title: cerebral organoid M20 , Day100, treatment=Mn, size=L

city: Atlanta

first: Maureen

last: Sampson

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

description: Library name: Sample12

data_processing:
The sequencing reads were aligned to the human genome and demultiplexed using cellranger-8.0.1 and GRCh38-2024-A.
Analysis was performed in R Studio using Seurat to generate a seurat object. For quality control, cells with <8% mitochondrial genes were excluded, and counts were filtered for 500-8000 range. Cells were integrated and normalized using SCT transform.
Assembly: GRCh38-2024-A
Supplementary files format and content: cellranger matrix files
Supplementary files format and content: R studio seurat object RDS file

source_name: cerebral organoid, Day 100

growth_protocol: Cerebral organoids were developed as previously described in Lancaster Nat Biotechnol 2017. On the first day, 18,000 cells were seeded in low attachment plates. After 5 days, embryoid bodies were formed and transferred to induction media (Stem Cell Technologies) to direct them towards neuronal fate. After another 2 days, cells were expanded in Matrigel droplets for 3 days, then moved to organoid maturation media (Stem Cell Technologies). After 2 weeks in culture, the Matrigel was removed from the organoids by mechanical dissociation and the organoids were grown on an orbital shaker. Maturation media was changed twice a week during organoids growth for up to 100 days in culture.

extract_protocol:
Organoid tissue was chopped using a scalpel and digested in 10ml with 25 U/ml papain (Worthington) and 12.5 U/ml DNAseI (Worthington) in a 5% CO2 incubator at 34°C on an orbital shaker at 123rpm for 45 min. Cells were washed with a protease inhibitor solution (ovomucoid). Following addition of Ovomucoid, the tissue was further triturated by pipetting and once single cell suspensions achieved, the cells were collected by centrifugation. All dissociation and trituration steps were performed in the presence of Protector RNAse inhibitor, transcription inhibitor actinomycin D, and translation inhibitor anisomycin. Up to 10,000 cells per organoid were captured with a Chromium GEM-X-Single Cell 3’ Chip kit v4 from 10X Genomics.
Libraries were prepared using Chromium Next GEM Single Cell 3’ Kit v4 with dual index labeling and sequenced on a standard Illumina platform.

treatment_protocol: Six organoids were untreated and six were exposed to 250μM manganese for 48h.

value: cerebral organoid, Day 100

value: TMOi001-A (Gibco cat #A18945, RRID:CVCL_RM92)

value: hiPSC cerebral organoid

value: Mn


title: paya_mng_167

status: Public on Jun 08 2026

type: genomic

city: Heidelberg

first: Philipp

last: Sievers

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

description: PAYA MNG

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
Average Beta
Unmethylated and methylated signal intensities

label: cy3, cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: PAYA MNG

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: material

value: FFPE

tag: Sex

value: Female

tag: age group

tag: methylation class

value: int

tag: localisation

value: supratentoriell


title: Embryo 4_6, Right side of microdissected heart field, stage E8.5i

type: SRA

city: Paris

first: Sigolène

middle: M

last: Meilhac

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine, Institut Pasteur

description: Library name: 4_6_R

library_source: transcriptomic

data_processing:
After demultiplexing, reads were trimmed to remove adapter sequences. Sequence quality was assessed using FastQC and Picard metrics. FASTQ files were mapped to the ENSEMBL Mus musculus GRCm39 reference genome using the Illumina STAR aligner and counted by featureCounts from the Subread package (v2.0.6).
Genes with low expression levels were filtered, using the filterByExpr function of edgeR R package [edgeR] with parameters min.count = 5, min.total.count = 10, large.n = 50 and min.prop = 0.2.
All differential analyses were carried out using the DESeq2 R package, with local fit type for dispersion estimation and ashr type to shrink the log2 fold changes.
An initial differential analysis was performed on wild-type samples to identify genes associated with asymmetry in wild type samples. The DESeq2 model was adjusted for the effect of the side (left/right) and embryo identifier to account for pairing. The resulting lists of differentially expressed genes (DEG) was refined by retaining “congruent” genes, defined as those exhibiting the same left-right trend across all samples. By using this list, asymmetry behaviour of mutant samples was divided into 3 laterality clusters.
A second differential analysis was then conducted to assess asymmetry variations between clusters, using a DESeq2 model adjusted for the effect of the side and embryo identifier, as well as to evaluate expression changes within each side, using a model adjusted for the cluster and sex. DEG were filtered to exclude genes not expressed in myocardial lineages and then refined to 1842 genes exhibiting diverse variation patterns.
Assembly: ENSEMBL Mus musculus GRCm39 reference genome
Supplementary files format and content: Processed data for all samples is in the file named: processed_data_file.txt
Supplementary files format and content: The file includes all available genes in the 1st column, under the column header "Geneid". To its right, there is a column per sample, with the sample name as a column header and matching "library name" in this Excel. Raw counts per gene (no filtering applied) are indicated.

molecule: polyA RNA

organism: Mus musculus

source_name: microdissected heart field

growth_protocol: Embryos were dissected at E8.5.

extract_protocol:
Total RNA was extracted in TRIzol-Chloroform and purified using the RNeasy Micro Elute Columns kit (QIAGEN) including DNAse treatment. RNA quality and quantity were measured on Fragment Analyzer (Agilent Technologies). All RQN were >9.1.
RNAseq libraries were prepared starting from 10 ng of total RNA using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina.
The cDNAs produced from the poly-A+ fraction were PCR amplified in 2 steps (9 cycles for the first amplification and -8 cycles for the second amplification). An equimolar pool of the final indexed RNA-Seq libraries was sequenced on an Illumina NovaSeq6000, with paired-end reads of 100 bases and a mean of ~80 million of reads/clusters was obtained per sample.

treatment_protocol: The heart field of E8.5i embryos was microdissected, divided into left and right halves, and flash frozen in liquid nitrogen

tag: tissue

value: microdissected heart field

tag: side

value: Right

value: Male

tag: heart looping_direction

value: Inverted

tag: genotype


title: cerebral organoid M7 , Day100, treatment=Mn, size=S

country: USA

description: Library name: Sample10

library_source: transcriptomic single cell

molecule: total RNA

tag: cell line

tag: cell type

tag: treatment


title: Flow, 120h, 1

city: Jena

first: Marc Thilo

last: Figge

state: Thuringen

address: Adolf-Reichwein-Straße 23

department: Applied System Biology

institute: HKI-Leibniz

description: Library name: Flow_1

data_processing:
Raw paired-end FASTQ files were quality-checked using FastQC.
Reads were aligned to the human reference genome GRCh38 using STAR.
Gene-level read counts were generated using featureCounts with Ensembl gene annotation.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file containing featureCounts gene-level raw counts for each sample, including gene annotation columns and per-sample count columns

source_name: C2BBe1, HUVECs, primary monocyte-derived macrophages

growth_protocol: Intestine-on-chips were built according to Feile et al. (Immunocompetent Intestine-on-Chip Model for Analyzing Gut Mucosal Immune Responses. J Vis Exp. 2024 May 24;(207). doi: 10.3791/66603)

extract_protocol:
RNA-extraction was performed using tha RNeasy Kit (Qiagen) to the manufacturer's recommendation.
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. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library 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 bioanalyzer for size distribution detection.

treatment_protocol: Flow chips were kept under flow for 120h while static chips were only perfused for 30minutes per day. 48h before the endpoint, LPS was added to the intestinal compartment of the chip.

value: 120h flow


title: Embryo 18_1, Right side of microdissected heart field, stage E8.5i

description: Library name: 18_1_R

value: Rightward


title: paya_mng_162

description: PAYA MNG

value: ben


title: Embryo 4_6, Left side of microdissected heart field, stage E8.5i

description: Library name: 4_6_L

value: Left


title: cerebral organoid M12 , Day100, treatment=Mn, size=L

description: Library name: Sample11


title: cerebral organoid M21 , Day100, treatment=Mn, size=L

description: Library name: Sample9


title: cerebral organoid M8 , Day100, treatment=Mn, size=S

description: Library name: Sample8


title: paya_mng_161

description: PAYA MNG


title: paya_mng_160

description: PAYA MNG


title: cerebral organoid M3 , Day100, treatment=Mn, size=S

description: Library name: Sample7


title: Embryo 3_7, Left side of microdissected heart field, stage E8.5i

description: Library name: 3_7_L


title: cerebral organoid C5 , Day100, treatment=Con, size=S

description: Library name: Sample5

value: Con


title: Embryo 3_7, Right side of microdissected heart field, stage E8.5i

description: Library name: 3_7_R


title: cerebral organoid C14 , Day100, treatment=Con, size=L

description: Library name: Sample6

value: cerebral organoid, Day 100


title: paya_mng_159

description: PAYA MNG


title: cerebral organoid C4 , Day100, treatment=Con, size=S

description: Library name: Sample4

value: TMOi001-A (Gibco cat #A18945, RRID:CVCL_RM92)


title: cerebral organoid C13 , Day100, treatment=Con, size=L

description: Library name: Sample3

value: hiPSC cerebral organoid


title: Embryo 2_7, Right side of microdissected heart field, stage E8.5i

description: Library name: 2_7_R


title: paya_mng_158

description: PAYA MNG


title: cerebral organoid C1 , Day100, treatment=Con, size=S

description: Library name: Sample1


title: paya_mng_157

description: PAYA MNG

value: spinal


title: RNA-seq: GFP control stable transfection (TREx) Rep 3

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

description: Library name: RNA_CL0180_GFP_TREx_RepC_E007623

data_processing:
RNA-seq reads were mapped to the hg38 genome using the nf-core RNA-seq pipeline with the default alignment options (STAR and Salmon).
Transcription abundance estimates were generated by Salmon
Assembly: hg38
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing CPM --binSize 10. The reads aligned to the forward strand were processed separately from the reads aligned to the reverse strand. The parameter --scaleFactor -1 was used when generating the reads on the reverse strand.

source_name: Flp-In T-REx-293

growth_protocol: Flp-In-293 cells were plated on 6 well plates in DMEM supplemented with 10% FBS, 0.1% Anti-anti, and 0.2% normocin. Two days later, the cells were transfected using Lipofectamine 2000, according to the manufacturer’s protocol, with 0.25 µg of vTR plasmid and 2.25 mg of the pOG44 Flp-Recombinase expression vector. Within three days, the media was changed to media containing hygromycin at 50 mg/mL and the hygromycin was gradually increased to 200 mg/mL to produce a pool of cells stably expressing the vTR. Doxycycline inducible Flp-In T-REx-293 cells were cultured in media also containing 100µg/mL zeocin. These cells were cultured in 1µg/mL doxycycline for overnight prior to collection.

