title: dusB_H2O2_replicate3

status: Public on Feb 11 2025

city: Paris

first: Louna

last: Fruchard

address: 28 Rue Du Docteur Roux

country: France

institute: Institut Pasteur

description: Library name: Sample12

data_processing:
Count data were analyzed using R version 3.2.0 and the Bioconductor package DESeq2 version 1.8.1
Data were normalized with DESeq2 and the “shorth” parameter
The dispersion estimation and statistical test for differential expression were performed with default parameters
The generalized linear model was set with a single covariate corresponding to the biological condition, biological replicates being included into each condition
Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg procedure and genes with an adjusted p-value lower than 0.001 were considered differentially expressed.
Assembly: V. cholerae N16961 accession numbers AE003852 and AE003853
Supplementary files format and content: excel or csv files containing number of reads and differencial expression values

organism: Vibrio cholerae O1 biovar El Tor str. N16961

source_name: bacterial culture

growth_protocol: growth in liquid MH up to OD 0,25

extract_protocol:
Cultures were centrifuged, and RNA was harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep Kit (20020595) was used with 7 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Krin et al., 2018, PMID: 29783948)

treatment_protocol: tobramycin 0,4 µg/ml

value: bacterial culture

tag: growth phase

value: exponential phase OD 0.25

value: delta-dusB

value: H2O2 10min 2mM


title: TM1

status: Public on Feb 12 2025

type: SRA

city: Hefei

first: Yue

last: Zhu

address: The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China

country: China

library_source: transcriptomic

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
The reads mapped the genome were calculated using featureCounts (v1.6.3).
Assembly: hg38
Supplementary files format and content: xlsx files include RPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: liver

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: liver

tag: cell line

tag: cell type

value: Human liver cancer cells

tag: treatment

value: TM


title: OE_1_KB16

city: Poznan

first: Katarzyna

last: Blaszczyk

state: Wielkopolska

address: ul. Uniwersytetu Poznańskiego 6/1.87

department: Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

description: SPOCK2 overexpression

data_processing:
RNA-seq raw paired-end reads were trimmed with fastp (Chen S., et al., 2018). Trimmed reads were aligned to Ensembl GRCh38 human genome with STAR (v2.7) (Dobin, A., et al. 2013) and counts were obtained using featureCounts v1.6.3 (Liao, Y., et al. 2014) . RNA-seq raw sequence reads analysis was performed using iDEP9.4 interactive platform) (Ge, S. X., et al. 2018). All aligned reads were normalized using DESeq2 package (Love M. I., et al., 2014).
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: normalized counts txt file

source_name: Pancreas

growth_protocol: The cells were cultured in Dulbecco’s modified Eagle’s medium containing 1g/L glucose (DMEM; Corning) supplemented with 2% BSA fraction V fatty acid free (Millipore), 50 μM 2-mercaptoethanol (Thermo Fisher Scientific), 10 mM nicotinamide (Sigma Aldrich), 5.5 μg/ml transferrin (Sigma Aldrich), 6.7 ng/ml selenite (Sigma Aldrich), 100 U/ml penicillin, and 100 μg/ml streptomycin on Geltrex (200 μg/ml) and fibronectin (4 μg/ml; Sigma Aldrich)-coated cell culture plates. Every 2 weeks cells were tested for mycoplasma presence. The cells were seeded at the density of 8x105 cells/cm² and were passaged every 7 days using Trypsin (GIBCO). The media was usually changed every 2-3 days. The cells were cultured at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted and purified using Trizol as previously described (Varshney et al., 2017).
RNAseq was performed according to the TruSeq RNA Library Prep Kit protocol

value: human pancreatic beta cell line

tag: genotype/variation

value: SPOCK2 OE


title: islets, Klf4-alphaKO, 1

city: Aurora

first: Lori

last: Sussel

state: Colorado

address: 1775 Aurora ct.

country: USA

institute: CU Anschutz

data_processing:
Fastqc for quality control
bbduk for adapter trimming
STAR for alignment
featurecounts for counts table
DESeq2 for DE analysis
Assembly: mm10
Supplementary files format and content: raw counts table in .txt format

molecule: polyA RNA

organism: Mus musculus

source_name: pancreatic islets

extract_protocol:
Total RNA from isolated islets was extracted using a Qiagen Rneasy Mini Kit
Tecan Universal Plus mRNA-seq library preparation kit with NuQuant

value: pancreatic islets

tag: genotype


title: CON3

institute: The First Affiliated Hospital of Anhui Medical University

value: DMSO


title: islets, Gcg-iCre control, 3


title: WT_beta

library_source: transcriptomic single cell

data_processing:
The raw scRNA-seq data were processed with bcl2fastq v2.20 to demultiplex samples and convert .bcl files to .fastq format. For initial data processing and some basic analyses 10xGenomics Cell Ranger pipelines and Seurat R package were used.
Assembly: hg38
Supplementary files format and content: tap-separated values files and matrix files

source_name: cell line

extract_protocol:
hPSC derived WT and SPOCK2 KO beta-cell spheroids, were dispersed with Tripsin, washed with 0.1% saponin – 1% BSA – PBS, filtered through 30 μm mesh filter. Afterwards cells were counted using Countess and adjusted to 700-1,200 cells/μl.
The scRNA-seq was performed with 10xGenomics platform and Illumina according to the manufacturer's protocol. Libraires were pair-end sequenced with depth of 40,000 reads per cell.

value: cell line

value: hPSC derived pancreatic beta cells

value: early beta cells, stage 7, day 21

value: WT


title: GIPZ_1_KB4

description: GIPZ control done with shRNA plazmid

value: GIPZ control


title: CON2


title: WT_MH_replicate1

description: Library name: Sample1

value: untreated


title: CON1


title: KD_2_KB14

description: SPOCK2 knock down done with shRNA plazmid

value: SPOCK2 KD


title: islets, Gcg-iCre control, 1


title: dusB_H2O2_replicate2

description: Library name: Sample11

value: bacterial culture

value: exponential phase OD 0.25


title: KD_1_KB8


title: WT_H2O2_replicate3

description: Library name: Sample9

value: H2O2 10min 2mM


title: dusB_H2O2_replicate1

description: Library name: Sample10

value: delta-dusB


title: WT_H2O2_replicate2

description: Library name: Sample8


title: S04_DCCs_IFNγ_1

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

data_processing:
RNAseq reads were aligned against the human genome hg19 using STAR-2.5.3a. Gene expression quantification was performed by calculating the read count at the gene level with RSEM.
Assembly: hg19
Supplementary files format and content: Gene expression data are provided as raw read counts.

source_name: Breast cancer

growth_protocol: standard animal cell culture methods were used

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
Followed Nugen Universal RNAseq Human Kit protocol

treatment_protocol: Disseminated cancer cells isolated from bone marrow of breast cancer patients.

value: Breast cancer

value: IFN-𝛾 treated, biological rep1


title: WT_H2O2_replicate1

description: Library name: Sample7


title: S02_DCCs_control_2

value: Disseminated cancer cells isolated from bone marrow of breast cancer patients

value: control, biological rep2


title: S03_DCCs_control_3

value: control, biological rep3


title: Mouse M1 founder tag sequencing, day 13 post C1498-FLARE injection

city: Lebanon

first: Rachel

middle: Danielle

last: Saxe

state: New Hampshire

address: 1 Medical Center Dr

institute: Dartmouth Cancer Center

description: Library name: sample5_M1_d13_ftag

library_source: genomic

data_processing:
Basecalling with BCL2fastq or BCL Convert
Assembly: mm10
Supplementary files format and content: FLARE lineage tracing barcode pipeline output with aligned reads and edit patterns (.stats files)

molecule: genomic DNA

extract_protocol:
Genomic DNA was extracted using the Qiagen Dneasy Blood and Tissue kit
Libraries were constructed with custom targeted PCR primers

value: AML, PBMC

tag: genetic modification

value: FLARE lineage recording


title: dusB_MH_replicate3

description: Library name: Sample6


title: dusB_MH_replicate2

description: Library name: Sample5


title: S06_DCCs_IFNγ_3

value: IFN-𝛾 treated, biological rep3


title: S05_DCCs_IFNγ_2

value: IFN-𝛾 treated, biological rep2


title: dusB_MH_replicate1

description: Library name: Sample4


title: WT_MH_replicate2

description: Library name: Sample2

value: WT


title: WT_MH_replicate3

description: Library name: Sample3


title: MCF7,IgG,Veh,Rep2, CUT&RUN

city: Jupiter

first: Jerome

last: Nwachukwu

state: Florida

address: 130 Scripps Way

department: Department of Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description: Library name: MCF7_IgG_rep2

data_processing:
Sequences were analyzed using the nf-core cutandrun pipeline (v3.2.2, doi: 10.5281/zenodo.5653535)
After adaptor trimming, reads were aligned to the human genome (GRCh38) using Bowtie2
Sorting and indexing using SAMtools
Normalization by counts Per Million mapped reads
Peak calling using MACS2 with a q-value < 0.01.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for control samples)
Library strategy: CUT&RUN

source_name: Breast

growth_protocol: Phenol red-free DMEM + 10% charcoal-stripped FBS for 3 days

extract_protocol:
CUT&RUN using the CUTANA kit (EpiCypher, cat no. 14-1048)
Illumina standard library construction (New England Biolabs) by the University of Florida ICBR NextGen DNA Sequencing Core Facility, RRID:SCR_019152

treatment_protocol: DMSO (Vehicle), 10 nM 17β-estradiol (E2), or 1 µM 4-hydroxytamoxifen (4OHT) for 1 hour

value: Breast

value: Epithelial

tag: cut&run antibody

value: normal rabbit IgG (EpiCypher, cat no. 13-0042, 1:50)

value: DMSO


title: MCF7,ERa,Veh,Rep2, CUT&RUN

description: Library name: MCF7_ERa_Vehicle_rep2

value: ERa (EpiCypher, cat no. 13-2011, 1:100)


title: MCF7,IgG,Veh,Rep1, CUT&RUN

description: Library name: MCF7_IgG_rep1


title: MCF7,ERa,E2,Rep1, CUT&RUN

description: Library name: MCF7_ERa_Estradiol_rep1

value: 10 nM E2


title: MCF7,ERa,E2,Rep2, CUT&RUN

description: Library name: MCF7_ERa_Estradiol_rep2


title: HEK293T viewpoint FHL2 Replica 3

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

library_source: other

data_processing:
Trimming (Cutadapt)
Alignment (HISAT2)
Assembly: hg38
Supplementary files format and content: bedgraph
Library strategy: 4C-Seq

molecule: other

growth_protocol: HEK293T cells were cultured in Dulbecco's Modified Eagle Medium (GibcoTM) with 10% fetal calf serum (FCS; Bio&Sell) and Penicillin-Streptomycin (Life Technologies) at 37°C / 5% CO2, and passaged manually at 80 - 90% confluency

extract_protocol:
The primary restriction enzyme digestion was performed with 800 U NlaIII or ApoI (New England Biolabs, R0125 and R3566). Following in situ ligation of digested chromatin, nuclei were lysed and the isolated DNA was digested with CviQI (New England Biolabs, R0639), circularized by ligation and purified.
The library was amplified by inverse PCR with viewpoints-specific primers coupled to Illumina adapters for sequencing. Following inverse PCR, the i5 and i7 Illumina adapters were used to generate NGS-compatible libraries as previously described 44. Amplicons were sequenced in a 50 bp paired-end mode on the Illumina NextSeq2000 platform.

