title: E45_Bla_CDX2_CR_rep2

data_processing:
library strategy: CUT&RUN
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq tracks, gene expression table for RNA-seq data

source_name: E4.5 blatocyst

extract_protocol:
Cells or embyos were lysed in wash buffer.
CUT&RUN was performed as previously reported (Skene et al., 2018; Skene and Henikoff, 2017) with modifications. Briefly, after removing the zona pellucida with Tyrode’s solution (Sigma-Aldrich, T1788) or 0.5% (m/v) Protease from Streptomyces griseus (Sigma-Aldrich, P8811), early embryos were incubated with Concanavalin-coated magnetic beads (Polyscience, 86057) for 10 min at room temperature on a thermomixer at 400 rpm. Samples were then incubated with primary antibody at a ratio of 1:100 at 4℃ for 3-5 hours on a thermomixer at 400 rpm. After washing for one time, beads were incubated with pA-MNase (to a final concentration of 400-700ng/mL) (a gift from Steven Henikoff lab) at 4℃ for 1 hours on a thermomixer at 400 rpm. After two times of washing, targeted digestion was performed by adding 2μL of 100mM CaCl2 for 30 mins on ice, followed by termination by adding an equal volume of 2  × stop buffer. Samples were then incubated at 37℃ for 20 mins for fragment releasing. The total samples or supernatants were digested with Proteinase K (NEB, P8107S) and purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v) followed by ethanol purification at -80℃ overnight. The next day, DNA was purified and subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Sequencing was done using the HiSeq X Ten system or  NovaSeq (Illumina) according to the manufacturer’s protocol.

value: wild type


title: PTKD_6h_rep3

status: Public on Nov 23 2023

type: SRA

city: Turku

first: Riitta

last: Lahesmaa

address: Tykistökatu 6 A

country: Finland

institute: Turku Bioscience Centre, University of Turku

library_source: transcriptomic

data_processing:
The base calling was done using bcl2fastq
Read alignment was done using  Rsubread (v. 2.0.0)
Genewise read counts were calculated using Rsubread (v. 2.0.0)
Assembly: human genome hg38
Supplementary files format and content: genewise read counts for each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: Th17-polarized cells_PTKD_6h

extract_protocol:
RNeasy Mini Kit (Qiagen)
Illumina TruSeq® Stranded mRNA sample protocol

tag: cell type

value: Th17-polarized cells

tag: genotype


title: PTKD_6h_rep1


title: E45_Bla_TFAP2C_CR_rep2

city: Beijing

first: Lijia

last: Li

address: Haidian District

department: School of Life Science

country: China

institute: Tsinghua University

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

growth_protocol: For collection of wildtypes E4.25 blastocyst, 4–6-week-old  female mice were injected with pregnant mare serum gonadotropin followed by human chorionic gonadotropin (hCG; Ningbo Hormone Product Co., Cat # 110251283 Ltd., China 10 IU) 48 hours before being mated with malemice. E4.25 blastocyst were flushed out from the uterus  at E4.25.

tag: strain

value: mix

tag: antibody


title: FAPs_208

city: Nuthetal

first: Tim

middle: Julius

last: Schulz

address: Arthur-Scheunert-Allee 114-116

country: Germany

institute: German Institute of Human Nutrition

library_source: transcriptomic single cell

data_processing:
The trimming was done with Trimgalore, the alignment was performed with STAR and the gene counting was done with featureCounts.
Assembly: mm10
Supplementary files format and content: tab-seperated value files

source_name: skeletal muscle

extract_protocol:
Muscle samples were isolated, minced and digested using Collagenase A for 45 min at 37 °C. Dispase II was added for 30 minutes to the muscle lysates. Muscles slurries were passed 10 times through a syringe and cell strainer and centrifugated. The pellet was re-suspended in Ammonium Chloride Potassium lysis buffer to eliminate red blood cells and centrifuged again. Cells were re-suspended in sorting buffer consisting of 100 µl Hank´s balanced salt solution (HBSS) containing 0.4% FBS. Fibro-adipogenic progenitors were isolated freshly using fluorescence-activated cell sorting (FACS) using the following surface marker profile: CD45-CD11b-CD31-SCA1+. For each single cell library, 4 independent chips using a commercial microfluidics platform (IFC, Fluidigm) were used with a capacity of capturing up to 96 individual cells per loaded chip. For each chip loading, cells were pooled from three mice (i.e. 4 pools per experimental group). Individual cell quality was checked as per manufacturers’ recommendation.
Successfully captured cells and corresponding cDNA samples of individuals cells were subsequently processed by Smart-Seq2 cDNA library preparation (Clontech) using the Nextera XT Indexing kit (Illumina). Quality control was performed using an Agilent Bioanalyzer DNA High Sensitivity Kit for electropherogram tracing.

tag: tissue

value: skeletal muscle

value: Fibro-adipogenic progenitors

tag: treatment

value: young


title: FAPs_206

value: aged


title: Scr_6h_rep1

source_name: Th17-polarized cells_Scr_6h


title: E45_Bla_CDX2_CR_rep1

value: Tfap2c (Abclonal, A7739)


title: FAPs_214


title: FAPs_205


title: E45_Bla_TFAP2C_CR_rep1


title: FAPs_204


title: FAPs_203


title: HUH-7 treat

city: wenzhou

first: Jin

last: Yuepeng

state: Zhejiang Province

address: Chashan Street, Ouhai District, Wenzhou City

institute: Wenzhou Medical University First Affiliated Hospital

description: with Flavokawain C

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 GrCM38/mm10 using CLC genomic benchwork (parameter- mismath cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
CORRECTION REQUESTED
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …

molecule: total RNA

source_name: LIVER

growth_protocol: cells were incubated at 37 ℃ in 5% CO2 and maintained in DMEM medium with 10% FBS and 100 U/mL penicillin and streptomycin.

extract_protocol:
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 Libraries Prep Kit following manufacturer's protocols.

treatment_protocol: The active compound in our study is a  pyrimidine derivative named Flavokawain C. The control group was cultured in nomral medium. The treated group was challenged in 10µM Flavokawain C for 48h.

value: LIVER

tag: cell line

value: human liver cancer cells HUH-7

value: epithelial cell

value: WT

value: treated with Flavokawain C (10µm) for 48h


title: GATA4_4D1WTday0 1

city: Nedlands

first: Kathryn

middle: Olivia

last: Farley

state: WA

address: 15 Hospital Avenue

department: Precision Health

country: Australia

institute: Telethon Kids Institute

data_processing:
UMItools (Smith T, et al, 2017) was used to de-duplicate our reads prior to alignment. All reads were aligned to the human genome (build GRCh38), using a modified version of the ENCODE ‘rna-seq-pipeline’ (https://github.com/ENCODE-DCC/rna-seq-pipeline), via the Cromwell wrapper software ‘caper’ (https://github.com/ENCODE-DCC/caper). Within the pipeline, reads were aligned to GRCh38 using the STAR aligner (v2.5.1b) (Dobin A et al, 2013) and known transcripts were quantified using Kallisto (v0.44.0) (Bray NL et al, 2016). We performed basic QC analysis of mapped reads using SAMStat (Lassmann et al, 2011).
We imported estimated gene abundances into R 4.1.2 (https://www.R-project.org/) using the tximport function (Soneson C, et al, 2016) We applied the standard RNAseq analysis using edgeR, limma and voom as described in (Law CW, et al, 2018).
Assembly: GRCh38

source_name: KOLF-2 cells, day 0

growth_protocol: KOLF-2 iPSCs were grown in TeSR-E8 medium (stemcell technologies). STEMdiff Cardiomyocyte Differentiation and Maintenance Kit (STEMCELL technologies) was used for cardiomyocyte differentiation.

extract_protocol:
At day 0 and day 20 of cardiac differentiation cells were collected for RNA extraction (RNeasy Minikit, with DNase on column treatment; Qiagen).   RNA integrity was determined via bioanalyser (Australian Genomics Research Facility (AGRF, Perth, Western Australia).
RNA sequencing was performed according to SureSelect Strand-Specific XT HS2 poly A RNA Library preparation for Illumina Multiplexed Sequencing, paired-end, 100bp, 30M read RNA sequencing on the NOVAseq 6000 platform (Illumina, USA) at Genomics WA (Perth. Australia).

value: KOLF-2 cells, day 0

value: induced pluripotent stem cells

value: cardiomyocyte differentiation

tag: clone id


title: FAPs_202


title: GATA4_4D1WTday20 1

source_name: KOLF-2 derived cardiomyocytes

value: KOLF-2 derived cardiomyocytes

value: Cardiomyocyte


title: E65_ExE_mzKO_RNA_rep2

data_processing:
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq tracks, gene expression table for RNA-seq data

source_name: E6.5 ExE

growth_protocol: E5.5 -E7.5 embryo tissues were collected via previously described (Harrison et al. 1995). Briefly, female mice and male mice  were mated naturally, and the time when the vaginal plug was observed the next day was considered E0.5.

extract_protocol:
Cells or embyos were lysed in lysis buffer containing RNase inhibitor.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing.

value: Tfap2c mzKO


title: E65_ExE_mzKO_RNA_rep3

value: mix


title: FAPs_201

value: skeletal muscle


title: Fetal heart, 10.40 weeks of gestation, sample 2 (smallRNAseq)

city: Toronto

first: Paul

last: Delgado Olguín

state: Ontario

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

description:
sample_40
all_unique_counts_smallRNAseq.txt

data_processing:
Raw sequence reads were trimmed, poor quality reads were removed, reads were aligned and annotated with COMPSRA.
Sequences were aligned to the human genome (hg38), and reads were annotated using several small RNA reference databases (miRbase, gtRNAdb, gencode, circBase, piRNABank, piRBase and piRNACluster).
Reads mapped to multiple genes were removed from further analysis and only single mapped genes were retained to avoid ambiguous results in downstream analyses, rendering a total of 40,229 annotated small RNAs
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes the raw counts of annotated and uniquely mapped small RNAs for each sample.

source_name: Fetal heart

extract_protocol:
whole hearts were stored at -80 °C in RNAlater Stabilization Solution (Thermo Fisher Scientific). After thawing, ventricles were isolated from the atria and major vessels. To eliminate blood inside the chambers, the ventricles were cut open, rinsed with PBS for 10 seconds and kept in TRIzol. Ventricles were then homogenized at 30 kHz for 1 min using TissueLyser II (Qiagen) and centrifugated to pellet the insoluble tissue. DNA-free RNA was extracted using a Direct-zol RNA MiniPrep kit (Zymo Research).
Small RNA libraries were prepared using the NEBNext Small RNA Library Prep Kit for Illumina with 1 ug starting material according to published protocol (NEBNext® Multiplex Small RNA Library Prep Set for Illumina® Set 1, Set 2, Index Primers 1–48 and Multiplex Compatible).
Small RNA-seq

value: Fetal heart

tag: age

value: 10.40 weeks of gestation


title: FAPs_200

value: Fibro-adipogenic progenitors

value: young


title: GATA4_3H1HDRday0 1

value: HDR


title: Fetal heart, 8.00 weeks of gestation (smallRNAseq)

description:
sample_38
all_unique_counts_smallRNAseq.txt

value: 8.00 weeks of gestation


title: GATA4_3H1HDRday20 1


title: Fetal heart, 8.50 weeks of gestation (smallRNAseq)

description:
sample_39
all_unique_counts_smallRNAseq.txt

value: 8.50 weeks of gestation


title: GATA4_3G2WTday20 1

value: WT


title: E65_ExE_control_RNA_rep2

value: Tfap2c control


title: Fetal heart, 10.50 weeks of gestation (smallRNAseq)

description:
sample_37
all_unique_counts_smallRNAseq.txt

value: 10.50 weeks of gestation


title: E65_Epi_mzKO_RNA_rep3

source_name: E6.5 epiblast

extract_protocol:
Cells or embyos were lysed in lysis buffer containing RNase inhibitor.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before be_x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0004_ആ߻倀므羰_x0000__x0000__x0000__x0000__x0000_饒୥


title: FAPs_199

value: aged


title: GATA4_3G2WTday0 1

value: KOLF-2 cells, day 0

value: induced pluripotent stem cells

value: cardiomyocyte differentiation


title: E65_ExE_control_RNA_rep1


title: FAPs_198


title: E65_Epi_mzKO_RNA_rep2

value: Tfap2c mzKO


title: Fetal heart, 16.60 weeks of gestation (smallRNAseq)

