title: Male_Hypox_GH_90min_pool2_G92_M16

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
G92_M16
Liver DNase-I released fragments.
processed data file: 05_Male_Hypox_GH_90min_DHS.xlsx

data_processing:
READ MAPPING: DNase-seq reads were aligned to the mm9 mouse genome using Bowtie2 (Langmead et al. 2009, Genome Biology) with default settings. Reads were filtered so that only uniquely-aligned reads were used for downstream analysis.
PEAK CALLING: Peaks were called using MACS2 (Zhang et al. 2008, Genome Biology) with default parameters without filtering for PCR duplicates. Peaks were filtered to remove blacklisted regions (www.sites.google.com/site/anshulkundaje/projects/blacklists) and also regions called as peaks that contain only PCR duplicated reads.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: MACS2 output Excel files for both the combined-sample and individual replicate samples for each treatment group. Individual samples (listed above) were combined at the FASTQ file level and processed through a custom DNase-seq pipeline as described. A separate Excel file is provided for each treatment group. The first sheet of each Excel file contains the data for the combined sample and the subsequent sheets contain the data for the individual samples. Each sheet is organized in the following way: the MACS2 command and argument list is provided at the top (rows 1-18), columns A-C represent genomic coordinates of the indicated peak; column D is the DHS peak width, column E is the absolute peak summit position, column F is the pileup height at peak summit, column G is the -log10(pvalue) for the peak summit, column H is the fold-change over background, column I is an integer score for display calculated as the -log10(qvalue), and column J is the peak name (unique identifier).

growth_protocol: Male and female CD1 mice (ICR strain), 7 weeks old, were purchased from Charles River Laboratories (Wilmington, MA) and kept on a 12-hour light/dark cycle with food and water without restriction.

extract_protocol:
DNA fragments were released from regions hypersensitive to DNase-I cutting and purified using a two step process: 1) sucrose gradient to isolate fragments less than 1-kb; followed by 2) SPRI bead purification isolating DNA fragments 125-400 bp. DNase-release fragments from n-2-3 individual livers in each group were pooled and then used for library preparation (3 livers for each pool indicated, except only 2 livers were pooled for Female_Hypox_pool1).
Samples were prepared for sequencing with NEBNext Ultra DNA library prep kit for Illumina according to the manufacturer's directions (New England Biolabs).

treatment_protocol: Mice were intact or were hypophysectomized by the supplier with the absence of weight gain and the lack of Mup protein in mouse urine as indicators of complete hypophysectomy (hypox). Hypophysectomized male mice were given a single intraperitoneal injection of vehicle (control) with or without recombinant rat GH at 125 ng of growth hormone (GH) per gram body weight and were euthanized by cervical dislocation 30, 90, or 240 min after GH injection (Connerney et al., 2017).

value: CD-1 (Charles River)

value: Male

value: 7 weeks

value: Hypox male + GH after 90 min


title: Male_Hypox_GH_240min_pool2_G92_M18

status: Public on Aug 21 2023

type: SRA

country: USA

description:
G92_M18
Liver DNase-I released fragments.
processed data file: 06_Male_Hypox_GH_240min_DHS.xlsx

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Liver

tag: strain

tag: tissue

value: Liver

tag: Sex

tag: age

tag: treatment

value: Hypox male + GH after 240 min


title: preop_P4

city: Minneapolis

first: Charles

middle: Scott

last: Cameron

state: Minnesota

address: 420 Delaware St SE

department: Pediatrics

institute: University of Minnesota-Twin Cities,

description:
Extracellular vesicle  total RNA
hiseq_counts

library_source: transcriptomic

data_processing:
Reads from the 128 samples that underwent total RNA sequencing were processed using the CHURP pipeline. Briefly, read quality was assessed with fastqc, and reads were trimmed using trimmomatic (v.33) to remove the first 3 base pairs of R2 (as these are from the SMART-seq Stranded adapter), adapters and low quality bases. Reads were aligned to hg38 using hisat2 and assigned to genes in Ensembl GrCh38 release 100 using Rsubread.
Assembly: HG38
Supplementary files format and content: text file containing count table

molecule: total RNA

organism: Homo sapiens

source_name: Serum Sample

extract_protocol:
RNA was harvested using ExoRNeasy Serum/Plasma Midi Kit (QIAGEN, Cat. No. 77144). 2.5 ng of total RNA was used for the construction of sequencing libraries.
SMART-Seq Stranded Kit (Cat. No. 634444) was used to generate cDNA libraries.

value: Serum Sample

tag: disease

value: Glioblastoma


title: Male_Hypox_GH_90min_pool1_G92_M15

description:
G92_M15
Liver DNase-I released fragments.
processed data file: 05_Male_Hypox_GH_90min_DHS.xlsx


title: GuineaPig, Liver, input, GuineaPig9,  do2424

city: London

first: Diego

last: Villar

address: 4 Newark Street, Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

data_processing:
ChIP-seq peak files were generated my MACS2 callPeak function (default parameters).
4C data was processed with pipe4C (Krijger et al. 2020)
Supplementary files format and content: MACS2 peak files for each ChIP and input combination (.narrowPeak extension)
Supplementary files format and content: 4C wig files for each 4C experiment

