title: D13Q_LAE_DEL_48

description: 10x Genomics

value: Airway epithelium

value: Delta, 48 hours post infection


title: leaf, CUT&Tag, rep2

status: Public on Jan 09 2025

type: SRA

city: Nanjing

first: Zexue

last: He

state: Jiangsu Province

address: Xuanwu District,1 Weigang

department: Agricultural College

country: China

institute: Nanjing Agricultural University

library_source: genomic

data_processing:
For data analyses, raw ZIP-seq data were cleaned by using Fastp (version 0.21.0)  to remove adapter sequences. All clean reads from two biological replicates were aligned to the MSU v7.0 reference genome for Oryza sativa (http://rice.plantbiology.msu.edu/) by utilizing the Burrows-Wheeler Aligner (BWA, version 0.7.17) with default settings of its mem algorithm. Any PCR duplicates were completely removed by using the Picard tool. The reads with a mapping quality score lower than 10 were filtered out by using SAMtools. Spearman rank correlation coefficient was calculated by using the multiBamSummary and plotCorrelation functions from the deepTools suite , which indicates the reproducibility and consistency between biologically replicated data.
Assembly: MSU v7.0
Supplementary files format and content: bw, (except for Input sample)
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Oryza sativa Japonica Group

source_name: leaf

growth_protocol: Pregerminated rice seeds of Nipponbare (Oryza sativa L., Japonica) were transferred into the soil and grew in a greenhouse at 28-30℃ with a 14h/10h light-dark cycle. Two-week old seedlings were harvested and quickly frozen in liquid nitrogen for storage at -80℃ until used.

extract_protocol:
5 μg purified genomic DNA was fragmented into size ranging from 100-500 bp. Fragmented DNA was denatured in Z-DNA reconstitution buffer (20 mM sodium citrate buffer, pH 7.2, 4M NaCl, 25% ethylene glycol, 250 µm Mn2+ and 0.7 M Mg2+) at 95℃ for 8 min, then slowly cooled down to room temperature for Z-DNA re-association.
For Z-DNA CUT&TAG, the detailed procedures were exactly followed according to the manual of the CUT&TAG kit (Cat#: TD904-01, Vazyme) produced by Vazyme.
ZIP-seq,CUT&TAG

tag: tissue

value: leaf

tag: group

value: ZDNA-CUT&Tag


title: leaf, 4acC-seq, ChIP-seq

data_processing:
For data analyses, raw ZIP-seq data were cleaned by using Fastp (version 0.21.0)  to remove adapter sequences. All clean reads from two biological replicates were aligned to the MSU v7.0 reference genome for Oryza sativa (http://rice.plantbiology.msu.edu/) by utilizing the Burrows-Wheeler Aligner (BWA, version 0.7.17) with default settings of its mem algorithm. Any PCR duplicates were completely removed by using the Picard tool. The reads with a mapping quality score lower than 10 were filtered out by using SAMtools. Spearman rank correlation coefficient was calculated by using the multiBamSummary and plotCorrelation functions from the deepTools suite , which indicates the reproducibility and consistency between biologically replicated data.
Assembly: MSU v7.0
Supplementary files format and content: bw, (except for Input sample)
Library strategy: 4acC-seq


title: 11_IFNgamma_treated_cell_R3

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

description: single-end, two lanes

library_source: transcriptomic

data_processing:
The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled, and sequenced on the Illumina HiSeq3000 system employing a single-end 101 cycles run at average read depths of 20 million reads/sample.
Sequencing data was demultiplexed using Illumina bcl2fastq version 2.20.0.422 BCL to FastQ file converter. The quality of raw reads was assessed with FastQC version 0.11.8.
Assembly: Reads were mapped to the GRCh38 human genome assembly
Supplementary files format and content: Tab delimited text file containing EnsemblID,Entrez,GeneSymbol and sample ID's in columns and for each gene with raw counts in rows

molecule: total RNA

organism: Homo sapiens

source_name: HaCaT

growth_protocol: HaCaT cells (Addex Biological) were grown in DMEM with 1 g/L -glucose and L-glutamine (Thermo Fisher Scientific) with 10% fetal bovine serum (FBS) at 5% CO2 without antibiotics. HaCaT cells were validated by short tandem repeat analysis at the Emory Integrated Genomics Core

extract_protocol:
RNeasy Mini kit (Qiagen, CA) with DNase digest and QIAcube automation stations. The RNA was quantified, and the quality was assessed by Bioanalyzer analysis (Agilent Technologies, Santa Clara, CA).
Clontech Smart-Seq V4 Ultra Low Input RNA kit (Takara Bio, Shiga, Japan) in combination with the Illumina NexteraXT kit (Illumina, San Diego, CA, USA), as per manufacturer’s instructions, with 10 ng of total RNA as input.

treatment_protocol: Human IFN-γ (Peprotech, NJ) and EGF (Promega, WI) were resuspended in DMEM (200 mg/mL and 2000 ng/ml respectively) and stored at -80°C.  For the treatment of cells, IFN-γ (1 ng/ml), EGF (1000 ng/ml), both, or neither was added to cells and cellular lysates were prepared 24 hours later (Qiagen, CA).

tag: cell line

value: HaCaT

tag: cell type

value: Keratinocyte

tag: treatment

value: IFNG


title: 11_male PDMCAO aged #2

city: Houston,

first: Gab Seok

last: Kim

state: TX

address: 6431 Fannin St.

department: Department of Neurology

institute: The University of Texas Health Science Center at Houston

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
processed by Cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

organism: Mus musculus

source_name: Brain

growth_protocol: male and female in young and aged mice

extract_protocol:
brains slice, Miltenyi Adult Brain Dissociation Kitt
10X Genomics

treatment_protocol: sham surgeried or PDCMAO (14 PSD)

value: Brain

value: aged

tag: genotype

value: male

value: PDMCAO


title: D02R_LAE_D614G

city: St Louis

first: Rita

last: Meganck

state: Missouri

address: 660 S Euclid Ave

institute: Washington University in St Louis

description: 10x Genomics

data_processing:
cellranger v6.1.2
SoupX
scDblFinder
Seurat v4
Minimal gene count>400, Percent mitochondrial genes<20%
Assembly: GRCh38, GENCODE v39
Supplementary files format and content: R data serialization (RDS) file, containing gene x cell (barcode) data matrices, dimension reduction embeddings, and cell meta-data.

source_name: Airway epithelium

growth_protocol: LAE/SAE cells were seeded onto the Transwell cell culture inserts. After confluency on the Transwell, the apical medium was removed and the cells were cultured on ALI condition with UNC-ALI medium at least for 4 weeks.

extract_protocol:
The cell dissociation procedure followed the manufacturer’s protocols for the 10x Genomics Chromium system with modifications. A 5 mM EDTA in Accutase solution (Sigma) was administered to both apical and basolateral HBE surfaces and cultures incubated for 20 min at 37 ˚C. The cells detached from the Transwell membrane were centrifuged (300g x 2 min at 4 C) and washed twice with 10% fetal bovine serum (FBS, Sigma) in Dulbecco's Modified Eagle Medium (DMEM, Sigma). The cells were then resuspended in DMEM with 10% FBS with gentle pipetting using wide-bore pipette tips and passed through a 40 µm cell strainer (Fisher Science #22363547) to remove clumps. Cell counting and viability were determined using an automated cell counter (Countess 3FL, Thermo).
Single-cell suspensions targeting approximately 10,000 cells were loaded onto a 10x Genomics Chromium Next GEM Chip G (10x Genomics) device following the manufacturer’s instructions. After GEM generation, the library preparation was performed following the instructions for the 10x Chromium Next GEM Single Cell 3’ GEM Library kit v3.1 (10x Genomics).

treatment_protocol: Infection with SARS-CoV-2 (MOI: 0.05) for 48 or 96 hours

value: Large airway epithelial

value: Primary air-liquid interface culture

tag: donor

value: D614G, 96 hours post infection


title: leaf, CUT&Tag, rep1


title: 10_female PDMCAO young #2

description: 10X Genomics

value: young

value: female


title: 10_EGF_treated_cells_R3

description: single-end, two lanes

value: EGF


title: D52Q_SAE_614_48

description: 10x Genomics

value: Airway epithelium

value: Small airway epithelial

value: D614G, 48 hours post infection


title: D18I_D3_Mock

description: 10x Genomics

value: Mock infection


title: leaf, ZIP-seq, igG

data_processing:
For data analyses, raw ZIP-seq data were cleaned by using Fastp (version 0.21.0)  to remove adapter sequences. All clean reads from two biological replicates were aligned to the MSU v7.0 reference genome for Oryza sativa (http://rice.plantbiology.msu.edu/) by utilizing the Burrows-Wheeler Aligner (BWA, version 0.7.17) with default settings of its mem algorithm. Any PCR duplicates were completely removed by using the Picard tool. The reads with a mapping quality score lower than 10 were filtered out by using SAMtools. Spearman rank correlation coefficient was calculated by using the multiBamSummary and plotCorrelation functions from the deepTools suite , which indicates the reproducibility and consistency between biologically replicated data.
Assembly: MSU v7.0
Supplementary files format and content: bw, (except for Input sample)
Library strategy: ZIP-seq

value: leaf

value: ZDNA-igG


title: D13Q_LAE_614_48

description: 10x Genomics


title: 9_male PDMCAO young #2

description: 10X Genomics


title: leaf, ZIP-seq, input

value: ZDNA-Input


title: iAT1_ replicate2

city: New York

first: Hans-Willem

last: Snoeck

state: NY

address: 650 west 168th street

institute: Columbia University Irving Medical Centre

description:
illumina V4 chemistry
HM008B

data_processing:
Samples were aligned to GRChProcessed reads were mapped against the human genome (GRCh38.p14) using Gencode v44. The number of reads per gene was counted using Salmon v.1.10.12 providing the count matrix. Differential gene expression was analyzed using DESeq2 v.1.30.1
Assembly: GRCh38 reference genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hESC-derived lung organoid

extract_protocol:
Total RNA was extracted  from iRAP,iAT1, D-IRAPs and submitted for sequencing.
Libraries were prepared and sequenced at the JP Sulzberger Columbia Genome Center High-Throughput Screening Center at Columbia University. Sequencing libraries were prepared using Illumina V4 chemistry workflow

value: hESC-derived lung organoid

value: Rockefeller University Embryonic Stem Cell Line 2 (RUES2)


title: iAT1_ replicate1

description:
illumina V4 chemistry
HM007B


title: 7_male PDMCAO aged #1

description: 10X Genomics

value: Brain

value: aged

value: male


title: 7_IFNgamma_treated_cell_R2

description: single-end, two lanes

value: HaCaT

value: Keratinocyte

value: IFNG


title: leaf, ZIP-seq, rep2

value: ZDNA-IP


title: 6_EGF_treated_cells_R2

description: single-end, two lanes

value: EGF


title: 6_female PDMCAO young #1

description: 10X Genomics

value: young

value: female

value: PDMCAO


title: 5_untreated_cells_R2

description: single-end, two lanes

value: Control


title: transitional AT2-like cells_replicate 1

description:
illumina V4 chemistry
HM005B


title: iRAP_replicate2

description:
illumina V4 chemistry
HM002B


title: 5_male PDMCAO young #1

description: 10X Genomics


title: 8_female PDMCAO aged #1

description: 10X Genomics


title: spleen_aCMP_scRNAseq

city: Minato-ku

first: Takaharu

last: Kimura

state: Tokyo

address: 4-6-1 Shirokanedai

country: Japan

institute: The University of Tokyo

description: Library name: Spleen_RNA

data_processing:
Sequencing data were mapped to the reference genome using CellRanger. Subsequent analysis was conducted using the Seurat and Signac R packages.
Assembly: mm10
Supplementary files format and content: CellRanger outputs files

molecule: nuclear RNA

source_name: Hematopoietic cells

growth_protocol: Fresh CMPs were directly collected from BM, exCMPs were collected from HSCs cultured for 7days and SPaCMPs were collected from the spleen 9 days after HSC transplantation.