description:
sample_36
all_unique_counts_smallRNAseq.txt

value: 16.60 weeks of gestation


title: HUH-7 control

description: without Flavokawain C

value: LIVER

value: human liver cancer cells HUH-7

value: epithelial cell

value: Cultured in common medium


title: FAPs_197

value: skeletal muscle

value: Fibro-adipogenic progenitors

value: young


title: GATA4_r1_3F2WTday20 1

value: KOLF-2 derived cardiomyocytes

value: Cardiomyocyte


title: E65_Epi_mzKO_RNA_rep1

value: mix


title: Fetal heart, 10.30 weeks of gestation (smallRNAseq)

description:
sample_35
all_unique_counts_smallRNAseq.txt

value: Fetal heart

value: 10.30 weeks of gestation


title: FAPs_196


title: Fetal heart, 16.00 weeks of gestation, sample 2 (smallRNAseq)

description:
sample_34
all_unique_counts_smallRNAseq.txt

value: 16.00 weeks of gestation


title: FAPs_195


title: GATA4_r3_3F2WTday20 3

value: WT


title: GATA4_r3_3F2WTday0 3

value: KOLF-2 cells, day 0

value: induced pluripotent stem cells

value: cardiomyocyte differentiation


title: Fetal heart, 9.00 weeks of gestation (smallRNAseq)

description:
sample_33
all_unique_counts_smallRNAseq.txt

value: 9.00 weeks of gestation


title: Fetal heart, 12.10 weeks of gestation (smallRNAseq)

description:
sample_32
all_unique_counts_smallRNAseq.txt

value: 12.10 weeks of gestation


title: FAPs_194

value: aged


title: E65_Epi_control_RNA_rep1

value: Tfap2c control


title: FAPs_193

value: skeletal muscle


title: GATA4_r2_3F2WTday20 2


title: E35_ICM_mzKO_RNA_rep5

source_name: E3.5 ICM

value: Tfap2c mzKO


title: GATA4_r2_3F2WTday0 2


title: E35_ICM_mzKO_RNA_rep4


title: FAPs_192

value: Fibro-adipogenic progenitors

value: young


title: Fetal heart, 18.20 weeks of gestation (smallRNAseq)

description:
sample_30
all_unique_counts_smallRNAseq.txt

value: 18.20 weeks of gestation


title: E35_ICM_mzKO_RNA_rep3

value: mix


title: Fetal heart, 19.00 weeks of gestation (smallRNAseq)

description:
sample_29
all_unique_counts_smallRNAseq.txt

value: Fetal heart

value: 19.00 weeks of gestation


title: FAPs_190


title: GATA4_r1_3F2WTday0 1


title: Fetal heart, 16.00 weeks of gestation, sample 1 (smallRNAseq)

description:
sample_31
all_unique_counts_smallRNAseq.txt

value: 16.00 weeks of gestation


title: GATA4_r1_2B2HDRday20 1

value: KOLF-2 derived cardiomyocytes

value: Cardiomyocyte

value: HDR


title: Fetal heart, 9.10 weeks of gestation (smallRNAseq)

description:
sample_28
all_unique_counts_smallRNAseq.txt

value: 9.10 weeks of gestation


title: GATA4_r1_2B2HDRday0 1

value: KOLF-2 cells, day 0

value: induced pluripotent stem cells

value: cardiomyocyte differentiation


title: GATA4_r3_2B2HDRday20 3


title: E65_Epi_control_RNA_rep3

value: Tfap2c control


title: FAPs_189

value: skeletal muscle

value: aged


title: E65_Epi_control_RNA_rep2


title: E35_ICM_mzKO_RNA_rep2

value: Tfap2c mzKO


title: E35_ICM_mzKO_RNA_rep1


title: E35_ICM_control_RNA_rep5


title: FAPs_188

value: Fibro-adipogenic progenitors

value: young


title: GATA4_r3_2B2HDRday0 3


title: FAPs_187


title: Fetal heart, 14.60 weeks of gestation, sample 2 (smallRNAseq)

description:
sample_25
all_unique_counts_smallRNAseq.txt

value: 14.60 weeks of gestation


title: GATA4_r2_2B2HDRday0 2


title: E35_ICM_control_RNA_rep4

value: mix


title: Fetal heart, 14.60 weeks of gestation, sample 1 (smallRNAseq)

description:
sample_24
all_unique_counts_smallRNAseq.txt

value: Fetal heart


title: GATA4_1D1HDRday20 1


title: FAPs_186


title: Fetal heart, 10.20 weeks of gestation (smallRNAseq)

description:
sample_23
all_unique_counts_smallRNAseq.txt

value: 10.20 weeks of gestation


title: E35_ICM_control_RNA_rep3


title: FAPs_185


title: E35_ICM_control_RNA_rep2

growth_protocol: For collection of wildtypes E3.5 ICM, 4–6-week-old  female mice were injected with pregnant mare serum gonadotropin followed by human chorionic gonadotropin (hCG; Ningbo Hormone Product Co., Cat # 110251283 Ltd., China 10 IU) 48 hours before being mated with malemice. Fertilized 8 cell were flushed out from the oviduct with HEPES-buffered CZB medium at E2.5 (68-70h). In vitro cultured was carried out for one day with the 8-cell embryo in KSOM medium to get blastocyst.


title: Fetal heart, 12.86 weeks of gestation (smallRNAseq)

description:
sample_22
all_unique_counts_smallRNAseq.txt

value: 12.86 weeks of gestation


title: 8cell_mzKO_RNA_rep3

source_name: 8-cell stage

growth_protocol: Embryos were collected from mice induced to superovulation by injections of 5 IU of pregnant mare's serum gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours_x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0004__x0000__x0000__x0000_므羰_x0000__x0000__x0000__x0000__x0000_


title: Fetal heart, 14.40 weeks of gestation (smallRNAseq)

description:
sample_27
all_unique_counts_smallRNAseq.txt

value: 14.40 weeks of gestation


title: E35_ICM_control_RNA_rep1


title: FAPs_184


title: Fetal heart, 11.40 weeks of gestation (smallRNAseq)

description:
sample_21
all_unique_counts_smallRNAseq.txt

value: 11.40 weeks of gestation


title: FAPs_183


title: GATA4_1D1HDRday0 1

value: HDR


title: Fetal heart, 12.40 weeks of gestation (smallRNAseq)

description:
sample_20
all_unique_counts_smallRNAseq.txt

value: 12.40 weeks of gestation


title: Fetal heart, 9.30 weeks of gestation (smallRNAseq)

description:
sample_19
all_unique_counts_smallRNAseq.txt

value: 9.30 weeks of gestation


title: hESC-derived microglia, TREX1-KO-2, rep2

city: La Jolla

first: Alysson

last: Muotri

state: California

address: 2880 Torrey Pines Scenic Drive, Room 3005

country: USA

institute: University of California - San Diego

data_processing:
Adapters were trimmed using cutadapt (version 1.16).
Reads were mapped to the reference human genome (hg38) using STAR (version 2.7.8a).
Gene counts were generated using featureCounts (version 2.0.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: embryonic stem cell

growth_protocol: Prior to initiating differentiation, PSC colonies were gently dissociated using a 1:1 solution of Accutase (Innovative Cell Technologies, San Diego, CA, USA) and PBS for 20 minutes at 37°C and seeded at a concentration of about 800,000 cells per 10cm matrigel-coated dish. Colonies were maintained in mTeSR™ Plus medium for about three days until the dish was about 70% confluent. The differentiation protocol consists of four sequential steps: primitive streak cell induction, hemangioblast-like hematopoietic precursors, myeloid differentiation, and monocyte generation. In the first step, primitive streak cells were induced by the addition of Bone Morphogenetic Protein - 4 (BMP-4, 80 ng/mL, Peprotech) to the mTeSR™ Plus medium with daily media changes for three days. In the second step (Day 4), cells were pushed to differentiate into hemangioblast-like hematopoietic precursors with the addition of a cocktail of three factors [Vascular Endothelial Growth Factor 121 (VEGF, 80 ng/mL, Peprotech), Stem Cell Factor (SCF, 100 ng/mL, Gemini Bio), and Fibroblast Growth Factor basic (bFGF, 25 ng/mL, Life Technologies)] in Microglial Precursor Differentiation Media (MPDM) which consists of StemPro-34 serum-free medium (SFM) (Thermo Fisher Scientific) supplemented with GlutaMax (2 mM, Thermo Fisher Scientific). In the third step (Day 6), the hematopoietic precursor cells were pushed towards myeloid differentiation with a different cocktail of factors [Fms-Like Tyrosine Kinase-3 ligand (FLT-3 ligand, 50 ng/mL, Gemini Bio), Interleukin-3 (IL-3, 50 ng/mL, Gemini Bio), Stem Cell Factor (SCF, 50 ng/mL, Gemini Bio), Thrombopoietin (TPO, 5 ng/mL, Peprotech), and Macrophage Colony Stimulating Factor (M-CSF, 50 ng/mL, Gemini Bio)] in the MPDM for twelve days with media changes on days 6 and 10. In step four (Day 13), cells were fated into the monocytic lineage with supplementation of a cocktail of factors [FLT-3 ligand (50 ng/mL, Gemini Bio), M-CSF (50 ng/mL, Gemini Bio), and Granulocyte Macrophage Colony-Stimulating Factor (GM-CSF, 25 ng/mL, Peprotech) in the MPDM with media changed twice a week. Cells produced in suspension in step 4 were recovered by centrifugation, resuspended in brain organoid media supplemented with M-CSF (50 ng/mL, Gemini Bio) and Interleukin-34 (IL-34, 50 ng/mL, BioLegend), replated and allowed to mature for one week prior to use in experiments.

extract_protocol:
Total RNA was obtained from microglia using the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany).
Total RNA was assessed for quality using an Agilent Tapestation 4200, and samples with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries using the Illumina® Stranded mRNA Prep (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions.

value: embryonic stem cell

value: H9 ESC

value: hESC-derived microglia-like cells

value: TREX1 KO


title: GATA4_r2_2B2HDRday20 2

value: KOLF-2 derived cardiomyocytes

value: Cardiomyocyte

value: cardiomyocyte differentiation


title: FAPs_181

value: skeletal muscle

value: Fibro-adipogenic progenitors

value: aged


title: 8cell_mzKO_RNA_rep2

value: Tfap2c mzKO

value: mix


title: Fetal heart, 12.00 weeks of gestation (smallRNAseq)

description:
sample_18
all_unique_counts_smallRNAseq.txt

value: Fetal heart

value: 12.00 weeks of gestation


title: hESC-derived microglia, TREX1-KO-2, rep1


title: FAPs_180


title: Fetal heart, 8.20 weeks of gestation (smallRNAseq)

description:
sample_17
all_unique_counts_smallRNAseq.txt

value: 8.20 weeks of gestation


title: 8cell_mzKO_RNA_rep1

growth_protocol: Embryos were collected from mice induced to superovulation by injections of 5 IU of pregnant mare's serum gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours_x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000_㽝㽛므羰_x0000__x0000__x0000__x0000__x0000_


title: FAPs_182

value: young


title: hESC-derived microglia, TREX1-KO-1, rep1


title: Fetal heart, 10.00 weeks of gestation (smallRNAseq)

description:
sample_16
all_unique_counts_smallRNAseq.txt

value: 10.00 weeks of gestation


title: 8cell_control_RNA_rep5

value: Tfap2c control


title: FAPs_179


title: 8cell_control_RNA_rep4


title: FAPs_178


title: hESC-derived microglia, control-2, rep1

value: embryonic stem cell

value: H9 ESC

value: control


title: 8cell_control_RNA_rep3


title: Fetal heart, 14.00 weeks of gestation, sample 2 (smallRNAseq)

description:
sample_13
all_unique_counts_smallRNAseq.txt

value: 14.00 weeks of gestation


title: hESC-derived microglia, control-1, rep1

value: hESC-derived microglia-like cells


title: hESC-derived microglia, control-1, rep2


title: FAPs_176


title: hESC-derived microglia, TREX1-KO-1, rep2

value: TREX1 KO


title: FAPs_177

value: skeletal muscle


title: 8cell_control_RNA_rep2

growth_protocol: Embryos were collected from mice induced to superovulation by injections of 5 IU of pregnant mare's serum gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to males.