organism: Cavia porcellus

extract_protocol:
Tissues were prepared by direct perfusion of the liver with PBS, followed by dicing the whole organs (liver and heart) in small pieces around 1cm3. Blood clots within the heart ventricles were removed. Cross-linking of the diced tissue was performed in 1% formaldehyde solution for 20 min, addition of 250 mM glycine and incubation for a further 10 min to neutralize the formaldehyde. After homogenization of cross-linked tissues in a dounce tissue grinder, samples were washed twice with PBS and lysed according to published protocols (SCHMIDT et al. 2009 for ChIP and Krijger et al. 2020 for 4C) to solubilize DNA-protein complexes. For ChIP, chromatin was fragmented to 300 bp average size by sonication on a Misonix sonicator 3000 with a 418 tip (1/16 inch diameter). Chromatin from 50-200 mg of dounced tissue was used for each ChIP experiment using antibodies against H3K4me3 (millipore 05-1339), H3K27ac (abcam ab4729), H3K4me1 (abcam ab8895), TBX5 (Insight bio sc-515536), RXRA (sc-553), FOXA1 (ab70382), HNF4A (ARP31946), CEBPA (sc-9314) and HNF6 (sc-13050). For 4C, locus-specific 4C templates were made using two rounds of enzyme digestion (primary and secondary) and ligation. Purified 4C templates were amplified by inverse PCR with bait-specific primers.
Illumina sequencing libraries were prepared from ChIP-enriched or 4C-enriched DNA using ThruPLEX DNA-seq library preparation kit (Takara Bio) or NEBNext Ultra II DNA Library Prep Kit for Illumina with up to 10ng of input DNA and 8-15 PCR cycles. After PCR, libraries were pooled in equimolar concentrations and sequenced on Illumina HiSeq 4000, NextSeq 500 or NovaSeq 6000 instruments.
ChIP-Seq, 4C-Seq

treatment_protocol: We performed chromatin immunoprecipitation experiments followed by high throughput sequencing (ChIP-seq) or 4C-seq using liver and heart tissue samples isolated from naked mole-rat, Damaraland mole-rat, guinea pig and mouse. At least two independent biological replicates from different animals were performed for each species and antibody. Wherever possible, tissues from young adult males were used. Tissues were prepared immediately post-mortem (typically within an hour) to maximize experimental quality. Post-mortem tissues were kept on ice until processed to minimize potential loss of protein-DNA interactions during post-mortem time. Sample allocations to experimental batches were randomised to ensure unbiased distributions of species, tissue, individual and sex, using the R/Bioconductor package OSAT (YAN et al. 2012).

tag: genotype

value: wild-type

tag: developmental stage

value: adult

tag: age (months)

value: male

tag: individual

tag: antibody

value: input


title: OSKM-shLuci-D0-rep2

city: guangzhou

first: gongcheng

last: Hu

state: guangdong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Raw reads were firstly trimmed adaptors and low quality reads using Trim Galore (v0.4.4), and then mapped to mouse mm10 genome using STAR (v2.5.2a).
Gene expression levels were quantified as read counts generated by RSEM (v1.2.22) with default settings. Raw tag counts were normalized using DESeq2 (v1.22.0).
Genome_build: mm10
Supplementary_files_format_and_content: .tsv file generated from normalized RNAseq data.

source_name: Reprogramming cells,knock down Ctrl

growth_protocol: The reprogramming cells were cultured with iCD1 medium.

extract_protocol:
Total RNA was extracted from cells by lysing with TRIzol.
The RNA samples were subject to library preparation using Vazyme mRNA-seq V3 Library Prep Kit for Illumina. The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.

treatment_protocol: 10,000 MEFs at passage 2 were plated in a 12-well plate and then infected twice with retroviral stocks generated with Plat-E cells. 3 volumes of the supernatants of the transfected Plat-E cells were mixed with 1 volume of fresh MEF medium containing polybrene at a final concentration of 8 μg/mL. For infecting OG2 MEFs, the medium of OG2 MEFs was replaced with 2 mL of infection mixture per well in a 12-well plate. Infected cells were cultured with iCD1 medium post infection and renewed daily.

tag: cell type

value: Reprogramming cells

value: knock down Ctrl

tag: time

value: day of reprogramming D0


title: preop_P3


title: GuineaPig, Liver, H3K27ac, GuineaPig7,  do3044


title: OSKM-shLuci-D5-rep1

value: day of reprogramming D5


title: GuineaPig, Liver, input, GuineaPig7,  do2422


title: Male_Hypox_GH_30min_pool2_G92_M14

description:
G92_M14
Liver DNase-I released fragments.
processed data file: 04_Male_Hypox_GH_30min_DHS.xlsx

value: Hypox male + GH after 30 min


title: GuineaPig, Liver, H3K4me1, GuineaPig9,  do3025


title: preop_P2


title: OSKM-shLuci-D0-rep1


title: Male_Hypox_GH_30min_pool1_G92_M13

description:
G92_M13
Liver DNase-I released fragments.
processed data file: 04_Male_Hypox_GH_30min_DHS.xlsx

value: CD-1 (Charles River)


title: Male_Hypox_GH_240min_pool1_G92_M17

description:
G92_M17
Liver DNase-I released fragments.
processed data file: 06_Male_Hypox_GH_240min_DHS.xlsx

value: Male


title: Female_Hypox_pool2_G92_M12

description:
G92_M12
Liver DNase-I released fragments.
processed data file: 03_Female_Hypox_DHS.xlsx

value: Female

value: 7 weeks

value: Hypox female


title: GuineaPig, Liver, H3K4me1, GuineaPig8,  do3024

value: Liver


title: GuineaPig, Liver, H3K4me3, GuineaPig8,  do2346


title: WT_S2d_3

city: Tianjin

first: Liu

last: Qian

address: Xi 7 Dao No.32 Airport Economic Area

institute: TIB CAS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Myceliophthora thermophila ATCC 42464 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
Assembly: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html)
Supplementary files format and content: tab-delimited text files including RPKM for each sample.

