title: VINC_ADI_PND21_312

description:
treatment: VINC
dose: ADI
sample number: 312


title: VINC_ADI_PND21_313

status: Public on Nov 04 2025

type: RNA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
treatment: VINC
dose: ADI
sample number: 313

hyb_protocol: Agilent : 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Arrays file were read and quantile normalized using the Bioconductor package limma. No background subtraction was performed. PND21 samples were normalized separately.

molecule: total RNA

organism: Rattus norvegicus

source_name: Testis

label_protocol: Agilent - Low RNA input QuickAmp starting from 200 ng total RNA

extract_protocol: Total RNAs were isolated from frozen testicular powder using TRIzol reagent (Invitrogen, Cergy Pontoise, France) coupled with column purification of RNA (High pure miRNA isolation kit, Roche Diagnostics, Meylan, France) and DNase treatment.

treatment_protocol: Antiandrogenic substances were administered in aqueous preparations. Pregnant females (20/group) were treated by gavage from gestation day (GD) 6 until postnatal (PND) day 21. After weaning, the offspring received the same test-substance as their mothers by oral gavage. Twenty males were selected to be raised until the weaning (Subset 1, PND21), the day of sexual maturation (Subset 2, puberty at PND30-40) or early adulthood (Subset 3, PND83±2). At each subset, testes were used for transcriptome and miRNome analyses. Three antiandrogenic substances were tested: Flutamide (FLUT), Prochloraz (PROC), Vinclozolin (VINC), at 3 doses. Flutamide: ADI = 0.0025mg/kg/d, NOAEL = 0.25mg/kg/d, LOAEL = 2.5mg/kg/d. Prochloraz: ADI=0.01 mg/kg/d, NOAEL=5 mg/kg/d, LOAEL=30 mg/kg/d. Vinclozolin: ADI=0.005 mg/kg/d, NOAEL=4 mg/kg/d, LOAEL=20 mg/kg/d

tag: background strain

value: Wistar

tag: age

value: postnatal day (PND) 21


title: PROC_LOAEL_PND21_392

description:
treatment: PROC
dose: LOAEL
sample number: 392


title: PROC_LOAEL_PND21_393

description:
treatment: PROC
dose: LOAEL
sample number: 393


title: VINC_ADI_PND21_311

description:
treatment: VINC
dose: ADI
sample number: 311


title: Downscaling 500 ES cells H2AZ

type: SRA

city: Copenhagen

first: Erkut

last: Ilaslan

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: Library name: 500-AZ-oc

library_source: genomic

data_processing:
Additional runs concatenated to first FastQ file. For samples with a 3rd run, these runs processed seperately.
FastQ files trimmed using Trim Galore.
Trimmed FastQ files mapped to mm10 using bowtie1 with -m 1 parameter.
BAM files sorted using SAMtools and converted to BED format using BEDtools.
BED files from 3rd run merged to the BED files contaning 1st and 2nd runs before downstream analysis in EaSeq (http://easeq.net). Gzip compressed WIG files generated using EaSeq. Scores represent fragments per kilobasepairs per million reads
Assembly: mm10
Supplementary files format and content: wig files containing mapped reads.

molecule: genomic DNA

organism: Mus musculus

source_name: E14 ES cells

growth_protocol: Postnatal day 7 (P7), P10, and P12 CD-1 females were used for collection of growing oocyte (GO) sample pools. C57BL/6NRj females aged 4 weeks were used for collecting NSN, SN and MII oocytes. To induce superovulation for collection of these three stages, the mice received an intraperitoneal injection with 5 international units (IU) of pregnant mare serum gonadotropin (PMSG; Prospec, HOR-272) at 2pm. For NSN and SN stages, the oocytes were collected ~45 hours after the PMSG injection. For collection of MII stage oocytes, an intraperitoneal injection with 5 IU of human chorionic gonadotropin (hCG; Sigma, C1063) was given 45-48 hours following PMSG injection. Subsequently, MII oocytes were collected 66-67 hours after the PMSG injection. Mouse E14 ES cells were obtained from a stock at passage P2 equal to those used for the mouse ENCODE project and cultured following the corresponding instructions (https://www.encodeproject.org/biosamples/ENCBS171HGC/). Prior to collection, cells were passaged once on gelatinized, feeder-free plates.

extract_protocol:
The samples were transferred to 1.5 ml tubes. SDS/RNase-free elution buffer (20 mM Tris–HCl/pH-7.5), 50 mM NaCl, 5 mM EDTA/pH-8.0) was added to 415 µl final volume, and the aqueous phase was sequentially extracted using equal volumes of phenol:chloroform:isoamylalcohol (Invitrogen, 15593-031) and chloroform:isoamylalcohol (Sigma-Aldrich, C0549). The 400 µl of the last aqueous phase were precipitated with 1 ml ice-cold ethanol, 11 µl linear acrylamide (Thermo Fisher Scientific, AM9520) and 44 µl 1 M sodium acetate (Invitrogen, AM9740) at least overnight at -80°C. For reconstitution, the pellets were centrifuged (swing-out, 16,000 x g, 4°C), and recovered using 15 µl of Qiagen EB (10 mM Tris, Qiagen, 19086) overnight at 4°C.
Sequencing libraries were prepared using the Qiaseq ultralow input kit (Qiagen, 180492 + 180310) with modifications to minimize material loses. These included prolonged incubations during the AMPure XP bead extractions (>15 min bead/sample incubation, >15 min DNA elution) (Beckman coulter, A63881), and an increased volume of beads (1.2 volume equivalents) during the second bead extraction. Double-stranded DNA concentration was determined using the Qubit HS DNA kit (ThermoFisher Scientific, Q32851), while DNA fragment size analyses were performed with TapeStation D1000 HS (Agilent, 5067-5585). Libraries were then and pooled in equimolar amounts. Sequential AMPure XP extractions (1.2 volume equivalents) were employed to drastically reduce adapter dimers from the pool prior to sequencing.

treatment_protocol: Oocytes were cross-linked in a solution of 50 µl M2 media, 50 µl PBS (Life Technologies, 14190-094), and a final concentration of 1% w/v formaldehyde (Sigma-Aldrich, F8775). After 8 min at room temperature, 14.3 µl 1 M Glycine (Merck, 67419) was added to inactivate the fixative. After 5 min at room temperature, ice cold PBS was used to wash the oocytes three times in a 0.6 ml tube (MaxymumRecovery, Axygen), resulting in a final volume of 10 µl. The fixative was added either in droplets under the microscope, or directly in the 0.6 ml tube followed by the washes and centrifugations at 700 x g for 10 min at 4°C with careful supernatant removal. Correspondingly, liquids were mixed by droplet pipetting or by gentle tube vortexing during cross-linking and glycine inactivation. Samples were snap-frozen in liquid nitrogen before storage at -80°C. Pelleted ES cells (around 20 million) were resuspended in 20 ml of a 1 % w/v formaldehyde (Sigma-Aldrich, F8775) solution in PBS with 20 mM of sodium butyrate (Sigma-Aldrich, 19-137), cross-linked at room temperature for 8 min, and inactivated using 2.4 ml of an aqueous 1.25 M glycine (Sigma, G8790) solution. Then, the pellet was washed twice with ice cold PBS supplemented with 20 mM of sodium butyrate (650 x g, 10 min, 4°C), cells were counted, diluted, and aliquoted into 0.6 ml tubes (MaxymumRecovery, Axygen) at different cell numbers. Finally, the cells were centrifuged, the supernatant removed, leaving 10 µl, and snap-frozen in liquid nitrogen before storage at -80°C.

tag: cell type

value: E14 ES cells


title: PROC_LOAEL_PND21_391

description:
treatment: PROC
dose: LOAEL
sample number: 391


title: Downscaling 100k ES cells H2AZ

description: Library name: 100k-AZ-std


title: PROC_NOAEL_PND21_384

description:
treatment: PROC
dose: NOAEL
sample number: 384


title: PROC_NOAEL_PND21_383

description:
treatment: PROC
dose: NOAEL
sample number: 383


title: P10 H2AZ Replicate B

description: Library name: p10-AZ-250-B

source_name: P10 Oocyte

value: P10 Oocyte


title: P10 Input Replicate A

description: Library name: p10-INP-A


title: P12 Input Replicate B

description: Library name: p12-INP-B

source_name: P12 Oocyte

value: P12 Oocyte


title: P7 H2AZ Replicate A

description: Library name: p7-AZ-250

source_name: P7 Oocyte

value: P7 Oocyte


title: PROC_NOAEL_PND21_381

description:
treatment: PROC
dose: NOAEL
sample number: 381


title: P10 Input Replicate B

description: Library name: p10-INP-B


title: P10 H2AZ Replicate A

description: Library name: p10-AZ-250-A


title: PROC_ADI_PND21_372

description:
treatment: PROC
dose: ADI
sample number: 372


title: FLUT_LOAEL_PND21_363

description:
treatment: FLUT
dose: LOAEL
sample number: 363


title: P7 Input Replicate A

description: Library name: p7-INP


title: PROC_NOAEL_PND21_382

description:
treatment: PROC
dose: NOAEL
sample number: 382


title: MII H2AZ Replicate A

description: Library name: MII-AZ-300

source_name: MII Oocyte

value: MII Oocyte


title: SN H2AZ Replicate A

description: Library name: SN-AZ-200

source_name: SN Oocyte

value: SN Oocyte


title: PROC_ADI_PND21_371

description:
treatment: PROC
dose: ADI
sample number: 371


title: FLUT_LOAEL_PND21_361

description:
treatment: FLUT
dose: LOAEL
sample number: 361


title: PROC_ADI_PND21_373

description:
treatment: PROC
dose: ADI
sample number: 373


title: NSN H2AZ Replicate A

description: Library name: NSN-AZ-200

source_name: NSN Oocyte

value: NSN Oocyte


title: PROC_ADI_PND21_374

description:
treatment: PROC
dose: ADI
sample number: 374


title: scATAC-seq PBMC C19 (healthy) donor HIP15_frozen

city: Saarbrucken

first: Irem

middle: Begüm

last: Gündüz

state: Saarland

address: Building A2.4

department: Bioinformatics

country: Germany

institute: Saarland University

description:
Library name: C19_ctrl_HIP15_frozen
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_ctrl; condition=healthy; processed data includes fragments.tsv.gz per sample.

data_processing:
Sequencing data were processed using Cell Ranger ATAC (v2.1.0).
Fragment files were filtered and analyzed with ArchR (v1.0.2), including quality control, dimensionality reduction, clustering, and peak calling.
Assembly: hg38
Supplementary files format and content: peak_matrix.mtx.gz — sparse matrix of peak accessibility counts per cell.
Supplementary files format and content: chromvar_matrix.mtx.gz — sparse matrix of TF activity scores inferred from chromatin accessibility.
Supplementary files format and content: peaks.tsv.gz — genomic coordinates of peaks

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Nuclei were isolated from cryopreserved PBMCs following the 10x Genomics Chromium Single Cell ATAC-seq protocol (CG000272). Lysis and washing steps were performed under ice-cold conditions.
Single-cell ATAC-seq libraries were prepared using the 10x Genomics Chromium Single Cell ATAC-seq kit according to the manufacturer’s protocol. Transposition, barcoding, and amplification were performed as specified in the 10x protocol.
Libraries were sequenced on the Illumina NovaSeq 6000 platform using paired-end 50 bp reads, following the 10x Genomics guidelines for scATAC-seq.

treatment_protocol: PBMCs were obtained from individuals in various conditions, including healthy controls, viral challenge (HIV, influenza), and environmental exposure (organophosphates). Treatment conditions are described per sample in the metadata.

tag: tissue

value: PBMC

tag: treatment

value: healthy

tag: batch


title: Blastocyst Input Replicate A

description: Library name: bla-INP

source_name: Blastocyst

value: Blastocyst


title: Morula Input Replicate A

description: Library name: mor-INP

source_name: Morula

value: Morula


title: FLUT_LOAEL_PND21_364

description:
treatment: FLUT
dose: LOAEL
sample number: 364


title: SN Input Replicate A

description: Library name: SN-INP


title: NSN Input Replicate A

description: Library name: NSN-INP


title: 8-cell Input Replicate A

description: Library name: 8c-INP

source_name: 8-cell embryo

value: 8-cell embryo


title: scATAC-seq PBMC C19 (healthy) donor HIP044

description:
Library name: C19_ctrl_HIP044
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_ctrl; condition=healthy; processed data includes fragments.tsv.gz per sample.