title: 8cell_control_RNA_rep1


title: Fetal heart, 9.50 weeks of gestation (smallRNAseq)

description:
sample_10
all_unique_counts_smallRNAseq.txt

value: 9.50 weeks of gestation


title: E65_ExE_mzKO_SOX2_CR_rep2

value: Sox2 (Abclonal, A11936)


title: Toll10B 2to4h CUT&Tag Dl Replicate 2

city: Stockholm

first: Mattias

last: Mannervik

address: Svante Arrhenius väg 20C

department: Dept. of Molecular Biosciences

country: Sweden

institute: Stockholm University

description:
Sequenced genomic DNA tagged by Tn5
Toll10B_2to4h_CUT&Tag_Dl_R2

data_processing:
library strategy: CUT&Tag
CUT&Tag-seq reads from each sequenced library were mapped to the Drosophila melanogaster (dm6) genome assembly using Bowtie2 with the default parameters . RPKM normalized CUT&Tag-seq coverage tracks were generated using the deepTools (v.3.5.1) package (default parameters with binSize = 2 (bases), normalizeUsing RPKM). The low read counts obtained from sequencing for the CUT&Tag samples 'gd7 2to4h CUT&Tag CycT Replicate 2', 'gd7 2to4h CUT&Tag BRD4 Replicate 2' and Toll10B 2to4h CUT&Tag 2SerP Replicate 2’ indicated these reactions had failed so they were excluded from the subsequent analysis .
Assembly: dm6
Supplementary files format and content: bigwigs for coverage

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: yw;PCNA-eGFP (wt) and Toll mutant (from gd7, Tollrm9/rm10 and Toll10B) embryos were collected from flies kept on potato-mash agar food and maintained at 25 degrees Celsius. Embryos were collected on apple juice plates with fresh yeast and aged at 25 degrees Celsius until they reached the range of hours after egg laying (AEL) for the required developmental stages.

extract_protocol:
Nuclear extraction was performed as described by 'Hainer, S.J., and Fazzio, T.G. (2019). High-Resolution Chromatin Profiling Using CUT&RUN. Curr Protoc Mol Biol 126, e85.' and CUT&TAG was performed essentially as described by 'Kaya-Okur, H.S., Wu, S.J., Codomo, C.A., Pledger, E.S., Bryson, T.D., Henikoff, J.G., Ahmad, K., and Henikoff, S. (2019). CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun 10, 1930.'. Nuclear extracts were prepared using a glass douncer and loose pestle in Nuclear Extraction buffer (20 mM HEPES pH 7.9, 10 mM KCl, 0.5 mM spermidine, 0.1% Triton X-100, 20% glycerol with protease inhibitor cocktail (Roche)) and centrifuged at 700 g for 10 min at 4°C. The nuclear pellets were resuspended in Nuclear Extraction buffer. Nuclei corresponding to 50 embryos per reaction (2-4 h AEL), 100 embryos (1.5-2 h AEL) or 200 embryos (60-80 min AEL) were incubated with 30 μl of BioMag®Plus Concanavalin A beads (Polysciences) (prepared in Binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1mM CaCl2, and 1 mM MnCl2)) on a nutator for 10 min at 4°C. Nuclei-bead complexes were resuspended in 100 μl Antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.05% digitonin, 2 mM EDTA pH 8.0 and 0.1% BSA supplemented with protease inhibitor cocktail (Roche)). For Toll mutant CUT&Tag, 1 μl of rabbit anti-BRD4/fs(1)h, rabbit anti-CycT, rabbit anti-Cdk9, rabbit anti-Rpb3 (a kind gift of John Lis), rabbit anti-RNA Polymerase II CTD repeat YSPTSPS (phosphor S5) (5SerP) (Abcam, ab5131) and rabbit anti-RNA Polymerase II CTD repeat YSPTSPS (phospho S2) (2SerP) (Abcam, ab5095) overnight at 4°C. For yw; PCNA-eGFP CUT&Tag, 1 μl of rabbit anti-BRD4/fs(1)h, rabbit anti-Cdk9 and rabbit anti-CBP. Following overnight incubation, tagmentation was performed using pA-Tn5 (Protein Science Facility, KI, Stockholm).
Tagmented DNA was PCR amplified using custom i5 and i7 PCR primers and Phusion® High-Fidelity PCR Master Mix with GC Buffer (NEB). PCR conditions were: 72°C for 5 min, 98°C for 30 s, followed by thermocycling (98°C for 10 s and 63°C for 10 s) for 13 cycles and final extension at 72°C for 1 min. Amplified libraries were purified using Agencourt AMPure XP beads (Beckman Coulter) (1.1:1 bead to sample volume ratio). Libraries were pair-end (2 x 37 bp) sequenced on an Illumina NextSeq 550 platform at the BEA core facility, Karolinska Institutet, Stockholm.

treatment_protocol: yw;PCNA-eGFP (60-80 min (nc 7-9), 1.5-2 h (nc 11-13) and 2-4 h AEL (nc14)), hand-sorted according to the developmental observed from the nuclear GFP signal, and Toll mutant embryos (2-4 h AEL) were dechorionated in dilute bleach, rinsed thoroughly with embryo wash buffer (PBS, 0.1% Triton X-100) and nuclei immediately extracted for CUT&Tag.

tag: developmental stage

value: Early embryonic stage (2-4 h AEL)

value: embryos

value: Toll10B mutant

value: guinea pig anti-Dl(gift of Christos Samakovlis)


title: FAPs_175

value: Fibro-adipogenic progenitors

value: aged


title: hESC-derived microglia, control-2, rep2


title: Fetal heart, 11.10 weeks of gestation (smallRNAseq)

description:
sample_9
all_unique_counts_smallRNAseq.txt

value: Fetal heart

value: 11.10 weeks of gestation


title: E65_ExE_mzKO_SOX2_CR_rep1

value: Tfap2c mzKO

value: mix


title: E65_ExE_mzKO_ATAC_rep1

extract_protocol:
Cells or embyos were lysed in lysis buffer.
The ATAC-seq procedure was performed as previously described (Wu et al. 2018). Briefly, cells were transferred into 6 μl of lysis buffer [10 mM tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.02% digitonin) in ice for 10 min. The ATAC reaction was performed by adding 4 μl of ddH2O, 4 μl of 5× TTBL, and 5 μl TTE mix V5 (Vazyme Biotech Co.,Ltd, catalog no. TD502) at 37°C for 30 min and then stopped by adding 5 μl of 5× TS stop buffer at room temperature for 5 min. DNA was extracted by phenol chloroform and ethanol purification after adding 40 ng of carrier RNA and 103 μl of tris-EDTA. Then, DNA was PCR-amplified with 10 μl of index (Vazyme Biotech Co.,Ltd, catalog no. TD202), 10 μl of 5× TAB and 1 μl tris-acetate-EDTA (Vazyme Biotech Co.,Ltd, catalog no. TD502) with the program of 72°C for 3 min, 98°C for 30 s, (98°C for 15 s, 60°C for 30 s, and 72°C for 3 min) with 18 cycles, and 72°C for 5 min.


title: FAPs_174


title: FAPs_173

value: young


title: FAPs_172


title: Tollrm9rm10 2to4h CUT&Tag Dl Replicate 1

description:
Sequenced genomic DNA tagged by Tn5
Tollrm9rm10_2to4h_CUT&Tag_Dl_R1

value: Tollrm9/rm10 mutant


title: Fetal heart, 14.00 weeks of gestation, sample 1 (smallRNAseq)

description:
sample_7
all_unique_counts_smallRNAseq.txt

value: 14.00 weeks of gestation


title: Fetal heart, 13.30 weeks of gestation (smallRNAseq)

description:
sample_14
all_unique_counts_smallRNAseq.txt

value: 13.30 weeks of gestation


title: FAPs_171

value: skeletal muscle


title: Fetal heart, 18.40 weeks of gestation (smallRNAseq)

description:
sample_12
all_unique_counts_smallRNAseq.txt

value: 18.40 weeks of gestation


title: FAPs_170


title: E65_ExE_control_SOX2_CR_rep1

value: Tfap2c control

value: Sox2 (Abclonal, A11936)


title: Fetal heart, 18.10 weeks of gestation (smallRNAseq)

description:
sample_6
all_unique_counts_smallRNAseq.txt

value: 18.10 weeks of gestation


title: gd7 2to4h CUT&Tag Dl Replicate 1

description:
Sequenced genomic DNA tagged by Tn5
gd7_2to4h_CUT&Tag_Dl_R1

value: Early embryonic stage (2-4 h AEL)

value: embryos

value: gd7 mutant


title: E65_ExE_control_ATAC_rep2


title: Toll10B 2to4h CUT&Tag Dl Replicate 1

description:
Sequenced genomic DNA tagged by Tn5
Toll10B_2to4h_CUT&Tag_Dl_R1

value: Toll10B mutant

value: guinea pig anti-Dl(gift of Christos Samakovlis)


title: Toll10B 2to4h CUT&Tag 2SerP Replicate 2

description: Sequenced genomic DNA tagged by Tn5

data_processing:
CUT&Tag-seq reads from each sequenced library were mapped to the Drosophila melanogaster (dm6) genome assembly using Bowtie2 with the default parameters . RPKM normalized CUT&Tag-seq coverage tracks were generated using the deepTools (v.3.5.1) package (default parameters with binSize = 2 (bases), normalizeUsing RPKM). The low read counts obtained from sequencing for the CUT&Tag samples 'gd7 2to4h CUT&Tag CycT Replicate 2', 'gd7 2to4h CUT&Tag BRD4 Replicate 2' and Toll10B 2to4h CUT&Tag 2SerP Replicate 2’ indicated these reactions had failed so they were excluded from the subsequent analysis .
Assembly: dm6
Supplementary files format and content: bigwigs for coverage
Library strategy: CUT&Tag

value: rabbit anti-2SerP (Abcam, ab5095)


title: gd7 2to4h CUT&Tag Dl Replicate 2

description:
Sequenced genomic DNA tagged by Tn5
gd7_2to4h_CUT&Tag_Dl_R2


title: Fetal heart, 15.30 weeks of gestation (smallRNAseq)

description:
sample_4
all_unique_counts_smallRNAseq.txt

value: Fetal heart

value: 15.30 weeks of gestation


title: E65_ExE_control_SOX2_CR_rep2

value: mix


title: Toll10B 2to4h CUT&Tag 2SerP Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: Tollrm9rm10 2to4h CUT&Tag Dl Replicate 2

description:
Sequenced genomic DNA tagged by Tn5
Tollrm9rm10_2to4h_CUT&Tag_Dl_R2

value: Tollrm9/rm10 mutant


title: E65_ExE_control_ATAC_rep1

value: C57BL/6J x  PWK/PhJ


title: FAPs_168

value: Fibro-adipogenic progenitors

value: aged


title: FAPs_169

value: skeletal muscle


title: Fetal heart, 15.60 weeks of gestation (smallRNAseq)

description:
sample_8
all_unique_counts_smallRNAseq.txt

value: 15.60 weeks of gestation


title: Fetal heart, 10.40 weeks of gestation, sample 1 (smallRNAseq)

description:
sample_3
all_unique_counts_smallRNAseq.txt

value: 10.40 weeks of gestation


title: A75-3

city: Weifang

first: Jiaqi

last: Guan

address: Shandong Second Medical University, No. 7166 Baotong West Street, Weicheng District, Weifang City (Fuyanshan Campus)

department: School of Clinical Medical

institute: Weifang Medical University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples.
The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar .Based on the hypergeometric distribution, GO , KEGG enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively.
Assembly: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/625/GCF_000003625.3_OryCun2.0/GCF_000003625.3_OryCun2.0_genomic.fna.gz
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Leporidae

source_name: Normal-BMSCs

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Bone marrow blood

value: finite cell line

value: bone marrow mesenchymal stem cells

value: Normal


title: FAPs_167

value: young


title: Fetal heart, 16.10 weeks of gestation (smallRNAseq)

description:
sample_2
all_unique_counts_smallRNAseq.txt

value: 16.10 weeks of gestation


title: Tollrm9rm10 2to4h CUT&Tag 2SerP Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (2-4 h AEL)

value: embryos

value: rabbit anti-2SerP (Abcam, ab5095)


title: FAPs_166


title: Tollrm9rm10 2to4h CUT&Tag 2SerP Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: Fetal heart, 14.50 weeks of gestation (smallRNAseq)

description:
sample_5
all_unique_counts_smallRNAseq.txt

value: Fetal heart

value: 14.50 weeks of gestation


title: A75-1


title: gd7 2to4h CUT&Tag 2SerP Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: gd7 mutant


title: Fetal heart, 17.00 weeks of gestation (smallRNAseq)

description:
sample_1
all_unique_counts_smallRNAseq.txt

value: 17.00 weeks of gestation


title: FAPs_165

value: Fibro-adipogenic progenitors

value: aged


title: Fetal heart, 8.30 weeks of gestation, sample 3 (RNAseq)

description:
31543
allcounts.txt

data_processing:
Raw sequence reads were trimmed using Trimmomatic 0.36.
Trimmed sequences were aligned to the reference human genome (hg38) using STAR version 2.5.3.
Total counts were quantified using FeatureCounts.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes the raw counts for each sample.