extract_protocol:
Total RNA was isolated using the mirVana RNA extraction kit
rRNA depleted, stranded libraries were generated by the sequencing center. Samples were sequenced at either Novogene or the Cincinnati Children’s Hospital Medical Center Genomics Sequencing Facility (CCHMC)

value: Flp-In T-REx-293

tag: transfection type

value: Stable cell line

tag: transfection plasmid

value: GFP control

tag: sequencing center

value: CCHMC


title: Embryo 2_7, Left side of microdissected heart field, stage E8.5i

description: Library name: 2_7_L

value: microdissected heart field

value: Female


title: RNA-seq: GFP control stable transfection (TREx) Rep 2

description: Library name: RNA_CL0180_GFP_TREx_RepB_E007622


title: Embryo 2_2, Right side of microdissected heart field, stage E8.5i

description: Library name: 2_2_R

value: Right

value: Male


title: RNA-seq: GFP control stable transfection (TREx) Rep 1

description: Library name: RNA_CL0180_GFP_TREx_RepA_E007621


title: paya_mng_156

description: PAYA MNG

value: FFPE


title: RNA-seq: GFP control transient transfection (CCHMC) Rep 3

description: Library name: RNA_GFP_only_CCHMC_RepC_E006390

value: Transient transfection


title: Embryo 2_2, Left side of microdissected heart field, stage E8.5i

description: Library name: 2_2_L

value: Rightward


title: RNA-seq: GFP control transient transfection (CCHMC) Rep 2

description: Library name: RNA_GFP_only_CCHMC_RepB_E006389


title: paya_mng_155

description: PAYA MNG

value: ben

value: posterior fossa


title: RNA-seq: GFP control transient transfection (CCHMC) Rep 1

description: Library name: RNA_GFP_only_CCHMC_RepA_E006388


title: paya_mng_153

description: PAYA MNG


title: Embryo 1_6, Right side of microdissected heart field, stage E8.5i

description: Library name: 1_6_R


title: RNA-seq: Puromycin control transient transfection (CCHMC) Rep 3

description: Library name: RNA_puro_only_CCHMC_RepC_E006387

value: puromycin control


title: Embryo 1_6, Left side of microdissected heart field, stage E8.5i

description: Library name: 1_6_L

value: Left


title: paya_mng_152

description: PAYA MNG

value: skull base


title: RNA-seq: Puromycin control transient transfection (CCHMC) Rep 2

description: Library name: RNA_puro_only_CCHMC_RepB_E006386


title: RNA-seq: nGFP tagged ZTA stable transfection Rep 3

description: Library name: RNA_CL0059_ZTA_RepF_E007010

value: nGFP tagged ZTA


title: RNA-seq: Puromycin control transient transfection (CCHMC) Rep 1

description: Library name: RNA_puro_only_CCHMC_RepA_E006385


title: cerebral organoid C12 , Day100, treatment=Con, size=L

description: Library name: Sample2

value: cerebral organoid, Day 100

value: TMOi001-A (Gibco cat #A18945, RRID:CVCL_RM92)

value: hiPSC cerebral organoid

value: Con


title: paya_mng_146

description: PAYA MNG

value: int

value: ventricel


title: RNA-seq: nGFP tagged ZTA stable transfection Rep 2

description: Library name: RNA_CL0059_ZTA_RepE_E007009

value: Stable cell line

value: CCHMC


title: scRNAseq

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

description: Library name: Sample 1

data_processing:
Demultiplexing, alignment, and barcode deconvolution via cellranger (v8.0.1)
Assembly: mm10
Supplementary files format and content: h5 matrix file for cellbarcode x gene

source_name: Large intestine

extract_protocol: 10X 3' GEX

value: Large intestine

value: Macrophages

tag: strain

tag: age

value: 8-12 weeks old


title: RNA-seq: nGFP tagged ZTA stable transfection Rep 1

description: Library name: RNA_CL0059_ZTA_RepD_E007008


title: RNA-seq: nGFP tagged EBNALP stable transfection (TREx) Rep 3

description: Library name: RNA_CL0154_EBNALP_RepC_E007181

value: Flp-In T-REx-293

value: nGFP tagged EBNALP


title: paya_mng_145

description: PAYA MNG

tag: material

value: FFPE

value: Male

value: spinal


title: RNA-seq: nGFP tagged EBNALP stable transfection (TREx) Rep 1

description: Library name: RNA_CL0154_EBNALP_RepA_E007179


title: RNA-seq: nGFP tagged EBNALP stable transfection (TREx) Rep 2

description: Library name: RNA_CL0154_EBNALP_RepB_E007180


title: HT29 Non Targeting Control rep#2

type: RNA

city: Boston

first: Teng

last: Teng

state: MA

address: 201 Brookline Ave Suite 901

institute: Tango Therapeutics

hyb_protocol: Nanostring protocol

scan_protocol: Nanostring scanning

data_processing: Nanostring/nCounter processing

label: Nanostring probe

source_name: human colorectal adenocarcinoma cell line

label_protocol: Nanostring labelling

growth_protocol: HT29 cells were cultured in DMEM supplemented with 10% FBS

extract_protocol: RNA from human cancer cell lines was isolated using the QIAGEN RNeasy Kit (Cat# 74004)

value: Colon

tag: gender

value: female

tag: morphology

value: epithelial

value: Non Targeting Control


title: paya_mng_143

description: PAYA MNG

tag: Sex

value: Female

tag: age group

tag: methylation class

value: posterior fossa


title: RNA-seq: nGFP tagged EBNA1 stable transfection Rep 3

description: Library name: RNA_CL0116_EBNA1_RepC_E006337

value: nGFP tagged EBNA1


title: HT29 Non Targeting Control rep#3

tag: tissue


title: HT29 Non Targeting Control rep#1


title: paya_mng_142

description: PAYA MNG

value: int

tag: localisation

value: supratentoriell


title: RNA-seq: nGFP tagged EBNA1 stable transfection Rep 2

description: Library name: RNA_CL0116_EBNA1_RepB_E006336

value: Stable cell line

value: CCHMC


title: RNA-seq: nGFP tagged EBNA1 stable transfection Rep 1

description: Library name: RNA_CL0116_EBNA1_RepA_E006335


title: paya_mng_140

description: PAYA MNG

value: ben


title: RNA-seq: cGFP tagged BMRF1 stable transfection Rep 3

description: Library name: RNA_CL0171_BMRF1_RepC_E007587

value: cGFP tagged BMRF1


title: RNA-seq: cGFP tagged BMRF1 stable transfection Rep 2

description: Library name: RNA_CL0171_BMRF1_RepB_E007586


title: HT29 EHMT2 KO rep#3

tag: genotype

value: EHMT2 KO


title: HT29 EHMT2 KO rep#2

tag: cell line


title: RNA-seq: cGFP tagged BMRF1 stable transfection Rep 1

description: Library name: RNA_CL0171_BMRF1_RepA_E007585


title: paya_mng_139

description: PAYA MNG

value: FFPE


title: RNA-seq: untaggged EBNA2 transient transfection Rep 3

description: Library name: RNA_EBNA2_only_RepC_E007436

value: Transient transfection

value: untagged EBNA2


title: HT29 EHMT2 KO rep#1

value: Colon


title: RNA-seq: untaggged EBNA2 transient transfection Rep 2

description: Library name: RNA_EBNA2_only_RepB_E007435


title: RNA-seq: untaggged EBNA2 transient transfection Rep 1

description: Library name: RNA_EBNA2_only_RepA_E007434


title: paya_mng_138

description: PAYA MNG


title: paya_mng_137

description: PAYA MNG


title: RNA-seq: nGFP taggged EBNA2 transient transfection Rep 3

description: Library name: RNA_EBNA2_nGFP_RepC_E007439

value: nGFP tagged EBNA2


title: HT29 EHMT1 KO rep#3

value: female

value: epithelial

value: EHMT1 KO


title: RNA-seq: nGFP taggged EBNA2 transient transfection Rep 2

description: Library name: RNA_EBNA2_nGFP_RepB_E007438


title: paya_mng_136

description: PAYA MNG

value: Female

value: skull base


title: HT29 EHMT1 KO rep#2


title: RNA-seq: nGFP taggged EBNA2 transient transfection Rep 1

description: Library name: RNA_EBNA2_nGFP_RepA_E007437


title: RNA-seq: cGFP taggged EBNA2 transient transfection Rep 2

description: Library name: RNA_EBNA2_cGFP_RepB_E007441

value: cGFP tagged EBNA2


title: HT29 EHMT1 KO rep#1


title: RNA-seq: untagged BMRF1 transient transfection Rep 3

description: Library name: RNA_BMRF1_only_RepC_E007485

value: untagged BMRF1


title: RNA-seq: cGFP taggged EBNA2 transient transfection Rep 1

description: Library name: RNA_EBNA2_cGFP_RepA_E007440


title: paya_mng_135

description: PAYA MNG

value: spinal


title: HT29 EHMT1/2 DKO rep#3

value: EHMT1/2 DKO


title: paya_mng_128

description: PAYA MNG

value: Frozen

value: ben

value: supratentoriell


title: RNA-seq: untagged BMRF1 transient transfection Rep 2

description: Library name: RNA_BMRF1_only_RepB_E007484

value: CCHMC


title: RNA-seq: untagged BMRF1 transient transfection Rep 1

description: Library name: RNA_BMRF1_only_RepA_E007483

value: Transient transfection


title: HT29 EHMT1/2 DKO rep#2


title: paya_mng_127

description: PAYA MNG

value: FFPE

value: Male


title: RNA-seq: nGFP tagged BMRF1 transient transfection Rep 3

description: Library name: RNA_BMRF1_nGFP_RepC_E007488

value: nGFP tagged BMRF1


title: HT29 EHMT1/2 DKO rep#1

value: Colon

value: female


title: RNA-seq: nGFP tagged BMRF1 transient transfection Rep 2

description: Library name: RNA_BMRF1_nGFP_RepB_E007487


title: RNA-seq: nGFP tagged BMRF1 transient transfection Rep 1

description: Library name: RNA_BMRF1_nGFP_RepA_E007486


title: paya_mng_126

description: PAYA MNG

value: ventricel


title: 4T1 cells-H-3

city: Changzhou

first: Tianhan

last: Xu

address: 68 Middle Gehu Road

country: China

institute: The Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University

description:
Library name: Sample6
FPKM_H3

data_processing:
The libraries were sequenced on an Illumina Novaseq X Plus platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp 1 and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: GRCm39.110
Supplementary files format and content: processed data.txt

source_name: mammary gland

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
Libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions.

value: mammary gland

value: HA


title: RNA-seq: cGFP tagged BMRF1 transient transfection Rep 3

description: Library name: RNA_BMRF1_cGFP_RepC_E007491

value: cGFP tagged BMRF1


title: RNA-seq: cGFP tagged BMRF1 transient transfection Rep 2

description: Library name: RNA_BMRF1_cGFP_RepB_E007490


title: paya_mng_125

description: PAYA MNG

value: Female


title: RNA-seq: cGFP tagged BMRF1 transient transfection Rep 1

description: Library name: RNA_BMRF1_cGFP_RepA_E007489


title: 4T1 cells-H-2

description:
Library name: Sample5
FPKM_H2


title: paya_mng_123

description: PAYA MNG


title: ChIP-seq: anti-RBPJ in GFP control stable transfection Rep 3

description: Library name: RBPJ_ChIP_CL0038_GFP_RepC_E007506

library_source: genomic

data_processing:
ChIP-seq alignment, quality control, and peak calling was performed using a version of the ChIP-Seq Transcription Factor Pipeline v2.2.0 from the ENCODE Project slightly modified to run within a Nextflow environment.
ChIP-seq reads were aligned to the human genome (hg38) using Bowtie2. Aligned reads were then sorted using samtools and duplicate reads were removed using Picard.
Peaks were called using the default parameters of MACS2.
Conservative overlap peaks, generated from the ENCODE pipeline, were obtained for each transfection plasmid and used for downstream analyses.
Assembly: hg38
Supplementary files format and content: Conservative overlap peaks in narrowPeak format.
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing CPM --binSize 10

extract_protocol:
Cells were crosslinked and nuclei were sonicated as described previously (Lu et al. 2015).
Libraries were prepared via ChIPmentation (Schmidl et al. 2015).

value: GFP control

tag: chip target

value: RBPJ

tag: antibody

tag: antibody lot_number


title: ChIP-seq: anti-RBPJ in GFP control stable transfection Rep 1

description: Library name: RBPJ_ChIP_CL0038_GFP_RepA_E007508

tag: transfection plasmid


title: 4T1 cells-H-1

description:
Library name: Sample4
FPKM_H1

tag: treatment


title: paya_mng_121

description: PAYA MNG


title: ChIP-seq: anti-RBPJ in cGFP tagged RTA stable transfection Rep 3

description: Library name: RBPJ_ChIP_CL0062_RTA_RepF_E007080

value: cGFP tagged RTA


title: 4T1 cells-B-3

description:
Library name: Sample3
FPKM_B3


title: ChIP-seq: anti-RBPJ in GFP control stable transfection Rep 2

description: Library name: RBPJ_ChIP_CL0038_GFP_RepB_E007507


title: paya_mng_120

description: PAYA MNG

value: int


title: ChIP-seq: anti-RBPJ in cGFP tagged RTA stable transfection Rep 2

description: Library name: RBPJ_ChIP_CL0062_RTA_RepE_E007079


title: 4T1 cells-B-2

description:
Library name: Sample2
FPKM_B2


title: ChIP-seq: anti-RBPJ in cGFP tagged RTA stable transfection Rep 1

description: Library name: RBPJ_ChIP_CL0062_RTA_RepD_E007078


title: ChIP-seq: anti-RBPJ in nGFP tagged EBNA2 stable transfection Rep 3

description: Library name: RBPJ_ChIP_CL0041_EBNA2_RepF_E007074

value: nGFP tagged EBNA2


title: paya_mng_119

description: PAYA MNG

value: mal


title: TLR4KO-MACT-SCV-3

city: Guelph

first: Umesh

middle: K.

