title: LLC-mouse-model, MW-TMPs, rep  2

city: Wuhan

first: Xinghui

last: Cao

address: Hangkong Road 13, Wuhan, China

institute: Huazhong University of Science and Technology

description:
Library name: Sample 8
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: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: subcutaneous tumor

extract_protocol:
When the intervention was completed, fresh subcutaneous tumors were stored in MACS tissue storage solution (#130100008) and cell suspensions were prepared by tissue homogenate.  The single-cell suspension was added to the single-cell sorting honeycomb plate and excessive magnetic beads with barcodes were put into the plate.
During the phase of cell lysis, the RNA was labeled as bounding to the barcode.  Subsequently, reverse transcription of RNA and cDNA synthesis were carried out to obtain cDNA library for subsequent sequencing.  Paired-end sequencing was conducted in the Nova seq6000 sequencing platform to get the transcriptome results.  BD Rhapsody Analysis pipeline was applied to identify the UMI sequence and the cell tag sequence alignment to the reference genome (GRCm39).

treatment_protocol: MW-TMPs

value: subcutaneous tumor

tag: strain

value: C57BL/6 mice

value: LLC

value: female

tag: age

value: 6-8 weeks

value: MW-TMPs


title: LLC-mouse-model, MW-TMPs, rep  3

status: Public on Feb 26 2025

type: SRA

country: China

description:
Library name: Sample 9
10X Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: Sex

tag: treatment


title: LLC-mouse-model, MW-TMPs, rep  1

description:
Library name: Sample 7
10X Genomics


title: CM, Day 0, RNA-Seq, Replicate 2

city: Frankfurt am Main

first: Marcel

last: Schulz

address: Theodor-Stern-Kai 7, Haus 26

country: Germany

institute: Goethe University and Uniklinikum Frankfurt

library_source: transcriptomic

data_processing:
Adaptor sequences were trimmed with TrimGalore [https://github.com/FelixKrueger/ TrimGalore] based on the library preparation protocol. Salmon was used for the estimation of gene expression values using transcript alignments from STAR v2.28
Assembly: mm10
Supplementary files format and content: salmon TPM

source_name: Cardiomyocytes

growth_protocol: see Methods in manuscript

extract_protocol:
Cardiomyocytes were enriched by performing repeated centrifugation steps (20 x g, 2 minutes). The supernatant of the centrifugation step was used to isolate hematopoietic cells, endothelial cells, and fibroblasts. Hematopoietic and endothelial cells were isolated by magnetic separation. Cells not bound to the magnetic beads or columns were used for cardiac fibroblast enrichment by a plating step with uncoated dishes. After 40 minutes, predominantly DDR2-positive fibroblasts adhered and were used for RNA isolation. Cells extracted from three mice were pooled to generate enough cells for one of four biological replicate sequencing samples for each timepoint. Total RNA was isolated from CM, EC, HC and FB using the Qiagen (Hilden, Germany) miRNeasy Kit involving column DNAse digestion. RNA quantity was fluorometrically measured using the Qubit 4 (Thermo Fisher) RNA HS Assay Kit and integrity of the RNA was verified using the Agilent Bioanalyzer RNA Pico chips.
Long RNA was converted into Illumina compatible libraries using the CATS Total RNA-seq Kit v2 with rRNA depletion (Diagenode). After the depletion, this procedure involves the fragmentation of RNA, 3 ́-polyadenylation and cDNA synthesis primed by oligo-T. Addition of a template switch oligo allows in combination with a suitable reverse transcriptase allows then the generation of double stranded cDNA with adaptor sequences for further amplification.

treatment_protocol: see Methods in manuscript

tag: cell type

value: Cardiomyocytes

value: Day 0


title: HC, Day 28, smallRNA-Seq, Replicate 1

description: small RNA sequencing

data_processing:
small RNA-seq analysis pipeline from nf-core [https://nf-co.re/smrnaseq]
Small RNAs were trimmed/qualitycheck using Trimgalore and then quantified using the small RNA-seq analysis pipeline from nf-core [https://nf-co.re/smrnaseq], where the full length of the small RNA reads were used for the pipeline.
The processed file is the result of samtools idxstats run on the sorted bowtie2 alignment files, aligned wiith the reference mm10 and thereafter mapped to miRBase v21 miRNAs.
Assembly: mm10
Supplementary files format and content: tab delimited files include reference sequence name, sequence length, # mapped read-segments and # unmapped read-segments

source_name: Hematopoietic cells

extract_protocol:
Cardiomyocytes were enriched by performing repeated centrifugation steps (20 x g, 2 minutes). The supernatant of the centrifugation step was used to isolate hematopoietic cells, endothelial cells, and fibroblasts. Hematopoietic and endothelial cells were isolated by magnetic separation. Cells not bound to the magnetic beads or columns were used for cardiac fibroblast enrichment by a plating step with uncoated dishes. After 40 minutes, predominantly DDR2-positive fibroblasts adhered and were used for RNA isolation. Cells extracted from three mice were pooled to generate enough cells for one of four biological replicate sequencing samples for each timepoint.
Small RNAs were converted into Illumina compatible libraries using the NEB Next small RNA library Kit from New England Biolabs (NEB), which involves 3´-ligation and 5´-ligation to small RNAs and therefore enriches for 5´-monophosphorylated and 3 ́-hydroxylated small RNAs, such as miRNA. Due to the varying RNA amounts available for each cell type, we used the following parameters for input of total RNA and PCR cycles: CM-500ng-14cycles, EC-50ng-16cycles, HC-150ng-15cycles, FB-150ng-15-cycles. After library amplification, we cut each library from 10% TBE (Tris-Borate-EDTA) PAGE gels, extracting the library size of approx. 140-150bp which corresponds to 20-30nt miRNAs. Libraries were then quantified using the Qubit dsDNA HS Assay (Thermo Fisher).

value: Hematopoietic cells

value: Day 28


title: FXS_1, Input

city: Cincinnati

first: Ziyuan

last: Guo

address: 3333 Burnet Ave

country: USA

institute: CCHMC

data_processing:
Raw reads in fastq format were trimmed to remove the adaptor sequence and the reads with adaptor contaminants and low-quality reads using Trim Galore (v 0.6.6)
Preprocessed reads were then aligned to the human genome (build GRCh38) using STAR (v2.7.9) with the default settings
m6A peaks were identified using exomePeak R package (v2.16.0), GO analysis was performed using clusterProfiler R package. m6A-RNA-related genomic features were visualized using Guitar R package (v2.14.0), de novo motif analysis was performed by homer (v4.11).
Assembly: GRCh38
Supplementary files format and content: bed
Library strategy: MeRIP-seq

organism: Homo sapiens

source_name: iPS

growth_protocol: iPSCs were expanded onto fresh vitronectin-coated plate with Essential 8 medium, passaged with ReleSRTM every 3-4 days

extract_protocol:
Total RNA was isolated from six-week-old cortical neurons and postmortem cortex tissues using TRIzol reagent and Phase Lock Gel Heavy
Purified mRNA samples were fragmented to 100-200 nucleotides.  10% fragmented RNA was set aside as an input sample, while the remaining RNA was used for m6A immunoprecipitation. The fragmented RNA was incubated with anti-m6A antibody and then with protein G magnetic beads. The m6A-enriched RNA was purified using TRIzol. The library was prepared following the instructions for Kapa RNA hyper prep kit. Both the input samples without IP and the m6A IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.

treatment_protocol: iPSCs were differentiated into cortical neurons and cultured for 6 weeks

value: iPS

value: iPS-derived cortical neuron

tag: genotype

value: FMR1 CGG repeats is over 200

tag: disease state

value: fragile X syndrome


title: Clam UF13D-0407

type: genomic

city: Stony Brook

first: Denis

last: Grouzdev

address: 100 Nicolls Rd

institute: Stony Brook University

description: UF Phase I

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Genotyping was performed at Neogen (Lincoln, Nebraska) on the Axiom 384HT arrays (Axiom HD Array [60K] Clam) following protocols outlined in the Axiom Assay 384HT Array Format Automated Workflow User Guide.

data_processing:
The raw genotyping data in CEL format was downloaded from the CAT website after the service and genotype annotation was analyzed using the Axiom software (v 5.4, Thermo Fisher) following the Best Practices Workflow with recommended threshold settings (DishQC ≥ 0.82, QC call rate ≥ 97%).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

organism: Mercenaria mercenaria

source_name: Clam UF13D-0407

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Adults M. mercenaria (12-14 months old) were collected from three farms in Cedar Key, Florida with one whole bag from each farm (1000-1200 clams). The clam seeds of each farm were originally sourced from different hatcheries. After purchase, the quahogs from each bag were cleaned at the farms using fresh water to remove sediment before being transported to the laboratory in a cooler (1 hr driving). After arriving at the laboratory, all quahogs were maintained in an indoor recirculating artificial seawater system equipped with a bead filter (Endurance 4000, Aquaculture Systems Technologies, Baton Rouge, LA) at 24 ± 0.55°C, 25 ppt salinity, and pH = 8.35. Quahogs were fed daily with a combination of microalgae, including Tetraselmis spp., Isochrysis spp., and Chaetoceros spp., at 50,000 cells/ml supplemented with commercial algal paste (Instant algae, Reed Mariculture, San Jose, CA, USA). System water quality was checked daily using a saltwater combination kit (AQ-4, Lamotte, Maryland, USA) for ammonia (< 0.01 mg/L), nitrite (< 0.01 mg/L), and nitrate levels (< 10 mg/L).

extract_protocol: The quahogs that died earliest (n = 330) were categorized as “dead” under the dichotomous phenotype, and the quahogs that died latest (n = 144) and survivors (n =231) were considered as “survived”. Genotyping of samples was performed on the previously described SNP microarray chip (Grouzdev et al., 2024). Fixed samples were shipped to the Center for Aquaculture Technologies (CAT, https://aquatechcenter.com, San Diego, CA) for this service. The total genomic DNA was extracted from sample sources (adductor muscle or hemocytes) using a magnetic bead-based extraction protocol. Briefly, fixed tissues (~10-15 mg) were subsampled and processed using mag-bind blood and tissue DNA kits (Omega BioTek, Norcross, GA) according to the manufacturer’s guidelines. Automated processing and liquid handling steps associated with the extraction protocol were performed using PurePrep 96 units (Molgen, San Diego, CA) according to kit and instrument-specific guidelines. Extracted gDNAs were assessed for yields and quality by spectrophotometry (Nanodrop, ThermoFisher) and 2% agarose gels targeting a minimum of 35 µl at >20 ng/µl of largely intact DNA (minimum 5KB).

treatment_protocol: The heat shock challenge was applied by increasing water temperature at 1°C per day from 24°C to a final temperature of 35°C using a heat pump with a temperature controller (Model No. DC24S, Aqualogic, San Diego, CA, USA). When the total dead quahog numbers reached about 50% of the total initial clam number, the temperature decreased from 35°C to 27°C within 24 hr and gradually to 24°C within another 24 hr. For easy reading, the heat challenge was separated into three phases (Figure 1): Phase I (13 days) – temperature increased from 24°C to 35°C and stayed at 35°C; Phase II (9 days) – temperature decreased from 35°C to 24°C with more clams died, and Phase III – temperature was maintained at 24°C and no quahog mortality was found in two days. Two HOBO pendant temperature loggers (UA-001–64, Onset, MA, USA) were submerged in the tank to record the temperature changes. No feeding was conducted after the temperature reached 28°C, and water quality was monitored twice a day.