extract_protocol:
Fresh CMPs, exCMPs, and SPaCMPs were sorted via fluorescence-activated cell sorting (FACS) using an Aria III cell sorter (BD) equipped with a 100 µm nozzle and appropriate filters and settings. Subsequently, nuclei were isolated according to the protocol of the Chromium Nuclei Isolation Kit.
Libraries were prepared using the Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics) and sequenced on an Illumina NovaSeq X platform.

treatment_protocol: For exCMPs collection, murine HSCs were cultured in Ham’s F12 medium (Wako), enriched with 10 mM HEPES (Thermo Fisher Scientific), recombinant cytokines murine TPO (100 ng/mL, Peprotech), and SCF (10 ng/mL, Peprotech), polyvinyl alcohol (PVA, 84% hydrolyzed, Sigma), as well as insulin-transferrin-selenium (ITS, Thermo Fisher Scientific, 1:100 dilution) and 1% Penicillin-Streptomycin-L-Glutamine (PSG, Wako).

value: Hematopoietic cells

value: CMP

value: Spleen aCMP

value: WT

value: Spleen after SCT

tag: library type

value: mRNA

tag: batch


title: 4_EGF_IFNgamma_treated_cells_R1

description: single-end, two lanes

value: EGF plus IFNG


title: 4_female sham aged #1

description: 10X Genomics

value: Brain

value: aged

value: sham


title: iRAP_replicate1

description:
illumina V4 chemistry
HM001B

value: hESC-derived lung organoid

value: Rockefeller University Embryonic Stem Cell Line 2 (RUES2)


title: 3_male sham aged #1

description: 10X Genomics

value: male


title: fresh_CMP_scATACseq

description: Library name: Fresh_ATAC

value: Fresh CMP

value: Fresh BM

value: ATAC


title: 3_IFNgamma_treated_cell_R1

description: single-end, two lanes

value: HaCaT

value: Keratinocyte

value: IFNG


title: fresh_CMP_scRNAseq

description: Library name: Fresh_RNA

value: Hematopoietic cells

value: CMP


title: 2_female sham young #1

description: 10X Genomics

value: Young

value: female


title: 9_untreated_cells_R3

description: single-end, two lanes

value: Control


title: VisiumHD_Spatial_Transcriptomics_ASS-ILD_bilateral_lung_transplantation

city: Beijing

first: Qingya

last: Shi

address: 30 Shuangqing Road, Haidian District

department: Tsinghua Medicine

institute: Tsinghua University

description: Library name: LTx

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to produce FASTQ files.
The sequences were mapped to the GRCh38 reference (Human Probe Set v2) for gene expression counting using Space Ranger's default parameters.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: cytassist_image.tiff: images captured by Visium CytAssist
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowers_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.parquet: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: lung tissue

extract_protocol:
The spatial transcriptomic sample was acquired at 39 weeks post-transplant via TBLB, and the pathological control specimen came from one of the five ASS-ILD patients without LTx via TBLC.
The Visium HD Spatial Gene Expression platform (Visium HD, 10X Genomics), capable of achieving single-cell scale spatial resolution, was utilized in this study. In accordance with the Visium HD FFPE Tissue Preparation Handbook (CG000684, 10X Genomics), tissue sections of 10 μm were prepared from FFPE blocks, ensuring high RNA quality (DV200 ≥ 30%). After H&E staining, probes were hybridized, ligated, eluted, and subsequently used for library construction based on the Visium HD Spatial Gene Expression Reagent Kits User Guide (CG000685). The resulting libraries were sequenced on the Illumina NovaSeq X platform using a paired-end approach.

value: lung tissue


title: expanded_CMP_scATACseq

description: Library name: Expandes_ATAC

value: Expanded CMP

value: WT

value: Ex vivo expansion


title: 8_EGF_IFNgamma_treated_cells_R2

description: single-end, two lanes

value: EGF plus IFNG


title: VisiumHD_Spatial_Transcriptomics_ASS-ILD_untreated

description: Library name: Non-LTx


title: transitional AT2-like cells_replicate 2

description:
illumina V4 chemistry
HM006B

value: hESC-derived lung organoid

value: Rockefeller University Embryonic Stem Cell Line 2 (RUES2)


title: leaf, ZIP-seq, rep1

value: leaf

value: ZDNA-IP


title: 1_untreated_cells_R1

description: single-end, two lanes

value: HaCaT


title: spleen_aCMP_scATACseq

description: Library name: Spleen_ATAC

value: Spleen aCMP

value: Spleen after SCT

value: ATAC


title: 1_male sham young #1

description: 10X Genomics

value: Brain

value: male

value: sham


title: expanded_CMP_scRNAseq

description: Library name: Expanded_RNA

value: Hematopoietic cells

value: CMP

value: mRNA


title: PBMCs, Figure_2E

status: Public on Jan 08 2025

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
Hybridized Probe-based RNA capture on 10x Barcoded Beads. Multiplexed pool with samples: BL05731_2e, PB04745_2e.
BL05731_FACS.csv
BL05731_FACS_sample_filtered_feature_bc_matrix.h5

data_processing:
10x Cell Ranger Pipeline
Scrublet Doublet Detection
Assembly: GRCh38
Supplementary files format and content: H5 cell by gene matrix, csv with doublet information, fcs files represent data for the flow cytometry results shown in our figure 2

source_name: Blood

extract_protocol:
Chromium Fixed RNA Profiling for Multiplexed Samples (CG000527)
PBMC enriched samples were processed according to the 10x Genomics protocol for Fixation of Cells and Nuclei (CG000478, Rev C). Probe hybridization was completed according to the 10x Genomics protocol for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673,  Rev A).
10x Genomics protocol for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673, Rev A).
Chromium Fixed RNA Profiling for Multiplexed Samples (CG000527)

value: Blood


title: 2_EGF_treated_cells_R1

description: single-end, two lanes

value: Keratinocyte

value: EGF


title: SAMPLE 72  28742_MUN_orange_M_skelmusc

type: RNA

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

department: Internal Medicine

institute: Wake Forest School of Medicine

hyb_protocol: Hybridization was performed at 58°C in GEX-HCB buffer (Illumina) at a concentration of 100 ng cRNA/μl, unsealed in a humidified chamber for 2 h.

scan_protocol: After washing and blocking, array signals were developed by a 10-min incubation in a 1 μg/ml Cy3-streptavidin and 1% blocking solution. Microarray scanning was performed in an iScan array scanner.

data_processing:
Data were uploaded to Genome Studio and quality filtered. Quality filtered data were uploaded to Partek Genomics Suite for normalization and statistical analyses.
Please note that the data was filtered based on quality scores >0.95 for at least 8 of 12 samples for one tissue and one diet. This ensured that tissue-specific and diet-specific quality transcripts were included, and allowed the comparison of the same set of transcripts among all tissues and diets.

label: biotin

organism: Papio hamadryas

source_name: skeletal muscle, MUN offspring, HFCS diet, male

label_protocol: Ambion Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA was extracted with Trizol reagent.

value: skeletal muscle

value: maternal under-nutrition

tag: diet

value: HFCS

tag: gender


title: SAMPLE 63  28497_CON_orange_F_skelmusc

source_name: skeletal muscle, CON offspring, HFCS diet, female

value: control

value: female


title: SAMPLE 68  28473_CON_orange_M_skelmusc

source_name: skeletal muscle, CON offspring, HFCS diet, male


title: SAMPLE 69  28476_CON_orange_M_skelmusc


title: SAMPLE 67  28428_CON_orange_M_skelmusc


title: SAMPLE 71  28609_MUN_orange_M_skelmusc


title: SAMPLE 65  28387_MUN_orange_F_skelmusc

source_name: skeletal muscle, MUN offspring, HFCS diet, female


title: SAMPLE 66  28392_MUN_orange_F_skelmusc


title: SAMPLE 64  28369_MUN_orange_F_skelmusc


title: SAMPLE 70  28389_MUN_orange_M_skelmusc


title: SAMPLE 60  28742_MUN_chow_M_skelmusc

source_name: skeletal muscle, MUN offspring, chow diet, male

value: chow


title: SAMPLE 59  28609_MUN_chow_M_skelmusc


title: SAMPLE 54  28392_MUN_chow_F_skelmusc

source_name: skeletal muscle, MUN offspring, chow diet, female


title: SAMPLE 56  28473_CON_chow_M_skelmusc

source_name: skeletal muscle, CON offspring, chow diet, male


title: SAMPLE 55  28428_CON_chow_M_skelmusc


title: SAMPLE 57  28476_CON_chow_M_skelmusc


title: SAMPLE 58  28389_MUN_chow_M_skelmusc


title: SAMPLE 61  27827_CON_orange_F_skelmusc


title: SAMPLE 53  28387_MUN_chow_F_skelmusc


title: B-PLL patient number 14

type: genomic

city: Barcelona

first: Jose Ignacio

last: Martin-Subero

state: Barcelona

address: c/Rosselló, 149-153

country: Spain

institute: IDIBAPS

hyb_protocol: According to manufacturer instructions

scan_protocol: According to manufacturer instructions

data_processing:
CpGs with a pvalue ≤0.01 in more than 10% of the samples were removed
SNP associated CpGs were removed
Sex associated CpGs were removed
Individual-specific CpGs were removed
The data was normalized using the SWAN algorithm after the filtering steps
The beta values range from 0 to 1, where 0 represents unmethylated and 1 methylated CpGs.