organism: Thermothelomyces thermophilus

source_name: Myceliophthora thermophila ATCC 42464

growth_protocol: M. thermophila strains were inoculated into 1×Vogel’s salt with 2% starch  as the sole carbon source and cultivated at 45 °C for 1 day and 2 days.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: timepoint

value: 2 day


title: WT_S2d_2


title: Female_Hypox_pool1_G92_M11

description:
G92_M11
Liver DNase-I released fragments.
processed data file: 03_Female_Hypox_DHS.xlsx


title: WT_S2d_1


title: GuineaPig, Liver, H3K4me3, GuineaPig7,  do2342


title: control_C9

value: Serum Sample

value: Healthy Control


title: control_C10


title: GuineaPig, Heart, input, GuineaPig8,  do17613

source_name: Heart

value: Heart

value: wild-type

value: adult


title: WT_S1d_3

value: 1 day


title: control_C8


title: Male_Hypox_pool2_G103_M2

description:
G103_M2
Liver DNase-I released fragments.
processed data file: 02_Male_Hypox_DHS.xlsx

value: Hypox male


title: Male_Hypox_pool1_G103_M1

description:
G103_M1
Liver DNase-I released fragments.
processed data file: 02_Male_Hypox_DHS.xlsx


title: GuineaPig, Heart, H3K4me1, GuineaPig8,  do17609

value: male


title: WT_S1d_2


title: control_C7


title: GuineaPig, Liver, H3K4me3, GuineaPig9,  do2350


title: preop_P1

value: Glioblastoma


title: Female_Control_pool4_G93_M18

description:
G93_M18
Liver DNase-I released fragments.
processed data file: 01_Female_Control_DHS.xlsx

value: Pituitary-intact female


title: control_C6


title: MtGM12_S2d_3


title: Female_Control_pool3_G93_M9

description:
G93_M9
Liver DNase-I released fragments.
processed data file: 01_Female_Control_DHS.xlsx

value: CD-1 (Charles River)


title: WT_S1d_1


title: control_C4


title: GuineaPig, Heart, H3K27ac, GuineaPig8,  do17608


title: GuineaPig, Heart, input, GuineaPig7,  do17598

value: input


title: control_C3


title: GuineaPig, Heart, H3K4me3, GuineaPig8,  do17607


title: Female_Control_pool1_G92_M7

description:
G92_M7
Liver DNase-I released fragments.
processed data file: 01_Female_Control_DHS.xlsx

value: Female


title: Female_Control_pool2_G92_M8

description:
G92_M8
Liver DNase-I released fragments.
processed data file: 01_Female_Control_DHS.xlsx

value: 7 weeks


title: MtGM12_S2d_2


title: GuineaPig, Heart, H3K4me1, GuineaPig7,  do17594


title: control_C2


title: Male_STAT5_Low_replicate10_G99_M11

description:
G99_M11
Liver DNase-I released fragments.
processed data file: 02_Male_STAT5_Low_DHS.xlsx

data_processing:
READ MAPPING: DNase-seq reads were aligned to the mm9 mouse genome using Bowtie2 (Langmead et al. 2009, Genome Biology) with default settings. Reads were filtered so that only uniquely-aligned reads were used for downstream analysis.
PEAK CALLING: Peaks were called using MACS2 (Zhang et al. 2008, Genome Biology) with default parameters without filtering for PCR duplicates. Peaks were filtered to remove blacklisted regions (www.sites.google.com/site/anshulkundaje/projects/blacklists) and also regions called as peaks that contain only PCR duplicated reads.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: MACS2 output Excel files for both the combined-sample and individual replicate samples for each treatment group. Individual samples (listed above) were combined at the FASTQ file level and processed through a custom DNase-seq pipeline as described. A separate Excel file is provided for each treatment group. The first sheet of each Excel file contains the data for the combined sample and the subsequent sheets contain the data for the individual samples. Each sheet is organized in the following way: the MACS2 command and argument list is provided at the top (rows 1-18), columns A-C represent genomic coordinates of the indicated peak; column D is the DHS peak width, column E is the absolute peak summit position, column F is the pileup height at peak summit, column G is the -log10(pvalue) for the peak summit, column H is the fold-change over background, column I is an integer score for display calculated as the -log10(qvalue), and column J is the peak name (unique identifier).  Note: the set of individual replicates that were combined is indicated in the name of the combined sample. For instance, for the Male_STAT5_High group, the combined sample is named "Male_Hi_combined", indicating that the Male_STAT5_High samples (n=8, listed above) were combined. Similarly, for the Male_STAT5_Low group, the combined samples is named "Male_Lo_combined", indicating that the Male_STAT5_Low samples (n=10, listed above) were combined. The name of each Excel sheet indicates the MACS2 DHS data for either the combined or individual replicate sample.

growth_protocol: Male CD1 mice (ICR strain), 8-10 weeks old, were purchased from Charles River Laboratories (Wilmington, MA) and kept on a 12-hour light/dark cycle with food and water without restriction.

