title: WT replicate 2

city: Illkirch

first: Susan

last: Chan

address: 1, rue Laurent Fries

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Genome_build: mm10
Supplementary_files_format_and_content: table with normalized data divided by median of transcripts length in kb

source_name: total RNA extracted from CD4+CD25+ sorted cells

extract_protocol: Full length cDNA were generated from 5 ng of total RNA  using SMART-SeqX v4 UltraX Low Input RNA Kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 10 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, USA) followed by 12 cycles of library amplification. Following purification with SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

tag: genotype


title: AcinarCer12w_rep2

status: Public on Oct 24 2023

type: SRA

city: New York

first: Rohit

last: Chandwani

state: NY

address: 413 East 69th St, BRB 1360G

department: Surgery

country: USA

institute: Weill Cornell Medicine

library_source: genomic

data_processing:
Read Trimming Fastq files containing ATAC-seq paired-end reads were trimmed for both base quality (q <=15) and Illumina adaptor sequences using TrimGalore v0.4.4
Alignment Trimmed reads were mapped to the mm9 mouse genome and BAMs were generated using Bowtie2 v2.3.4.1
Sorting and indexing BAMs were sorted and indexed using Samtools v1.8
Remove duplicates PCR Duplicates were removed using Picard MarkDuplicates v2.16
Peak-calling Peak calling was performed using MACS2 v2.1.2
Peak aggregation The peaks from all samples were then were merged within a 500 bp window to create a full peak atlas using in house bash and python scripts
Counting reads Raw read counts were tabulated over this peak atlas using FeatureCounts v1.6.3
Generation of normalized abundance measurements The raw read counts were normalized using the median of ratios normalization method in DESeq2 v1.22.2
Assembly: mm9
Supplementary files format and content: bigwig files

molecule: genomic DNA

organism: Mus musculus

source_name: Pancreas

extract_protocol:
tdTomato+ acinar cells were FACS sorted. Standard ATAC-seq protocol was followed (Buenrostro et al. 2013).
Illumina Nextera kit

tag: strain

value: WT

tag: biological context

value: Pancreatitis

tag: recovery duration

value: 12 weeks


title: knockin, control 2

city: Philadelphia

first: Dong

last: Li

state: PA

address: 3615 Civic Center BLVD

institute: Children's Hospital of Philadelphia

library_source: transcriptomic

data_processing:
aligned onto the human reference genome
features were counted by featureCounts
DESeq2 was then used to detected differentially expressed genes
Assembly: GRCh37
Supplementary files format and content: tabl-delimited text file includes raw coutns for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: H9 human pluripotent stem cells

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen)
RNA libararies were prepared using Illumina TruSeq Library Prep Kit folloiwing manufacturer's protocols

tag: cell line

value: H9 human pluripotent stem cells

value: wild type


title: AcinarCer12w_rep1


title: GRZ_D_male9_d100_skin

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v1.8.4.
The RNA sequencing reads were aligned to the N. furzeri genome assembly (assembly version Nfu_20150522, gene annotation version 150922)  using STAR 2.5.1b (parameters: --alignIntronMax 100000, --outSJfilterReads Unique) (PMID: 23104886).
For each gene, all reads that map uniquely to one genomic position were counted with FeatureCounts 1.5.0 under default settings (PMID: 24227677).
Assembly: Genome Nfu_20150522 and annotation 20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (https://nfingb.leibniz-fli.de) (PMID: 26638077)
Supplementary files format and content: csv file containing raw read counts per gene over all samples

molecule: total RNA

organism: Nothobranchius furzeri

source_name: skin

extract_protocol:
Brain and skin tissue samples were prepared from each specimen and RNA was extracted using the RNeasy Mini Kit (Quiagen).
Library preparation was done using Illumina’s TruSeq RNA v2 kit following the manufacturer’s instruction.

value: GRZ-D

tag: tissue

value: skin

tag: Sex

value: male

tag: age in_days


title: Helios KO replicate 1

country: France

value: Helios KO


title: knockin, control 1


title: AcinarCer6w_rep1

value: 6 weeks


title: GRZ_D_male9_d100_brain

source_name: brain

value: brain


title: WT replicate 1


title: knockin, control 4


title: GRZ_D_male8_d100_skin


title: ChIP_HAND2_IMR32_BRM014_rep2

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: HAND2 ChIP-seq in IMR32 cells treated with BRM014

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie v2.4.1.
Fragments with read qualities greater than 10 were considered for further analysis.
All bigWig files are unscaled counts and require scaling before comparison across samples.
Assembly: hg38
Supplementary files format and content: Unscaled bigWig files of genome-wide coverage

growth_protocol: Cells were cultured in 10% FBS DMEM medium using standard approaches.

extract_protocol:
Lysates were obtained from sonicated nuclei crosslinked with either 1% formaldehyde and 2 mM disuccinimidyl glutarate (double cross-linking) for ASCL1, or 1% formaldehyde alone (single cross-linking) for all other targets. Protein-DNA complexes were isolated by immunoprecipitation.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with either either DMSO or 1 uM BRM014 for 1 h

tag: chip antibody

tag: treatment


title: ChIP_HAND2_IMR32_DMSO_rep1

description: HAND2 ChIP-seq in IMR32 cells treated with DMSO

value: DMSO


title: ChIP_HAND2_IMR32_DMSO_rep2


title: 5-FU H3K27ac

city: Koto-ku

first: Jin

last: Lee

state: Tokyo

country: Japan

institute: Japanese Foundation for Cancer Research

data_processing:
Raw FASTQ file were checked quality using FastQC (version 0.11.9)
and removed adapters using Trimmomatic (version 0.39).
The reads were aligned to GRCh38 genome using bwa mem (version 0.7.17)
Peaks were called using MACS3 (version 3.0.0b3) with significance cut-off q-value < 0.01
Assembly: bigWig files were generated using deeptools. (version 3.5.1)
Supplementary files format and content: GRCh38
Supplementary files format and content: bigWig, narrowPeak (except for Input samples)

growth_protocol: JSC15-3 cells were cultured with ACL4 and Ham's F12 supplemented with  Antibiotic-Antimycotic Solution in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Chromatin immunoprecipitation (ChIP) assay was performed using SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) Kit (Cell Signaling Technology) according to the manufacturer’s instructions.
Sequence libraries were constructed with NEBNest UltraⅡ DNA library Prep Kit for Illumina (New England Biolabs, Inc.) according to the manufacture's instructions.

treatment_protocol: JSC15-3 cells were treated with 3 μM of 5-FU for 5 days.

value: H3K27ac (ab4729, Abcam)

tag: cell type

value: gastric cancer patient-derived cells

value: 3 μM 5-FU for 5 days


title: 5-FU H3K27me3

value: H3K27me3 (#9733, Cell Signaling Technology)


title: DMSO H3K27me3

value: DMSO for 5 days


title: DMSO H3K27ac


title: ChIP_HAND2_IMR32_BRM014_rep1

value: WT


title: GRZ_D_male2_d147_skin


title: He KO replicate 2


title: ChIP_ISL1_IMR32_BRM014_rep2

description: ISL1 ChIP-seq in IMR32 cells treated with BRM014

value: Anti-ISL1, DSHB mix of #40.2D6 Lot 1, #39.4D5 Lot 1, #39.3F7 Lot 1, and #40.3A4 Lot 1


title: Diac50a

city: New Haven

first: Valerie

last: Horsley

address: 260 Whitney

institute: Yale University

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Assembly: GRCh38
Supplementary files format and content: Supplementary files format and content: H5 matrix, seurat object and h5ad of combined processed files.

source_name: Foot ulcer

extract_protocol:
Skin wounds specimens were collected in PBS with 1% Pen/Strep. Tissues were cleaned with 10% betadine, twice in 70% ethanol, and twice in PBS. Tissues digestion was performed to achieve single cell suspensions in DMEM with 700-1200 cells per uL.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: Foot ulcer

value: Non-Diabetic


title: Diac44c


title: Diac44b


title: ChIP_ISL1_IMR32_BRM014_rep1


title: FU Input


title: ChIP_H3K4me1_IMR32_DMSO_rep1

description: H3K4me1 ChIP-seq in IMR32 cells treated with DMSO

value: Anti-H3K4me1, Abcam, #ab8895, Lot GR257926-1


title: GRZ_D_male13_d100_skin

value: GRZ-D


title: Diac50b

source_name: Ankle ulcer

value: Ankle ulcer


title: ChIP_GATA3_IMR32_DMSO_rep2

description: GATA3 ChIP-seq in IMR32 cells treated with DMSO

value: Anti-GATA3, Thermo Fisher #MA1028, Lot XH352307


title: DMSO Input


title: Diac44a


title: GRZ_D_male8_d100_brain

value: male


title: GRZ_D_male13_d100_brain


title: GRZ_D_male7_d100_skin

value: skin


title: JSC15-3 5-FU siBRD4 (2)

description:
readcount_RNA-seq.csv
TPM.csv

data_processing:
Raw FASTQ file were checked quality using FastQC (version 0.11.9) and removed adapters using Trimmomatic (version 0.39).
The reads were aligned to hg38 using STAR (version 2.7.9a).
Gene expression was quantified using FeatureCounts of Subread package (version 2.0.1).
Filtering low expression genes and normalization were performed using edgeR.
To exclude contaminated RNA such as rRNA, we extracted and analyzed protein coding genes. Expression of each RNA was transformed to CPM.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes TPM values for each sample after protein coding gene extraction.

extract_protocol:
(1) JSC15-3 cells were treated with 3 µM 5-FU for 5 days, and (2) JSC15-3 cells were transfected with siNCT(negative control) and siBRD4 and treated with or without 3 µM 5-FU for 5 days. RNA was extracted using RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
Sequence libraries were constructed with TruSeq stranded mRNA library preparation kit(Illumina) according to the manufacture's instructions.

value: BRD4 knockdown

value: 5-FU for 5 days


title: ChIP_GATA3_IMR32_DMSO_rep1

value: DMSO


title: GRZ_D_male12_d100_skin


title: Diac39


title: Diac38


title: JSC15-3 DMSO siBRD4 (2)

description:
readcount_RNA-seq.csv
TPM.csv

value: gastric cancer patient-derived cells


title: GRZ_D_male12_d100_brain

value: brain


title: Diac37

value: Diabetic


title: GRZ_D_male11_d100_skin


title: JSC15-3 5-FU siNCT (2)

description:
readcount_RNA-seq.csv
TPM.csv


title: ChIP_GATA3_IMR32_BRM014_rep1

description: GATA3 ChIP-seq in IMR32 cells treated with BRM014


title: JSC15-3 DMSO siNCT (2)

description:
readcount_RNA-seq.csv
TPM.csv

value: DMSO for 5 days


title: ChIP_EBF3_IMR32_DMSO_rep2

description: EBF3 ChIP-seq in IMR32 cells treated with DMSO

value: Anti-EBF3, Invitrogen #PA5-30985, Lot YD3904578

value: WT


title: GRZ_D_male11_d100_brain


title: ChIP_EBF3_IMR32_DMSO_rep1


title: JSC15-3 5-FU (1)

description:
readcount_RNA-seq.csv
TPM.csv


title: Diac34

value: Foot ulcer


title: Diac35


title: ChIP_EBF3_IMR32_BRM014_rep2

description: EBF3 ChIP-seq in IMR32 cells treated with BRM014


title: GRZ_D_male10_d100_skin


title: ChIP_EBF3_IMR32_BRM014_rep1


title: GRZ_D_male6_d49_skin


title: GRZ_D_male10_d100_brain


title: JSC15-3 DMSO (1)

description:
readcount_RNA-seq.csv
TPM.csv


title: Hc9

city: kiel

first: Archana

last: Bhardwaj

address: Rosalind-Franklin-Straße 12

institute: Institute of Clinical Molecular Biology (IKMB)

data_processing:
Libraries were prepared using TruSeq Stranded total RNA RiboZero GOLD, Illumina
Samples were paired-end sequenced (2 × 150 bp reads) for 300 cycles to a depth of 1,000 million base reads on a NovaSeq6000 instrument, Illumina
FASTQ files were generated using bcl2fastq software v2.20
Differential gene expression (DGE) from RNA-seq data was determined with linear models using DESeq2 v4.1.3 and significance decided by Benjamini-Hochberg false discovery rate (FDR) adjusted p-values <0.05
Assembly: Ensembl GRCh38 genome version, release 92

source_name: Colon, whole mucosa

extract_protocol:
Biopsies preserved in AllProtect were homogenized in RLT buffer from RNeasy Mini Kit supplemented with 1% 2-mercaptoethanol in a TissueLyser II instrument (all from Qiagen, Hilden, Germany). Total RNA from homogenized biopsy samples was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
TruSeq ribozero gold kit

treatment_protocol: Biopsies were preserved in AllProtect at -80ºC until RNA was isolated.