value: Adductor muscle


title: FXS_1, MeRIP


title: UHC_7, Input

value: FMR1 CGG repeats is 30

value: healthy


title: Clam UF138S-0662

description: UF Phase III

value: Hemocytes in ethanol


title: LLC-mouse-model, UV-TMPs, rep  3

description:
Library name: Sample 6
10X Genomics

value: subcutaneous tumor

value: C57BL/6 mice

value: UV-TMPs, Positive


title: LLC-mouse-model, UV-TMPs, rep  2

description:
Library name: Sample 5
10X Genomics

value: LLC

value: female

value: 6-8 weeks


title: HC, Day 14, smallRNA-Seq, Replicate 3

description: small RNA sequencing

value: Day 14


title: Clam UF136S-0640

description: UF Phase II


title: LLC-mouse-model, UV-TMPs, rep  1

description:
Library name: Sample 4
10X Genomics


title: UHC_6, Input


title: UHC_7, MeRIP


title: HC, Day 14, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Hematopoietic cells


title: HC, Day 14, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: UHC_6, MeRIP


title: LLC-mouse-model, PBS, rep  3

description:
Library name: Sample 3
10X Genomics

value: PBS, Negative control


title: Clam UF142D-0365

description: UF Phase I


title: HC, Day 14, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: Clam UF133S-0661

description: UF Phase III


title: HC, Day 7, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Day 7


title: LLC-mouse-model, PBS, rep  2

description:
Library name: Sample 2
10X Genomics


title: UHC_5, Input

value: iPS

value: iPS-derived cortical neuron


title: LLC-mouse-model, PBS, rep  1

description:
Library name: Sample 1
10X Genomics


title: Clam UF131D-0455

description: UF Phase I


title: HC, Day 7, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: UHC_5, MeRIP


title: HC, Day 7, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: MT_4

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description:
Library name: MT_4
Smo MUT replicate 4

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm38/mm10 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for all 8 samples

source_name: embryos

extract_protocol:
Pregnant dams were harvested, embryos were dissected, and each embryo was placed in a 1.5-mL Eppendorf tube and flash frozen in liquid nitrogen, then stored at -80°C while genotyping was performed
RNA sequencing libraries for each sample were prepared with 1 mg total RNA by using the TruSeq RNA Sample Prep v2 Kit (Illumina) per the manufacturer’s instructions, and sequencing was completed on the Illumina NovaSeq 6000.

value: embryos

value: Smo MUT


title: UHC_4, Input

value: FMR1 CGG repeats is 30


title: Clam UF137D-0429

description: UF Phase I

value: Adductor muscle


title: Clam UF127D-0401

description: UF Phase I


title: MT_3

description:
Library name: MT_3
Smo MUT replicate 3


title: Clam UF125P-0484

description: UF Phase I


title: HC, Day 7, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: Clam UF123D-0386

description: UF Phase I


title: UHC_3, Input

value: healthy


title: MT_1

description:
Library name: MT_1
Smo MUT replicate 1


title: MT_2

description:
Library name: MT_2
Smo MUT replicate 2


title: WT_4

description:
Library name: WT_4
Smo WT replicate 4

value: Smo WT


title: HC, Day 3, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Day 3


title: HC, Day 3, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: Clam UF11D-0439

description: UF Phase I

source_name: Clam UF11D-0439


title: Clam UF132P-0597

description: UF Phase II


title: UHC_3, MeRIP


title: UHC_2, Input


title: HC, Day 3, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: HC, Day 3, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: WT_3

description:
Library name: WT_3
Smo WT replicate 3


title: Clam UF118P-0483

description: UF Phase I


title: UHC_2, MeRIP


title: WT_2

description:
Library name: WT_2
Smo WT replicate 2


title: UHC_1, Input


title: Clam UF117S-0353

description: UF Phase I


title: UHC_1, MeRIP


title: HC, Day 1, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Day 1


title: HC, Day 1, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: WT_1

description:
Library name: WT_1
Smo WT replicate 1


title: Clam UF116D-0461

description: UF Phase I


title: UHC_4, MeRIP


title: Brain, IFNgR KO, Day 14 post-craniotomy infection

city: White/Caucasian

first: Tammy

last: Kielian

state: NE

address: 985900 Nebraska Medical Center

institute: UNMC

description:
Library name: KO_Brain
KO_Brain
IFNgR_scRNA-seq.h5

data_processing:
Sequencing data was aligned to the mouse genome using 10X Genomics Cell Ranger before importing into Partek Flow Genomics Suite (RRID: SCR_011860) for the remainder of the analysis.
A standard quality control pipeline was implemented to safeguard against contamination by low-quality cells/reads.
Resulting single-cell count matrices were normalized within Partek Flow using counts per million, add 1, and log base 2 transformed. Samples were then integrated for all downstream analyses.
Assembly: mm10
Supplementary files format and content: Hierarchical Data Format .h5 files containing count matricies for each sample

molecule: polyA RNA

source_name: Brain

extract_protocol:
Mice were euthanized at the indicated intervals using an overdose of inhaled isoflurane prior to tissue collection. The vasculature was perfused with sterile 1X PBS, whereupon the brain was collected and placed in 1X PBS supplemented with 10% FBS on ice. For brain samples, the ipsilateral hemisphere of the brain was removed and disrupted by passing through a 70 µm cell strainer and rinsed with 1X PBS. Tissues were disrupted with collagenase IV (Cat. #C9891, Sigma-Aldrich) and DNase I (Cat. #AAJ62229MC, Fisher Scientific) for 15 min at 37°C followed by the addition of FBS to inactivate enzymatic digestion, whereupon the cell suspension was subjected to Percoll density gradient centrifugation (25% Percoll (GE Heatlhcare) with 3% FBS) at 520 x g for 20 min with no brake. The upper myelin layer down to the pellet was discarded, and the pellet was resuspended in 1X PBS to obtain a single cell suspension. For galea samples, galea was dissected from infected mice and placed into sterile 1X PBS supplemented with 10% FBS on ice. This tissue was then homogenized using the blunt end of a syringe and passed through a 70 µm cell strainer and rinsed with 1X PBS to obtain a single cell suspension. Target CD45+ cell populations were enriched via FACS before submission to a core facility at UNMC for scRNA-seq.
Illumina-compatible cDNA libraries were quantified with a Qubit-30 Fluorometer and assessed using a fragment analyzer before loading on a Novaseq6000 instrument at a final concentration of 300pM for generation of 75 bp pair-end reads.

value: Brain

value: CD45+ Immune Cells

value: IFNgR KO

tag: treatment/time point

value: Day 14 post-craniotomy infection


title: Clam UF121S-0660

description: UF Phase III

value: Hemocytes in ethanol


title: FXS_7, FXS

data_processing:
Raw reads in fastq format were trimmed to remove the adaptor sequence and the reads with adaptor contaminants and low-quality reads using Trim Galore (v 0.6.6)
Preprocessed reads were then aligned to the human genome (build GRCh38) using STAR (v2.7.9) with the default settings
Gene counts were obtained using FeatureCounts (v2.0.3)
Differential expression gene (DEGs) analysis was conducted using the R statistical package DESeq2 with an P of 0.05 and a fold change threshold of log2 (fold change) > ±1
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

growth_protocol: iPSCs were expanded onto fresh vitronectin-coated plate with Essential 8 medium, passaged with ReleSRTM every 3–4 days

extract_protocol:
Total cellular RNA was isolated using  TRIzol reagent and Phase Lock Gel Heavy
Libraries were generated from 1 μg of total RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB), as per the manufacturer’s protocol.

value: FMR1 CGG repeats is over 200

value: fragile X syndrome


title: Clam UF115S-0659

description: UF Phase III


title: Brain, Wildtype, Day 14 post-craniotomy infection

description:
Library name: WT_Brain
WT_Brain
IFNgR_scRNA-seq.h5

value: WT


title: HC, Day 1, smallRNA-Seq, Replicate 2

description: small RNA sequencing

value: Hematopoietic cells


title: FXS_6, FXS

value: iPS

value: iPS-derived cortical neuron


title: HC, Day 1, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: Clam UF114D-0441

description: UF Phase I


title: Galea, IFNgR KO, Day 14 post-craniotomy infection

description:
Library name: KO_Galea
KO_Galea
IFNgR_scRNA-seq.h5

source_name: Galea

value: Galea


title: HC, Day 0, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Day 0


title: FXS_5, FXS


title: Clam UF113D-0471

description: UF Phase I

value: Adductor muscle


title: HC, Day 0, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: Galea, Wildtype, Day 14 post-craniotomy infection

description:
Library name: WT_Galea
WT_Galea
IFNgR_scRNA-seq.h5


title: Clam UF111D-0460

description: UF Phase I


title: FXS_3, FXS


title: Clam UF112D-0477

description: UF Phase I


title: HC, Day 0, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: paneth cells, PBS+TNF, replicate 4

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
checking read quality with fastqc v0.12
data were mapped with the STAR (2.7.10a) to the mouse reference genome/transcriptome (mm39/gencode v28) using default paremeters, --quantMode GeneCounts to obtain read counts per sample immediatly from STAR
per sample read couns were merged into a count matrix and further processed in R using the DESeq2 libary
Assembly: mm39
Supplementary files format and content: tab delimited text file with count matrix of raw counts

source_name: small intestine

extract_protocol:
RNA was obtained with the Aurum Total RNA Mini kit (Bio-Rad) according to the manufacturer’s protocol
RNA-seq libraries were prepared using the illumina TruSeq Stranded mRNA kit using the manufacturers instructions

treatment_protocol: mice were injected first with PBS or DEX, one hour afterwared they were injected again with either PBS or TNF. mice were sample 3 hours after the second injection

value: small intestine

value: purified paneth cells

value: 1h PBS + 3h TNF


title: paneth cells, PBS+TNF, replicate 2


title: Clam UF110D-0451

description: UF Phase I


title: paneth cells, PBS+TNF, replicate 3


title: Clam UF109S-0612

description: UF Phase II


title: FB, Day 28, smallRNA-Seq, Replicate 4

description: small RNA sequencing

source_name: Fibroblasts

value: Fibroblasts

value: Day 28


title: paneth cells, PBS+TNF, replicate 1


title: HC, Day 0, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: Clam UF108D-0352

description: UF Phase I


title: Clam UF107D-0428

description: UF Phase I


title: UHC_6, Control

value: FMR1 CGG repeats is 30

value: healthy


title: FB, Day 28, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: paneth cells, PBS+PBS, replicate 4

value: 1h PBS + 3h PBS


title: UHC_5, Control


title: paneth cells, PBS+PBS, replicate 3


title: FB, Day 28, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: FB, Day 28, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: FXS_2, FXS

value: FMR1 CGG repeats is over 200


title: Clam UF106D-0438

description: UF Phase I


title: paneth cells, PBS+PBS, replicate 2


title: Clam UF105D-0392

description: UF Phase I


title: FXS_1, FXS

value: fragile X syndrome


title: UHC_3, Control


title: paneth cells, PBS+PBS, replicate 1


title: Clam UF102P-0492

description: UF Phase I


title: UHC_2, Control


title: paneth cells, DEX+TNFS, replicate 4

value: 1h DEX + 3h TNF


title: FB, Day 14, smallRNA-Seq, Replicate 3

description: small RNA sequencing

value: Day 14


title: UHC_7, Control

value: iPS


title: paneth cells, DEX+TNFS, replicate 3


title: UHC_1, Control

value: iPS-derived cortical neuron


title: FB, Day 14, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: Clam UF101S-0658

description: UF Phase III

value: Hemocytes in ethanol


title: HeLa-S3, 300min, G1, Nucleus

city: Cologne

first: Achim

last: Tresch

state: North Rhine-Westphalia

address: Paul-Schallueck-Str. 10

department: Institute of Medical Statistics and Computational Biology

institute: University of Cologne

data_processing:
Reads were mapped with NextGenMap ( Sedlazeck et al. (2013), version 0.5.5), settings: -5 12 -b --slam-seq2 –max-polya 4 --strata -l. Reads were filtered out if their mapping quality value is lower than 2 and their sequence identity is lower than 95%. Reads that passed these quality filters were assigned to known 3’UTRs (overlapping 3’UTRs on the same strand were merged to prevent double counting). We excluded known SNPs reported in the GRCh38 NCBI dbSNP database.  Additionally, potential SNPs and RNA editing sites were called by calculating position-wise mismatch rates for each covered genomic position in control (i.e., no 4sU labeling) samples. If the mismatch rate was higher than 5%, the genomic position was masked. Subsequently, the T>C conversions were quantified from each sequencing read.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file including counts for each 3UTR
Library strategy: SLAM-seq

growth_protocol: HeLa-S3 cells were cultured at 37°C in DMEM supplemented with 10\% FBS Superior (Sigma, S0615) and 1X penicillin-streptomycin (Gibco, 15070063).