treatment_protocol: i4C was performed on HEK293T WT cells. Viewpoints were localized in PDE4C, FHL2, and MEIS1-AS3

value: Viewpoint FHL2


title: HEK293T viewpoint PDE4C Replica 3

value: Viewpoint PDE4C


title: HEK293T viewpoint MEIS1-AS3 Replica 2

value: Viewpoint MEIS1-AS3


title: HEK293T viewpoint MEIS1-AS3 Replica 3


title: S01_DCCs_control_1

value: Breast cancer

value: Disseminated cancer cells isolated from bone marrow of breast cancer patients

value: control, biological rep1


title: HEK293T viewpoint FHL2 Replica 2


title: HEK293T viewpoint PDE4C Replica 1


title: HEK293T viewpoint FHL2 Replica 1


title: IMR90 cells, IR, 53BP1 OE, rep 2

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

data_processing:
Sequenced reads were aligned using STAR with a 2-pass pipeline.
Raw counts were generated using htseq.
FPKM values were computed by Cufflinks
Assembly: hg19
Supplementary files format and content: FPKM matrix contains FPKM values for each sample and each gene
Supplementary files format and content: Raw count matrix contains raw counts for each sample and each gene

growth_protocol: IMR90 primary human fibroblasts were grown at 37°C, 3.5% O2, 5% CO2, in Dulbecco’s modified Eagle’s medium (Gibco 10313-121) with 10% FBS (Corning 35-0-11-CV), 1% penicillin/streptomycin (Gibco 15140-122) and 2 mM glutamine (Gibco 25030-081). Cells were checked routinely for mycoplasma contamination.

extract_protocol:
Cells were lysed in Trizol (Ambion 15596026) and RNA was isolated using  a commercial kit (Zymo Directzol)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For 53BP1 exogenous expression, lentivirus was generated from 293T cells. Concentrated virus was titrated to the minimum amount required for >90% cell viability after puromycin selection. Cells were infected overnight with 8 ug/mL polybrene. IR senescence was induced by 20 Gray x-ray irradiation of 20-30% confluent cells. Cells were split after returning to confluence in 3 days.

value: fibroblast

value: 53BP1 OE

value: 10 days post 20 Gy IR


title: MCF7,ERa,Veh,Rep1, CUT&RUN

description: Library name: MCF7_ERa_Vehicle_rep1


title: HEK293T viewpoint PDE4C Replica 2


title: IMR90 cells, IR, empty vector, rep 1

value: empty vector


title: CVS 70561, Female, IVF

type: genomic

city: Los Angeles

first: Margareta

middle: D

last: Pisarska

address: 8635 West Third Street Suite 160

department: Obstetrics and Gynecology

institute: Cedars-Sinai Medical Center

hyb_protocol: Bisulphite converted DNA was amplified and hybridized to the human Infinium MethylationEPIC BeadChip array (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using standard recommended Illumina scanner settings.

data_processing:
Raw IDAT files were preprocessed and normalized using the Bioconductor R package "minfi", with preprocessQuantile() function, a stratified quantile normalization method which is ideal for smaller methylation differences, such as from samples of the same tissue type. The Bioconductor R pipeline "methylationArrayAnalysis" was used, leaving 865,859 probes. The matrix of normalized M values was filtered and used for differentially methylated probes (DMPs) analysis using a generalized linear model adjusted for fetal sex. Briefly, masked (unreliable) probes were dropped using column "MASK_general" from Dr Wanding Zhou's updated annotation of the EPIC array, specifically file "EPIC.hg38.manifest.tsv.gz" version 9/9/2018 downloaded from <https://zwdzwd.github.io/InfiniumAnnotation>. Non-autosomal probes were also dropped. For the infertility study, only CpG probes were used (cg prefix in probeIDs), but not CpH probes (ch prefix) or probes with single nucleotide polymorphisms (rs prefix). See the associated publications for more details.
processed value definition:  M value

label: Cy3 and Cy5

source_name: First trimester placenta - chorionic villi

label_protocol: Standard Illumina protocol

growth_protocol: Fresh chorionic villi tissue discarded after clinical visit for chorionic villus sampling was collected with informed consent, then quickly preserved with RNAlater RNA stabilizing reagent (QIAGEN) and stored at -80C until further processing. Tissue was not cultured.

extract_protocol: Genomic DNA and total RNA were separately isolated from the same tissue using the two column kit, AllPrep DNA/RNA/miRNA Mini Kit (QIAGEN). Thawed tissue was treated with the RLT Plus lysis buffer from the QIAGEN kit and homogenized by passing through three progressively thinner needles (22G, 25G, 27G) attached to a single-use RNase-free syringe. The homogenate was passed through the spin columns and washed following manufacturer instructions. Genomic DNA was eluted with 100 uL of EB buffer pre-warmed to 70C for improved yield.

treatment_protocol: Some patients received fertility treatments to achieve pregnancy, prior to enrollment in research.

value: Wild type

tag: fetal sex

value: Female

value: IVF:in vitro fertilization

tag: infertility treatment

value: Infertility treatment

tag: gestational age at cvs (days)

tag: maternal bmi

tag: fetal ethnicity

value: NonHispanic

tag: mode of delivery

value: Vaginal

value: No


title: IMR90 cells, IR, empty vector, rep 2


title: CVS 70284, Male, IVF

value: First trimester placenta - chorionic villi

value: Male

value: C-Section


title: CVS 70353, Female, IVF


title: CVS 70517, Female, IVF


title: CVS 70239, Male, IVF


title: CVS 70349, Female, IVF


title: IMR90 cells, proliferating, 53BP1 OE, rep 3

value: Cultured 10 days


title: CVS 70146, Male, IVF


title: IMR90 cells, IR, empty vector, rep 3


title: IMR90 cells, proliferating, 53BP1 OE, rep 1


title: HEK293T viewpoint MEIS1-AS3 Replica 1

value: Viewpoint MEIS1-AS3


title: IMR90 cells, proliferating, empty vector, rep 3


title: IMR90 cells, proliferating, 53BP1 OE, rep 2


title: CVS 70094, Male, IVF


title: IMR90 cells, IR, 53BP1 OE, rep 3


title: IMR90 cells, proliferating, empty vector, rep 2


title: IMR90 cells, proliferating, empty vector, rep 1


title: CVS 72094, Female, NIFT

value: NIFT:non-IVF fertility treatment

value: Bulk placenta in GSE215421


title: IMR90 cells, IR, 53BP1 OE, rep 1

value: fibroblast

value: 53BP1 OE


title: MCF7-NUTF2 biol rep 3

data_processing:
Reads were aligned using Hisat2 (Version 2.2.1)
Reads were counted using featureCounts program in the Subread (Version 2.0.1) package
Assembly: hg38
Supplementary files format and content: comma separated value (.csv) files containing raw read counts

growth_protocol: Phenol red-free DMEM + 10% FBS for 3 days

extract_protocol:
Total RNA was extracted using the RNeasy kit (QIAGEN). mRNA was selectively isolated from total RNA (500ng input) using poly-T oligos attached to magnetic beads according to the manufacturer’s guidelines in the NEBNext poly(A) mRNA magnetic isolation module (Cat. #: E7490, NEB, Ipswich, MA).
The library preparation from the enriched mRNA was conducted according to NEBNext Ultra II Directional RNA kit

value: Breast

value: Epithelial


title: CVS 72089, Male, IVF

value: Wild type


title: CVS 70198, Male, IVF

value: IVF:in vitro fertilization


title: MCF7-NUTF2 biol rep 2


title: MCF7-NUTF2 biol rep 1


title: CVS 72066, Female, NIFT

value: Female

value: Infertility treatment


title: CVS 72057, Male, NIFT

value: NonHispanic

value: Vaginal


title: CVS 72064, Female, IVF

value: First trimester placenta - chorionic villi

value: No


title: CVS 72056, Male, IVF

value: Male

value: C-Section


title: CVS 71998, Female, Spontaneous

value: unassisted/spontaneous


title: MCF7-Empty biol rep 2


title: MCF7-Empty biol rep 1


title: CVS 71991, Male, IVF


title: CVS 72175, Male, Spontaneous

value: Bulk placenta in GSE109082


title: CVS 71968, Female, NIFT

value: NIFT:non-IVF fertility treatment

value: Hispanic


title: CVS 71990, Female, Spontaneous

value: Bulk placenta in GSE215421


title: CVS 71961, Female, IVF


title: CVS 72160, Male, Spontaneous


title: CVS 71959, Female, IVF


title: heart.Het.1292524

city: Tarrytown

first: Gabor

last: Halasz

state: New York

address: 777 old saw mill river road

institute: Regeneron Pharmaceuticals

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292524

data_processing:
Raw sequence data (BCL files) were converted to FASTQ format via Illumina bcl2fastq v2.17.
Reads were decoded based on their barcodes and read quality was evaluated with FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were mapped to the mouse genome (NCBI GRCm38) using ArrayStudio software (OmicSoft Corp. (Cary, NC) allowing two mismatches
Reads mapped to the exons of a gene were summed at the gene level.
Assembly: NCBI GRCm38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample
Supplementary files format and content: tab-delimited text file contains TPM values for each sample

source_name: heart

extract_protocol:
Total RNA was purified from tissues using MagMAX™-96 for Microarrays Total RNA Isolation kit (Life Technologies (Carlsbad, CA)), according to manufacturer’s specifications. Genomic DNA was removed using MagMAX Turbo DNase buffer and TURBO DNase from the MagMAX kit listed above. Messenger RNA was purified from total RNA using Dynabeads mRNA purification kit (Invitrogen (Waltham, MA)).
Strand-specific RNA sequencing (RNA-seq) libraries were prepared using KAPA mRNA-Seq Library Preparation kit (Kapa Biosystems (Wilmington, MA)). After mRNA quality control analysis, RNA-seq libraries were prepared and long read sequencing (75bp, single end, 15M reads) was used for all samples. Sequencing was performed on Illumina HiSeq®2500 by a multiplexed single-read run with 33 cycles.