label: not provided

source_name: Peripheral Blood

label_protocol: According to manufacturer instructions

extract_protocol: According to manufacturer instructions

value: Peripheral Blood

tag: subject status

value: B-PLL patient

value: Peripheral Blood Mononuclear Cells


title: SAMPLE 52  28369_MUN_chow_F_skelmusc


title: SAMPLE 62  28385_CON_orange_F_skelmusc


title: B-PLL patient number 32


title: B-PLL patient number 29


title: B-PLL patient number 27


title: B-PLL patient number 35


title: B-PLL patient number 5


title: SAMPLE 42  28392_MUN_orange_F_fat

source_name: fat, MUN offspring, HFCS diet, female

value: adipose


title: SAMPLE 47  28609_MUN_orange_M_fat

source_name: fat, MUN offspring, HFCS diet, male

value: male


title: B-PLL patient number 13


title: B-PLL patient number 37


title: SAMPLE 51  28497_CON_chow_F_skelmusc

source_name: skeletal muscle, CON offspring, chow diet, female


title: B-PLL patient number 38


title: B-PLL patient number 9


title: B-PLL patient number 24


title: SAMPLE 41  28387_MUN_orange_F_fat


title: SAMPLE 49  27827_CON_chow_F_skelmusc


title: SAMPLE 48  28742_MUN_orange_M_fat


title: SAMPLE 50  28385_CON_chow_F_skelmusc


title: SAMPLE 46  28389_MUN_orange_M_fat


title: B-PLL patient number 36


title: SAMPLE 43  28428_CON_orange_M_fat

source_name: fat, CON offspring, HFCS diet, male


title: SAMPLE 40  28369_MUN_orange_F_fat


title: B-PLL patient number 6


title: B-PLL patient number 33


title: B-PLL patient number 10


title: B-PLL patient number 18


title: SAMPLE 39  28497_CON_orange_F_fat

source_name: fat, CON offspring, HFCS diet, female


title: SAMPLE 37  27827_CON_orange_F_fat


title: SAMPLE 34  28389_MUN_chow_M_fat

source_name: fat, MUN offspring, chow diet, male


title: SAMPLE 30  28392_MUN_chow_F_fat

source_name: fat, MUN offspring, chow diet, female


title: SAMPLE 31  28428_CON_chow_M_fat

source_name: fat, CON offspring, chow diet, male


title: SAMPLE 36  28742_MUN_chow_M_fat


title: SAMPLE 27  28497_CON_chow_F_fat

source_name: fat, CON offspring, chow diet, female


title: SAMPLE 38  28385_CON_orange_F_fat


title: SAMPLE 28  28369_MUN_chow_F_fat


title: B-PLL patient number 22


title: SAMPLE 45  28476_CON_orange_M_fat


title: SAMPLE 44  28473_CON_orange_M_fat


title: SAMPLE 33  28476_CON_chow_M_fat


title: SAMPLE 32  28473_CON_chow_M_fat


title: B-PLL patient number 1


title: B-PLL patient number 4


title: SAMPLE 35  28609_MUN_chow_M_fat


title: B-PLL patient number 30


title: SAMPLE 26  28385_CON_chow_F_fat


title: SAMPLE 25  27827_CON_chow_F_fat


title: SAMPLE 29  28387_MUN_chow_F_fat


title: SAMPLE 24  228742_MUN_orange_M_liv

source_name: liver, MUN offspring, HFCS diet, male

value: liver


title: SAMPLE 14  228385_CON_orange_F_liv

source_name: liver, CON offspring, HFCS diet, female


title: SAMPLE 17  228387_MUN_orange_F_liv

source_name: liver, MUN offspring, HFCS diet, female


title: SAMPLE 13  227827_CON_orange_F_liv


title: SAMPLE 10  228389_MUN_chow_M_liv

source_name: liver, MUN offspring, chow diet, male


title: SAMPLE 11  228609_MUN_chow_M_liv


title: SAMPLE 19  228428_CON_orange_M_liv

source_name: liver, CON offspring, HFCS diet, male


title: SAMPLE 16  228369_MUN_orange_F_liv


title: SAMPLE 15  228497_CON_orange_F_liv


title: SAMPLE 22  228389_MUN_orange_M_liv


title: SAMPLE 21  228476_CON_orange_M_liv


title: 843, lung, -Streptozocin, +MA-SARS-CoV-2

city: Philadelphia

first: Sara

last: Kass-Gergi

state: PA

address: 3900 Spruce St

department: Medicine

institute: University of Pennsylvania

data_processing:
Raw data (raw reads) in fastq.gz format were processed through a general pipeline as describe previously (13). Reads were aligned to the mm10 mouse genome using Kallisto and imported into R Studio for analysis via the TxImport package. Data was then normalized using the trimmed mean of M values normalization method in the EdgeR package
Assembly: mm10
Supplementary files format and content: FPKM matrix

source_name: lung

extract_protocol:
Lung tissue was placed in TRIzol® reagent (ThermoFisher, PN 15596018) RNA was extracted using Direct-zol RNA Miniprep Plus kit from Zymo.
cDNA synthesis, sequencing library generation, and sequencing was performed on an Illumina HiSeq platform by GENEWIZ Co. Ltd.

value: lung

value: WT

value: -Streptozocin, +MA-SARS-CoV-2


title: SAMPLE 20  228473_CON_orange_M_liv


title: SAMPLE 12  228742_MUN_chow_M_liv


title: SAMPLE 8  228473_CON_chow_M_liv

source_name: liver, CON offspring, chow diet, male


title: SAMPLE 9  228476_CON_chow_M_liv


title: SAMPLE 7  228428_CON_chow_M_liv


title: 841, lung, -Streptozocin, +MA-SARS-CoV-2


title: SAMPLE 23  228609_MUN_orange_M_liv


title: 840, lung, -Streptozocin, -MA-SARS-CoV-2

value: -Streptozocin, -MA-SARS-CoV-2


title: SAMPLE 4  228369_MUN_chow_F_liv

source_name: liver, MUN offspring, chow diet, female


title: SAMPLE 1  227827_CON_chow_F_liv

source_name: liver, CON offspring, chow diet, female


title: SAMPLE 6  228392_MUN_chow_F_liv


title: SAMPLE 2  228385_CON_chow_F_liv


title: SAMPLE 5  228387_MUN_chow_F_liv


title: SAMPLE 3  228497_CON_chow_F_liv


title: 838, lung, -Streptozocin, -MA-SARS-CoV-2


title: 831, lung, +Streptozocin, -MA-SARS-CoV-2

value: +Streptozocin, -MA-SARS-CoV-2


title: 842, lung, -Streptozocin, +MA-SARS-CoV-2


title: 829, lung, +Streptozocin, +MA-SARS-CoV-2

value: +Streptozocin, +MA-SARS-CoV-2


title: SAMPLE 18  228392_MUN_orange_F_liv

value: maternal under-nutrition


title: Ctrl, -Met, -IAA, rep4

city: University Park

first: James

last: Lee

address: 406 South Frear Building

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

data_processing:
Paired-end reads of 50 bp were processed with fastp (version 0.23.2) to remove low quality reads. Processed reads were aligned to S. cerevisiae genome (sacCer3) with BWA (version 0.7.17). Aligned bam files were deduplicated with Picard MarkDuplicates (version 3.0.0). bigwig files were generated by deeptools bamCoverage (version 3.5.1) for visualization purposes. To detect differentially methylated NDRs, aligned reads on each NDR were counted by Subread featureCounts (version 2.0.3) using a list of NDR coordinates generated from a previous study, with the following parameters “-p -O”. Fold change and P-value were generated by DEseq2 (1.38.0) without outliers filtering. log2 (Fold Change) > 0.7 and the adjusted P-value < 0.05 were used as the cutoff for identifying differentially methylated regions.
Assembly: sacCer3
Supplementary files format and content: table generated by DEseq2
Supplementary files format and content: bigwig

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown in 50 mL synthetic media with/without methionine at 30°C to OD660 = 0.3.

extract_protocol:
Standard MeDIP protocol for preparation of methylated genomic DNA
MeDIP-Seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L). Next generation sequencing was performed on NextSeq 2000 (Illumina).

treatment_protocol: β-estradiol (Sigma, 50-28-2) was added to a final concentration of 2 nM allowing the LacI-NLS-M.CviPI fusion protein to express.

tag: strain

tag: chip antibody

tag: condition

value: 2nM β-estradiol, without met, without IAA

value: MATa, leu2-3,112, his3-11, trp1-1, ura3-1, can1-100, ade2-1,ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2MET4::MET4-AID-Hygromycin


title: Ctrl, -Met, -IAA, rep1


title: MET6_VP, -Met, -IAA, rep3

value: MATa, leu2-3,112, his3-11, trp1-1, ura3-1, can1-100, ade2-1,ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, SHC1 (MET6)::256XLacO::HIS3, MET4::MET4-AID-Hygromycin


title: MET6_VP, -Met, -IAA, rep4


title: 832, lung, +Streptozocin, -MA-SARS-CoV-2


title: 830, lung, +Streptozocin, +MA-SARS-CoV-2


title: Ctrl, -Met, -IAA, rep2


title: 827, lung, +Streptozocin, +MA-SARS-CoV-2


title: MET6_VP, -Met, -IAA, rep2


title: MET6_VP, -Met, -IAA, rep1


title: MET6_VP, -Met, +IAA, rep4

value: 2nM β-estradiol, without met, 500 μM IAA


title: Ctrl, -Met, +IAA, rep1


title: Ctrl, -Met, +IAA, rep4


title: Ctrl, -Met, +IAA, rep3


title: Ctrl, -Met, -IAA, rep3


title: MET6_VP, -Met, +IAA, rep3


title: Ctrl, -Met, +IAA, rep2


title: MET6_VP, -Met, +IAA, rep2


title: Ctrl, +Met, -IAA, rep4

value: 2nM β-estradiol, 10X met, without IAA


title: MET6_VP, -Met, +IAA, rep1


title: Ctrl, +Met, -IAA, rep2


title: Ctrl, +Met, -IAA, rep3


title: Ctrl, +Met, -IAA, rep1


title: MET6_VP, +Met, -IAA, rep4


title: MET6_VP, +Met, -IAA, rep3


title: MET6_VP, +Met, -IAA, rep2


title: Ctrl, +Met, +IAA, rep4

value: 2nM β-estradiol, 10X met, 500 μM IAA


title: Ctrl, +Met, +IAA, rep3


title: Ctrl, +Met, +IAA, rep2


title: MET6_VP, +Met, +IAA, rep3


title: MET6_VP, +Met, +IAA, rep4


title: Ctrl, -Met, rep2

value: 2nM β-estradiol, without met

value: MATa, leu2-3,112, his3-11, trp1-1, ura3-1, can1-100, ade2-1,ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2


title: MET6_VP, +Met, -IAA, rep1


title: Ctrl, -Met, rep1


title: MET6_VP, +Met, +IAA, rep1


title: Ctrl, +Met, rep2

value: 2nM β-estradiol, 10X met


title: MET13_VP, -Met, rep2

value: MATa, leu2-3,112, his3-11, trp1-1, ura3-1, can1-100, ade2-1,ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, MET13::256XLacO::HIS3


title: Ctrl, +Met, rep1


title: MET13_VP, -Met, rep1


title: MET13_VP, +Met, rep2


title: Ctrl, +Met, +IAA, rep1


title: MET6_VP, +Met, +IAA, rep2


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D45 rep1

city: San Francisco

first: Benoit

middle: G.