extract_protocol:
whole hearts were stored at -80 °C in RNAlater Stabilization Solution (Thermo Fisher Scientific). After thawing, ventricles were isolated from the atria and major vessels. To eliminate blood inside the chambers, the ventricles were cut open, rinsed with PBS for 10 seconds and kept in TRIzol. Ventricles were then homogenized at 30 kHz for 1 min using TissueLyser II (Qiagen) and centrifugated to pellet the insoluble tissue. DNA-free RNA was extracted using a Direct-zol RNA MiniPrep kit (Zymo Research).
RNA-seq libraries were prepared using a NEBNext Ultra RNA Library Prep Kit for Illumina with the NEBNext Poly(A) mRNA Magnetic Isolation Module and 1 ug of starting material.

value: 8.30 weeks of gestation


title: FAPs_164

value: skeletal muscle


title: gd7 2to4h CUT&Tag 2SerP Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: Fetal heart, 16.60 weeks of gestation (RNAseq)

description:
31539
allcounts.txt

value: 16.60 weeks of gestation


title: A72-2

source_name: PMOP-BMSCs

value: Bone marrow blood

value: finite cell line

value: Osteoporosis


title: A72-3

value: bone marrow mesenchymal stem cells


title: A75-2

value: Normal


title: FAPs_162

value: young


title: Fetal heart, 16.10 weeks of gestation (RNAseq)

description:
31520
allcounts.txt

value: 16.10 weeks of gestation


title: Fetal heart, 8.50 weeks of gestation, sample 2 (RNAseq)

description:
31519
allcounts.txt

value: 8.50 weeks of gestation


title: FAPs_161


title: A72-1


title: Replicate2_RSC_Input_Abf1

city: Göttingen

first: Elisa

last: Oberbeckmann

address: Justus-von-Liebig Weg 11

department: Molecular Biology

institute: University Medical Center Göttingen

description:
plasmid DNA
Abf1-2MNase-merge-RSC_120-180-cov.bw

data_processing:
Sequencing data was mapped to the SacCer3 (R64) genome using Bowtie (Langmead et al. 2009).
After mapping, data was imported into R Studio using GenomicAlignments (Lawrence et al. 2013) and only fragments smaller than 91 bp were kept.
Genome coverage was calculated and bigwigs were exported.
Assembly: SacCer3/R64-1-1
Supplementary files format and content: bigwig containing ChIP-seq data with fragments smaller than 91 bp only

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: For a high assembly degree, 46 µg of plasmid library DNA were mixed with 40 µg of recombinant S. cerevisiae histone octamers in 400 µL assembly buffer (10 mM HEPES-NaOH pH 7.6, 2 M NaCl, 0.5 mM EDTA pH 8, 0.05% IGEPAL CA-630, 0.2 µg/µL BSA). Samples were transferred to Slide-A-Lyzer dialysis cups which were placed in a 3 L beaker containing 300 mL high salt buffer (10 mM HEPES-NaOH pH 7.6, 2 M NaCl, 1 mM EDTA, 0.05% IGEPAL CA-630). Samples were gradually dialyzed against a total of 3 L low salt buffer (10 mM HEPES-NaOH pH 7.6, 50 mM NaCl, 0.5 mM EDTA, 0.05% IGEPAL CA-630) while stirring via a peristaltic pump over 12-14 hours at room temperature. After complete transfer of low salt buffer, samples were dialyzed against 1 L low salt buffer for 1 hour at room temperature with stirring. The chromatin was then centrifuged for 1 minute at 10,000 rpm at room temperature and the supernatant was transferred to a fresh protein low-binding tube. We refer to the in vitro reconstituted chromatin as “SGD chromatin”. DNA concentration of the SGD chromatin was measured using a spectrophotometer (Nanodrop) and it was stored in low salt buffer at 4ºC.

extract_protocol:
DNA was eluted with 1x STOP-Buffer (20 mM Tris-HCL pH 7.5, 0.3% SDS, 10 mM EDTA, 150 mM NaCl, 125 ng/ul Glycogen, 5% Proteinase K (NEB), reversed crosslinked for 2 h at 65°C  and supernatant was subjected to ethanol precipitation.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) using the manufacturer's protocol.

treatment_protocol:
Remodeling reactions contained 1) 30 µL of SGD chromatin corresponding to about ~2.1 µg of DNA assembled into nucleosomes 2) transcription factors (TFs) Reb1 or Abf1 and 3) one of the chromatin remodeling enzymes, in assembly buffer (25.6 mM HEPES-NaOH pH 7.6, 3 mM MgCl2, 2.5 mM ATP, 1.25 mM TCEP, 10 mM creatine phosphate, 0.25 mM EGTA, 56 mM KOAc, 0.28 mM DTT, 13.4% glycerol, 10 µg/mL creatine kinase) for a total reaction volume of 100 µL. The TFs, Reb1 or Abf1 containing a C-terminal Strep-tag®II, were added at a final concentration of 50 nM each. The remodeling enzymes Chd1, ISW2, and INO80 were added to a final concentration of 24 nM and RSC was added to a final concentration of 12 nM.
SGD chromatin was was incubated with formaldehyde (FA) at a final concentration of 0.05% and cross-linking was continued for 5 minutes at 30ºC. The cross-linking reactions were quenched with Quenching Buffer (50 mM Tris-HCl pH 7.5, 20 mM lysine and 80 mM aspartate final concentration) for 15 minutes at 30ºC. Cross-linked chromatin was supplemented with 0.4 Ku/µL final concentration of MNase (New England Biolabs) in a total reaction volume of 200 µL containing digestion buffer (10 mM Tris-Cl pH 7.6, 1.7 mM CaCl2). The reaction was incubated at 30ºC for 5 minutes then stopped with STOP-Buffer (final concentration: 5 mM Tris-HCl pH 7.5, 10 mM EDTA and 1 mM EGTA). 5% of the sample was kept as input and subjected to MNase-seq. The rest was incubated with 10 ul prewashed with MagStrep "type3" Strep-Tactin® bead suspension (IBA) on a rotating wheel at 4°C for 1-3 h. Afterwards, beads were washed 4x with 500 ul TST rotating for 5 minutes at 4°C.

tag: source

value: in vitro-reconstituted chromatin

tag: atp-dependent remodeler_and_tfs_used

value: Abf1, RSC

tag: cross-linking condition

value: 0.05% Formaldehyde

tag: chip antibody

value: none (Input)

value: whole cell


title: Tollrm9rm10 2to4h CUT&Tag 5SerP Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (2-4 h AEL)

value: embryos

value: Tollrm9/rm10 mutant

value: rabbit anti-5SerP (Abcam, ab5131)


title: Fetal heart, 17.00 weeks of gestation (RNAseq)

description:
31513
allcounts.txt

value: Fetal heart

value: 17.00 weeks of gestation


title: FAPs_160

value: skeletal muscle

value: Fibro-adipogenic progenitors


title: Fetal heart, 15.30 weeks of gestation (RNAseq)

description:
31514
allcounts.txt

value: 15.30 weeks of gestation


title: FAPs_159

value: aged


title: Toll10B 2to4h CUT&Tag 5SerP Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Toll10B mutant


title: Replicate2_INO80_Input_Abf1

description:
plasmid DNA
Abf1-2MNase-merge-INO80_120-180-cov.bw

value: Abf1, INO80


title: gd7 2to4h CUT&Tag 5SerP Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: gd7 mutant


title: Replicate2_TFs-only_Input_Abf1

description:
plasmid DNA
Abf1-2MNase-merge-TFs_120-180-cov.bw

value: in vitro-reconstituted chromatin

value: Abf1, no remodeler


title: FAPs_158


title: FAPs_163


title: Fetal heart, 14.60 weeks of gestation, sample 2 (RNAseq)

description:
31419
allcounts.txt

value: 14.60 weeks of gestation


title: Toll10B 2to4h CUT&Tag 5SerP Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: Replicate1_RSC_Input_Abf1

value: Abf1, RSC

value: 0.05% Formaldehyde

value: none (Input)

value: whole cell


title: Toll10B 2to4h CUT&Tag Rpb3 Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (2-4 h AEL)

value: embryos

value: rabbit anti-Rpb3 (gift of John Lis)


title: FAPs_157

value: skeletal muscle

value: young


title: Toll10B 2to4h CUT&Tag Rpb3 Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: Fetal heart, 14.60 weeks of gestation, sample 1 (RNAseq)

description:
31413
allcounts.txt

value: Fetal heart


title: Replicate2_Chd1_Input_Abf1

description:
plasmid DNA
Abf1-2MNase-merge-Chd1_120-180-cov.bw

value: Abf1, Chd1


title: FAPs_156

value: Fibro-adipogenic progenitors

value: aged


title: Fetal heart, 12.40 weeks of gestation (RNAseq)

description:
31228
allcounts.txt

value: 12.40 weeks of gestation


title: Tollrm9rm10 2to4h CUT&Tag Rpb3 Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Tollrm9/rm10 mutant


title: Replicate2_ISW2_Input_Abf1

description:
plasmid DNA
Abf1-2MNase-merge-ISW2_120-180-cov.bw

value: in vitro-reconstituted chromatin

value: Abf1, ISW2


title: Tollrm9rm10 2to4h CUT&Tag 5SerP Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: rabbit anti-5SerP (Abcam, ab5131)


title: Replicate1_Chd1_Input_Abf1

value: 0.05% Formaldehyde


title: Replicate1_ISW2_Input_Abf1

value: none (Input)


title: Fetal heart, 10.00 weeks of gestation (RNAseq)

description:
31217
allcounts.txt

value: 10.00 weeks of gestation


title: gd7 2to4h CUT&Tag 5SerP Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (2-4 h AEL)

value: gd7 mutant


title: FAPs_155


title: Fetal heart, 16.00 weeks of gestation, sample 4 (RNAseq)

description:
31185
allcounts.txt

value: 16.00 weeks of gestation


title: FAPs_154

value: skeletal muscle


title: Fetal heart, 14.00 weeks of gestation, sample 2 (RNAseq)

description:
31507
allcounts.txt

value: 14.00 weeks of gestation


title: Tollrm9rm10 2to4h CUT&Tag Rpb3 Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: embryos

value: rabbit anti-Rpb3 (gift of John Lis)


title: gd7 2to4h CUT&Tag Rpb3 Replicate 2

description: Sequenced genomic DNA tagged by Tn5


title: FAPs_153

value: Fibro-adipogenic progenitors

value: young


title: Replicate1_INO80_Input_Abf1

value: Abf1, INO80

value: whole cell


title: Replicate1_TFs-only_Input_Abf1

value: in vitro-reconstituted chromatin

value: Abf1, no remodeler


title: gd7 2to4h CUT&Tag Rpb3 Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: FAPs_152


title: FAPs_191


title: Replicate1_ control_Input_Abf1

description:
plasmid DNA
Abf1-2MNase-merge-control_120-180-cov.bw

value: no TF, no remodeler


title: Fetal heart, 8.00 weeks of gestation (RNAseq)

description:
30664
allcounts.txt

value: Fetal heart

value: 8.00 weeks of gestation


title: Toll10B 2to4h CUT&Tag BRD4 Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Toll10B mutant

value: rabbit anti-BRD4/fs(1)h (gift of Renato Paro, kindly provided by Nicola Iovino)


title: Replicate2_RSC_Input_Reb1

description:
plasmid DNA
Reb1-2MNase-merge-RSC_120-180-cov.bw

value: Reb1, RSC

value: 0.05% Formaldehyde

value: none (Input)


title: Toll10B 2to4h CUT&Tag BRD4 Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (2-4 h AEL)


title: Fetal heart, 14.00 weeks of gestation, sample 1 (RNAseq)

description:
30476
allcounts.txt

value: 14.00 weeks of gestation


title: Fetal heart, 11.10 weeks of gestation (RNAseq)

description:
30475
allcounts.txt

value: 11.10 weeks of gestation


title: FAPs_150

value: skeletal muscle

value: Fibro-adipogenic progenitors


title: Replicate2_Chd1_Input_Reb1

description:
plasmid DNA
Reb1-2MNase-merge-Chd1_120-180-cov.bw

value: Reb1, Chd1


title: Replicate2_ISW2_Input_Reb1

description:
plasmid DNA
Reb1-2MNase-merge-ISW2_120-180-cov.bw

value: Reb1, ISW2

value: whole cell


title: Fetal heart, 13.60 weeks of gestation (RNAseq)

description:
30454
allcounts.txt

value: 13.60 weeks of gestation


title: Tollrm9rm10 2to4h CUT&Tag BRD4 Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: embryos