value: heart


title: heart.Het.1292547

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292547


title: heart.WT.1292548

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292548


title: heart.WT.1292549

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292549


title: heart.WT.1292546

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292546


title: CVS 71910, Male, Spontaneous


title: CVS 71890, Male, IVF


title: heart.WT.1292520

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292520


title: CVS 71853, Female, NIFT


title: CVS 71887, Female, Spontaneous


title: CVS 71832, Female, NIFT


title: CVS 71825, Female, IVF


title: CVS 71766, Male, NIFT


title: MCF7-Empty biol rep 3

value: Breast

value: Epithelial


title: liver.Het.1292519

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292519

value: liver


title: heart.Het.1292521

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292521


title: liver.WT.1292517

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292517


title: liver.WT.1292518

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292518


title: CVS 71752, Male, NIFT

value: Wild type


title: heart.WT.1292525

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292525


title: liver.WT.1292515

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292515


title: CVS 71642, Female, IVF

value: Female

value: IVF:in vitro fertilization

value: Infertility treatment


title: CVS 71696, Female, IVF

value: First trimester placenta - chorionic villi

value: Vaginal


title: liver.Het.1292514

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292514


title: liver.WT.1292513

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292513


title: CVS 71997, Male, Spontaneous

value: Male

value: No

value: NonHispanic


title: heart.Het.1292523

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292523


title: CVS 71625, Female, Spontaneous

value: unassisted/spontaneous

value: Bulk placenta in GSE109082


title: liver.WT.1292511

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292511


title: liver.WT.1292510

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292510


title: CVS 71595, Male, IVF

value: C-Section


title: CVS 71623, Male, Spontaneous

value: Bulk placenta in GSE215421


title: CVS 71587, Female, IVF

value: Hispanic


title: heart.Het.1292522

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292522

value: heart


title: liver.Het.1292512

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292512


title: liver.Het.1292509

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292509


title: CVS 71536, Male, Spontaneous


title: CVS 71529, Male, NIFT

value: NIFT:non-IVF fertility treatment


title: liver.WT.1292508

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292508

value: liver


title: kidney.WT.1292507

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292507

source_name: kidney

value: kidney


title: kidney.WT.1292503

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292503


title: kidney.WT.1292506

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292506


title: CVS 71526, Female, NIFT

value: Wild type

value: Female


title: kidney.WT.1292499

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292499


title: CVS 71483, Female, IVF

value: IVF:in vitro fertilization

value: Infertility treatment


title: kidney.WT.1292498

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292498


title: kidney.Het.1292505

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292505


title: kidney.Het.1292504

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292504


title: kidney.Het.1292497

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292497


title: U2OS cells, CHRONO overexpressed clone2, rep3

city: Hefei,

first: Qin

last: Zhou

state: Anhui

address: 111 Jiulong Road, Hefei, Anhui, China

institute: Anhui university

data_processing:
SOAPnuke software filter parameters: " -n 0.01 -l 20 -q 0.4 --adaMR 0.25 --ada_trim --polyX 50",
1. Filter adapter: if the sequencing read matches 25.0% or more of the adapter sequence(maximum 2 base mismatches are allowed), cut the adapter;2. Filter low-quality data: if the bases with a quality value of less than 20 in the sequencing readaccount for 40.0% or more of the entire read, discard the entire read;3. Remove N: if the N content in the sequencing read accounts for 1.0% or more of the entire read,discard the entire read;4. Remove polyX: if the length of polyX (X can be A, T, G or C) in the sequencing read exceeds50bp, discard the entire read;5. Obtain Clean reads: the output read quality value system is set to Phred+33.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes RPKM values for all sample

source_name: Bone

growth_protocol: U2OS cells were maintained in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5%CO2 at 37 ℃

extract_protocol:
RNA was harvest using Trizol reagent (Qiagen)，1µg of total RNA was used for the construction of sequencing libraries.
1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly Atail;2. mRNA molecules were fragmented into small pieces;3. The fragmented mRNA was synthesized into first strand cDNA using random primers;4. The second strand cDNA was synthesized;5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated tothe ends of these 3' adenylated cDNA fragments;6. PCR amplification and purification;7. Library quality control;8. Library circularization;9. The library was amplified to make DNA nanoball (DNB);10. Sequencing on DNBSEQ (DNBSEQ Technology) platform.

value: Bone

value: Human Osteosarcoma Cells

value: CHRONO overexpressed


title: CVS 71523, Male, Spontaneous

value: First trimester placenta - chorionic villi

value: Male

value: No

value: NonHispanic

value: Vaginal


title: U2OS cells, CHRONO overexpressed clone2, rep1


title: CVS 71468, Female, NIFT

value: Bulk placenta in GSE215421


title: CVS 71462, Male, NIFT

value: C-Section


title: lung.Het.1292495

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292495

source_name: lung

value: lung


title: liver.Het.1292516

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292516

value: liver


title: CVS 71466, Male, Spontaneous

value: unassisted/spontaneous

value: Bulk placenta in GSE109082


title: U2OS cells, CHRONO overexpressed clone2, rep2


title: kidney.WT.1292501

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292501

value: kidney


title: CVS 71477, Female, Spontaneous

value: Wild type

value: Female

value: Hispanic


title: kidney.Het.1292502

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292502


title: CVS 71465, Male, IVF

value: IVF:in vitro fertilization

value: Infertility treatment


title: kidney.Het.1292500

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292500


title: kidney.WT.1292496

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292496


title: U2OS cells, CHRONO overexpressed clone1, rep3

value: Bone

value: Human Osteosarcoma Cells

value: CHRONO overexpressed


title: CVS 71457, Male, NIFT

value: First trimester placenta - chorionic villi

value: Male

value: NIFT:non-IVF fertility treatment

value: NonHispanic

value: No


title: lung.WT.1292494

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292494

value: lung


title: lung.WT.1292493

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292493


title: CVS 71452, Female, IVF

value: C-Section

value: Bulk placenta in GSE215421


title: U2OS cells, CHRONO overexpressed clone1, rep1


title: lung.WT.1292490

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292490


title: lung.WT.1292491

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292491


title: CVS 71432, Female, NIFT


title: lung.Het.1292489

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292489


title: lung.Het.1292488

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292488


title: CVS 71423, Male, NIFT


title: lung.WT.1292485

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292485


title: CVS 71417, Female, IVF


title: lung.Het.1292484

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292484


title: U2OS cells, WT, rep1

value: WT


title: U2OS cells, WT, rep3


title: DM biol rep 3

city: Calgary

first: Deepika

last: Dogra

state: Alberta

address: 3330 Hospital Dr NW

department: Department of Medical Genetics

country: Canada

institute: University of Calgary

data_processing:
Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts.
Genes with zero values in more than 4 samples were exlcuded from the analysis
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include log normalised counts for each sample

organism: Danio rerio

source_name: heads

growth_protocol: Adult zebrafish (TL and AB strains) were maintained at 28°C in a 14-hour light/10-hour dark cycle under standard aquaculture conditions, and fertilized eggs were collected via natural spawning.

extract_protocol:
Trizol based RNA extraction and column purification
purified RNA with RIN>7 were sent for sequencing
NextSeq2000 P2 100 cycle

treatment_protocol: untreated

value: heads

value: untreated


title: DM biol rep 2


title: heart.Het.1292479

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292479

value: heart


title: lung.Het.1292487

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292487


title: lung.WT.1292477

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292477


title: DM biol rep 1


title: lung.Het.1292486

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292486


title: CVS 71407, Male, NIFT

value: Wild type


title: lung.WT.1292476

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292476


title: CVS 71425, Female, IVF

value: Female

value: IVF:in vitro fertilization

value: Infertility treatment


title: U2OS cells, CHRONO overexpressed clone1, rep2

value: Bone

value: Human Osteosarcoma Cells

value: CHRONO overexpressed


title: CVS 71354, Female, IVF

value: First trimester placenta - chorionic villi

value: Vaginal


title: lung.WT.1292492

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292492


title: lung.WT.1292475

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292475


title: lung.Het.1292474

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292474


title: 5b biol rep 3


title: CVS 71352, Male, IVF

value: Male

value: NonHispanic

value: No


title: U2OS cells, WT, rep2


title: 5b biol rep 2


title: lung.Het.1292471

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292471

value: lung


title: CVS 71320, Female, NIFT

value: NIFT:non-IVF fertility treatment

value: Bulk placenta in GSE215421


title: lung.WT.1292469

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292469


title: lung.Het.1292466

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292466


title: lung.Het.1292470

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292470


title: CVS 71347, Female, NIFT

value: C-Section


title: CVS 71319, Female, IVF

value: Hispanic


title: lung.WT.1292467

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292467


title: CVS 71313, Male, Spontaneous

value: Wild type

value: unassisted/spontaneous

value: Bulk placenta in GSE109082


title: heart.WT.1292478

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292478

value: heart


title: 5b biol rep 1

value: heads

value: untreated


title: lung.WT.1292468

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292468


title: lung.Het.1292472

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292472


title: lung.WT.1292465

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292465


title: 5a biol rep 2


title: CVS 71310, Male, NIFT

value: Infertility treatment


title: lung.WT.1292464

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292464


title: lung.Het.1292463

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292463


title: 5a biol rep 3


title: 5a biol rep 1


title: WT biol rep 3

value: WT


title: lung.Het.1292462

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292462


title: CVS 71309, Female, NIFT

value: First trimester placenta - chorionic villi

value: Female

value: Vaginal


title: lung.WT.1292461

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292461


title: lung.Het.1292460

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292460


title: CVS 71304, Female, NIFT

value: No


title: lung.Het.1292473

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292473

value: lung


title: lung.WT.1292459

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292459


title: lung.Het.1292457

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292457


title: lung.Het.1292458

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292458


title: Islets, GCGR-KO mice, scRNA-seq

city: Xiamen, Fujian

first: jianxin

last: jia

address: Xiamen University, Xiamen, Fujian

institute: Xiamen University

data_processing:
Cell Ranger Single-Cell Software Suite (v5.0.1;10x Genomics) was used for sample demultiplexing, alignment, filtering, and UMI counting.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreatic islets