extract_protocol:
At each time point, 3 million cells were fractionated to obtain nuclear and cytosolic fractions based on Mayer et al. (2015) with the following modifications: Nuclear pellets were washed with nuclear wash buffer (PBS with 1X cOmplete Protease Inhibitor (Roche, 11873580001)) and resuspended in 1400 µl TRIzol (Invitrogen, 15596026). Similarly, a time series in the G1 cell cycle phase (12 hours release time after double thymidine blocking) was measured at 0, 15, 45, 75, 145, 180, 240 and 300 minutes. Prior to phenol extraction of RNA, 1.9 µl of 1:100 diluted ERCC ExFold RNA Spike-In Mixes (Invitrogen, 4456739) per 1 million cells was added to each sample.
The 4sU RNA was alkylated according to Herzog et al. (2017), and poly-A enriched SLAM-seq libraries were generated using the 3'-QuantSeq-REV protocol (Lexogen).

treatment_protocol: A double thymidine block was used for cell cycle synchronisation at the G1/S boundary. Briefly, Hela-S3 cells were blocked with 2.5 mM thymidine for 18 hours. The cells were released from the block by two washes with pre-warmed medium, followed by incubation for 9 hours in fresh medium supplemented with 24 µM 2-deoxycytidine. The second G1/S block was again performed by adding 2.5 mM thymidine for 18 hours. Finally, cells were released by two washes with pre-warmed media and incubated for 6 hours (late G2) in DMEM containing 24 µM 2-deoxycytidine before labelling with 500 µM 4sU (Glentham Life Sciences, GN6085) for 0, 15, 45, 75, 120 and 180 minutes.


title: Clam UF100D-0427

description: UF Phase I


title: UHC_4, Control


title: HeLa-S3, 240min, G1, Nucleus


title: paneth cells, DEX+TNFS, replicate 1


title: FB, Day 7, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Day 7


title: HeLa-S3, 180min, G1, Nucleus


title: paneth cells, DEX+PBS, replicate 4

value: 1h DEX + 3h PBS


title: FB, Day 14, smallRNA-Seq, Replicate 4

description: small RNA sequencing


title: HeLa-S3, 145min, G1, Nucleus


title: FB, Day 7, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: paneth cells, DEX+PBS, replicate 2

value: small intestine


title: HeLa-S3, 75min, G1, Nucleus


title: Clam SC94D-0768

description: SC Phase I

source_name: Clam SC94D-0768

value: Adductor muscle


title: paneth cells, DEX+PBS, replicate 3

value: purified paneth cells


title: FB, Day 3, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Fibroblasts

value: Day 3


title: FB, Day 14, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: HeLa-S3, 45min, G1, Nucleus


title: FB, Day 7, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: Clam SC93D-0767

description: SC Phase I

source_name: Clam SC93D-0767


title: HeLa-S3, 15min, G1, Nucleus


title: Clam SC9D-0794

description: SC Phase I

source_name: Clam SC9D-0794


title: paneth cells, DEX+TNFS, replicate 2


title: paneth cells, DEX+PBS, replicate 1


title: HeLa-S3, 0min, G1, Nucleus


title: Clam SC92D-0732

description: SC Phase I

source_name: Clam SC92D-0732


title: paneth cell, WT control, replicate 4

data_processing:
Reads were subjected to QC with fastqc (v0.12.0)
reads were mapped to the mm39 reference genome using the STAR (v2.7.0a) aligner with the --quantMode GeneCounts option to immediatly obtain counts per genes for each sample
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Assembly: mm39
Supplementary files format and content: A tab delimited text file with raw counts for each sample

extract_protocol:
The small intestine was isolated and a single cell suspension was prepared from the material. Cells were sorted using FACS and paneth cells were collected for RNA isolation. RNA was isolated using an aurum total RNA mini kit accorting to the manufacturers instructions
library preparation was done with the illumina truseq stranded mRNA library kit according to the manufacturers instructions

value: WT


title: FB, Day 3, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: FB, Day 3, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: Clam SC89D-0729

description: SC Phase I

source_name: Clam SC89D-0729


title: Clam SC99D-0718

description: SC Phase I

source_name: Clam SC99D-0718


title: paneth cell, WT control, replicate 3


title: Clam SC88P-0928

description: SC Phase II

source_name: Clam SC88P-0928


title: FB, Day 7, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: FB, Day 3, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: Clam SC98D-0753

description: SC Phase I

source_name: Clam SC98D-0753


title: Clam SC85D-0762

description: SC Phase I

source_name: Clam SC85D-0762


title: HeLa-S3, 120min, Mitosis, Nucleus


title: FB, Day 1, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Day 1


title: paneth cell, WT control, replicate 1


title: FB, Day 1, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: HeLa-S3, 75min, Mitosis, Nucleus


title: Clam SC82P-0921

description: SC Phase II

source_name: Clam SC82P-0921


title: Clam SC78S-0981

description: SC Phase III

source_name: Clam SC78S-0981


title: paneth cell, diphtheria toxin, replicate 4

value: DT TG


title: FB, Day 1, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: paneth cell, diphtheria toxin, replicate 3


title: FB, Day 1, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: Clam SC75S-0980

description: SC Phase III

source_name: Clam SC75S-0980


title: HeLa-S3, 180min, Mitosis, Nucleus


title: FB, Day 0, smallRNA-Seq, Replicate 3

description: small RNA sequencing

value: Day 0


title: HeLa-S3, 15min, Mitosis, Nucleus


title: HeLa-S3, 300min, G1, Cytosol


title: paneth cell, diphtheria toxin, replicate 2


title: FB, Day 0, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: Clam SC73S-0979

description: SC Phase III

source_name: Clam SC73S-0979


title: HeLa-S3, 0min, Mitosis, Nucleus


title: paneth cell, diphtheria toxin, replicate 1


title: Clam SC6D-0738

description: SC Phase I

source_name: Clam SC6D-0738


title: paneth cells, zinc supplemented water, replicate 4

data_processing:
Reads were subjected to QC with fastqc (v0.12.0)
reads were mapped to the mm39 reference genome using the STAR (v2.7.10a) aligner with the --quantMode GeneCounts option to immediatly obtain counts per genes for each sample
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Assembly: mm39
Supplementary files format and content: A tab delimited text file with raw counts for each sample

treatment_protocol: Mice wre put on Milli-Q or zinc supplemented (25mM ZnSO4) water for 7 days. Afterwars, mice were injected with TNF and samples were taken after 3 hours.

tag: treatment 1

value: TNF, 3h

tag: treatment 2

value: 25 mM ZnSO4


title: paneth cell, WT control, replicate 2


title: HeLa-S3, 240min, G1, Cytosol


title: HeLa-S3, 180min, G1, Cytosol


title: HeLa-S3, 45min, Mitosis, Nucleus


title: Clam SC67P-0920

description: SC Phase II

source_name: Clam SC67P-0920


title: FB, Day 0, smallRNA-Seq, Replicate 4

description: small RNA sequencing


title: FB, Day 0, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: paneth cells, zinc supplemented water, replicate 3

source_name: small intestine


title: Clam SC65D-0723

description: SC Phase I

source_name: Clam SC65D-0723


title: paneth cells, zinc supplemented water, replicate 2


title: HeLa-S3, 75min, G1, Cytosol


title: EC, Day 28, smallRNA-Seq, Replicate 4

description: small RNA sequencing

source_name: Endothelial cells

value: Endothelial cells

value: Day 28


title: paneth cells, zinc supplemented water, replicate 1


title: HeLa-S3, 145min, G1, Cytosol


title: Clam SC64D-0795

description: SC Phase I

source_name: Clam SC64D-0795


title: EC, Day 28, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: paneth cells, Milli-Q water, replicate 4

value: Milli-Q water


title: Clam SC69P-0945

description: SC Phase II

source_name: Clam SC69P-0945


title: EC, Day 28, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: HeLa-S3, 45min, G1, Cytosol


title: Clam SC59P-0951

description: SC Phase II

source_name: Clam SC59P-0951


title: HeLa-S3, 15min, G1, Cytosol


title: Clam SC58D-0717

description: SC Phase I

source_name: Clam SC58D-0717


title: paneth cells, Milli-Q water, replicate 3


title: EC, Day 14, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Day 14


title: EC, Day 28, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: HeLa-S3, 0min, G1, Cytosol


title: Clam SC56D-0707

description: SC Phase I

source_name: Clam SC56D-0707


title: paneth cells, Milli-Q water, replicate 1


title: Clam SC52D-0781

description: SC Phase I

source_name: Clam SC52D-0781


title: EC, Day 14, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: HeLa-S3, 120min, Mitosis, Cytosol


title: paneth cells, TNF replicate 3

data_processing:
checking read quality with fastqc v0.12
data were mapped with the STAR (2.7.10a) to the mouse reference genome/transcriptome (mm39/gencode v28) using default paremeters, --quantMode GeneCounts to obtain read counts per sample immediatly from STAR
per sample read couns were merged into a count matrix and further processed in R using the DESeq2 libary
Assembly: mm39
Supplementary files format and content: tab delimited tekst file with count matrix of raw counts

treatment_protocol: mice were injected with PBS or TNF. The small intestine was isolaed after 3 hours and PC were purified using a cell sorter for RNA isolation

tag: time

value: 3 hours

value: TNF


title: paneth cells, TNF replicate 4

value: small intestine


title: HeLa-S3, 180min, Mitosis, Cytosol


title: HeLa-S3, 75min, Mitosis, Cytosol


title: EC, Day 14, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: EC, Day 14, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: EC, Day 7, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Day 7


title: Clam SC51D-0731

description: SC Phase I

source_name: Clam SC51D-0731

value: Adductor muscle


title: Clam SC50D-0716

description: SC Phase I

source_name: Clam SC50D-0716


title: paneth cells, TNF replicate 1

value: purified paneth cells


title: paneth cells, TNF replicate 2


title: Clam SC4D-0811

description: SC Phase I

source_name: Clam SC4D-0811


title: Clam SC55D-0742

description: SC Phase I

source_name: Clam SC55D-0742


title: Clam SC49S-0973

description: SC Phase III

source_name: Clam SC49S-0973

value: Hemocytes in ethanol


title: HeLa-S3, 0min, Mitosis, Cytosol


title: paneth cells, PBS, replicate 4

value: WT

value: PBS


title: EC, Day 7, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: EC, Day 7, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: paneth cells, Milli-Q water, replicate 2


title: paneth cells, PBS, replicate 3


title: Clam SC47S-0972

description: SC Phase III

source_name: Clam SC47S-0972


title: Clam SC45D-0765

description: SC Phase I

source_name: Clam SC45D-0765


title: B6_MZT-4B

city: Shenyang

first: Meihui

last: Tian

address: No.77, Puhe Road

department: School of Forensic Medicine

institute: China Medical University

data_processing:
Small RNA sequences were annotated using the software SPORTS1.1 with one mismatch tolerance (SPORTS1.1 parameter setting: -M1).
Reads were mapped to the genomic tRNA database GtRNAdb and Transfer RNA related Fragments database tRFdb.
The tsRNAs were annotated based on both pre-tRNA and mature tRNA sequences.Mature tRNA sequences were derived from the GtRNAdb sequences using the following procedures: (1) predicted introns were removed; (2) a CCA sequence was added to the 3′ ends of all tRNAs; and (3) a G nucleotide was added to the 5′ end of histidine tRNAs.
tRFs from tRFdb sequences annotated by the mapping results with three specific regions: extreme 5’ end (tRF-5), extreme 3’ end (tRF-3) of mature tRNA and 3’ trailer region (tRF-1) of primary tRNA genes.
Differentially expressed tsRNAs analysis was performed using the R package DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes output for each sample
Supplementary files format and content: tab-delimited text file includes summary for each sample

source_name: monozygotic twin

extract_protocol:
Total RNA was extracted using TRIzol Reagent (1 ml; Invitrogen; 15596018). Small RNAs of 15–50 nucleotides was selected.
The adapters of RNA-seq libraries were obtained from the QIAseq® miRNA Library Kit (QIAGEN: 331505).