title: P12 Input Replicate A

description: Library name: p12-INP


title: FLUT_NOAEL_PND21_354

description:
treatment: FLUT
dose: NOAEL
sample number: 354


title: FLUT_LOAEL_PND21_362

description:
treatment: FLUT
dose: LOAEL
sample number: 362


title: scATAC-seq PBMC C19 (healthy) donor HIP043

description:
Library name: C19_ctrl_HIP043
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_ctrl; condition=healthy; processed data includes fragments.tsv.gz per sample.


title: FLUT_ADI_PND21_344

description:
treatment: FLUT
dose: ADI
sample number: 344


title: FLUT_NOAEL_PND21_352

description:
treatment: FLUT
dose: NOAEL
sample number: 352


title: scATAC-seq PBMC C19 (healthy) donor HIP045

description:
Library name: C19_ctrl_HIP045
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_ctrl; condition=healthy; processed data includes fragments.tsv.gz per sample.


title: FLUT_NOAEL_PND21_353

description:
treatment: FLUT
dose: NOAEL
sample number: 353


title: FLUT_NOAEL_PND21_351

description:
treatment: FLUT
dose: NOAEL
sample number: 351


title: FLUT_ADI_PND21_342

description:
treatment: FLUT
dose: ADI
sample number: 342


title: 8-cell H2AZ Replicate A

description: Library name: 8c-AZ-460


title: Huvec cells,WT,low glucose (5 mM),12 hours,biological replicate 2

city: Ganzhou

first: Weijian

last: Zhu

address: No. 1, Hexie Blvd

country: China

institute: Gannan Medical University

description: Library name: Huvec_L2_FRAS210119348_1r

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to the human reference genome (GRCh38/hg38) using CLC Genomics Workbench (parameters: mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8)
Read count extraction and normalization were performed using CLC Genomics Workbench
Differential expression analysis was performed using the DESeq2 package (v1.38.3) in R.
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited text files including raw gene-level read counts for each sample.
Supplementary files format and content: txt files include FPKM values for each Sample

source_name: umbilical vein

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

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.5 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells adherent for 2 days (designated as Day 0, or D0) were cultured for 12 hours in MEM medium (Thermo Fisher Scientific) containing either 25 mM (high glucose) or 5 mM (low glucose) D-glucose.

value: umbilical vein

tag: cell line

value: HUVEC

value: endothelial cell

tag: genotype

value: WT

value: low glucose(5 mM)


title: Huvec cells,WT,low glucose (5 mM),12 hours,biological replicate 1

description: Library name: Huvec_L1_FRAS210119347_1r


title: FLUT_ADI_PND21_343

description:
treatment: FLUT
dose: ADI
sample number: 343

value: Wistar

value: postnatal day (PND) 21


title: CTRL_PND21_303

description:
treatment: CTRL
dose: --
sample number: 303


title: FLUT_ADI_PND21_341

description:
treatment: FLUT
dose: ADI
sample number: 341


title: Huvec cells,WT,low glucose (5 mM),12 hours,biological replicate 3

description: Library name: Huvec_L3_FRAS210119349_1r


title: CTRL_PND21_304

description:
treatment: CTRL
dose: --
sample number: 304


title: scATAC-seq PBMC C19 (healthy) donor HIP023_frozen

description:
Library name: C19_ctrl_HIP023_frozen
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_ctrl; condition=healthy; processed data includes fragments.tsv.gz per sample.


title: Huvec cells,WT,high glucose (25 mM),12 hours,biological replicate 3

description: Library name: Huvec_H3_FRAS210119346_1r

value: high glucose(25 mM)


title: WT_ZT12_CR_rep2

city: Neuherberg

first: fabiana

last: quagliarini

address: Ingolstaedter Landstr 1

institute: helmholtz munich

data_processing:
Sequence quality was checked using FastQC and MultiQC
Adapter reads were trimmed using Trimmomatics
Reads were aligned using Salmon to mm10
Salmon quant.sf files were imported in R using tximport to generate read counts
Raw read counts were transformed by variance  stabilizing transformation (VST) method.
Assembly: mm10
Supplementary files format and content: tab-separate files containing raw read counts from Salmon
Supplementary files format and content: tab-separate files containing VST counts from DESeq2

molecule: polyA RNA

source_name: Mouse liver

growth_protocol: C57BL/6J mice were fed with chow diet

extract_protocol:
RNA was extracted using the QIAZOL reagent. 1 μg of RNA was used for library preparation.
Libraries were prepped from 1µg total RNA with the Illumina TruSeq RNA library prep kit v2 chemistry in an automated system (Agilent Bravo liquid handling) platform).

treatment_protocol: Mice were either night-restricted fed (NRF), or NRF + reduced calorie intake across the weeks with end point of 40% less calories

value: Mouse liver

tag: strain

value: Caloric Restriction (CR)


title: WT_ZT12_CR_rep3


title: MII Input Replicate A

description: Library name: MII-INP

value: MII Oocyte


title: CTRL_PND21_302

description:
treatment: CTRL
dose: --
sample number: 302


title: CTRL_PND21_301

description:
treatment: CTRL
dose: --
sample number: 301


title: P12 H2AZ Replicate A

description: Library name: p12-AZ-200

value: P12 Oocyte


title: Huvec cells,WT,high glucose (25 mM),12 hours,biological replicate 1

description: Library name: Huvec_H1_FRAS210119344_1r


title: Huvec cells,WT,high glucose (25 mM),12 hours,biological replicate 2

description: Library name: Huvec_H2_FRAS210119345_1r


title: WT_ZT12_AL_rep3

value: Night Restricted Feeding (NR)


title: Blastocyst H2AZ Replicate A

description: Library name: bla-AZ-460


title: WT_ZT12_AL_rep2


title: scATAC-seq PBMC C19 (mild) donor 86

description:
Library name: C19_mild_86
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_mild; condition=mild; processed data includes fragments.tsv.gz per sample.

value: PBMC

value: mild


title: t5h_reox_rep_3

city: Villeubanne

first: Julie

last: hesnard

state: FRANCE

address: HESNARD

institute: Institut Lumière Matière

description:
Library name: Sample 18
raw_t5h_reox_rep_3-MACE_Seq

data_processing:
Deduplication based on UMIs (Unique Molecular Identifier) was performed using in-house
FastQC (0.11.9) was used to assess the quality of sequencing reads
Processed sequencing reads were mapped with a reference genome (Ensembl Dictyostelium discoideum 2_7) using Bowtie2 (2.4.4, [3])
Quantification of mapped reads to each gene was performed using HTSeq (version 2.0.2)
Raw counts were geometric-mean-normalized using DESeq2 (version 1.38). TPM-normalized by dividing each count with the sum of all counts for each sample multiplied by one million. Quantification of mapped reads to each transcript was performed using HTSeq (version 2.0.2).
Assembly: Ensembl Dictyostelium discoideum 2_7
Supplementary files format and content: raw count for each sample

organism: Dictyostelium discoideum

growth_protocol: AX3 cultured axenically with HL5 medium (HLF2; Formedium, UK) containing 100 mM glucose and 1/1000 penicillin-streptomycin (P/S) (15140-122; Gibco, USA). Cells were grown at 22 °C under agitation at 180 rpm.

extract_protocol:
Total RNAs were extracted (RNeasy Plus Mini Kit, 74134, Qiagen, Germany) quantified and adjusted at 100 ng for librairy preparation.
The librairy was constructed following the manufacturer’s instructions (Rapide MACE-seq kit, GenXpro GmbH, Germany)

treatment_protocol: AX3 cells were placed under hypoxic conditions (1% O2) for 24 hours and then reoxygenated for 5 hours (20% O2)

tag: development stage

value: vegetative

value: Dictyostelium wild type cell

value: reoxygenation (21% after 24h at 1%O2)

tag: time


title: Morula H2AZ Replicate A

description: Library name: mor-AZ-460

value: Morula


title: t1h_reox_rep_3

description:
Library name: Sample 17
raw_t1h_reox_rep_3-MACE_Seq


title: scATAC-seq PBMC C19 (healthy) donor HIP02_frozen

description:
Library name: C19_ctrl_HIP02_frozen
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_ctrl; condition=healthy; processed data includes fragments.tsv.gz per sample.

value: healthy


title: scATAC-seq PBMC C19 (mild) donor 83

description:
Library name: C19_mild_83
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_mild; condition=mild; processed data includes fragments.tsv.gz per sample.


title: 8wk_Control_LSK_3

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

country: USA

institute: Washington University In St Louis

description: Library name: 23

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 101 top-level assembly with STAR version 2.7.9a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3.
Assembly: Mouse Ensembl GRCm38.101
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Bone marrow

extract_protocol:
Quiagen Rneasy Plus RNA Etraction Kit
Clontech SMRTr

value: Bone marrow

value: LSK


title: 8wk_Control_LSK_2

description: Library name: 22


title: 8wk_Control_LSK_1

description: Library name: 21


title: t5h_rep_3

description:
Library name: Sample 15
raw_t5h_rep_3-MACE_Seq

value: WT

value: hypoxia (1% O2)


title: WT_ZT12_CR_rep1


title: scATAC-seq PBMC C19 (healthy) donor EV08

description:
Library name: C19_ctrl_EV08
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_ctrl; condition=healthy; processed data includes fragments.tsv.gz per sample.


title: WT_ZT12_AL_rep1


title: t5h_reox_rep_2

description:
Library name: Sample 12
raw_t5h_reox_rep_2-MACE_Seq


title: scATAC-seq PBMC C19 (mild) donor 66D7

description:
Library name: C19_mild_66D7
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_mild; condition=mild; processed data includes fragments.tsv.gz per sample.


title: t24h_rep_3

description:
Library name: Sample 16
raw_t24h_rep_3-MACE_Seq


title: t1h_rep_3

description:
Library name: Sample 14
raw_t1h_rep_3-MACE_Seq


title: 8wk_ME_LSK_4

description: Library name: 20


title: 8wk_Control_LSK_4

description: Library name: 24


title: t1h_reox_rep_2

description:
Library name: Sample 11
raw_t1h_reox_rep_2-MACE_Seq


title: t24h_rep_2

description:
Library name: Sample 10
raw_t24h_rep_2-MACE_Seq


title: scATAC-seq PBMC C19 (mild) donor 66D0

description:
Library name: C19_mild_66D0
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_mild; condition=mild; processed data includes fragments.tsv.gz per sample.


title: 8wk_ME_LSK_3

description: Library name: 19


title: t1h_rep_2

description:
Library name: Sample 8
raw_t1h_rep_2-MACE_Seq


title: scATAC-seq PBMC C19 (severe) donor 564B

description:
Library name: C19_sev_564B
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_sev; condition=severe; processed data includes fragments.tsv.gz per sample.

value: severe


title: t1h_reox_rep_1

description:
Library name: Sample 5
raw_t1h_reox_rep_1-MACE_Seq


title: 8wk_ME_LSK_2

description: Library name: 18


title: P14_Control_LSK_4

description: Library name: 16


title: t0_rep_2

description:
Library name: Sample 7
raw_t0_rep_2-MACE_Seq


title: t5h_rep_1

description:
Library name: Sample 3
raw_t5h_rep_1-MACE_Seq


title: scATAC-seq PBMC C19 (severe) donor 564A

description:
Library name: C19_sev_564A
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_sev; condition=severe; processed data includes fragments.tsv.gz per sample.


title: t5h_rep_2

description:
Library name: Sample 9
raw_t5h_rep_2-MACE_Seq


title: P14_Control_LSK_2

description: Library name: 14


title: t5h_reox_rep_1

description:
Library name: Sample 6
raw_t5h_reox_rep_1-MACE_Seq


title: scATAC-seq PBMC C19 (mild) donor 67

description:
Library name: C19_mild_67
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_mild; condition=mild; processed data includes fragments.tsv.gz per sample.


title: t0_rep_3

description:
Library name: Sample 13
raw_t0_rep_3-MACE_Seq


title: scATAC-seq PBMC C19 (severe) donor 560

description:
Library name: C19_sev_560
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_sev; condition=severe; processed data includes fragments.tsv.gz per sample.


title: scATAC-seq PBMC C19 (moderate) donor 556

description:
Library name: C19_mod_556
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_mod; condition=moderate; processed data includes fragments.tsv.gz per sample.

value: moderate


title: t24h_rep_1

description:
Library name: Sample 4
raw_t24h_rep_1-MACE_Seq


title: scATAC-seq PBMC C19 (moderate) donor 559

description:
Library name: C19_mod_559
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_mod; condition=moderate; processed data includes fragments.tsv.gz per sample.


title: mVSMCs, THOC5 OE Pi _THOC5 rep 2 (RIP-Seq)

city: Wuhan

first: yuyao

last: wang

address: 1095 Jiefang Avenue, Wuhan City, Hubei Province

institute: Tongji Hospital affiliated to Tongji Medical College of Huazhong University of Science & Technology