extract_protocol:
DNA fragments were released from regions hypersensitive to DNase-I cutting and purified using a two step process: 1) sucrose gradient to isolate fragments less than 1-kb; followed by 2) SPRI bead purification to select DNA fragments 125-400 bp.
Samples were prepared for sequencing with NEBNext Ultra DNA library prep kit for Illumina according to the manufacturer's directions (New England Biolabs).

treatment_protocol: Fresh livers were collected from individual untreated, pituitary-intact male mice. Portions of each liver were used to prepare a protein extract for analysis of liver STAT5 activity by electrophoretic mobility shift assay (EMSA) (Connerney et al., 2017) to identify individual mouse livers as STAT5-high activity (n=8) and STAT5-low activity DNase-seq samples (n=10) at the time the mice were euthanized.

value: Male

value: 8-10 weeks


title: MtGM12_S1d_3


title: control_C1


title: Male_STAT5_Low_replicate9_G99_M9

description:
G99_M9
Liver DNase-I released fragments.
processed data file: 02_Male_STAT5_Low_DHS.xlsx

value: Liver


title: GuineaPig, Heart, H3K27ac, GuineaPig7,  do17593


title: MtGM12_S1d_2


title: GuineaPig, Heart, H3K4me3, GuineaPig7,  do17592


title: Male_STAT5_Low_replicate8_G99_M7

description:
G99_M7
Liver DNase-I released fragments.
processed data file: 02_Male_STAT5_Low_DHS.xlsx


title: MP46-1-OxBS

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

data_processing:
Paired-end reads were trimmed with fastx toolkit v0.0.13 with these parameters : -f 8 -Q 33. Adapters were removed using Cutadapt v1.8-2. Cleaned reads were aligned with bismark v0.12.5 with default parameters onto the Human reference Genome Hg19. Only reads mapping uniquely on the genome were conserved. Methylation calls were extracted after duplicate removal. Only CG dinucleotides covered by a minimum of 5 reads were conserved for the rest of the analysis.
Differentially methylated regions (DMR) were assigned when a methylation difference of 30% occurs at least on 10 CpGs in a minimum of 500bp windows; windows are merged if distant between two DMRs is less than 500bp.
Assembly: hg19
Supplementary files format and content: text file and CpG methylation

source_name: PDX of uveal melanoma

growth_protocol: Normal uveal melanocytes from an healthy donors, obtained after enucleations were dissociated and maintained in culture from choroidal membranes from Pr Simon Saule’s lab and Dr Geraldine Liot. After enzymatic (with collagenase) and mechanical dissociation, primary cells were cultured in HAM/F12 supplemented with 10% FBS, Penicillin 100 U/mL, Streptomycin 100 U/mL, 2mM L-glutamine, 2.5µg/mL Amphotericin B. Extemporaneously completed media was supplemented with 0.1mM IBMX, 10ng/µL of Cholera toxin (10 ng/ml final), and 10mg/mL FGF and filter with a 0.22µm filter. Cell were maintained in a humidified atmosphere with 5% CO2 at 37°C , and culture medium was exchanged twice a week.   MP41 and MP46 xenograft tumors were harvested before they reached a volume of 1 cm3 following ethical rules, and processed immediately for dissociation, immunolabelling and sorting based on Crépin R, Gentien D et al. et al protocol (2017).

extract_protocol:
Genomic DNA was extracted using QIAamp DNA Mini kit, and quality controls were achieved using a Nanodrop ND1000 to evaluate DNA purity and Qubit™ dsDNA BR/HS Assays to evaluate double strand DNA concentration
Whole genome DNA methylation analysis was carried out with a Cambridge Epigenetics kit (TrueMethyl kit) that corresponds to an oxidative bisulfite reaction, to identify and analyze only 5-methylcytosine (5-mC). Briefly 400ng of genomic DNA were used to first perform an oxidation reaction, that converts 5-hydroxymethylcytosine (5-hmC) to 5- formylcytosine(5fC), thus after a bisulfite conversion, unmodified C and 5FC will be converted into uracils and sequenced as thymines contrary to 5mC that remains sequence as a cytosine
Libraries were sequenced on an Illumina Hiseq as paired end 100bp for methylation analysis to identify Differenetial Methylated Region (DMR) between UM model vs NM.

value: UM sorted cells

tag: origin

value: MP46 PDX

tag: biological and technical replicate

value: Biological replicate 1 - technical replicate 1 - RunB178


title: DMR, Liver, input, DMR4,  do17611

organism: Fukomys damarensis

value: wild-type

value: 48 (estimated)


title: MP41-1-OxBS

value: MP41 PDX


title: MtGM12_S1d_1

value: 1 day


title: DMR, Liver, input, DMR1,  do17610

value: adult

value: male


title: Male_STAT5_Low_replicate7_G92_M6

description:
G92_M6
Liver DNase-I released fragments.
processed data file: 02_Male_STAT5_Low_DHS.xlsx


title: Male_STAT5_Low_replicate6_G92_M4

description:
G92_M4
Liver DNase-I released fragments.
processed data file: 02_Male_STAT5_Low_DHS.xlsx


title: Male_STAT5_Low_replicate5_G74A_M9

description:
G74A_M9
Liver DNase-I released fragments.
processed data file: 02_Male_STAT5_Low_DHS.xlsx


title: MtGM12_S2d_1

value: 2 day


title: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 ΔPA14_03790 mutant at OD 2 replicate 1

