sorted into CD45+ and CD45- populations using BD FACSAria (BD Biosciences). Each population was transferred into separate 75 mm flow cytometry tubes, centrifuged for 5 minutes at 250 g at 4˚C, and the supernatant was discarded. After staining with the hashtag (2, 4, and 6 (M1/42, 30-F11)) and TotalSeq-C surface (CD11c (N418), CD163 (S15049I), F4/80 (BM8), and Ly-6G (1A8)) antibodies, cell viability and count were reassessed. The 10x Genomics Chromium Controller was utilized to generate GEM bead emulsions using the Single Cell 5′ Library & Gel Bead Kit (10x Genomics) according to the manufacturer's protocol.
After generating GEM bead emulsions, we performed the synthesis and amplification of cDNA, followed by library preparation steps using 10x Genomics kits according to the manufacturer's protocol.

value: prostate

value: CD45+ cells

value: FVB/NJ injected with MyC-CaP

value: degarelix (androgen-deprivation therapy (ADT))

tag: library type

value: ADT


title: shSTAU1-2 0h biorep1 stability STAU1

value: Biological replicate 1

value: shSTAU1 #2


title: shSTAU1-2 4h biorep1 stability STAU1

value: shSTAU1 #2, 4h after actinomycin treatment


title: mouse inner ear organoid, day 11, rep2


title: mouse inner ear organoid, day 8, rep1


title: shSTAU1-1 4h biorep1 stability STAU1

value: shSTAU1 #1, 4h after actinomycin treatment


title: PROseq_Isolated_keratinocytes_Rep2

value: Skin

value: Keratinocytes


title: P21 knockin replicate1

value: Brain

value: Knockin


title: PROseq_Isolated_keratinocytes_Rep1


title: shSTAU1-1 0h biorep1 stability STAU1

value: Primary keratinocytes

value: shSTAU1 #1


title: mouse inner ear organoid, day 4, rep2

value: inner ear organoid

value: 4 days in vitro


title: mouse inner ear organoid, day 4, rep1


title: AMF rep2

city: China Shenzhen

first: Yang

last: Wang

address: Sun Yat-Sen University Shenzhen Campus

institute: Sun Yat-Sen University

data_processing:
Illumina RTA software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR 2.7.0 with default parameters
The gene expression level was calculated by featureCounts with default parameters.
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: HepG2l cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted by using EASYspin RNA Mini Kit (Aidlab RN07).
RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111).

treatment_protocol: HepG2 cells were treated with DMSO or 90 μM AMF for 48 h.

value: Human hepatoblastoma

value: WT

value: AMF


title: MyD88 KO nTERT Ctrl-IgG4

city: Chicago

first: kyle

last: amber

state: IL

address: 707 S Wood St

institute: Rush University

data_processing:
Bowtie (version 1.2.3), RSEM (version 1.3.3) with standard parameters
Assembly: Hg38/gencode.v42
Supplementary files format and content: TXT file containing raw TPM, FPKM, counts

growth_protocol: Cells were grown in KC-SFM medium (ThermoFisher) supplemented with 30 μg/ml bovine pituitary extract, 0.2 ng/ml epidermal growth factor, and 0.3 mM calcium chloride.

extract_protocol:
Qiagen RNeasy Mini Kit
Poly (A) mRNA was subsequently extracted and enriched from total RNA utilizing oligo (dT)-attached magnetic beads according to the manufacturer’s (Illumina) instructions. Enriched and purified mRNA was fragmented into approximately 200 nt short mRNA, followed by first-strand cDNA synthesis using random hexamers as primers. Second-strand cDNA was constructed in a buffer containing dNTPs, DNA polymerase I and RNaseH. Appropriate fragments were isolated and enriched by PCR amplification.

treatment_protocol: Treated overnight with affinity purified BP-IgG or Ctrl-IgG

value: MyD88 KO nTERT

value: keratinocyte

value: Ctrl-IgG


title: shControl 4h biorep1 stability STAU1

value: Biological replicate 1

value: Control shRNA, 4h after actinomycin treatment


title: MyD88 KO nTERT Ctrl-IgG3


title: shControl 0h biorep1 stability STAU1

value: Control shRNA


title: AMF rep1


title: PROseq_Isolated_keratinocytes_Rep3

value: Skin


title: mouse inner ear organoid, day 3, rep2

value: 3 days in vitro


title: DMSO rep2

value: DMSO


title: DMSO rep1


title: shSTAU1-4 biorep2 adipocyte

description: NovaSeq X Plus

data_processing:
Lexogen reads were processed according to the manufacturer’s recommendation, mapped with STAR (v. 2.7) to the Gencode M32 genome (“basic” annotations), and genes quantified with FeatureCounts (from Rsubread v.2.10.5). Quantifications were analyzed with DESeq2 (v.1.38.3), with apeGLM shrinkage.
Assembly: GRCm39 (M32)
Supplementary files format and content: Reads per gene quantified with FeatureCounts (from Rsubread v.2.10.5).

growth_protocol: 3T3-L1 (ATCC, CL-173) cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) media (Gibco, #11995-065) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin at 37°C with 5% CO2. 3T3-L1 cells were induced to differentiation in DMEM supplied with 10% FBS, 1% penicillin–streptomycin, 0.5 mM IBMX, 1 µM dexamethasone, 10 µg/mL insulin.