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastqc
Trimmed sequence reads were mapped to mm 10 using bowtie2
peak calling was detected by MACS2 in RIP-Seq
Read count extraction and normalization were performed using samtools
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes scale counts for each Sample tab

source_name: Primary mouse vascular smooth muscle cells

extract_protocol:
The total RNA of cells were extracted by GeneJet RNA Purification Kit (Thermo Scientific, K0732). According to the manufacturer's instructions. The Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit (Millipore 17-700) was used to perform RNA immunoprecipitation (RIP).
1µg total RNA was prepared to generate a sequencing library by TruSeqTM RNA Library Prep Kit V2 (Illumina, RS-122-2002). For RIP-Seq library generation, rRNA was removed using the Ribo-offTM rRNA Depletion Kit (Vazyme N406).

value: THOC5 overexppression

value: Osteogenic medium


title: mVSMCs, THOC5 OE Pi_input  rep 1 (RIP-Seq)

value: Primary mouse vascular smooth muscle cells


title: t1h_rep_1

description:
Library name: Sample 2
raw_t1h_rep_1-MACE_Seq


title: scATAC-seq PBMC C19 (severe) donor 558

description:
Library name: C19_sev_558
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_sev; condition=severe; processed data includes fragments.tsv.gz per sample.


title: scATAC-seq PBMC C19 (severe) donor 555_2

description:
Library name: C19_sev_555_2
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_sev; condition=severe; processed data includes fragments.tsv.gz per sample.


title: P14_Control_LSK_3

description: Library name: 15


title: mVSMCs, THOC5 OE Pi_input  rep 2 (RIP-Seq)


title: mVSMCs, GFP OE Pi _THOC5 rep 2 (RIP-Seq)


title: RKO cells, shControl, biol rep 1

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

description: Library name: Sample 4

data_processing:
All libraries were sequenced on the Illumina HiSeq X Ten instrument, and 150 bp paired-end reads were generated.
Sequencing reads were aligned back to the human genome (hg38) by TopHat 2.
Read count extraction was performed using GFOLD software.
The expression matrix of all samples was subjected to the Bayesian workflow for differential gene modeling based on the “edgeR” and “limma” R packages.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include reads count for each Sample

source_name: RKO

growth_protocol: RKO cell lines stably expressing TRIP6-specific shRNA (shRNA/TRIP6 ) or scrambled shRNA control (shRNA/Control) were constructed using a lentiviral shRNA technique. The cells were infected with the lentivirus, and 36 h later, cells were selected using 5 μg/ml puromycin for 2–3 weeks.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
RNA-seq

value: RKO

value: a poorly differentiated colon carcinoma cell line

value: scrambled shRNA control (shRNA/Control) using a lentiviral shRNA technique


title: scATAC-seq PBMC C19 (severe) donor 557

description:
Library name: C19_sev_557
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_sev; condition=severe; processed data includes fragments.tsv.gz per sample.

value: PBMC


title: mVSMCs, GFP OE Pi _input rep 2 (RIP-Seq)


title: t0_rep_1

description:
Library name: Sample 1
raw_t0_rep_1-MACE_Seq

value: vegetative

value: Dictyostelium wild type cell


title: mVSMCs, THOC5 OE Pi _THOC5 rep 1 (RIP-Seq)


title: RKO cells, shTRIP6, biol rep 3

description: Library name: Sample 3

value: TRIP6 knockdown

value: TRIP6-specific shRNA (shRNA/TRIP6) using a lentiviral shRNA technique


title: P14_Control_LSK_1

description: Library name: 13

value: Bone marrow


title: 8wk_ME_LSK_1

description: Library name: 17

value: LSK


title: RKO cells, shControl, biol rep 3

description: Library name: Sample 6

value: WT


title: RKO cells, shControl, biol rep 2

description: Library name: Sample 5


title: P14_ME_LSK_4

description: Library name: 12


title: P14_ME_LSK_2

description: Library name: 10


title: mVSMCs, GFP OE Pi _input rep 1 (RIP-Seq)


title: scATAC-seq PBMC C19 (mild) donor 132D0

description:
Library name: C19_mild_132D0
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_mild; condition=mild; processed data includes fragments.tsv.gz per sample.

value: mild


title: scATAC-seq PBMC C19 (mild) donor 52

description:
Library name: C19_mild_52
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_mild; condition=mild; processed data includes fragments.tsv.gz per sample.


title: mVSMCs, GFP OE Pi _THOC5 rep 1 (RIP-Seq)


title: P14_ME_LSK_1

description: Library name: 9


title: P14_ME_LSK_3

description: Library name: 11


title: RKO cells, shTRIP6, biol rep 2

description: Library name: Sample 2


title: E16_Control_LSK_2

description: Library name: 6

source_name: Liver

value: Liver


title: scATAC-seq of chronic PBMC from donor hiv9

description:
Library name: HIV_chr_hiv9
Single-cell ATAC-seq of PBMCs from chronic condition

value: chronic


title: Muscle mononuclear cell fractions cell 2, C6

city: BLACKSBURG

first: Zhendong

last: Tan

state: VA

address: 175 West Campus Drive

institute: Virginia Tech

description:
Library name: C6
10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed using Cell Ranger (v3.0.2, 10x Genomics) with default parameters to align to the bovine reference genome (Bos_taurus.ARS-UCD1.2). Ambient RNA contamination was removed using CellBender (v0.2.0). Filtered output files were imported into Seurat (v5.2.0) for quality control and downstream analysis. Cells with 300–3,000 detected genes and <10,000 UMIs were retained. Data from six scRNA-seq libraries were normalized, scaled, and integrated using the Harmony algorithm. Contamination scores were estimated using decontX (v1.4.0), and cells with scores >0.2 were excluded. Dimensionality reduction and clustering were performed in Seurat using principal component analysis (PCA) and UMAP (dims = 1:30, seed.use = 45).
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: Matrix Market format files (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz) containing raw UMI counts per gene per cell for each sample.

organism: Bos taurus

source_name: Skeletal muscle

extract_protocol:
Stromal vascular fractions (SVFs) were isolated from intramuscular fat (IMF) and subcutaneous fat (SF) depots of adult Angus crossbred steers by collagenase digestion and centrifugation. Mononuclear cell fractions (MCFs) were isolated from the longissimus dorsi muscle of newborn Angus crossbred bull calves by enzymatic digestion and filtration. Freshly isolated cells were subjected to debris removal using the Debris Removal Solution (Miltenyi Biotec, Cat# 130-109-398) according to the manufacturer’s instructions, followed by dead cell removal using the Dead Cell Removal Kit (Miltenyi Biotec, Cat# 130-090-101) and MACS magnetic separation. Purified viable cells were resuspended in PBS containing 0.04% bovine serum albumin (BSA), filtered through a 40 μm strainer, and kept on ice prior to library preparation.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v3 (10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s protocol. Briefly, viable cells were resuspended in PBS containing 0.04% bovine serum albumin (BSA), adjusted to 1,000 cells/μL, and loaded onto a Chromium Chip B for Gel Bead-in-Emulsion (GEM) generation and barcoding on a Chromium Controller (10x Genomics). Reverse transcription and cDNA amplification (11 PCR cycles) were performed, followed by library construction. Library quality was assessed using an Agilent High Sensitivity TapeStation (Agilent Technologies, Santa Clara, CA, USA). Libraries were sequenced on an Illumina NovaSeq 6000 (paired-end 150 bp) at the Novogene-UC Davis Sequencing Center according to the 10x Genomics Single Cell 3′ v3 protocol.

value: Skeletal muscle

tag: description

value: Bull

value: mononuclear cell fractions cell

tag: Stage

value: Calf


title: mVSMCs, Pi_input rep 2 (RIP-Seq)

value: Primary mouse vascular smooth muscle cells

value: Osteogenic medium


title: scATAC-seq PBMC C19 (mild) donor 057

description:
Library name: C19_mild_057
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_mild; condition=mild; processed data includes fragments.tsv.gz per sample.

value: PBMC


title: RKO cells, shTRIP6, biol rep 1

description: Library name: Sample 1

value: RKO

value: a poorly differentiated colon carcinoma cell line


title: Subcutaneous fat stromal vascular fraction cell 2, S2

description:
Library name: S2
10X Genomics

source_name: Adipose tissue

value: Adipose tissue

value: Steer

value: stromal vascular fraction cell

value: Adult


title: scATAC-seq PBMC C19 (moderate) donor 555_1

description:
Library name: C19_mod_555_1
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_mod; condition=moderate; processed data includes fragments.tsv.gz per sample.

value: moderate


title: scATAC-seq PBMC C19 (moderate) donor 055

description:
Library name: C19_mod_055
Single-cell ATAC-seq (10x Chromium) of PBMCs; cohort=C19; group=C19_mod; condition=moderate; processed data includes fragments.tsv.gz per sample.


title: mVSMCs, Pi_THOC5 rep 2 (RIP-Seq)

value: WT


title: mVSMCs, Pi_input rep 1 (RIP-Seq)


title: scATAC-seq of acute PBMC from donor hiv7

description:
Library name: HIV_acu_hiv7
Single-cell ATAC-seq of PBMCs from acute condition

value: acute


title: E16_Control_LSK_1

description: Library name: 5

value: Liver

value: LSK


title: E16_ME_LSK_4

description: Library name: 4


title: mVSMCs, Pi_THOC5 rep 1 (RIP-Seq)


title: Subcutaneous fat stromal vascular fraction cell 1, S1

description:
Library name: S1
10X Genomics


title: Muscle mononuclear cell fractions cell 1, C5

description:
Library name: C5
10X Genomics

value: Skeletal muscle

value: Bull


title: mVSMCs, Ctrl_THOC5 rep 2 (RIP-Seq)

value: Growth medium


title: Intramuscular fat stromal vascular fraction cell 2, M2

description:
Library name: M2
10X Genomics


title: scATAC-seq of healthy PBMC from donor hiv6

description:
Library name: HIV_ctrl_hiv6
Single-cell ATAC-seq of PBMCs from healthy condition

value: healthy


title: scATAC-seq of chronic PBMC from donor hiv5

description:
Library name: HIV_chr_hiv5
Single-cell ATAC-seq of PBMCs from chronic condition

value: chronic


title: E16_ME_LSK_3

description: Library name: 3


title: E16_Control_LSK_3

description: Library name: 7


title: Intramuscular fat stromal vascular fraction cell 1, M1

description:
Library name: M1
10X Genomics


title: mVSMCs, Ctrl_THOC5 rep 1 (RIP-Seq)

value: Primary mouse vascular smooth muscle cells


title: E16_ME_LSK_1

description: Library name: 1


title: mVSMCs, Ctrl_input rep 1 (RIP-Seq)


title: CR, FOXO1_ChIP, rep2

data_processing:
Reads were aligned to mm10 using BWA, with MEM algorithm
Multimappers and duplicates were removed using Samtools and Picard
Peaks were called with MACS2, using q-value = 0.1, and blacklisted regions were filtered with bedtools intersect 70%
For FoxO1, BAM files of the two replicates were merged and then merged BAM was used for peak calling input, with cutoff q-value = 10^-5
BiqWig files were made using deeptools BamtoBigWig tool
Peak universe, a data frame containing peaks across samples, were made with multiIntersect from bedtools
Assembly: mm10
Supplementary files format and content: biqWig, NarrowPeak

source_name: mouse liver

growth_protocol: Mice fed only during the night,  caloric restricted, and night-restricted-fed and corticosterone supplemented mice. All mice were fed using regular chow diet

extract_protocol:
Snap frozen livers were lysed and fixed with 4% formaldehyde for 15 minutes at room temperature. After quenching and cell lysis, chromatin was sonicated using Diagenode Bioruptor.
Libraries from ChIP DNA were prepared with the KAPA Hyperprep Kit (Kapa Biosystems), Illumina compatible adapters were synthesized by IDT (Integrated DNA Technologies). Adapter-ligated libraries were size selected (360-610bp) in a Pippin Gel station (Sage Science) using 2% dye free gels (Sage Science). Library concentrations were estimated by RT-PCR with the KAPA Library Quantification Kit (Kapa Biosystems). Quality of the libraries was evaluated with the Agilent High Sensitivity DNA Kit in a 2100 Bioanalyzer (Agilent).