extract_protocol:
The pancreatic islets were isolated from 8-12-week-old male C57BL/6J mice. After euthanasia, the pancreas was perfused by injection of 2-4 mL digestion buffer (Hanks' Balanced Salt Solution containing type IV collagenase into the common bile duct. The pancreas was then dissected and then incubated at 37°C for 10 minutes followed by gently shaking for 3-6 minutes. Density gradient centrifugation was performed, and individual islets with high purity were hand-picked under a dissecting microscope. To prepare the single-cell suspension, the purified islets were digested with 0.25% trypsin-EDTA and filtered through a 40 μm cell strainer. Cell viability was evaluated by trypan blue staining, followed by microscopy to ensure that cell viability was greater than 90%, and over 90% of cells were singlets.
Following preparation of islet single-cell suspension, the single cells were loaded onto 3’ library chips for the Chromium Single Cell 3’ Library (v3) according to the manufacturer’s recommendations (10X Genomics)

value: Pancreatic islets

value: GCGR-KO


title: lung.Het.1292454

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292454


title: lung.WT.1292453

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292453


title: CVS 71265, Male, Spontaneous

value: Male

value: NonHispanic

value: Bulk placenta in GSE215421


title: lung.WT.1292456

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292456


title: Islets, WT mice, scRNA-seq


title: lung.WT.1292450

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292450


title: lung.Het.1292455

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292455


title: lung.Het.1292452

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292452


title: RAW264.7 cell SMART-Cas9-3

city: Shenzhen

first: Jingqin

last: Chen

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

description: Library name: Sample6

data_processing:
lllumina Casava1.7 software used for basecalling.
Assembly: GRCm38
Supplementary files format and content: gene-count-matrix

extract_protocol:
RAW264.7 cells were collected, and flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 μg was collected using the lllumina Trumina TruSrq Sample Pre Kit (Cat#FC-122-1001).
RNA libraries were prepared for sequencing using standard lllumina proocols

value: Macrophage

value: RhoA knockout

value: RANKL/M-CSF


title: RAW264.7 cell SMART-Cas9-2

description: Library name: Sample5


title: CVS 71240, Male, NIFT

value: Wild type

value: NIFT:non-IVF fertility treatment

value: C-Section


title: lung.Het.1292451

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292451


title: RAW264.7 cell SMART-Cas9-1

description: Library name: Sample4


title: lung.WT.1292448

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292448


title: CVS 71253, Male, Spontaneous

value: unassisted/spontaneous


title: CVS 71238, Male, IVF

value: First trimester placenta - chorionic villi

value: IVF:in vitro fertilization

value: Infertility treatment


title: lung.WT.1292447

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292447


title: WT biol rep 2

value: heads

value: WT

value: untreated


title: RAW264.7 cell Control-3

description: Library name: Sample3

value: wt


title: WT biol rep 1


title: lung.Het.1292446

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292446

value: lung


title: RAW264.7 cell Control-2

description: Library name: Sample2


title: lung.WT.1292445

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292445


title: CVS 71266, Male, Spontaneous

value: Male

value: No

value: NonHispanic

value: Vaginal

value: Bulk placenta in GSE109082


title: CVS 71246, Female, IVF

value: Wild type

value: Female

value: Bulk placenta in GSE215421


title: CVS 71197, Female, Spontaneous

value: unassisted/spontaneous

value: Hispanic


title: lung.Het.1292443

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292443


title: lung.Het.1292449

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292449


title: lung.Het.1292442

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292442


title: lung.Het.1292444

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292444


title: lung.WT.1292441

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292441


title: RAW264.7 cell Control-1

description: Library name: Sample1

value: Macrophage

value: RANKL/M-CSF


title: lung.WT.1292439

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292439


title: CVS 71134, Male, Spontaneous

value: First trimester placenta - chorionic villi


title: lung.Het.1292436

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292436


title: lung.Het.1292440

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292440


title: CVS 71098, Female, Spontaneous


title: CVS 71117, Female, NIFT

value: NIFT:non-IVF fertility treatment

value: Infertility treatment

value: C-Section


title: lung.Het.1292438

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292438

value: lung


title: CVS 71235, Female, IVF

value: IVF:in vitro fertilization


title: lung.WT.1292435

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292435


title: lung.WT.1292434

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292434


title: lung.WT.1292433

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292433


title: KO 48_4

city: HUDDINGE

first: Ivan

middle: Martinov

last: Vlassakev

address: HÄLSOVÄGEN 7C

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

description: Library name: Sample L19

data_processing:
Raw non-demultiplexed fastq files were processed using zUMIs (version 2.4.1 or newer) with STAR (v2.5.4b) to generate expression profiles for both the 5′ ends containing UMIs as well as combined full-length and UMI data.
Mouse cDNA was mapped against mm10 genome with CAST SNPs masked with N to avoid mapping bias. Data were quantified with gene annotations from Ensembl GRCm38.91.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

growth_protocol: AML12 cells were cultured in 10% fetal bovine serum in growth media comprised of Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12, HEPES, 100 U/mL Penicillin/streptomycin, 1% Insulin-Transferrin-Selenium solution (Gibco) and 40 ng/mL dexamethasone.

extract_protocol:
RNA from cells was extracted using commercial kits (MACHEREY-NAGEL GmbH & Co. KG) according to the provided instructions.
High-sensitivity DNA chip (Agilent Bioanalyzer) were used to check library size distribution. All cDNA concentrations were quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Scientific). Tagmentation was carried out in 2 µl, consisting of 1× tagmentation buffer (10 mM Tris, pH 7.5, 5 mM MgCl2, 5% DMF), 0.08–0.1 µl ATM (Illumina XT DNA sample preparation kit), 1 µl cDNA and water. Library amplification of the tagmented samples was performed using 1.5 µl custom designed Nextera index primers. After tagmentation, samples were pooled, and the pool was purified with Ampure XP beads. Libraries were sequenced at the 75-bp single end, 50-bp single end or 150-bp paired end on a high-output flow cell using an Illumina NextSeq500 instrument, an Illumina HiSeq3000 instrument or a NovaSeq S4 flow cell 150-bp paired end.

treatment_protocol: Cells were grown until 90% confluence was reached prior to conducting experiments. To synchronise the circadian clock, we induced a 1-h dexamethasone pulse.

value: liver

value: immortalized murine hepatocytes


title: KO 42_4

description: Library name: Sample H19


title: KO 48_3

description: Library name: Sample K19


title: KO 48_2

description: Library name: Sample J19


title: KO 48_1

description: Library name: Sample I19


title: CVS 71074, Male, NIFT

value: Male

value: NonHispanic

value: Vaginal

value: No


title: lung.Het.1292432

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.Het.1292432


title: lung.WT.1292431

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292431


title: CVS 71060, Male, Spontaneous

value: Wild type

value: Bulk placenta in GSE215421


title: heart.Het.1292429

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292429

value: heart


title: KO 42_3

description: Library name: Sample G19


title: heart.Het.1292428

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292428


title: CVS 71059, Male, NIFT


title: CVS 71141, Female, Spontaneous

value: Female

value: unassisted/spontaneous

value: Bulk placenta in GSE109082


title: KO 42_2

description: Library name: Sample F19


title: CVS 71057, Female, NIFT

value: First trimester placenta - chorionic villi

value: NIFT:non-IVF fertility treatment

value: Hispanic


title: heart.WT.1292427

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292427


title: lung.WT.1292437

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292437

value: lung


title: heart.WT.1292425

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292425


title: heart.WT.1292424

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292424


title: KO 36_4

description: Library name: Sample D19


title: heart.Het.1292426

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292426


title: CVS 71075, Male, IVF

value: IVF:in vitro fertilization

value: Infertility treatment

value: C-Section


title: KO 36_3

description: Library name: Sample C19

value: liver

value: immortalized murine hepatocytes


title: CVS 71055, Male, Spontaneous

value: Male

value: NonHispanic


title: heart.Het.1292423

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292423


title: heart.Het.1292422

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292422


title: CVS 71050, Male, NIFT

value: Wild type

value: No


title: KO 36_2

description: Library name: Sample B19


title: heart.WT.1292420

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292420

value: heart


title: heart.Het.1292419

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292419


title: heart.WT.1292418

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292418


title: KO 36_1

description: Library name: Sample A19


title: CVS 71045, Male, Spontaneous

value: Bulk placenta in GSE215421


title: lung.WT.1292430

description:
Dchs1_counts.txt
Dchs1_TPM.txt
lung.WT.1292430


title: heart.Het.1292417

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292417


title: CVS 71032, Male, IVF


title: KO 30_4

description: Library name: Sample P18


title: heart.Het.1292416

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292416


title: KO 42_1

description: Library name: Sample E19


title: heart.Het.1292415

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292415


title: heart.Het.1292414

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292414


title: CVS 71022, Female, Spontaneous

value: Female

value: unassisted/spontaneous

value: Vaginal


title: CVS 71019, Female, NIFT

value: First trimester placenta - chorionic villi

value: NIFT:non-IVF fertility treatment


title: KO 30_3

description: Library name: Sample O18


title: KO 30_2

description: Library name: Sample N18


title: heart.WT.1292413

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292413


title: heart.Het.1292411

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292411


title: heart.WT.1292412

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292412


title: heart.Het.1292410

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292410


title: heart.WT.1292409

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292409


title: heart.WT.1292421

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292421


title: CVS 71049, Male, Spontaneous


title: CVS 70993, Male, Spontaneous


title: CVS 70992, Female, Spontaneous


title: KO 24_4

description: Library name: Sample L18


title: KO 30_1

description: Library name: Sample M18


title: KO 24_3

description: Library name: Sample K18


title: heart.Het.1292406

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292406


title: CVS 70982, Male, Spontaneous


title: heart.WT.1292408

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292408


title: heart.WT.1292407

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292407


title: heart.Het.1292405

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292405


title: heart.WT.1292404

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292404


title: KO 24_2

description: Library name: Sample J18


title: CVS 70980, Female, IVF


title: KO 24_1

description: Library name: Sample I18


title: heart.WT.1292402

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292402


title: heart.Het.1292403

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292403


title: CVS 70977, Female, Spontaneous


title: heart.Het.1292401

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292401


title: KO 18_3

description: Library name: Sample G18


title: heart.Het.1292398

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292398


title: KO 18_4

description: Library name: Sample H18


title: CVS 70927, Female, Spontaneous

value: Hispanic


title: CVS 70951, Male, Spontaneous


title: heart.WT.1292400

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292400


title: heart.WT.1292399

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292399


title: heart.WT.1292397

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292397


title: heart.Het.1292394

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292394


title: KO 18_2

description: Library name: Sample F18


title: CVS 70909, Male, NIFT


title: WT 48_4

description: Library name: Sample L17

value: wild-type (control)