value: Human peripheral blood


title: EC, Day 3, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Day 3


title: paneth cells, PBS, replicate 2

source_name: small intestine


title: Clam SC43D-0780

description: SC Phase I

source_name: Clam SC43D-0780


title: A6_MZT-4A


title: B5_MZT-3B


title: HeLa-S3, 45min, Mitosis, Cytosol


title: EC, Day 3, smallRNA-Seq, Replicate 3

description: small RNA sequencing

source_name: Endothelial cells


title: EC, Day 3, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: paneth cell, SPF Zn, replicaat 2

data_processing:
quality control was done with fastqc (v0.12.0)
reads weremapped to the mm39 reference genome using the STAR (v2.7.0a) aligner with the --quantMode GeneCounts option to immediatly obtain counts per genes for each sample
The DESeq2 package was used to process the counts and determine differential gene expression
Assembly: mm39
Supplementary files format and content: A tab delimited text file with raw counts for each sample

extract_protocol:
Cells were sorted using a FACS and paneth cells were collected for RNA isolation. RNA was isolated using an aurum total RNA mini kit accorting to the manufacturers instructions
library preparation was done with the illumina truseq stranded mRNA library kit according to the manufacturers instructions

treatment_protocol: mice were put on Milli-Q or zinc supplemented water for 7 weeks (200 mM ZnSO4). Antibiotics treated mice were give 3 weeks of broad spectrum antibiotics in the last 3 weeks of the ZnSO4 or Milli-Q treatement

value: 200 mM ZnSO4 water

tag: microbiome context

value: SPF


title: paneth cell, SPF Zn, replicaat 3


title: EC, Day 3, smallRNA-Seq, Replicate 1

description: small RNA sequencing

value: Endothelial cells


title: Clam SC399D-0779

description: SC Phase I


title: Clam SC3D-0810

description: SC Phase I

source_name: Clam SC3D-0810


title: A5_MZT-3A


title: Clam SC394S-1045

description: SC Phase III


title: paneth cell, SPF Zn, replicaat 1


title: B4_MZT-2B


title: EC, Day 7, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: paneth cell, SPF MQ, replicaat 3


title: B3_MZT-1B


title: paneth cells, PBS, replicate 1


title: EC, Day 1, smallRNA-Seq, Replicate 3

description: small RNA sequencing

value: Day 1


title: EC, Day 1, smallRNA-Seq, Replicate 4

description: small RNA sequencing


title: Clam SC392D-0705

description: SC Phase I


title: paneth cell, SPF MQ, replicaat 2

value: Milli-Q water


title: paneth cell, SPF MQ, replicaat 1


title: EC, Day 1, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: Clam SC391D-0821

description: SC Phase I


title: A3_MZT-1A


title: SW1353 cells, miR-455 inhibitor , 48 hours (2)

city: Norwich

first: Ian

last: Clark

state: Norfolk

address: Earlham Road

country: United Kingdom

institute: University of East Anglia

data_processing:
FASTQC followed by TrimGalore to trim adapter sequences and low quality reads
Transcripts obtained from Ensembl and Kallisto to map reads to all transcripts
Sleuth used to identify differential expression
Assembly: hg38
Supplementary files format and content: Excel files of normalised counts for each sample

extract_protocol:
Total RNA was purified using Trizol
Libraries constructed and sequenced by Novogene

value: chondrosarcoma

value: miR-455 inhibitor


title: SW1353 cells, miR-455 inhibitor , 48 hours (3)


title: Clam SC38P-0919

description: SC Phase II

source_name: Clam SC38P-0919


title: EC, Day 1, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: paneth cell, Germ-free Zn, replicaat 4

value: germ-free


title: Clam SC386D-0737

description: SC Phase I


title: Clam SC393D-0750

description: SC Phase I


title: SW1353 cells, miR-455 inhibitor , 48 hours (1)


title: paneth cell, Germ-free Zn, replicaat 3

value: small intestine


title: A4_MZT-2A


title: paneth cell, Germ-free Zn, replicaat 2


title: Clam SC37S-0971

description: SC Phase III

source_name: Clam SC37S-0971


title: SW1353 cells, miR-455 inhibitor control , 48 hours (3)

value: miR-455 inhibitor control


title: EC, Day 0, smallRNA-Seq, Replicate 2

description: small RNA sequencing

value: Day 0


title: EC, Day 0, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: Clam SC371D-0759

description: SC Phase I

value: Adductor muscle


title: SW1353 cells, miR-455 inhibitor control , 48 hours (2)


title: paneth cell, Germ-free MQ, replicaat 3

value: purified paneth cells


title: CM, Day 28, smallRNA-Seq, Replicate 4

description: small RNA sequencing

source_name: Cardiomyocytes

value: Cardiomyocytes

value: Day 28


title: SW1353 cells, miR-455 inhibitor control , 48 hours (1)


title: CM, Day 28, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: Clam SC36D-0752

description: SC Phase I

source_name: Clam SC36D-0752


title: Clam SC368D-0808

description: SC Phase I


title: CM, Day 28, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: SW1353 cells, miR-455 mimic , 48 hours (2)

value: miR-455 mimic


title: SW1353 cells, miR-455 mimic , 48 hours (3)


title: paneth cell, Germ-free MQ, replicaat 2


title: EC, Day 0, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: paneth cell, Germ-free MQ, replicaat 1


title: Clam SC363D-0726

description: SC Phase I


title: Clam SC35S-0970

description: SC Phase III

source_name: Clam SC35S-0970

value: Hemocytes in ethanol


title: HeLa-S3, 15min, Mitosis, Cytosol


title: paneth cell, SPF Zn + antibiotica, replicaat 4

value: 200 mM ZnSO4 water

value: antibiotics


title: CM, Day 28, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: paneth cell, SPF Zn + antibiotica, replicaat 3


title: CM, Day 14, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Day 14


title: SW1353 cells, miR-455 mimic control, 48 hours (3)

value: miR-455 mimic control


title: paneth cell, SPF Zn + antibiotica, replicaat 2


title: Clam SC359D-0730

description: SC Phase I


title: CM, Day 14, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: paneth cell, Germ-free Zn, replicaat 1


title: SW1353 cells, miR-455 mimic control, 48 hours (2)


title: CM, Day 14, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: Clam SC352D-0727

description: SC Phase I


title: paneth cell, SPF MQ + antibiotica, replicaat 4

value: Milli-Q water


title: Clam SC34P-0950

description: SC Phase II

source_name: Clam SC34P-0950


title: SW1353 cells, miR-455 mimic control, 48 hours (1)

value: chondrosarcoma


title: CM, Day 14, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: Clam SC349D-0778

description: SC Phase I


title: Clam SC347D-0766

description: SC Phase I


title: CD3/CD28 treated 17q12DS patient 2

city: NEW HAVEN

first: HYEON JUN

last: SHIN

state: CT

address: 1 Gilbert St

institute: Yale University School of Medicine

data_processing:
Illumina NovaSeq Control Software v1.8 used for basecalling.
Low-quality reads were trimmed and adaptor contamination was removed using Trim Galore (v0.5.0). Trimmed reads were mapped to the human reference genome (hg38) using HISAT2 (v2.1.0)36.
Gene expression levels were quantified using StringTie (v1.3.3b)37 with gene models (v27) from the GENCODE project. Differentially expressed genes were identified using DESeq2 (v 1.22.1)38.
Assembly: mm10
Supplementary files format and content: tab-delimited tsv files include read count values for each Sample

source_name: CD4+ T cells

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 SENSE mRNA-Seq Library Prep Kit  (Cat#001.96) standard protocols.

tag: individual

value: 17q12DS patient 2

value: CD4+ T cells

value: CD3/CD28 treated


title: paneth cell, SPF MQ + antibiotica, replicaat 3

value: small intestine


title: paneth cell, SPF MQ + antibiotica, replicaat 2


title: CD3/CD28 treated 17q12DS patient 1

value: 17q12DS patient 1


title: SW1353 cells, miR-455 mimic , 48 hours (1)


title: Clam SC346P-0926

description: SC Phase II

value: Adductor muscle


title: paneth cell, SPF MQ + antibiotica, replicaat 1

value: purified paneth cells


title: CM, Day 7, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Cardiomyocytes

value: Day 7


title: CM, Day 7, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: Untreated 17q12DS patient 1

value: Untreated


title: CM, Day 7, smallRNA-Seq, Replicate 3

description: small RNA sequencing


title: Untreated 17q12DS patient 2


title: in vivo Ago2 KO brain cells, replicate 2

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

description: 10x Genomics

data_processing:
CellRanger v4.0.0 used for demultiplexing + read mapping + barcode assignment + UMI counting
Seurat v3.2.3 used for quality control + normalization + sample integration + dimensionality reduction + cell clustering
CellChat v1.6 used for cell-cell communication analysis
Assembly: GRCm38
Supplementary files format and content: Filtered feature-barcode count matrices from CellRanger

molecule: nuclear RNA

source_name: brain

growth_protocol: Mice were maintained on a 12-hour light/dark cycle with ad libitum access to regular chow food in accordance to requirements established by the Johns Hopkins University Animal Care and Use Committee (ACUC) and the Landesamt für Gesundheit und Soziales (LAGeSo).

extract_protocol:
Snap frozen hemispheres of mice at age P14 were minced on ice into 1 mm x 1 mm pieces, dounced in 2 ml ice cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2 U/ul recombinant RNase inhibitor (Takara)) and lysed on ice for 5 minutes. Lysis was stopped by adding 10 ml of ice-cold PBS-BSA (1% BSA, 0.2 U/ul RNase inhibitor), the suspension was filtered through a 40 mm cell strainer and centrifuged at 4°C, 500g for 5 minutes. Nuclei were washed two times with PBS-BSA, counted and assessed for quality.
Immediately before loading nuclei on the 10x Chromium, nuclei were washed and concentrated to remove potential ambient RNA. Post wash between 2000 and 5000 nuclei were loaded onto the 10X Chromium System for nuclei encapsulation as per the manufacturer’s instructions in Chromium Single Cell 3’ Reagents kit v3 user guide RevC. Libraries were prepared using Single Cell 3’ v3 chemistry. Briefly, RNA was reverse transcribed in the gel bead emulsion and cDNA amplified adding three additional PCR cycles to compensate for low RNA content of nuclei as compared to cells. Subsequently, libraries were fragmented and indexed. Final libraries were quantified and assessed for fragments size using the Agilent 4200 Tapestation System. Libraries were pooled and sequenced on a NovaSeq 6000 (Illumina).