value: mouse liver

value: Caloric Restriction (CR)


title: scATAC-seq of healthy PBMC from donor hiv8

description:
Library name: HIV_ctrl_hiv8
Single-cell ATAC-seq of PBMCs from healthy condition

value: PBMC


title: scATAC-seq of chronic PBMC from donor hiv3

description:
Library name: HIV_chr_hiv3
Single-cell ATAC-seq of PBMCs from chronic condition


title: mVSMCs, THOC5 OE Pi rep 2 (RNA-Seq)

value: THOC5 overexppression

value: Osteogenic medium


title: E16_Control_LSK_4

description: Library name: 8


title: VINC_LOAEL_PND83_734

description:
treatment:  VINC
dose: LOAEL
sample ID: 734

hyb_protocol: Agilent : 55 degree_C during 20 hours

data_processing: The R package AgiMicroRna was used to extract the TotalGenesignal value from the Agilent result files, and perform quantile normalization separately for each age group.

source_name: Testis

label_protocol: Agilent - miRNA Complete Labeling and Hyb Kit starting from 100 ng total RNA

value: Wistar

value: postnatal day (PND) 83


title: mVSMCs, THOC5 OE Pirep 1 (RNA-Seq)


title: HashTag

city: Kashiwa

first: BIN

last: WU

state: Chiba

address: #304, 6-6-2, Kashiwanoha

department: Research

country: Japan

institute: ImmunoGeneTeqs

data_processing:
After adapter trimming and quality filtering, base composition of sequencing data was analyzed by FastQC-v0.11.9.
Pair-end Fastq files (R1: cell barcode reads, R2: RNA reads) of sample LOBLMday14WTA were processed as follows. Adapter trimming, quality filtering, and phase-shift base removal of sequencing data was performed by using Cutadapt 4.1.Filtered cell barcode and cDNA reads were annotated and mapped to reference genome (build GRCm39 release-107) by using STARsolo (2.7.10a) and known BD Rhapsody cell barcodes by the following parameters:–clipAdapterType CellRanger4 –outSAMmultNmax 1 –outFilterScoreMinOverLread 0 –outFilterMatchNminOverLread 0 –outFilterMultimapScoreRange 0 –seedSearchStartLmax 30 –soloType CB_UMI_Complex –soloUMIdedup NoDedup –soloMultiMappers Rescue –soloFeatures Gene GeneFull –soloCBmatchWLtype EditDist_2 –soloUMIlen 8 –soloAdapterSequence NNNNNNNNNGTGANNNNNNNNNGACA –soloCBposition 2_0_2_8 2_13_2_21 3_1_3_9 –soloUMIposition 3_10_3_17. We do not perform UMI compression because BD Rhapsody UMI length (8-base and directly attatched polyT) is not sufficient to avoid UMI collision (minimum 10-base is required, Perukhov et al Genome Biol 2018). Resulted non-umi count data was converted to genes x cells matrix file and inflection threshold of the barcode rank plot was detected by using DropletUtils package in R version 4.2.2 Patched (2022-11-10 r83330). Valid cell barcodes and backgrounds from inflection threshold * 0.9 to inflection threshold * 1.1 were separated by Dropkick package (Heiser et al Genome Biol 2022).
For STAR index build, small RNA annotations were filtered out from gencode.vM30 gtf file.
Assembly: GRCm39 release-107
Supplementary files format and content: tab-delimited text files include raw tag-count values for each sample

source_name: lung

growth_protocol: Lung organoids were generated by co-culturing murine lung fibroblasts and epithelial cells. Briefly, single-cell suspension was obtained from murine lungs by enzymatic digestion by collagenase and DNase I as described previously (Tsukui et al., 2015), and lung fibroblasts and epithelial cells were isolated by cell sorting. Resulted cells were suspended in MTEC Plus medium (described below) to yield 4 x 10^6 cells/ml of fibroblasts and 2 x 10^5 cells/ml of lung epithelial cells per well. 1x10^5 lung fibroblast and 5 x 10^3 lung epithelial cells/25µL were combined and suspended with an equal volume of Matrigel (BD Biosciences) at 4°C, and 90µL of the suspension was seeded onto each insert (BD Biosciences or Greiner) placed on a 24-well culture dish. Then, cells were cultured at 37°C for 30 min, 500 µL of MTEC Plus medium were added, and further cultured at 37°C with 5% CO2 in a humidified atmosphere. The MTEC Plus medium used for culture consisted of medium DMEM/F-12 (Sigma-Aldrich), mouse epidermal cell growth factor (25 ng/mL; R&D Systems), pituitary extract (30 µg/mL; Sigma-Aldrich), and insulin-transferrin-sodium selenite (1×; Thermo Fisher Scientific), penicillin/streptomycin (1×; Sigma-Aldrich), cholera toxin (100 ng/mL; Sigma-Aldrich), and fetal bovine serum (5%). Retinoic acid (Sigma-Aldrich) was added at the time of medium addition, and Y-27632 Rho-associated kinase inhibitor (10 μM; Fujifilm Wako Pure Chemicals) only immediately after seeding. The culture medium was changed every two days for 14 days.

extract_protocol:
Lungs were minced into 0.5 mm2 with a razor blade and digested with Collagenase solution [RPMI-1640 (Nacalai Tesque) supplemented with 10% FBS (MP Bio Japan), 10 mM HEPES pH7.2-7.4 (Cytiva (Global Life Sciences Technologies Japan)), 0.2% Collagenase (Fujifilm Wako Pure Chemicals), 2 kU/mL DNase I (Merck)] , and 0.96 mg/mL Dispase (Roche) at 37 ºC for 50 minutes. Cell suspensions were washed and resuspended with 25% Percoll PLUS (Cytiva). After under layered 65% Percoll PLUS, cell suspensions were centrifuged at 20ºC for 1,000 ×g for 20 minutes, and the middle layer was collected. Resultant cell suspensions were washed and resuspended with 1000 μL of preparation medium [RPMI-1640 supplemented with 5% FBS and 10 mM HEPES]. Each single-cell suspension cell concentration was counted using Flow-count fluorospheres (Beckman Coulter) and a Cytoflex flow cytometer (Beckman Coulter). Cells were stained with 2.5 μg/ml of Totalseq anti-mouse Hashtag-A antibodies (BioLegend) at 4ºC for 30 minutes and washed thrice with Cell Staining Buffer (BioLegend) and pooled.
Pooled single-cell suspensions were subjected to a BD Rhapsody system with BD Rhapsody Targeted & Abseq Reagent kit (BD Biosciences) following the manufacture’s instructions. 20000 cells were subjected to the BD Rhapsody workflow. After reverse transcription, Exonuclease I treatment of the resultant BD Rhapsody beads was performed at 37ºC for 60 minutes with 1,200 rpm on a Thermomixer C with Thermotop. Resultant beads were immediately chilled on ice; the supernatant was removed and washed with 1 mL of WTA wash buffer [10 mM Tris-HCl (pH 8.0), 50 mM NaCl, 1 mM EDTA, and 0.05% Tween-20], 200 μL of BD Rhapsody lysis buffer (for inactivation of enzyme), once with 1 ml of WTA wash buffer, twice with 500 μL of WTA wash buffer, resuspended with 200 μL of Beads resuspension buffer. During the washing step, beads-containing DNA LoBind tubes (Eppendorf Japan) were replaced twice. Exonuclease I-treated BD Rhapsody beads were subjected to TAS- Seq workflow for cDNA and/or hashtag library amplification (Shichino S., bioRxiv, 2021). 150 ng of amplified cDNA libraries was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina. Ligated products were purified by AmPure XP beads and 9 cycles of Barcoding PCR were performed. Resultant products were purified twice by double size selection with 0.5× → 0.3× (final 0.8×) AmPure XP beads and eluted with 30 μL of 10 mM Tris-HCl pH8.0. Size distribution of amplified products was analyzed by MultiNA system with appropriate dilutions. Resultant libraries and barcoded hashtag libraries were quantified using the KAPA Library Quantification Kit. Pooled libraries were sequenced by Illumina Novaseq 6000 sequencer.
BD Rhapsody WTA

treatment_protocol: Lung organoid were stimulated with 0.3 ug/ml bleomycin for 48 hours from day 8 post co-culture.

value: lung

value: epithelial cells, fibroblats

value: C57BL/6J or C57BL/6-Tg

value: WT or CAG-EGFP

value: Bleomycin


title: scATAC-seq of chronic PBMC from donor hiv12

description:
Library name: HIV_chr_hiv12
Single-cell ATAC-seq of PBMCs from chronic condition


title: mVSMCs, Ctrl_input rep 2 (RIP-Seq)

value: WT


title: WTA


title: scATAC-seq of acute PBMC from donor hiv11

description:
Library name: HIV_acu_hiv11
Single-cell ATAC-seq of PBMCs from acute condition

value: acute


title: CR, FOXO1_ChIP, rep1


title: mVSMCs, GFP OE Pi rep 1 (RNA-Seq)


title: VINC_LOAEL_PND83_733

description:
treatment:  VINC
dose: LOAEL
sample ID: 733


title: E16_ME_LSK_2

description: Library name: 2

value: Liver

value: LSK


title: mVSMCs, GFP OE Pi rep 2 (RNA-Seq)

value: Primary mouse vascular smooth muscle cells


title: scATAC-seq of healthy PBMC from donor hiv10

description:
Library name: HIV_ctrl_hiv10
Single-cell ATAC-seq of PBMCs from healthy condition

value: healthy


title: NR+CORT, GR_ChIP, rep2

data_processing:
Reads were aligned to mm10 using BWA, with MEM algorithm
Multimappers and duplicates were removed using Samtools and Picard
Peaks were called with MACS2, using p-value = 0.1, and blacklisted regions were filtered with bedtools intersect 70%
BiqWig files were made using deeptools BamtoBigWig tool
Peak universe, a data frame containing peaks across samples, were made with multiIntersect from bedtools
Assembly: mm10
Supplementary files format and content: biqWig, NarrowPeak

value: mouse liver

value: Night restricted feeding (NRF) + corticosterone  (CORT) supplementation


title: mVSMCs, THOC5 OE rep 2 (RNA-Seq)

value: THOC5 overexppression

value: Growth medium


title: VINC_NOAEL_PND83_724

description:
treatment:  VINC
dose: NOAEL
sample ID: 724

value: Wistar


title: scATAC-seq of acute PBMC from donor hiv1

description:
Library name: HIV_acu_hiv1
Single-cell ATAC-seq of PBMCs from acute condition

value: PBMC


title: VINC_LOAEL_PND83_732

description:
treatment:  VINC
dose: LOAEL
sample ID: 732

value: postnatal day (PND) 83


title: scATAC-seq of acute PBMC from donor hiv4

description:
Library name: HIV_acu_hiv4
Single-cell ATAC-seq of PBMCs from acute condition


title: VINC_NOAEL_PND83_723

description:
treatment:  VINC
dose: NOAEL
sample ID: 723


title: mVSMCs, THOC5 OE rep 1 (RNA-Seq)


title: scATAC-seq of healthy PBMC from donor hiv2

description:
Library name: HIV_ctrl_hiv2
Single-cell ATAC-seq of PBMCs from healthy condition


title: VINC_NOAEL_PND83_722

description:
treatment:  VINC
dose: NOAEL
sample ID: 722


title: CR, GR_ChIP, rep2

value: Caloric Restriction (CR)


title: mVSMCs, GFP OE rep 2 (RNA-Seq)


title: scATAC-seq of medium PBMC from donor 01S0004826

description:
Library name: OP_med_01S0004826
Single-cell ATAC-seq of PBMCs from medium condition

value: medium


title: VINC_NOAEL_PND83_721

description:
treatment:  VINC
dose: NOAEL
sample ID: 721


title: VINC_LOAEL_PND83_731

description:
treatment:  VINC
dose: LOAEL
sample ID: 731


title: mVSMCs, GFP OE rep 1 (RNA-Seq)


title: scATAC-seq of low PBMC from donor 01S0004814

description:
Library name: OP_low_01S0004814
Single-cell ATAC-seq of PBMCs from low condition

value: low


title: VINC_ADI_PND83_717

description:
treatment:  VINC
dose: ADI
sample ID: 717


title: scATAC-seq of low PBMC from donor 01S0004784

description:
Library name: OP_low_01S0004784
Single-cell ATAC-seq of PBMCs from low condition


title: NR, GR_ChIP, rep1

value: Night restricted feeding (NRF)


title: CR_ZT20_GRLKO_rep3

value: Mouse liver

value: GRfl/fl x Alb-Cre


title: NR, GR_ChIP, rep2


title: Wild type, thymus, H3K4me3-IP

city: Seoul

first: Min-Hee

last: Kang

state: Seoul

address: 120 Neungdong-ro

department: Stem Cell and Regenerative Biotechnology

country: South Korea

institute: Konkuk University

description: Library name: WT-thymus-K4me3-IP

data_processing:
Raw reads (single-end, 75 bp) were quality-checked using FastQC v0.11.9.
Adapters and low-quality bases were trimmed using Trimmomatic v0.39.
Trimmed reads were aligned to the Sus scrofa reference genome (Sscrofa11.1) using BWA-MEM v0.7.17.
Peak calling was performed using MACS2 v2.2.7.1 with a q-value cutoff of 0.01. For each H3K4me3 sample, the corresponding Input DNA sample was used as the control.
Assembly: Sscrofa11.1
Supplementary files format and content: Processed data are provided as bigWig (signal tracks) files.