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

department: Molecular Bacteriology

country: Germany

institute: Helmholtz Center for Infection Research

description: 211207__mgu19__RNAseq_RZ__PA14_d03790__PL__1

data_processing:
cutadapt ( --nextseq-trim=20 -g TTTTT;min_overlap=1 -G GGGGGGG;min_overlap=3 -m 36)
bowtie2 ( --very-sensitive-local -I 100 -X 1200 --fr )
featurecounts (-p -Q 20 10 -t CDS,tRNA,rRNA -g locus --extraAttributes name)
Assembly: NC_008463.1
Supplementary files format and content: reads_per_gene.csv - reads per gene with samples in separate columns

organism: Pseudomonas aeruginosa UCBPP-PA14

growth_protocol: Bacterial subcultures were grown in liquid LB, at 37 °C and 180 rpm shaking until OD 2.0

extract_protocol:
RNA extraction was done as previously described (Schinner et al., 2020)
Illumina TruSeq kit

treatment_protocol: Bacterial cell pellets were resuspended in RNAprotect.

tag: cell line

value: bacteria

value: RNAprotect


title: DMR, Liver, H3K4me1, DMR4,  do17604


title: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 ΔPA14_03790 mutant at OD 2 replicate 2

description: 211207__mgu19__RNAseq_RZ__PA14_d03790__PL__2

tag: strain


title: Male_STAT5_Low_replicate4_G74A_M8

description:
G74A_M8
Liver DNase-I released fragments.
processed data file: 02_Male_STAT5_Low_DHS.xlsx

value: CD-1 (Charles River)

tag: tissue


title: MP46C_H3K4me3

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

data_processing:
The quality control of the fastq files was performed using FastQC.
The sequences were aligned on hg19 assembly using bowtie2. Duplicates were marked and filtered out using Picard tools MarkDuplicates and samtools.
The peak calling was performed using macs2 callpeak function. The parameter --broad was used for the Histone samples, not for the transcription factor samples.
Assembly: hg19
Supplementary files format and content: bigWig ChIP-seq profiles

extract_protocol:
ChIP of H2AUb, H3K4me and H3K27me3 were performed from 6 millions of cells originating from Patient Derived Tumour grafts; magnetic Dynabeads coupled to Protein A were used for the IP (Invitrogen). Sonication was performed to obtain fragment size of 150-300 bp. Chip of H3K27Ac and CTCF were performed according the Diagneode protocols. The chromatin was prepared using the iDeal ChIP-seq Kit for Transcription Factors (Diagenode Cat# C01010170). Chromatin was sheared using Bioruptor® Pico sonication device (Diagenode Cat# B01060001) combined with the Bioruptor® Water cooler for 10 cycles using a 30’’ [ON] 30’’ [OFF] settings to obtain fragment size of 150-300 bp. Per H3K27Ac and CTCF ChIP,  2 millions of cells were prepared in 100μl. The library preparation has been conducted by Diagenode ChIP-seq/ChIP-qPCR Profiling service (Diagenode Cat# G02010000). Libraries were prepared using IP-Star® Compact Automated System (Diagenode Cat# B03000002) from input and ChIP’d DNA using MicroPlex Library Preparation Kit v3 (96 indexes) (Diagenode Cat# C05010004). Optimal library amplification was assessed by qPCR using KAPA SYBR® FAST (Sigma-Aldrich) on LightCycler® 96 System (Roche) and by using High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent). Libraries were then purified using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analised by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent).
Libraries were prepared accordingly to manufactures (TruSeq ChIP sample Prep Kit, Illumina). Sequencing was performed on a Illumina Hi-Seq 2500 (H2Aub, H3K4me3, H3k27me3) and on a Illumina NovaSeq (ChIPseq H3K27Ac, CTCF)

treatment_protocol: Cells obtained from subcultre or cell sorting were counted and 6 million cells were resuspended in 1xPBS with 1%, v/v freshly opened formaldehyde at a concentration of  1x106 cells per 1ml PBS. Cells were icubated at room temperature for 15 minutes with gentle rocking. A glycine solution was added to a final concentration of 0.125M to quench the reaction. The mixture was incubated at room temperature for 5 minutes on rocker. Cells were centrifuged for 5 minutes at 300xG (1000rpm) at 4°C. The supernatant was discarded  into an appropriate collection container, and cells were resuspended in 1ml of cold 1X PBS and spin for 5 minutes at 00xG (1000rpm) at 4°C. The supernatant was discarded. This washing step was repeated one more time, the supernatant was removed and cell pellets were flash-freezon in a dry ice/ethanol bath and stored at -80°C before ChIPseq experiments

tag: type of sample

value: Biological replicate 2 - technical replicate 1


title: DMR, Liver, H3K27ac, DMR4,  do17603

tag: Sex


title: MP46C_H3K27me3


title: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 ΔPA14_23130 mutant at OD 2 replicate 2

description: 211207__mgu19__RNAseq_RZ__PA14_d23130__PL__2

tag: treatment


title: Male_STAT5_Low_replicate3_G74A_M7

description:
G74A_M7
Liver DNase-I released fragments.
processed data file: 02_Male_STAT5_Low_DHS.xlsx