value: Colon, whole mucosa

tag: subject status

value: healthy controls (Hc)


title: ChIP_ASCL1_IMR32_DMSO_rep2

description: ASCL1 ChIP-seq in IMR32 cells treated with DMSO


title: ChIP_GATA3_IMR32_BRM014_rep2


title: Diac32


title: Hc10


title: ChIP_ASCL1_IMR32_DMSO_rep1


title: Hc8


title: Diac36


title: Female 20 PBS Control

city: Grand Rapids

first: Joseph

last: Patterson

state: MI

address: 400 Monroe NW

institute: Michigan State University

description:
RNA underwent ribosomal reduction (TruSeq RNA Library Preparation Kit from Illumina)
DGE_sleuth_object_female_WT_040921

data_processing:
FastQC tool (version 0.11.7) was run on raw .fastq files to generate quality control (QC) plots
Read counts were quantified and quasi-mapped to a Rattus norvegicus index transcriptome using the salmon tool (version 0.11.3). Index transcriptome was generated using the “RTR.fa.gz” file from PMID: 32749457. During read quantification in salmon, the --numBootstraps parameter was set to 30 bootstraps for each sample.
Quantified RNASeq reads were then processed for downstream analyses using the prepare_fish_for_sleuth function in the wasabi R package (version 1.0.1)
The sleuth R package (version 0.30.0) was used to test wasabi-processed RNASeq data for differential transcript expression (DTE)
To avoid inclusion of low-quality data, only transcripts with greater than 10 estimated counts in at least 50% of the samples were included in downstream DTE analyses. After filtering by this count cutoff, DTE models were generated in the sleuth package using a combination of the sleuth_prep, sleuth_fit, sleuth_lrt, and sleuth_wt functions. The sleuth_prep function initialized the sleuth object and read in the target mapping and bootstrap information from the provided annotation database and wasabi-processed data, respectively. The sleuth_fit function was then used to produce two smoothed linear models – “full” and “reduced.” In sleuth, the “full” model was fit using a smoothed linear model for experimental treatment (control vs. PFF), whereas the “reduced” model was fit assuming equal abundances by treatment. Next, the sleuth_lrt function was used to run a likelihood ratio test (LRT), which identified transcripts with a significantly improved fit in the “full” model compared to “reduced.” Lastly, the sleuth_wt function was used to run a separate Wald test on the abundance data, generating beta values – approximations of log fold change – for each tested transcript.
Assembly: Rat transcriptome from PMID: 32749457

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
Laser captured tissue was dissected into Trizol, then RNA isolated using a Zymo (R1016) RNA Clean and Concentrator Kit. RNA quality and quantity were assessed with an Agilent 2100 Bioanalyzer with the 6000 Pico Kit (5067-1513).
Libraries were prepared from 10 ng of total RNA using a TruSeq RNA Library Preparation kit ribosomal reduction from Illumina

treatment_protocol: Rats received intrastriatal injections of mouse alpha-synuclein preformed fibrils (16 micrograms total) or equal volume of sterile PBS as a control

value: Brain

tag: brain region

value: Substantia nigra pars compacta

value: Female

tag: cycle (if_female)

value: Estrus

value: Taconic #12141; NTac:SD-Tg (TH-EGFP) 24Xen

value: Intrastriatal injection of sterile Dulbecco's PBS


title: Female 22 PBS Control

value: Metestrus


title: GRZ_D_male6_d49_brain

value: GRZ-D

value: male


title: GRZ_D_male5_d49_skin

value: skin


title: Female 19 PBS Control

value: Proestrus


title: Hc7


title: ChIP_ASCL1_IMR32_BRM014_rep2

description: ASCL1 ChIP-seq in IMR32 cells treated with BRM014


title: GRZ_D_male5_d49_brain

value: brain


title: Female 18 PBS Control


title: Hc6


title: GRZ_D_male4_d49_skin


title: Hc5


title: GRZ_D_male4_d49_brain


title: ATAC_SKNDZ_DMSO_1h_rep2

description: ATAC-seq in SKNDZ cells treated with DMSO

data_processing:
ATAC-seq reads were aligned to the hg38 genome assembly using Bowtie v2.4.1.
Fragments with read qualities greater than 10 were considered for further analysis. 200 bp pseudofragments were created at the positions corresponding to the transposition sites, and peak calls were made using MACS 2.1.2 without modeling of fragment size. Reads within peaks were counted using bedtools.
The table of all counts was processed using DESeq2, using default parameters.
Bigwig files were created based on 200 bp pseudofragments, with intermediate files created using bedtools 2.28.0. All bigWig files are unscaled and require scaling before comparison across samples.
Assembly: hg38
Supplementary files format and content: Unscaled bigWig files of genome-wide coverage

source_name: SK-N-DZ

growth_protocol: Cells were cultured in 10% FBS MEM medium using standard approaches.

extract_protocol:
Nuclei were permeabilized and transposed according to the Omni-ATAC protocol.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with either 1 uM BRM014 or an equivalent volume of DMSO for 1 h prior to library construction.

value: SK-N-DZ

value: DMSO


title: Female 14 PFF treated

description:
RNA underwent ribosomal reduction (TruSeq RNA Library Preparation Kit from Illumina)
DGE_sleuth_object_female_LRT_040921

value: Intrastriatal injection of mouse alpha-synuclein preformed fibrils


title: Hc4

value: Colon, whole mucosa


title: GRZ_D_male3_d49_skin


title: ATAC_SKNDZ_DMSO_1h_rep1

value: WT


title: Female 13 PFF treated

value: Brain


title: Hc3

value: healthy controls (Hc)


title: GRZ_D_male3_d49_brain


title: GRZ_D_male2_d49_skin


title: Male 11 PBS Control

description:
RNA underwent ribosomal reduction (TruSeq RNA Library Preparation Kit from Illumina)
DGE_sleuth_object_male_WT_060921

value: Substantia nigra pars compacta

value: Male


title: Hc2


title: ATAC_SKNDZ_BRM014_1h_rep1

description: ATAC-seq in SKNDZ cells treated with BRM014


title: GRZ_D_male2_d49_brain


title: ATAC_SKNDZ_BRM014_1h_rep2


title: Hc1


title: ATAC_KELLY_DMSO_1h_rep2

description: ATAC-seq in KELLY cells treated with DMSO

source_name: KELLY

value: KELLY


title: GRZ_D_male1_d49_skin


title: LC8

value: lymphocytic colitis (LC)


title: LC7


title: ChIP_ASCL1_IMR32_BRM014_rep1


title: Female 16 PFF treated

value: Female

value: Taconic #12141; NTac:SD-Tg (TH-EGFP) 24Xen


title: Male 10 PBS Control

value: Intrastriatal injection of sterile Dulbecco's PBS


title: ATAC_KELLY_BRM014_1h_rep2

description: ATAC-seq in KELLY cells treated with BRM014


title: GRZ_D_male1_d49_brain

value: GRZ-D

value: male


title: Female 12 PFF treated

value: Metestrus


title: Male 8 PBS Control


title: ATAC_KELLY_BRM014_1h_rep1


title: GRZ_D_female8_d49_skin

value: skin

value: female


title: LC6


title: Male 5 PFF treated

description:
RNA underwent ribosomal reduction (TruSeq RNA Library Preparation Kit from Illumina)
DGE_sleuth_object_male_LRT_060921

value: Intrastriatal injection of mouse alpha-synuclein preformed fibrils


title: Male 9 PBS Control


title: LC5

value: Colon, whole mucosa


title: ATAC_IMR32_DMSO_1h_rep2

description: ATAC-seq in IMR32 cells treated with DMSO

value: WT

value: DMSO


title: ATAC_KELLY_DMSO_1h_rep1


title: Male 4 PFF treated

value: Brain


title: GRZ_D_female8_d49_brain

value: brain


title: GRZ_D_female7_d49_skin


title: Male 2 PFF treated

value: Substantia nigra pars compacta

value: Male


title: GRZ_D_female7_d49_brain


title: Male 3 PFF treated


title: LC2

value: lymphocytic colitis (LC)


title: LC4


title: LC1


title: ATAC_IMR32_BRM014_1h_rep1

description: ATAC-seq in IMR32 cells treated with BRM014


title: GRZ_D_female6_d49_brain


title: ATAC_IMR32_BRM014_1h_rep2


title: M2 cells

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

description: untreated

data_processing:
STAR 2.6.1 aligned to HG38
Quantified to Ensembl human genome 92
Normalized via Log2 Counts per million with offset of 1
Log normal shrinkage was used to remove batch effect between runs
Counts with a maximum of less than 2 were filtered out for a normal distribution
Assembly: HG38
Supplementary files format and content: tab-delimited text files, includes RPKM values for each sample

source_name: M2 machrophages

growth_protocol: U937 cells were cultured in RPMI-1640 supplemented with 10% FCS.

extract_protocol:
Total RNA was extracted from the cells according to manufacturer’s protocols with the RNeasy Mini Kit (Qiagen).
Libraries were prepared using the NEB Ultra II Library Preparation Kit and NEBNext® Multiplex Oligos for Illumina (Dual Index Primers Set 1) (New England BioLabs) following the manufacturer’s protocol.

treatment_protocol: U937 cells were differentiated into M1 and M2 macrophages in a two-step process by addition of TPA (10 nM, 3 days) followed by addition of IFN-γ or IL-4 , respectively.

value: U937 cells

tag: differentiation status

value: untreated


title: Male 1 PFF treated

value: Taconic #12141; NTac:SD-Tg (TH-EGFP) 24Xen


title: GRZ_D_female6_d49_skin

value: GRZ-D


title: GRZ_D_male7_d100_brain

value: male


title: CC4

value: collagenous colitis (CC)


title: M2 exo

description: MSC-exosome exposed

value: MSC-exosome exposed


title: ATAC_IMR32_DMSO_1h_rep1


title: MZCS_0403_male6_d39_skin

value: skin


title: CC3


title: M1 cells

description: untreated

source_name: M1 machrophages


title: ARVF_SoftGel_Passage6_rep3

city: Aurora

first: Timothy

last: McKinsey

state: CO

institute: University of Colorado Anschutz Medical Campus

data_processing:
Read quality of FastQ files was assessed using FastQC (v 0.11.5), with mean Phred scores higher than 30 for all bases.
Biological replicate paired-end sample FastQ's were aligned and mapped to the Rnor_6.0 building using the RefSeq genome annotation file from USCS (August 2018) with the HISAT2 aligner (v 2.1.0) with default parameters.
Once aligned, the replicate files were quantified and FPKM normalized to determine the overall gene expression using Cufflinks and Cuffnorm (v 2.2.1).
Samples were assessed using pairwise replicate correlation. All samples with >97% correlation scores were retained.
Each of the replicates per condition were then averaged and formatted as a GCT file to compare each condition using a single column for one group and another single column for a different group.
Differential expression was performed with Cuffnorm FPKM reads. Significance of expression values were calculated with R's standard two-tailed t-test and genes were selected based on FDR values >95% and log 2 fold changes >|0.58|
Assembly: Rnor_6.0
Supplementary files format and content: Excel workbook; raw counts

source_name: Heart

growth_protocol: Adult rat ventricular fibroblasts were cultured in DMEM/F-12 containing 20% fetal bovine serum

extract_protocol:
Total RNA was collected from ARVFs from three biological replicates using the Direct-zol RNA Miniprep Kit (Zymo Research R2051) according to the manufacturer’s instructions.
The University of Colorado Genomics and Microarray core facility performed mRNA selection and cDNA library preparation followed by 2x150 base pair fragment sequencing on an Illumina NovaSeq 6000 sequencing system.

treatment_protocol: ARVFs were cultured on tissue culture polystyrene or transferred to two-dimensional soft poly(ethylene glycol) norbornene hydrogel at passage 3 and passage 6 for 48 hours.