organism: Sus scrofa

source_name: Thymus

extract_protocol:
Chromatin was prepared from tissues by formaldehyde cross-linking, followed by cell lysis and sonication to shear DNA to an average length of 200-500 bp.
ChIP libraries were prepared using the TruSeq ChIP Sample Prep Kit (Illumina) according to the manufacturer's protocol. Immunoprecipitation was performed using an anti-H3K4me3 antibody (ab8580, Abcam).

value: Thymus

value: Wild type

value: 3 months


title: scATAC-seq of high PBMC from donor 01S0004754

description:
Library name: OP_high_01S0004754
Single-cell ATAC-seq of PBMCs from high condition

value: high


title: VINC_ADI_PND83_714

description:
treatment:  VINC
dose: ADI
sample ID: 714


title: VINC_ADI_PND83_716

description:
treatment:  VINC
dose: ADI
sample ID: 716


title: NR+CORT, GR_ChIP, rep1

value: mouse liver

value: Night restricted feeding (NRF) + corticosterone (CORT) supplementation


title: Wild type, spleen, H3K4me3-IP

description: Library name: WT-spleen-K4me3-IP

source_name: Spleen

value: Spleen


title: scATAC-seq of high PBMC from donor 01S0004700

description:
Library name: OP_high_01S0004700
Single-cell ATAC-seq of PBMCs from high condition

source_name: PBMC


title: Wild type, spleen, Input

description: Library name: WT-spleen-Input


title: CR_ZT20_GRLKO_rep2


title: VINC_ADI_PND83_712

description:
treatment:  VINC
dose: ADI
sample ID: 712


title: scATAC-seq of medium PBMC from donor 01S0004676

description:
Library name: OP_med_01S0004676
Single-cell ATAC-seq of PBMCs from medium condition


title: CR_ZT20_GRLKO_rep1


title: PROC_LOAEL_PND83_794

description:
treatment:  PROC
dose: LOAEL
sample ID: 794


title: CR, GR_ChIP, rep1


title: Wild type, lymph node, Input

description: Library name: WT-lymph-node-Input

source_name: Lymph node

value: Lymph node


title: PROC_LOAEL_PND83_793

description:
treatment:  PROC
dose: LOAEL
sample ID: 793

value: Wistar


title: CR_ZT20_WT_rep3

value: GRfl/fl


title: Wild type, lymph node, H3K4me3-IP

description: Library name: WT-lymph-node-K4me3-IP


title: CR_ZT20_WT_rep2


title: PROC_LOAEL_PND83_792

description:
treatment:  PROC
dose: LOAEL
sample ID: 792

value: postnatal day (PND) 83


title: Wild type thymus, Input

description: Library name: WT-thymus-Input


title: scATAC-seq of high PBMC from donor 01S0004526

description:
Library name: OP_high_01S0004526
Single-cell ATAC-seq of PBMCs from high condition

value: PBMC


title: RAG2 Knockout, thymus, Input

description: Library name: Rag2-KO-thymus-Input

value: RAG2 Knockout


title: scATAC-seq of high PBMC from donor 01S0004718

description:
Library name: OP_high_01S0004718
Single-cell ATAC-seq of PBMCs from high condition


title: CR_ZT20_WT_rep1

value: Caloric Restriction (CR)


title: scATAC-seq of high PBMC from donor 01S0004508

description:
Library name: OP_high_01S0004508
Single-cell ATAC-seq of PBMCs from high condition


title: PROC_LOAEL_PND83_791

description:
treatment:  PROC
dose: LOAEL
sample ID: 791


title: CR_ZT16_GRLKO_rep3


title: RAG2 Knockout, thymus, H3K4me3-IP

description: Library name: Rag2-KO-thymus-K4me3-IP


title: RAG2 Knockout, spleen, Input

description: Library name: Rag2-KO-spleen-Input


title: CR_ZT16_GRLKO_rep2


title: PROC_NOAEL_PND83_784

description:
treatment:  PROC
dose: NOAEL
sample ID: 784


title: scATAC-seq of low PBMC from donor 01S0004478

description:
Library name: OP_low_01S0004478
Single-cell ATAC-seq of PBMCs from low condition

value: low


title: RAG2 Knockout, spleen, H3K4me3-IP

description: Library name: Rag2-KO-spleen-K4me3-IP


title: PROC_NOAEL_PND83_783

description:
treatment:  PROC
dose: NOAEL
sample ID: 783


title: CR_ZT16_GRLKO_rep1

value: Mouse liver


title: scATAC-seq of high PBMC from donor 01S0004460

description:
Library name: OP_high_01S0004460
Single-cell ATAC-seq of PBMCs from high condition


title: scATAC-seq of high PBMC from donor 01S0004538

description:
Library name: OP_high_01S0004538
Single-cell ATAC-seq of PBMCs from high condition


title: RAG2 Knockout, lymph node, Input

description: Library name: Rag2-KO-lymph-node-Input


title: CR_ZT16_WT_rep3


title: scATAC-seq of high PBMC from donor OP_9

description:
Library name: OP_high_OP_9
Single-cell ATAC-seq of PBMCs from high condition


title: PROC_NOAEL_PND83_782

description:
treatment:  PROC
dose: NOAEL
sample ID: 782


title: CR_ZT16_WT_rep2


title: PROC_NOAEL_PND83_781

description:
treatment:  PROC
dose: NOAEL
sample ID: 781


title: RAG2 Knockout, lymph node, H3K4me3-IP

description: Library name: Rag2-KO-lymph-node-K4me3-IP


title: CR_ZT16_WT_rep1


title: scATAC-seq of medium PBMC from donor OP_8

description:
Library name: OP_med_OP_8
Single-cell ATAC-seq of PBMCs from medium condition

value: medium


title: PROC_ADI_PND83_774

description:
treatment:  PROC
dose: ADI
sample ID: 774


title: Thymus, Wild-type

description: Library name: WT_THY

data_processing:
Raw reads were quality-checked using FastQC v0.11.9.
Adapters and low-quality bases were trimmed using Trimmomatic v0.39.
Trimmed reads were aligned to the Sus scrofa reference genome (Sscrofa11.1) using STAR aligner v2.7.9a.
Gene expression abundance was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values using Cufflinks v2.2.1.
Assembly: Sscrofa11.1
Supplementary files format and content: A single tab-delimited text file containing a matrix of raw read counts and FPKM, with genes in rows and samples in columns.

extract_protocol:
Total RNA was extracted from tissues using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
RNA-seq libraries were prepared using the Truseq Stranded Total RNA Sample Preparation Kit (Illumina)  following the manufacturer's protocol.

value: Thymus


title: scATAC-seq of high PBMC from donor OP_7

description:
Library name: OP_high_OP_7
Single-cell ATAC-seq of PBMCs from high condition


title: PROC_ADI_PND83_773

description:
treatment:  PROC
dose: ADI
sample ID: 773


title: scATAC-seq of high PBMC from donor 01S0004484

description:
Library name: OP_high_01S0004484
Single-cell ATAC-seq of PBMCs from high condition


title: CR_ZT12_GRLKO_rep3

value: GRfl/fl x Alb-Cre


title: PROC_ADI_PND83_772

description:
treatment:  PROC
dose: ADI
sample ID: 772


title: Spleen, Wild-type

description: Library name: WT_SPL

value: Wild type

value: 3 months


title: scATAC-seq of low PBMC from donor OP_6

description:
Library name: OP_low_OP_6
Single-cell ATAC-seq of PBMCs from low condition


title: Lymph node, Wild-type

description: Library name: WT_LN


title: CR_ZT12_GRLKO_rep2


title: PROC_ADI_PND83_771

description:
treatment:  PROC
dose: ADI
sample ID: 771


title: Thymus, RAG2-KO

description: Library name: RAG2_KO_THY


title: scATAC-seq of low PBMC from donor OP_5

description:
Library name: OP_low_OP_5
Single-cell ATAC-seq of PBMCs from low condition


title: Spleen, RAG2-KO

description: Library name: RAG2_KO_SPL


title: scATAC-seq of high PBMC from donor OP_4

description:
Library name: OP_high_OP_4
Single-cell ATAC-seq of PBMCs from high condition

value: high


title: CR_ZT12_WT_rep3


title: FLUT_LOAEL_PND83_764

description:
treatment:  FLUT
dose: LOAEL
sample ID: 764


title: FLUT_LOAEL_PND83_763

description:
treatment:  FLUT
dose: LOAEL
sample ID: 763


title: scATAC-seq of high PBMC from donor OP_24

description:
Library name: OP_high_OP_24
Single-cell ATAC-seq of PBMCs from high condition


title: Lymph node, RAG2-KO

description: Library name: RAG2_KO_LN


title: CR_ZT12_WT_rep2


title: scATAC-seq of high PBMC from donor OP_3

description:
Library name: OP_high_OP_3
Single-cell ATAC-seq of PBMCs from high condition


title: FLUT_LOAEL_PND83_762

description:
treatment:  FLUT
dose: LOAEL
sample ID: 762


title: placental labyrinth of GD 20.5 SD rats

city: Tokyo

first: Pharmaceutics

last: Keio

address: 1-5-30 Shibakoen, Minato-ku

department: Pharmacy

institute: Keio University

description:
Library name: Sample 2
Column name in Raw_counts.csv: rat_LZ

data_processing:
Before adaptor trimming, a published RNA-seq dataset from size-filtered, syncytiotrophoblast-enriched fractions of human placental villous tissue (accession number GSE182381) was utilized. The original human placental samples were obtained from uncomplicated, full-term, singleton pregnancies delivered by the cesarean section.
RNA-seq reads were firstly cleaned by processing FASTQ format data with Trimmomatic (ver 0.3.9) software.
Salmon (ver 1.9.0) was then employed to map the clean reads to the reference genome assembly (human: GRCh38.p14, mouse: GRCm39, rat: GRCr8) and the read counts for RefSeq genes with the accession number prefixes NM_ were extracted.
RefSeq IDs were converted to gene symbols using the bitr function from the clusterProfiler (ver. 4.14.6) package and organism-specific annotation packages (human: org.Hs.eg.db (ver. 3.20.0), mouse: org.Mm.eg.db (ver. 3.20.0), rat: org.Rn.eg.db (ver. 3.20.0)).
The count values for each sample were summarized as “Raw_counts.csv”. If the corresponding gene was not present for a species, the count value was set to NA. However, in the downstream analysis, it was treated as 0 instead of NA for convenience.
Assembly: GRCm39, GRCr8, GRCh38.p14
Supplementary files format and content: The CSV file includes raw counts by gene symbols for each sample.

source_name: placental labyrinth

extract_protocol:
Total RNA was extracted from the placental labyrinth of gestational day (GD) 17.5 C57BL/6J mice and GD20.5 SD rats using ISOGEN II (Nippon Gene, Tokyo, Japan). Equal amounts of RNA from three to four different litters were then pooled as one biological sample
The RNA-seq library preparation and sequencing of the samples were performed by Rhelixa (Tokyo, Japan). Used kits there were "NEBNext® Poly(A) mRNA Magnetic Isolation Module (for PolyA selection)" and "NEBNext® Ultra™ ll Directional RNA Library Prep Kit".