value: Male

tag: age


title: DMR, Liver, H3K4me3, DMR4,  do17602

tag: genotype


title: DMR, Liver, H3K4me1, DMR1,  do17601

tag: developmental stage


title: Male_STAT5_Low_replicate2_G74A_M6

description:
G74A_M6
Liver DNase-I released fragments.
processed data file: 02_Male_STAT5_Low_DHS.xlsx

value: 8-10 weeks


title: DMR, Liver, H3K27ac, DMR1,  do17600

value: Liver

tag: age (months)


title: MP46A_H3K27me3

value: UM sorted cells

value: Biological replicate 1 - technical replicate 1


title: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 at OD 2 replicate 1

source_name: PA14 WT

value: PA14 WT

value: WT


title: MP46A_H3K4me3

value: MP46 PDX


title: NM1-OxBS

source_name: normal choroidal melanocytes Donor #9

value: Primary Culture

value: heathly donnor

value: Biological replicate 1 - technical replicate 1 - RunB178


title: DMR, Liver, H3K4me3, DMR1,  do17599

value: wild-type

value: adult

value: 48 (estimated)

value: male

tag: individual


title: Male_STAT5_Low_replicate1_G74A_M5

description:
G74A_M5
Liver DNase-I released fragments.
processed data file: 02_Male_STAT5_Low_DHS.xlsx

value: CD-1 (Charles River)


title: sig-MeJA-24h-3

city: Jinju

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

country: South Korea

institute: Gyeongsang National University

data_processing:
A quality control application for high throughput sequence data using FastQC Version 0.11.8
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt  Version 1.15
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using Trimmomatic Version 0.38
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Assembly: Capsicum annuum v1.6
Supplementary files format and content: tab-delimited text files include the values of read count for each sample

molecule: polyA RNA

organism: Capsicum annuum

source_name: Leaves

extract_protocol:
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols

value: Leaves

value: MeJA


title: DMR, Liver, input, DMR2,  do17595

value: 36 (estimated)

tag: antibody

value: input


title: MP46A_H2Aub

value: UM sorted cells


title: Male_STAT5_High_replicate8_G99_M10

description:
G99_M10
Liver DNase-I released fragments.
processed data file: 01_Male_STAT5_High_DHS.xlsx

value: Liver

value: Male

value: 8-10 weeks


title: sig-MeJA-24h-2

value: WT


title: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 ΔPA14_23130 mutant at OD 2 replicate 1

description: 211207__mgu19__RNAseq_RZ__PA14_d23130__PL__1

tag: cell type

value: bacteria

value: RNAprotect


title: MP46C_H2Aub

value: MP46 PDX

value: Biological replicate 2 - technical replicate 1


title: MP41B_H3K27me3

value: MP41 PDX


title: DMR, Liver, H3K4me1, DMR2,  do17585

value: wild-type

value: adult


title: Male_STAT5_High_replicate7 _G99_M8

description:
G99_M8
Liver DNase-I released fragments.
processed data file: 01_Male_STAT5_High_DHS.xlsx

value: CD-1 (Charles River)


title: MP41B_H3K4me3


title: sig-MeJA-12h-3

value: Leaves


title: MP41B_H2Aub


title: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 at OD 2 replicate 2

value: PA14 WT


title: DMR, Heart, input, DMR4,  do16813

value: Heart

value: 48 (estimated)

value: male


title: sig-MeJA-24h-1

value: MeJA


title: MP41_H3K27me3

value: UM sorted cells

value: Biological replicate 1 - technical replicate 1


title: MP41_H3K4me3


title: sig-MeJA-12h-2

value: WT


title: Male_STAT5_High_replicate3_G92_M1

description:
G92_M1
Liver DNase-I released fragments.
processed data file: 01_Male_STAT5_High_DHS.xlsx

value: Liver

value: Male

value: 8-10 weeks


title: DMR, Heart, input, DMR2,  do16812

value: 36 (estimated)

value: input


title: sig-MeJA-12h-1


title: Male_STAT5_High_replicate5_G92_M3

description:
G92_M3
Liver DNase-I released fragments.
processed data file: 01_Male_STAT5_High_DHS.xlsx


title: Male_STAT5_High_replicate4 _G92_M2

description:
G92_M2
Liver DNase-I released fragments.
processed data file: 01_Male_STAT5_High_DHS.xlsx


title: Male_STAT5_High_replicate6_G99_M6

description:
G99_M6
Liver DNase-I released fragments.
processed data file: 01_Male_STAT5_High_DHS.xlsx


title: Male_STAT5_High_replicate2_G74A_M4

description:
G74A_M4
Liver DNase-I released fragments.
processed data file: 01_Male_STAT5_High_DHS.xlsx


title: MP41_H2Aub

value: MP41 PDX


title: sig-MeJA-6h-3


title: DMR, Heart, H3K27ac, DMR4,  do16808

value: wild-type

value: adult


title: sig-MeJA-6h-2

value: Leaves


title: Male_STAT5_High_replicate1 _G74A_M3

description:
G74A_M3
Liver DNase-I released fragments.
processed data file: 01_Male_STAT5_High_DHS.xlsx

value: CD-1 (Charles River)


title: DMR, Liver, H3K27ac, DMR2,  do17584


title: DMR, Heart, H3K4me3, DMR4,  do16807

value: Heart


title: sig-MeJA-6h-1


title: DMR, Heart, H3K4me1, DMR2,  do16806


title: MP46_3

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description: DNAse treatment