value: Tollrm9/rm10 mutant


title: FAPs_148

value: aged


title: FAPs_149


title: gd7 2to4h CUT&Tag BRD4 Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: gd7 mutant


title: Replicate2_INO80_Input_Reb1

description:
plasmid DNA
Reb1-2MNase-merge-INO80_120-180-cov.bw

value: in vitro-reconstituted chromatin

value: Reb1, INO80


title: FAPs_147


title: Replicate2_TFs-only_Input_Reb1

description:
plasmid DNA
Reb1-2MNase-merge-TFs_120-180-cov.bw

value: Reb1, no remodeler

value: 0.05% Formaldehyde


title: Tollrm9rm10 2to4h CUT&Tag BRD4 Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (2-4 h AEL)

value: rabbit anti-BRD4/fs(1)h (gift of Renato Paro, kindly provided by Nicola Iovino)


title: gd7 2to4h CUT&Tag BRD4 Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: Replicate2_ control_Input_Reb1_Abf1

description:
plasmid DNA
Reb1-2MNase-merge-control_120-180-cov.bw

value: no TF, no remodeler

value: none (Input)


title: Fetal heart, 16.50 weeks of gestation (RNAseq)

description:
30320
allcounts.txt

value: Fetal heart

value: 16.50 weeks of gestation


title: FAPs_151

value: skeletal muscle

value: Fibro-adipogenic progenitors

value: young


title: Fetal heart, 18.00 weeks of gestation (RNAseq)

description:
31163
allcounts.txt

value: 18.00 weeks of gestation


title: Toll10B 2to4h CUT&Tag CycT Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: embryos

value: Toll10B mutant

value: rabbit anti-CycT (gift of Akira Nakamura)


title: Replicate1_RSC_Input_Reb1

value: in vitro-reconstituted chromatin

value: Reb1, RSC

value: whole cell


title: Fetal heart, 11.40 weeks of gestation (RNAseq)

description:
30141
allcounts.txt

value: 11.40 weeks of gestation


title: FAPs_145

value: aged


title: Replicate1_Chd1_Input_Reb1

value: Reb1, Chd1

value: 0.05% Formaldehyde


title: Toll10B 2to4h CUT&Tag CycT Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (2-4 h AEL)


title: FAPs_144


title: Fetal heart, 14.40 weeks of gestation (RNAseq)

description:
30448
allcounts.txt

value: Fetal heart

value: 14.40 weeks of gestation


title: Fetal heart, 9.00 weeks of gestation, sample 2 (RNAseq)

description:
30119
allcounts.txt

value: 9.00 weeks of gestation


title: FAPs_143

value: skeletal muscle

value: Fibro-adipogenic progenitors


title: Tollrm9rm10 2to4h CUT&Tag CycT Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Tollrm9/rm10 mutant


title: Fetal heart, 12.86 weeks of gestation (RNAseq)

description:
30354
allcounts.txt

value: 12.86 weeks of gestation


title: Replicate1_ISW2_Input_Reb1

value: Reb1, ISW2

value: none (Input)


title: Fetal heart, 16.00 weeks of gestation, sample 3 (RNAseq)

description:
30109
allcounts.txt

value: 16.00 weeks of gestation


title: FAPs_146

value: young


title: Replicate1_INO80_Input_Reb1

value: in vitro-reconstituted chromatin

value: Reb1, INO80

value: whole cell


title: FAPs_142


title: Fetal heart, 9.40 weeks of gestation, sample 2 (RNAseq)

description:
30087
allcounts.txt

value: 9.40 weeks of gestation


title: Replicate1_TFs-only_Input_Reb1

value: Reb1, no remodeler

value: 0.05% Formaldehyde


title: Fetal heart, 8.50 weeks of gestation, sample 1 (RNAseq)

description:
30103
allcounts.txt

value: Fetal heart

value: 8.50 weeks of gestation


title: gd7 2to4h CUT&Tag CycT Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (2-4 h AEL)

value: embryos

value: gd7 mutant

value: rabbit anti-CycT (gift of Akira Nakamura)


title: FAPs_141

value: skeletal muscle

value: Fibro-adipogenic progenitors

value: aged


title: Fetal heart, 10.30 weeks of gestation (RNAseq)

description:
29953
allcounts.txt

value: 10.30 weeks of gestation


title: Replicate1_ control_Input_Reb1

value: no TF, no remodeler

value: none (Input)


title: FAPs_140


title: gd7 2to4h CUT&Tag CycT Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: Toll10B 2to4h CUT&Tag Cdk9 Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Toll10B mutant

value: rabbit anti-Cdk9 (gift of Akira Nakamura)


title: FAPs_139

value: young


title: Replicate2_RSC_IP_Abf1

description:
plasmid DNA
Abf1-2ChIP-merge-RSC_38-90-cov.bw

value: in vitro-reconstituted chromatin

value: Abf1, RSC

value: Strep-Tactin® (IBA)

value: whole cell


title: FAPs_138


title: Replicate2_Chd1_IP_Abf1

description:
plasmid DNA
Abf1-2ChIP-merge-Chd1_38-90-cov.bw

value: Abf1, Chd1

value: 0.05% Formaldehyde


title: Fetal heart, 18.20 weeks of gestation (RNAseq)

description:
29835
allcounts.txt

value: Fetal heart

value: 18.20 weeks of gestation


title: Toll10B 2to4h CUT&Tag Cdk9 Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (2-4 h AEL)

value: embryos


title: Fetal heart, 18.40 weeks of gestation (RNAseq)

description:
29554
allcounts.txt

value: 18.40 weeks of gestation


title: FAPs_137

value: skeletal muscle

value: Fibro-adipogenic progenitors

value: aged


title: Tollrm9rm10 2to4h CUT&Tag Cdk9 Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Tollrm9/rm10 mutant


title: Replicate2_ISW2_IP_Abf1

description:
plasmid DNA
Abf1-2ChIP-merge-ISW2_38-90-cov.bw

value: Abf1, ISW2


title: FAPs_136

value: young


title: Tollrm9rm10 2to4h CUT&Tag Cdk9 Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: rabbit anti-Cdk9 (gift of Akira Nakamura)


title: Fetal heart, 9.10 weeks of gestation, sample 2 (RNAseq)

description:
29504
allcounts.txt

value: 9.10 weeks of gestation


title: Replicate2_INO80_IP_Abf1

description:
plasmid DNA
Abf1-2ChIP-merge-INO80_38-90-cov.bw

value: in vitro-reconstituted chromatin

value: Abf1, INO80

value: Strep-Tactin® (IBA)


title: Fetal heart, 16.00 weeks of gestation, sample 2 (RNAseq)

description:
29443
allcounts.txt

value: 16.00 weeks of gestation


title: gd7 2to4h CUT&Tag Cdk9 Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: gd7 mutant


title: Tollrm9rm10 2to4h CUT&Tag CycT Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: rabbit anti-CycT (gift of Akira Nakamura)


title: Replicate2_TFs-only_IP_Abf1

description:
plasmid DNA
Abf1-2ChIP-merge-TFs_38-90-cov.bw

value: Abf1, no remodeler

value: 0.05% Formaldehyde

value: whole cell


title: FAPs_135

value: skeletal muscle


title: gd7 2to4h CUT&Tag Cdk9 Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (2-4 h AEL)

value: embryos


title: FAPs_134

value: Fibro-adipogenic progenitors

value: aged


title: Fetal heart, 8.20 weeks of gestation (RNAseq)

description:
29431
allcounts.txt

value: Fetal heart

value: 8.20 weeks of gestation


title: FAPs_133


title: Replicate1_RSC_IP_Abf1

description:
plasmid DNA
Reb1-2ChIP-merge-RSC_38-90-cov.bw

value: Abf1, RSC


title: Fetal heart, 13.30 weeks of gestation (RNAseq)

description:
29439
allcounts.txt

value: 13.30 weeks of gestation


title: wt nc14 CUT&Tag BRD4 Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: yw; PCNA-eGFP

value: rabbit anti-BRD4/fs(1)h (gift of Renato Paro, kindly provided by Nicola Iovino)


title: Replicate2_ control_IP_Abf1

description:
plasmid DNA
Abf1-2ChIP-merge-control_38-90-cov.bw

value: in vitro-reconstituted chromatin

value: no TF, no remodeler

value: Strep-Tactin® (IBA)


title: FAPs_132


title: Fetal heart, 11.30 weeks of gestation (RNAseq)

description:
29420
allcounts.txt

value: 11.30 weeks of gestation


title: wt nc14 CUT&Tag BRD4 Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: wt nc11to13 CUT&Tag BRD4 Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (1.5-2 h AEL)


title: FAPs_131


title: Replicate1_Chd1_IP_Abf1

description:
plasmid DNA
Reb1-2ChIP-merge-Chd1_38-90-cov.bw

value: Abf1, Chd1

value: 0.05% Formaldehyde

value: whole cell


title: FAPs_130

value: skeletal muscle

value: young


title: Replicate1_ISW2_IP_Abf1

description:
plasmid DNA
Reb1-2ChIP-merge-ISW2_38-90-cov.bw

value: Abf1, ISW2


title: Fetal heart, 9.10 weeks of gestation, sample 1 (RNAseq)

description:
29412
allcounts.txt

value: Fetal heart

value: 9.10 weeks of gestation


title: Fetal heart, 10.50 weeks of gestation, sample 2 (RNAseq)

description:
29417
allcounts.txt

value: 10.50 weeks of gestation


title: Replicate1_INO80_IP_Abf1

description:
plasmid DNA
Reb1-2ChIP-merge-INO80_38-90-cov.bw

value: Abf1, INO80


title: wt nc11to13 CUT&Tag BRD4 Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: embryos

value: yw; PCNA-eGFP


title: Fetal heart, 12.00 weeks of gestation (RNAseq)

description:
29404
allcounts.txt

value: 12.00 weeks of gestation


title: wt nc7to9 CUT&Tag BRD4 Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (60-80 min AEL)

value: rabbit anti-BRD4/fs(1)h (gift of Renato Paro, kindly provided by Nicola Iovino)


title: Replicate1_TFs-only_IP_Abf1

description:
plasmid DNA
Reb1-2ChIP-merge-TFs_38-90-cov.bw

value: in vitro-reconstituted chromatin

value: Abf1, no remodeler

value: Strep-Tactin® (IBA)


title: Fetal heart, 12.20 weeks of gestation (RNAseq)

description:
29401
allcounts.txt

value: 12.20 weeks of gestation


title: wt nc7to9 CUT&Tag BRD4 Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: FAPs_128

value: Fibro-adipogenic progenitors

value: aged


title: Replicate1_ control_IP_Abf1

description:
plasmid DNA
Reb1-2ChIP-merge-control_38-90-cov.bw

value: no TF, no remodeler

value: 0.05% Formaldehyde

value: whole cell


title: Fetal heart, 16.00 weeks of gestation, sample 1 (RNAseq)

description:
29399
allcounts.txt

value: Fetal heart

value: 16.00 weeks of gestation


title: wt nc14 CUT&Tag CBP Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (2-4 h AEL)

value: rabbit anti-CBP (homemade)


title: FAPs_127

value: skeletal muscle


title: FAPs_129

value: young


title: Fetal heart, 11.00 weeks of gestation (RNAseq)

description:
29305
allcounts.txt

value: 11.00 weeks of gestation


title: Replicate2_RSC_IP_Reb1

value: Reb1, RSC


title: FAPs_126


title: Fetal heart, 9.30 weeks of gestation (RNAseq)

description:
29298
allcounts.txt

value: 9.30 weeks of gestation


title: Replicate2_Chd1_IP_Reb1

value: in vitro-reconstituted chromatin

value: Reb1, Chd1


title: wt nc14 CUT&Tag CBP Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: embryos

value: yw; PCNA-eGFP


title: FAPs_125

value: Fibro-adipogenic progenitors


title: Fetal heart, 10.40 weeks of gestation, sample 2 (RNAseq)

description:
29282
allcounts.txt

value: 10.40 weeks of gestation


title: wt nc11to13 CUT&Tag CBP Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (1.5-2 h AEL)


title: wt nc11to13 CUT&Tag CBP Replicate 2

description: Sequenced genomic DNA tagged by Tn5


title: FAPs_124

value: aged


title: FAPs_123


title: wt nc7to9 CUT&Tag CBP Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (60-80 min AEL)


title: Replicate2_TFs-only_IP_Reb1

value: Reb1, no remodeler

value: 0.05% Formaldehyde

value: Strep-Tactin® (IBA)

value: whole cell


title: Replicate2_INO80_IP_Reb1

value: Reb1, INO80


title: Fetal heart, 8.30 weeks of gestation, sample 2 (RNAseq)