value: Heart

value: Fibroblast

value: Wild-type

value: Soft Gel; Passage 6


title: ARVF_SoftGel_Passage6_rep2


title: LC3

value: Colon, whole mucosa


title: ARVF_SoftGel_Passage6_rep1


title: M1 exo

description: MSC-exosome exposed


title: CC2


title: MZCS_0403_male4_d39_skin


title: MZCS_0403_male4_d39_brain

value: brain


title: CC1


title: ARVF_Plastic_Passage6_rep2

value: Plastic; Passage 6


title: ARVF_Plastic_Passage6_rep1


title: GS359_T2_ctrl_tmz, scRNAseq

city: Rotterdam

first: Martine

last: Lamfers

address: Dr. Molewaterplein 40

department: Neurosurgery

country: Netherlands

institute: Erasmus MC

description: SORTseq

data_processing:
Read alignment and count matrix was performed by Single Cell Discoveries, Utrecht. The poisson counting statistics corrected and UMI corrected counts were used for the analysis
Annotation of the count data with the per cell information was performed based on the FACS sorting layout of the 384-well plates
Assembly: hg38
Supplementary files format and content: count matrix (Tab-separated values files; NT=not treated and PT=temozolomide)

growth_protocol: Cells were grown in serum-free medium. Cell cultures were grown in Dulbecco’s modified Eagle’s medium-F12, supplemented with 1% Penicillin/Streptomycin, 2% B27, 20 ng/mL bFGF, 20 ng/mL EGF, and 5 μg/mL Heparin.

extract_protocol:
Cells were detached from culture plates with Accutase, resuspended in HBSS, and individual cells were FACS sorted into 384-well plates
The libraries were constructed according to the SORTseq protocol. Briefly, single cells sorted into 384-well plates were submitted for scRNAsequencing at Single Cell Discoveries, Utrecht. Libraries were constructed based on a semi-robotized implementation of the CELseq2 library protocol, and submitted for paired-end sequencing

treatment_protocol: Cells were treated weekly for 90 days using 1/4 of each cell culture specific IC50

value: Brain

value: patient-derived

value: glioblastoma

value: IDH-wildtype

value: not treated, temozolomide


title: GS359_T0_ctrl, scRNAseq

description: SORTseq

value: not treated


title: MZCS_0403_male3_d39_skin

value: male


title: GS359_T1_ctrl_tmz, scRNAseq

description: SORTseq


title: MZCS_0403_male3_d39_brain


title: GR

city: Zhengzhou

first: Kenan

last: Zhang

address: Jianshe Street

country: China

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Raw data were preprocessed by using fastp version0.19.6.
Filtered reads were aligned to the genome (GRCh38, hg38) assembly using Bowtie2.
Peaks were called using MACS version2.
Assembly: GRCh38, hg38
Supplementary files format and content: bigwig files were generated using deepTools.
Supplementary files format and content: peak txt files containing the specific binding region.
Library strategy: CUT&Tag

source_name: renal cell carcinoma

growth_protocol: Caki-1 cells were maintained according to the ATCC’s recommendation.

extract_protocol:
CUT&Tag was performed using NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (for Illumina) (Novoprotein) according to manufacturer’s instructions. In brief, Caki-1 cells were collected and bounded to Concanavalin A–coated beads. Subsequently, cells were resuspended in antibody buffer and incubated with primary antibodies against GR and secondary antibodies in order. The samples were incubated with pA-Tn5 transposase. After transposon activation and tagmentation, DNA was isolated, amplified, and purified to construct library.
The library for sequencing was constructed and NovoNGS DNA Clean beads were used for purification steps. The library was quantified with NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (for Illumina) and sequenced on an Illumina novaseq 150PE.

treatment_protocol: Untreated

value: Caki-1 cells

value: renal cell carcinoma

value: GR

value: untreated


title: ARVF_SoftGel_Passage3_rep3

value: Heart

value: Fibroblast

value: Soft Gel; Passage 3


title: MZCS_0403_male1_d39_skin

value: skin


title: ARVF_SoftGel_Passage3_rep2

value: Wild-type


title: GS785_T0_ctrl, scRNAseq

description: SORTseq


title: MZCS_0403_male6_d39_brain

value: brain


title: GS772_T0_ctrl; GS789_T0_ctrl, scRNAseq

description: SORTseq

value: Brain


title: GS785_T1_tmz, scRNAseq

description: SORTseq

value: patient-derived

value: temozolomide


title: MZM_0403_male7_d35_skin


title: MZCS_0403_male1_d39_brain


title: ARVF_Plastic_Passage6_rep3

value: Plastic; Passage 6


title: ARVF_SoftGel_Passage3_rep1


title: ARVF_Plastic_Passage3_rep3

value: Plastic; Passage 3


title: KO-iMGLs, LPS treated, biol rep 1

city: Beijing

first: Xiaodan

last: Hu

address: Medical Building 304

institute: Tsinghua University

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequenced reads were trimmed for adapator sequence, and masked for low-complexity or low-quality seqence, then mapped to GRCh38
The gene expression count matrix was obtained by Cufflinks
Assembly: Homo_sapiens.GRCh38.87
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: iMGLs were maintained in differentiation medium in humidified medium with 5% CO2 at 37°C

extract_protocol:
Cells were digested into single cells and suspended in culture medium. Then total RNAs were extracted using TRIzol reagent
mRNA-seq library was prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, E7530) according to the manufacturer’s instruction

value: human pluripotent stem cells, H1

value: microglia

value: KO

value: LPS


title: KO-iMGLs, LPS treated, biol rep 2


title: KO-iMGLs, LPS and BMS treated, biol rep 1

value: LPS and BMS


title: WT-iMGLs, LPS treated, biol rep 2

value: WT


title: MZM_0403_male7_d35_brain

value: male


title: ARVF_Plastic_Passage3_rep2

value: Heart

value: Fibroblast


title: KO-iMGLs, LPS and BMS treated, biol rep 2


title: GS772_T1_ctrl_tmz, scRNAseq

description: SORTseq

value: glioblastoma

value: IDH-wildtype

value: not treated, temozolomide


title: GS789_T1_ctrl, scRNAseq

description: SORTseq

value: Brain

value: not treated


title: MZM_0403_male4_d35_skin

value: skin


title: MZM_0403_male4_d35_brain

value: brain


title: ARVF_Plastic_Passage3_rep1

value: Wild-type

value: Plastic; Passage 3


title: KO-iMGLs, biol rep 3

value: human pluripotent stem cells, H1

value: microglia

value: control


title: GS785_T1_ctrl; GS789_T1_tmz, scRNAseq

description: SORTseq

value: patient-derived


title: KO-iMGLs, biol rep 2

value: KO


title: Kcnj16_m1 [BX109]

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida, College of medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website 2 directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: reference genome was built using Hisat2 v2.0.5 a
Supplementary files format and content: FPKM

source_name: Kidney

extract_protocol:
RNA was extracted using the Trizol reagent according to the manufacturer's protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification). The library was checked with Qubit and real-time PCR for quantification and a bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Kidney

tag: strain background

value: Dahl Salt Sensitive rat

value: male


title: KO-iMGLs, biol rep 1


title: GS785_T2_ctrl_tmz, scRNAseq

description: SORTseq

value: glioblastoma


title: GS789_T2_ctrl_tmz, scRNAseq

description: SORTseq

value: IDH-wildtype


title: Kcnj16_m1 [BX104]


title: MZM_0403_male2_d35_skin


title: MZM_0403_male2_d35_brain


title: WT-iMGLs, biol rep 3

value: WT


title: Kcnj16_m1 [BX103]


title: ChIP_input_IMR32_DMSO_rep2

description: Input control DNA in IMR-32 cells treated with DMSO

source_name: IMR-32 cells

growth_protocol: IMR-32 cells were cultured in 10% FBS MEM medium using standard approaches.

extract_protocol:
Lysates were obtained from sonicated nuclei crosslinked with formaldehyde, and protein-DNA complexes were isolated by immunoprecipitation.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 1 uM BRM014 or DMSO for 24 h.

tag: marker

value: DMSO

tag: chip antibody vendor

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: MZM_0403_male13_d35_skin

tag: strain


title: WT-iMGLs, biol rep 1

value: Brain

tag: cell line

tag: genotype


title: Kcnj16_m1 [BX101]

tag: tissue

tag: Sex


title: ChIP_input_IMR32_DMSO_rep1

tag: chip antibody


title: WT-iMGLs, LPS treated, biol rep 1

tag: treatment

value: LPS


title: MZM_0403_male12_d35_skin

value: skin

tag: age in_days


title: ChIP_input_IMR32_BRM014_rep2

description: Input control DNA in IMR-32 cells treated with BRM014


title: SS_WT [BX108]


title: MZM_0403_male13_d35_brain

value: brain


title: S8PB.RNA

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) pipeline (v1.12.1).
Downstream analyses were mainly conducted with Seurat R package (v4.1.1).
Assembly: human: hg38; EBV: GCF_002402265.1
Supplementary files format and content: barcodes.tsv:
Supplementary files format and content: genes.tsv
Supplementary files format and content: matrix.mtx

source_name: peripheral blood

extract_protocol:
Individual cells were isolated by density gradient centrifugation using Ficoll-Paque Plus medium (GE Healthcare) and washed with Ca/Mg-free PBS. After removal of red blood cells, the remaining were isolated by centrifuged at 400g for 10 min at 4°C. The supernatant was discarded and the cells were resuspended by phosphate buffered saline to obtain single-cell suspension, which were then loaded onto microwell chip using the Singleron Matrix®Single Cell Processing System.
The scRNA-seq libraries were constructed according to the protocol of the FocuSCOPE® Single Cell mRNA x EBV Library Kit (Singleron).

value: peripheral blood

tag: cell type_enrichment

tag: disease

value: healthy control

tag: subject

value: subject 8


title: Kcnj16_m1 [BX102]


title: ChIP_input_IMR32_BRM014_rep1


title: MZM_0403_male12_d35_brain


title: WT-iMGLs, biol rep 2

value: human pluripotent stem cells, H1

tag: cell type

value: microglia

value: control


title: GRZ_D_male6_d35_skin

value: GRZ-D


title: ChIP_SUZ12_IMR32_DMSO_rep2

description: anti-SUZ12 ChIP in IMR-32 cells treated with DMSO

value: Active Motif


title: SS_WT [BX107]

value: Kidney

tag: strain background

value: Dahl Salt Sensitive rat

value: male


title: S8BM.RNA

source_name: bone marrow

value: bone marrow


title: S7PB.RNA

value: subject 7


title: S7BM.RNA


title: SS_WT [BX074]


title: GRZ_D_male6_d35_brain


title: ChIP_SUZ12_IMR32_BRM014_rep2

description: anti-SUZ12 ChIP in IMR-32 cells treated with BRM014

tag: marker

value: WT


title: SS_WT [BX073]


title: GRZ_D_male5_d35_skin


title: S6PB.RNA

value: EBV-HLH

value: subject 6


title: ChIP_SUZ12_IMR32_BRM014_rep1

tag: chip antibody vendor


title: GRZ_D_male5_d35_brain

value: brain


title: GRZ_D_male4_d35_skin

value: skin


title: ChIP_RING1B_IMR32_DMSO_rep2

description: anti-RING1B ChIP in IMR-32 cells treated with DMSO

value: DMSO

value: Cell Signaling

tag: chip antibody cat. #


title: S6BM.RNA


title: ChIP_RING1B_IMR32_DMSO_rep1

tag: chip antibody lot/batch #


title: S5BM.RNA

value: CAEBV

value: subject 5


title: GRZ_D_male4_d35_brain

tag: strain


title: S4TPB.RNA

value: peripheral blood

value: hematopoietic stem cell transplantation

value: subject 4


title: S4TBM.RNA


title: ChIP_RING1B_IMR32_BRM014_rep1

description: anti-RING1B ChIP in IMR-32 cells treated with BRM014


title: GRZ_D_male3_d35_brain

value: GRZ-D


title: GRZ_D_male3_d35_skin


title: S4PB.RNA


title: ChIP_RING1B_IMR32_BRM014_rep2


title: GRZ_D_male2_d35_brain


title: S4HC.RNA


title: ChIP_SUZ12_IMR32_DMSO_rep1

value: Active Motif


title: ChIP_H3K4me3_IMR32_DMSO_rep1

description: anti-H3K4me3 ChIP in IMR-32 cells treated with DMSO

value: Millipore


title: S5PB.RNA


title: ChIP_H3K4me3_IMR32_BRM014_rep2

description: anti-H3K4me3 ChIP in IMR-32 cells treated with BRM014


title: SS_WT [BX095]

value: Kidney

value: Dahl Salt Sensitive rat

value: male


title: GRZ_D_male1_d35_skin


title: S4BM.RNA

value: bone marrow


title: ChIP_H3K4me3_IMR32_BRM014_rep1

value: WT


title: Differentiated placenta stem cells, replicate 6

type: RNA

city: Hamilton

first: Sonya

last: Kouthouridis

state: ON

address: 1280 Main St W

department: Chemical Engineering

country: Canada

institute: McMaster University

description: Gene expression data from placental stem cells RCB-4940 cultured in differentiation medium for 8 days

hyb_protocol: Samples were hybridized for 16 hr at 45°C using Affymetrix WT PLUS Kit.