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Count on FAST DB gene annotations (GenoSplice) and normalization using Deseq
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes deseq normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2016_1 were also provide

extract_protocol:
Total RNA was extracted using miRNeasy kits following supplier recommendations, including a DNAse step. Quality controls were achieved using a Nanodrop ND1000 to evaluate RNA purity and concentration, and on automated electrophoresis to monitor RNA integrity (Bioanalyzer RNA 6000 Nano/Pico kits).
TruSeq Stranded mRNA

value: MP46 PDX

value: Biological replicate 3 - technical replicate 1 - Run 224


title: sig-MeJA-3h-3

value: MeJA


title: DMR, Heart, H3K27ac, DMR2,  do16805

value: male


title: Protoplasts of basal root tips, replicate 1, scRNAseq

city: Beijing

first: Jian

last: Gao

address: No.8 Futong East Street, Chaoyang District, Beijing 100102, China

institute: International Center for Bamboo and Rattan

description:
10x Genomics
Moso bamboo

library_source: transcriptomic single cell

data_processing:
The Cell Ranger (version 5.0.1) was used for sample demultiplexing, barcode processing and single-cell 3’ gene counting, and scRNA-seq data were aligned to the Moso Genome (http://172.26.100.143/#/) 66 using STAR. Combined with the annotation information of the Moso Genome (GTF file), the reads aligned to the genome were divided into exons, introns and intergenic regions (at least 50% of the bases were aligned to exons, introns and intergenic regions of reads).
Assembly: http://forestry.fafu.edu.cn/db/PhePacBio/
Supplementary files format and content: Tab-separated values files and matrix files

organism: Phyllostachys edulis

source_name: root

extract_protocol:
The basal root tips (~2 cm) were washed clean and cut into 1–2 mm strips, which  were added to a sterile petri dish with 25 ml sterile enzyme solution (3% cellulase R-10, 0.7% macerozyme R-10, 0.2% pectinase Y-23, 0.3% hemicellulose, 0.1% BSA, 0.01 M CaCl2, 20 mM MES and 0.6 M mannitol) in a vacuum pump at 23°C for 20-30 min, and then the mixture was moved in an incubator with shaking at 65 rpm/min for 3 h at 23°C to release basal root protoplasts. Those protoplasts were filtered with a 40-µm cell strainer and then centrifuged at a speed of 100 g/min for 2 min at 23°C, and after the supernatant was sucked out, 0.6 M mannitol was added to resuspend all protoplasts. After separating root protoplasts, they needed to be purified by sucrose density gradient centrifugation. The total viability of protoplasts needed to reach above 85%, which was further confirmed with trypan blue staining. The concentration of basal root protoplasts was adjusted to 1000 cells/µL.
After the protoplast suspensions were put into the 10 x Chromium instrument, the library was constructed using the 10 x Genomics Chromium Single Cell 3'kit (V3). The specific experimental operation steps were implemented according to the scRNA-seq experimental manual of LC-Bio Technology (Hangzhou, China). The Illumina NovaSeq 6000 was used to sequence the library, which demanded a minimum sequencing depth of 20,000 reads per cell.

value: Protoplast

value: root

value: 6-8 weeks old


title: sig-MeJA-3h-2

value: WT


title: MP41_3

description: DNAse treatment

value: UM sorted cells

value: Biological replicate 1 technical replicate 2- Run 224


title: DMR, Heart, H3K4me1, DMR4,  do16809

value: 48 (estimated)


title: XCV3-48h-3


title: DMR, Heart, H3K4me3, DMR2,  do16804

value: 36 (estimated)


title: XCV3-48h-2


title: NM_6

description: DNAse treatment

source_name: normal choroidal melanocytes Patient #3

value: Primary Culture

value: heathly donnor

value: Biological replicate 1 - technical replicate 1- Run B224


title: sig-MeJA-3h-1

value: Leaves


title: XCV3-48h-1


title: sig-MeJA-1h-2


title: MP41_Input

value: MP41 PDX

value: Biological replicate 1 - technical replicate 1

value: DNA Input


title: NM_4

description: DNAse treatment

source_name: normal choroidal melanocytes Patient #1


title: XCV3-24h-3


title: NM_5

description: DNAse treatment

source_name: normal choroidal melanocytes Patient #2


title: sig-MeJA-1h-1

value: MeJA


title: Protoplasts of basal root tips, replicate 2, scRNAseq

description:
10x Genomics
Moso bamboo


title: NM_3

description: DNAse treatment

value: Biological replicate 1 - technical replicate 2 - Run B224


title: MP41_4

description: DNAse treatment

value: Biological replicate 3 - technical replicate 1


title: sig-SA-24h-3

value: SA


title: MP46_2

description: DNAse treatment

value: MP46 PDX

value: Biological replicate 2 - technical replicate 1- Run B116


title: XCV3-24h-2

value: WT


title: XCV3-24h-1


title: XCV3-12h-3


title: sig-SA-24h-2


title: MP46_1

description: DNAse treatment

value: UM sorted cells

value: Biological replicate 1 - technical replicate 1- Run B116


title: sig-MeJA-1h-3


title: sig-SA-24h-1


title: MP41_2

description: DNAse treatment


title: XCV3-12h-2


title: sig-SA-12h-3


title: MP41_1

description: DNAse treatment


title: XCV3-12h-1


title: Tc+medium[WEHI] biological replicate 7

type: RNA

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description: Gene expression from WT mouse CXCL12-abundant reticular cells

hyb_protocol: Labeled fragments were hybridized to Affymetrix Clariom S Mouse arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: Primary murine CD8+ T cells, after 48 hr culture in supernatant of WEHI cells