treatment_protocol: no treatment

value: brain cells

value: brain

value: Slc17a6-Cre, Ago2 flox/flox


title: CM, Day 7, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: Clam SC340D-0793

description: SC Phase I


title: CD3/CD28 treated Healthy control 2

value: Healthy control 2


title: CM, Day 3, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Day 3


title: in vivo Ago2 KO brain cells, replicate 1

description: 10x Genomics


title: EC, Day 0, smallRNA-Seq, Replicate 4

description: small RNA sequencing

value: Endothelial cells

value: Day 0


title: paneth cell, SPF Zn + antibiotica, replicaat 1

value: 200 mM ZnSO4 water

value: antibiotics


title: CD3/CD28 treated Healthy control 1

value: Healthy control 1

value: CD4+ T cells

value: CD3/CD28 treated


title: Clam SC332S-1039

description: SC Phase III

value: Hemocytes in ethanol


title: in vivo Ago2 WT brain cells, replicate 2

description: 10x Genomics

value: Slc17a6-Cre, Ago2 wt/wt


title: Clam SC32S-0969

description: SC Phase III

source_name: Clam SC32S-0969


title: in vivo Ago2 WT brain cells, replicate 1

description: 10x Genomics


title: CM, Day 3, smallRNA-Seq, Replicate 3

description: small RNA sequencing

value: Cardiomyocytes


title: Clam SC31P-0929

description: SC Phase II

source_name: Clam SC31P-0929

value: Adductor muscle


title: Clam SC320S_1036

description: SC Phase III


title: Clam SC344S-1043

description: SC Phase III


title: GMC01, scRNAseq

city: Hengyang

first: Weizhi

last: Zhao

state: Hunan

address: 28 West Changsheng Road

institute: University of South China

description: singleron

data_processing:
Gene expression matrices were generated from raw reads using scopetools (https://anaconda.org/singleronbio/scopetools) by filtering out reads lacking polyT tails and extracting cell barcodes and unique molecular identifiers (UMI).  Subsequently, adapters and polyA tails were trimmed, and the reads were aligned onto the GRCh38 reference genome using Ensemble (v92) gene annotation.  The count of UMIs per gene per cell was calculated by grouping reads with the same cell barcode, UMI, and gene.
Normalization and analysis of differentially expressed genes (DEGs) were carried out using multifactor analysis (GMC vs. Control) in the R program package limma (v3.50.3).
From the obtained DEGs, upregulated and downregulated genes were separately analyzed for pathway enrichments as previously described. Gene Ontology (GO) term enrichments, covering biological process, cellular component, and molecular function, as well as Kyoto Encyclopedia of Genes and Genomes pathway enrichments, were constructed using Metascape (http://metascape.org)
The human version of the functional genomics tool PROGENy (v1.16.0), the human version of DoRothEA (v1.6.0) and the human version of MatrisomeDB were used to deduce the the characteristics of GMC samples.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Iliotibial band tissue

extract_protocol:
After collection, fresh fascial samples were stored at 4 °C in the GEXSCOPE Tissue Preservation Solution (Cat# 1200050001, Singleron Biotechnologies, Nanjing, China) and processed within 24 h. The samples underwent three washes with Hanks Balanced Salt Solution and were then minced into small pieces measuring 1–2 mm3. Subsequently, they were digested in GEXSCOPE Tissue Dissociation Mix Buffer Solution (Cat# 1200000044, Singleron Biotechnologies, Nanjing, China) inside a thermostatic oscillator at 37 °C and 180 rpm for 15 min. Tissue lysates were filtered through a 40 µm sterile strainer (Cat# 352340, Corning, New York, USA), and any remaining red blood cells were eliminated by incubating in Red Blood Cell Lysis Buffer (Cat# 00‑4333‑57, ThermoFisher, Waltham, USA) at 4 °C for 10 min. The viability of finial single‑cell suspensions was determined using Trypan Blue (Cat# T8154, Sigma, St. Louis, USA) and acridine orange/propidium iodide staining (Cat# CS2‑0106, Nexcelom, Lawrence, USA).
ScRNA‑seq libraries were constructed according to the manufacturer’s protocol (GEXSCOPE Single Cell RNA seq Kit, Singleron Biotechnologies, Nanjing, China). The resulting scRNA‑seq libraries were sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired‑end reads, aiming for a sequence depth of approximately 30,000 reads per cell.

value: Iliotibial band tissue


title: Untreated Healthy control 1

value: Untreated


title: CM, Day 1, smallRNA-Seq, Replicate 3

description: small RNA sequencing

data_processing:
small RNA-seq analysis pipeline from nf-core [https://nf-co.re/smrnaseq]
Small RNAs were trimmed/qualitycheck using Trimgalore and then quantified using the small RNA-seq analysis pipeline from nf-core [https://nf-co.re/smrnaseq], where the full length of the small RNA reads were used for the pipeline.
The processed file is the result of samtools idxstats run on the sorted bowtie2 alignment files, aligned wiith the reference mm10 and thereafter mapped to miRBase v21 miRNAs.
Assembly: mm10
Supplementary files format and content: tab delimited files include reference sequence name, sequence length, # mapped read-segments and # unmapped read-segments

value: Day 1


title: OVX2_IP

city: Fuzhou

first: 佳泳

last: 吴

address: 20 Cha Zhong Road

institute: The First Affiliated Hospital of Fujian Medical University

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for m6A-modification peak calling and the significant methylation was identified by exomepeak2 , and the m6A peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the m6A peaks contained the consensus of m6A motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of m6A regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
Assembly: rn6
Supplementary files format and content: The processed data files is in CSV format, containing the expression levels and m6A methylation status changes for each gene.

source_name: bone

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched
mRNA-seq and MeRIP-seq

value: bone

value: Wild type

value: ovariectomy


title: OVX4_IP


title: CM, Day 1, smallRNA-Seq, Replicate 4

description: small RNA sequencing


title: OVX3_IP


title: CM, Day 1, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: Clam SC30P-0935

description: SC Phase II

data_processing:
The raw genotyping data in CEL format was downloaded from the CAT website after the service and genotype annotation was analyzed using the Axiom software (v 5.4, Thermo Fisher) following the Best Practices Workflow with recommended threshold settings (DishQC ≥ 0.82, QC call rate ≥ 97%).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: Clam SC30P-0935


title: 6_C-267

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: blood

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan). According to the SMART-Seq kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: blood

value: Peripheral Blood Mononuclear Cell


title: Clam SC319P-0925

description: SC Phase II


title: CM, Day 3, smallRNA-Seq, Replicate 2

description: small RNA sequencing

extract_protocol:
Cardiomyocytes were enriched by performing repeated centrifugation steps (20 x g, 2 minutes). The supernatant of the centrifugation step was used to isolate hematopoietic cells, endothelial cells, and fibroblasts. Hematopoietic and endothelial cells were isolated by magnetic separation. Cells not bound to the magnetic beads or columns were used for cardiac fibroblast enrichment by a plating step with uncoated dishes. After 40 minutes, predominantly DDR2-positive fibroblasts adhered and were used for RNA isolation. Cells extracted from three mice were pooled to generate enough cells for one of four biological replicate sequencing samples for each timepoint.
Small RNAs were converted into Illumina compatible libraries using the NEB Next small RNA library Kit from New England Biolabs (NEB), which involves 3´-ligation and 5´-ligation to small RNAs and therefore enriches for 5´-monophosphorylated and 3 ́-hydroxylated small RNAs, such as miRNA. Due to the varying RNA amounts available for each cell type, we used the following parameters for input of total RNA and PCR cycles: CM-500ng-14cycles, EC-50ng-16cycles, HC-150ng-15cycles, FB-150ng-15-cycles. After library amplification, we cut each library from 10% TBE (Tris-Borate-EDTA) PAGE gels, extracting the library size of approx. 140-150bp which corresponds to 20-30nt miRNAs. Libraries were then quantified using the Qubit dsDNA HS Assay (Thermo Fisher).

value: Day 3


title: Untreated Healthy control 2

value: Healthy control 2


title: Clam SC311P-0942

description: SC Phase II


title: OVX1_IP


title: 3_19-178


title: 4_20-269


title: NC4_IP


title: 2_19-42


title: CM, Day 1, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: Clam SC309D-0776

description: SC Phase I


title: CM, Day 0, smallRNA-Seq, Replicate 3

description: small RNA sequencing

value: Day 0


title: NC2_IP


title: 1_19-14


title: Clam SC300D-0816

description: SC Phase I


title: CM, Day 3, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: 5_20-384


title: 5_20-377


title: NC3_IP


title: 4_20-316


title: CM, Day 0, smallRNA-Seq, Replicate 1

description: small RNA sequencing


title: CM, Day 0, smallRNA-Seq, Replicate 4

description: small RNA sequencing


title: Clam SC2S-0962

description: SC Phase III

source_name: Clam SC2S-0962


title: CM, Day 0, smallRNA-Seq, Replicate 2

description: small RNA sequencing


title: OVX3_Input


title: OVX4_Input


title: Clam SC297P-0943

description: SC Phase II


title: ATR fl/fl, iKO (4-OHT), rep5

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

data_processing:
Sequence information was extracted in FastQ format using Illumina’s bcl2fastq v.1.8.4
The reads were aligned to the mouse reference genome (GRCm38 with the Ensembl genome annotation release 91) using STAR 2.5.4b (parameters: --alignIntronMax 100000, --outSJfilterReads Unique, --outSAMmultNmax 1, --outFilterMismatchNoverLmax 0.04) (PMID: 23104886)
For each gene, all reads that map uniquely to one genomic position were counted with FeatureCounts 1.5.0 (multi-mapping or multi-overlapping reads were discarded, stranded mode was set to “–s 2”) (PMID: 24227677)
Assembly: GRCm38
Supplementary files format and content: comma separated values (csv) file containing raw read counts per gene per sample.

source_name: murine embryonic

extract_protocol:
Please refer to Zhou et al., DNA Repair (Amst), 11, 2012 (PMID: 22078264)
Library preparation was done using TruSeq stranded total RNA RiboZero Gold kit (Illumina) following the manufacturer’s description.

value: murine embryonic

value: primary MEF

value: fibroblast

value: mutant, ATR-iKO


title: Clam SC290S-1031

description: SC Phase III

extract_protocol: The quahogs that died earliest (n = 330) were categorized as “dead” under the dichotomous phenotype, and the quahogs that died latest (n = 144) and survivors (n =231) were considered as “survived”. Genotyping of samples was performed on the previously described SNP microarray chip (Grouzdev et al., 2024). Fixed samples were shipped to the Center for Aquaculture Technologies (CAT, https://aquatechcenter.com, San Diego, CA) for this service. The total genomic DNA was extracted from sample sources (adductor muscle or hemocytes) using a magnetic bead-based extraction protocol. Briefly, fixed tissues (~10-15 mg) were subsampled and processed using mag-bind blood and tissue DNA kits (Omega BioTek, Norcross, GA) according to the manufacturer’s guidelines. Automated processing and liquid handling steps associated with the extraction protocol were performed using PurePrep 96 units (Molgen, San Diego, CA) according to kit and instrument-specific guidelines. Extracted gDNAs were assessed for yields and quality by spectrophotometry (Nanodrop, ThermoFisher) and 2% agarose gels targeting a minimum of 35 µl at >20 ng/µl of largely intact DNA (minimum 5KB).