description:
29279
allcounts.txt

value: Fetal heart

value: 8.30 weeks of gestation


title: wt nc7to9 CUT&Tag CBP Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: rabbit anti-CBP (homemade)


title: Fetal heart, 8.30 weeks of gestation, sample 1 (RNAseq)

description:
29260
allcounts.txt


title: Replicate2_ control_IP_Reb1

value: in vitro-reconstituted chromatin

value: no TF, no remodeler


title: FAPs_122

value: skeletal muscle


title: wt nc14 CUT&Tag Cdk9 Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (2-4 h AEL)

value: embryos

value: yw; PCNA-eGFP

value: rabbit anti-Cdk9 (gift of Akira Nakamura)


title: Fetal heart, 19.00 weeks of gestation (RNAseq)

description:
29243
allcounts.txt

value: 19.00 weeks of gestation


title: Replicate1_RSC_IP_Reb1

value: Reb1, RSC


title: FAPs_121

value: Fibro-adipogenic progenitors

value: young


title: wt nc14 CUT&Tag Cdk9 Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: FAPs_120

value: aged


title: Replicate2_ISW2_IP_Reb1

value: Reb1, ISW2

value: 0.05% Formaldehyde

value: Strep-Tactin® (IBA)

value: whole cell


title: Replicate1_Chd1_IP_Reb1

value: Reb1, Chd1


title: Fetal heart, 11.4 weeks of gestation (RNAseq)

description:
29235
allcounts.txt

value: Fetal heart

value: 11.4 weeks of gestation


title: Replicate1_ISW2_IP_Reb1

value: in vitro-reconstituted chromatin


title: Fetal heart, 15.60 weeks of gestation (RNAseq)

description:
29223
allcounts.txt

value: 15.60 weeks of gestation


title: wt nc11to13 CUT&Tag Cdk9 Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (1.5-2 h AEL)

value: embryos


title: wt nc11to13 CUT&Tag Cdk9 Replicate 1

description: Sequenced genomic DNA tagged by Tn5

value: yw; PCNA-eGFP

value: rabbit anti-Cdk9 (gift of Akira Nakamura)


title: FAPs_119

value: skeletal muscle


title: FAPs_118

value: Fibro-adipogenic progenitors


title: Replicate1_INO80_IP_Reb1

value: Reb1, INO80


title: Fetal heart, 10.40 weeks of gestation, sample 1 (RNAseq)

description:
29209
allcounts.txt

value: 10.40 weeks of gestation


title: FAPs_117

value: young


title: Replicate1_TFs-only_IP_Reb1

value: Reb1, no remodeler

value: 0.05% Formaldehyde


title: wt nc7to9 CUT&Tag Cdk9 Replicate 2

description: Sequenced genomic DNA tagged by Tn5

value: Early embryonic stage (60-80 min AEL)


title: wt nc7to9 CUT&Tag Cdk9 Replicate 1

description: Sequenced genomic DNA tagged by Tn5


title: Fetal heart, 18.10 weeks of gestation (RNAseq)

description:
29217
allcounts.txt

value: 18.10 weeks of gestation


title: Replicate1_ control_IP_Reb1

value: no TF, no remodeler

value: Strep-Tactin® (IBA)

value: whole cell


title: Fetal heart, 14.50 weeks of gestation (RNAseq)

description:
29257
allcounts.txt

value: Fetal heart

value: 14.50 weeks of gestation


title: FAPs_115

value: aged


title: Toll10B 2to4h ChIP CBP Replicate 2

description: Sequenced ChIP DNA from CBP IP

data_processing:
ChIP-seq reads from each sequenced library were mapped to the Drosophila melanogaster (dm6) genome assembly using Bowtie2 with the default parameters. RPKM normalized ChIP-seq coverage tracks were generated using the deepTools (v.3.5.1) package (default parameters with binSize = 2 (bases), normalizeUsing RPKM). Bigwig files of the mean RPKM were produced using the deepTools 'bigwigCompare' tool.
Assembly: dm6
Supplementary files format and content: bigwig for coverage

source_name: Embryos

growth_protocol: Toll mutant (from gd7, Tollrm9/rm10 and Toll10B) embryos were collected from flies kept on potato-mash agar food and maintained at 25 degrees Celsius. Embryos were collected on apple juice plates with fresh yeast and aged at 25 degrees Celsius until they reached the range of hours after egg laying (AEL) for the required developmental stage.

extract_protocol:
To prepare chromatin, embryos were homogenized in a glass dounce homogenizer by 20 strokes with a tight pestle in A1 buffer (15 mM HEPES pH 7.6, 15 mM NaCl, 60 mM KCl, 4 mM MgCl2, 0.5 mM DTT, 0.5% Triton X-100 and protease inhibitor tablets (Roche)), centrifuged at 3500 g for 5 min at 4°C and the supernatant discarded. The remaining nuclear pellet was resuspended in 200 μl of sonication buffer (15 mM HEPES pH 7.6, 140 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.1% sodium deoxycholate, 1% Triton X-100 and protease inhibitor tablets (Roche)) supplemented with 0.5% SDS and 0.2% n-lauroylsarcosine and sonicated using a Bioruptor (Diagenode) with high power settings to obtain an average fragment size distribution of 200-500 bp, Sonicated chromatin was centrifuged at 13,000 rpm for 10 min at 4°C and diluted 5-fold in sonication buffer to reduce the concentration of detergents. Immunoprecipitations (IPs) were performed with 10 μg rabbit anti-CBP (homemade) Chromatin was incubated with anti-CBP overnight at 4°C and equal amounts of Protein A and G Dynabeads (Invitrogen), pre-blocked with BSA (1 mg/ml), were incubated with the samples for 4 h at 4°C. Chromatin corresponding to 10% of the amount in each IP was withdrawn to serve as an input for qPCR. Samples were subjected to 10 min washes with Wash A (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 0.1% SDS, 0.1% Sodium Deoxycholate and 1% Triton X-100), Wash B (Wash A adjusted to 500 mM NaCl), Wash C (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% Sodium Deoxycholate and 0.5% IGEPAL CA-630) and Tris-EDTA (TE) buffer. Beads were resuspended in 100 μl TE and treated with RNase A (20 μg/ml) at 55°C for 30 min before SDS (to 0.75%) and Tris-HCl (to 50mM) were added and crosslinks reversed at 65°C for overnight. Eluted ChIP DNA was treated with Proteinase K at 55°C for 2 h and purified with the ChIP DNA Clean & Concentrator kit (ZymoResearch, D5205).
ChIP-sequencing was performed using 2-5 ng of ChIP DNA in biological duplicates. Libraries were prepared with the NEBNext® Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) and single-end (1 x 75 bp) sequenced on the Illumina NextSeq 550 platform at the BEA core facility, Karolinska Institutet, Stockholm.

treatment_protocol: Formaldehyde fixation and chromatin preparation were performed essentially as described in 'Blythe, S.A., and Wieschaus, E.F. (2015). Zygotic genome activation triggers the DNA replication checkpoint at the midblastula transition. Cell 160, 1169-1181.'. Toll mutant embryos (2-4 h AEL) were dechorionated in dilute bleach, rinsed thoroughly with embryo wash buffer (PBS, 0.1% Triton X-100) and crosslinked in a mixture of 2 ml fixation buffer (PBS, 0.5% Triton X-100) and 6 ml heptane with 100 μl of 37% formaldehyde (Sigma-Aldrich, F8775) for 15 min at room temperature. Crosslinking was quenched by the addition of 125 mM glycine, embryos were washed (PBS, 0.5% Triton X-100), snap frozen in liquid nitrogen and stored at -80 degrees Celsius.

value: Toll10B mutant

value: Early embryonic stage (2-4 h AEL)

value: rabbit anti-CBP (homemade)

tag: spike-in


title: FAPs_116

value: skeletal muscle

value: Fibro-adipogenic progenitors


title: Micro-C Replicate5_INO80_circular

description:
plasmid DNA
INO80_circ_rep1_rep2_Filtered_ShiftbyOrientation_80.txt

data_processing:
Analysis was performed using the MCC pipeline as described in Hua et al. (2021). Briefly, adapter sequences were removed using Trim Galore (Babraham Institute, v.0.3.1) and paired-end reads were reconstructed using FLASH (v.1.2.11) (Magoč & Salzberg, 2011). Reconstructed reads were then mapped to the ~3 Mbp plasmid library (chrV:5,599 to chrX:106,749) with the non-stringent aligner BLAT (Kent, 2002). Uninformative reads (e.g. plasmid backbone) were discarded, while the mapped reads in the FASTQ files were further mapped to the SacCer3 reference genome using Bowtie2 (Langmead & Salzberg, 2012). The aligned reads were then processed to identify the ligation junction and remove PCR duplicates using MCCanalyser.pl. The unique ligation junctions were identified if the fragment ends were less than 5 bp apart in the original read and separated by mapping with BLAT and Bowtie2.
The pairwise interaction list was further filtered for interactions that are inter-chromosomal, and interactions are less than 147 bp apart. The ligation junction was further shifted by 80 bp to map the nucleosome dyad. The read pair orientation was determined based on the direction of the read.
Assembly: SacCer3
Supplementary files format and content: Text file containing a list of the chimeric pairs, the base pair coordinates shifted from the ligation junction, strand information, direction of read (upstream or downstream of the ligation junction), read pair orientations, and distance between pairs
Library strategy: in vitro Micro-C

extract_protocol:
The chromatin was reverse cross-linked with the addition of 1 mg/mL Proteinase K (Life Technologies) and 0.5% SDS at 65ºC for ≥3 hours. For DNA extraction, the reaction was supplemented with glycogen and subjected to ethanol precipitation. The ligation products were assessed using Fragment Analyzer. A successful ligation is indicated by the increase in fragment sizes of > 320 bp. Unligated mono-nucleosomal fragments were further removed by purification with 0.9 volume of AMPure XP beads.
Approximately 150-200 ng of each library was sonicated to a mean fragment size of 200 bp using a Covaris S220 Ultrasonicator (peak incident power 175; duty factor 10%; cycles per burst 200; treatment time 250s). Bead cleanup with AMPure XP beads was then performed and the fragment size was assessed using Fragment Analyzer. Libraries were indexed using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) using 170-200 ng input. The manufacturer’s protocol was followed with the following deviations: To maximize library complexity and yield, the PCR was performed in duplicate per ligation reaction using Herculase II reagents (Agilent Technologies). The parallel library preparations and PCR reactions were subsequently pooled for each reaction. The quality of the indexed library and molar concentration were measured using Fragment Analyzer and Qubit.

treatment_protocol:
Remodeling reactions contained 1) 30 µL of SGD chromatin corresponding to about ~2.1 µg of DNA assembled into nucleosomes 2) transcription factors (TFs) Reb1 and Abf1 if indicated and 3) one of the chromatin remodeling enzymes, in assembly buffer (25.6 mM HEPES-NaOH pH 7.6, 3 mM MgCl2, 2.5 mM ATP, 1.25 mM TCEP, 10 mM creatine phosphate, 0.25 mM EGTA, 56 mM KOAc, 0.28 mM DTT, 13.4% glycerol, 10 µg/mL creatine kinase) for a total reaction volume of 100 µL. The GRFs, Reb1 and Abf1, were added at a final concentration of 50 nM each. The remodeling enzymes Chd1, ISW2, and INO80 were added to a final concentration of 24 nM and RSC was added to a final concentration of 12 nM.
SGD chromatin was was incubated with Disuccinimidyl glutarate (DSG) at final concentrations of 0.75 mM for 20 minutes at 30ºC after which it was added with formaldehyde (FA) at a final concentration of 0.05% and cross-linking was continued for another 10 minutes at 30ºC. The cross-linking reactions were quenched with Quenching Buffer (10 mM Tris-HCl pH 7.5, 2 mM lysine and 8 mM aspartate final concentration) for 15 minutes at 30ºC. Cross-linked chromatin was supplemented with 0.4 Ku/µL final concentration of MNase (New England Biolabs) in a total reaction volume of 200 µL containing digestion buffer (10 mM Tris-Cl pH 7.6, 1.7 mM CaCl2). The reaction was incubated at 30ºC for 5 minutes then stopped with STOP-Buffer (final concentration: 5 mM Tris-HCl pH 7.5, 10 mM EDTA, 200 mM NaCl and 1 mM EGTA). The cross-linked and MNase-digested chromatin was purified using an Amicon Ultra 50 kDa centrifugal filter to remove <100 bp fragments. The chromatin was loaded and filled to 1 mL with low salt buffer (20 mM HEPES-NaOH, 50 mM NaCl, 0.5 mM EDTA, 0.05% IGEPAL CA-630) and concentrated to 200 µL by centrifugation (2000 g, 2 minutes). It was again filled to 1 mL with low salt buffer and concentrated to 200 µL for two more times. In the last centrifugation step, the sample was concentrated to ~100 µL.