title: heart.WT.1292392

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292392


title: heart.WT.1292395

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292395


title: CVS 70905, Male, IVF

value: IVF:in vitro fertilization

value: Infertility treatment


title: heart.WT.1292393

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292393


title: CVS 70904, Female, NIFT

value: C-Section


title: heart.Het.1292391

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292391


title: heart.Het.1292390

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292390


title: CVS 70899, Female, IVF


title: heart.Het.1292389

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292389


title: WT 48_2

description: Library name: Sample J17

value: liver

value: immortalized murine hepatocytes


title: CVS 70897, Female, IVF

value: NonHispanic


title: heart.WT.1292396

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292396


title: heart.WT.1292388

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292388


title: KO 18_1

description: Library name: Sample E18


title: heart.WT.1292387

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292387


title: WT 48_1

description: Library name: Sample I17


title: CVS 70895, Female, Spontaneous

value: Wild type


title: heart.WT.1292385

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292385


title: CVS 70889, Female, Spontaneous

value: No


title: WT 42_4

description: Library name: Sample H17


title: WT 42_3

description: Library name: Sample G17


title: heart.Het.1292384

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292384

value: heart


title: kidney.Het.1292381

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292381

value: kidney


title: WT 48_3

description: Library name: Sample K17


title: CVS 70885, Female, Spontaneous

value: Female


title: WT 42_2

description: Library name: Sample F17


title: heart.Het.1292383

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292383


title: CVS 70859, Female, Spontaneous

value: unassisted/spontaneous

value: Bulk placenta in GSE215421


title: kidney.Het.1292380

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292380


title: kidney.WT.1292379

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292379


title: WT 42_1

description: Library name: Sample E17


title: WT 36_4

description: Library name: Sample D17


title: CVS 70862, Male, Spontaneous

value: First trimester placenta - chorionic villi

value: Male


title: kidney.Het.1292378

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292378


title: kidney.Het.1292377

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292377


title: CVS 70844, Male, NIFT

value: NIFT:non-IVF fertility treatment

value: Hispanic

value: Vaginal


title: kidney.WT.1292376

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292376


title: kidney.WT.1292375

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292375


title: CVS 70837, Female, Spontaneous


title: heart.Het.1292386

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.Het.1292386


title: kidney.Het.1292374

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292374


title: kidney.Het.1292373

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292373


title: CVS 70833, Female, Spontaneous


title: WT 36_3

description: Library name: Sample C17

value: wild-type (control)


title: CVS 70819, Male, Spontaneous

value: Bulk placenta in GSE109082

value: Bulk placenta and decidua in GSE131874


title: WT 36_1

description: Library name: Sample A17

value: liver

value: immortalized murine hepatocytes


title: heart.WT.1292382

description:
Dchs1_counts.txt
Dchs1_TPM.txt
heart.WT.1292382


title: WT 36_2

description: Library name: Sample B17


title: WT 30_4

description: Library name: Sample P16


title: CVS 70814, Male, Spontaneous

value: Wild type

value: C-Section


title: WT 30_3

description: Library name: Sample O16


title: kidney.Het.1292368

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292368


title: kidney.Het.1292367

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292367


title: kidney.WT.1292369

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292369


title: kidney.WT.1292372

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292372


title: WT 30_2

description: Library name: Sample N16


title: kidney.Het.1292365

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292365


title: CVS 70785, Female, Spontaneous

value: No


title: kidney.Het.1292364

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292364

value: kidney


title: kidney.Het.1292363

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292363


title: kidney.WT.1292366

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292366


title: CVS 70789, Female, Spontaneous

value: Female

value: NonHispanic


title: WT 30_1

description: Library name: Sample M16


title: CVS 70772, Female, NIFT

value: Infertility treatment

value: Bulk placenta in GSE215421


title: CVS 70768, Male, NIFT

value: First trimester placenta - chorionic villi

value: Male


title: kidney.WT.1292362

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292362


title: kidney.Het.1292360

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292360


title: WT 24_4

description: Library name: Sample L16


title: kidney.WT.1292371

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292371


title: kidney.WT.1292359

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292359


title: kidney.WT.1292370

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292370


title: WT 24_3

description: Library name: Sample K16


title: CVS 70739, Male, Spontaneous

value: unassisted/spontaneous


title: WT 24_2

description: Library name: Sample J16


title: CVS 70734, Male, Spontaneous


title: kidney.Het.1292355

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292355


title: kidney.Het.1292358

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292358


title: CVS 70729, Female, Spontaneous

value: Hispanic

value: Vaginal


title: kidney.Het.1292354

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292354


title: WT 24_1

description: Library name: Sample I16

value: wild-type (control)


title: WT 18_4

description: Library name: Sample H16


title: CVS 70726, Female, Spontaneous


title: kidney.WT.1292352

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292352


title: WT 18_3

description: Library name: Sample G16


title: kidney.WT.1292351

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292351


title: CVS 70716, Male, IVF

value: IVF:in vitro fertilization


title: kidney.Het.1292350

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292350


title: WT 18_2

description: Library name: Sample F16

value: liver


title: kidney.Het.1292361

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292361


title: kidney.WT.1292348

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292348


title: kidney.Het.1292347

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292347


title: WT 18_1

description: Library name: Sample E16

value: immortalized murine hepatocytes


title: kidney.WT.1292346

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292346


title: CVS 70706, Female, Spontaneous

value: Wild type

value: Bulk placenta in GSE109082


title: kidney.WT.1292344

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292344


title: kidney.Het.1292357

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292357


title: kidney.WT.1292345

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292345


title: kidney.WT.1292356

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292356


title: CVS 70699, Male, Spontaneous

value: No


title: ZT20_4 KO

description: Library name: Sample H5

source_name: eWAT

extract_protocol:
RNA from all samples was extracted via the Qiagen kit according to manufacturer's instructions.
High-sensitivity DNA chip (Agilent Bioanalyzer) were used to check library size distribution. All cDNA concentrations were quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Scientific). Tagmentation was carried out in 2 µl, consisting of 1× tagmentation buffer (10 mM Tris, pH 7.5, 5 mM MgCl2, 5% DMF), 0.08–0.1 µl ATM (Illumina XT DNA sample preparation kit), 1 µl cDNA and water. Library amplification of the tagmented samples was performed using 1.5 µl custom designed Nextera index primers. After tagmentation, samples were pooled, and the pool was purified with Ampure XP beads. Libraries were sequenced at the 75-bp single end, 50-bp single end or 150-bp paired end on a high-output flow cell using an Illumina NextSeq500 instrument, an Illumina HiSeq3000 instrument or a NovaSeq S4 flow cell 150-bp paired end.

value: eWAT

value: full-body Bmal1-KO


title: kidney.Het.1292342

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292342

value: kidney


title: CVS 70688, Female, Spontaneous

value: Female

value: NonHispanic


title: CVS 70682, Male, NIFT

value: First trimester placenta - chorionic villi

value: NIFT:non-IVF fertility treatment

value: Infertility treatment

value: C-Section

value: Bulk placenta in GSE215421


title: kidney.Het.1292343

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292343


title: kidney.Het.1292353

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292353


title: kidney.WT.1292340

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292340


title: ZT20_2 KO

description: Library name: Sample F5


title: CVS 70632, Male, Spontaneous

value: Male

value: unassisted/spontaneous

value: Vaginal


title: kidney.Het.1292341

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292341


title: kidney.WT.1292339

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292339


title: ZT20_1 KO

description: Library name: Sample E5


title: kidney.WT.1292349

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292349


title: kidney.WT.1292338

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292338


title: ZT20_3 KO

description: Library name: Sample G5


title: CVS 70629, Male, NIFT


title: CVS 70625, Female, Spontaneous


title: kidney.Het.1292337

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292337


title: spn1 K192N 128U MNase Rep2

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description: spn1 K192N 128U MNase

data_processing:
Sequencing reads were trimmed using Cutadapt (Martin, 2011): Illumina adapter sequences were removed, and reads were trimmed to 140 bp. Reads less than 35 bp were discarded. Trimmed reads were aligned to the sacCer3 version of Saccharomyces cerevisiae genome using bowtie2 (Langmead & Salzberg, 2012). Samtools (Li et al., 2009) and bedtools (Quinlan & Hall, 2010) were used for processing aligned reads from sam to bed files. Coverage at 1 bp windows genome-wide for specific fragment lengths was calculated as the number of reads that mapped at each window, normalized by the factor N:  N = 139712364/(Total number of mapped reads). 139712364 was a number chosen arbitrarily.  Coverage of fragment centers for specific fragment lengths was also calculated similarly at 1 bp windows.
Assembly: sacCer3
Supplementary files format and content: Normalized coverage of fragment centers for fragments 80-170 bp in the bigWig format.

organism: Saccharomyces cerevisiae

growth_protocol: All Saccharomyces cerevisiae strains were grown in yeast extract, peptone, and dextrose (YPD; 2% dextrose) media at 30°C. The strains used in this study were previously created as described (Li et al., 2018 PMID:  29300974; Thurston et al., 2018 PMID:  30301740; Zhang et al., 2008 PMID:  18086892). Strains were transformed with a covering plasmid expressing wild-type SPN1 flanked by the TOA1 promoter and terminator. Endogenous SPN1 was replaced by a LEU2 fragment flanked by the SPN1 promoter and terminator through homologous recombination. Plasmids containing wild-type SPN1, spn1K192N, or spn1141-305 under the control of their native promoter and terminator were introduced into strains by plasmid shuffling.