last: Bruneau

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

description:
Library name: Atrial_D45_rep1
aCM_d45.1

data_processing:
The .fastq files were analyzed using nf-core Nextflow RNA-seq pipeline aligning to hg38 reference genome and using STAR for alignment and Salmon quantification.
Assembly: hg38
Supplementary files format and content: .tsv format of gene counts and tpm values

growth_protocol: Cells were grown in 1 well of a 6- or 12-well dish per replicate.

extract_protocol:
Cells were dissociated in 0.25% Trypsin-EDTA for 10 mins, followed by quenching in 15%FBS in DPBS. Cells were lifted off the dish and resuspended to single cells by repeatedly using P1000 pipette and then transferred to a 1.5 ml tube and centrifuged at 300 x g for 5 min at room temperature. Pellets were snap frozen in dry ice. Total RNA was isolated using Qiagen RNeasy micro kit (Qiagen #74004) with QIAshredder (Qiagen #79656) and eluted in 25 µl water. RNA concentration was determined using Nanodrop and quality was checked using Agilent Bioanalyzer.
RNA-seq libraries were generated using Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit were prepared as per manufacturer’s instructions using 400 ng of input RNA. Library concentration was quantified using Qubit Fluorometer and dsDNA HS Assay Kit and quality assessed on Agilent Bioanalyzer.

value: cardiomyocyte

value: atrial cardiomyocyte differentation


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D20 rep3

description:
Library name: Atrial_D20_rep3
aCM_d20.3

value: WT


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D20 rep2

description:
Library name: Atrial_D20_rep2
aCM_d20.2


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D45 rep2

description:
Library name: Atrial_D45_rep2
aCM_d45.2


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D45 rep3

description:
Library name: Atrial_D45_rep3
aCM_d45.3


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D20 rep1

description:
Library name: Atrial_D20_rep1
aCM_d20.1


title: MET13_VP, +Met, rep1


title: splenic cDC2-1

city: Shimotuga

first: Yasushi

last: Sawanobori

state: Tochigi

address: Kitakobayashi 880, Mibu

institute: Dokkyo medical university

description: Gene expression data from rat splenic classic cDC2

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The microarray was outsourced to Kurabo (Osaka, Japan) and performed using the Clariom™ S Assay, rat (Thermo Fisher Scientific). At least 250 ng of RNA was delivered for outsourcing. RNA integrity numbers were at least 7.9. The data were initially analyzed with the Transcriptome Analysis Console (TAC) v4.0.3 ((Thermo Fisher Scientific).

label: CD172a-FITC, CD161-PE, OX6-AF647, CD45R-APC-eF780, CD103-biotin, streptavidin-PE-Cy7, CD45-Pacific Blue

organism: Rattus norvegicus

source_name: Lewis rat splenic PI-CD45+MHCII+CD103+CD172a+ cells

label_protocol: not provided

extract_protocol:
For splenic DC analysis and isolation, cells from digested spleens were resuspended in 15% OptiPrep (Axis-Shield, Oslo, Norway) in PBS(-) and placed in centrifuge tubes. Layers of 11.5% OptiPrep/PBS(-) and PBS(-) were overlaid on the cell suspension. The tubes were centrifuged at 600 g for 25 minutes at room temperature with gentle acceleration and braking. Cells between the 15% and 11.5% OptiPrep layers were collected as DC-containing low-density cells and washed with PBS(-).  For thymic DC analysis and isolation, cells from digested thymi were resuspended at 5 × 10⁸ cells/ml in PBS, and anti-rat MHCII antibody (BioLegend, San Diego, CA, USA) was added at a concentration of 0.5 µg/ml. Cells were incubated at 4°C for 30 minutes and washed with 0.5% BSA and 2 mM EDTA/PBS(-) (MACS buffer). Cells were then resuspended at 20 × 10⁸ cells/ml in MACS buffer, and 20% anti-mouse IgG microbeads (Miltenyi Biotech, North Rhine-Westphalia, Germany) were added. The cells were incubated at 4°C for 15 minutes, washed twice with MACS buffer, filtered through 50 m nylon mesh pieces, and resuspended at 1.5 × 10⁸ cells/ml in MACS buffer. The cells were isolated using the Possel program of autoMACS (Miltenyi Biotech). To increase yield, the negative fraction was subjected to the Possel program again. Later, this isolation method was substituted with a single run of the Posseld2 program.  For thymic and splenic macrophage isolation, cells from digested thymi or spleens were resuspended at 5 × 10⁸ cells/ml in PBS. Mouse gamma globulin (Jackson ImmunoResearch, West Grove, PA, USA) was added at 20 µg/ml to block nonspecific binding, and the cells were incubated at 4°C for 10 minutes. Biotinylated anti-CD11b/c antibody was added at 0.25 µg/ml, and the cells were incubated at 4°C for 10 minutes, followed by washing with MACS buffer. Cells were then resuspended at 1 × 109 cells/ml in MACS buffer, and 10% streptavidin microbeads (Miltenyi Biotech) were added. After incubation at 4°C for 15 minutes, the cells were washed twice with MACS buffer, filtered with 50 m nylon mesh pieces, and resuspended at 1.5 × 10⁸ cells/ml in MACS buffer. The cells were isolated using the Posselds program of autoMACS.
Sorted cells from 8- to 11-week-old Lewis rats were dissolved into ISOGEN (NIPPON GENE, Tokyo, Japan), and RNA was extracted following the manufacturer’s protocol. To ensure DNA removal, the RNA samples were treated with RNase-free DNase I (Takara Bio, Shiga, Japan) following the manufacturer’s protocol. RNA was precipitated with Ethachinmate (NIPPON GENE) and dissolved in sterilized water. All cell types were analyzed using two samples each. Some samples were pooled from multiple animals to ensure sufficient RNA yields.
The prepared cells were stained following the standard flow cytometry protocol to isolate DC subsets and macrophages. The stained cells were sorted using FACSAria™ III cell sorter (BD, Franklin Lakes, NJ, USA) and collected in HBSS supplemented with 1.25 mM Ca2+, 1.45% BSA, and 2% FCS.

value: spleen


title: splenic cDC2-2


title: thymic macrophage-2

description: Gene expression data from rat thymic HIS36+ macrphages

label: HIS36-PE, OX6-AF647, CD45R-APC-eF780, CD45-Pacific Blue

source_name: Lewis rat thymic PI-CD45+CD45R-HIS36+ cells

value: thymus


title: splenic cDC1-2

description: Gene expression data from rat splenic cDC1

source_name: Lewis rat splenic PI-CD45+MHCII+CD103+CD172a- cells


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D11 rep3

description:
Library name: Atrial_D11_rep3
aCM_d11.3


title: splenic macrophage-2

description: Gene expression data from rat splenic HIS36+ macrphages

source_name: Lewis rat splenic PI-CD45+CD45R-HIS36+ cells


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D11 rep2

description:
Library name: Atrial_D11_rep2
aCM_d11.2


title: splenic CD103- DC-like-1

description: Gene expression data from rat splenic CD103- dendritic cells

source_name: Lewis rat splenicc PI-CD45+MHCII+CD103-CD45R-CD172a+ cells


title: thymic CD103- DC-like-2

description: Gene expression data from rat thymic CD103- dendritic cells

label: CD172a-FITC, OX6-AF647, CD45R-APC-eF780, CD103-biotin, streptavidin-PE-Cy7, CD45-Pacific Blue

source_name: Lewis rat thymic PI-CD45+MHCII+CD103-CD45R-CD172a+ cells


title: splenic cDC1-1


title: thymic cDC1-2

description: Gene expression data from rat thymic cDC1

source_name: Lewis rat thymic PI-CD45+MHCII+CD103+CD172a- cells


title: thymic cDC2-2

description: Gene expression data from rat thymic classic cDC2

source_name: Lewis rat thymic PI-CD45+MHCII+CD103+CD172a+ cells


title: splenic CD103- DC-like-2

source_name: Lewis rat splenic PI-CD45+MHCII+CD103-CD45R-CD172a+ cells


title: thymic cDC2-1


title: thymic cDC1-1


title: splenic macrophage-1


title: thymic macrophage-1


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D6 rep3

description:
Library name: Atrial_D6_rep3
aCM_d6.3

value: cardiac precursor


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D6 rep2

description:
Library name: Atrial_D6_rep2
aCM_d6.2


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D11 rep1

description:
Library name: Atrial_D11_rep1
aCM_d11.1


title: thymic CD103- DC-like-1


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D4 rep3

description:
Library name: Atrial_D4_rep3
aCM_d4.3

value: cardiac mesoderm


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D2 rep3

description:
Library name: Atrial_D2_rep3
aCM_d2.3


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D4 rep2

description:
Library name: Atrial_D4_rep2
aCM_d4.2


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D6 rep1

description:
Library name: Atrial_D6_rep1
aCM_d6.1


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D2 rep2

description:
Library name: Atrial_D2_rep2
aCM_d2.2


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D2 rep1

description:
Library name: Atrial_D2_rep1
aCM_d2.1


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with TBX5in/del rep1

description: Library name: TBX5_null_rep1

data_processing:
Hi-C 3.0 data were processed using 4D Nucleome (4DN) Hi-C data Processing Pipeline (v0.2.7) (https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline), which generated .mcool file with iterative correction and eigenvector decomposition (ICE) normalization.
Reads were mapped to GRCh38 using bwa.
Valid HiC alignments were filtered using pairtools.
Biological replicates were merged using https://github.com/4dn-dcic/docker-4dn-hic/blob/master/scripts/run-merge-pairs.s
The pairs files were converted to cool files using cooler.
Assembly: hg38
Supplementary files format and content: .mcool file of interaction contact frequencies at different resolutions

growth_protocol: WTc11 iPSCs and WTc11 iPSCs with genome-edited mutations for TBX5 (TBX5in/+ and TBX5in/del) were previously generated and characterized in both ventricular (Kathiriya 2021) and atrial cardiomyocyte (CM) differentiations (Kathiriya biorxiv). WTc11 iPSCs used for atrial and ventricular time course Hi-C 3.0 experiments were grown on hESC-qualified Matrigel (Corning #354277). Human iPSCs for all other experiments were grown on growth factor-reduced basement membrane Matrigel (Corning #356231) in mTeSR-1 (StemCell Technologies #85850) or mTeSR+ medium (StemCell Technologies #100-0276). iPSCs were routinely passaged using ReLesR (StemCell Technologies #100-0483). For CM differentiations, iPSCs were dissociated using Accutase (StemCell Technologies #07920) and seeded into 6-well or 12-well plates. Cells were grown for three day until 70-90% confluency and induced using Stemdiff Cardiomyocyte Ventricular (StemCell Technologies #05010) or Atrial (StemCell Technologies #100-0215) kits, according to manufacturer’s instructions.