last: Shandilya

state: Ontario

address: 50 Stone Rd E

department: Animal Biosciences

country: Canada

institute: University of Guelph

description: Library name: Sample 15

data_processing:
CLC genomics workbench v 25.0.1
Sequence reads were trimmed for adaptor sequences using CLC genomics workbench.
Trimmed sequences were mapped to zebrafish reference genome (GRCz11)  using CLC genomics workbench
Read count extraction and normalization were performed using CLC genomics benchwork
Assembly: mm10
Supplementary files format and content: Each files include raw counts, RPKM, TPM, Gene ID and name for each sample

organism: Bos taurus

source_name: Mammary gland

growth_protocol: Wild-type bovine mammary epithelial MAC-T cells and CRISPR-Cas9-generated TLR4-knockout MAC-T cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and penicillin–streptomycin at 100 U/mL. Cells were cultured at 37°C in a humidified incubator containing 5% CO₂ and propagated under standard conditions until approximately 80% confluence before experimental challenge.

extract_protocol:
Total RNA was isolated from infected and control wild-type and TLR4-knockout MAC-T cells using the RNeasy Mini Kit according to the manufacturer’s instructions. Residual genomic DNA was removed by DNase I digestion. RNA quantity and purity were assessed spectrophotometrically using A260/A280 absorbance ratios, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer. RNA samples with RNA integrity numbers greater than 7 were selected for downstream library preparation and sequencing.
RNA libraries for RNA-seq were prepared using the Illumina Seq library preparation kit using the manufacturer's instructions.

treatment_protocol: Wild-type and TLR4-knockout MAC-T cells were seeded into 24-well plates at a density of 5 × 10⁴ cells per well and cultured until approximately 80% confluence. Cells were then exposed to either Staphylococcus aureus parental strain 3231, its isogenic small colony variant Heba3231, or an equivalent volume of sterile carrier medium as the uninfected control. Bacterial challenge was performed at a multiplicity of infection of 25:1 for 3.5 h at 37°C in 5% CO₂. After addition of bacteria, plates were briefly centrifuged at 250 × g for 2 min to facilitate bacterial–cell contact. Following treatment, cells were collected in TRIzol and stored at −80°C until RNA isolation.

value: Mammary gland

value: TLR4 KO MACT-T

tag: cell type

value: Unknown

value: TLR4 knockout

value: SCV-Infected

tag: batch


title: ChIP-seq: anti-RBPJ in nGFP tagged EBNA2 stable transfection Rep 2

description: Library name: RBPJ_ChIP_CL0041_EBNA2_RepE_E007073


title: CandR-iMGT-Myh6-eGFP-MEFs, siChst7, D1, IgG, BiolRep2

city: Baltimore

first: Chulan

last: Kwon

state: MD

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

institute: Johns Hopkins University

description:
Library name: d1_siChst7_2_CandR_IgG
30 M read

data_processing:
Bowtie2 was used to map reads to mm10
MACS3 called peaks
Assembly: mm10
Supplementary files format and content: The narrowpeaks files are the output from MACS3
Library strategy: CUT&Run

growth_protocol: The cells were cultured in plates precoated with 0.1% gelatin (Stem Cell Technologies, #7903) and maintained in Fibroblast Culture Medium (FCM) consisting of DMEM (Corning, #10-013-CV), 10% fetal bovine serum (FBS; VWR, #89510-186), and 1% antibiotic-antimycotic solution (Gibco, #15240062) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
At Day 1 post-MGT overexpression, cells were harvested and frozen in 90% FBS with 10% DMSO using a controlled-rate freezing container (Mr. Frosty) at –80C. Approximately 250,000 cells were used per condition.
CUTandRUN DNA samples sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7645L) along with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1, NEB #E7600S). DNA libraries were cleaned up using AMPure XP reagent, Bechman Coulter, A63881).

treatment_protocol: On siRNA transfection day (day −1), cells were detached using 0.25% trypsin-EDTA (Thermo Fisher, #25200056) for 3 min at 37°C, neutralized with fibroblast culture medium (FCM), centrifuged, and resuspended in induction cardiac reprogramming medium (iCRM), consisting of DMEM, 20% Medium 199 (Gibco, #11150-059), 10% FBS, and 1% A/A. Cells were plated in 6-well plates at a density of 300,000 cells per well and transfected with siJunb, siH1f0, or siControl. The following day (day 0), 1 μg/mL doxycycline hydrochloride (Dox; Sigma, #D3072) diluted in iCRM was added to induce MGT expression.

value: mouse embryonic fibroblasts

tag: treatment 1

tag: treatment 2

value: Doxy induced (MGT) cardiac reprogramming

value: IgG

tag: time

value: Day 1 post-MGT


title: paya_mng_118

description: PAYA MNG

tag: material

value: FFPE

tag: Sex

value: Male

value: ben

value: supratentoriell


title: TLR4KO-MACT-SCV-2

description: Library name: Sample 14


title: ChIP-seq: anti-RBPJ in nGFP tagged EBNA2 stable transfection Rep 1

description: Library name: RBPJ_ChIP_CL0041_EBNA2_RepD_E007072

value: RBPJ


title: paya_mng_116

description: PAYA MNG

tag: age group

tag: methylation class


title: CandR-iMGT-Myh6-eGFP-MEFs, siChst7, D1, IgG, BiolRep1

description:
Library name: d1_siChst7_1_CandR_IgG
30 M read


title: TLR4KO-MACT-SCV-1

description: Library name: Sample 13

tag: tissue


title: CandR-iMGT-Myh6-eGFP-MEFs, siControl, D1, IgG, BiolRep1

description:
Library name: d1_siControl_1_CandR_IgG
30 M read

value: siCtrl


title: ChIP-seq: anti-GFP in nGFP tagged ZTA stable transfection Rep 3

description: Library name: ChIP_CL0059_ZTA_RepF_E006829

value: nGFP tagged ZTA

value: GFP

value: Abcam ab290


title: paya_mng_110

description: PAYA MNG

value: Female

tag: localisation

value: skull base


title: TLR4KO-MACT-PS-3

description: Library name: Sample 12

value: Mammary gland

tag: cell line

value: TLR4 KO MACT-T

value: Unknown

tag: genotype

value: TLR4 knockout

value: PS-Infected


title: CandR-iMGT-Myh6-eGFP-MEFs, siChst7, D1, JUNB, BiolRep2

description:
Library name: d1_siChst7_2_CandR_JUNB
30 M read

value: mouse embryonic fibroblasts

value: Doxy induced (MGT) cardiac reprogramming

tag: antibody

value: JUNB

value: Day 1 post-MGT


title: ChIP-seq: anti-GFP in nGFP tagged ZTA stable transfection Rep 2

description: Library name: ChIP_CL0059_ZTA_RepE_E006828

tag: chip target

tag: antibody lot_number


title: paya_mng_109

description: PAYA MNG

value: FFPE

value: Male

value: int

value: supratentoriell


title: TLR4KO-MACT-PS-2

description: Library name: Sample 11

tag: treatment


title: CandR-iMGT-Myh6-eGFP-MEFs, siChst7, D1, JUNB, BiolRep1

description:
Library name: d1_siChst7_1_CandR_JUNB
30 M read

tag: cell type


title: paya_mng_108

description: PAYA MNG

value: ben


title: ChIP-seq: anti-GFP in nGFP tagged ZTA stable transfection Rep 1

description: Library name: ChIP_CL0059_ZTA_RepD_E006827

tag: transfection plasmid

value: nGFP tagged ZTA

value: GFP

value: Abcam ab290


title: TLR4KO-MACT-PS-1

description: Library name: Sample 10

value: Mammary gland

tag: batch


title: CandR-iMGT-Myh6-eGFP-MEFs, siControl, D1, JUNB, BiolRep2

description:
Library name: d1_siControl_2_CandR_JUNB
30 M read

tag: treatment 1

value: siCtrl

tag: treatment 2


title: ChIP-seq: anti-GFP in nGFP tagged EBNALP stable transfection (TREx) Rep 3

description: Library name: ChIP_CL0154_EBNALP_RepC_E007184

value: Flp-In T-REx-293

value: nGFP tagged EBNALP


title: paya_mng_107

description: PAYA MNG

tag: material


title: MACT-SCV-3

description: Library name: Sample 9

value: MAC-T cell

value: Unknown

value: WT

value: SCV-Infected


title: CandR-iMGT-Myh6-eGFP-MEFs, siControl, D1, JUNB, BiolRep1

description:
Library name: d1_siControl_1_CandR_JUNB
30 M read

value: mouse embryonic fibroblasts

value: Doxy induced (MGT) cardiac reprogramming

value: JUNB

tag: time

value: Day 1 post-MGT


title: ChIP-seq: anti-GFP in nGFP tagged EBNALP stable transfection (TREx) Rep 2

description: Library name: ChIP_CL0154_EBNALP_RepB_E007183


title: paya_mng_104

description: PAYA MNG

value: FFPE

tag: Sex

value: Female

tag: age group

value: posterior fossa


title: MACT-SCV-2

description: Library name: Sample 8

tag: tissue


title: paya_mng_292

description: PAYA MNG

tag: methylation class

value: ben

tag: localisation

value: skull base


title: ChIP-seq: anti-GFP in nGFP tagged EBNALP stable transfection (TREx) Rep 1

description: Library name: ChIP_CL0154_EBNALP_RepA_E007182

tag: cell line

value: GFP

value: Abcam ab290


title: paya_mng_103

description: PAYA MNG


title: MACT-SCV-1

description: Library name: Sample 7

value: Mammary gland

tag: genotype


title: paya_mng_275

description: PAYA MNG


title: ChIP-seq: anti-GFP in nGFP tagged EBNA3C stable transfection Rep 3

description: Library name: ChIP_CL0057_EBNA3C_RepI_E006826

value: nGFP tagged EBNA3C

tag: chip target

tag: antibody


title: paya_mng_102

description: PAYA MNG

value: mal


title: MACT-PS-3

description: Library name: Sample 6

value: MAC-T cell

value: Unknown

tag: treatment

value: PS-Infected


title: paya_mng_271

description: PAYA MNG

value: supratentoriell


title: ChIP-seq: anti-GFP in nGFP tagged EBNA3C stable transfection Rep 2

description: Library name: ChIP_CL0057_EBNA3C_RepH_E006825

tag: antibody lot_number


title: paya_mng_099

description: PAYA MNG

value: Male


title: paya_mng_262

description: PAYA MNG


title: MACT-PS-2

description: Library name: sample 5

tag: cell type

value: WT


title: ChIP-seq: anti-GFP in nGFP tagged EBNA3C stable transfection Rep 1

description: Library name: ChIP_CL0057_EBNA3C_RepG_E006824

tag: transfection plasmid


title: paya_mng_098

description: PAYA MNG


title: MACT-PS-1

description: Library name: Sample 4

tag: batch


title: paya_mng_260

description: PAYA MNG


title: ChIP-seq: anti-GFP in nGFP tagged EBNA2 stable transfection Rep 3

description: Library name: ChIP_CL0041_EBNA2_RepI_E007071

value: nGFP tagged EBNA2


title: paya_mng_094

description: PAYA MNG

value: FFPE

value: int


title: MAC-T-3

description: Library name: Samples 3

value: Control-Uninfected


title: paya_mng_259

description: PAYA MNG

value: ben


title: ChIP-seq: anti-GFP in nGFP tagged EBNA2 stable transfection Rep 2

description: Library name: ChIP_CL0041_EBNA2_RepH_E007070


title: paya_mng_093

description: PAYA MNG

value: Female

value: posterior fossa


title: MAC-T-2

description: Library name: Sample 2


title: paya_mng_250

description: PAYA MNG

value: orbital


title: paya_mng_087

description: PAYA MNG

value: Frozen


title: ChIP-seq: anti-GFP in nGFP tagged EBNA2 stable transfection Rep 1

description: Library name: ChIP_CL0041_EBNA2_RepG_E007069

value: GFP

value: Abcam ab290


title: MAC-T-1

description: Library name: Sample 1

value: Mammary gland

value: MAC-T cell


title: paya_mng_249

description: PAYA MNG


title: ChIP-seq: anti-GFP in nGFP tagged EBNA1 stable transfection Rep 3

description: Library name: ChIP_CL0116_EBNA1_RepC_E006340

value: nGFP tagged EBNA1


title: paya_mng_085

description: PAYA MNG

value: supratentoriell


title: paya_mng_235

description: PAYA MNG

value: Male

value: skull base


title: IL10RAKO-MACT-SCV-3

description: Library name: Sample 15

growth_protocol: Wild-type bovine mammary epithelial MAC-T cells and CRISPR-Cas9-generated  IL10RA-knockout MAC-T cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and penicillin–streptomycin at 100 U/mL. Cells were cultured at 37°C in a humidified incubator containing 5% CO₂ and propagated under standard conditions until approximately 80% confluence before experimental challenge.