extract_protocol:
Yeast cultures (3 ml) were grown to OD600 = 0.7-1.0 at 30°C, then used to inoculate yeast cultures (400 ml) grown to OD600 = 1.0 at 28°C. Cells are centrifuged at 5000 x rpm for 10 minutes at 4°C and the supernatant is decanted. The cell pellets are resuspended in 30 ml of sorbitol buffer (50mM Tris-Cl pH 7.5, 1M sorbitol, 10mM MgCl2) containing 10mM 𝛽-mercaptoethanol (𝛽ME) and 1mM phenylmethylsulfonyl fluoride (PMSF). The cell pellets were resuspended in sorbitol buffer with 𝛽ME and PMSF and centrifuged at max rpm for 5 minutes at 4°C twice, and the cell pellets were weighed afterward. Pellets were then suspended in 0.66ml sorbitol buffer with 𝛽ME and PMSF per gram of cells. 20 µl of the cell suspension was set aside for monitoring cell wall digestion, and the remainder was incubated at 30°C with gentle agitation for 10 minutes.  Spheroplasting was performed by adding 0.34 ml of Zymolase (10mg/ml) per gram of cells to the sorbitol-cell suspension, followed by incubation at 30°C. Spheroplasting was monitored by determining the OD600 of 4 µl of cell suspension with or without Zymolase combined with 4 µl of 1% SDS and 992 µl of ddH2O. When the OD600 of the cells with Zymolase was ~10% of the cells without Zymolase, sorbitol buffer with PMSF was slowly added until the final volume is 30 ml. Spheroplasts were collected by centrifugation at max rpm for 5 minutes, followed by decanting of the supernatant. The spheroplasts were washed in 5 ml of sorbitol buffer two additional times, then suspended in Ficoll buffer (18% Ficoll 400, 20mM Tris-Cl pH 7.5, 0.5mM MgCl2). Each spheroplast suspension was transferred to a 50 ml Potter-Elvehjem homogenizer and homogenized on ice with six up-down even strokes with a handheld drill at max rpm. The suspensions were transferred to chilled 25 ml centrifuge tubes, and the remaining cells were pelleted at 6400 x rpm for 5 minutes at 4°C. The supernatant containing yeast nuclei was transferred to new centrifuge tubes and pelleted at 15,000 x rpm at 4°C. Nuclei were suspended in 10 ml of MNase digestion buffer (20 mM Tris-Cl pH 8.0, 1.5 mM CaCl2, 150 mM NaCl, and 1 mM PMSF). The OD600 of the nuclei suspension was determined by a 1:10 dilution in digestion buffer, which should be ~0.2 for nuclei from 1 gram of cells. Nuclei were pelleted at 15,000 x rpm for 30 minutes at 4°C and suspended in digestion buffer at a ratio of 2.4 ml for OD600 = 0.2. 400 µl aliquots of the nuclei suspension were prepared for MNase digestion and incubated at 37°C for 10 minutes. Nuclei were digested with a range of MNase concentrations (0U, 32U, 64U, 128U, and 256U) at 37°C for 10 minutes. 100 µl of stop solution (50mM EDTA, 2.5% SDS, 0.25mg/ml Proteinase K) was added to each reaction, then samples were incubated at 37°C overnight. Samples were extracted twice with phenol:chloroform, once with chloroform, and precipitated with ethanol. The DNA was washed with 70% ethanol, dried at room temperature, then suspended in 100 µL of TE buffer (pH 7.5) and 3 µL of RNaseA (10 mg/mL). Reactions were incubated overnight at 37°C, followed by ethanol precipitation, a wash with 70% ethanol, and drying at room temperature. The precipitated DNA was resuspended in 100µl of TE buffer (10mM Tris-Cl, pH 8.0 and 1mM EDTA, pH 8.0), and 10µl was subjected to agarose gel electrophoresis.
MNase-protected DNA fragments were made into sequencing libraries using the single stranded library protocol as previously described (Ramani et al., 2019; Snyder et al., 2016). In brief, 10ng DNA was dephosphorylated using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific cat. EF0651), denatured, and incubated overnight with CircLigaseII (Lucigen cat. CL9025K) and 0.093-0.125 µM biotinylated CL78 primer (Snyder et al., 2016) at 60ºC with shaking every 5 minutes. DNA fragments were then denatured and bound to magnetic streptavidin M-280 beads (Invitrogen cat. 11205D) for 30 minutes at room temperature with nutation. Beads were washed, and second-strand synthesis was performed using Bst 2.0 DNA polymerase (NEB cat. M0537) with an increasing temperature gradient of 15-31ºC with shaking at 1750 rpm. Beads were washed, and a 3’ gap fill was performed using T4 DNA polymerase (Thermo Scientific cat. EL0011) for 30 minutes at room temperature. Beads were washed, and a double-stranded adapter was ligated using T4 DNA ligase (Thermo Scientific cat. EP0062) for 2 hours at room temperature with shaking at 1750 rpm. Beads were washed and resuspended in 30 µL 10 mM TET buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 0.05% Tween-20). DNA was denatured at 95ºC for 3 min, and DNA libraries were collected after immediate magnetic separation. Quantitative real-time PCR was performed on DNA libraries using iTAQ Supermix (Bio-Rad cat. 1725124), and Ct values were used to determine the number of PCR cycles needed to amplify each library. PCR was performed with KAPA HiFi DNA polymerase (Kapa Biosystems cat. KK2502) using barcoded indexing primers for Illumina. Primer dimers were removed from the libraries using AMPure beads (Beckman Coulter cat. A63881). Libraries were eluted in 0.1X TE, and concentrations were determined using Qubit. The length distribution of each library was assessed by the Agilent Bioanalyzer using the D1000 or HSD1000 cassette. Libraries were sequenced for 150 cycles in paired-end mode on the NovaSeq 6000 system at the University of Colorado Cancer Center Genomics Shared Resource.

value: BY4741 spn1delta::LEU2 + pCR312


title: spn1 141-305 128U MNase Rep2

description: spn1 141-305 128U MNase

value: BY4741 spn1delta::LEU2 + pAA344


title: Zt16_3 KO

description: Library name: Sample C5


title: CVS 70623, Female, IVF

value: Wild type

value: IVF:in vitro fertilization


title: CVS 70594, Male, IVF

value: No


title: kidney.Het.1292335

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.Het.1292335


title: Zt16_1 KO

description: Library name: Sample A5

value: eWAT

value: full-body Bmal1-KO


title: Zt16_2 KO

description: Library name: Sample B5


title: kidney.WT.1292336

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292336

value: kidney


title: CVS 70579, Male, NIFT

value: NonHispanic


title: spn1 141-305 32U MNase

description: spn1 141-305 32U MNase


title: WT 128U MNase Rep2

description: WT 128U MNase

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0


title: spn1 K192N 32U MNase

description: spn1 K192N 32U MNase


title: liver.WT.1292333

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292333

value: liver


title: kidney.WT.1292334

description:
Dchs1_counts.txt
Dchs1_TPM.txt
kidney.WT.1292334


title: CVS 70551, Male, Spontaneous

value: First trimester placenta - chorionic villi


title: Zt12_4 KO

description: Library name: Sample P4


title: liver.Het.1292332

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292332


title: CVS 70540, Female, IVF

value: Female

value: Infertility treatment


title: Zt12_2 KO

description: Library name: Sample N4


title: CVS 70529, Male, IVF

value: Male

value: C-Section

value: Bulk placenta in GSE215421


title: spn1 141-305 128U MNase Rep1

description: spn1 141-305 128U MNase


title: spn1 K192N 128U MNase Rep1

description: spn1 K192N 128U MNase

value: BY4741 spn1delta::LEU2 + pCR312


title: liver.WT.1292331

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292331


title: Zt12_3 KO

description: Library name: Sample O4


title: Zt16_4 KO

description: Library name: Sample D5


title: liver.Het.1292330

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292330


title: CVS 70514, Male, Spontaneous

value: unassisted/spontaneous


title: WT 128U MNase Rep1

description: WT 128U MNase


title: CVS 70507, Male, Spontaneous

value: Wild type

value: Hispanic


title: liver.WT.1292329

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292329


title: ZT8_3 KO

description: Library name: Sample K4


title: CVS 70461, Male, NIFT

value: NIFT:non-IVF fertility treatment

value: No


title: liver.WT.1292328

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292328


title: ZT8_2 KO

description: Library name: Sample J4

value: eWAT

value: full-body Bmal1-KO


title: CVS 70435, Female, IVF

value: IVF:in vitro fertilization

value: NonHispanic


title: liver.Het.1292327

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292327

value: liver


title: WT 32U MNase

description: WT 32U MNase

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0


title: CVS 70281, Male, Spontaneous

value: First trimester placenta - chorionic villi


title: ZT8_1 KO

description: Library name: Sample I4


title: liver.WT.1292326

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292326


title: liver.WT.1292325

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292325


title: Zt12_1 KO

description: Library name: Sample M4


title: liver.WT.1292324

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292324


title: T-cells scramble guide dCAS9-DNMT3A Day 21 Replica 2

hyb_protocol: DNA was bisulfite converted, amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChips (Illumina)  according to the standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan)

data_processing:
dye bias correction, pOOBAH, ssnoob normalization, remove of non-CpG probes, remove of probes with SNP and remove of flagged probes in manifest b5 file
Processed data: T_cell_hyper_beta_detp.csv includes normalized beta-values.

label: Cy5 and Cy3

source_name: primary T-cells

growth_protocol: Human primary T-cells were then cultured in TexMacs medium (Miltenyi Biotec) with 10% FCS (Bio&Sell), IL-2 (50 IU/mL, GibcoTM) and Penicillin Streptomycin 100U/ml (GibcoTM) at 37°C / 5% CO2.

extract_protocol: Genomic DNA was isolated using the Macherey Nagel Tissue kit.

treatment_protocol: Transfection of T cells was performed using the NEON transfection system (Invitrogen). 5 million T cells were transfected with 5μg of plasmids for CRISPR-constructs and 5μg of gRNA plasmids inside of a NEON 100ul pipet tip with 1 pulse (20ms) at 2100V. After 24 hours, cells were resuspended in MACS buffer for flowcytometric sorting for double positive cells (BD FACSAriaTM fusion) and further cultured in TexMACS medium as indicated above for up to 21 days.