scan_protocol: Affymetrix GeneChip™ 3000 instrument system

data_processing: SST-RMA gene-level probeset summary with standard settings of the Transcriptome Analysis Console (TAC; version 4.0.3; Thermo Fisher Scientific)

label: biotin

source_name: trophoblast stem cell monolayer cultured 8 days

label_protocol: Total RNA was amplified using the WT PLUS Reagent Kit (Thermo Fisher Scientific Inc., Waltham, USA).

growth_protocol: Blastocyst-derived placental stem cells (PSCs, RCB-4940, female) were cultured in PSC expansion medium (PSCM) consisting of DMEM/F12 + GlutaMAX supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% penicillin-streptomycin, 0.3% BSA, 1% ITS media supplement, 1.5 ug/ml L-ascorbic acid, 50 ng/ml EGF, 2 uM CHIR99021, 0.5 uM A83-01, 1 uM SB431542, 0.8 mM VPA and 5 uM Y27632 or PSC differentiation medium consisting of DMEM/F12 + GlutaMAX supplemented with 0.1 mM 2-mercaptoethanol, 0.5% penicillin-streptomycin, 0.3% BSA, 1% ITS media supplement, 2.5 uM Y27632, 2 uM forskolin, and 4% KSR. BeWo 30 cells were cultured in expansion medium consisting of DMEM supplemented with 10% FBS and 1% penicillin-streptomycin and then differentiation medium consisting of DMEM supplemented with 10% FBS, 1% penicillin-streptomycin, 50 uM forskolin and 50 ng/mL of EGF.

extract_protocol: Samples were lysed and RNA extraction was performed using the PurelinkTM RNA Mini kit (Thermo Fisher Scientific, 12183018A) following the manufacturer’s instructions.

treatment_protocol: Cells were cultured according to their expansion or differentiation protocols.

tag: culture medium type

value: Differentiation

tag: culture days

tag: seeding density


title: Differentiated placenta stem cells, replicate 5


title: GRZ_D_male1_d35_brain

extract_protocol:
Brain and skin tissue samples were prepared from each specimen and RNA was extracted using the RNeasy Mini Kit (Quiagen).
Library preparation was done using Illumina’s TruSeq RNA v2 kit following the manufacturer’s instruction.

tag: tissue

value: brain

tag: Sex


title: S3PB.RNA

tag: treatment

value: subject 3


title: Differentiated placenta stem cells, replicate 4


title: Differentiated placenta stem cells, replicate 1


title: Differentiated placenta stem cells, replicate 3


title: ChIP_H3K4me3_IMR32_DMSO_rep2

value: DMSO

tag: chip antibody


title: GRZ_D_male2_d35_skin

source_name: skin

value: skin

tag: age in_days


title: ChIP_H3K27me3_IMR32_DMSO_rep2

description: anti-H3K27me3 ChIP in IMR-32 cells treated with DMSO


title: MZM_0403_male6_d21_skin


title: Undifferentiated placenta stem cells, replicate 3

description: Gene expression data from placental stem cells RCB-4940 cultured in expansion medium for 8 days

value: Expansion


title: Undifferentiated placenta stem cells, replicate 6


title: S3HC.RNA

tag: cell type_enrichment

tag: disease

value: CAEBV


title: ChIP_H3K27me3_IMR32_DMSO_rep1


title: MZM_0403_male6_d21_brain

source_name: brain


title: Undifferentiated placenta stem cells, replicate 2

tag: cell type


title: S3BM.RNA

tag: subject


title: Undifferentiated placenta stem cells, replicate 4


title: ChIP_H3K27me3_IMR32_BRM014_rep2

description: anti-H3K27me3 ChIP in IMR-32 cells treated with BRM014

tag: marker


title: MZM_0403_male5_d21_skin


title: ChIP_H3K27me3_IMR32_BRM014_rep1

tag: chip antibody vendor


title: MZM_0403_male5_d21_brain


title: K562.LTR.growth.B3

city: Xiamen

first: Dongyang

last: Xu

state: Fujian

address: 668 Jimei Road

institute: Huaqiao University

description: K562 insertional mutagenesis cell library grown for 48 hours plus one month after lentivirus transfection bioreplica 3

data_processing:
Only paired-end raw reads with the read 2 starting with LTR tag “GCCTTGTGTGTGGTAGATCCACAGATCAAGGATATCTTGTCTTCGTTGGGAGTGAATTAGCCCTTCCA” and each base of each read having Phred quality score > 20 were selected.
Such reads were aligned to the GRCh37/hg19 using BWA-MEM (v0.7.12) with default settings.
Only read-pairs where both read 1 and 2 uniquely mapped to the genome with appropriate configuration and spacing were kept.
The insertion position was defined as the first base upstream of the LTR tag in the read 2.
Read count of each insertion position was calculated and normalized to total number of uniquely aligned reads of each sample.
Assembly: GRCh37/hg19
Supplementary files format and content: Processed data are in BED files containing coordinates of lentivirus insertion sites. The 5th column shows the normalized count of each insertion position.

growth_protocol: Human liver hepatocellular carcinoma cell line HepG2 and human chronic myeloid leukemia cell line K562 were maintained in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (ExCell Bio, Uruguay) and 1% penicillin-streptomycin (Gibco) at 37℃ in 5% CO2.

extract_protocol:
DNA was isolated with TIANamp Genomic DNA Kit (Tiangen)
1 μg of genomic DNA was used as the template for a linear PCR in a 50 μl reaction system containing 1x Taq Buffer, 2.5 U Taq DNA polymerase (Tiangen), 4 μl of 2.5 mM dNTP mix (Takara), and 0.3 μM biotinated primer 3-LTR_prime (5’-biotin-GCTCAACTGGTACTAGCTTGTAGCACCATCC-3’), which anneals to the 3’ LTR region of the lentivirus vector. 50 cycles of linear PCR were performed with 2.5 U Taq DNA polymerase (Tiangen) added at the beginning and immediately after 25 cycles of the reaction. PCR conditions were as follows: 94℃ for 5 min; 50 cycles of 94℃ for 30 s, 55℃ for 30 s and 72℃ for 30 s; 72℃ for 5 min. After the linear amplification, the PCR products were mixed with 10 μl of BeaverBeadsTM Streptavidin (Beaver) and incubated for 2 h at room temperature with shaking (400 rpm) in a metal bath. Beads were then collected with a magnetic stand and washed with 300 μl Binding/Wash buffer (10 mM Tris-HCl (pH 7.5), 1 M NaCl, 1 mM EDTA, 0.1% Tween-20) for 6 times, and with 65°C H2O for twice. For the second strand synthesis, beads were resuspended in a 24 μl reaction volume containing 1x Klenow Fragment Buffer (NEB), 2 μl of 2.5 mM dNTP mix (Takara), 6.25 μM P5_N6 primer (5’-CTACACGACGCTCTTCCGATCTNNNNNN-3’) and pre-incubated at 15℃ for 20 min. Then, 2 U of Klenow polymerase (NEB) were added and the mixtures were incubated at the following conditions: slow ramp at 0.5℃ per minute from 15℃ to 25℃ followed by 30 min incubation; then slow ramp at 0.5℃ per minute to 37℃ followed by 1 h incubation. Beads were captured with a magnetic stand and washed gently with 300 μl of 4℃ water. To construct the library for NGS, nested PCR was performed. First, beads were resuspended in a 25 μl PCR reaction volume containing 1x Taq Buffer, 1.25 U Taq DNA polymerase (Tiangen), 2 μl of 2.5 mM dNTP mix (Takara), 0.5 μM of primer P5 (5’-CTACACGACGCTCTTCCGATCT-3’) and 0.5 μM of primer 3-LTR_Nest (5’-CCTGGTGTGTAGTTCTGCCAATCAG-3’). PCR conditions were as follows: 94℃ for 3 min; 20 cycles of 94℃ for 30 s, 55℃ for 30 s and 72℃ for 30 s; 72℃ for 7 min. Second, 5 μl of the PCR products from the previous step were used for the next round of PCR in 50 μl volume containing 1x Taq Buffer, 2.5 U Taq DNA polymerase (Tiangen), 4 μl of 2.5mM dNTP mix (Takara), 0.4 μM of primer Illumina_P5 (5’-AATGATACGGCGACCACCGAGAtctACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and 0.4 μM of primer Illumina_P7-3LTR (5’- CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCCTTGTGTGTGGTAGATCCACAG-3’). PCR conditions were as follows: 94℃ for 3 min; 15 cycles of 94℃ for 30 s, 55℃ for 30 s and 72℃ for 30 s; 72℃ for 7 min. PCR products were purified with 1.2x volumes of VAHTS DNA Clean Beads (Vazyme) to a final volume of 21 μl. The concentration of PCR products was measured by Qubit 3.0 fluorometer using Equalbit dsDNA HS Assay Kit (Vazyme). To achieve a better coverage, five libraries were prepared in parallel from 1 μg of genomic DNA and pooled together.

tag: cell line

value: human chronic myeloid leukemia cell

tag: transfection

value: lentiviral insertional mutagenesis library


title: Undifferentiated placenta stem cells, replicate 1


title: ATAC_IMR32_WT_DMSO_Slate_rep2

description: ATAC-seq in late S IMR-32 cells treated with DMSO vehicle control

treatment_protocol: IMR-32 cells expressing tFucci(CA)5 were treated with either 1 uM BRM014 or an equivalent volume of DMSO for 4 h. Immediately prior to transposition, cells were sorted based on the FUCCI fluorescent cell cycle indicator status.

value: IMR-32 cells

tag: phase

value: S late


title: K562.LTR.growth.B2

description: K562 insertional mutagenesis cell library grown for 48 hours plus one month after lentivirus transfection bioreplica 2


title: Differentiated BeWo b30 cell, replicate 5

description: Gene expression data from BeWo b30 cells cultured in expansion medium for 2 days and differentiation medium for 2 more days.