extract_protocol:
Total RNA was extracted using the RNeasy Plus kit (QIAGEN, 74136).
QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen, 191.96) following manufacturer’s protocol with UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen, 018.96)

value: Adipocyte

value: shRNA against STAU1, #4


title: MyD88 KO nTERT Ctrl-IgG1


title: DDX50 STAU1 Glc dms26

data_processing:
UMIs were moved to read name and fixed sequenced removed using umi_tools extract, after which bbduk.sh removed adapters AGA TCG GAA GAG CGT CGT GTA GGG AAA GAG TGT and AGA TCG GAA GAG CAC ACG TCT GAA CTC CAG TCA. Reads were then mapped to a bowtie2 genome of stabilized RNAs and expression-matched random RNAs using RNAFramework rf-map. Mapped reads were deduplicated with umi_tools, quantified with RNAFramework/rf-count, then normalized. For comparison of unnormalized reaction rates between conditions, the quantifications output from rf-count were used. Finally, RNAs were folded with the parameters --temperature 37 --dotplot -sh --vienna-rnasubopt ViennaRNA/bin/RNAsubopt --vienna-rnafold ViennaRNA/bin/RNAfold.
Assembly: hg38
Supplementary files format and content: TPM at the subset of genes investigated for structure.
Library strategy: DMS-seq

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500). Cells were induced to differentiate by the addition of 1.2 mM calcium for 4 days at full confluence.

extract_protocol:
Total RNA was extracted from day 4 differentiated keratinocytes using RNeasy Plus (QIAGEN, 74136).
DMS labeled RNA was first purified using the Dynabeads™ mRNA DIRECT™ Purification Kit (Invitrogen, 61012). 12 μL poly(A) beads per sample were washed twice with binding buffer (100 mM Tris-HCl pH 7.5, 500 mM NaCl, 10 mM EDTA, 1% SDS), then added to purified RNA in 600 μL of binding buffer, incubated for 3-5 minutes at room temperature with mixing to bind RNA to the beads, washed with the kit’s buffers according to the kit’s instructions, and eluted in 11 μL of 10 mM Tris-HCl (pH 7.5) by heating at 65-80°C for 2 minutes. Purified poly(A) RNA was converted to a sequencing library with the SMARTer® Stranded Total RNA-SeqKit v3 Pico Input Mammalian kit (Takara, 634485) following the manufacturer’s instructions and using a 1.5 min 94°C initial incubation in First-Strand buffer and 7 cycles during the first PCR reaction.

treatment_protocol: Total RNA was extracted from day 4 differentiated keratinocytes using RNeasy Plus (QIAGEN, 74136). 1 µg of total RNA was used for each experiment. RNA was diluted to 200ng/µL with RNase free water and heated for 1 min at 95 °C, then placed on ice. RNA was subsequentially diluted in refolding buffer to 90 µL before protein or glucose were added to the mix. A total of 6 conditions were explored (DMS was not added at this step): 1. No DMS+200ng BSA; 2. DMS+200ng BSA; 3. DMS+200ng BSA+1 mM glucose; 4. DMS+200ng DDX50; 5. DMS+150ng STAU1; 6. DMS+200ng DDX50+150ng STAU1+1mM glucose. Mixtures were incubated at 37 °C for 10 min on thermomixer. After incubation, 10 μL 1.7M DMS (diluted in ethanol) or 10 μL ethanol (for no DMS samples) was added to the mixtures and RNA labeled by incubation at 37 °C for 5 min on a thermomixer while shaking at 500rpm. To quench, 60 μL β-mercaptoethanol was added to the mixture immediately and labeled RNA was purified.

value: Primary keratinocytes


title: mouse inner ear organoid, day 3, rep1

value: inner ear organoid


title: shSTAU1-4 biorep1 adipocyte

description: NovaSeq X Plus


title: MyD88 KO nTERT-BP-IgG5

value: BP-IgG


title: DDX50 STAU1 Glc dms25


title: MyD88 KO nTERT-BP-IgG4


title: DDX50 KR STAU1 Glc dms22


title: MyD88 KO nTERT-BP-IgG3


title: shSTAU1-2 biorep1 adipocyte

description: NovaSeq X Plus

value: shRNA against STAU1, #2


title: DDX50 KR STAU1 Glc dms21


title: MyD88 KO nTERT Ctrl-IgG2


title: DDX50 KR dms20


title: MyD88 KO nTERT-BP-IgG2


title: MyD88 KO nTERT-BP-IgG1


title: shDDX50-2 biorep2 adipocyte

description: NovaSeq X Plus

value: shRNA against DDX50, #2


title: shDDX50-2 biorep1 adipocyte

description: NovaSeq X Plus


title: STAU1 dms27


title: DDX50 KR dms19


title: GBCT19

city: Shanghai

first: Shengli

last: Li

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
Stringtie was used to assemble transcripts from mapped reads.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: Gallbladder tissue

extract_protocol:
Tissues were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) was used with 3 ug of total RNA for the construction of sequencing libraries. RNA-seq libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using RNAseq protocols

value: Gallbladder

tag: tumor status

value: Primary tumor

tag: gender

value: Male

tag: patient age

tag: tumor stage


title: GBCT16

value: Female


title: GBCT20


title: GBCT18


title: shDDX50-1 biorep2 adipocyte

description: NovaSeq X Plus

tag: cell type

value: shRNA against DDX50, #1


title: DDX50 STAU1 Glc dms18


title: nTERT-BP-IgG5

value: nTERT

value: keratinocyte


title: GBCT15


title: nTERT-BP-IgG4

value: Skin


title: shSTAU1-2 biorep2 adipocyte

description: NovaSeq X Plus


title: GBCT14


title: DDX50 STAU1 Glc dms17


title: nTERT-BP-IgG3


title: GBCT13


title: shControl biorep2 adipocyte

description: NovaSeq X Plus

value: Control shRNA


title: DDX50 STAU1 dms16


title: GBCT17


title: GBCT12


title: shControl biorep1 adipocyte

description: NovaSeq X Plus