value: primary T-cells

value: scramble guide + dCAS9-DNMT3A/3L

tag: time point

value: isolation after 21 days of culture


title: ZT4_2 KO

description: Library name: Sample F4


title: CVS 70088, Female, NIFT

value: Female

value: Infertility treatment

value: C-Section

value: Bulk placenta in GSE215421


title: ZT4_4 KO

description: Library name: Sample H4


title: liver.Het.1292323

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292323


title: T-cells scramble guide dCAS9-DNMT3A Day 21 Replica 1


title: ZT4_3 KO

description: Library name: Sample G4


title: ZT8_4 KO

description: Library name: Sample L4


title: ZT4_1 KO

description: Library name: Sample E4


title: liver.Het.1292322

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292322


title: ZT0_4 KO

description: Library name: Sample D4


title: T-cells HyperCpGs targeted dCAS9-DNMT3A Day 21 Replica 2

value: guides HyperCpGs (PDE4C, FHL2, ELOVL2, KLF14, and TEAD1) + dCAS9-DNMT3A/3L


title: T-cells HyperCpGs targeted dCAS9-DNMT3A Day 21 Replica 1


title: HRSV at 15H, biological rep2

type: RNA

city: Singapore

first: Richard

middle: J

last: Sugrue

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description: Gene expression data from HRSV infected Hep2 15 hpi rep 2

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45˚C on Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with GeneChip Operating Software 5.0 (GCOS 5.0) using Affymetrix default analysis settings. Further analysis was done in GeneSpring 11.0. The normalization was done using internal and external control genes as assigned by Affymetrix. The target intensity of each array on a given time point was first filtered by the flagging of Present (P) in 3 replicates at one time-point, which then further calculated in fold change up- or downregulation with respect to the signal intensity in MOCK infected cells, after analyzed by ANOVA with p value ≤ 0.05.

label: biotin

source_name: HRSV infected Hep2 15 hpi rep 2

label_protocol: Biotinylated mRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: The cells were grown in DMEM 10% Fetal Bovine Serum (FBS)100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2

extract_protocol: RNA extraction was performed using RNAeasy MiniKit (Qiagen) according to the manufacturer's instruction at 4˚C

treatment_protocol: The cells were infected with HRSV MOI=5 in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 33˚C, 5% CO2

value: Hep2 cells


title: HRSV at 8H, biological rep3

description: Gene expression data from HRSV infected Hep2 8 hpi rep 3

source_name: HRSV infected Hep2 8 hpi rep 3


title: HRSV at 15H, biological rep3

description: Gene expression data from HRSV infected Hep2 15 hpi rep 3

source_name: HRSV infected Hep2 15 hpi rep 3


title: HEK293T scramble guide dCAS9-DNMT3A Day 3 Replica 3

description:
scrambleCTRL_D3_R3
isolation after 3 days of culture

data_processing:
dye bias correction, pOOBAH, ssnoob normalization, remove of non-CpG probes, remove of probes with SNP and remove of flagged probes in manifest b5 file
processed value definition: average beta-value

treatment_protocol: HEK293T cells were transfected with the TransIT®-LT1 transfection reagent (Mirus Bio) in 6-well plates with 1.25μg of plasmids for the CRISPR-construct and 1.25μg of plasmids for single gRNA. We either pooled two gRNAs targeting PDE4C or up to nine gRNAs for multiplexed editing. After 24 hours we selected the transfected cells either by puromycin treatment (2 ug/ml for 2 days) or flowcytometric sorting for double positive cells (BD FACSAriaTM fusion).


title: ZT0_3 KO

description: Library name: Sample C4


title: liver.Het.1292319

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292319

source_name: liver


title: ZT0_2 KO

description: Library name: Sample B4


title: HEK293T scramble guide dCAS9-DNMT3A Day 3 Replica 2

description:
scrambleCTRL_D3_R2
isolation after 3 days of culture


title: ZT0_1 KO

description: Library name: Sample A4


title: HRSV at 15H, biological rep1

description: Gene expression data from HRSV infected Hep2 15 hpi rep 1

source_name: HRSV infected Hep2 15 hpi rep 1


title: liver.WT.1292318

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292318


title: HEK293T scramble guide dCAS9-DNMT3A Day 3 Replica 1

description:
scrambleCTRL_D3_R1
isolation after 3 days of culture


title: HRSV at 12H, biological rep3

description: Gene expression data from HRSV infected Hep2 12 hpi rep 3

source_name: HRSV infected Hep2 12 hpi rep 3


title: liver.Het.1292317

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292317


title: HRSV at 12H, biological rep1

description: Gene expression data from HRSV infected Hep2 12 hpi rep 1

source_name: HRSV infected Hep2 12 hpi rep 1


title: HRSV at 8H, biological rep1

description: Gene expression data from HRSV infected Hep2 8 hpi rep 1

source_name: HRSV infected Hep2 8 hpi rep 1


title: HRSV at 12H, biological rep2

description: Gene expression data from HRSV infected Hep2 12 hpi rep 2

source_name: HRSV infected Hep2 12 hpi rep 2


title: HEK293T HypoCpGs targeted dCAS9-DNMT3A Day 3 Replica 3

description:
DNMT3A_HypoCpGs_D3_R3
isolation after 3 days of culture

value: guides HypoCpGs (AKAP8L, CSNK1D, IGSF11, MEIS1-AS3, COL1A1) + dCAS9-DNMT3A/3L


title: HEK293T HypoCpGs targeted dCAS9-DNMT3A Day 3 Replica 2

description:
DNMT3A_HypoCpGs_D3_R2
isolation after 3 days of culture


title: HRSV at 4H, biological rep3

description: Gene expression data from HRSV infected Hep2 4 hpi rep 3

source_name: HRSV infected Hep2 4 hpi rep 3


title: liver.Het.1292320

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292320


title: HRSV at 4H, biological rep1

description: Gene expression data from HRSV infected Hep2 4 hpi rep 1

source_name: HRSV infected Hep2 4 hpi rep 1


title: HRSV at 8H, biological rep2

description: Gene expression data from HRSV infected Hep2 8 hpi rep 2

source_name: HRSV infected Hep2 8 hpi rep 2


title: ZT20_1 LRE

description: Library name: Sample M3

value: eWAT

value: LRE


title: ZT20_4 LRE

description: Library name: Sample P3


title: ZT20_2 LRE

description: Library name: Sample N3


title: liver.WT.1292316

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292316


title: liver.Het.1292321

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292321


title: Zt8_4 LRE

description: Library name: Sample L3


title: ZT20_3 LRE

description: Library name: Sample O3


title: HRSV at 0H, biological rep2

description: Gene expression data from mock infected Hep2 rep 2

source_name: Mock infected Hep2 rep 2


title: HEK293T HypoCpGs targeted dCAS9-DNMT3A Day 3 Replica 1

description:
DNMT3A_HypoCpGs_D3_R1
isolation after 3 days of culture


title: liver.WT.1292315

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292315


title: HRSV at 4H, biological rep2

description: Gene expression data from HRSV infected Hep2 4 hpi rep 2

source_name: HRSV infected Hep2 4 hpi rep 2


title: HEK293T scramble guide dCAS9-DNMT3A Day 15 Replica 3

description:
scrambleCTRL_D15_R3
isolation after 15 days of culture

data_processing:
dye bias correction, pOOBAH, ssnoob normalization, remove of non-CpG probes, remove of probes with SNP and remove of flagged probes in manifest b5 file
*processed value definition: average beta-value


title: liver.Het.1292312

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292312


title: liver.Het.1292314

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292314


title: liver.Het.1292313

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292313


title: Zt8_3 LRE

description: Library name: Sample K3


title: Zt8_2 LRE

description: Library name: Sample J3


title: liver.Het.1292311

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292311


title: HEK293T scramble guide dCAS9-DNMT3A Day 15 Replica 1

description:
scrambleCTRL_D15_R1
isolation after 15 days of culture


title: HEK293T HypoCpGs targeted dCAS9-DNMT3A Day 15 Replica 3

description:
DNMT3A_HypoCpGs_D15_R3
isolation after 15 days of culture


title: Zt8_1 LRE

description: Library name: Sample I3


title: HEK293T HypoCpGs targeted dCAS9-DNMT3A Day 15 Replica 2

description:
DNMT3A_HypoCpGs_D15_R2
isolation after 15 days of culture


title: liver.Het.1292310

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292310


title: HEK293T HypoCpGs targeted dCAS9-DNMT3A Day 15 Replica 1

description:
DNMT3A_HypoCpGs_D15_R1
isolation after 15 days of culture


title: HEK293T scramble guide dCAS9-DNMT3A Day 15 Replica 2

description:
scrambleCTRL_D15_R2
isolation after 15 days of culture


title: liver.WT.1292309

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292309


title: Zt16_4 LRE

description: Library name: Sample H3


title: HRSV at 0H, biological rep3

description: Gene expression data from mock infected Hep2 rep 3

source_name: Mock infected Hep2 rep 3


title: Zt16_3 LRE

description: Library name: Sample G3

source_name: eWAT


title: HEK293T control (PDE4C guides only) Replica 3

value: guides PDE4C

value: isolation after 14 days of culture


title: liver.Het.1292308

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292308

value: liver


title: Zt16_2 LRE

description: Library name: Sample F3


title: liver.WT.1292307

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292307


title: HEK293T control (PDE4C guides only) Replica 2


title: liver.WT.1292306

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292306


title: HRSV at 0H, biological rep1

description: Gene expression data from mock infected Hep2 rep 1

source_name: Mock infected Hep2 rep 1


title: PSMB10WT_IFNγ_24hr_rep5

city: Borstel

first: Yuqin

last: Wang

address: Parkallee 26

institute: FZB

description: Gene expression after 24hr in IFNγ treated PSMB10WT skin fibroblast

hyb_protocol: 1650 ng of Cy3-labelled cRNA was fragmented according to Low Input Quick Amp Labelling Kit Protocol (Agilent) with 2xHI-RPM Hybridization Buffer for 30 min at 60°C. Hybridization on Agilent Human Whole Genome 4x44k V2 arrays was performed at 65°C for 17h under constant rotation in a hybidization oven. Washing was performed using the GE Wash buffer 1 (Agilent) at RT and Ge Wash Buffer 2 (Agilent) at 37°C for each 1 min. Washed slides were air-dried and immediately scanned.

scan_protocol: Slides were immediately scannend on an Agilent SureScan Scanner with Dye Channel =Green, 5 µm Resolution and scanning area=61 x 21.6 mm.

data_processing: Agilent Feature Extraction Software V 11.5 was used with default options (GE 1-color protocol) to extract raw data. Txt files were imported into GeneSpring software Version 13 under omission of compromised flags. Flags were accepted if at least 100 percent of samples in any 1 out of 7 conditions were detected.

source_name: PSMB10WT skin fibroblast, IFNγ stimulation, 24hr

label_protocol: Cy3-labelling of total RNA was conducted with the Low Input Quick Amp Labelling Kit (Agilent) according to manufacturer´s instructions. Dye incorporation rate and specific yield was calculated using an NanoDrop spectrophotometer.