value: placental labyrinth

value: SD

tag: developmental stage

value: gestational day (GD) 20.5


title: CR_ZT12_WT_rep1


title: scATAC-seq of low PBMC from donor OP_23

description:
Library name: OP_low_OP_23
Single-cell ATAC-seq of PBMCs from low condition


title: FLUT_LOAEL_PND83_761

description:
treatment:  FLUT
dose: LOAEL
sample ID: 761

value: Wistar


title: CR_ZT8_GRLKO_rep3


title: si3m rep_2

city: Shanghai

first: Zilun

last: Wei

address: 180 Fenglin Road

department: Shanghai Institute of Cardiovascular Diseases

institute: Zhongshan Hospital

data_processing:
Adaptors in pair-end RNA-seq reads were trimmed by Trimmomatic (V0.40)
Trimmed sequence reads were mapped to rn6 using HISAT2 (v2.2.1)
QC and Ribo-Seq analysis performed by R package, eg.ggplot2, limma, DESeq2,etc
Read count extraction and normalization were performed using featurecount tool.
Supplementary files format and content: rn6
Supplementary files format and content: tab-delimited text files include count values for each Sample
Library strategy: Ribo-seq

source_name: Myocardial cells

growth_protocol: NRVMs were derived from embryonic rat myocardium. NRVMs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
The preparative extraction of ribosome-protected fragments was required with 0.1 mg/mL cycloheximide to stall ribosomes prior to lysis and stabilize polyribosomes. Flash freezing in liquid nitrogen followed by physical disruption in lysis buffer. After ultracentrifugation for 3 h at 35,000 rpm, gradients were passed through a UV detector (Bio-Rad, USA), and the absorption at 254 nm was recorded. The fraction containing monosomes and polysomes were collected and concentrated separately, followed by total RNA extraction.
The sequencing library was prepared by VAHTS Small RNA Library Prep Kit for Illumina for its high data quality, simplicity, economic efficiency.

value: Myocardial cells

value: NRVM

value: siRNA

tag: sirna


title: FLUT_NOAEL_PND83_754

description:
treatment:  FLUT
dose: NOAEL
sample ID: 754

value: postnatal day (PND) 83


title: scATAC-seq of low PBMC from donor OP_22

description:
Library name: OP_low_OP_22
Single-cell ATAC-seq of PBMCs from low condition

value: PBMC


title: CR_ZT8_GRLKO_rep2

value: Caloric Restriction (CR)


title: scATAC-seq of high PBMC from donor OP_21

description:
Library name: OP_high_OP_21
Single-cell ATAC-seq of PBMCs from high condition


title: si3m rep_1


title: siNT rep_2

value: control


title: CR_ZT12_GRLKO_rep1

value: Mouse liver


title: FLUT_NOAEL_PND83_752

description:
treatment:  FLUT
dose: NOAEL
sample ID: 752


title: FLUT_NOAEL_PND83_753

description:
treatment:  FLUT
dose: NOAEL
sample ID: 753


title: CR_ZT8_GRLKO_rep1


title: siNT rep_1


title: CR_ZT8_WT_rep3

value: GRfl/fl


title: scATAC-seq of medium PBMC from donor OP_2

description:
Library name: OP_med_OP_2
Single-cell ATAC-seq of PBMCs from medium condition

value: medium


title: si3m rep3

data_processing:
Adaptors in pair-end RNA-seq reads were trimmed by Trimmomatic (V0.40)
Trimmed sequence reads were mapped to rn6 using HISAT2 (v2.2.1)
QC and Ribo-Seq analysis performed by R package, eg.ggplot2, limma, DESeq2,etc
Read count extraction and normalization were performed using featurecount tool and R limma package.
differential analysis was performed by DESeq2 R package
Supplementary files format and content: rn6
Supplementary files format and content: tab-delimited text files include count values for each Sample

extract_protocol:
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.


title: CR_ZT8_WT_rep2


title: FLUT_NOAEL_PND83_751

description:
treatment:  FLUT
dose: NOAEL
sample ID: 751

extract_protocol: Total RNAs were isolated from frozen testicular powder using TRIzol reagent (Invitrogen, Cergy Pontoise, France) coupled with column purification of RNA (High pure miRNA isolation kit, Roche Diagnostics, Meylan, France) and DNase treatment.


title: scATAC-seq of low PBMC from donor OP_19

description:
Library name: OP_low_OP_19
Single-cell ATAC-seq of PBMCs from low condition

data_processing:
Sequencing data were processed using Cell Ranger ATAC (v2.1.0).
Fragment files were filtered and analyzed with ArchR (v1.0.2), including quality control, dimensionality reduction, clustering, and peak calling.
Assembly: hg38
Supplementary files format and content: peak_matrix.mtx.gz — sparse matrix of peak accessibility counts per cell.
Supplementary files format and content: chromvar_matrix.mtx.gz — sparse matrix of TF activity scores inferred from chromatin accessibility.
Supplementary files format and content: peaks.tsv.gz — genomic coordinates of peaks

value: low


title: FLUT_ADI_PND83_744

description:
treatment:  FLUT
dose: ADI
sample ID: 744


title: CR_ZT8_WT_rep1


title: si3m rep2


title: scATAC-seq of medium PBMC from donor OP_18

description:
Library name: OP_med_OP_18
Single-cell ATAC-seq of PBMCs from medium condition


title: CR_ZT4_GRLKO_rep3

value: GRfl/fl x Alb-Cre


title: siNT rep2


title: CR_ZT4_GRLKO_rep2


title: CR_ZT4_GRLKO_rep1


title: scATAC-seq of high PBMC from donor OP_16

description:
Library name: OP_high_OP_16
Single-cell ATAC-seq of PBMCs from high condition

value: high


title: siNT rep3


title: FLUT_ADI_PND83_742

description:
treatment:  FLUT
dose: ADI
sample ID: 742


title: scATAC-seq of low PBMC from donor OP_20

description:
Library name: OP_low_OP_20
Single-cell ATAC-seq of PBMCs from low condition


title: scATAC-seq of high PBMC from donor OP_15

description:
Library name: OP_high_OP_15
Single-cell ATAC-seq of PBMCs from high condition


title: scATAC-seq of high PBMC from donor OP_14

description:
Library name: OP_high_OP_14
Single-cell ATAC-seq of PBMCs from high condition


title: CTRL_PND83_704

description:
treatment:  CTRL
dose: --
sample ID: 704


title: FLUT_ADI_PND83_741

description:
treatment:  FLUT
dose: ADI
sample ID: 741


title: rat_IgG_CLIP

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Clip-Seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
Clip-Seq reads were aligned to the UCSC rn6/hg19 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create Clip-Seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing homer v4.11 with the significance cut-off q-value <=0.05
Assembly: rn6 for rat genome/hg19 for human genome
Supplementary files format and content: tab txt format
Library strategy: Clip-Seq

extract_protocol:
3’ end of the RNA carries a monophosphate due to RNase A mediated cleavage; calf intestinal alkaline phosphatase (CIAP) was added to remove the monophosphate so that the RNA can be ligated to the 5’-end of adenylated 3’ linker consequently. On the other hand, 5’ end of RNA lacks a phosphate group due to RNase A cleavage, 1 ml of [ɣ-32P] ATP (Perkin Elmer, USA) was added into the immunoprecipitates. RNA was then purified and precipitated through acidic phenol, chloroform and ethanol and resuspended in 5 ml of RNase-free water.
The first few steps in sequence analysis were done by using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). First, the 3’ adaptor sequences were removed from reads by using fastx_clipper. The rest was trimmed from the 3’ end so that the remaining reads have Phred quality of 25 or higher. After clipping and trimming, reads of 20nt or longer were collapsed to generate a set of unique sequences. The sequences were aligned to abundant contaminant sequences (Illumina adaptor/primer sequences and rat/human ribosomal DNA complete repeating unit, queried in GenBank accession) with GSNAP (V2021-12-17) with 10% mismatch rate137. Filtered reads that do not match to any contaminant and have sufficient sequence complexity were aligned to UCSC (the University of California, Santa Cruz) rn6 for rat genome assembly and hg19 for human with GSNAP (V2021-12-17) with options of 10% mismatch rate, no terminal clipping, and splice site annotations from RefSeq (https://www.ncbi.nlm.nih.gov/refseq/, V2022-9-16). The alignment results were filtered to leave only the single best hit with minimum edit distance (up to two edits) to obtain a set of single hit reads. Those with multiple best hits were ignored as repetitive sequences. The alignments were annotated with RefSeq (https://www.ncbi.nlm.nih.gov/refseq/, V2022-9-16), RepeatMasker (http://repeatmasker.org/, V4.1.3), miRBase (https://www.mirbase.org/, V22.1), Rfam (https://rfam.xfam.org/, V14.8) and GtRNAdb (http://gtrnadb.ucsc.edu/, V19.0) by using intersectBed of BEDTools (https://bedtools.readthedocs.io/en/latest/index.html, V2.28.0).

treatment_protocol: NRVMs grown on four 100 mm dishes were rinsed and irradiated with 600 mJ/cm of UV-B by using CL-1000 ultraviolet crosslinker (UVP). UV-irradiated cells were harvested and treated with DNase I and RNase A. 20μL eIF3m antibody (11423-1-AP, Proteintech) or IgG was used for immunoprecipitation of eIF3m-RNA complex or the negative control.

tag: clip antibody

value: IgG


title: siNT rep1


title: CR_ZT4_WT_rep3

data_processing:
Sequence quality was checked using FastQC and MultiQC
Adapter reads were trimmed using Trimmomatics
Reads were aligned using Salmon to mm10
Salmon quant.sf files were imported in R using tximport to generate read counts
Raw read counts were transformed by variance  stabilizing transformation (VST) method.
Assembly: mm10
Supplementary files format and content: tab-separate files containing raw read counts from Salmon
Supplementary files format and content: tab-separate files containing VST counts from DESeq2


title: FLUT_ADI_PND83_743

description:
treatment:  FLUT
dose: ADI
sample ID: 743


title: CTRL_PND83_702

description:
treatment:  CTRL
dose: --
sample ID: 702


title: CTRL_PND83_703

description:
treatment:  CTRL
dose: --
sample ID: 703


title: scATAC-seq of high PBMC from donor OP_12

description:
Library name: OP_high_OP_12
Single-cell ATAC-seq of PBMCs from high condition

extract_protocol:
Nuclei were isolated from cryopreserved PBMCs following the 10x Genomics Chromium Single Cell ATAC-seq protocol (CG000272). Lysis and washing steps were performed under ice-cold conditions.
Single-cell ATAC-seq libraries were prepared using the 10x Genomics Chromium Single Cell ATAC-seq kit according to the manufacturer’s protocol. Transposition, barcoding, and amplification were performed as specified in the 10x protocol.
Libraries were sequenced on the Illumina NovaSeq 6000 platform using paired-end 50 bp reads, following the 10x Genomics guidelines for scATAC-seq.


title: scATAC-seq of high PBMC from donor OP_13

description:
Library name: OP_high_OP_13
Single-cell ATAC-seq of PBMCs from high condition


title: CR_ZT4_WT_rep2


title: rat_EIF3M_CLIP


title: CR_ZT4_WT_rep1


title: si3m rep1


title: siMt2 rep 3


title: scATAC-seq of high PBMC from donor OP_11

description:
Library name: OP_high_OP_11
Single-cell ATAC-seq of PBMCs from high condition


title: CR_ZT0_GRLKO_rep3


title: VINC_LOAEL_PND30-40_532

description:
treatment:  VINC
dose: LOAEL
sample ID: 532

value: postnatal day (PND) 30-40


title: siMt2 rep 2


title: CR_ZT0_GRLKO_rep2


title: scATAC-seq of day30 PBMC from donor flu341_4

description:
Library name: Influenza_d30_flu341_4
Single-cell ATAC-seq of PBMCs from day30 condition

value: day 30 after challenge


title: siMt2 rep 1


title: scATAC-seq of day6 PBMC from donor flu341_3

description:
Library name: Influenza_d6_flu341_3
Single-cell ATAC-seq of PBMCs from day6 condition

value: day 6 after challenge


title: VINC_NOAEL_PND30-40_524

description:
treatment:  VINC
dose: NOAEL
sample ID: 524

value: Wistar


title: CR_ZT0_GRLKO_rep1


title: VINC_LOAEL_PND30-40_531

description:
treatment:  VINC
dose: LOAEL
sample ID: 531


title: VINC_LOAEL_PND30-40_534

description:
treatment:  VINC
dose: LOAEL
sample ID: 534


title: CR_ZT0_WT_rep3


title: scATAC-seq of healthy PBMC from donor flu341_1

description:
Library name: Influenza_ctrl_flu341_1
Single-cell ATAC-seq of PBMCs from healthy condition

value: healthy

value: right before challenge


title: scATAC-seq of day3 PBMC from donor flu341_2

description:
Library name: Influenza_d3_flu341_2
Single-cell ATAC-seq of PBMCs from day3 condition

value: day 3 after challenge


title: scATAC-seq of day30 PBMC from donor flu206_4

description:
Library name: Influenza_d30_flu206_4
Single-cell ATAC-seq of PBMCs from day30 condition

value: PBMC


title: CR_ZT0_WT_rep2

value: Caloric Restriction (CR)


title: VINC_NOAEL_PND30-40_523

description:
treatment:  VINC
dose: NOAEL
sample ID: 523


title: CR_ZT0_WT_rep1


title: VINC_LOAEL_PND30-40_533

description:
treatment:  VINC
dose: LOAEL
sample ID: 533


title: NRF_ZT20_GRLKO_rep3

value: Night Restricted Feeding (NR)