source_name: trophoblast cell line monolayer cultured 4 days

value: BeWo b30

tag: culture medium type


title: MZM_0403_male4_d21_skin

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v1.8.4.
The RNA sequencing reads were aligned to the N. furzeri genome assembly (assembly version Nfu_20150522, gene annotation version 150922)  using STAR 2.5.1b (parameters: --alignIntronMax 100000, --outSJfilterReads Unique) (PMID: 23104886).
For each gene, all reads that map uniquely to one genomic position were counted with FeatureCounts 1.5.0 under default settings (PMID: 24227677).
Assembly: Genome Nfu_20150522 and annotation 20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (https://nfingb.leibniz-fli.de) (PMID: 26638077)
Supplementary files format and content: csv file containing raw read counts per gene over all samples

tag: strain


title: MZM_0403_male4_d21_brain


title: K562.LTR.growth.B1

description: K562 insertional mutagenesis cell library grown for 48 hours plus one month after lentivirus transfection bioreplica 1


title: K562.LTR.control.B3

description: K562 insertional mutagenesis cell library grown for 48 hours after lentivirus transfection bioreplica 3


title: ATAC_IMR32_WT_DMSO_Slate_rep1


title: ATAC_IMR32_WT_DMSO_Searly_rep2

description: ATAC-seq in early S IMR-32 cells treated with DMSO vehicle control

value: S early


title: MZM_0403_male3_d21_skin


title: ATAC_IMR32_WT_DMSO_Searly_rep1


title: MZM_0403_male2_d21_skin


title: ATAC_IMR32_WT_DMSO_G2M_rep2

description: ATAC-seq in G2/M IMR-32 cells treated with DMSO vehicle control


title: ATAC_IMR32_WT_DMSO_G2M_rep1


title: MZM_0403_male2_d21_brain


title: ATAC_IMR32_WT_DMSO_G1late_rep2

description: ATAC-seq in late G1 IMR-32 cells treated with DMSO vehicle control

value: G1 late


title: MZM_0403_male1_d21_skin

value: male


title: ATAC_IMR32_WT_DMSO_G1late_rep1


title: MZM_0403_male3_d21_brain


title: ATAC_IMR32_WT_DMSO_G1early_rep2

description: ATAC-seq in early G1 IMR-32 cells treated with DMSO vehicle control

value: G1 early


title: HepG2.LTR.control.B2

description: HepG2 insertional mutagenesis cell library grown for 48 hours after lentivirus transfection bioreplica 2

value: human liver hepatocellular carcinoma cell


title: ATAC_IMR32_WT_DMSO_G1early_rep1


title: MZCS_0403_male6_d21_skin


title: ATAC_IMR32_WT_BRM014_Slate_rep2

description: ATAC-seq in late S IMR-32 cells treated with BRM014


title: MZM_0403_male1_d21_brain


title: ATAC_IMR32_WT_BRM014_Slate_rep1


title: HepG2.LTR.control.B1

description: HepG2 insertional mutagenesis cell library grown for 48 hours after lentivirus transfection bioreplica 1


title: ATAC_IMR32_WT_BRM014_Searly_rep2

description: ATAC-seq in early S IMR-32 cells treated with BRM014


title: HepG2.LTR.growth.B3

description: HepG2 insertional mutagenesis cell library grown for 48 hours plus one month after lentivirus transfection bioreplica 3


title: HepG2.LTR.growth.B2

description: HepG2 insertional mutagenesis cell library grown for 48 hours plus one month after lentivirus transfection bioreplica 2


title: HepG2.LTR.control.B3

description: HepG2 insertional mutagenesis cell library grown for 48 hours after lentivirus transfection bioreplica 3


title: K562.LTR.control.B2

description: K562 insertional mutagenesis cell library grown for 48 hours after lentivirus transfection bioreplica 2


title: HepG2.LTR.growth.B1

description: HepG2 insertional mutagenesis cell library grown for 48 hours plus one month after lentivirus transfection bioreplica 1


title: K562.LTR.control.B1

description: K562 insertional mutagenesis cell library grown for 48 hours after lentivirus transfection bioreplica 1


title: MZCS_0403_male5_d21_skin


title: RNA-4sU_SKNDZ_DMSO_rep1

description: mRNA in 4sU-treated SK-N-DZ cells treated with DMSO

data_processing:
RNA-seq reads were aligned to the hg38 genome assembly using HISAT-3n
Fragments with read qualities greater than 10 were considered for further analysis. Of these, reads mapping to the coding strand of exonic regions containing 5 or more T>C conversions were counted using htseq, with gene definitions obtained from the refGene table of RefSeq genes in the UCSC Table Browser.
The table of all counts was processed using DESeq2, using default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file including total numbers of reads containing 5 or more T>C conversions overlapping each transcript for each sample.

source_name: SK-N-DZ cells

growth_protocol: IMR-32 cells were cultured in 10% FBS MEM medium using standard approaches, KELLY and SK-N-DZ were cultured in 10% FBS DMEM medium using standard approaches.

extract_protocol:
RNA was extracted from cells at ~50% confluency using TRIzol reagent. RNA from 4sU-treated cells was thiol-modified by exposure to iodoacetate, or left untreated. Following this step, mRNA was enriched by poly(dT) capture. RNA was fragmented, converted to DNA, then size-selected for 200-400 bp DNA fragments before PCR amplification.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Non-engineered cells were treated with either 1 uM BRM014 or an equivalent volume of DMSO. Engineered auxin-inducible degron (SMARCA4-mAID) cells were treated with either 500 uM auxin (indole-3-acetic acid) or an equivalent volume of ethanol. Cells were treated 500 uM 4-thio-uridine (4sU) for 2 h prior to harvesting, or left untreated.

value: SK-N-DZ

tag: genotype

value: WT


title: MZCS_0403_male6_d21_brain

tag: tissue

value: brain


title: RNA-4sU_SKNDZ_DMSO_rep2

value: DMSO


title: ATAC_IMR32_WT_BRM014_Searly_rep1


title: MZCS_0403_male4_d21_skin

value: skin

tag: Sex


title: MZCS_0403_male5_d21_brain


title: RNA-4sU_SKNDZ_BRM014_rep2

description: mRNA in 4sU-treated SK-N-DZ cells treated with BRM014

tag: treatment


title: RNA-4sU_SKNDZ_BRM014_rep1


title: MZCS_0403_male3_d21_skin


title: ATAC_IMR32_WT_BRM014_G1late_rep2

description: ATAC-seq in late G1 IMR-32 cells treated with BRM014


title: MZCS_0403_male4_d21_brain


title: ABC5

type: protein

city: Dallas

first: Chengsong

last: Zhu

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

description: 8 positive controls (Higcontrol 1,HIgcontrol2,HIgcontrol3,HIgcontrol4  and MIgcontrol1,MIgcontrol2,MIgcontrol3 and MIgcontrol4) were also imprinted on the arrays as positive controls.

hyb_protocol: not provided

scan_protocol: not provided

data_processing: NFI were normalized by robust linear model using build-in Ig control with various dilutions

molecule: protein

source_name: cell culture supernatent

label_protocol: Mouse supernatent samples were first treated with DNAse I to remove free-DNA and then applied onto antoantigen arrays with 1:50 dilution. The autoantibodies binding to the antigens on the array were detected with cy3-labeled anti-human IgG  and the array slides were scanned with Genepix 4400A scanner with laser wavelengths 532nm for cy3 and 635nm for cy5 to generate Tiff images.  Genepix Pro 7.0 software is used to analyze the image and generate the Genepix report (GPR) files (Molecular Devices, Sunnyvale, California, USA). The net fluorescent intensity (NFI) of each antigen was generated by subtracting the local background and negative control (Phosphate buffered saline or simplified as PBS) signal.

extract_protocol: Serum samples from recipients collected as per routine protocol as defined above were procured from histocompatibility lab after IRB approval. Sera of all subjects were aliquoted and stored at -80ºC.

tag: slide

tag: block


title: PBS

tag: condition

value: Negative control


title: ATAC_IMR32_WT_BRM014_G2M_rep2

description: ATAC-seq in G2/M IMR-32 cells treated with BRM014


title: AdV-D24-ICOSL-CD40L + Pseudovirus SARS-CoV-2 100 VP/mL [S5]

city: Warsaw

first: Monika

middle: Maria

last: Staniszewska

address: Poleczki 19

department: CEZAMAT

country: Poland

institute: Warsaw University of Technology

description:
"S5" column
AdV1+pseudo-SARS-CoV-2 IC100

data_processing:
Reads were trimmed of nucleotides from both ends if their quality in the Phred scale was below 30, afterwards only reads longer than 40 bp were kept (cutadapt 3.5-m 40 --quality-base 30).
Reads were aligned to the Vero_WHO_p1.0 reference genome using the align function from the Rsubread package (ver. 2.8.2)
Only reads with the flags 99, 147, 83, or 163 were kept for further analysis.
Reads were assigned to genes, as defined by the RefSeq annotation (GCF_015252025.1_Vero_WHO_p1.0_genomic.gtf) using the featureCounts function from Rsubread package (ver. 2.8.2).
Assembly: Vero_WHO_p1.0 reference genome with RefSeq annotation (GCF_015252025.1_Vero_WHO_p1.0_genomic.gtf)
Supplementary files format and content: counts.csv - comma separated value text file format with gene id, gene position and the number of assigned reads. Column names: "GeneID",  "Chr" , "Start" , "End" , "Strand", "S1", "S2" , "S3" , "S4", "S5", "S6".

organism: Chlorocebus aethiops

source_name: kidney

growth_protocol: The VERO E6 cells were cultured in the Eagle’s Minimum Essential Media (EMEM) ATCC supplemented with 1% of penicillin/streptomycin (Gibco Laboratories, USA) and 10% fetal bovine serum.

extract_protocol: We prepared 1 × 106 cryo-conserved cells of Vero E6 treated with the platform factors (plus untreated control) for RNA isolation. We obtained 25 µL of the total volume of each sample containing ≥ 1 µg RNA with a concentration of ≥ 40 ng/µL.

treatment_protocol: We previously designed adenovirus AdV-D24- inducible co-stimulator ligand (ICOSL)-CD40L (AdV1) which selectively replicates in cancer but not in healthy cells and it is armed with two potent co-stimulatory molecules: inducible co-stimulator ligand (ICOSL) and CD40 ligand (CD40L, CD154). We tested several mechanisms by which adenoviruses (AdV1 or AdV2 without ICOSL and CD40L) act as adjuvants and tested the efficiency of adenoviruses in combination with recombinant spike protein rRBD in the induction of innate and adaptive immunity. The following adenoviruses in the stock concentration were used: AdV-D24-ICOSL-CD40L (5.2 × 1011 VP/mL) named AdV1 and AdV5.3-d24-E3 (7.7 × 1012 VP/mL) named AdV2. The viral particle concentration was calculated using the method described by Sobotka et al. 2022. The extinction coefficient was 1.1 × 1012 viral particles per OD 260 unit. We calculated VP using Equation (3): VP = A260 × dilution factor × 1.1 × 1012/mL, (3) where the 260 nm/280 nm ratio was 2.0 and the absorbance at 260 nm was 0.1–1.0 OD unit. Adenoviruses were characterized by performing titration (VP/mL) expanded in the NCI-H226 cell line growing in the RPMI 1640 Medium (Gibco Laboratories, USA) supplemented with 1% of penicillin/streptomycin (Gibco Laboratories, USA) and 10% fetal bovine serum (FBS, Gibco Laboratories, USA). The OD-260-SDS method was used to determine the concentration of virus particles (VP/mL) in NCI-H226 (extinction coefficient of 1.1 × 1012/Abs 260 unit) growing in ATCC-formulated RPMI-1640 Medium (ATCC USA) supplemented with fetal bovine serum (ATCC, USA) to a final concentration of 10%. The TCID50 assay was also performed to quantify viral titers by determining the concentration at which 50% of the infected cells display cytopathic effect CPE; AdV1: 3.2 × 103 TCID50/mL and AdV2: 3.2 × 106 TCID50/mL. Due to the high variability of these assays, the ratio between TCID50/VP =1:9, in the study ratio, VP/mL/IU/mL was used and was comparable between tested stocks. The viruses were documented by scanning electron microscopy SEM Hitachi SU8230 (Japan).

value: kidney

value: Vero E6

value: infection with AdV-D24-ICOSL-CD40L + Pseudovirus SARS-CoV-2 100 VP/mL


title: AdV-D24-WT + Pseudovirus SARS-CoV-2 100 VP/mL [S6]

description:
"S6" column
AdV2+pseudo-SARS-CoV-2 IC100

value: infection with AdV-D24-WT + Pseudovirus SARS-CoV-2 100 VP/mL


title: Pseudovirus SARS-CoV-2 100 VP/mL [S4]

description:
"S4" column
Pseudo-SARS-CoV-2 IC100

value: infection with Pseudovirus SARS-CoV-2 100 VP/mL


title: AdV-D24-ICOSL-CD40L-100 VP/mL [S2]

description:
"S2" column
AdV1 IC100

value: infection with AdV-D24-ICOSL-CD40L-100 VP/mL


title: AdV-D24-WT 100 VP/mL [S3]

description:
"S3" column
AdV2 IC100

value: infection with AdV-D24-WT 100 VP/mL


title: VeroE6 cell line untreated (Control) [S1]

description:
"S1" column
Control

value: untreated


title: MZCS_0403_male2_d21_skin

city: Jena

first: Philipp

last: Koch

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

value: male

tag: age in_days


title: MZCS_0403_male3_d21_brain


title: ATAC_IMR32_WT_BRM014_G2M_rep1

city: Houston

first: H. Courtney

last: Hodges

institute: Baylor College of Medicine

value: IMR-32 cells


title: MZCS_0403_male2_d21_brain


title: MZ5


title: Female brain,replicate 3, scRNA_seq

first: IOZ

last: CAS

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

description: 10X Genomics

data_processing:
Alignment, barcode assignment, and UMI counting were preceesed by CellRanger pipelines v4.0.0
Assembly: https://doi.org/10.11922/sciencedb.01162
Supplementary files format and content: Tab-separated values files and matrix files

organism: Hylyphantes graminicola

source_name: Brain

extract_protocol:
Brains (35–40 mixed-aged adults) were dissected in cold 1X PBS solution using fine forceps and transferred to a tube containing MACS ® Tissue Storage Solution. The brain tissue was dissociated into single cells using the Adult Brain Dissociation kit.
Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.