value: Hemocytes in ethanol


title: 2_19-139


title: Clam SC29S-0968

description: SC Phase III

source_name: Clam SC29S-0968


title: 3_19-177


title: OVX2_Input


title: OVX1_Input


title: Clam SC289D-0764

description: SC Phase I

value: Adductor muscle


title: Clam SC305D-0806

description: SC Phase I


title: ATR fl/fl, iKO (4-OHT), rep4

growth_protocol: Please refer to Zhou et al., DNA Repair (Amst), 11, 2012 (PMID: 22078264)


title: 1_18-42


title: NC4_Input

value: sham operation


title: ATR fl/fl, iKO (4-OHT), rep3

treatment_protocol: Please refer to Zhou et al., DNA Repair (Amst), 11, 2012 (PMID: 22078264)


title: NC1_IP


title: 5_20-385


title: NC3_Input


title: Clam SC288D-0823

description: SC Phase I


title: ATR fl/fl, iKO (4-OHT), rep1


title: ATR fl/fl, iKO (4-OHT), rep2


title: 4_19-13


title: Clam SC285P-0933

description: SC Phase II


title: Clam SC287D-0735

description: SC Phase I


title: NC2_Input


title: ATR fl/fl, untreated, rep4

value: wildtype, fl/fl

value: control


title: NC1_Input

value: bone


title: 2_16-35


title: ATR fl/fl, untreated, rep5


title: Clam SC284S-1029

description: SC Phase III


title: Clam SC282P-0941

description: SC Phase II


title: ATR fl/fl, untreated, rep3


title: ATR fl/fl, untreated, rep2


title: 1_15-86


title: 6_C-621


title: Clam SC280P-0948

description: SC Phase II


title: MiR-455 null, 3 month old 1

data_processing:
FASTQC followed by TrimGalore to trim adapter sequences and low quality reads
Transcripts obtained from Ensembl and Kallisto to map reads to all transcripts
Sleuth used to identify differential expression
Assembly: mm10
Supplementary files format and content: Excel files of normalised counts for each sample

source_name: Knee cartilage

extract_protocol:
Total RNA was purified using a combination of Trizol and miRVana
Libraries constructed and sequenced by Novogene

value: Knee cartilage

value: chondrocyte

value: miR-455 null


title: ATR fl/fl, untreated, rep1


title: Clam SC27P-0944

description: SC Phase II

source_name: Clam SC27P-0944


title: 5_C-350

value: blood

value: Peripheral Blood Mononuclear Cell


title: Wild-type, 3 month old 3

value: wild-type


title: 4_19-211


title: Clam SC278D-0733

description: SC Phase I


title: Wild-type, 3 month old 2


title: Clam SC275P-0932

description: SC Phase II


title: 3_16-47


title: Wild-type, 3 month old 1


title: Clam SC273D-0805

description: SC Phase I


title: 2_15-92


title: 1076FBSButyrate

city: Doha

first: Cristina

last: Maccalli

address: Doha

country: Qatar

institute: Sidra Medicine

description:
Library name: 1076FBSButyrate_0701466331
Lexogen 3'DGE

data_processing:
quality check of raw data was done using FastQC version 0.11.9.
Alignment was done using STAR (version 2.6.1) and reads were mapped to the hg38 genome.
FeatureCounts (v2.0.0) was used to estimate the expression counts of the genes.
Read count data were filtered for lowly expressed genes that would keep genes with a total read count of more than 50. Sample read counts were adjusted for library size and normalized using the Trimmed Mean of M-values (TMM) method using Bioconductor package EdgeR (v4.2.0).
Data were log2 transformed. Differential expression analyses were performed using the limma R package (v3.6.0) from the Bioconductor R project.
Assembly: hg38 genome
Supplementary files format and content: csv file containing normalized read count for all samples
Supplementary files format and content: csv file containing Log2 transformed data of differential expression in CIC and FBS treated vs untreated. File contatin also p value and statistics.

source_name: Cell line

growth_protocol: CICs were cultured as colon-spheres in Advanced DMEM/F12 medium  containing 20 ng/ml of EGF , 50 ng/ml FGF-2. Differenciated cells were cultured in the presence of RPMI 1640 supplemented with 10% FBS

extract_protocol:
RNA extraction and purification from CICs and FBS cell lines were performed using the AllPrep DNA/RNA Mini Kit  The amount and the quality of nucleic acids have been assessed by the Nanodrop 8000 and Qubit PicoGreen assay and RNA RIN threshold has been determined by the 2100 BioAnalyzer.
QuantSeq 3’mRNA-Seq Library Prep Kit-FWD (Lexogen) and using the KAPA HiFi Library quantification kit.The final library pool was sequenced on Illumina NextSeq 500 with High Output 75 bp single end read kit, at a depth of 8 million reads per library.

treatment_protocol: CIC and FBS the cell lines were cultured in Opti-MEM™ I Reduced Serum Medium in 6-well plates and transfected with 50 nM of either mimics or inhibitors of miR-15a or miR-196a using the NEON transfection kit. Cells were also transfected with 50 nM of either mirVana miRNA mimic Negative Control #1 or mirVana miRNA inhibitor Negative Control #1. Following 4 hrs, the complete medium was then added to the cells, and cells were cultured in vitro for 48 hrs for further assessments. Also, CIC and FBS cell lines were incubated with the following agents: Butyrate alone (1mM) for 12 hrs, or IFN-γ (1000 IU/ml) for 48 hrs + Butyrate (1mM); or HDACi (vorinostat) (1.25 μM) for 24 hrs.

value: Cell line

value: FBS

value: Butyrate


title: 1076FBSIFNg+Butyrate

description:
Library name: 1076FBSIFNg+Butyrate_0701466321
Lexogen 3'DGE

value: IFNg+Butyrate


title: mouse liver fed with ethanol diet, AAV-shFAF2-4

city: Indianapolis

first: Zhihong

last: Yang

institute: Indiana University

data_processing:
For the bioinformatics analysis, HISAT was used to map reads to the genome after removing adaptor contamination, low quality bases and undetermined bases. The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. StringTie was used to perform expression level for mRNAs by calculating FPKM (Fragments per kilobase of exon per million fragments).
Assembly: The mapped reads of each sample were assembled using StringTie.
Supplementary files format and content: excel file includes raw counts for each sample
Supplementary files format and content: Excel file includes FPKM values for each sample

source_name: Liver

extract_protocol:
Direct-Zol RNA kits
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

value: Liver


title: Clam SC271D-0706

description: SC Phase I


title: MiR-455 null, 3 month old 3


title: MiR-455 null, 3 month old 2


title: 1_14-81


title: mouse liver fed with ethanol diet, AAV-shFAF2-3


title: Clam SC270S-0955

description: SC Phase II


title: 4_19-203


title: 3_18-20


title: 1076FBSUT-R

description:
Library name: 1076FBSUT-R_0701466311
Lexogen 3'DGE

value: Untreated


title: mouse liver fed with ethanol diet, AAV-shFAF2-2


title: 1076FBSmiR-196amimic2

description:
Library name: 1076FBSmiR-196amimic2_0701466351
Lexogen 3'DGE


title: 1076CSCmiR-196amimic2

description:
Library name: 1076CSCmiR-196amimic2_0701466301
Lexogen 3'DGE

value: CIC


title: mouse liver fed with ethanol diet, AAV-shFAF2-1


title: 1076CSCHDACi

description:
Library name: 1076CSCHDACi_0701466291
Lexogen 3'DGE

value: HDACi


title: 1076FBSHDACi

description:
Library name: 1076FBSHDACi_0701466341
Lexogen 3'DGE


title: mouse liver fed with ethanol diet, AAV-Null_4


title: Clam SC269D-0804

description: SC Phase I

value: Adductor muscle


title: 1076CSCButyrate

description:
Library name: 1076CSCButyrate_0701466281
Lexogen 3'DGE


title: Clam SC267S-0954

description: SC Phase II


title: 1_19-07


title: mouse liver fed with ethanol diet, AAV-Null_3


title: 1076CSCIFNg+Butyrate

description:
Library name: 1076CSCIFNg+Butyrate_0701466271
Lexogen 3'DGE


title: mouse liver fed with ethanol diet, AAV-Null_2


title: 3_C-598


title: 1076CSCUT-R

description:
Library name: 1076CSCUT-R_0701466261
Lexogen 3'DGE


title: Clam SC260S-1023

description: SC Phase III

value: Hemocytes in ethanol


title: 1247FBSmiR-196amimic2

description:
Library name: 1247FBSmiR-196amimic2_0701466251
Lexogen 3'DGE


title: Clam SC256D-0725

description: SC Phase I


title: mouse liver fed with ethanol diet, AAV-Null_1


title: 1_19-180


title: 3_19-154


title: Clam SC253D-0775

description: SC Phase I


title: 4_pt-s96


title: Clam SC268P-0934

description: SC Phase II


title: CD8 Tcells,PBS,PBCD83

city: 郑州市

first: yimeng

last: xia

address: 郑州市经八路

institute: 郑州大学第二附属医院

data_processing:
Raw paired-end fastq reads were filtered by TrimGaloreto discard the adapters and low quality bases via calling the Cutadapt tool. The clean reads obtained were then aligned to the mm10/hg19 mouse/human genome using HISAT2, followed by reference genome-guided transcriptome assembly and gene expression quantification using StringTie . Differentially expressed genes (DEGs) were identified by DEseq2(for sample with replications) or edgeR (for sample with no replication) with a cut-off value of log2|fold-change|>1 and p-adjust <0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424), which yielded > 2 μg of total RNA per sample.
Illumina library construction was performed according to the manufacturer's instructions (Illumina,USA).