title: siNT rep 2

value: Myocardial cells

value: NRVM

value: siRNA

value: control


title: scATAC-seq of day6 PBMC from donor flu206_3

description:
Library name: Influenza_d6_flu206_3
Single-cell ATAC-seq of PBMCs from day6 condition


title: LU01

city: Guangxi Zhuang Autonomous Region

first: wang

last: zhen

address: 1303 East Education Road, Yulin City, Guangxi, China

institute: Yulin Normal University

data_processing:
The sequences were further processed with a bioinformatic pipeline tool, BMKCloud (www.biocloud.net) online platform. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Assembly: The left files (read1 files) from all libraries/samples were pooled into one big left.fq.gz file, and right files (read2 files) into one big right.fq.gz file. Transcriptome assembly was accomplished based on the left.fq.gz and right.fq.gz using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default
Supplementary files format and content: fastq,fasta

organism: Ichthyophis bannanicus

source_name: Lung

extract_protocol:
The purity, concentration and integrity of RNA samples are tested using advanced molecular biology equipment to ensure the use of qualified samples for transcriptome sequencing.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina®(NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Lung


title: VINC_NOAEL_PND30-40_521

description:
treatment:  VINC
dose: NOAEL
sample ID: 521


title: scATAC-seq of medium PBMC from donor OP_10

description:
Library name: OP_med_OP_10
Single-cell ATAC-seq of PBMCs from medium condition

value: medium


title: VINC_NOAEL_PND30-40_522

description:
treatment:  VINC
dose: NOAEL
sample ID: 522


title: VINC_ADI_PND30-40_514

description:
treatment:  VINC
dose: ADI
sample ID: 514


title: NRF_ZT20_GRLKO_rep2

source_name: Mouse liver

extract_protocol:
RNA was extracted using the QIAZOL reagent. 1 μg of RNA was used for library preparation.
Libraries were prepped from 1µg total RNA with the Illumina TruSeq RNA library prep kit v2 chemistry in an automated system (Agilent Bravo liquid handling) platform).

value: Mouse liver

value: GRfl/fl x Alb-Cre


title: siNT rep 3


title: scATAC-seq of day3 PBMC from donor flu206_2

description:
Library name: Influenza_d3_flu206_2
Single-cell ATAC-seq of PBMCs from day3 condition


title: VINC_ADI_PND30-40_513

description:
treatment:  VINC
dose: ADI
sample ID: 513

value: postnatal day (PND) 30-40


title: NRF_ZT20_GRLKO_rep1


title: siNT rep 1


title: scATAC-seq of healthy PBMC from donor flu206_1

description:
Library name: Influenza_ctrl_flu206_1
Single-cell ATAC-seq of PBMCs from healthy condition


title: TE03

value: Testis


title: VINC_ADI_PND30-40_512

description:
treatment:  VINC
dose: ADI
sample ID: 512

value: Wistar


title: scATAC-seq of day30 PBMC from donor flu03_4

description:
Library name: Influenza_d30_flu03_4
Single-cell ATAC-seq of PBMCs from day30 condition

value: day 30 after challenge


title: NRF_ZT20_WT_rep4

value: GRfl/fl


title: ST03

source_name: Stomach

value: Stomach


title: NRF_ZT20_WT_rep3


title: scATAC-seq of day6 PBMC from donor flu03_3

description:
Library name: Influenza_d6_flu03_3
Single-cell ATAC-seq of PBMCs from day6 condition

value: PBMC

value: day 6 after challenge


title: scATAC-seq of day3 PBMC from donor flu03_2

description:
Library name: Influenza_d3_flu03_2
Single-cell ATAC-seq of PBMCs from day3 condition

value: day 3 after challenge


title: ST02


title: ST01


title: PROC_LOAEL_PND30-40_594

description:
treatment:  PROC
dose: LOAEL
sample ID: 594


title: NRF_ZT20_WT_rep1

value: Night Restricted Feeding (NR)


title: VINC_ADI_PND30-40_511

description:
treatment:  VINC
dose: ADI
sample ID: 511


title: scATAC-seq of day30 PBMC from donor flu02_4

description:
Library name: Influenza_d30_flu02_4
Single-cell ATAC-seq of PBMCs from day30 condition


title: NRF_ZT20_WT_rep2


title: OV03

source_name: Ovary

value: Ovary


title: NRF_ZT16_GRLKO_rep3


title: scATAC-seq of healthy PBMC from donor flu03_1

description:
Library name: Influenza_ctrl_flu03_1
Single-cell ATAC-seq of PBMCs from healthy condition

value: healthy

value: right before challenge


title: OV01


title: LU03

value: Lung


title: PROC_LOAEL_PND30-40_592

description:
treatment:  PROC
dose: LOAEL
sample ID: 592


title: scATAC-seq of day6 PBMC from donor flu02_3

description:
Library name: Influenza_d6_flu02_3
Single-cell ATAC-seq of PBMCs from day6 condition


title: LU02


title: PROC_LOAEL_PND30-40_593

description:
treatment:  PROC
dose: LOAEL
sample ID: 593


title: TE02


title: NRF_ZT16_GRLKO_rep1


title: PROC_NOAEL_PND30-40_584

description:
treatment:  PROC
dose: NOAEL
sample ID: 584


title: PROC_LOAEL_PND30-40_591

description:
treatment:  PROC
dose: LOAEL
sample ID: 591


title: scATAC-seq of day3 PBMC from donor flu02_2

description:
Library name: Influenza_d3_flu02_2
Single-cell ATAC-seq of PBMCs from day3 condition


title: TE01


title: NRF_ZT16_WT_rep4


title: PROC_NOAEL_PND30-40_582

description:
treatment:  PROC
dose: NOAEL
sample ID: 582


title: scATAC-seq of healthy PBMC from donor flu02_1

description:
Library name: Influenza_ctrl_flu02_1
Single-cell ATAC-seq of PBMCs from healthy condition


title: scATAC-seq of day30 PBMC from donor flu01_4

description:
Library name: Influenza_d30_flu01_4
Single-cell ATAC-seq of PBMCs from day30 condition


title: NRF_ZT16_WT_rep3


title: HE03

source_name: Heart

value: Heart


title: NRF_ZT16_WT_rep2

value: Mouse liver


title: HE01


title: PROC_NOAEL_PND30-40_581

description:
treatment:  PROC
dose: NOAEL
sample ID: 581


title: scATAC-seq of day3 PBMC from donor flu01_2

description:
Library name: Influenza_d3_flu01_2
Single-cell ATAC-seq of PBMCs from day3 condition


title: scATAC-seq of day6 PBMC from donor flu01_3

description:
Library name: Influenza_d6_flu01_3
Single-cell ATAC-seq of PBMCs from day6 condition


title: NRF_ZT16_GRLKO_rep2

value: GRfl/fl x Alb-Cre


title: KI03

source_name: Kidney

value: Kidney


title: PROC_ADI_PND30-40_573

description:
treatment:  PROC
dose: ADI
sample ID: 573

value: postnatal day (PND) 30-40


title: PROC_ADI_PND30-40_572

description:
treatment:  PROC
dose: ADI
sample ID: 572

value: Wistar


title: PROC_ADI_PND30-40_574

description:
treatment:  PROC
dose: ADI
sample ID: 574


title: NRF_ZT16_WT_rep1


title: scATAC-seq of healthy PBMC from donor flu01_1

description:
Library name: Influenza_ctrl_flu01_1
Single-cell ATAC-seq of PBMCs from healthy condition


title: KI02


title: NRF_ZT12_GRLKO_rep3


title: KI01


title: dTAG_mCherry_003

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

description: Library name: Sample 12

data_processing:
Fastp (paired-end) was used to remove adapter sequences, reads with Q<25, and reads less than 30bp long
Remaining reads were aligned to the reference human genome (hg38) using the STAR aligner with default settings
FeatureCounts was used to obtain raw read count values.
DESeq2 was used to obtain differentially expressed genes, and genes with a Log2FC >1.5 and FDR <0.05 were considered significant.
Assembly: hg38
Supplementary files format and content: Tab-delimited txt file contains raw counts for each sample.

source_name: Blood

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin (Pen/Strep)

extract_protocol:
total RNA was extracted with Trizol (Invitrogen) according to the manufacturer’s protocol.
500ng total RNA was used as input for the Illumina TruSeq® Stranded mRNA Library Prep kit (20020594) following the manufacturer’s protocol.

treatment_protocol: OCI-AML3 degron cells were seeded in RPMI supplemented with polybrene (7μg/ml) and 2.5μl of concentrated viral particles. Cells were spin-infected at 1100rpm for 2 hrs at room temperature and returned to the incubator overnight. 48 hours after transduction, cells were treated with 500nM dTAG-13 or DMSO. mCherry+ cells were FACS isolated 24 hours after dTAG-13 addition.

value: Blood

value: AML

value: NPM1c-degron; mCherry

value: dTAG


title: dTAG_mCherry_002

description: Library name: Sample 11


title: FLUT_LOAEL_PND30-40_564

description:
treatment:  FLUT
dose: LOAEL
sample ID: 564


title: NRF_ZT12_GRLKO_rep1


title: FLUT_LOAEL_PND30-40_563

description:
treatment:  FLUT
dose: LOAEL
sample ID: 563


title: HE02


title: dTAG_mCherry_001

description: Library name: Sample 10


title: FLUT_LOAEL_PND30-40_562

description:
treatment:  FLUT
dose: LOAEL
sample ID: 562


title: LI02

source_name: Liver

value: Liver


title: NRF_ZT12_WT_rep4

value: GRfl/fl


title: NRF_ZT12_GRLKO_rep4

value: Night Restricted Feeding (NR)


title: LI01


title: dTAG_FL-NPM1c_003

description: Library name: Sample 9

value: NPM1c-degron; FL-NPM1c-mCherry


title: SP03

value: Spleen


title: NRF_ZT12_WT_rep2


title: dTAG_FL-NPM1c_002

description: Library name: Sample 8


title: PROC_ADI_PND30-40_571

description:
treatment:  PROC
dose: ADI
sample ID: 571


title: NRF_ZT12_WT_rep1


title: SP01


title: dTAG_Cbodynull_003

description: Library name: Sample 6

value: NPM1c-degron; Cbodynull-mCherry


title: FLUT_NOAEL_PND30-40_553

description:
treatment:  FLUT
dose: NOAEL
sample ID: 553


title: FLUT_NOAEL_PND30-40_554

description:
treatment:  FLUT
dose: NOAEL
sample ID: 554


title: SP02


title: dTAG_FL-NPM1c_001

description: Library name: Sample 7


title: NRF_ZT12_GRLKO_rep2


title: LI03


title: NRF_ZT8_GRLKO_rep4


title: dTAG_Cbodynull_002

description: Library name: Sample 5


title: NRF_ZT8_GRLKO_rep3


title: dTAG_Cbodynull_001

description: Library name: Sample 4


title: SK02

source_name: Skin

value: Skin


title: SK03


title: NRF_ZT8_GRLKO_rep2


title: NTC_DMSO_003

description: Library name: Sample 3


title: FLUT_LOAEL_PND30-40_561

description:
treatment:  FLUT
dose: LOAEL
sample ID: 561

source_name: Testis


title: NRF_ZT8_GRLKO_rep1


title: NRF_ZT12_WT_rep3


title: NTC_DMSO_002

description: Library name: Sample 2


title: FLUT_NOAEL_PND30-40_551

description:
treatment:  FLUT
dose: NOAEL
sample ID: 551


title: BL03


title: SK01


title: FLUT_ADI_PND30-40_543

description:
treatment:  FLUT
dose: ADI
sample ID: 543


title: NTC_DMSO_001

description: Library name: Sample 1


title: FLUT_ADI_PND30-40_544

description:
treatment:  FLUT
dose: ADI
sample ID: 544


title: FLUT_NOAEL_PND30-40_552

description:
treatment:  FLUT
dose: NOAEL
sample ID: 552


title: NRF_ZT8_WT_rep4


title: NRF_ZT8_WT_rep3


title: NRF_ZT8_WT_rep2


title: Huvec cells,WT,low glucose (5 mM),12 hours

description: Library name: HUVEC_LowGlucose

data_processing:
CUT&Tag libraries were prepared and sequenced by Novogene (Tianjin, China) on the Illumina NovaSeq platform, generating 150 bp paired-end reads.
Raw reads in fastq format were processed using fastp (v0.20.0). Adapter sequences were removed, and reads were filtered by removing those containing more than 5 'N' bases, those with >40% of bases having quality scores <15, and those shorter than 15 bp after trimming. Clean reads were retained for downstream analysis. Q20, Q30, and GC content were also calculated during this step.
The reference genome and annotation files were downloaded from the official genome website. Clean reads were aligned to the reference genome using BWA (v0.7.12). Low-quality alignments were filtered out by retaining only uniquely mapped reads with a mapping quality score (MAPQ) ≥ 13 for downstream analysis.
Peak calling was performed using MACS2 (v2.1.0) with the parameters: -q 0.05 -f AUTO --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all. Peaks were identified using a q-value cutoff of < 0.05.
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig,narrowPeak

source_name: umbilical vein

extract_protocol:
Nuclei were isolated from fresh or lightly fixed cells and incubated with a primary antibody specific to the target protein. After washing, cells were incubated with a secondary antibody conjugated to a pA-Tn5 transposase fusion protein. The tethered Tn5 transposase was activated by magnesium to simultaneously cleave and tag DNA at antibody-bound sites. Tagged fragments were then extracted for library preparation.
CUT&Tag libraries were constructed using the CUT&Tag_Novogene Kit following the manufacturer's protocol. Briefly, Concanavalin A (ConA) magnetic beads were used to immobilize cells or nuclei. Membrane permeability was enhanced by digitonin treatment. Target protein binding was achieved via a specific primary antibody, followed by incubation with a secondary antibody. Protein A-Tn5 transposase was then recruited to the target region in a directed manner, enabling in situ tagmentation and simultaneous addition of sequencing adapters. The tagmented DNA fragments were PCR amplified to generate sequencing-ready libraries. Post-amplification libraries were purified using AMPure XP beads (Beckman Coulter) and evaluated for quality using the Agilent Bioanalyzer 2100 system.