extract_protocol:
Total RNA was isolated from infected and control wild-type and  IL10RA-knockout MAC-T cells using the RNeasy Mini Kit according to the manufacturer’s instructions. Residual genomic DNA was removed by DNase I digestion. RNA quantity and purity were assessed spectrophotometrically using A260/A280 absorbance ratios, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer. RNA samples with RNA integrity numbers greater than 7 were selected for downstream library preparation and sequencing.
RNA libraries for RNA-seq were prepared using the Illumina Seq library preparation kit using the manufacturer's instructions.

treatment_protocol: Wild-type and  IL10RA-knockout MAC-T cells were seeded into 24-well plates at a density of 5 × 10⁴ cells per well and cultured until approximately 80% confluence. Cells were then exposed to either Staphylococcus aureus parental strain 3231, its isogenic small colony variant Heba3231, or an equivalent volume of sterile carrier medium as the uninfected control. Bacterial challenge was performed at a multiplicity of infection of 25:1 for 3.5 h at 37°C in 5% CO₂. After addition of bacteria, plates were briefly centrifuged at 250 × g for 2 min to facilitate bacterial–cell contact. Following treatment, cells were collected in TRIzol and stored at −80°C until RNA isolation.

value: IL10RA KO MACT-T

value: IL10RA knockout

value: SCV-Infected


title: ChIP-seq: anti-GFP in nGFP tagged EBNA1 stable transfection Rep 2

description: Library name: ChIP_CL0116_EBNA1_RepB_E006339


title: paya_mng_083

description: PAYA MNG

value: FFPE

value: int


title: paya_mng_233

description: PAYA MNG

value: Female

value: ben


title: ChIP-seq: anti-GFP in nGFP tagged EBNA1 stable transfection Rep 1

description: Library name: ChIP_CL0116_EBNA1_RepA_E006338


title: paya_mng_082

description: PAYA MNG


title: IL10RAKO-MACT-SCV-2

description: Library name: Sample 14


title: IL10RAKO-MACT-SCV-1

description: Library name: Sample 13


title: paya_mng_231

description: PAYA MNG


title: paya_mng_081

description: PAYA MNG

value: spinal


title: IL10RAKO-MACT-PS-3

description: Library name: Sample 12

value: PS-Infected


title: ChIP-seq: anti-GFP in cGFP tagged BMRF1 stable transfection Rep 3

description: Library name: ChIP_CL0171_BMRF1_RepC_E007584

value: cGFP tagged BMRF1

value: GFP


title: paya_mng_230

description: PAYA MNG


title: paya_mng_080

description: PAYA MNG


title: ChIP-seq: anti-GFP in cGFP tagged BMRF1 stable transfection Rep 2

description: Library name: ChIP_CL0171_BMRF1_RepB_E007583

value: Abcam ab290


title: IL10RAKO-MACT-PS-2

description: Library name: Sample 11

value: Mammary gland


title: paya_mng_226

description: PAYA MNG


title: ChIP-seq: anti-GFP in cGFP tagged BMRF1 stable transfection Rep 1

description: Library name: ChIP_CL0171_BMRF1_RepA_E007582


title: paya_mng_079

description: PAYA MNG

value: posterior fossa


title: IL10RAKO-MACT-PS-1

description: Library name: Sample 10


title: paya_mng_220

description: PAYA MNG

value: supratentoriell


title: ATAC-seq: GFP control stable transfection Rep 3

description: Library name: ATAC_CL0038_GFP_RepC_E006356_E006520

data_processing:
ATAC-seq alignment, quality control, and peak calling was performed using a version of the DNA Accessibility Pipeline v2.2.0 from the ENCODE Project slightly modified to run within a Nextflow environment.
ATAC-seq reads were aligned to the human genome (hg38) using Bowtie2. Aligned reads were then sorted using samtools and duplicate reads were removed using Picard.
Peaks were called using the default parameters of MACS2.
Conservative overlap peaks, generated from the ENCODE pipeline, were obtained for each transfection plasmid and used for downstream analyses.
Assembly: hg38
Supplementary files format and content: Conservative overlap peaks in narrowPeak format.
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing CPM --binSize 10

extract_protocol:
Transposase Tn5 with sequencing adapter sequences was used to cut the accessible DNA as detailed in Buenrostro et al. 2015
The resulting accessible DNA sequences were isolated, and libraries were prepared from 50,000 cells from each cell line using the OMNI ATAC protocol as detailed in Corces et al 2017

value: GFP control


title: paya_mng_077

description: PAYA MNG

value: Male


title: paya_mng_219

description: PAYA MNG


title: MACT-SCV-3

description: Library name: Sample 9

value: MAC-T cell

value: WT


title: ATAC-seq: GFP control stable transfection Rep 2

description: Library name: ATAC_CL0038_GFP_RepB_E006355_E006519


title: MACT-SCV-2

description: Library name: Sample 8

value: SCV-Infected


title: paya_mng_076

description: PAYA MNG

value: FFPE


title: paya_mng_207

description: PAYA MNG


title: ATAC-seq: GFP control stable transfection Rep 1

description: Library name: ATAC_CL0038_GFP_RepA_E006354_E006518


title: paya_mng_075

description: PAYA MNG

value: skull base


title: paya_mng_200

description: PAYA MNG


title: MACT-SCV-1

description: Library name: Sample 7


title: ATAC-seq: nGFP tagged ZTA stable transfection Rep 3

description: Library name: ATAC_CL0059_ZTA_RepF_E006671

value: nGFP tagged ZTA


title: paya_mng_074

description: PAYA MNG

value: int


title: MACT-PS-3

description: Library name: Sample 6


title: ATAC-seq: nGFP tagged ZTA stable transfection Rep 2

description: Library name: ATAC_CL0059_ZTA_RepE_E006670


title: paya_mng_199

description: PAYA MNG

value: Female

value: ben


title: paya_mng_070

description: PAYA MNG

value: Frozen


title: MACT-PS-2

description: Library name: sample 5

value: PS-Infected


title: ATAC-seq: nGFP tagged ZTA stable transfection Rep 1

description: Library name: ATAC_CL0059_ZTA_RepD_E006669


title: paya_mng_069

description: PAYA MNG

value: spinal


title: paya_mng_192

description: PAYA MNG


title: ATAC-seq: cGFP tagged RTA stable transfection Rep 3

description: Library name: ATAC_CL0062_RTA_RepC_E005563

value: cGFP tagged RTA


title: MACT-PS-1

description: Library name: Sample 4

value: Mammary gland


title: paya_mng_066

description: PAYA MNG


title: MAC-T-3

description: Library name: Sample 3

value: Control-Uninfected


title: paya_mng_191

description: PAYA MNG

value: supratentoriell


title: paya_mng_065

description: PAYA MNG

value: Male

value: mal


title: ATAC-seq: cGFP tagged RTA stable transfection Rep 2

description: Library name: ATAC_CL0062_RTA_RepB_E005562


title: paya_mng_190

description: PAYA MNG

value: posterior fossa


title: MAC-T-2

description: Library name: Sample 2

value: MAC-T cell

value: WT


title: ATAC-seq: cGFP tagged RTA stable transfection Rep 1

description: Library name: ATAC_CL0062_RTA_RepA_E005561


title: paya_mng_058

description: PAYA MNG

value: FFPE


title: MAC-T-1

description: Library name: Sample 1


title: ATAC-seq: nGFP tagged EBNALP stable transfection (TREx) Rep 3

description: Library name: ATAC_CL0154_EBNALP_RepC_E007187

value: Flp-In T-REx-293

value: nGFP tagged EBNALP


title: paya_mng_189

description: PAYA MNG

value: Female


title: paya_mng_057

description: PAYA MNG

value: ben


title: paya_mng_188

description: PAYA MNG


title: Lemna aequinoctialis, experiment, Indole-3-lactic acid 3

city: Seoul

first: SoHee

last: Park

address: 84, Heukseok-ro

country: South Korea

institute: Chung-ang university

description: Library name: Lemna aequinoctialis-Indole-3-lactic acid 3

data_processing:
Data processing was performed by FASTQ filtering. Raw reads were filtered to remove adapter sequences, poly-N reads, and low-quality reads.
Clean reads were de novo assembled using Trinity (v2.15.1), and the assembled transcripts were clustered using Corset (v1.09).
The clean reads were mapped to the Trinity-assembled transcriptome using RSEM (v1.3.3), and gene-level read counts were generated.
Differential gene expression analysis was performed using DESeq2 (v1.42.0) based on the read count data.
Assembly: RSEM
Supplementary files format and content: Excel files include raw read counts for each sample
Supplementary files format and content: Excel files include FPKM values for each sample

organism: Lemna aequinoctialis

source_name: Lemna aequinoctialis plant cell

growth_protocol: L. aequinoctialis was cultured in Diamond 200 mL flasks of liquid medium at 25 ± 1 °C, exposed to light intensities of 81–84 µmol m⁻² s⁻¹, and under a 16-h light and 8-h dark cycle for 28 days in an incubator (NEX-202 M, EYELA, Nexus Technologies, Seoul, South Korea).