extract_protocol:
CMs were grown in 3 wells of a 6-well dish per replicate, with all 3 wells pooled together after dissociation for the crosslinking step (approximately 10 million cells). CMs were dissociated in 0.25% Trypsin-EDTA for 10 mins, followed by quenching in 15%FBS in DPBS. CMs were lifted off the dish and resuspended to single cells by repeatedly using P1000 pipette and then transferred to a 15 ml tube and centrifuged at 800 rpm for 5 min at room temperature. Pellets were washed once in 5 ml HBSS before resuspending entire cell pellet in exactly 10 ml HBSS. 16% methanol-free formaldehyde was added to a final concentration of 1% and samples incubated on nutator at room temperature for 10 min. Samples were quenched with 2.5 M glycine to a final concentration of 0.125 M and incubated on nutator at room temperature for 5 min, then 15 min at 4˚C and followed by centrifugation at 1000 x g for 5 min at room temperature. Samples were washed once in DPBS. Pellets were resuspended in 1 ml of 3 mM DSG in PBS, transferred to 1.5 ml tubes and incubated on nutator for 40 min. Samples were quenched with 2.5 M glycine to a final concentration of 0.125 M and incubated on nutator at room temperature for 5 min. Samples were centrifuged at 2000 x g for 5 min at RT. Cell pellets were resuspended in 5 mg/ml BSA in DPBS, to prevent cells sticking to tube after DSG crosslinking, and centrifuged at 2000 x g for 5 min at 4˚C. Supernatant was carefully removed and cell pellets were snap frozen in liquid nitrogen and stored at -80˚C.
Samples were processed for Hi-C using Arima-HiC+ kit (Arima Genomics). >1 µg per sample was used as determined by Arima’s Estimating Input Amount Protocol using Qubit Fluorometer and dsDNA HS Assay Kit (ThermoFisher Scientific #Q32854) Samples were processed by following manufacturer’s user guide for mammalian cell lines with one exception: DNA was digested using 50 U DpnII (New England Biolabs #R0543M) and 50 U DdeI (New England Biolabs #R0175L) restriction enzymes in 1x NEB Buffer 3.1 for 60 min at 37˚C. All samples passed Arima-QC1 Quality Control. Sequencing libraries were prepared by following Arima’s user guide for Library Prep Using KAPA Hyper Prep Kit (Roche #7962347001). Between 1.5-4 µg of DNA was fragmented in 130 µl microtube (Covaris #520045) using a Covaris S2 sonicator for 55s at 10% duty cycle, intensity 4, 200 cycles per burst in a water bath maintained at 4˚C. An average fragment size of 400 bp was verified using Agilent 2100 Bioanalyzer. Between 400-1000 ng of size-selected DNA was used for biotin enrichment, end repair, dA-tailing and adapter ligation. The number of PCR cycles was determined following Arima-QC2 Quality Control using KAPA Library Quantification Kit (Roche KK4824) and libraries were amplified to at least 10 nM. All samples passed Arima-QC2 Quality Control. DNA cleanup steps were done using Ampure XP beads (Beckman Coulter #A63881). Final libraries were quantified using Qubit Fluorometer and dsDNA HS Assay Kit and assessed on Agilent BioAnalyzer. Pooled, equimolar libraries were sequenced using NovaSeq technology (Illumina).


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with  TBX5in/+ rep2

description: Library name: TBX5_Het_rep2


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with  TBX5in/+ rep1

description: Library name: TBX5_Het_rep1


title: Hi-C of Homo sapiens: ventricular  cardiomyocyte differentiation from WTC11 at D11 rep2

description: Library name: Ventricular_D11_rep2


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WT WTC11 rep1

description: Library name: TBX5_WT_rep1


title: Hi-C of Homo sapiens: WTC11 rep2

description: Library name: D0_rep2

value: iPSC


title: Hi-C of Homo sapiens: ventricular  cardiomyocyte differentiation from WTC11 at D23 rep2

description: Library name: Ventricular_D23_rep2


title: Hi-C of Homo sapiens: ventricular  cardiomyocyte differentiation from WTC11 at D6 rep2

description: Library name: Ventricular_D6_rep2


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with TBX5in/del rep2

description: Library name: TBX5_null_rep2


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D45 rep4

description: Library name: Atrial_D45_rep4

data_processing:
Fastq files were aligned to the hg38 reference genome using bowtie2. Reads were filtered to include of those with a mapq score of 30 or greater and removing duplicate reads using SAMtools. Blacklisted regions were removed using BEDtools. Chip-seq peaks were called on each individual replicate relative to input using macs2 and the narrowpeaks parameter. CTCF ChIP bigwig files for visualization were generated using deepTools2 bamCoverage.
Assembly: hg38
Supplementary files format and content: .narrowPeak of peaks and .bw of signal profiles

growth_protocol: Cells were grown in one 6-well plate per replicate, with all 6 wells pooled together after dissociation for the crosslinking step (approximately 20 million cells). Each plate was one biological replicate. To generate TBX5-bio cell line, a codon-optimized BioTAP (Alekseyenko 2014) tag was inserted immediately after the start methionine codon in the N-terminus of the endogenous TBX5 locus using ribonucleoprotein (RNP) complexes of sgRNA (GCCCTCGTCTGCGTCGGCCA, ordered from Synthego) and SpCas9-NLS ‘HiFi’ protein (QB3 MacroLab, University of California Berkeley). This tag can be biotinylated by endogenous biotin ligases. The BioTAP tag was codon optimized for integration using HDR Alt-R gene blocks donor template (IDT). RNPs were prepared by mixing 1 µl of 40 µM Cas9 with 1.2 µl of 100 µM sgRNA and made to a total volume of 10 µl with Lonza P3 transfection buffer (Lonza #197179) and incubated at room temperature for 10 min. 250000 WTc11 iPSCs were resuspended in 12.2 µl Lonza P3 transfection buffer and nucleofected with 1 µg codon-optimized BioTAP donor template and 10 µl RNPs using Lonza Nucleofector 4D system in 96-well format using DS-138 settings. After nucleofection, mTeSR1 supplemented with CloneR (StemCell Technologies #05888) was added to cells and incubated for 10 min at 37˚C, before transferring cells into a single well of a matrigel-coated 48-well plate. The following day, media was replaced with fresh mTeSR1. The cells were expanded into a 12-well plate. Single cells were dissociated with Accutase and were sorted into 96-well plates for colony selection using Namocell Hana single-cell dispenser. Plates were cultured in mTeSR1 supplemented with CloneR for 3 days post sorting to ensure survival and then replaced with mTeSR1. Colonies were screened by PCR using primers pairs flanking the whole insertion site (F: 5’-TCCTCAGAGCAGAACCTTGC, R: 5’-CTTACCTGCTGGGTGAAGG), 5’ integration site (F: 5’-AAACTGCTCCCTCCTGTCAC, R: 5’-ATTTTCATGGCCTCAAGCAC) and 3’ integration site (F: 5’-CCGATGGTAAGGTCGAGAAG, R: 5’-CGAGGTCTCCTTACCTGCTG). Amplicon from whole insertion site PCR was amplified and verified by Sanger sequencing. Copy number variation was determined by droplet digital PCR (Bio-Rad QX200 Droplet Reader) and using the RPP30 assay (Bio-Rad #10031243) and comparing to custom primers (F: 5’-GCGTTTATCTCCGTCTCCATTT and R: 5’- GGACTGTCAGTAAGATCCTTGTT) and probe (5’- CAAGCACCGTTTGCCCTGCTTTAA) for the knock-in TBX5-biotin allele. The cells were determined to have a normal karyotype.