growth_protocol: Skin fibroblasts of patient(PSMB10G209R) and neonatal individual of comparative age(PSMB10wt) were cultured in 50ug/mL PureCol(Advanced BioMatrix) coated cell culture plates. The medium for cultivation comprised of DMEM high glucose (4.5 g/L)  GlutaMAX™ (Thermo Fisher Scientific) supplemented with 10 % (v/v) fetal bovine serum (FBS) (Capricorn Scientific), 100 U/mL penicillin/streptomycin (Gibco, Thermo Fisher Scientific). phSF were grown in a humidified environment with 5% CO2 at 37 °C and passaged into new cell culture plate twice a week when reach confluency of 80-90%.

extract_protocol: Total RNA from PSMB10WT and PSMB10G209R skin fibroblast were extracted using TriZol and quality controlled by Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 Nano Kit according to manufacturer´s instructions.

treatment_protocol: Recombinant Human IFN-γ were dissolved in PBS, aliquoted and stored in -80°C. 200,000 skin fibroblasts were seeded in 6-well plate the day before the treatment. Change new medium of pre-planted cell after it reaches 70% confluency. Add 75U/ml Recombinant Human IFN-γ into new medium. Cells  treated with IFN-γ were then cultured for 24 hours.

value: skin

tag: age

value: neonatal


title: Zt16_1 LRE

description: Library name: Sample E3


title: PSMB10WT_ctrl_24hr_rep5

description: Gene expression after 24hr in control treated PSMB10WT skin fibroblast

source_name: PSMB10WT skin fibroblast, ctrl, 24hr


title: ZT12_4 LRE

description: Library name: Sample D3


title: PSMB10WT_IFNγ_24hr_rep2


title: PSMB10WT_IFNγ_24hr_rep1


title: PSMB10WT_IFNγ_24hr_rep3


title: PSMB10WT_IFNγ_24hr_rep4


title: HEK293T PDE4C targeted CRISPRoff Replica 3

value: guides PDE4C + CRISRoff v2.1


title: PSMB10WT_ctrl_24hr_rep3


title: PSMB10WT_ctrl_24hr_rep4


title: HEK293T PDE4C targeted CRISPRoff Replica 2


title: liver.WT.1292305

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292305


title: PSMB10WT_ctrl_24hr_rep2


title: liver.Het.1292304

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292304


title: HEK293T PDE4C targeted CRISPRoff Replica 1


title: ZT12_2 LRE

description: Library name: Sample B3


title: PSMB10WT_ctrl_24hr_rep1


title: ZT12_1 LRE

description: Library name: Sample A3


title: liver.WT.1292302

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292302


title: HEK293T control (PDE4C guides only) Replica 1


title: liver.Het.1292303

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292303


title: PSMB10G209R_IFNγ_24hr_rep5

description: Gene expression after 24hr in IFNγ treated PSMB10G209R skin fibroblast

source_name: PSMB10G209R skin fibroblast, IFNγ stimulation, 24hr


title: ZT12_3 LRE

description: Library name: Sample C3


title: PSMB10G209R_IFNγ_24hr_rep4


title: HEK293T PDE4C targeted dCAS9-DNMT3A Replica 2

value: guides PDE4C + dCAS9-DNMT3A/3L


title: ZT4_3 LRE

description: Library name: Sample O2


title: HEK293T PDE4C targeted dCAS9-DNMT3A Replica 1


title: liver.WT.1292300

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292300

source_name: liver


title: ZT4_2 LRE

description: Library name: Sample N2


title: liver.Het.1292299

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292299


title: PSMB10G209R_IFNγ_24hr_rep3


title: donor3, unstimulated, 250000 cells, replicate 1

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

description: Library name: d3_un_rep1

data_processing:
Raw sequences were processed with HICUP 0.8.3 for QC, alignment to the Hg38 genome with Bowtie2, and filtering of invalid ligation products. The resulting BAM alignment files were converted to the multiresolution ".hic" format using built-in tools in HICUP, and normalised using 'Juicer pre' with the default settings.
Assembly: Hg38
Supplementary files format and content: ".hic" format is a highly compressed binary format that contains genomic contact matrices from multiple resolutions (5k, 10k, 25k, 50k, 100k, 250k, 500k, 1M and 2.5M) and using a range of normalisations (VC, VC_SQRT, SCALE and KR), as well as raw observed and expected values, and Pearson correlation matrices. These files can be visualised directly using the java software Juicebox.

source_name: blood

growth_protocol: Healthy human donor blood cones were ordered from NHS Blood and Transplant Services, UK under UCL Research Ethics Committee Approval reference 3138/001. This agreement ensures donor anonymity and so donations do not come with any demographic information. The contents of each cone were diluted in 8ml 1xPBS and layered onto 15ml Ficoll in x4 50ml tubes. Tubes were subjected to centrifugation at 2000rpm for 20 min at RT. Peripheral blood mononuclear cells (PBMCs) were aspirated using a transfer pipette and washed 2x in 10ml 2mM EDTA 1xPBS in 15ml conical tubes 350xg 5 min at room temperature, RT). A third wash was done at 200xg 5 mins at RT to maximise platelet removal. PBMCs were spun at 350xg and resuspended in x1 Mojosort buffer (1xPBS, 2mM EDTA, 0.5% BSA) and diluted to 1x108 PMBCs/ml. All cell counts were done using a OLS CASY cell counter. mCD4+ T cells were isolated by magnetic separation Biolegend (480064) following manufactures protocol. Purity was assessed by flow cytometry.

extract_protocol:
Cells were counted and spun into pellets of the required numbers (50000, 250000, or 1000000) at 5000xg for 5 mins. Supernatant was removed until <20ul of liquid + cell pellet remained. The pellets were snap frozen on dry ice and then stored in at -70oC until processing. All pellets were committed to the mammalian cell low input Arima Genomics Inc workflow (https://arimagenomics.com/wp-content/files/User-Guide-Arima-HiC-for-Mammalian-Cell-Lines.pdf, September, 2024) with the following modifications; conditioning incubation time 20 mins, restriction enzyme cutting time 1hr. Proximally ligated DNA samples were QC for biotin nucleotide incorporation if enough material was available. Sonication was done using a S220 Covaris machine (Imperial College London) with the manufacturer’s recommended settings to achieve ~400bp fragment peaks. Fragment distribution was assessed using an Agilent TapeStation 4150 using a dsDNA D1000 or D5000 cartridge.
Final libraries were QC before shipment by Qubit dsDNA assay and TapeStation as above. Libraries were submitted for sequencing to Novogene(UK)

treatment_protocol:
Isolated T cells were activated at 2.5x106/ml in RPMI 10% FBS 0.5% Penicillin/Streptomycin solution (Gibco, 15070063). The base of 24-well culture dishes was treated 45 mins with 1ml 1xPBS containing anti-CD3 antibody Biolegend (317326) clone OKT at 476ng/ml Plates were washes x1 with 1xPBS. Added on day-0 only was anti-CD28 antibody Biolegend (302902) clone CD28.2 at 1000ng/ml. T cells were allowed to expand in wells for x3 days with 1000U/ml IL-2 (Prepotech, 200-02) added daily. For days 4 and 5 T cells were transferred to T25 untreated culture flasks with additional RPMI added to prevent medium exhaustion (assessed by colour change pink to yellow). 1000U/ml IL-2 was added on each of these days.
Fluorescent antibody panel (Live/Dead(blue), L23105), CD3 Biolegend(317336), CD4 Biolegend(317414), CD45RO Biolegend(304204), CD69 Biolegend(310910), CD25 Biolegend(302606) was validated for specificity using fluorescence minus one. 3x105 cells were pelleted 4oC 350xg 5 min and suspended in 100μl 1xPBS 0.001% Live/Dead(blue) dye. 1μl of each fluorescent antibody was added and briefly vortexed before incubation at 4oC for 30 mins. Stained cells were spun and washed x1 with 0.5ml ice-cold 1xPBS 1% FBS 2mM EDTA 0.01% sodium azide, with final suspensions in 300μl. Samples were run on a BD LSR Fortessa with baseline voltage setting (except CD25, in which the voltage was reduced by 50 units) with gating and analysis done in FlowJo v_10.8.1.

value: blood

value: primary CD4+ memory T-cells

tag: donor


title: liver.WT.1292298

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292298

tag: tissue


title: ZT0_4 LRE

description: Library name: Sample L2


title: HEK293T PDE4C targeted dCAS9-DNMT3A Replica 3

tag: cell line


title: liver.WT.1292297

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292297


title: donor3, IL2, 250000 cells, replicate 1

description: Library name: d3_il2_rep1

tag: cell type

value: IL2 activation


title: ZT0_3 LRE

description: Library name: Sample K2


title: ZT4_4 LRE

description: Library name: Sample P2


title: liver.Het.1292296

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292296


title: PSMB10G209R_IFNγ_24hr_rep1


title: donor2, unstimulated, 250000 cells, replicate 1

description: Library name: d2_un_rep1

tag: treatment


title: ZT0_2 LRE

description: Library name: Sample J2


title: donor3, IL2+TCR, 250000 cells, replicate 1

description: Library name: d3_ab_rep1

value: IL2+TCR activation


title: liver.Het.1292301

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292301


title: PSMB10G209R_ctrl_24hr_rep4

description: Gene expression after 24hr in control treated PSMB10G209R skin fibroblast

source_name: PSMB10G209R skin fibroblast, ctrl, 24hr


title: liver.WT.1292295

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292295


title: PSMB10G209R_ctrl_24hr_rep3


title: PSMB10G209R_ctrl_24hr_rep2


title: PSMB10G209R_IFNγ_24hr_rep2


title: PSMB10G209R_ctrl_24hr_rep5


title: ZT4_1 LRE

description: Library name: Sample M2


title: ZT0_1 LRE

description: Library name: Sample I2


title: liver.WT.1292294

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292294


title: donor1, unstimulated, 50000 cells, replicate 2

description: Library name: d1_Un_u50_rep2


title: donor2, IL2, 250000 cells, replicate 1

description: Library name: d2_il2_rep1


title: liver.WT.1292292

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292292


title: ZT20_4 WT

description: Library name: Sample H2

value: WT


title: ZT20_3 WT

description: Library name: Sample G2


title: donor2, IL2+TCR, 250000 cells, replicate 1

description: Library name: d2_ab_rep1


title: liver.Het.1292291

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292291