extract_protocol:
Total RNA was extracted from plant tissues using the Monarch Total RNA Miniprep Kit (New England Biolabs, Massachusetts, USA; Cat. No. T2010S). The tissue was disrupted in 400 µL of 1× DNA/RNA Protection Reagent using a TacoPrep Bead Beater for 13 s, and the homogenized lysate was centrifuged at 16,000 × g for 2 min to remove plant debris. The supernatant was mixed with 400 µL of RNA lysis buffer, and genomic DNA was removed using a gDNA removal column by centrifugation at 16,000 × g for 30 s. An equal volume of 95% ethanol was added to the flow-through, and the mixture was loaded onto an RNA purification column. The column was washed with RNA wash buffer and centrifuged, and total RNA was eluted with 50 µL of nuclease-free water. The isolated RNA was stored at −80 °C until further analysis. RNA quantity and quality were assessed using a Nanodrop spectrophotometer, an Agilent 5400 Fragment Analyzer System, agarose gel electrophoresis, Qubit, real-time PCR, and a bioanalyzer. RNA sequencing libraries were constructed by purifying mRNA from total RNA using poly-T oligo-attached magnetic beads, followed by mRNA fragmentation, first- and second-strand cDNA synthesis, end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Qualified libraries were sequenced on an Illumina NovaSeq X Plus platform using 150-bp paired-end sequencing.
RNA-Seq

value: Lemna aequinoctialis plant cell

value: Indole-3-lactic acid (ILA)


title: paya_mng_056

description: PAYA MNG


title: paya_mng_198

description: PAYA MNG

value: int


title: paya_mng_179

description: PAYA MNG


title: Lemna aequinoctialis, experiment, Indole-3-lactic acid 2

description: Library name: Lemna aequinoctialis-Indole-3-lactic acid 2


title: ATAC-seq: nGFP tagged EBNALP stable transfection (TREx) Rep 1

description: Library name: ATAC_CL0154_EBNALP_RepA_E007185


title: ATAC-seq: nGFP tagged EBNALP stable transfection (TREx) Rep 2

description: Library name: ATAC_CL0154_EBNALP_RepB_E007186


title: paya_mng_055

description: PAYA MNG


title: paya_mng_178

description: PAYA MNG


title: Lemna aequinoctialis, experiment, Indole-3-lactic acid 1

description: Library name: Lemna aequinoctialis-Indole-3-lactic acid 1


title: ATAC-seq: nGFP tagged EBNA3C stable transfection Rep 3

description: Library name: ATAC_CL0057_EBNA3C_RepF_E006550

value: nGFP tagged EBNA3C


title: paya_mng_053

description: PAYA MNG

value: orbital


title: Lemna aequinoctialis, Control 3

description: Library name: Lemna aequinoctialis-Control 3


title: paya_mng_177

description: PAYA MNG


title: ATAC-seq: nGFP tagged EBNA3C stable transfection Rep 2

description: Library name: ATAC_CL0057_EBNA3C_RepE_E006549_E006805


title: paya_mng_052

description: PAYA MNG


title: paya_mng_176

description: PAYA MNG

value: skull base


title: Lemna aequinoctialis, Control 2

description: Library name: Lemna aequinoctialis-Control 2


title: ATAC-seq: nGFP tagged EBNA3C stable transfection Rep 1

description: Library name: ATAC_CL0057_EBNA3C_RepD_E006548_E006804


title: paya_mng_051

description: PAYA MNG


title: Lemna aequinoctialis, Control 1

description: Library name: Lemna aequinoctialis-Control 1


title: paya_mng_175

description: PAYA MNG

value: supratentoriell


title: paya_mng_049

description: PAYA MNG

value: Frozen


title: ATAC-seq: nGFP tagged EBNA3B stable transfection Rep 3

description: Library name: ATAC_CL0055_EBNA3B_RepC_E005560

value: nGFP tagged EBNA3B


title: EryP_KO_Stag2_Rep_3

city: New York

first: Varun

middle: Saichandan

last: Sudunagunta

state: NY

address: 650 W 168th, Black Building, 1110B

department: Division of Hematology/Oncology, Department of Medicine

institute: Columbia University Vagelos College of Physicians and Surgeons

description: Library name: VS007

data_processing:
nf-core/cutandrun pipeline (v3.2.2)
Raw reads underwent adapter trimming and quality filtering, followed by alignment to the mm10 reference genome using Bowtie2. A blacklist file was applied to remove known sequencing artifacts and nonspecific binding regions
Read coverage was computed with BEDTools (v2.30.0), normalized to Counts Per Million (CPM), and converted to BigWig format using bedGraphToBigWig for visualization
Peak calling was performed using both MACS2(v2.2.7.1) and SEACR (v1.3)(65) to identify narrow and broad peaks.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: Lineage-specified erythroid progenitor (EryP)

extract_protocol:
CUT&RUN assays were performed using the CUTANA ChIC/CUT&RUN Kit (EpiCypher) on 200,000 EryPs (Stag2 WT or KO) for Stag2, following the manufacturer’s instructions. After cell permeabilization and anti-Stag2 antibody binding, micrococcal nuclease (MNase) was activated to cleave DNA near bound protein sites, and released fragments were collected for downstream library preparation.
Approximately 5 ng of CUT&RUN DNA per sample was processed using the EpiCypher CUT&RUN Library Prep Kit, again following standard protocols. After end repair and adapter ligation, library quantity and fragment size distribution were checked using an Agilent 4150 TapeStation (D5000 ScreenTapes).

value: KO

value: STAG2 (A302-580, Bethyl)


title: paya_mng_174

description: PAYA MNG


title: ATAC-seq: nGFP tagged EBNA3B stable transfection Rep 2

description: Library name: ATAC_CL0055_EBNA3B_RepB_E005559


title: paya_mng_047

description: PAYA MNG


title: EryP_KO_Stag2_Rep_2

description: Library name: VS006

value: Lineage-specified erythroid progenitor (EryP)


title: paya_mng_173

description: PAYA MNG

value: FFPE

value: Male


title: ATAC-seq: nGFP tagged EBNA3B stable transfection Rep 1

description: Library name: ATAC_CL0055_EBNA3B_RepA_E005558


title: EryP_KO_Stag2_Rep_1

description: Library name: VS005


title: paya_mng_172

description: PAYA MNG


title: ATAC-seq: nGFP tagged EBNA3A stable transfection Rep 3

description: Library name: ATAC_CL0053_EBNA3A_RepF_E006547_E006802

value: nGFP tagged EBNA3A


title: paya_mng_046

description: PAYA MNG

value: Female


title: EryP_WT_Stag2_Rep_3

description: Library name: VS004

value: WT


title: paya_mng_154

description: PAYA MNG


title: paya_mng_045

description: PAYA MNG

value: ben


title: GRA knockin, Dex, biol rep2

city: RTP

first: Thomas

last: Randall

state: NC

address: 101 TW Alexander

institute: NIEHS

description: Library name: Sample 17

data_processing:
Alignment using STAR (V 2.5.1).
Read count was produced with featureCount (subread, Version 1.5.1)
Statistical analysis done with DEseq2 (v 1.38.3)
DEG was obtained using adjusted pvalue <0.05
Assembly: mm39/genecode_vM34
Supplementary files format and content: readcounts in txt format

source_name: hippocampus

extract_protocol:
The hippocampus was collected after the 6 hour PBS or Dex treatment.  Total RNA was isolated from the hippocampus using Qiagen RNeasy mini kit.
The integrity of the total RNA was determined using the TapeStation (Agilent Technologies), and RNA concentration was assessed using a Qubit (ThermoFisher Scientific).  A TruSeq RNA kit (Illumina, San Diego, CA) was utilized to prepare the poly(A)-enriched RNA-seq libraries that were sequenced on the Illumina NovaSeq 6000 in a 75-base paired-end mode according to the manufacturer’s protocol.

treatment_protocol: Adrenalectomized wild-type and homozygous GRA knockin mice were injected IP with PBS (vehicle) or dexamethasone (Dex) (1mg/kg).  After a 6-hour treatment time, mice were euthanized and the hippocampus removed.

value: hippocampus

value: male

tag: strain

value: GRA knockin

value: Dex


title: 4859, LOW RFI

first: Victoria

last: Asselstine

address: 553 Gordon St #501

description: Library name: Sample 38

data_processing:
Data was processed using CLC genomics workbench
the raw sequence data was trimmed using the automatic trimmer function of CLC Genomics Workbench (CLC Bio, Aarhus, Denmark) using a quality trimming score = 0.05.
After the reads were trimmed, quality control was performed using the NGS quality control tool of CLC Genomics Workbench
The trimmed sequence reads were then aligned to the annotated ARS_UCD1.2 bovine reference genome using the CLC Genomics Workbench
Alignment parameters included a length fraction of 0.8 and a similarity of 0.8, mismatch cost = 2, deletion cost = 3, insert cost = 3, minimum contig length = 200 base pairs (bp) were allowed
Read cound and normalization was performed using CLC genomics workbench
Assembly: ARS_UCD1.2
Supplementary files format and content: csv file with raw counts per gene and sample

source_name: Milk Somatic Cells

extract_protocol:
Milk samples were collected using a 3 cm plastic cannula to ensure no bacteria contaminated the sample. Milk was kept on ice and immediately processed for RNA extraction using Trizol reagent to preserve the integrity of RNA.
Library construction was performed using the TruSeq RNA sample preparation kit

value: Milk Somatic Cells

tag: breed

value: Holstein dairy


title: undescended testis (UD), Shih-tzu, age 30 months

city: Poznań

first: Arkadiusz

last: Kajdasz

state: wielkopolskie

address: ul. Z. Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

description: Library name: 6906_UD

data_processing:
Quality of raw reads were checked with fastqc (v0.11). Reads were mapped to the dog genome (CanFam3.1, downloaded from Ensembl database) with bowtie2 including --local setting (v2.4.2). SAM files were converted to BAM files with samtools (v1.11). Reads mapped to miRNA sequences were counted with featureCounts (v2.0.1) using annotation file downloaded from miRBase (v22, annotation file release date 2018-03-05).
Assembly: CanFam3.1
Supplementary files format and content: tab-delimited text files includes raw counts of miRNA for each Sample

organism: Canis lupus familiaris

source_name: testis

extract_protocol:
Total RNA from testicular tissue was isolated using an miRNeasy Mini Kit (Qiagen) according to manufacturer protocol.
The concentration of miRNA was measured with Qubit RNA BR Assay Kit (Invitrogen) on a Qubit 2.0 fluorometer (Invitrogen). The purity was analyzed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific). The RNA integrity number (RIN) values were checked on a 2100 Bioanalyzer instrument (Agilent) using RNA 6000 Nano kit (Agilent). For each sample, 200 ng of total RNA was used for library preparation with NEXTflex Small RNA-Seq Kit v3 (Bioo Scientific).

value: testis

tag: disease

value: undescended testis (UD)

value: Shih-tzu

tag: age

value: 30 months


title: ATAC-seq: nGFP tagged EBNA3A stable transfection Rep 2

description: Library name: ATAC_CL0053_EBNA3A_RepE_E006546_E006803


title: paya_mng_043

description: PAYA MNG

extract_protocol: Illumina protocol

tag: material

tag: Sex

tag: age group

value: tentorial


title: EryP_WT_Stag2_Rep_2

description: Library name: VS003

value: Lineage-specified erythroid progenitor (EryP)

value: STAG2 (A302-580, Bethyl)


title: paya_mng_151

description: PAYA MNG

value: FFPE

value: Male

tag: methylation class

tag: localisation

value: ventricel


title: ATAC-seq: nGFP tagged EBNA3A stable transfection Rep 1

description: Library name: ATAC_CL0053_EBNA3A_RepD_E006545_E006801

tag: cell line

value: nGFP tagged EBNA3A


title: paya_mng_042

description: PAYA MNG

value: Female

value: ben

value: skull base


title: paya_mng_150

description: PAYA MNG

value: int

value: orbital


title: EryP_WT_Stag2_Rep_1

description: Library name: VS002

tag: genotype

value: WT


title: ATAC-seq: nGFP tagged EBNA2 stable transfection Rep 3

description: Library name: ATAC_CL0041_EBNA2_RepC_E005554

value: nGFP tagged EBNA2


title: paya_mng_040

description: PAYA MNG

value: supratentoriell


title: paya_mng_149

description: PAYA MNG


title: paya_mng_037

description: PAYA MNG


title: EryP_WT_IgG

description: Library name: VS001

value: IgG


title: ATAC-seq: nGFP tagged EBNA2 stable transfection Rep 2

description: Library name: ATAC_CL0041_EBNA2_RepB_E005553


title: EryP_HiC_KO_Rep_4

description:
Library name: VSS007
Stag2_KO_merged.mcool

data_processing:
nf-core/hic pipeline (v.2.1.0)
Reads were aligned to the mouse reference genome mm10 using a prebuilt Bowtie2 index, and library digestion was specified as Arima (Arima restriction enzyme cocktail, ^GATC,G^ANTC). Within pipeline, read pairs were mapped to mm10 with Bowtie2 and filtered to retain valid Hi-C pairs following standard Hi-C processing logic (removal of low mapping quality reads, invalid ligation products, and duplicates). HiC-Pro-compatible mapping summaries and intermediate files were produced (HiC-Pro mapping outputs enabled) to facilitate QC and troubleshooting. For each replicate, contact matrices were generated at multiple resolutions (5 kb, 10 kb, 25 kb, 50 kb, 100 kb, 250 kb, 500 kb, 1 Mb, 2.5 Mb, 10 Mb) and stored in the cooler ecosystem as .cool and multi-resolution .mcool files. Matrices were balanced using iterative correction (ICE balancing as implemented in the cooler ecosystem), and downstream analyses used raw counts for statistical testing of interactions unless otherwise stated, while balanced matrices were used for visualization and structural feature inference.
Assembly: mm10
Supplementary files format and content: .mcool (individual replicates and merged)

extract_protocol:
Hi-C was performed using the low cell input modification of the Arima High Coverage Hi-C Kit on 130,000-250,000 EryPs (Stag2 WT and KO), following the manufacturer's instructions.
Approximately 5 ng of CUT&RUN DNA per sample was processed using the EpiCypher CUT&RUN Library Prep Kit, again following standard protocols. After end repair and adapter ligation, library quantity and fragment size distribution were checked using an Agilent 4150 TapeStation (D5000 ScreenTapes).