value: umbilical vein

value: HUVEC

value: endothelial cell

value: WT

value: low glucose(5 mM)


title: FLUT_ADI_PND30-40_541

description:
treatment:  FLUT
dose: ADI
sample ID: 541

value: Wistar

value: postnatal day (PND) 30-40


title: BL02

value: Blood


title: BL01


title: Huvec cells,WT,high glucose (25 mM),12 hours

description: Library name: HUVEC_HighGlucose

value: high glucose(25 mM)


title: CTRL_PND30-40_504

description:
treatment:  CTRL
dose: --
sample ID: 504


title: 2-cell Input Replicate A

description: Library name: 2c-INP

data_processing:
Additional runs concatenated to first FastQ file. For samples with a 3rd run, these runs processed seperately.
Samples sequenced for revision were clipped to 51 bp length to preserve comparability to rest of the samples using Trim Galore --hardtrim5 51 parameter.
FastQ files trimmed using Trim Galore.
Trimmed FastQ files mapped to mm10 using bowtie1 with -m 1 parameter.
BAM files sorted using SAMtools and converted to BED format using BEDtools.
BED files from 3rd run merged to the BED files contaning 1st and 2nd runs before downstream analysis in EaSeq (http://easeq.net). Gzip compressed WIG files generated using EaSeq. Scores represent fragments per kilobasepairs per million reads.
Assembly: mm10
Supplementary files format and content: wig files containing genomic location and score of deduplicated mapped reads

source_name: 2-cell embryo

growth_protocol: Postnatal day 7 (P7), P10, and P12 CD-1 females were used for collection of growing oocyte (GO) sample pools. C57BL/6NRj females aged 4 weeks were used for collecting NSN, SN and MII oocytes. To induce superovulation for collection of these three stages, the mice received an intraperitoneal injection with 5 international units (IU) of pregnant mare serum gonadotropin (PMSG; Prospec, HOR-272) at 2pm. For NSN and SN stages, the oocytes were collected ~45 hours after the PMSG injection. For collection of MII stage oocytes, an intraperitoneal injection with 5 IU of human chorionic gonadotropin (hCG; Sigma, C1063) was given 45-48 hours following PMSG injection. Subsequently, MII oocytes were collected 66-67 hours after the PMSG injection. Mouse E14 ES cells were obtained from a stock at passage P2 equal to those used for the mouse ENCODE project and cultured following the corresponding instructions (https://www.encodeproject.org/biosamples/ENCBS171HGC/). Prior to collection, cells were passaged once on gelatinized, feeder-free plates.  Zygote, 2-Cell and 4-Cell embryos: To perform in vitro fertilization, sperm from C57BL/6NRj male mouse was collected directly from the cauda epididymis of a recently euthanized male and incubated in a 35 mm dish containing 90 µl of FERITUP preincubation media (Cosmo-Bio; KYD-002-EX) In parallel, a fertilization dish (30 mm) was prepared by placing a 90 µl droplet of human tubal fluid (HTF) medium supplemented with 2 mM reduced glutathione (Sigma; G4251), and covering it with NidOil. The HTF medium (100ml) was prepared in-house (593.8 mg NaCl (Sigma; S-5886), 35 mg KCl (Sigma; P-5405), 4.9 mg MgSO₄·7H₂O (Sigma; M-7774), 5.4 mg KH₂PO₄ (Sigma; P-5655), 57 mg CaCl₂ (Sigma; C-5670), 210 mg NaHCO₃ (Sigma; S-5761), 0.34 ml sodium lactate (Sigma; L-7900), 3.7 mg sodium pyruvate (Sigma; P-4562), 50 mg glucose (Sigma; G-6152), 49.55 mg Methyl-b-cyclodextrin (Sigma; C-4555), 0.5 ml penicillin/streptomycin (Gibco; 15140-122), 400 mg BSA (Sigma; A-7030), 0.04 ml phenol red (Sigma; P-0290), dissolved in Milli-Q water to a final volume of 100 ml). The fertilization dish was equilibrated at 37 °C in a 5% CO₂ incubator. Female C57BL/6NRj mice were superovulated via intraperitoneal injection of pregnant mare serum gonadotropin (PMSG; Prospec; HOR-272), followed 48 hours later by human chorionic gonadotropin (hCG; Sigma; CG5). The dosage of each hormone (5  IU) was administered to mice aged 4 weeks. Fifteen hours after hCG administration, the mice were euthanized, and their oviducts were dissected and placed into the fertilization dish. Cumulus-oocyte complexes were retrieved from the ampulla and transferred into the fertilization droplet. Following a 30-minute pre-incubation period, between 1 and 10 µl of motile sperm was added to the fertilization droplet. The dish was then incubated for three hours at 37 °C in 5% CO₂. To remove cumulus cells and excess sperm, embryos were washed through seven sequential droplets of Advanced KSOM medium (Sigma; MR-101) placed in a 60 mm dish, which had been pre-equilibrated under the same conditions and covered with NidOil. Zygotes were collected approximately four hours post-fertilization, at which point pronuclei were clearly visible. Embryos at the two-cell stage were collected 24 hours post-fertilization, and those at the four-cell stage were retrieved after approximately 48 hours. All samples were subsequently processed for pico-ChIP sequencing.  8-cell embryos: The same procedure was followed for superovulation and copulation as described above, but with different timing for the hormone injections: PMSG at 3pm and hCG 48h later. At 68h after the hCG injection, the females were euthanized by cervical dislocation and the ovaries with oviducts and upper uterine horns were removed and transferred for processing in a petri dish with M2 medium. One by one, the ovary was removed, the infundibulum was located and slid onto a flushing needle. Embryos were isolated by flushing M2 medium through the oviduct. 8-cell embryos were collected and washed in fresh M2 medium before Tyrode’s acid treatment, further washing in M2, and cross-linking.  Morulas and blastocysts: Follicle growth was stimulated in 3.5–4 week old females (C57BL/6NRj, Janvier Labs) by an intraperitoneal (IP) injection with 5 IU PMSG at 2pm. Around 45 h later, 5 IU hCG (Chorulon, MSD Animal Health) was IP injected to induce ovulation. Directly after hCG injection, females were housed 1:1 with stud males of the same strain for copulation. The following morning at 8am, females were removed from the males' cages and euthanized by cervical dislocation. The ovaries with oviducts and upper uterine horns were removed in one piece, placed in a microtube with 1 ml of M2 medium and immediately transferred for processing. Under a stereomicroscope, zygotes surrounded by cumulus cells were isolated from the ampulla in a petri dish with M2 medium at 37°C. To remove the cumulus cells, zygotes were briefly put in hyaluronidase solution (HYASE-10X, Vitrolife) diluted 1:10 in M2 medium. The zygotes were then washed in three consecutive wells of 0.5 ml M2 medium covered with OVOIL-100 paraffin oil (Vitrolife). Normally fertilized zygotes, identified by the presence of two pronuclei, were selected and transferred to a pre-equilibrated micro-droplet culture dish (Vitrolife) containing 25 μl of G-1 PLUS culture medium (Vitrolife) per well, covered with paraffin oil, with approximately 10 zygotes per droplet. The zygotes were incubated at 37 °C with 6% CO₂. Late morulas (n = 11) and blastocysts (n = 14) were collected at developmental day 3.5, as embryos originated from natural copulation of several mice, and therefore development was not fully synchronized. The zona pellucida was removed using Tyrode’s acid treatment, and the embryos were then washed in fresh M2 medium and cross-linked as described below (picoChIP-seq > Oocyte and embryo cross-linking).

extract_protocol:
The samples were transferred to 1.5 ml tubes. SDS/RNase-free elution buffer (20 mM Tris–HCl/pH-7.5), 50 mM NaCl, 5 mM EDTA/pH-8.0) was added to 415 µl final volume, and the aqueous phase was sequentially extracted using equal volumes of phenol:chloroform:isoamylalcohol (Invitrogen, 15593-031) and chloroform:isoamylalcohol (Sigma-Aldrich, C0549). The 400 µl of the last aqueous phase were precipitated with 1 ml ice-cold ethanol, 11 µl linear acrylamide (Thermo Fisher Scientific, AM9520) and 44 µl 1 M sodium acetate (Invitrogen, AM9740) at least overnight at -80°C. For reconstitution, the pellets were centrifuged (swing-out, 16,000 x g, 4°C), and recovered using 15 µl of Qiagen EB (10 mM Tris, Qiagen, 19086) overnight at 4°C.
Sequencing libraries were prepared using the Qiaseq ultralow input kit (Qiagen, 180492 + 180310) with modifications to minimize material loses. These included prolonged incubations during the AMPure XP bead extractions (>15 min bead/sample incubation, >15 min DNA elution) (Beckman coulter, A63881), and an increased volume of beads (1.2 volume equivalents) during the second bead extraction. Double-stranded DNA concentration was determined using the Qubit HS DNA kit (ThermoFisher Scientific, Q32851), while DNA fragment size analyses were performed with TapeStation D1000 HS (Agilent, 5067-5585). Libraries were then and pooled in equimolar amounts. Sequential AMPure XP extractions (1.2 volume equivalents) were employed to drastically reduce adapter dimers from the pool prior to sequencing.

value: 2-cell embryo


title: CTRL_PND30-40_503

description:
treatment:  CTRL
dose: --
sample ID: 503


title: NRF_ZT8_WT_rep1

value: Mouse liver


title: NRF_ZT4_GRLKO_rep3

value: GRfl/fl x Alb-Cre


title: Zygote Input Replicate A

description: Library name: zyg-INP

source_name: Zygote

value: Zygote


title: V20-003_EOT

city: Duarte

first: Edward

middle: C.

last: Dominguez

state: CA

address: 1500 E. Duarte Rd.

department: Toni Stephenson Lymphoma Ctr

institute: City of Hope

data_processing:
Partek Flow was utilized for data analysis. Trimming of adapters and bases for Fastq files was performed with ParteK software. Mapping to the reference index hg38 was performed with STAR.  Counts were then normalized to 1.0e4 CPM. Gene set enrichment analysis (GSEA) (Subramanian, Tamayo, et al. (2005), PNAS 102, 15545-15550, http://www.broad.mit.edu/gsea/) was performed using Hallmark pathways.
Assembly: quantified to hg38 - Ensembl Transcripts release 102
Supplementary files format and content: Excel file with normalized counts

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll gradient and resuspended in ACK lysing buffer (Life Technologies) for red blood cell lysis. Total RNA was extracted using Homogenizer Mini Columns and the E.Z.N.A Total RNA Kit I (Omega Bio-Tek).
Pre-made libraries partial lane sequencing (PE150)

tag: diagnosis

value: DLBCL

value: Voruciclib

value: Post-Treatment

tag: outcome

value: Progressive Disease

value: PBMC


title: V20-003_C1D8


title: P10 Input Replicate D

description: Library name: p10-INP-D

source_name: P10 oocyte

value: P10 oocyte


title: NRF_ZT4_GRLKO_rep2

value: Night Restricted Feeding (NR)