extract_protocol:
Cells were dissociated in 0.25% Trypsin-EDTA for 10 mins, followed by quenching in 15%FBS in DPBS. Cells were lifted off the dish and resuspended to single cells by repeatedly using P1000 pipette and then transferred to a 15 ml tube and centrifuged at 800 rpm for 5 min at room temperature. Pellets were washed once in 10 ml DPBS plus 1x protease inhibitors (DBPS+PI) before resuspending entire cell pellet in exactly 10 ml DPBS+PI. 16% methanol-free formaldehyde (ThermoFisher Scientific #28908) was added to a final concentration of 1% and samples incubated on nutator at room temperature for 10 min. Samples were quenched with 2.5 M glycine to a final concentration of 0.125 M and incubated on nutator at room temperature for 5 min, followed by centrifugation at 500 x g for 5 min at 4˚C. Samples were washed once in ice cold DPBS+PI, before being transferred to 2 ml protein lo-bind rubes, centrifuged at 2500 x g at 4˚C. for 5 min and cell pellets were snap frozen in liquid nitrogen and stored at -80˚C.  TBX5-bio cross-linked cells were thawed on ice and resuspended in 1 ml of ice cold cell lysis buffer (25 mM Tris-HCl, pH 7.4, 85 mM KCl, 0.25% Triton X-100 and 1x Protease inhibitors in ddH2O) and incubated at 4˚C rotating for 30 minutes. Sample were centrifuged at 2500 x g for 5 min at 4˚C and resuspended in 1 ml nuclear lysis buffer (0.5% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, and 1x protease inhibitors in ddH2O). Samples were transferred to 1 ml millitube (Covaris #520130) and sheared using a Covaris S2 sonicator for 15 min at 5% duty cycle, intensity 5, 200 cycles per burst in a water bath maintained at 4˚C. After shearing, 5 µl of each sample was kept for reverse crosslinking and the remaining sonicated sample was transferred to a new protein lo-bind tube and snap frozen in liquid nitrogen. The 5 µl sample was made up to 100 µl and incubated for 30 min at 37˚C with 1 µl RNase A, followed addition of 12 µl 5 M NaCl and reverse crosslinking with 1 µl proteinase K at 65˚C overnight. The following day the reverse crosslinked samples were purified using Qiagen MinElute PCR Purification kit (Qiagen #28006) and DNA quantified using Qubit Fluorometer and dsDNA HS Assay Kit (ThermoFisher Scientific #Q32854). Samples were run on an Agilent 2100 Bioanalyzer to verify that chromatin was sheared to fragments between 100-500bp in size. Based on these measurements, the amount of DNA in each lysed sample could be extrapolated and equal amounts of sheared chromatin could be used per ChIP. Sheared samples were thawed quickly at 37˚C and the equivalent of 55 µg of chromatin was transferred to a 5 ml protein lo-bind tube for ChIP and made up to 1 ml in nuclear lysis buffer. 50 µl (5%) of each sample was collected as input and stored at 4˚C until reverse crosslinking step. ChIP samples were then diluted 1:5 with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100, 167 mM NaCl and 1x protease inhibitors in ddH2O). 50 µl of pre-washed Dynabeads MyOne Streptavidin T1 beads (ThermoFisher Scientific #65601) were added to each sample and incubated overnight with rotation at 4˚C. The following day, beads were collected using a magnetic stand and transferred to 2 ml protein lo-bind tubes and washed with 1 ml twice of the following wash buffers: wash buffer 1 (2% SDS in ddH2O), wash buffer 2 (0.1% sodium deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 500 mM NaCl in ddH2O), wash buffer 3 (250 mM LiCl, 0.5% IGEPAL CA-630 [Sigma #I8896], 0.5% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl pH 8.0 in ddH2O) and TE buffer (10 mM Tris-HCl pH 7.5 and 1 mM EDTA ddH2O).  After adding each wash buffer, beads were vortexed for 15 s, spun briefly and collected against a magnet. DNA was eluted with 150 µl elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0 in ddH2O) shaking at 1000 rpm at 65˚C overnight. The following day, beads were collected on a magnetic stand and supernatant was transferred to a new DNA lo-bind tube. Both ChIP and input samples were incubated at 37˚C for 30 min at 37˚C with 1.5 µl RNase A, followed addition of 18 µl 5 M NaCl and reverse crosslinking with 1.5 µl proteinase K at 65˚C for 6 hours. DNA was purified using Qiagen MinElute PCR Purification kit (Qiagen #28006). CTCF ChIP-seq was performed generally as above with changes detailed here. The following buffers were used: cell lysis buffer recipe (20 mM Tris-HCl pH 8.0, 85 mM KCl, 0.5% IGEPAL CA-630 and 1x protease inhibitors in ddH2O), nuclear lysis buffer recipe (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, and 1x protease inhibitors in ddH2O), wash buffer 1 recipe (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS and 1% Triton X-100 in ddH2O), wash buffer 2 recipe (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS and 1% Triton X-100 in ddH2O) and wash buffer 3 (250 mM LiCl, 1% IGEPAL CA-630 [Sigma #I8896], 1% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl pH 8.0 in ddH2O) and elution buffer (1% SDS, 100 mM NaHCO3 in ddH2O). 70 µg of chromatin was used per sample. After diluting in dilution buffer, each ChIP sample was incubated rotating at 4˚C overnight with 6 µg antibody (combination of both Active Motif #61311 [discontinued] and Abcam #ab128873 used in each sample) and the following day incubated with 50 µl prewashed Magna ChIP protein A/G beads (Sigma #16-663) for 4 hours at 4˚C. Bead washes were performed by resuspending beads in 1 ml buffer using P1000 pipette, spinning briefly and collecting on magnet. Following the bead washes, DNA was eluted in 50 µl shaking at 37˚C, transferring to new tube and repeating bead elution to pool eluates to a total volume of 100 µl. Both ChIP and input samples were incubated at 37˚C for 30 min at 37˚C with 1 µl RNase A, followed by addition of 12 µl 5 M NaCl and reverse crosslinking with 1 µl proteinase K at 65˚C overnight. DNA was purified using ChIP DNA Clean and Concentrator kit (Zymo Research #D5205).
For Illumina sequencing library preparation, the entire ChIP sample or 2 µl of each input was used. End repair was performed in a 100 µl reaction with 15 U T4 DNA polymerase (New England Biolabs #M0203L), 5 U Klenow fragment DNA polymerase (New England Biolabs, #M0210L), 50 U T4 PNK (New England Biolabs #M0201L), 400 µM dNTP (Promega #U1511) and 1x T4 DNA ligase buffer w 10 mM ATP (New England Biolabs #B0202S) in nuclease-free water for 30 min at room temperature, followed by 1.6x bead:sample AmpureXP purification. Entire eluate was used for A-tailing in a 50 µl reaction with 1 mM dATP (New England Biolabs #N0440S), 15 U Klenow 3’>5’ exonuclease (New England Biolabs #M0212L) and 1x NEB buffer 2 in nuclease-free water for 30 min at 37˚C, followed by 1.6x bead:sample AMPureXP purification. Entire eluate was used for adapter ligation in a 50 µl reaction with 6000 U T4 DNA ligase (New England Biolabs #M0202L), 20 nM annealed and uniquely indexed adapters and 1x T4 DNA ligase buffer with 10 mM ATP (New England Biolabs #B0202S) in nuclease-free water for 2 hours at room temperature, followed by 1x bead:sample AMPureXP purification. Adapters were prepared by annealing following HPLC purified oligos: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T and 5’Phos-GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG where * represents a phosphothiorate bond and NNNNNN is a Truseq index sequence.The entire eluate was used for PCR amplification in a 50 µl reaction with 1x NEB Next High-Fidelity 2x PCR master mix (New England Biolabs #M0541L), 10 µM primers (F: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA, R: 5’-CAAGCAGAAGACGGCATACGAGAT) in nuclease free water, using thermocycler settings 98˚C for 30 sec; 16 cycles of 98˚C for 10 sec, 58˚C for 40 sec and 72˚C for 30 sec; 72˚C for 5 min and followed by 0.8x bead:sample AMPureXP purification. DNA was quantified using Qubit Fluorometer and dsDNA HS Assay Kit and quality assessed on Agilent Bioanalyzer.


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WT WTC11 rep2

description: Library name: TBX5_WT_rep2


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D45 rep2

description: Library name: Atrial_D45_rep2


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D20 rep4

description: Library name: Atrial_D20_rep4


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D20 rep1

description: Library name: Atrial_D20_rep1


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D45 rep3

description: Library name: Atrial_D45_rep3


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D20 rep2

description: Library name: Atrial_D20_rep2


title: RNA-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D4 rep1

description:
Library name: Atrial_D4_rep1
aCM_d4.1


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D11 rep1

description: Library name: Atrial_D11_rep1


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D11 rep2

description: Library name: Atrial_D11_rep2


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D20 rep5

description: Library name: Atrial_D20_rep5


title: PBMCs, Figure_1_ADT

description: Antibody-derived oligonucleotide (ADT)

library_source: other

data_processing:
Supplementary files format and content: Cell by ADT matrix
10x Cell Ranger Pipeline
Scrublet Doublet Detection
Assembly: GRCh38
Supplementary files format and content: H5 cell by gene matrix, csv with doublet information, fcs files represent data for the flow cytometry results shown in our figure 2
Library strategy: ADT

molecule: protein

source_name: Blood

extract_protocol:
10x Genomics protocol for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673, Rev A).
PBMC enriched samples were processed according to the 10x Genomics protocol for Fixation of Cells and Nuclei (CG000478, Rev C). Probe hybridization was completed according to the 10x Genomics protocol for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673,  Rev A).
10x Genomics protocol for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673, Rev A).
Chromium Fixed RNA Profiling for Multiplexed Samples (CG000527)

value: Blood

value: ADT


title: Marathon; 1:1; 9-143-31

city: Chicago

first: Chang

last: Ye

state: Illinois

institute: University of Chicago

description:
9-143-31
CAM-seq on HEK293T polyA enriched RNA

data_processing:
Sequencing adapters were trimmed from the 3′ ends of read 1 and read 2 using the Cutadapt tool. Low-quality and short reads were filtered out by applying ‘-q 20 –max-n 0 -m 20’ arguments. 10nt of a random sequence in the 5’ end of read 1were extracted as a unique molecular barcode for each sequence. Processed reads were mapped to human  genomes (GRCh38) accordingly using hisat2-3n tool.
Assembly: GRCh38
Supplementary files format and content: TSV
Library strategy: CAM-seq

molecule: polyA RNA

growth_protocol: HEK293T cells were obtained from the American Type Culture Collection (ATCC). Cells were maintained in DMEM medium at 37 °C with 5.0% CO2 in a Heracell VIOS 160i incubator (Thermo Scientific).

extract_protocol:
Cellular or plant total RNA was extracted from cells or plant tissue using TRIzol reagent (Ambion by Life Technologies) and Direct-zol RNA miniprep kit (Zymo Research) following the manufacturer’s protocol. After RNA extraction, two rounds of Poly(A) enrichment were conducted using DynaBeads mRNA Direct Purification kit (Thermo Fisher Scientific) following the manufacturer’s protocol with some modifications.
Following the CAM-seq treatment, RNA samples were purified and sequencing libraries were prepared using the cDNA ligation method. Briefly, the RNA was end-repaired and ligated with a 3' adapter, then reverse transcribed into cDNA under various enzymatic and RT conditions. Subsequently, the cDNA was ligated with a cDNA adapter. The sequencing libraries were then amplified using a dual-index primer for Illumina sequencing.


title: PBMCs, Figure_1_RNA

description: Hybridized Probe-based RNA capture on 10x Barcoded Beads Mulitplexed pool with samples: BL05111, BL05113, BL05402, PB05111, PB05113, PB05402

data_processing:
10x Cell Ranger Pipeline
Scrublet Doublet Detection
Assembly: GRCh38
Supplementary files format and content: H5 cell by gene matrix, csv with doublet information, fcs files represent data for the flow cytometry results shown in our figure 2, fcs files represent data for the flow cytometry results shown in our figure 2

value: mRNA


title: HIV; 1:400; 9-143-30

description:
9-143-30
CAM-seq on HEK293T polyA enriched RNA


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D45 rep1

description: Library name: Atrial_D45_rep1


title: PBMCs, Figure_5

description: Hybridized Probe-based RNA capture on 10x Barcoded Beads. Mulitplexed pool with samples: BL05012_5, BL05111_5, BL05731_5, PB02183_5