value: KO


title: paya_mng_148

description: PAYA MNG

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
Average Beta
Unmethylated and methylated signal intensities


title: ATAC-seq: nGFP tagged EBNA2 stable transfection Rep 1

description: Library name: ATAC_CL0041_EBNA2_RepA_E005552


title: paya_mng_034

description: PAYA MNG


title: EryP_HiC_KO_Rep_3

description:
Library name: VSS006
Stag2_KO_merged.mcool


title: ATAC-seq: nGFP tagged EBNA1 stable transfection Rep 3

description: Library name: ATAC_CL0116_EBNA1_RepC_E006343

value: nGFP tagged EBNA1


title: paya_mng_033

description: PAYA MNG

value: posterior fossa


title: paya_mng_147

description: PAYA MNG


title: EryP_HiC_KO_Rep_2

description:
Library name: VSS005
Stag2_KO_merged.mcool

value: Lineage-specified erythroid progenitor (EryP)


title: paya_mng_144

description: PAYA MNG

value: FFPE


title: paya_mng_031

description: PAYA MNG

value: spinal


title: ATAC-seq: nGFP tagged EBNA1 stable transfection Rep 2

description: Library name: ATAC_CL0116_EBNA1_RepB_E006342


title: paya_mng_134

description: PAYA MNG

value: Male


title: EryP_HiC_KO_Rep_1

description:
Library name: VSS004
Stag2_KO_merged.mcool


title: paya_mng_028

description: PAYA MNG


title: ATAC-seq: nGFP tagged EBNA1 stable transfection Rep 1

description: Library name: ATAC_CL0116_EBNA1_RepA_E006341


title: EryP_HiC_WT_Rep_3

description:
Library name: VSS003
Stag2_WT_merged.mcool


title: paya_mng_133

description: PAYA MNG

value: mal


title: ATAC-seq: cGFP tagged BMRF1 stable transfection Rep 3

description: Library name: ATAC_CL0171_BMRF1_RepC_E007581

value: cGFP tagged BMRF1


title: paya_mng_027

description: PAYA MNG

value: Female

value: ben


title: EryP_HiC_WT_Rep_2

description:
Library name: VSS002
Stag2_WT_merged.mcool


title: paya_mng_132

description: PAYA MNG


title: paya_mng_026

description: PAYA MNG


title: ATAC-seq: cGFP tagged BMRF1 stable transfection Rep 2

description: Library name: ATAC_CL0171_BMRF1_RepB_E007580


title: 4832, HIGH RFI

description: Library name: Sample 33

tag: tissue

value: Milk Somatic Cells

value: Holstein dairy


title: EryP_HiC_WT_Rep_1

description:
Library name: VSS001
Stag2_WT_merged.mcool

value: WT


title: paya_mng_131

description: PAYA MNG


title: ATAC-seq: cGFP tagged BMRF1 stable transfection Rep 1

description: Library name: ATAC_CL0171_BMRF1_RepA_E007579


title: paya_mng_025

description: PAYA MNG

value: ventricel


title: paya_mng_130

description: PAYA MNG

value: tentorial


title: Sl3_48h_R3

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

institute: INRAE

description: Library name: Sl3-48h_3

data_processing:
Sequenced reads were mapped to PN40024.v4 grapevine transcriptome (https://integrape.eu/resources/genes-genomes/genome-accessions/) using STAR with parameters  --alignIntronMax 60000 --alignMatesGapMax 60000 -- quantMode GeneCounts
Assembly: PN40024.v4 grapevine transcriptome (https://integrape.eu/resources/genes-genomes/genome-accessions/)
Supplementary files format and content: Matrix tables (tab-delimited text files) with either raw values or normalized (DESeq2) values for all features.

organism: Vitis vinifera

source_name: Infected grape berries

growth_protocol: Infected Vitis vinifera grapes were infected with Botrytis cinerea Vv3 or Sl3 strain and were incubated for 24h or 48h.

extract_protocol:
Total RNA was extracted according to the total RNA isolation protocol described by Reid et al. (2006), but with 10M rather than 8M LiCl, and resuspended in RNAse/DNAse-free water. The total RNA was then treated with a DNA-freeTM kit to remove any trace of DNA (Ambion – Applied Biosystems).
Illumina TruSeq Stranded mRNA Sample Prep kit was used to prepare all RNA-seq libraries, following the manufacturer’s instructions. Sequencing was performed by the Integragen platform. Samples were run on an Illumina HiSeq 4000 in paired mode, 2x75 bp.

value: Infected grape berries

tag: agent

value: Botrytis cinerea


title: Ter119_WT_ATAC_Rep3

description: Library name: AV006 ATAC

library_source: genomic single cell

data_processing:
Demultiplexed data was processed using the Cellranger count pipeline
For this Multi-ome, we did not process the scRNA portion of the data.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: gene_score_counts.tsv gene_score_feature_metadata.tsv gene_score_sample_metadata.tsv metadata.tsv
Supplementary files format and content: gene_score_feature_metadata.tsv
Supplementary files format and content: gene_score_sample_metadata.tsv
Supplementary files format and content: metadata.tsv

source_name: Ter119+ erythroblast

extract_protocol:
Nuclei were isolated from sorted Ter119+ erythroblasts as per 10X Genomics protocol
As per 10X multiome protocol

value: Ter119+ erythroblast

tag: library type

value: ATAC


title: paya_mng_023

description: PAYA MNG

value: int

value: orbital


title: Ter119_WT_GEX_Rep3

description: Library name: AV006 RNA

tag: cell type

value: mRNA


title: paya_mng_129

description: PAYA MNG

value: FFPE

value: Male

value: supratentoriell


title: Sl3_48h_R2

description: Library name: Sl3-48h_2


title: paya_mng_020

description: PAYA MNG

value: Female


title: Ter119_WT_ATAC_Rep2

description: Library name: AV005 ATAC


title: paya_mng_117

description: PAYA MNG

value: skull base


title: paya_mng_019

description: PAYA MNG

value: Frozen

value: ben


title: Sl3_48h_R1

description: Library name: Sl3-48h_1


title: Ter119_WT_GEX_Rep2

description: Library name: AV005 RNA

value: WT


title: paya_mng_115

description: PAYA MNG

value: spinal


title: Sl3_24h_R4

description: Library name: Sl3-24h_4


title: Ter119_KO_ATAC_Rep3

description: Library name: AV004 ATAC

value: KO


title: paya_mng_114

description: PAYA MNG


title: Sl3_24h_R3

description: Library name: Sl3-24h_3

value: Infected grape berries


title: Ter119_KO_GEX_Rep3

description: Library name: AV004 RNA


title: paya_mng_015

description: PAYA MNG


title: paya_mng_113

description: PAYA MNG


title: Sl3_24h_R2

description: Library name: Sl3-24h_2

value: Botrytis cinerea


title: paya_mng_013

description: PAYA MNG


title: paya_mng_018

description: PAYA MNG


title: paya_mng_112

description: PAYA MNG


title: Ter119_WT_ATAC_Rep1

description: Library name: AV003 ATAC

value: Ter119+ erythroblast


title: Vv3_48h_R3

description: Library name: Vv3-48h_3


title: Ter119_WT_GEX_Rep1

description: Library name: AV003 RNA


title: paya_mng_008

description: PAYA MNG


title: paya_mng_007

description: PAYA MNG


title: Vv3_48h_R2

description: Library name: Vv3-48h_2


title: paya_mng_111

description: PAYA MNG

value: posterior fossa


title: paya_mng_101

description: PAYA MNG


title: Ter119_KO_ATAC_Rep2

description: Library name: AV002 ATAC

value: ATAC


title: paya_mng_006

description: PAYA MNG


title: Vv3_48h_R1

description: Library name: Vv3-48h_1


title: Ter119_KO_GEX_Rep2

description: Library name: AV002 RNA


title: paya_mng_100

description: PAYA MNG


title: Vv3_24h_R4

description: Library name: Vv3-24h_4


title: paya_mng_005

description: PAYA MNG

value: mal


title: Ter119_KO_ATAC_Rep1

description: Library name: AV001 ATAC


title: paya_mng_092

description: PAYA MNG


title: Vv3_24h_R3

description: Library name: Vv3-24h_3


title: paya_mng_003

description: PAYA MNG


title: Ter119_KO_GEX_Rep1

description: Library name: AV001 RNA

value: mRNA


title: paya_mng_091

description: PAYA MNG

value: FFPE

value: int


title: Vv3_24h_R2

description: Library name: Vv3-24h_2


title: paya_mng_002

description: PAYA MNG


title: EryP_Feb18_KO_Gata1_Rep_3

description: Library name: VS065

data_processing:
nf-core/cutandrun pipeline (v3.2.2)
Raw reads underwent adapter trimming and quality filtering, followed by alignment to the hg38 reference genome using Bowtie2. A blacklist file was applied to remove known sequencing artifacts and nonspecific binding regions
Read coverage was computed with BEDTools (v2.30.0), normalized to Counts Per Million (CPM), and converted to BigWig format using bedGraphToBigWig for visualization
Peak calling was performed using both MACS2(v2.2.7.1) and SEACR (v1.3)(65) to identify narrow and broad peaks.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: Unipotent erythroid progenitor (EryP)

extract_protocol:
CUT&RUN assays were performed using the CUTANA ChIC/CUT&RUN Kit (EpiCypher) on 500,000 EryPs (Stag2 WT or KO) for Gata1, following the manufacturer’s instructions. After cell permeabilization and anti-Gata1 antibody binding, micrococcal nuclease (MNase) was activated to cleave DNA near bound protein sites, and released fragments were collected for downstream library preparation.
Approximately 5 ng of CUT&RUN DNA per sample was processed using the EpiCypher CUT&RUN Library Prep Kit, again following standard protocols. After end repair and adapter ligation, library quantity and fragment size distribution were checked using an Agilent 4150 TapeStation (D5000 ScreenTapes).

value: Unipotent erythroid progenitor (EryP)

tag: treatment

value: GATA1 (Abcam; ab11852)


title: paya_mng_090

description: PAYA MNG

value: Male

value: supratentoriell


title: PrimPol2-BrdU-Seq

city: Birmingham

first: Marco

last: Saponaro

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Paired-end BrdU-seq reads were aligned to the hg38 genome assembly using Bowtie 2 v.2.3.3.1 (Langmead et al., 2012).
BAM files were sorted and indexed using SAMtools v.1.4 (Li et al., 2009).
The reads that mapped to region DAC blacklisted for mappability by the ENCODE project were removed.
Coverage calcualtion was done using the function “quantify” in EaSeq, from the start to the end of the gene of all annotated genes
Assembly: hg38
Supplementary files format and content: .txt, containing the quantifications over each gene as above described

source_name: skin; foreskin

growth_protocol: Human immortalized fibroblasts (BJ-hTERT cells) were cultured in DMEM (Sigma-Aldrich) supplemented with 10 % FBS, 2 mM L-glutamine and penicillin/streptomycin in 5 % CO2 at 37°C.