value: Brain


title: Female brain,replicate 2, scRNA_seq

description: 10X Genomics


title: Female brain,replicate 1, scRNA_seq

description: 10X Genomics


title: FO5


title: MZCS_0403_male1_d21_skin


title: MZCS_0403_male1_d21_brain


title: GRZ_D_male8_d21_skin

value: GRZ-D


title: ABC4


title: ATAC_IMR32_WT_BRM014_G1late_rep1

value: G1 late


title: MZ4


title: GRZ_D_male8_d21_brain

value: brain


title: ATAC_IMR32_WT_BRM014_G1early_rep1

description: ATAC-seq in early G1 IMR-32 cells treated with BRM014

value: G1 early


title: FO3


title: GRZ_D_male7_d21_brain


title: MZ2


title: Male brain,replicate 1, scRNA_seq

description: 10X Genomics


title: ChIP_input_SKNDZ_rep1

description: Input control DNA in SK-N-DZ cells

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie v2.4.1.
Fragments with read qualities greater than 10 were considered for further analysis. Fragments were extended to 200 bp, Reads within coding regions were counted using bedtools.
Bigwig files were created by extending fragments to 200 bp, with intermediate files created using bedtools 2.28.0. All bigWig files are unscaled and require scaling before comparison across samples.
Genome_build: hg38
Supplementary_files_format_and_content: Unscaled bigWig files of genome-wide coverage

treatment_protocol: No treatments were performed.

value: SK-N-DZ

value: WT

tag: chip antibody

value: none (input)

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: RNA-4sU_KELLY_DMSO_rep2

description: mRNA in 4sU-treated KELLY cells treated with DMSO

source_name: KELLY cells

value: KELLY

value: DMSO


title: RNA-4sU_KELLY_unconv_rep2

description: mRNA in untreated KELLY cells


title: RNA-4sU_KELLY_DMSO_rep1


title: RNA-4sU_KELLY_unconv_rep1

description: mRNA in untreated KELLY cells


title: RNA-4sU_IMR32_DMSO_rep2

description: mRNA in 4sU-treated IMR-32 cells treated with DMSO


title: RNA-4sU_IMR32-mAID_EtOH_rep1

description: mRNA in 4sU-treated SMARCA4-mAID IMR-32 cells treated with ethanol

value: ethanol


title: RNA-4sU_KELLY_BRM014_rep2

description: mRNA in 4sU-treated KELLY cells treated with BRM014


title: ChIP_SMARCA4_SKNDZ_rep2

description: anti-SMARCA4 ChIP in SK-N-DZ cells

tag: chip antibody vendor

value: Cell Signaling


title: ChIP_SMARCA4_SKNDZ_rep1

description: anti-SMARCA4 ChIP in SK-N-DZ cells

tag: cell line


title: Male brain,replicate 2, scRNA_seq

description: 10X Genomics


title: FO4


title: ATAC_IMR32_WT_BRM014_G1early_rep2


title: RNA-4sU_KELLY_BRM014_rep1


title: ABC3


title: RNA-4sU_IMR32_DMSO_rep1


title: GRZ_D_male6_d21_brain


title: RNA-4sU_IMR32-mAID_auxin_rep2

description: mRNA in 4sU-treated SMARCA4-mAID IMR-32 cells treated with auxin

value: auxin


title: MZ1


title: MZ3


title: RNA-4sU_IMR32-mAID_auxin_rep1


title: ChIP_SMARCA4_IMR32_rep1

description: anti-SMARCA4 ChIP in IMR-32 cells


title: cerebellum-after-bone-marrow-transplant-at-12-months-KO4

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

description: reaching this exceptional age after bone-marrow transplant

hyb_protocol: Following fragmentation, 5.5ug of ss-cDNA were hybridized for 16 hr at 45C on Clariom D Mouse Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene ChIP Scanner 3000 7G.

data_processing: Data analysis was done with the Transcriptome Analysis Console (TAC) 4.0.1 (Applied Biosystems) using default parameters.

source_name: ZFE Klinikum Goethe University Frankfurt

label_protocol: The fragmented 5.5 μg of single-stranded cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the  proprietary DNA Labeling Reagent that is covalently linked to biotin (GeneChip™ WT PLUS Reagent Kit, Affymetrix).

growth_protocol: Ageing of mutants and sex- / age-matched WT animals until 12 months was closely monitored after the intervention, continuously assuring that lymphoma and immunological deficits were not threatening the mice. Dissection 4 ATM-null versus matched WT mice occurred after cervical dislocation, snap-freezing the fresh cerebellar tissue in liquid nitrogen

extract_protocol: RNA extraction from frozen tissue samples was performed with the TRIzol Reagent (Sigma Aldrich, St. Louis, USA) following manufacturer’s instructions. cDNA synthesis was done from 1 µg of total RNA using the SuperScript IV VILO kit (Thermo Scientific, Waltham, USA) according to the user’s manual. Single-stranded cDNA library was generated from DNase treated 1 μg of total RNA using GeneChipTM WT PLUS Reagent Kit (Applied Biosystems, Thermo Scientific, Waltham, USA).

treatment_protocol: Bone-marrow transplantation: As conditioning regimen, the recipient mice received 0.125 mg/ml anti-CD4 antibody (clone GK1.5, Sigma, Steinheim, Germany) and 0.125 mg/ml anti-CD8 antibody (clone 53–6.7, Sigma) 7 days before bone marrow transplantation (BMT), and then a second dose of each antibody together with 200 mg/kg cyclophosphamide (80 mg/ml, Sigma-Aldrich, St. Louis, Missouri, USA) 1 day before BMT for nonmyeloablative conditioning. Bone marrow cells were harvested in sterile manner from CD-90.2 depleted donor animals on the day of BMT, and 5 x 106 bone marrow cells were injected intravenously into conditioned recipients

value: cerebellum

value: ATM-null (JAX strain 002753)

tag: age

value: 12 months old


title: ChIP_input_IMR32_rep1

description: Input control DNA in IMR-32 cells


title: GRZ_D_male7_d21_skin

address: Beutenbergstraße 11

value: skin

value: male


title: ChIP_SMARCA4_IMR32_rep2

address: 1 Baylor Plaza, BCM 229

description: anti-SMARCA4 ChIP in IMR-32 cells


title: RNA-4sU_IMR32-mAID_EtOH_rep2


title: cerebellum-after-bone-marrow-transplant-at-12-months-KO3


title: ChIP_input_KELLY_rep1

description: Input control DNA in KELLY cells


title: GRZ_D_male6_d21_skin

value: GRZ-D


title: ABC2


title: GRZ_D_male3_d21_brain


title: cerebellum-after-bone-marrow-transplant-at-12-months-KO1


title: ChIP_SMARCA4_KELLY_rep2

description: anti-SMARCA4 ChIP in KELLY cells


title: GRZ_D_male2_d21_skin


title: ABC1


title: GRZ_D_male3_d21_skin


title: ChIP_SMARCA4_KELLY_rep1

description: anti-SMARCA4 ChIP in KELLY cells


title: RNA-4sU_IMR32_BRM014_rep2

description: mRNA in 4sU-treated IMR-32 cells treated with BRM014


title: ATAC_IMR32_WT_BRM014_rep2

description: ATAC-seq in IMR-32 cells treated with BRM014

data_processing:
ATAC-seq reads were aligned to the hg38 genome assembly using Bowtie v2.4.1.
Fragments with read qualities greater than 10 were considered for further analysis. 200 bp pseudofragments were created at the positions corresponding to the transposition sites, and peak calls were made using MACS 2.1.2 without modeling of fragment size. Reads within peaks were counted using bedtools.
The table of all counts was processed using DESeq2, using default parameters.
Bigwig files were created based on 200 bp pseudofragments, with intermediate files created using bedtools 2.28.0. All bigWig files are unscaled and require scaling before comparison across samples.
Genome_build: hg38
Supplementary_files_format_and_content: Unscaled bigWig files of genome-wide coverage

extract_protocol:
Nuclei were permeabilized and transposed according to the Omni-ATAC protocol.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Non-engineered IMR-32 cells (WT) were treated with either 1 uM BRM014 or an equivalent volume of DMSO for 24 h prior to library construction. Engineered cells (SMARCA4-mAID) were treated with either 500 uM auxin (indole-3-acetic acid) or an equivalent volume of ethanol for 24 h prior to library construction.


title: GRZ_D_male5_d21_brain


title: RNA-4sU_IMR32_BRM014_rep1


title: cerebellum-at-12-months-WT3

description: sex/age-matched control

value: WT in 129/SvEV


title: FO1


title: GRZ_D_male4_d21_skin


title: ATAC_IMR32_SMARCA4-mAID_auxin_rep1

description: ATAC-seq in SMARCA4-EGFP-mAID IMR-32 cells treated with auxin


title: FO2


title: ATAC_IMR32_WT_DMSO_rep2

description: ATAC-seq in IMR-32 cells treated with DMSO vehicle control


title: GRZ_D_male5_d21_skin


title: Differentiated BeWo b30 cell, replicate 4

description: Gene expression data from BeWo b30 cells cultured in expansion medium for 2 days and differentiation medium for 2 more days.

tag: cell type

value: BeWo b30

value: Differentiation

tag: culture days

tag: seeding density


title: GRZ_D_male4_d21_brain

tag: strain

value: brain


title: cerebellum-at-12-months-WT1

description: sex/age-matched control

tag: tissue

tag: genotype


title: ATAC_IMR32_WT_DMSO_rep1

value: WT

tag: treatment


title: ATAC_IMR32_SMARCA4-mAID_EtOH_rep1

description: ATAC-seq in SMARCA4-EGFP-mAID IMR-32 cells treated with ethanol vehicle control


title: cerebellum-after-bone-marrow-transplant-at-12-months-KO2


title: ATAC_IMR32_WT_BRM014_rep1


title: cerebellum-at-12-months-WT4

description: sex/age-matched control


title: 21288Tam_NS3

status: Public on Oct 23 2023

city: College Station

first: Jesse

last: Starkey

state: Texas

address: Minnie Bell Heep Center, Suite 412 2475 TAMU

department: Entomology

institute: Texas A&M University

data_processing:
Tuxedo Suite
Individual samples were processed with FastQC, and the bioinformatic analysis was performed within the Discovery environment of Cyverse
Which included Tophat for mapping reads to the genome (RefSeq GCF_016802725.1) and Cufflink applications
Differentially expressed genes (DEGs) were determined between treatments via the CuffDiff application with the q-value threshold set to 0.05
Assembly: RefSeq GCF_016802725.1
Supplementary files format and content: .xlsx
Supplementary files format and content: DEGs between different treatments

organism: Solenopsis invicta

source_name: whole body

extract_protocol:
Total RNA extractions were done using the OMNI International Tissue RNA kits (OMNI International, Kennesaw, GA). 1ug of total RNA was used for the construction of the libraries.
RNA libraries for RNA-seq were prepared using Illumina NovaSeq 6000 SP X.

value: whole body

value: S-hydroprene


title: 21288Tam_NA4

value: Acetone


title: 21288Tam_NA2


title: 21288Tam_N4

value: Nurse


title: ATAC_IMR32_SMARCA4-mAID_auxin_rep2


title: cerebellum-at-12-months-WT2

description: sex/age-matched control


title: 21288Tam_NS4


title: 21288Tam_F3

value: Forager


title: 21288Tam_F1


title: ATAC_IMR32_SMARCA4-mAID_EtOH_rep2

value: ethanol


title: 21288Tam_NS2


title: 21288Tam_N3


title: koPfRsdA_1

first: Zili

last: Song

address: Beichen West Road 1

institute: Institute of Microbiology, Chinese Academy of Sciences

data_processing:
Data quality control by fastp software (version 0.19.7)
The reads was quickly and accurately compared with the reference genome using HISAT2 software.
Read count extraction and normalization were performed using subread software.
Assembly: GCF_000516985.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Pestalotiopsis fici

source_name: Mycelium

growth_protocol: P. fici was cultured on PDA medium at 25℃ for 5 days.