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D20 rep6

description: Library name: Atrial_D20_rep6


title: Marathon; 1:40; 9-143-32

description:
9-143-32
CAM-seq on HEK293T polyA enriched RNA


title: Bst2.0; 1:400; 9-143-24

description:
9-143-24
CAM-seq on HEK293T polyA enriched RNA


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D20 rep3

description: Library name: Atrial_D20_rep3


title: HIV; 1:40; 9-143-29

description:
9-143-29
CAM-seq on HEK293T polyA enriched RNA


title: Bst2.0; 1:1; 9-143-22

description:
9-143-22
CAM-seq on HEK293T polyA enriched RNA


title: MMLv; 1:40; 9-143-26

description:
9-143-26
CAM-seq on HEK293T polyA enriched RNA


title: MMLv; 1:400; 9-143-27

description:
9-143-27
CAM-seq on HEK293T polyA enriched RNA


title: HIV; 1:1; 9-143-28

description:
9-143-28
CAM-seq on HEK293T polyA enriched RNA


title: WarmStart; 1:400; 9-143-21

description:
9-143-21
CAM-seq on HEK293T polyA enriched RNA


title: WarmStart; 1:40; 9-143-20

description:
9-143-20
CAM-seq on HEK293T polyA enriched RNA


title: MMLv; 1:1; 9-143-25

description:
9-143-25
CAM-seq on HEK293T polyA enriched RNA


title: AMW; 1:40; 9-143-17

description:
9-143-17
CAM-seq on HEK293T polyA enriched RNA


title: WarmStart; 1:1; 9-143-19

description:
9-143-19
CAM-seq on HEK293T polyA enriched RNA


title: AMW; 1:400; 9-143-18

description:
9-143-18
CAM-seq on HEK293T polyA enriched RNA


title: AMW; 1:1; 9-143-16

description:
9-143-16
CAM-seq on HEK293T polyA enriched RNA


title: RevertAid; 1:400; 9-143-15

description:
9-143-15
CAM-seq on HEK293T polyA enriched RNA


title: RevertAid; 1:40; 9-143-14

description:
9-143-14
CAM-seq on HEK293T polyA enriched RNA


title: RevertAid; 1:1; 9-143-13

description:
9-143-13
CAM-seq on HEK293T polyA enriched RNA


title: SSII; 1:400; 9-143-12

description:
9-143-12
CAM-seq on HEK293T polyA enriched RNA


title: SSII; 1:1; 9-143-10

description:
9-143-10
CAM-seq on HEK293T polyA enriched RNA


title: Marathon; 1:400; 9-143-33

description:
9-143-33
CAM-seq on HEK293T polyA enriched RNA


title: SSIV; 1:1; 9-143-7

description:
9-143-7
CAM-seq on HEK293T polyA enriched RNA


title: SSIV; 1:400; 9-143-9

description:
9-143-9
CAM-seq on HEK293T polyA enriched RNA


title: 839, lung, -Streptozocin, -MA-SARS-CoV-2

value: lung

value: -Streptozocin, -MA-SARS-CoV-2


title: SSIII; 1:1; 9-143-4

description:
9-143-4
CAM-seq on HEK293T polyA enriched RNA


title: SSIII; 1:400; 9-143-6

description:
9-143-6
CAM-seq on HEK293T polyA enriched RNA


title: SSII; 1:40; 9-143-11

description:
9-143-11
CAM-seq on HEK293T polyA enriched RNA


title: SSIII; 1:40; 9-143-5

description:
9-143-5
CAM-seq on HEK293T polyA enriched RNA


title: maxima; 1:400; 9-143-3

description:
9-143-3
CAM-seq on HEK293T polyA enriched RNA


title: PBMCs, Figure_4

description: Hybridized Probe-based RNA capture on 10x Barcoded Beads. Mulitplexed pool with samples: BL05013_4, BL05045_4, BL05113_4, BL05759_4, BL05760_4, PB02183_4


title: 31

city: Québec

first: Ricardo

middle: Perecin

last: Nociti

state: Québec

address: 2425, Rue de l'Agriculture

department: Animal Science

country: Canada

institute: Université Laval

data_processing:
Trimgalore / cutadapt
STAR
featurecounts
DESEQ2
PCIT / CETF
Assembly: ARS-UCD 1.2
Supplementary files format and content: Raw counts for each sample in .csv file
Supplementary files format and content: NDA

organism: Bos taurus

source_name: Blastocyst

extract_protocol:
The SMART-Seq®HT kit (Takara Bio, USA)
NextEra XT Stranded mRNA Sample Prep kit following manufacturer instructions

value: Blastocyst

value: unknown

value: TOP


title: maxima; 1:1; 9-143-1

description:
9-143-1
CAM-seq on HEK293T polyA enriched RNA


title: SSIV; 1:40; 9-143-8

description:
9-143-8
CAM-seq on HEK293T polyA enriched RNA


title: 29


title: maxima; 1:40; 9-143-2

description:
9-143-2
CAM-seq on HEK293T polyA enriched RNA


title: 27

value: ENC


title: 30


title: 25

value: CON


title: 26


title: Input_R61_NeuN+_Rep24

city: strasbourg

first: Charles

last: DECRAENE

address: 12 rue Goethe

department: UMR 7364 CNRS

country: France

institute: CNRS

description: Library name: Input_R61_NeuN+_Rep24

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bclconvert 3.8.4.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: Striatum

extract_protocol:
NeuN+ and NeuN- sorted nuclei preparations from R6/1 and WT mice were divided to allow immunoprecipitation of the same extract with H3K9ac (Ab4441, Abcam), H3K18ac (C15410139, Diagenode) and IgG control (C15410206, Diagenode) with 50 000 nuclei/CUT&Tag. CUT&Tag was essentially performed as described by Kaya-Okur et al. (2020). Briefly, concanavalinA-coated beads (93569S, Cell signaling) were added to nuclei suspension at room temperature under rotation to attach nuclei. Then corresponding primary antibodies were incubated overnight at 4 °C. Beads-nuclei complex were washed and incubated 1h at RT with proteinA-Transposase5 complex (C01070001, Diagenode) to a final concentration of 1:250. Tagmentation was done by incubating samples 1h in MgCl2 at 37°C, then proteins were eliminated by 1h incubation in SDS and Proteinase K at 55°C. DNA was recovered using Qiagen MinElute PCR Purification Kit.
CUT&Tag libraries were prepared from the eluted double-strand DNA using NEBNext HiFi 2x PCR master mix (BioLabs) and Illuminas compatible indexes (20091654, Illumina Nextera) (13 cycles). Amplified libraries were purified and size-selected using SPRI select beads (B23317, Beckmann Coulter) at 1.3 time, two times consecutively.

value: Striatum

value: No antibody


title: R61_H3K9ac_NeuN+_Rep4

description: Library name: R61_H3K9ac_NeuN+_Rep4

value: H3K9ac (Ab4441, Abcam)


title: WT_H3K9ac_NeuN+_Rep5

description: Library name: WT_H3K9ac_NeuN+_Rep5

value: WT


title: R61_H3K9ac_NeuN+_Rep2

description: Library name: R61_H3K9ac_NeuN+_Rep2


title: 23


title: Bst2.0; 1:40; 9-143-23

description:
9-143-23
CAM-seq on HEK293T polyA enriched RNA


title: WT_H3K9ac_NeuN+_Rep4

description: Library name: WT_H3K9ac_NeuN+_Rep4


title: BTS11_2D_5_OM2

city: Cambridge

first: Sarah

last: Inglesfield

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

data_processing:
*library strategy: post-bisulphite adaptor tagging (PBAT) bisulphite-Seq
adapter and quality trimming using Trim Galore (v0.6.2)
mapped to GRCh38 using Bismark v0.23.1
Assembly: GRCh38
Supplementary files format and content: DNA methylation values are provided for 100-CpG windows with at least 10 informative CpGs, spanning all autosomes.  Data is provided as a text file.

growth_protocol: Two cell lines of hTSCs (BTS11 and CT29) were obtained from the Arima lab upon written request (Okae et al., 2018). BTS refers to cell lines derived from a blastocyst stage embryo whilst CT originates from 1st trimester placental cytotrophoblast cells.  BTS11 and CT29 were initially cultured using the previously described protocol (Okae et al., 2018) with an updated concentration of CHIR99021 to 4µM (Sheridan et al., 2021). Samples were grown in Okae Media (OM) (Okae et al., 2018) or Trophoblast Organoid Media (TOM), detailed below, for 4 weeks. These cells were initially grown in standard 2D conditions until 80% confluent, then technical replicates of each cell line were either maintained in 2D culture conditions or moved into Matrigel for 3D culture. The conversion of 2D cultures into 3D trophoblast organoid was achieved by plating a single cell suspension onto 25µl Matrigel doplets in 48 well plates and culture followed the published protocol (Turco et al., 2018) for a total of 4 passages. During this time, cultures were overlaid with TOM media: Advanced DMEM/F12 (Thermo Fisher Scientific), N2 supplement (Thermo Fisher Scientific, 17502048, B27 supplement minus vitamin A (Thermo Fisher Scientific, 12587010; at manufacturer's recommended concentration), Primocin 100 μg/ml (InvivoGen, ant-pm), N-acetyl-L cysteine 1.25 mM (Sigma-Aldrich, A9165), L-glutamine 2 mM (Sigma-Aldrich, 25030024), recombinant human EGF 50 ng/ml (Peprotech, AF10015), CHIR99021 1.5 μM (Tocris, 4423), recombinant human R-spondin-1 80 ng/ml (R&D systems, 4645-RS-01M/CF), recombinant human FGF-2 100 ng/ml (Peprotech, 100-18B), recombinant human HGF 50 ng/ml (Peprotech, 100-39), A83-01 500 nM (Tocris, 2939), prostaglandin E2 2.5 μM (Sigma-Aldrich, P0409), and Y-27632 2 μM (Millipore, 688000).  After 4 weeks of culture, cells were dissociated at single cell suspension (Sheridan et al., 2020) and counted on a haemocytometer. Aliquots of 5000 cells were frozen in PBS at -80°C before proceeding to the bisulphite-sequencing.

extract_protocol:
Aliquots of 5000 cells suspended in PBS were thawed and then lysed in 10mM Tris buffer with 0.5% SDS and proteinase K at 37°C for 1 hour.
Bisulphite conversion was done using the EZ DNA Methylation Direct Kit (Zymo Research), as per the manufacturers protocol. First and then second strand synthesis was performed on eluted DNA using Klenow Fragment (3’->5’ exo-) enzyme (New England Biolabs) and customised 9bp random sequence containing biotin-conjugated adaptors. Using Phusion High-Fidelity DNA polymerase (New England Biolabs), libraries were amplified for 10 cycles in a 50uL reaction.

treatment_protocol: The BTS11 cell line was transduced with lentiviral particles of either pLV[Exp]-EGFP:T2A:Puro-EF1A>ORF_Stuffer (control) (VectorBuilder VB010000-9389rbj) or pLV[Exp]-EGFP:T2A:Puro-EF1A>hDNMT3L[NM_013369.3] (VectorBuilder VB900013-3690ksg) to overexpress DNMT3L. In both cases, the lentiviral particles were packaged by VectorBuilder. The BTS11 cells were transduced with the lentivirus supplemented with 8 μg/ml polybrene (Millipore, TR-1003-G) for 24 hours. After 48 hours, the cells were selected by adding 1 µg/ml puromycin to the medium for 7 days.