value: in vitro-reconstituted chromatin

value: Abf1, Reb1, INO80

value: 0.75 mM DSG, 0.05% Formaldehyde

tag: restriction enzyme


title: Fetal heart, 10.50 weeks of gestation, sample 1 (RNAseq)

description:
29205
allcounts.txt

value: 10.50 weeks of gestation


title: Fetal heart, 9.40 weeks of gestation, sample 1 (RNAseq)

description:
29183
allcounts.txt

value: 9.40 weeks of gestation


title: Fetal heart, 12.10 weeks of gestation (RNAseq)

description:
29186
allcounts.txt

value: 12.10 weeks of gestation


title: Toll10B 2to4h ChIP CBP Replicate 1

description: Sequenced ChIP DNA from CBP IP


title: FAPs_114


title: FAPs_113


title: Toll10B 2to4h ChIP Input Replicate 2

description: Sequenced ChIP Input DNA


title: Micro-C Replicate5_INO80_linearized

description:
plasmid DNA
INO80_lin_rep1_rep2_Filtered_ShiftbyOrientation_80.txt

value: BamHI


title: Micro-C Replicate4_INO80_circular


title: Micro-C Replicate4_INO80_linearized


title: Toll10B 2to4h ChIP Input Replicate 1

description: Sequenced ChIP Input DNA


title: L131_Sepsis_ADT

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

institute: Monash Bioinformatics Platform

description:
PBMC, Baby A12 Day 40 blood draw; 'Enterobacter bloodstream infection', ADT
ADT: TotalSeq™-B0139 anti-human TCR γ/δ, TotalSeq™-B0072 anti-human CD4, TotalSeq™-B0080 anti-human CD8a

library_source: other

data_processing:
Single cell data were processed individually by cellranger 5.0.1 using cellranger multi mode against the cellranger reference refdata-gex-GRCh38-2020-A. This mode was used to process gene expression data and antibody capture data for each sample simultaneously.
Data were then further processed in R (v4.0.2), using Seurat (v4.0.1), scater (v1.18.6) and harmony (v1.0 immunogenics lab) packages. Individual count matrices were loaded into Seurat and scater for processing. Demultiplexing was performed using Seurat's HTODemux function. The isOutlier function from scater was used to detect library size outliers, cells with low number of genes expressed and cells with a high percentage of mitochondrial reads. After the samples had been demultiplexed, further quality control and data normalisation was performed using the basic Seurat workflow
The six individual Seurat ojects were then merged to created one combined Seurat object before Harmony was used to performed integration with the RunHarmony function. This was to batch correct the sorted CD3+ samples (EL Pre and EL sepsis)
Cell annotation was performed using the SingleR package against the Monaco reference from the celldex package
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5 - this contains the gene counts, HTO/ADT counts produced by the cellranger pipeline
Library strategy: CITE-seq

molecule: protein

source_name: blood

extract_protocol:
PBMC were extracted from whole neonatal blood and frozen at -80C. Paired samples from the same baby were thawed on the day of the experiment and incubated with Totalseq antibodies or hashtag reagents prior to sorting of live PBMC (4/5 babies) or CD3+ T cells (1/5 babies).
Cells were loaded onto a 10x Chromium Chip A using reagents from the Chromium Single-Cell 3’ gene expression and antibody derived tag (ADT) libraries were prepared according to the manufacturer’s instructions. Samples were sequenced with the Illumina NextSeq 500 platform, or Hiseq 2500 High Output platform dependent on the experiment. For libraries names beginning 'EL_Pre' or 'EL_Sepsis'  sorted cells were loaded onto a 10x Genomics Chromium controller and 5’ gene expression and ADT libraries were prepared.

value: blood

value: PBMC


title: FAPs_111

source_name: skeletal muscle

value: young


title: Tollrm9rm10 2to4h ChIP CBP Replicate 2

description: Sequenced ChIP DNA from CBP IP

value: Tollrm9/rm10 mutant


title: Micro-C Replicate2_RSC_noTFs

description:
plasmid DNA
RSC-noTF_rep1_rep2_Filtered_ShiftbyOrientation_80.txt

value: RSC

value: whole cell


title: L131_Sepsis_GEX

description: PBMC, Baby A12 Day 40 blood draw; 'Enterobacter bloodstream infection', GEX

data_processing:
Single cell data were processed individually by cellranger 5.0.1 using cellranger multi mode against the cellranger reference refdata-gex-GRCh38-2020-A. This mode was used to process gene expression data and antibody capture data for each sample simultaneously.
Data were then further processed in R (v4.0.2), using Seurat (v4.0.1), scater (v1.18.6) and harmony (v1.0 immunogenics lab) packages. Individual count matrices were loaded into Seurat and scater for processing. Demultiplexing was performed using Seurat's HTODemux function. The isOutlier function from scater was used to detect library size outliers, cells with low number of genes expressed and cells with a high percentage of mitochondrial reads. After the samples had been demultiplexed, further quality control and data normalisation was performed using the basic Seurat workflow
The six individual Seurat ojects were then merged to created one combined Seurat object before Harmony was used to performed integration with the RunHarmony function. This was to batch correct the sorted CD3+ samples (EL Pre and EL sepsis)
Cell annotation was performed using the SingleR package against the Monaco reference from the celldex package
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5 - this contains the gene counts, HTO/ADT counts produced by the cellranger pipeline


title: L131_Pre_GEX

description: PBMC, Baby A12 Day 34 blood draw; 'Proximal non-sepsis sample', GEX


title: FAPs_108

value: aged


title: Micro-C Replicate2_Chd1_noTFs

description:
plasmid DNA
Chd1-noTF_rep1_rep2_Filtered_ShiftbyOrientation_80.txt


title: Fetal heart, 9.00 weeks of gestation, sample 1 (RNAseq)

description:
29182
allcounts.txt

value: Fetal heart

value: 9.00 weeks of gestation


title: FAPs_109

value: skeletal muscle

value: Fibro-adipogenic progenitors


title: EL_Sepsis_ADT

description:
sorted CD3+ T cells, Baby A13 Day 13 blood draw; CoNS bloodstream infection, ADT
ADT: TotalSeq™-C0080 anti-human CD8a, TotalSeq™-C0154 anti-human CD27,  TotalSeq™-C0072 anti-human CD4
HTO: TotalSeq™-C0252 anti-human Hashtag 2

value: sorted CD3+ T cells


title: Tollrm9rm10 2to4h ChIP Input Replicate 1

description: Sequenced ChIP Input DNA

value: Early embryonic stage (2-4 h AEL)


title: gd7 2to4h ChIP CBP Replicate 2

description: Sequenced ChIP DNA from CBP IP

value: gd7 mutant

value: rabbit anti-CBP (homemade)


title: FAPs_107


title: Tollrm9rm10 2to4h ChIP Input Replicate 2

description: Sequenced ChIP Input DNA


title: EL_Sepsis_GEX

description: sorted CD3+ T cells, Baby A13 Day 13 blood draw; CoNS bloodstream infection, GEX


title: gd7 2to4h ChIP CBP Replicate 1

description: Sequenced ChIP DNA from CBP IP


title: FAPs_112


title: EL_Pre_ADT

description:
sorted CD3+ T cells, Baby A13 Day 6 blood draw; 'Proximal non-sepsis sample', ADT
ADT: TotalSeq™-C0080 anti-human CD8a, TotalSeq™-C0154 anti-human CD27,  TotalSeq™-C0072 anti-human CD4
HTO: TotalSeq™-C0251 anti-human Hashtag 1


title: Micro-C Replicate2_ISW2_noTFs

description:
plasmid DNA
ISW2-noTF_rep1_rep2_Filtered_ShiftbyOrientation_80.txt

value: in vitro-reconstituted chromatin

value: 0.75 mM DSG, 0.05% Formaldehyde


title: Micro-C Replicate2_INO80_noTFs

description:
plasmid DNA
INO80-noTF_rep1_rep2_Filtered_ShiftbyOrientation_80.txt


title: FAPs_106


title: gd7 2to4h ChIP Input Replicate 2

description: Sequenced ChIP Input DNA


title: Micro-C Replicate2_noTFs

description:
plasmid DNA
SGD-only_rep1_rep2_Filtered_ShiftbyOrientation_80.txt

value: no remodeler


title: Micro-C Replicate1_RSC_noTFs


title: Tollrm9rm10 2to4h ChIP CBP Replicate 1

description: Sequenced ChIP DNA from CBP IP


title: FAPs_105


title: EL_Pre_GEX

description: sorted CD3+ T cells, Baby A13 Day 6 blood draw; 'Proximal non-sepsis sample', GEX

value: blood


title: gd7 2to4h ChIP Input Replicate 1

description: Sequenced ChIP Input DNA


title: FAPs_104

value: young


title: FAPs_110


title: L131_Pre_ADT

description:
PBMC, Baby A12 Day 34 blood draw; 'Proximal non-sepsis sample', ADT
ADT: TotalSeq™-B0139 anti-human TCR γ/δ, TotalSeq™-B0072 anti-human CD4, TotalSeq™-B0080 anti-human CD8a

value: PBMC


title: Micro-C Replicate1_ISW2_noTFs


title: Control

city: Wuhan

first: Guojun

last: Guo

state: Hubei

address: 1277# Jiefang Avenue

department: Hand Surgery

institute: Union Hospital of Tongji medical college, Huazhong University of Science & Technology

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Assembly: Rattus norvegicus
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

organism: Rattus norvegicus

source_name: dorsal root ganglia

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adaptor ligated and library amplification.
RNA libraries were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: dorsal root ganglia


title: DPN

description: 10x Genomics


title: Micro-C Replicate1_Chd1_noTFs

value: whole cell


title: FAPs_102

value: aged


title: Toll10B 5h  PRO-seq Replicate 2

description:
Toll10B_5h_PRO_R2
Sequenced biotinylated nuclear run-on RNA

data_processing:
Library strategy: PRO-seq
PRO-seq reads from each sequencing library were mapped to the Drosophila melanogaster (dm6) genome assembly using Bowtie2 with the default parameters. Strand separated RPKM normalized (bigwig) PRO-seq coverage tracks from individual replicates were generated using the deepTools (v.3.5.1) package 'bamCoverage' (default parameters with binSize = 2 (bases), normalizeUsing RPKM) . Strand separated files of the mean RPKM signal from both replicates were produced by first merging the read alignment (bam) files produced by Bowtie2 for each replicate using samtools merge (Samtools), from which bigwig files were obtained using the  'bamCoverage' tool (deepTools). In order to better visualize the signal from pausing and gene body regions simultaneously, the bin size was extended to 10 bases when producing the merged bigwig files.
Assembly: dm6
Supplementary files format and content: bigwig for coverage

growth_protocol: Wild-type (from yw;PCNA-eGFP)  and Toll mutant (from gd7, Tollrm9/rm10 and Toll10B) embryos were collected from flies kept on potato-mash agar food and maintained at 25 degrees Celsius. Embryos were collected on apple juice plates with fresh yeast and aged at 25 degrees Celsius until they reached the range of hours after egg laying (AEL) for the required developmental stage.

extract_protocol:
Precision Run-On sequencing (PRO-seq) and the more sensitive qPRO-seq were performed according to the papers 'Kwak, H., Fuda, N.J., Core, L.J., and Lis, J.T. (2013). Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339, 950-953.' and 'Judd, J., Wojenski, L.A., Wainman, L.M., Tippens, N.D., Rice, E.J., Dziubek, A., Villafano, G.J., Wissink, E.M., Versluis, P., Bagepalli, L., et al. (2020). A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq). bioRxiv, 2020.2005.2018.102277.'. Embryos were resuspended in cold nuclear extraction buffer A (10 mM Tris-HCl pH 7.5, 300 mM sucrose, 10 mM NaCl, 3 mM CaCl2, 2 mM MgCl2, 0.1% Triton X, 0.5 mM DTT, protease inhibitor cocktail (Roche) and 4 u/ml RNase inhibitor (SUPERaseIN, Ambion)), transferred to a dounce homogenizer and dounced with the loose pestle for 20 strokes. To remove large debris, the suspension was passed through mesh followed by douncing with a tight pestle for 10 strokes. Nuclei were pelleted at 700 g for 10 min at 4°C and washed twice in buffer A and once in buffer D (10 mM Tris-HCl pH 8, 25% glycerol, 5mM MgAc2, 0.1 mM EDTA, 5 mM DTT). For PRO-seq, isolated nuclei corresponding to approximately 10 million cells, and for qPRO-seq from 1 million cells, were resuspended in buffer D and stored at -80°C for subsequent nuclear run-on (NRO) reactions with biotinylated nucleotides.
Library construction was performed according to the papers  'Kwak, H., Fuda, N.J., Core, L.J., and Lis, J.T. (2013). Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339, 950-953.' and 'Judd, J., Wojenski, L.A., Wainman, L.M., Tippens, N.D., Rice, E.J., Dziubek, A., Villafano, G.J., Wissink, E.M., Versluis, P., Bagepalli, L., et al. (2020). A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq). bioRxiv, 2020.2005.2018.102277.'. Samples were sequenced single-end (1x75 bp) on the Illumina NextSeq 550 platform at the BEA core facility, Karolinska Institutet, Stockholm.