value: PBS


title: 1247FBSButyrate

description:
Library name: 1247FBSButyrate_0701466231
Lexogen 3'DGE


title: 2_19-73


title: Clam SC252D-0820

description: SC Phase I


title: 3_pt-s91


title: CD8 Tcells,PBS,PBCD82


title: Clam SC249D-0803

description: SC Phase I


title: 1247FBSIFNg+Butyrate

description:
Library name: 1247FBSIFNg+Butyrate_0701466221
Lexogen 3'DGE


title: CD8Tcells,PBS,PBCD81


title: 1247FBSUT-R

description:
Library name: 1247FBSUT-R_0701466211
Lexogen 3'DGE


title: 1_C-106


title: Clam SC247P-0947

description: SC Phase II


title: 2_C-227


title: 1247CSCmiR-196amimic2

description:
Library name: 1247CSCmiR-196amimic2_0701466201
Lexogen 3'DGE


title: Clam SC254D-0757

description: SC Phase I


title: 2_C-113


title: CD8Tcells,PolyIC,PoCD83

value: adjuvant PolyIC


title: Clam SC244D-0802

description: SC Phase I


title: 1247CSCHDACi

description:
Library name: 1247CSCHDACi_0701466191
Lexogen 3'DGE


title: 5_16-43


title: CD8Tcells,PolyIC,PoCD82


title: CD8 Tcells,PBS,PBCD84


title: 1247FBSHDACi

description:
Library name: 1247FBSHDACi_0701466241
Lexogen 3'DGE


title: 1247CSCButyrate

description:
Library name: 1247CSCButyrate_0701466181
Lexogen 3'DGE


title: Clam SC242D-0763

description: SC Phase I


title: 4_15-71


title: 1247CSCIFNg+Butyrate

description:
Library name: 1247CSCIFNg+Butyrate_0701466171
Lexogen 3'DGE


title: CD8Tcells,PolyIC,PoCD81


title: 3_15-58


title: Clam SC23D-0812

description: SC Phase I

source_name: Clam SC23D-0812


title: CD8Tcells,Zfp760WT,ZWCD84

value: Zfp760 wildtype peptide


title: 1247CSCUT-R

description:
Library name: 1247CSCUT-R_0701466161
Lexogen 3'DGE


title: Clam SC232D-0774

description: SC Phase I


title: 2_15-32


title: Clam SC245P-0924

description: SC Phase II


title: CD8Tcells,Zfp760WT,ZWCD83


title: CD8Tcells,PolyIC,PoCD84


title: 6_19-158


title: 1247FBSmiR-9mimic

description:
Library name: 1247FBSmiR-9mimic_0701466151
Lexogen 3'DGE


title: 1_15-11


title: Clam SC230P-0940

description: SC Phase II


title: CD8Tcells,Zfp760WT,ZWCD82


title: 4_C-593


title: 1247FBSUT2

description:
Library name: 1247FBSUT2_0701466131
Lexogen 3'DGE


title: Clam SC225D-0720

description: SC Phase I


title: Clam SC227S-0958

description: SC Phase II


title: CD8 Tcells,Zfp760MT,ZMCD84

value: Zfp760 mutant peptide


title: Clam SC224S-1011

description: SC Phase III


title: 1247CSCUT2

description:
Library name: 1247CSCUT2_0701466121
Lexogen 3'DGE


title: CD8 Tcells,Zfp760MT,ZMCD83


title: 2_C-291

value: blood


title: Clam SC223S-1010

description: SC Phase III


title: 1_C-153

value: Peripheral Blood Mononuclear Cell


title: 1076FBSmiR-299mimic

description:
Library name: 1076FBSmiR-299mimic_0701466111
Lexogen 3'DGE


title: 1076CSCmiR-299mimic

description:
Library name: 1076CSCmiR-299mimic_0701466101
Lexogen 3'DGE


title: 4_C-478


title: CD8 Tcells,Zfp760MT,ZMCD82


title: Clam SC217S-1009

description: SC Phase III


title: 1247FBSmiR-299mimic

description:
Library name: 1247FBSmiR-299mimic_0701466091
Lexogen 3'DGE


title: CD8 Tcells,Zfp760MT,ZMCD81


title: 3_C-315


title: Clam SC216D-0724

description: SC Phase I


title: 1247CSCmiR-9mimic

description:
Library name: 1247CSCmiR-9mimic_0701466141
Lexogen 3'DGE


title: CD8Tcells,Zfp760WT,ZWCD81


title: Clam SC214D-0713

description: SC Phase I


title: 1_C-115


title: 3_C-358


title: CD8 Tcells,Ddx21WT,DWCD83

value: Ddx21 wildtype peptide


title: CD8Tcells,Ddx21WT,DWCD84


title: H1792_ACBI1,rep2

city: HOUSTON

first: Yonathan

last: Lissanu

state: TEXAS

address: 1515 Holcombe Blvd

department: Cardiovascular and Thoracic Surgery

institute: md anderson cancer centre

data_processing:
Raw sequencing reads were aligned to human reference genome hg38 and transcriptome gene annotation GENCODE V44 using TopHat2 v2.1.1. HTseq-count v0.11.0 was used to count the expression level of each gene.
Assembly: hg38
Supplementary files format and content: Text file containing gene expression

source_name: Lung

growth_protocol: The cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin–streptomycin at 37 °C with 5% CO2. Cell lines were cultured till 90% confluency and kept at low passage numbers and maintained at 37 °C in a humidified 5% CO2-containing incubator.

extract_protocol:
Total RNA was isolated from cells using the RNAeasy Mini kit (Qiagen) followed by purification using the RNeasy Mini Kit (Cat# 74104, Qiagen) according to manufacturer’s instructions.
Libraries were constructed using the NEBNext Ultra II DNA Library prep kit according to manufacturer’s instructions

treatment_protocol: Cells were plated in 10cm dishes and treated with DMSO, 1mM ACBI1 for 96hours.

value: Lung

value: Lung cancer

value: WT


title: CD8 Tcells,Ddx21WT,DWCD81


title: Clam SC212D-0755

city: Stony Brook

first: Denis

last: Grouzdev

institute: Stony Brook University

description: SC Phase I


title: H1792_DMSO,rep2

value: DMSO


title: Clam SC210S-1007

description: SC Phase III


title: 1076FBSmiR-378dinhibition

description:
Library name: 1076FBSmiR-378dinhibition_0701466071
Lexogen 3'DGE

value: Cell line

value: FBS


title: CD8 Tcells,Ddx21MT,DMCD83

value: Ddx21 mutant peptide


title: H1792_DMSO,rep1


title: 1076CSCmiR-4461inhibition

description:
Library name: 1076CSCmiR-4461inhibition_0701466021
Lexogen 3'DGE

value: CIC


title: Clam SC20P-0949

description: SC Phase II

source_name: Clam SC20P-0949

value: Adductor muscle


title: 1247CSCmiR-299mimic

description:
Library name: 1247CSCmiR-299mimic_0701466081
Lexogen 3'DGE


title: 1247FBSmiR-378dinhibition

description:
Library name: 1247FBSmiR-378dinhibition_0701466051
Lexogen 3'DGE


title: CD8 Tcells,Ddx21MT,DMCD84


title: 1076FBSmiR-4461inhibition

description:
Library name: 1076FBSmiR-4461inhibition_0701466031
Lexogen 3'DGE


title: H1792_ACBI1,rep1


title: CD8 Tcells,Ddx21WT,DWCD82


title: 2_C-229


title: Clam SC215D-0756

description: SC Phase I


title: Clam SC209P-0923

description: SC Phase II


title: CD8 Tcells,Ddx21MT,DMCD82


title: Clam SC213S-1008

description: SC Phase III

value: Hemocytes in ethanol


title: Clam SC208D-0787

description: SC Phase I


title: ASeq2-44A,rep2

library_source: genomic

data_processing:
Raw sequencing reads were aligned to human reference genome hg38 using BWA alignment tool.
Assembly: hg38
Supplementary files format and content: peak calling

extract_protocol:
After ATAC-Seq, the transposed DNA samples were purified by Qiagen minElute column.
ATAC-seq libraries are prepared based on Howard Chang protocol from Nature Methods, 2017. qPCR was used to determine the optimal PCR cycles to prevent over-amplification of transposed DNA. Purified transposed DNA is subjected to total of 11 cycles of qPCR amplification to make ATAC-Seq libraries.


title: ASeq1-44A,rep1


title: CD8 Tcells,Ddx21MT,DMCD81


title: Clam SC207P-0939

description: SC Phase II


title: 1076FBSmiR-196ainhibition

description:
Library name: 1076FBSmiR-196ainhibition_0701465991
Lexogen 3'DGE


title: ASeq2-44D,rep2


title: 1076CSCmiR-196ainhibition

description:
Library name: 1076CSCmiR-196ainhibition_0701465981
Lexogen 3'DGE


title: Clam SC206D-0712

description: SC Phase I


title: ASeq1-44D,rep1


title: CD4 Tcells,PBS,PBCD42

value: PBS


title: 1247FBSmiR-196ainhibition

description:
Library name: 1247FBSmiR-196ainhibition_0701465971
Lexogen 3'DGE


title: CD4 Tcells,PBS,PBCD44


title: CD4 Tcells,PBS,PBCD43


title: ASeq2-19A,rep2


title: 1247FBSmiR-4461inhibition

description:
Library name: 1247FBSmiR-4461inhibition_0701466011
Lexogen 3'DGE


title: 1247CSCmiR-196ainhibition

description:
Library name: 1247CSCmiR-196ainhibition_0701465961
Lexogen 3'DGE


title: Clam SC205D-0700

description: SC Phase I


title: CD4 Tcells,PolyIC,PoCD44

value: adjuvant PolyIC


title: ASeq1-19A,rep1


title: 1076FBSmiR-15ainhibition

description:
Library name: 1076FBSmiR-15ainhibition_0701465951
Lexogen 3'DGE


title: ASeq2-19D,rep2


title: Clam SC203D-0800

description: SC Phase I


title: CD4 Tcells,PBS,PBCD41


title: 1247CSCmiR-4461inhibition

description:
Library name: 1247CSCmiR-4461inhibition_0701466001
Lexogen 3'DGE


title: 1076CSCmiR-15ainhibition

description:
Library name: 1076CSCmiR-15ainhibition_0701465941
Lexogen 3'DGE


title: ASeq1-19D,rep1


title: CD4 Tcells,PolyIC,PoCD42


title: HCC44_ACBI,rep2


title: Clam SC202D-0817

description: SC Phase I


title: 1247FBSmiR-15ainhibition

description:
Library name: 1247FBSmiR-15ainhibition_0701465931
Lexogen 3'DGE


title: CD4 Tcells,PolyIC,PoCD43


title: Clam SC201S-1006

description: SC Phase III


title: 1247CSCmiR-15ainhibition

description:
Library name: 1247CSCmiR-15ainhibition_0701465921
Lexogen 3'DGE


title: CD4 Tcells,PolyIC,PoCD41


title: Clam SC1D-0824

description: SC Phase I

source_name: Clam SC1D-0824


title: Clam SC204D-0773

description: SC Phase I


title: CD4 Tcells,Zfp760WT,ZWCD44

value: Zfp760 wildtype peptide


title: 1076FBSmiR-196amimic

description:
Library name: 1076FBSmiR-196amimic_0701465911
Lexogen 3'DGE


title: Clam SC198D-0772

description: SC Phase I


title: HCC44_DMSO,rep2


title: 1076CSCmiR-196amimic

description:
Library name: 1076CSCmiR-196amimic_0701465901
Lexogen 3'DGE


title: CD4 Tcells,Zfp760WT,ZWCD43


title: CD4 Tcells,Zfp760WT,ZWCD41


title: 1247FBSmiR-196amimic

description:
Library name: 1247FBSmiR-196amimic_0701465891
Lexogen 3'DGE


title: HCC44_DMSO,rep1


title: Clam SC194D-0749

description: SC Phase I


title: Clam SC191P-0922

description: SC Phase II


title: H1975_ACBI1,rep2


title: CD4 Tcells,Zfp760MT,ZMCD43

value: Zfp760 mutant peptide


title: 1076FBSmiR-15amimic

description:
Library name: 1076FBSmiR-15amimic_0701465871
Lexogen 3'DGE


title: Clam SC18D-0761

description: SC Phase I

source_name: Clam SC18D-0761


title: H1975_ACBI1,rep1


title: CD4 Tcells,Zfp760MT,ZMCD44


title: HCC44_ACBI1,rep1


title: H1975_DMSO,rep2


title: Clam SC193D-0748

description: SC Phase I


title: 1247FBSmiR-15amimic

description:
Library name: 1247FBSmiR-15amimic_0701465851
Lexogen 3'DGE


title: CD4 Tcells,Zfp760MT,ZMCD42


title: Clam SC195S-1004

description: SC Phase III


title: CD4 Tcells,Zfp760WT,ZWCD42


title: Clam SC188P-0931

description: SC Phase II


title: Clam SC187P-0938

description: SC Phase II


title: CD4 Tcells,Ddx21WT,DWCD44


title: 1247CSCmiR-15amimic

description:
Library name: 1247CSCmiR-15amimic_0701465841
Lexogen 3'DGE


title: H1975_DMSO,rep1


title: 1247CSCmiR-196amimic

description:
Library name: 1247CSCmiR-196amimic_0701465881
Lexogen 3'DGE


title: 1076FBSUT

description:
Library name: 1076FBSUT_0701465831
Lexogen 3'DGE

value: Untreated


title: 5637 cells, KO2, rep1

city: Wuhan

first: Jingtian

last: Yu

address: 169 Donghu

institute: Wuhan University

description:
gene_count_matrix_WT_KO.txt
5637-KO2-1_S103

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The total reads are compared with the reference genome (clean data were mapped to the reference genome of Homo_sapiens.GRCh38 from NCBI using STRA software (version 2.5.3a) with default parameters.） to obtain comprehensive transcript information.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor)
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: 5637 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: Transfection of siRNA followed LipofectamineTM 3000 Reagent’s (L3000015, Invitrogen) protocol.