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 for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufacturer's protocols.

value: Mycelium

value: PfRsdA knockout


title: koPfCsdA_2

value: PfCsdA knockout


title: 21288Tam_F4


title: LEW - immune-enriched - scRNAseq

city: Toronto

first: Delaram

last: Pouyabahar

address: 160 College St

department: Molecular Genetics

institute: University of Toronto

description: 10x Genomics Single Cell 3’ v3

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger 3.1.0 pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Rattus_norvegicus.custom_6.0.98-
Supplementary files format and content: Matrix files (.mtx)

source_name: liver

growth_protocol: The animals were co-housed in the Animal Research Center facility at Princess Margaret Research Tower and were fed a standard diet of sterilized water and laboratory blocks.

extract_protocol: Samples were prepared as outlined by the 10x Genomics Single Cell 3′ v2 Reagent Kit user guide. Briefly, the samples were washed twice in PBS (Life Technologies) + 0.04% BSA (Sigma) and re-suspended in PBS + 0.04% BSA. Sample viability was assessed via Trypan Blue (Thermo Fisher) and using a haemocytometer (Thermo Fisher). Following counting, the appropriate volume for each sample was calculated for a target capture of 10,000 cells for TLH and 9000 cells for immune-enriched samples. Samples below the required cell concentration as defined by the user guide (i.e., <400 cells/µl) were pelleted and re-suspended in a reduced volume and counted again using a haemocytometer prior to loading onto the 10x Genomics single-cell-A chip. After droplet generation, samples were transferred onto a pre-chilled 96-well plate (Eppendorf), heat-sealed and reverse transcription was performed using a Veriti 96-well thermal cycler (Thermo Fisher). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x followed by a Silane DynaBead clean-up (Thermo Fisher) as outlined in the user guide. Purified cDNA was amplified for 12 cycles before being cleaned up using SPRIselect beads (Beckman). Samples were diluted 4:1 (elution buffer (Qiagen):cDNA) and run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell 3′ Reagent Kits v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).  The molarity of each library was calculated based on library size as measured using a bioanalyzer (Agilent Technologies) and qPCR amplification data (Kappa/Roche).  Samples were pooled and normalized to 10 nM, then diluted to 2 nM using elution buffer (Qiagen) with 0.1% Tween20 (Sigma). Each 2 nM pool was denatured using 0.1 N NaOH at equal volumes for 5 min at room temperature. Library pools were further diluted to 20 pM using HT-1 (Illumina) before being diluted to a final loading concentration of 14 pM. 150 μl from the 14 pM pool was loaded into each well of an 8-well strip tube and loaded onto a cBot (Illumina) for cluster generation. Samples were sequenced on a HiSeq 2500 with the following run parameters: Read 1—26 cycles, read 2—98 cycles, index 1—8 cycles. A median sequencing depth of 50,000 reads/cell was targeted for each sample.

value: liver

tag: cell dissociation

value: Immune-enriched (additional wash)

value: Lewis

tag: Sex

value: M

tag: disease state

value: healthy


title: koPfRsdA_2


title: 21288Tam_NA3


title: PfWT_3

value: P. fici wild type


title: 21288Tam_N1


title: PfWT_2


title: 5AzadC_H3K9me3_CUTTag_Rep3

city: Rochester

first: Fanju

last: Meng

address: 601 Elmwood Avenue

department: Biomedical Genetics

institute: University of Rochester Medical Center

data_processing:
Raw sequencing reads were processed with Cutadapt (v2.7) to remove adapters
Then sequencing reads were aligned to zebrafish genome (GRCz11) using Bowtie2(v2.2.5), and then PCR duplicates were marked and removed using Picard MarkDuplicates(v2.5.0)
Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters: --normalizeUsing RPKM --binSize 10
Assembly: Zv11
Supplementary files format and content: bigWig files, RPKM normalized genome browser track
Library strategy: CUT&Tag

organism: Danio rerio

source_name: whole embryos

growth_protocol: Adult wild type AB/Tuebingen zebrafish were maintained on a 14h:10h light:dark cycle

extract_protocol: Around 100,000 cells from 6hpf embryos were used for CUT&Tag and library construction according to standard methods. Polyclonal H3K9me3 antibody from Active Motif (Cat. 39062) was used.

treatment_protocol: Newly fertilized eggs were collected immediately after spawning, and placed around 50 per well in a 6 well plate. Embryos were treated with 100uM 5Aza-dC (treatment starts from 1-cell stage), or with 0.1% DMSO for control group.

value: whole embryos

tag: developmental stage

value: 6hour post fertilization

value: wild type


title: koPfCsdA_1


title: koPfCsdA_3


title: PfWT_1


title: 5AzadC_H3K9me3_CUTTag_Rep1


title: DMSO_H3K9me3_CUTTag_Rep3

value: DMSO


title: koPfRsdA_3


title: DMSO_H3K9me3_CUTTag_Rep1


title: LEW2-snRNAseq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger 3.1.0, and 10x Genomics Space Ranger 1.1.0  pipelines
Assembly: Rattus_norvegicus.custom_6.0.98-
Supplementary files format and content: Matrix files (.mtx)

extract_protocol: Samples were prepared as outlined by the 10x Genomics Single Cell 3’ v2 (scRNA-seq TLH samples) and v3 (immune-enriched samples and snRNA-seq samples) Reagent Kit user guides and as described previously (Andrews et al., 2022; MacParland et al., 2018). Briefly, following cell counting (using Trypan blue exclusion for single cell and SYBR green II for single nuclei), we targeted the capture of 9000 cells and loaded them onto the 10x Genomics Single cell A Chips for the total liver homogenate,and B Chips for the immune-enriched and snRNA-seq samples. Visium spatial transcriptomics were sequined at 60,000 reads per spot with 2400 and 2500 number of spots for sample A1 and B1, respectively. cDNA libraries were prepared as per the Single Cell 3′ Reagent Kits v3 user guide and Visium Spatial Gene Expression Reagent Kits user guide for spatial transcriptomics. scRNA-seq TLH were sequenced on a HiSeq 2500. Visium spatial transcriptomics, snRNA-seq and immune-enriched samples were sequenced on a NovaSeq 6000.

value: Total Liver Homogenate (CST nuclei extraction)

tag: assay

value: 10x Genomics Single Cell 3’ v3


title: LEW1-snRNAseq


title: Rat_A1_VIS (sample A)

value: Wistar

value: 10x Genomics Spatial 3’ v1


title: DA2-snRNAseq

value: Dark Agouti


title: DA1-snRNAseq


title: 5AzadC_H3K9me3_CUTTag_Rep2


title: DMSO_H3K9me3_CUTTag_Rep2


title: H2A.ZmCherry_5AzadC_12hpf_totalRNA_Rep2

data_processing:
Sequencing reads were mapped with STAR with default setting (v2.7.2a)
Count tables were generated by featureCounts (v2.0.3 in subread) using GRCz11.102.gtf with paired-end mode.
Differentially expressed genes were identified using DESeq2 (v1.22.2 in R/3.5.1)
Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters: --normalizeUsing RPKM --binSize 10
Genome_build: Zv11
Supplementary_files_format_and_content: bigWig files and txt files

source_name: zebrafish embryos

extract_protocol:
Treated embryos were collected in Trizol at 12hpf, and grinded with motar and pestle. Total RNA was extracted with phenol:chloroform:isoamyl alcohol, then aqueous layer were purified with Zymo Direct-zol RNA Miniprep kit.
Total RNA-seq libraries were constructed.

treatment_protocol: Newly fertilized eggs were collected immediately after spawning, and placed around 50 per well in a 6 well plate. Embryos were treated with 5 mL 100uM 5Aza-dC , or with 0.1% DMSO for control group.

value: 12hour post fertilization

value: H2A.Z overexpression


title: H2A.ZmCherry_5AzadC_12hpf_totalRNA_Rep1


title: H2A.ZmCherry_5AzadC_12hpf_totalRNA_Rep3


title: H2A.ZmCherry_DMSO_12hpf_totalRNA_Rep3


title: H2A.ZmCherry_DMSO_12hpf_totalRNA_Rep2


title: H2AZmCherry_5AzadC_H2AZ_CUTTag_Rep3

data_processing:
Sequencing reads were aligned to zebrafish genome (GRCz11) using Bowtie2, and then PCR duplicates were marked and removed using Picard
Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters: --normalizeUsing RPKM --binSize 10
Assembly: Zv11
Supplementary files format and content: bigWig files
Library strategy: CUT&Tag

extract_protocol: Around 100,000 cells from 6hpf embryos were used for CUT&Tag and library construction according to standard methods. Polyclonal H2A.Z antibody from Active Motif (Cat. 39113) was used.

treatment_protocol: Newly fertilized eggs were collected immediately after spawning, and placed around 50 per well in a 6 well plate. Embryos were treated with 100uM 5-AzadC (treatment starts from 1-cell stage), or with 0.1% DMSO for control group.

value: zebrafish embryos


title: GRZ_D_male1_d21_skin

value: GRZ-D

value: skin

value: male

tag: age in_days


title: GRZ_D_male1_d21_brain

value: brain


title: GRZ_D_male2_d21_brain


title: H2A.ZmCherry_DMSO_12hpf_totalRNA_Rep1


title: KO1

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

institute: University of Ulm

description: adipose tissue collected at postnatal day six

data_processing:
Firstly,we remove the reads mapped to rRNA and get raw data.
Then the sequencing reads which containing low-quality, adaptor-polluted and high content of unknown base (N) reads, should be processed to be removed before downstream analyses.
We map clean reads to reference transcripts using Bowtie2.
Lastly we calculate gene expression level for each sample with  RSEM.
Genome_build: Based on the gene expression level, we can identify  DEGs (Differentially expression genes) between WT and KO samples. We used DEseq2 algorithms to detect the DEGs.
Supplementary_files_format_and_content: Excel showing DEGs.

source_name: inguinal adipose tissue

growth_protocol: SPF animal maintenance

extract_protocol: TRIZOL extraction from tissue

tag: genotype/variation

value: KO


title: WT3

value: WT


title: KO2


title: WT2


title: KO3


title: WT1


title: WT_5AzadC_12hpf_totalRNA_Rep3


title: H2AZmCherry_5AzadC_H2AZ_CUTTag_Rep2

value: 6hour post fertilization


title: H2AZmCherry_DMSO_H2AZ_CUTTag_Rep3


title: H2AZmCherry_5AzadC_H2AZ_CUTTag_Rep1


title: WT_5AzadC_12hpf_totalRNA_Rep1

value: wild type


title: H2AZmCherry_DMSO_H2AZ_CUTTag_Rep2

value: DMSO


title: H2AZmCherry_DMSO_H2AZ_CUTTag_Rep1


title: WT_DMSO_12hpf_totalRNA_Rep2


title: WT_DMSO_12hpf_totalRNA_Rep3


title: WT_5AzadC_12hpf_totalRNA_Rep2


title: DA - immune-enriched - scRNAseq

description: 10x Genomics Single Cell 3’ v3

value: liver

value: Immune-enriched (additional wash)

value: M

value: healthy


title: DAC_control_ATAC_rep1

data_processing:
Sequencing reads were aligned to zebrafish genome (GRCz11) using Bowtie2, and then PCR duplicates were marked and removed using Picard
Peak calling was performed using MACS2 with the following parameters: -f BAMPE --nomodel using bam files of triplicates
Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters: --normalizeUsing RPKM --binSize 10
Differential peaks were identified by DiffBind using ATAC narrowPeak and associated bam files for each replicate with default setting, using cutoff threshold of adjusted p-value < 0.05 and absolute value of log2FC at 0.5.
Assembly: Zv11
Supplementary files format and content: bigWig files and txt files

source_name: whole embryo

extract_protocol:
Around 100,000 cells from 6hpf embryos were used for nuclei isolation and ATAC-seq. Genomic DNA were extracted using Zymo Research DNA Clean & Concentrator-5 (D4014)
ATAC-Seq libraries were generated using NEBNext High-Fidelity 2X PCR Master Mix (M-541S) according to standard method.