extract_protocol:
Cells were fixed in 1 % formaldehyde for 10 min at room temperature. Then, glycine was added to a final concentration of 0.125 M and the reaction was incubated for 5 min at room temperature. Fixed cells were washed twice with ice-cold PBS, and lysed for 5 min in ice-cold ChIP cell lysis buffer (5 mM HEPES pH 8.0, 85 mM KCl, 0.5 % NP-40 alternative, protease inhibitors). Nuclei were pelleted by centrifugation at 3900 g for 5 min at 4ºC, and lysed for 5 min in ChIP nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS, protease inhibitors) and incubated 5 minutes on ice. Lysates were sonicated using VCX130 (Sonics & Materials, Inc) with the following settings: 8 cycles, 30 % Amp, 15 s ON, 25 s OFF. Sonicated chromatin was centrifuged at 17000 g at 4ºC for 10 min and the supernatant was stored at -80ºC until immunoprecipitation. Before immunoprecipitation, 15 µl of Dynabeads Protein A was washed twice with 900 µl 5 mg/ml BSA in PBS and reacted for 1 h or more with 3 µg of the corresponding antibody (Phospho-Histone H2A.X: ab2893, Abcam; H3: ab1791, Abcam) in 500 µl of 5 mg/ml BSA in PBS at room temperature. The beads were washed again with 900 µl 5 mg/ml BSA in PBS before use. The concentration of sonicated chromatin was quantified by using Quick Start Bradford protein 1x dye reagent (Bio-Rad). 50 µl chromatin were used as Input. 0.6 mg of chromatin was 1:5 diluted with ChIP dilution buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, protease inhibitors), and incubated with prepared beads overnight at 4ºC with rotation. Chromatin bound to beads was washed twice in ChIP low salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), twice in ChIP high salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl),  twice in ChIP LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 % NP40 alternative, 1 % sodium deoxycholate, 1 mM EDTA), and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA). Most of the TE buffer was removed after the beads were centrifuged at 3000 rpm for 3 min and put on Magnet. The remaining TE was removed after the beads were centrifuged again at 13200 rpm for 1 min and put on Magnet. The beads were resuspended in 50 µl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS) and incubated at 65°C for 10 min followed by centrifugation at 12000 rpm for 1 min. The supernatant was transferred to a new DNA low binding tube (Sarstedt) and incubated at 65°C overnight for de-crosslinking. Reverse cross-linked supernatant was mixed with 50 µl of TE and incubated with RNase A at 37°C for 1 h. The supernatant was further incubated with 0.7 mg/ml proteinase K at 55°C for 2 h. DNA was purified by DNA Clean & Concentrator-5 and eluted with 8 µl EB (10 mM Tris-HCl pH 8.5). The purified DNA was quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). 1 ng of DNA was used to construct DNA library according to Illumina's Nextera XT DNA Library Preparation Kit protocol. After being cleaned up, indexed libraries were quantified, normalized and pooled, sequenced on Illumina NextSeq system
NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads following manufacturer’s protocol
paired end on 4 lanes (L1-L4)

tag: condition

value: PrimPol siRNA2

value: skin; foreskin

value: BJ hTERT

value: fibroblasts

tag: chip antibody

value: anti-BrdU antibody, Sigma-Aldrich


title: paya_mng_001

description: PAYA MNG

source_name: PAYA MNG

value: Female

value: ben

value: ventricel


title: paya_mng_089

description: PAYA MNG

value: spinal


title: EryP_Feb18_KO_Gata1_Rep_2

description: Library name: VS064

value: KO


title: Pomalidomide, 5uM, Single ZF, 3

city: Lausanne

first: Nicolas

last: Thomä

address: Rte Cantonale

country: Switzerland

institute: EPFL

description:
Library name: Pomalidomide 5 Single ZF3
Single_Pomalidomide_processed.txt

library_source: other

data_processing:
Data was processed and matched to its expected sequence with Mutscan. Then the logFC was calculated with edgeR and Limma (Singe/Dual) or Loess (DMS). Additional details in the corresponding manuscript.
Assembly: Reference sequences were used for alignment
Supplementary files format and content: Tab delimmited text files. Contains count, logFC, Pvalues and dna sequence for alignment.

molecule: other

organism: Saccharomyces cerevisiae

extract_protocol:
For all Single ZF, Dual Z and Bonsai libraries, DNA was extracted using a custom yeast Miniprep protocol. For the DMS library, DNA was extracted using a custom yeast Midiprep protocol.
Sequencing libraries wer constructed by PCR with primers containing the illumina adapters

value: Pomalidomide, 5uM, Single ZF


title: EryP_Feb18_KO_Gata1_Rep_1

description: Library name: VS063


title: PrimPol1-BrdU-Seq

value: PrimPol siRNA1


title: Pomalidomide, 5uM, Single ZF, 2

description:
Library name: Pomalidomide 5 Single ZF2
Single_Pomalidomide_processed.txt


title: paya_mng_086

first: Philipp

last: Sievers

address: Im Neuenheimer Feld 224

description: PAYA MNG

value: FFPE

value: skull base


title: Pomalidomide, 5uM, Single ZF, 1

description:
Library name: Pomalidomide 5 Single ZF1
Single_Pomalidomide_processed.txt


title: EryP_Feb18_WT_Gata1_Rep_2

description: Library name: VS061

value: Unipotent erythroid progenitor (EryP)

value: WT

value: GATA1 (Abcam; ab11852)


title: paya_mng_084

description: PAYA MNG

value: supratentoriell


title: PAPRi2-BrdU-Seq

value: skin; foreskin


title: paya_mng_073

description: PAYA MNG


title: Pomalidomide, 15uM, Single ZF, 3

description:
Library name: Pomalidomide 15 Single ZF 3
Single_Pomalidomide_processed.txt

data_processing:
Data was processed and matched to its expected sequence with Mutscan. Then the logFC was calculated with edgeR and Limma (Singe/Dual) or Loess (DMS). Additional details in the corresponding manuscript.
Assembly: Reference sequences were used forr alignment
Supplementary files format and content: Tab delimmited text files. Contains count, logFC, Pvalues and dna sequence for alignment.

extract_protocol:
For all Single ZF and Dual ZF libraries, DNA was extracted using a custom yeast Miniprep protocol. For the DMS library, DNA was extracted using a custom yeast Midiprep protocol.
Sequencing libraries wer constructed by PCR with primers containing the illumina adapters

value: Pomalidomide5uM, Single ZF


title: EryP_Feb18_WT_Gata1_Rep_1

description: Library name: VS060


title: Pomalidomide, 15uM, Single ZF, 2

description:
Library name: Pomalidomide 15 Single ZF 2
Single_Pomalidomide_processed.txt


title: PARPi1-BrdU-Seq

value: BJ hTERT

value: fibroblasts


title: paya_mng_072

description: PAYA MNG

value: Male

value: posterior fossa


title: RAD6i2-BrdU-Seq

value: anti-BrdU antibody, Sigma-Aldrich


title: Pomalidomide, 15uM, Single ZF, 1

description:
Library name: Pomalidomide 15 Single ZF 1
Single_Pomalidomide_processed.txt


title: paya_mng_071

description: PAYA MNG

value: Female


title: Pig#34,No NRP+HOPE 2h

first: Diana

last: Albino

department: Surgery

institute: Columbia University

description:
Library name: Sample9
column name name in TPM_values.csv: P34.DCD

data_processing:
Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification. After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Sus Scrofa reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the geneid feature in the annotation file. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. The Benjamini–Hochberg correction was applied to generate adjusted p-values. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison.
Assembly: The trimmed reads were mapped to the Sus Scrofa reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary files format and content: csv file for normalized data for Arm1 and Arm2

organism: Sus scrofa

source_name: Myocardium

extract_protocol:
Total RNA was extracted using the Rneasy Mini Kit (Qiagen) as per manufacturer guidelines. RNA purity was assessed on a NanoDrop spectrophotometer. RNA samples were quantified using Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA inputs were normalized to 100ng.
ERCC RNA Spike-In Mix (Cat: #4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on a flowcell. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software.

treatment_protocol: Myocardial biopsies were collected at the end of experiment, flash-frozen in liquid nitrogen and stored at -80°C.

value: Myocardium

value: Cardiomyocytes

value: No NRP+ HOPE

tag: time


title: RAD6i1-BrdU-Seq


title: DMSO, Single ZF, 3

description:
Library name: DMSO Single ZF 3
Single_Pomalidomide_processed.txt

value: DMSO, Single ZF


title: paya_mng_064

institute: University Hospital Heidelberg, Intitute of Pathology

description: PAYA MNG

value: FFPE

value: int

value: skull base


title: DMSO, Single ZF, 2

description:
Library name: DMSO Single ZF 2
Single_Pomalidomide_processed.txt


title: ATRi2-BrdU-Seq


title: Pig#33,No NRP+HOPE 2h

description:
Library name: Sample8
column name name in TPM_values.csv: P33.DCD

value: No NRP+HOPE


title: Pig#31,No NRP+HOPE 2h

description:
Library name: Sample7
column name name in TPM_values.csv: P31.DCD


title: ATRi1-BrdU-Seq


title: DMSO, Single ZF, 1

description:
Library name: DMSO Single ZF 1
Single_Pomalidomide_processed.txt


title: Pig#30,NRP+HOPE 24h

description:
Library name: Sample6
column name name in TPM_values.csv: P30.DCD

value: NRP+HOPE


title: paya_mng_054

description: PAYA MNG

value: ben


title: ATMi2-BrdU-Seq

value: skin; foreskin


title: HeLa_FLAG_2

city: Chiba

first: Masaki

last: Fukuyo

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

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: HeLa

growth_protocol: HeLa cells were cultured in Iscove's modified Dulbecco's medium supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was collected using the MagNA pure compact RNA isolation kit (Roche Diagnostics)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Cells were incubated in Iscove's modified Dulbecco's medium supplemented with 10% FBS and 1% penicillin-streptomycin. HeLa cells were transfected with 4ug FLAG vector for non-target, FIR-FLAG, FIRΔexon2-FLAG, or untreated samples using Lipofectamine 2000, and they were exposed to 2 days for selection.  HeLa cells were transfected with each 25uM siRNAs using Lipofectamine 2000, and they were exposed to 2 days for selection.