treatment_protocol: Naive yw;PCNA-eGFP (60-80 min AEL), hand-sorted according to the developmental observed from the nuclear GFP signal, and Toll mutant embryos (2.5-3 h and 4.5-5 h AEL) were dechorionated in dilute bleach, rinsed thoroughly with embryo wash buffer (PBS, 0.1% Triton X-100), snap frozen in liquid nitrogen and stored at -80 degrees Celsius.

value: Toll10B mutant

value: Early embryonic stage (4.5-5 h AEL)

tag: molecule subtype

value: Nascent RNA


title: Toll10B 5h  PRO-seq Replicate 1

description:
Toll10B_5h_PRO_R1
Sequenced biotinylated nuclear run-on RNA


title: FAPs_101

data_processing:
The trimming was done with Trimgalore, the alignment was performed with STAR and the gene counting was done with featureCounts.
Assembly: mm10
Supplementary files format and content: tab-seperated value files

extract_protocol:
Muscle samples were isolated, minced and digested using Collagenase A for 45 min at 37 °C. Dispase II was added for 30 minutes to the muscle lysates. Muscles slurries were passed 10 times through a syringe and cell strainer and centrifugated. The pellet was re-suspended in Ammonium Chloride Potassium lysis buffer to eliminate red blood cells and centrifuged again. Cells were re-suspended in sorting buffer consisting of 100 µl Hank´s balanced salt solution (HBSS) containing 0.4% FBS. Fibro-adipogenic progenitors were isolated freshly using fluorescence-activated cell sorting (FACS) using the following surface marker profile: CD45-CD11b-CD31-SCA1+. For each single cell library, 4 independent chips using a commercial microfluidics platform (IFC, Fluidigm) were used with a capacity of capturing up to 96 individual cells per loaded chip. For each chip loading, cells were pooled from three mice (i.e. 4 pools per experimental group). Individual cell quality was checked as per manufacturers’ recommendation.
Successfully captured cells and corresponding cDNA samples of individuals cells were subsequently processed by Smart-Seq2 cDNA library preparation (Clontech) using the Nextera XT Indexing kit (Illumina). Quality control was performed using an Agilent Bioanalyzer DNA High Sensitivity Kit for electropherogram tracing.

value: skeletal muscle

tag: cell type

value: Fibro-adipogenic progenitors


title: Micro-C Replicate1_INO80_noTFs


title: Toll10B 3h  PRO-seq Replicate 2

description:
Toll10B_3h_PRO_R2
Sequenced biotinylated nuclear run-on RNA

value: Early embryonic stage (2.5-3 h AEL)


title: FAPs_103


title: Micro-C Replicate1_noTFs


title: 10_µg_mL_Poly_IC_3

city: Boston

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
The sample is aligned to GRCm38 transcriptome and quantified using Kallisto, Cellranger and RSEM
Assembly: GRCm38
Supplementary files format and content: gzipped abundance.tsv output from Kallisto, Cellranger and RSEM

source_name: cells

growth_protocol: Cells in vitro were cultured in adherent culture or encapsulated in droplets ("droplets" contained in title)

extract_protocol:
In vivo: Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes. In vitro: Cells from culture were lysed in RLT and processed by Qiagen RNeasy kit protocol.
Libraries were prepared by NEBNext Low Input kit.

treatment_protocol: In vivo: Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse. ICV injection: AREG or PBS was administered via ICV injection. In vitro: Cells were stimulated with AREG or Poly(I:C) or LPS or IL1b/TNFa.

value: Astrocyte

tag: genotype

value: fetal


title: 10_µg_mL_Poly_ICplus100_ng_mL_AREG_1

tag: strain


title: 10_µg_mL_Poly_ICplus100_ng_mL_AREG_2


title: FAPs_100


title: FAPs_98


title: Tollrm9/rm10 5h  PRO-seq Replicate 2

description:
Tollrm9/rm10_5h_PRO_R2
Sequenced biotinylated nuclear run-on RNA

value: Tollrm9/rm10 mutant


title: MNase-Seq Replicate5_INO80_linearized

description: plasmid DNA

data_processing:
Sequencing data was mapped to the SacCer3 (R64) genome using Bowtie (Langmead et al. 2009).
After mapping, data was imported into R Studio using GenomicAlignments (Lawrence et al. 2013) and only fragments between 125-205 bp length were kept.
Nucleosome dyad length was reduced to 50 bp and smoothed by a 10 bp rolling window. Genome coverage was calculated.
Assembly: SacCer3/R64-1-1
Supplementary files format and content: bigwig containing sorted and smoothed nucleosome fragments

extract_protocol:
The chromatin was reverse cross-linked with the addition of 1 mg/mL Proteinase K (Life Technologies) and 0.5% SDS at 65ºC for ≥3 hours. For DNA extraction, the reaction was supplemented with glycogen and subjected to ethanol precipitation.
Approximately 15-20 ng of each library was indexed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) using the manufacturer's protocol.

treatment_protocol:
Remodeling reactions contained 1) 30 µL of SGD chromatin corresponding to about ~2.1 µg of DNA assembled into nucleosomes 2) transcription factors (TFs) Reb1 and Abf1 if indicated and 3) one of the chromatin remodeling enzymes, in assembly buffer (25.6 mM HEPES-NaOH pH 7.6, 3 mM MgCl2, 2.5 mM ATP, 1.25 mM TCEP, 10 mM creatine phosphate, 0.25 mM EGTA, 56 mM KOAc, 0.28 mM DTT, 13.4% glycerol, 10 µg/mL creatine kinase) for a total reaction volume of 100 µL. The GRFs, Reb1 and Abf1, were added at a final concentration of 50 nM each. The remodeling enzymes Chd1, ISW2, and INO80 were added to a final concentration of 24 nM and RSC was added to a final concentration of 12 nM.
SGD chromatin was was incubated with Disuccinimidyl glutarate (DSG) at final concentrations of 0.75 mM for 20 minutes at 30ºC after which it was added with formaldehyde (FA) at a final concentration of 0.05% and cross-linking was continued for another 10 minutes at 30ºC. The cross-linking reactions were quenched with Quenching Buffer (50 mM Tris-HCl pH 7.5, 20 mM lysine and 80 mM aspartate final concentration) for 15 minutes at 30ºC. Cross-linked chromatin was supplemented with 0.4 Ku/µL final concentration of MNase (New England Biolabs) in a total reaction volume of 200 µL containing digestion buffer (10 mM Tris-Cl pH 7.6, 1.7 mM CaCl2). The reaction was incubated at 30ºC for 5 minutes then stopped with STOP-Buffer (final concentration: 5 mM Tris-HCl pH 7.5, 10 mM EDTA, 200 mM NaCl and 1 mM EGTA). The chromatin was then purified using an Amicon Ultra 50 kDa centrifugal filter to remove <100 bp fragments.

value: in vitro-reconstituted chromatin

value: Abf1, Reb1, INO80

value: 0.75 mM DSG, 0.05% Formaldehyde

value: BamHI


title: MNase-Seq Replicate4_INO80_circular

description: plasmid DNA


title: FAPs_99


title: MNase-Seq Replicate5_INO80_circular

description: plasmid DNA


title: FAPs_97

value: young


title: 10_µg_mL_Poly_IC_2


title: MNase-Seq Replicate2_RSC_noTFs

description: plasmid DNA

value: RSC


title: MNase-Seq Replicate4_INO80_linearized

description: plasmid DNA

value: whole cell


title: Tollrm9/rm10 3h  PRO-seq Replicate 2

description:
Tollrm9/rm10_3h_PRO_R2
Sequenced biotinylated nuclear run-on RNA


title: Toll10B 3h  PRO-seq Replicate 1

description:
Toll10B_3h_PRO_R1
Sequenced biotinylated nuclear run-on RNA


title: FAPs_96

value: aged


title: FAPs_95


title: 10_µg_mL_Poly_ICplus100_ng_mL_AREG_3


title: Vehicle_3


title: Vehicle_2


title: MNase-Seq Replicate2_Chd1_noTFs

description: plasmid DNA


title: MNase-Seq Replicate2_INO80_noTFs

description: plasmid DNA


title: gd7 5h  PRO-seq Replicate 1

description:
gd7_5h_PRO_R1
Sequenced biotinylated nuclear run-on RNA

value: gd7 mutant


title: gd7 3h  PRO-seq Replicate 2

description:
gd7_3h_PRO_R2
Sequenced biotinylated nuclear run-on RNA


title: gd7 5h  PRO-seq Replicate 2

description:
gd7_5h_PRO_R2
Sequenced biotinylated nuclear run-on RNA

value: Early embryonic stage (4.5-5 h AEL)


title: 10_µg_mL_Poly_IC_1


title: FAPs_93


title: Microglia_LPS_3

value: Microglia

value: WT


title: Microglia_LPS_2


title: gd7 3h  PRO-seq Replicate 1

description:
gd7_3h_PRO_R1
Sequenced biotinylated nuclear run-on RNA

value: Nascent RNA


title: Tollrm9/rm10 3h  PRO-seq Replicate 1

description:
Tollrm9/rm10_3h_PRO_R1
Sequenced biotinylated nuclear run-on RNA

value: Early embryonic stage (2.5-3 h AEL)


title: FAPs_92

value: skeletal muscle

value: Fibro-adipogenic progenitors


title: FAPs_91


title: FAPs_94


title: wt naive  PRO-seq Replicate 2

description:
wt_naive_PRO_R2
Sequenced biotinylated nuclear run-on RNA

value: yw; PCNA-eGFP

value: Early embryonic stage (60-80 min AEL)


title: wt naive  PRO-seq Replicate 1

description:
wt_naive_PRO_R1
Sequenced biotinylated nuclear run-on RNA


title: Vehicle_1

value: Astrocyte

value: fetal


title: MNase-Seq Replicate2_ISW2_noTFs

description: plasmid DNA

value: in vitro-reconstituted chromatin

value: 0.75 mM DSG, 0.05% Formaldehyde


title: Microglia_LPS_1


title: Microglia_LPS_4


title: MNase-Seq Replicate2_noTFs

description: plasmid DNA

value: no remodeler


title: MNase-Seq Replicate1_ISW2_noTFs

description: plasmid DNA

value: whole cell


title: MNase-Seq Replicate1_RSC_noTFs

description: plasmid DNA

value: RSC


title: MNase-Seq Replicate1_Chd1_noTFs

description: plasmid DNA


title: FAPs_90

value: young


title: wt naive qPRO-seq Replicate 2

description:
wt_naive_qPRO_R2
Sequenced biotinylated nuclear run-on RNA


title: Microglia_Vehicle_4


title: MNase-Seq Replicate1_noTFs

description: plasmid DNA


title: Microglia_Vehicle_3


title: Tollrm9/rm10 5h  PRO-seq Replicate 1

description:
Tollrm9/rm10_5h_PRO_R1
Sequenced biotinylated nuclear run-on RNA

value: Tollrm9/rm10 mutant

value: Early embryonic stage (4.5-5 h AEL)


title: Microglia_Vehicle_2

value: Microglia

value: WT


title: wt naive qPRO-seq Replicate 1

description:
wt_naive_qPRO_R1
Sequenced biotinylated nuclear run-on RNA

value: Nascent RNA


title: Microglia_Vehicle_1


title: MNase-Seq Replicate1_INO80_noTFs

description: plasmid DNA


title: FAPs_89

value: skeletal muscle


title: FAPs_87

value: Fibro-adipogenic progenitors

value: aged


title: FAPs_85


title: FAPs_88


title: FAPs_86


title: Astrocytes_ST2_KO_3

value: 13 weeks


title: FAPs_84


title: Astrocytes_ST2_KO_1

value: Astrocyte


title: Astrocytes_ST2_KO_2


title: FAPs_83