treatment_protocol: Newly fertilized eggs were collected immediately after spawning, and placed around 50 per well in a 6 well plate. Embryos were treated with 5 mL 100uM Decitabine (DAC) or 3.12uM TDCIPP , or with 0.1% DMSO as control group.

value: whole embryo

tag: developmental stages


title: DAC_control_ATAC_rep3


title: TDCIPP_control_ATAC_rep2


title: TDCIPP_control_ATAC_rep3


title: DAC_treat_ATAC_rep3

value: DAC


title: TDCIPP_treat_ATAC_rep2

value: TDCIPP


title: TDCIPP_treat_ATAC_rep3


title: DAC_control_ATAC_rep2


title: DAC_treat_ATAC_rep1


title: Rat_B1_VIS (sample B)

value: Wistar

value: 10x Genomics Spatial 3’ v1


title: DAC_treat_ATAC_rep2


title: TDCIPP_treat_ATAC_rep1


title: WT_DMSO_12hpf_totalRNA_Rep1

value: 12hour post fertilization


title: SAM24387959 Thyroid aN1aN2-2 (pool of 6 mice)

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

data_processing:
Sample demultiplexing, barcode processing and single cell 3' gene counting were performed using 10X Cell Ranger. Only cells with a mitochondrial UMI fraction <0.25 were considered for analysis.
Per-gene UMI counts were normalized by the total number of transcripts per cell, scaled by the median number of transcripts across all cells and log-transformed for downstream analysis.
Dataset alignment (between 1st and 2nd processing dates), cell clustering, visualization and differential expression analysis were performed as prescribed in the OSCA book (https://osca.bioconductor.org) (Amezquita et al., 2019).
The pipeline merged together single-cell data generated from multiple batches. For each batch, it ran the quality control, normalization and variance modelling steps, and then applied MNN correction to merge all batches into a single coordinate space. Dimensionality reduction and clustering on the merged data were performed to obtain a common grouping for all cells.
The analysis used the top 20 principal components for clustering and visualization, the 50 nearest neighbors (k=50) for graph-based clustering and performed marker detection using the AUC with a log-fold change threshold of 1.
For differential expression, treated samples were contrasted with control samples, genes were ranked based on the π statistic (π=logFC * -log10(p-val)) (Xiao et al., 2014) and subsequently gene set enrichment was performed using the clusterProfiler::GSEA function.
For topic analysis, we extracted the top 50 genes associated with specific topics and performed a hypergeometric test using the clusterProfiler::enricher function. To characterize cells based on the activity of transcriptional programs, we performed topic modeling using functions from the CountClust R package (Dey et al., 2017). We evaluated a range between 2 to 15 topics for their fit using the FitGoM function. A total of 7 topics were selected to represent the data after inspecting the AIC and BIC statistics. Top genes associated with each topic were identified by applying the ExtractTopFeatures function, which uses the relative gene expression profile of the GoM clusters and applies a KL-divergence based method to obtain a list of top features that drive each of the clusters.
Assembly: GRCm38 mouse genome (NCBI Build 38)
Supplementary files format and content: csv, count matrix

source_name: Thyroid

extract_protocol:
Thyroid tissue was extracted from mice at the time of necropsy. To generate single cells, thyroids were cut with a razon blade and digested for 30min at 42°C. The digestion was done with 0.05mg/ml Liberase TM (Sigma, 5401127001) diluted in Advanced DMEM/F12, 10mM HEPES, 1% Glutamax, 1% P/S and 1:1000 Rock inhibitor (Y27632, StemCell 72304). After digestion, centrifuge the cells at 1200rpm/5min, wash them with Advanced DMEM/F12, 10mM HEPES, 1% Glutamax, 1% P/S and filter them through a 70um strainer. After digestion and wash, cells were centrifuged at 1200rpm/5min and resuspended in PBS 3% FBS. Given the low number of cells obtained from a single mouse thyroid, the thyroids from six mice were pooled into one sample.
Chromium Single Cell 3’ Library and Gel bead kit v2, following the manufacturer’s manual (CG00052 Chromium Single Cell 3 Reagent Kits v2 User Guide RevA; 10x Genomics). Cell density and viability of the single-cell suspensions were determined by Vi-CELL XR cell counter (Beckman Coulter). All of the processed samples had more than 85% viable cells. Cell density was used to impute the volume of single-cell suspension needed in the RT master mix, aiming to achieve ~8000 cells per sample. cDNAs and libraries were prepared following the manufacturer’s manual (10X Genomics). Libraries were profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and quantified using Kapa Library Quantification Kit (Kapa Biosystems, Wilmington, MA). Each library was sequenced in one lane of HiSeq4000 (Illumina) following the manufacturer’s sequencing specification (10X Genomics).

treatment_protocol: Male C57BL/6 mice at 10-14 weeks of age were obtained from Jackson Laboratories (strain ID: 00664). Mice were injected intraperitoneally with a single dose of blocking antibodies diluted in PBS at the following concentrations: anti-ragweed isotype control (40MPK); anti-Jag1+anti-jag2 (20MPK each) or anti-Notch1+ anti-Notch2 (5MPK, 10MPK) .

value: Thyroid

tag: diagnostics

value: Normal

value: anti-Notch1 and anti-Notch2 antibodies, 7 days


title: SAM24387958 Thyroid aN1aN2-1 (pool of 6 mice)


title: SAM24387960 Thyroid aN1aN2-3 (pool of 6 mice)


title: SAM24381185 Thyroid aJ1aJ2-3 (pool of 6 mice)

value: anti-Jag1 and anti-Jag2 antibodies 7 days


title: SAM24381186 Thyroid aJ1aJ2-4 (pool of 6 mice)


title: SAM24381184 Thyroid RW-2 (pool of 6 mice)

value: RW 7 days


title: TDCIPP_control_ATAC_rep1

value: 6hour post fertilization

value: wild type


title: Differentiated BeWo b30 cell, replicate 2

data_processing: SST-RMA gene-level probeset summary with standard settings of the Transcriptome Analysis Console (TAC; version 4.0.3; Thermo Fisher Scientific)

extract_protocol: Samples were lysed and RNA extraction was performed using the PurelinkTM RNA Mini kit (Thermo Fisher Scientific, 12183018A) following the manufacturer’s instructions.

value: BeWo b30

tag: culture medium type

value: Differentiation


title: K562, etoposide or imatinib treated, RACE and RT-PCR targeted sequencing for novel transcripts, nanopore sequencing

description: polyA+ RNA from each drug treated samples was mixed and used for cDNA synthesis, transcripts identified by Insertion-based Screen for functional Elements and Transcripts (InSETs) were targeted enriched by Rapid amplification of cDNA ends (RACE) and RT-PCR, followed by nanopore sequencing

data_processing:
Reads were aligned to the GRCh37/hg19 using Minimap2 (v2.17-r941) in spliced alignment mode with the command “minimap2 -ax splice --secondary=no”, and the option “--secondary=no” was used to suppress secondary alignments.
Supplementary and low-quality alignments were filtered out using SAMTools (v1.10) with the command “samtools view -F0x900 -q 60”.
Assembly: GRCh37/hg19
Supplementary files format and content: Processed data are in BED files containing coordinates of novel transcripts. The 5th column shows the read count of each transcript.

growth_protocol: Human chronic myeloid leukemia cell line K562 was maintained in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (ExCell Bio, Uruguay).

extract_protocol:
RNA was isolated with TRNzol Universal (Tiangen) and E.Z.N.A. Total RNA Kit I (Omega). The polyA+ fraction was isolated from each total RNA by Library Preparation VAHTSTM mRNA Capture Beads (Vazyme). Equal amount of polyA+ RNA from each sample was mixed and used for cDNA synthesis for RACE and RT-PCR.
RACE and RT-PCR were performed to targeted enrich for InSETs, then sequencing library was prepared by Ligation Sequencing Kit (SQK-LSK109) (Oxford Nanopore Technologies Inc., Oxford, UK) by Baocheng Corporation (Hangzhou).

treatment_protocol: K562 cells (0.5 million cells/ml) were grown in a 6-well plate for 16 h and treated with either 80 μM etoposide or 1 μM imatinib for 0 h, 6 h, 24 h, or 36 h.

tag: cell line

tag: cell type

value: human chronic myeloid leukemia cell line

value: wild-type

value: cells were treated with either 80 μM etoposide or 1 μM imatinib for 0 h, 6 h, 24 h, or 36 h


title: BAT aJ1aJ2+T3T4 7d-10

data_processing:
Sequencing reads were aligned to the mouse genome (NCBI Build 38) using GSNAP (Wu and Nacu, 2010) version ‘2013-10-10’, allowing a maximum of two mismatches per 50 base pair sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap’).
Lastly, gene expression levels were quantified by calculating the number of reads mapped to the exons of each RefSeq gene using the HTSeqGenie R package.
Transcript annotation was based on the RefSeq database NCBI Annotation Releases 104 for mouse.
Read counts were scaled by library size, quantile normalized and precision weights calculated using the “voom” R package (Law et al., 2014).
Differential expression analysis on the normalized count data was performed using the “limma” R package (Ritchie et al., 2015) by contrasting treated samples with control samples, respectively. Gene expression was considered significantly different across groups if we observed an |log2-fold change| ≥ 1 (estimated from the model coefficients) associated with an FDR adjusted P-value ≤ 0.05. In addition, gene expression was obtained in the form of normalized Reads Per Kilobase gene model per Million total reads (nRPKM) as described previously (Srinivasan et al., 2016).
Assembly: mouse genome (NCBI Build 38)
Supplementary files format and content: csv (count and fpkm matrix)

source_name: Brown adipose tissue

extract_protocol:
Total RNA was extracted from  tissues with Trizol (Invitrogen) following the provider’s recommendations. After adding isopropanol, the samples were transferred into RNAeasy extraction column (Qiagen), washed and eluded following the manufacturer protocol.
The libraries were sequenced on Illumina HiSeq 4000 (Illumina). We obtained on average 40 million single-end RNA-seq reads (50bp) per sample.

treatment_protocol: Male C57BL/6 mice at 10-14 weeks of age were obtained from Jackson Laboratories (strain ID: 00664). Mice were injected intraperitoneally with a single dose of blocking antibodies diluted in PBS at the following concentrations: anti-ragweed isotype control (40MPK); anti-Jag1+anti-jag2 (20MPK each); anti-Notch1+ anti-Notch2 (5MPK, 10MPK) , anti-Notch1+ anti-Notch2+ anti-Notch3 (5MPK, 10MPK, 20MPK). Exogenous administration of thyroxine (T4) and 3-Iodotrionine (T3) was performed daily starting at day 2 of the antibody treatment with a dose 1ug/g BW of T4 and 0.05μg/g BW T3.

value: Brown adipose tissue

value: anti-Jag1 and anti-Jag2 antibodies +T3T4 7 days


title: BAT RW+T3T4 7d-5

value: RW +T3T4 7 days


title: SAM24381183 Thyroid RW-1 (pool of 6 mice)


title: BAT aJ1aJ2+T3T4 7d-6


title: BAT RW+T3T4 7d-3


title: BAT RW+T3T4 7d-4


title: BAT aJ1aJ2+T3T4 7d-8


title: SAM24372772 single cell thyroid RW (pool of 6 mice)


title: SAM24372773 single cell thyroid aJ1aJ2 7 days (pool of 6 mice)


title: BAT RW+T3T4 7d-2


title: BAT aJ1aJ2+T3T4 7d-9


title: BAT aJ1aJ2+T3T4 7d-7


title: BAT aJ1aJ2 7d-10


title: BAT aJ1aJ2 7d-9


title: BAT aJ1aJ2 7d-8


title: BAT aJ1aJ2 7d-7


title: BAT aJ1aJ2 7d-6


title: BAT RW+T3T4 7d-1


title: BAT RW 7d-3


title: BAT RW 7d-5


title: BAT RW 7d-4