value: Tumor cells

value: RBPMS-KO


title: CD4 Tcells,Zfp760MT,ZMCD41


title: 1076CSCmiR-15amimic

description:
Library name: 1076CSCmiR-15amimic_0701465861
Lexogen 3'DGE


title: Clam SC186D-0786

address: 100 Nicolls Rd

description: SC Phase I


title: CD4 Tcells,Ddx21WT,DWCD42

value: Ddx21 wildtype peptide


title: CD4 Tcells,Ddx21WT,DWCD43


title: 1247CSCUT

description:
Library name: 1247CSCUT_0701465801
Lexogen 3'DGE


title: 1076CSCUT

description:
Library name: 1076CSCUT_0701465821
Lexogen 3'DGE


title: 5637 cells, WT2, rep1

description:
gene_count_matrix_WT_KO.txt
5637-WT2-1_S100


title: 1247FBSUT

description:
Library name: 1247FBSUT_0701465811
Lexogen 3'DGE


title: 5637 cells, WT2, rep3

description:
gene_count_matrix_WT_KO.txt
5637-WT2-3_S102


title: 5637 cells, KO2, rep3

description:
gene_count_matrix_WT_KO.txt
5637-KO2-3_S105


title: 5637 cells, WT2, rep2

description:
gene_count_matrix_WT_KO.txt
5637-WT2-2_S101


title: 5637 cells, KO2, rep2

description:
gene_count_matrix_WT_KO.txt
5637-KO2-2_S104


title: Clam SC179S-1002

description: SC Phase III


title: CD4 Tcells,Ddx21MT,DMCD43


title: Clam SC175D-0822

description: SC Phase I


title: Clam SC184D-0815

description: SC Phase I


title: 5637 cells, KO1, rep2

description:
gene_count_matrix_WT_KO.txt
5637-KO1-2_S98


title: CD4 Tcells,Ddx21MT,DMCD42


title: CD4 Tcells,Ddx21WT,DWCD41


title: Clam SC185D-0792

description: SC Phase I


title: CD4 Tcells,Ddx21MT,DMCD41


title: CUT-RUN-SM4-A1

data_processing:
Raw sequencing reads were aligned to human reference genome hg38 using Bowtie2 v2.4.5
Assembly: hg38
Supplementary files format and content: peak calling
Library strategy: CUT&RUN

growth_protocol: The cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin–streptomycin at 37 °C with 5% CO2.

extract_protocol:
Total DNA was isolated from cells using the RNAeasy Mini kit (Qiagen) followed by purification using the RNeasy Mini Kit according to manufacturer’s instructions.
Libraries were constructed using the NEBNext Ultra II DNA Library prep kit according to manufacturer’s instructions

value: Lung

value: Lung cancer


title: Clam SC174S-1000

description: SC Phase III


title: 1076CSCmiR-378dinhibition

description:
Library name: 1076CSCmiR-378dinhibition_0701466061
Lexogen 3'DGE


title: CUT-RUN-POS-D2

description: Positive control

value: WT

value: DMSO


title: CD4 Tcells,Ddx21MT,DMCD44


title: 5637 cells, KO1, rep3

description:
gene_count_matrix_WT_KO.txt
5637-KO1-3_S99


title: Clam SC172D-0747

description: SC Phase I


title: CUT-RUN-POS-D1

description: Positive control


title: 5637 cells, WT1, rep3

description:
gene_count_matrix_WT_KO.txt
5637-WT-3_S96


title: lonp1_OE_OE_ptenf_f_528

city: Shanghai

first: Xingming

last: Zhang

address: No. 270, Dong'an Road, Xuhui District, Shanghai

institute: Fudan University Shanghai Cancer Center

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: tissue

extract_protocol:
TRIzol® reagent (Thermo Fisher Scientific) was utilized for total RNA extraction from PCa cells according to the manufacturer’s instructions.
Total RNA was purified using the RNA Clean XP Kit (A63987, Beckman Coulter,  Kraemer Boulevard Brea, CA, USA) and DNase set (79254, QIAGEN, Germany). Complementary DNA was synthesized with 1 μg of total RNA using VAHTS® mRNA-seq V2 Library Prep Kit for Illumina (NR603, Vazyme, Nanjing, China),  followed by amplification and subjected to paired-end150 (PE150) Hiseq. Each  sample contained pooled RNA from 3 biological replicates and was mixed with  equal mass to minimize variation across samples.

value: tissue

tag: tissue type

value: prostate

value: PB-Cre; Pten knockout and lonp1 knockin


title: 5637 cells, KO1, rep1

description:
gene_count_matrix_WT_KO.txt
5637-KO1-1_S97


title: CUT-RUN-SM4-A2


title: Clam SC170P-0918

description: SC Phase II

value: Adductor muscle


title: lonp1_OE_OE_ptenf_f_522


title: Clam SC16S-0964

description: SC Phase III

source_name: Clam SC16S-0964

value: Hemocytes in ethanol


title: 5637 cells, WT1, rep2

description:
gene_count_matrix_WT_KO.txt
5637-WT-2_S95


title: CUT-RUN-SM4-D2


title: lonp1_OE_OE_ptenf_f_404


title: CUT-RUN-SM4-D1


title: Clam SC17D-0819

description: SC Phase I

source_name: Clam SC17D-0819


title: Clam SC169D-0785

description: SC Phase I


title: CUT-RUN-NFKB-A1

description: NFKB


title: CUT-RUN-NFKB-A2

description: NFKB


title: U-2OS Clone#12 cells, 8h DOX REP2

city: Munich

first: Stephan

last: Hamperl

state: Bayern

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz-Zentrum Munich

data_processing:
Paired-end reads were trimmed using trim_galore (version 0.6.10) (Krueger et al., 2023) with the parameter --quality 28
Reads were mapped to the genome using bowtie2 (version 2.5.1) with the parameters --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --dovetail -I 10 -X 700
Aligned reads were filtered by samtools (version 1.17) with the parameter -q 12
Duplicated reads were removed using picard MarkDuplicates (version 3.0.0) with the parameter -REMOVE_DUPLICATES TRUE
Genome coverages were created using deeptools bamCoverage (version 3.5.2) (Ramírez et al., 2016) with parameters --blackListFileName hg38-blacklist.v2.bed --ignoreForNormalization MT --binSize 20 --smoothLength 60 –extendReads --maxFragmentLength 700 --normalizeUsing "CPM"
Assembly: hg38
Supplementary files format and content: bigWig with normalized BrdU-seq coverage
Library strategy: BrdU-IP-seq

source_name: U-2OS Clone#12

growth_protocol: U-2OS Clone#12 cells were grown in DMEM (GIBCO) containing 10% FBS, 2mM L-glutamine, and penicillin/streptomycin, in a 5% CO2 environment at 37°C

extract_protocol:
Genomic DNA was isolated by phenol-chloroform extraction. 20 µg/sample of DNA were sonicated on a Covaris E220 focused sonicator for 10 min.
Libraries were constructed using NEBNext Ultra II DNA Library Kit with Purification Beads (E7103S, E7103L) and NEBNext Multiplex Oligos for Illumina (E6440S) according to manufacturer's instructions

treatment_protocol: U-2OS Clone#12 cells were synchronized by double thymidine block. Cells were released into S-phase by replacing thymidine containing medium by fresh culturing medium or kept in thymidine containing medium for G1 conditions. Simultaneous to S-phase release  0 or 1 µg/mL Doxycycline was added.

value: U-2OS Clone#12

value: U-2OS Tet-ON

tag: antibody

value: BrdU (BD Biosciences #347580)


title: U-2OS Clone#12 cells, 8h DOX REP1


title: ptenf_f_585

value: PB-Cre; Pten knockout


title: ptenf_f_588


title: Clam SC165S-0999

description: SC Phase III


title: ptenf_f_79


title: CUT-RUN-NFKB-D2

description: NFKB


title: Clam SC164D-0722

description: SC Phase I


title: CUT-RUN-NFKB-D1

description: NFKB


title: lonp1_OE_OE_350

value: PB-Cre; lonp1 knockin


title: U-2OS Clone#12 cells, 8h REP1


title: U-2OS Clone#12 cells, 6h DOX REP2


title: Clam SC15D-0760

description: SC Phase I

source_name: Clam SC15D-0760


title: Clam SC159S-0998

description: SC Phase III


title: lonp1_OE_OE_344


title: Clam SC158P-0930

description: SC Phase II


title: lonp1_OE_OE_345


title: CUT-RUN-NEG-D1

description: Negative control


title: U-2OS Clone#12 cells, 6h DOX REP1


title: U-2OS Clone#12 cells, 6h REP2


title: Clam SC168D-0741

description: SC Phase I


title: WT395

value: PB-Cre


title: H2122PAR-3,rep2

source_name: lung

extract_protocol:
Total RNA was isolated from cells using the RNAeasy Mini kit (Qiagen) followed by purification using the RNeasy Mini Kit according to manufacturer’s instructions.
Libraries were constructed using the NEBNext Ultra II DNA Library prep kit according to manufacturer’s instructions

value: lung

value: vehicle


title: Clam SC155D-0739

description: SC Phase I


title: U-2OS Clone#12 cells, 6h REP1


title: WT371


title: H2122PAR-1,rep1


title: U-2OS Clone#12 cells, 8h REP2


title: U-2OS Clone#12 cells, 4h DOX REP2


title: WT353


title: H2122KO-1,rep3

value: SMARCA4 KO


title: CUT-RUN-NEG-D2

description: Negative control

value: Lung

value: Lung cancer


title: Clam SC152D-0740

description: SC Phase I


title: Clam SC14D-0818

description: SC Phase I

source_name: Clam SC14D-0818


title: U-2OS Clone#12 cells, 4h DOX REP1


title: U-2OS Clone#12 cells, 4h REP2


title: Clam SC148D-0784

description: SC Phase I


title: H2122PAR-6,rep3

value: WT


title: H2122KO-1,rep1


title: 5637 cells, WT1, rep1

description:
gene_count_matrix_WT_KO.txt
5637-WT-1_S94

value: Tumor cells


title: Clam SC146D-0799

description: SC Phase I


title: IECs, WT-2

first: Yue

last: Xu

address: 上海市徐汇区华山路

institute: 上海交通大学

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

source_name: colon

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

value: IECs

value: DSS


title: IECs, WT-3


title: H2122KO-1,rep2


title: IECs, WT-1


title: Clam SC145D-0814

description: SC Phase I

value: Adductor muscle


title: U-2OS Clone#12 cells, 4h REP1

value: U-2OS Clone#12


title: U-2OS Clone#12 cells, 2h DOX REP2

value: U-2OS Tet-ON


title: hiPSC_FS_NPCs_rep3

city: Kyoto

first: Kenji

last: Osafune

address: Shogoin-Kawahara-cho 53

department: Center for iPS Cell Research and Application (CiRA)

institute: Kyoto University

data_processing:
Raw reads were trimmed and quality-filtered using Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16).
Trimmed reads were mapped to the human GRCh38 genome using STAR (version 2.7.2b).
Read counts on annotated genes were quantified using featureCounts (version 1.6.1), and FPKM values were calculated by normalizing to total counts and transcript length.
Differential expression and Gene Ontology (GO) enrichment analysis were performed using iDEP (version 0.96).
Assembly: GRCh38.p13 (hg38)
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was extracted from hiPSC-NPCs and hiPSC-FS-NPCs using the RNeasy Mini Kit (Qiagen), and the quality of the RNA was assessed using a Bioanalyzer (Agilent) to ensure that the RNA integrity number (RIN) was above 7.0.
After poly(A)+ enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs), double-stranded cDNA libraries were prepared using the SMARTer Stranded Total RNA Sample Prep Kit-HI Mammalian (Clontech).

value: Induced pluripotent stem cells

value: differentiation into nephron progenitor cells followed by differentiation into nephron organoids


title: IECs, NSD2-FF-VILCRE3


title: hiPSC_FS_NPCs_rep2


title: U-2OS Clone#12 cells, 2h DOX REP1

value: BrdU (BD Biosciences #347580)


title: IECs, NSD2-FF-VILCRE2


title: hiPSC_FS_NPCs_rep1


title: Clam SC13D-0770

description: SC Phase I

source_name: Clam SC13D-0770


title: IECs, NSD2-FF-VILCRE1


title: Clam SC139D-0783

description: SC Phase I


title: U-2OS Clone#12 cells, 2h REP1


title: hiPSC_NPCs_rep2

value: wild type

value: differentiation into nephron progenitor cells