value: HeLa

value: control vector


title: Pig#29,NRP+SCS 2h

description:
Library name: Sample5
column name name in TPM_values.csv: P29.DCD

value: NRP+SCS


title: paya_mng_050

city: Heidelberg

description: PAYA MNG

value: Frozen

value: Male


title: ATMi1-BrdU-Seq

value: BJ hTERT

value: fibroblasts

value: anti-BrdU antibody, Sigma-Aldrich


title: Pig#28,NRP+HOPE 24h

description:
Library name: Sample4
column name name in TPM_values.csv: P28.DCD

value: Myocardium

value: Cardiomyocytes


title: paya_mng_048

description: PAYA MNG

value: FFPE

value: Female

value: posterior fossa


title: RNAPII 22h Ser2 ATRi ChIP-Seq

data_processing:
Single-end ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie 2 v.2.3.3.1 (Langmead et al., 2012).
BAM files were sorted and indexed using SAMtools v.1.4 (Li et al., 2009).
The reads that mapped to region DAC blacklisted for mappability by the ENCODE project were removed.
Metagene were generated using the function “average” in EaSeq
Assembly: hg38
Supplementary files format and content: .txt, containing the quantifications over each gene as above described

extract_protocol:
Cells were fixed in 1 % formaldehyde for 10 min at room temperature. Then, glycine was added to a final concentration of 0.125 M and the reaction was incubated for 5 min at room temperature. Fixed cells were washed twice with ice-cold PBS, and lysed for 5 min in ice-cold ChIP cell lysis buffer (5 mM HEPES pH 8.0, 85 mM KCl, 0.5 % NP-40 alternative, protease inhibitors). Nuclei were pelleted by centrifugation at 3900 g for 5 min at 4ºC, and lysed for 5 min in ChIP nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS, protease inhibitors) and incubated 5 minutes on ice. Lysates were sonicated using VCX130 (Sonics & Materials, Inc) with the following settings: 8 cycles, 30 % Amp, 15 s ON, 25 s OFF. Sonicated chromatin was centrifuged at 17000 g at 4ºC for 10 min and the supernatant was stored at -80ºC until immunoprecipitation. Before immunoprecipitation, 15 µl of Dynabeads Protein A was washed twice with 900 µl 5 mg/ml BSA in PBS and reacted for 1 h or more with 3 µg of the corresponding antibody (Phospho-Histone H2A.X: ab2893, Abcam; H3: ab1791, Abcam) in 500 µl of 5 mg/ml BSA in PBS at room temperature. The beads were washed again with 900 µl 5 mg/ml BSA in PBS before use. The concentration of sonicated chromatin was quantified by using Quick Start Bradford protein 1x dye reagent (Bio-Rad). 50 µl chromatin were used as Input. 0.6 mg of chromatin was 1:5 diluted with ChIP dilution buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, protease inhibitors), and incubated with prepared beads overnight at 4ºC with rotation. Chromatin bound to beads was washed twice in ChIP low salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), twice in ChIP high salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl),  twice in ChIP LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 % NP40 alternative, 1 % sodium deoxycholate, 1 mM EDTA), and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA). Most of the TE buffer was removed after the beads were centrifuged at 3000 rpm for 3 min and put on Magnet. The remaining TE was removed after the beads were centrifuged again at 13200 rpm for 1 min and put on Magnet. The beads were resuspended in 50 µl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS) and incubated at 65°C for 10 min followed by centrifugation at 12000 rpm for 1 min. The supernatant was transferred to a new DNA low binding tube (Sarstedt) and incubated at 65°C overnight for de-crosslinking. Reverse cross-linked supernatant was mixed with 50 µl of TE and incubated with RNase A at 37°C for 1 h. The supernatant was further incubated with 0.7 mg/ml proteinase K at 55°C for 2 h. DNA was purified by DNA Clean & Concentrator-5 and eluted with 8 µl EB (10 mM Tris-HCl pH 8.5). The purified DNA was quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). 1 ng of DNA was used to construct DNA library according to Illumina's Nextera XT DNA Library Preparation Kit protocol. After being cleaned up, indexed libraries were quantified, normalized and pooled, sequenced on Illumina NextSeq system
NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads following manufacturer’s protocol
single end on 4 lanes (L1-L4)

value: 22h Ser2 ATRi

value: Ser2-RPB1, Abcam


title: Pig#27,NRP+HOPE 24h

description:
Library name: Sample3
column name name in TPM_values.csv: P27.DCD

value: NRP+HOPE


title: HeLa_FIRΔexon2_FLAG_2


title: paya_mng_044

description: PAYA MNG

value: ben

value: supratentoriell


title: paya_mng_063

description: PAYA MNG

value: orbital


title: RNAPII 22h Ser2 DMSO ChIP-Seq

value: 22h Ser2 DMSO

value: skin; foreskin


title: HeLa_FIRΔexon2_FLAG_1

value: HeLa


title: paya_mng_036

description: PAYA MNG

value: Male


title: RNAPII 19h Ser2 ATRi ChIP-Seq

value: 19h Ser2 ATRi

value: BJ hTERT

value: fibroblasts


title: HeLa_FIR_FLAG_2

value: FIR-FLAG


title: Pig#25,NRP+SCS 2h

description:
Library name: Sample2
column name name in TPM_values.csv: P25.DCD

value: Myocardium

value: Cardiomyocytes

value: NRP+SCS


title: Pig#24,NRP+SCS 2h

description:
Library name: Sample1
column name name in TPM_values.csv: P24.DCD


title: paya_mng_035

description: PAYA MNG

value: FFPE

value: Female


title: RNAPII 19h Ser2 DMSO ChIP-Seq

value: 19h Ser2 DMSO

value: Ser2-RPB1, Abcam


title: HeLa_FIR_FLAG_1


title: 014_Baseline

city: Rochester

first: Emma

last: Durrenberger

state: Minnesota

address: 200 First St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description:
Library name: sample_27
014_Baseline

data_processing:
Libraries were multiplexed and sequenced in a single lane using the standard protocol for the Illumina NovaSeq 6000 and the NovaSeq XP 4-Lane kit for individual lane loading. The flow cell was sequenced as 100 X 2 paired-end reads using the NovaSeq S4 sequencing kit and NovaSeq Control Software v1.8.0. Base-calling was performed with Illumina’s RTA version 3.4.4.
The raw RNA sequencing paired-end reads were processed through the Mayo RNA-Seq bioinformatics pipeline, MAP-RSeq version 3.1.5. MAP-RSeq uses STAR to align reads to the reference human genome build hg38. Gene and exon expression quantification were performed using the Subread package to obtain both raw and normalized (FPKM – Fragments Per Kilobase per Million mapped reads) reads. Finally, comprehensive analyses were run on the aligned reads to assess the quality of the sequenced libraries.
Assembly: hg38
Supplementary files format and content: merged_gene_count.tsv tsv file containing merged raw gene counts for all samples
Supplementary files format and content: merged_gene_count_fpkm_by_read.tsv tsv file containing gene count fpkm by read for all samples

source_name: blood

extract_protocol:
Total RNA concentration and quality were determined using Qubit fluorometry (ThermoFisher Scientific, Waltham, MA) and the Agilent Fragment Analyzer (Santa Clara, CA). The total RNA underwent globin depletion using GLOBINclear (ThermoFisher Scientific, Waltham, MA) and a clean-up with DNase I (Zymo Research, Irvine, CA) treatment.
cDNA libraries were prepared using 100 ng of total RNA according to the manufacturer’s instructions for the Illumina Stranded mRNA Prep, Ligation (Illumina, San Diego, CA). The concentration and size distribution of the completed libraries were determined with the Agilent TapeStation and Qubit fluorometry.

value: blood

value: PBMCs

tag: time point

value: Baseline


title: 013_Week_12

description:
Library name: sample_26
013_Week_12


title: paya_mng_022

description: PAYA MNG

value: ben


title: Healthy human epidermis scRNA-seq donor 3

city: Vienna

first: Hannes

last: Kühtreiber

state: Vienna

address: Lazarettgasse 14

department: Department of Dermatology

country: Austria

institute: Medical University Vienna

description: Library name: Epidermis3

data_processing:
Raw sequencing data were demultiplexed using the 10x Genomics Cell Ranger fastq pipeline.
Reads were aligned to the human GRCh38 reference genome using the 10x Genomics Cell Ranger count pipeline.
Cell barcodes and unique molecular identifiers were counted using Cell Ranger count to generate gene-barcode matrices for each donor sample.
Assembly: GRCh38
Supplementary files format and content: Matrix Market format gene-barcode matrix generated from 10x Genomics single-cell RNA-seq data. Files include matrix.mtx, barcodes.tsv, and features.tsv or genes.tsv, containing UMI count data for cell barcodes and detected genes.

source_name: Viable epidermal cells isolated from healthy adult human abdominal skin obtained from abdominoplasty; 10x Genomics Chromium single-cell RNA-seq.

growth_protocol: Primary human skin samples were obtained from three healthy adult donors undergoing abdominoplasty.

extract_protocol:
Skin samples were obtained from three healthy adult donors during abdominoplasty. From each skin sample, six biopsies were digested with Dispase II overnight at 4 °C to separate the epidermis. Half of the separated epidermis was dissociated using the GentleMACS Human Whole Skin dissociation kit for 2.5 hours at 37 °C according to the manufacturer’s instructions. The other half was digested with 0.05% Trypsin-EDTA and DNase I for 7 minutes at 37 °C. Dissociated cell suspensions were pooled, processed using the GentleMACS OctoDissociator, sequentially filtered through 100 µm and 40 µm cell strainers, stained with DAPI for 10 seconds, resuspended in 0.04% BSA in PBS, washed twice, and sorted for viable cells using an AriaFusion high-speed cell sorter.
Single-cell gene expression libraries were generated using the 10x Genomics Chromium platform with the Single Cell 3′ v2 chemistry. Immediately after cell sorting, single-cell suspensions were processed for Gel Bead-in-Emulsion generation, cDNA synthesis, and library preparation. GEM generation, library preparation, and RNA sequencing were performed by the Biomedical Sequencing Core Facility of the Center for Molecular Medicine, Vienna, Austria. Biopsy acquisition, cell suspension preparation, and loading on the Chromium instrument were completed within 3.5 hours. Libraries were sequenced on an Illumina HiSeq 3000/4000 instrument.

treatment_protocol: No treatment

value: skin epidermis

value: viable epidermal cells

tag: batch

value: donor 3


title: RNAPII 16h Ser2 ATRi ChIP-Seq

value: 16h Ser2 ATRi

value: skin; foreskin

value: BJ hTERT


title: HeLa_LP2000_2

value: HeLa

value: Lipofectamine 2000


title: paya_mng_021

description: PAYA MNG

tag: material

value: int

value: ventricel


title: Healthy human epidermis scRNA-seq donor 2

description: Library name: Epidermis2

value: donor 2


title: paya_mng_088

description: PAYA MNG

value: FFPE

tag: Sex

value: Male

value: skull base


title: HeLa_LP2000_1


title: CTR siRNA2-BrdU-Seq

value: CTR siRNA2

value: fibroblasts

value: anti-BrdU antibody, Sigma-Aldrich


title: RNAPII 16h Ser2 DMSO ChIP-Seq

value: 16h Ser2 DMSO

value: Ser2-RPB1, Abcam


title: EryP_Feb18_WT_Gata1_Rep_3

description: Library name: VS062

value: Unipotent erythroid progenitor (EryP)

value: WT

value: GATA1 (Abcam; ab11852)


title: Healthy human epidermis scRNA-seq donor 1

description: Library name: Epidermis1

value: skin epidermis

value: viable epidermal cells

value: donor 1


title: HeLa_siFIRΔexon2_3

value: HeLa


title: ALV2, 15uM, Dual ZF, 3

description:
Library name: ALV2 Dual ZF 3
ALV2_processed.txt

value: ALV25uM, Dual ZF


title: paya_mng_017

description: PAYA MNG

tag: age group

value: ben


title: paya_mng_016

description: PAYA MNG

value: FFPE

value: Female

tag: methylation class


title: RNAPII 22h total ATRi ChIP-Seq

value: 22h total ATRi

value: skin; foreskin

value: BJ hTERT

value: Rpb1 NTD antibody, Cell Signaling


title: HeLa_siFIRΔexon2_1


title: ALV2, 15uM, Dual ZF, 2

description:
Library name: ALV2 Dual ZF 2
ALV2_processed.txt


title: paya_mng_014

description: PAYA MNG

value: int

tag: localisation

value: skull base


title: RNAPII 22h total DMSO ChIP-Seq

value: 22h total DMSO

tag: cell line

value: fibroblasts


title: EryP_Feb18_WT_IgG

description: Library name: VS058

value: Unipotent erythroid progenitor (EryP)

tag: genotype

value: WT

value: IgG


title: HeLa_siFIR_2

value: siFIR


title: paya_mng_004

description: PAYA MNG

value: Male

value: tentorial


title: ALV2, 15uM, Dual ZF, 1

description:
Library name: ALV2 Dual ZF 1
ALV2_processed.txt

value: ALV25uM, Dual ZF


title: RNAPII 19h total ATRi ChIP-Seq

value: 19h total ATRi

tag: tissue


title: HeLa_siFIR_1

value: HeLa


title: DMSO 2, Dual ZF, 3

description:
Library name: DMSO 2 Dual ZF 3
ALV2_processed.txt

value: DMSO 2, Dual ZF


title: HeLa_siGL2_2

value: sicontrol


title: RNAPII 19h total DMSO ChIP-Seq

value: 19h total DMSO

value: skin; foreskin

value: BJ hTERT