value: Trophoblast stem cells

value: 2D culture in okae media in 5% Oxygen


title: CT29_2D_5_OM2


title: WT_H3K9ac_NeuN+_Rep3

description: Library name: WT_H3K9ac_NeuN+_Rep3


title: BTS11_2D_5_OM1


title: R6_H3K9ac_NeuN+_Rep3

description: Library name: R6_H3K9ac_NeuN+_Rep3


title: Input_NeuN+_Rep3

description: Library name: Input_NeuN+_Rep3

value: NeuN+


title: R6_H3K27me3_NeuN+_Rep3.bw

extract_protocol:
NeuN+ sorted nuclei preparations from R6/1 and WT mice were divided to allow immunoprecipitation of the same extract with H3K27me3 (C15410195, Diagenode),   H2AK119ub (8240, cell signaling), and IgG control (C15410206, Diagenode) with 75 000 nuclei/CUT&Tag. CUT&Tag was essentially performed as described by Kaya-Okur et al. (2020). Briefly, concanavalinA-coated beads (93569S, Cell signaling) were added to nuclei suspension at room temperature under rotation to attach nuclei. Then corresponding primary antibodies were incubated overnight at 4 °C. Beads-nuclei complex were washed and incubated 1h at RT with proteinA-Transposase5 complex (C01070001, Diagenode) to a final concentration of 1:250. Tagmentation was done by incubating samples 1h in MgCl2 at 37°C, then proteins were eliminated by 1h incubation in SDS and Proteinase K at 55°C. DNA was recovered using Qiagen MinElute PCR Purification Kit.
CUT&Tag libraries were prepared from the eluted double-strand DNA using NEBNext HiFi 2x PCR master mix (BioLabs) and Illuminas compatible indexes (20091654, Illumina Nextera) (13 cycles). Amplified libraries were purified and size-selected using SPRI select beads (B23317, Beckmann Coulter) at 1.3 time, two times consecutively.

value: H3K27me3:C15410195, Diagenode


title: 28


title: 24


title: Input_NeuN+_Rep2.bw


title: R6_H3K27me3_NeuN+_Rep2.bw


title: WT_H2AK119ub_NeuN+_Rep3.bw

value: H2AK119ub (8240, cell signaling)


title: R6_H2AK119ub_NeuN+_Rep3.bw


title: Input_WT_NeuN+_Rep45

description: Library name: Input_WT_NeuN+_Rep45


title: WT_H3K27me3_NeuN+_Rep2.bw


title: Input_NeuN+_Rep1.bw


title: R6_H2AK119ub_NeuN+_Rep2.bw


title: WT_H2AK119ub_NeuN+_Rep2.bw


title: Input_NeuN+_Rep3.bw


title: R6_H3K27me3_NeuN+_Rep1.bw


title: WT_H3K27me3_NeuN+_Rep1.bw


title: R6_H2AK119ub_NeuN+_Rep1.bw


title: WT_H2AK119ub_NeuN+_Rep1.bw


title: CT29_2D_5_OM1


title: Input_R61.rep2

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq None.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: bigwig

extract_protocol:
P3013
ChIPseq was performed with striatal tissues from R6/1 and WT mice as described by Alcala-Vida et al. (2021) using antibody targeting H2AK119ub (8240, cell signaling). Briefly, pooled tissues were cut into small fragments, fixed in 1% formaldehyde and incubated for 15 min at room temperature. Cross-linking was stopped by the addition of glycine to final concentration 0.125 M. Tissue fragments were washed with cold PBS supplemented with protease inhibitors. The tissues were then mechanically homogenized in sonication buffer (50mM HEPES pH7.9, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC, 0.1% SDS, 1x PIC) and sonicated to obtain DNA fragments < 500 bp using Covaris E220Ultrasonicator (Covaris). The soluble chromatin fraction was pretreated with protein A Agarose/Salmon Sperm DNA (16-157, Sigma-Aldrich) for 45 min at 4 °C. Subsequently, samples were incubated overnight at 4 °C with corresponding primary antibodies. Protein A Agarose/Salmon Sperm DNA was then added and the mixture was incubated for 3h at 4 °C in a shaker. Agarose beads were washed, protein–DNA complexes were eluted from the beads and de-crosslinked overnight with RNAse A at 65 °C. Proteins were eliminated by 2 h incubation at 45 °C with Proteinase K, and DNA recovered using Qiagen MiniElute PCR Purification Kit.
P3013 : ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 3 to 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + 2 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.
P2959 : ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7  cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.


title: R6_H2AK119ub.rep2


title: WT_H2AK119ub.rep2


title: Input_WT.rep2


title: WT_H3K27me3_NeuN+_Rep3.bw


title: R61_H2AK119ub.rep1

extract_protocol:
P2959
ChIPseq was performed with striatal tissues from R6/1 and WT mice as described by Alcala-Vida et al. (2021) using antibody targeting H2AK119ub (8240, cell signaling). Briefly, pooled tissues were cut into small fragments, fixed in 1% formaldehyde and incubated for 15 min at room temperature. Cross-linking was stopped by the addition of glycine to final concentration 0.125 M. Tissue fragments were washed with cold PBS supplemented with protease inhibitors. The tissues were then mechanically homogenized in sonication buffer (50mM HEPES pH7.9, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC, 0.1% SDS, 1x PIC) and sonicated to obtain DNA fragments < 500 bp using Covaris E220Ultrasonicator (Covaris). The soluble chromatin fraction was pretreated with protein A Agarose/Salmon Sperm DNA (16-157, Sigma-Aldrich) for 45 min at 4 °C. Subsequently, samples were incubated overnight at 4 °C with corresponding primary antibodies. Protein A Agarose/Salmon Sperm DNA was then added and the mixture was incubated for 3h at 4 °C in a shaker. Agarose beads were washed, protein–DNA complexes were eluted from the beads and de-crosslinked overnight with RNAse A at 65 °C. Proteins were eliminated by 2 h incubation at 45 °C with Proteinase K, and DNA recovered using Qiagen MiniElute PCR Purification Kit.
P3013 : ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 3 to 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + 2 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.
P2959 : ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7  cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.


title: Input_R61.rep1


title: Input_KI_10m

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq None.
Assembly: mm10
Supplementary files format and content: Bigwig

extract_protocol:
NeuN+ and NeuN- sorted nuclei preparations from R6/1 and WT mice were divided to allow immunoprecipitation of the same extract with H3K27ac (ab4729, Abcam), H3K27me3 (C15410195, diagenode) and IgG control (C15410206, Diagenode), using 50000 nuclei/CUT&Tag. CUT&Tag was essentially performed as described by Kaya-Okur et al. (2020). Briefly, concanavalinA-coated beads (93569S, Cell signaling) were added to nuclei suspension at room temperature under rotation to attach nuclei. Then corresponding primary antibodies were incubated overnight at 4 °C. Beads-nuclei complex were washed and incubated 1h at RT with proteinA-Transposase5 complex (C01070001, Diagenode) to a final concentration of 1:250. Tagmentation was done by incubating samples 1h in MgCl2 at 37°C, then proteins were eliminated by 1h incubation in SDS and Proteinase K at 55°C. DNA was recovered using Qiagen MinElute PCR Purification Kit.
CUT&Tag libraries were prepared from the eluted double-strand DNA using NEBNext HiFi 2x PCR master mix (BioLabs) and Illuminas compatible indexes (20091654, Illumina Nextera) (13 cycles). Amplified libraries were purified and size-selected using SPRI select beads (B23317, Beckmann Coulter) at 1.3 time, two times consecutively.


title: Input_WT_10m


title: Input_KI_2m


title: WT_10m_H3K27me3_rep3


title: Input_WT_6m


title: KI_10m_H3K27me3_rep1


title: WT_10m_H3K27me3_rep2


title: KI_6m_H3K27me3_rep3


title: KI_10m_H3K27me3_rep3


title: KI_6m_H3K27me3_rep2


title: WT_6m_H3K27me3_rep2


title: KI_6m_H3K27me3_rep1


title: Control wox5-1 root Replicate 2

city: Freiburg im Breisgau

first: Thomas

last: Laux

address: Schänzlestr. 1

department: Institut für Biologie III

country: Germany

institute: Albert-Ludwigs-Universität Freiburg

description: Agilent array was hybridized with both wox5-1 (Cy5) and input control (Cy3) samples differentially labeled with Cy5 and Cy3 dye, respectively.

hyb_protocol: DNA was hybridized using SureHyb hybridization chambers according to the Agilent hybridization protocol (Agilent Mammalian ChIP-on-chip protocol, Version 10.2, 2011).

scan_protocol: Images were obtained using an Agilent microarray scanner (Model G2505C).

data_processing: Signal extraction and initial data processing were done using the Agilent's Feature Extraction Software. Additional data processing was done used Ringo software (Toedling, J. et al., 2007).

organism: Arabidopsis thaliana

source_name: Control (input) non-immunoprecipitated chromatin fragments

label_protocol: DNA was labeled using SureHyb hybridization chambers according to the Agilent labeling protocol (Agilent Mammalian ChIP-on-chip protocol, Version 10.2, 2011).

growth_protocol: Seeds were surface sterilized, placed at 4°C for 3 days, and grown on 0.5x MS media, 1% agar without sucrose. Plates were placed vertically in a growth chamber with 16 hours of light and 8 hours of darkness at 23 °C.

extract_protocol: The ChIP was performed as described before (Pi, L. et al., 2015) with minor modifications. Precipitated DNA was eluted with 3x 100 µL elution buffer (0.1 M glycine, 0.5 M NaCl, 0.05 % Tween-20, pH 2.8) and neutralized by adding 50 µL 1 M Tris (pH 9.0) for each elution step. Proteinase K (Roche) was added to a final concentration of 0.5 mg/mL to elute DNA and input DNA which were then incubated at 65 °C overnight. After that, equal amounts of proteinase K were added and incubated at 65 °C for 4 hours. DNA was precipitated by adding 2.5x volume of 100% ethanol, 10% sodium acetate (3M, pH 5.4), and 1 µL glycogen at -20 °C overnight and collected by centrifugation at 13000 g for 30 minutes at 4 °C. ChIP-DNA and input DNA were amplified using the WGA2 amplification kit (Sigma-Aldrich). Amplified DNA was purified with the PCR purification kit (Qiagen).

treatment_protocol: 5 days old seedlings of 35S:WOX5-GR and wox5-1 were treated with 10 μM DEX for 4 hrs. 5 mm root tips were harvested and cross-linked with 1% formaldehyde.

tag: ecotype

value: Root tips of 5-day old seedlings

value: Control wox5-1

source_name: Chromatin fragments precipitated with anti-WOX5 antibody


title: WT_6m_H3K27me3_rep1