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: Primary murine T cells were isolated from the spleen, activated with CD3/CD28 Dynabeads and cultured in complete RPMI with 2-ME. WEHI 3B cells and BMDCs were cultured for 48 hrs in complete RPMI. Supernatants were sterile filtered and used as substitute culture medium for the T cell culture.

extract_protocol: RNA was isolated using the miRNeasy Mini Kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: CD8+ T cells were reisolated after 48 hrs by MACS cell separation.

value: murine CD8+ T cells

value: spleen

value: wildtype


title: sig-SA-12h-2


title: XCV3-6h-3


title: NM_2

description: DNAse treatment

source_name: normal choroidal melanocytes Donor #11

value: Primary Culture

value: heathly donnor

value: tBiological replicate 1 - technical replicate 1 - Run B116


title: XCV3-6h-2

value: Leaves


title: sig-SA-12h-1


title: NM_1

description: DNAse treatment

value: Biological replicate 1 - technical replicate 1 - Run B116


title: Tc+medium[WEHI] biological replicate 6


title: Tc+medium[WEHI] biological replicate 2


title: XCV3-6h-1


title: Tc+medium[WEHI] biological replicate 1


title: sig-SA-6h-3


title: Tc+medium[WEHI] biological replicate 5


title: Tc+Tc (fresh medium) biological replicate 7

source_name: Primary murine CD8+ T cells, after 48 hr culture in fresh medium


title: Tc+medium[WEHI] biological replicate 4


title: pancreatic tumor, 10952_S3

city: La Jolla

first: Nirakar

last: Rajbhandari

state: Ca

address: 2880 Torrey Pines Scenic Dr

institute: University of California San Diego

data_processing:
Mouse single-cell RNA sequencing was aligned to the 10x genomics pre-built mm10 reference and feature-barcode matrices were generated using Cellranger v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Secondary analysis was performed using the Seurat v3.1/4.0 R packages.Cells were filtered for a minimum of 500 features, a maximum of 2,500 features, and a mitochondrial percentage less than 10% per cell.
Assembly: mm10
Supplementary files format and content: Each unprocessed sample condition file has three corresponding processed output files: barcodes.tsv, features.tsv, and matrix.mtx

source_name: Pancreatic

growth_protocol: Msi2-Myc mice were crossed to R26R-LSL-tdTomato mice. tdTomato+ (i.e MYC-expressing) epithelial cells from Msi2-Myc; R26-LSL-tdTomato mice were sorted and analyzed at 5 weeks (t=5) post-tamoxifen treatment on a FACS III Aria. We orthotopically transplanted the tdTomato+ cells into the pancreas of recipient (NSG) mice. At end-stage, tumors were harvested and sorted EpCAM+ cells were submitted for scRNA-seq.

extract_protocol:
All mouse pancreatic tumors were aseptically taken out from tumor-bearing mice, washed with cold 1x PBS (GIBCO, Life Technologies), and minced into 1-2 mm pieces using scalpel blades immediately following resection. Tumor pieces were collected into a 50 ml Falcon tube containing 10 mL Gey’s balanced salt solution (GBSS, Sigma, #G9779), 5 mg Collagenase P (Roche, #11249002001), and 0.2 µg DNase I (Roche, #4716728001). Samples were incubated for 20 to 30 minutes at 37oC, then pipetted and returned to 37oC for 15 minutes. Samples were re-pipetted then passed through a 70 µm nylon mesh (Corning). Red blood cells were lysed using RBC lysis buffer (eBioscience, #00-4333-57), and remaining tumor cells were washed, resuspended in GBSS (GIBCO, Life Technologies) containing 2.5% FBS and 2 mM EDTA for staining, FACS analysis, and cell sorting.
Sorted cells were washed once and resuspended in 1x PBS with 0.05% BSA. Sorted cells were manually counted and viability was assessed using Trypan Blue staining. Up to 16,000 cells were loaded into one well of the 10x chip to produce Gel Bead-in-Emulsions (GEMs) and capture individual cells. We utilized the Chromium Single Cell 3' Reagent Version 1 Kit (10X Genomics).  GEMs underwent reverse transcription to barcode RNA before cleanup and cDNA amplification. Libraries were prepared with the Chromium Single Cell 3' Reagent Version 3 Kit. Each sample was sequenced on HiSeq4000 (Illumina) in Rapid Run Mode with paired-end sequencing parameters for an average depth of 50,000 reads per cell.

value: Pancreatic

value: epithelial +EpCAM

value: Msi2-Myc; R26-LSL-tdTomato

value: 5 weeks Tamoxifen


title: sig-SA-6h-1

value: SA


title: sig-SA-6h-2


title: XCV3-3h-3


title: pancreatic tumor, 10951_S2


title: Tc+medium[WEHI] biological replicate 3


title: XCV3-3h-2


title: pancreatic tumor, 10950_S1


title: Tc+Tc (fresh medium) biological replicate 6


title: Tc+Tc (fresh medium) biological replicate 5


title: Retina, Rbpms-CreERT2/CreERT2, rep3

city: Augusta

first: Lin

last: Gan

state: Geogia

address: 1120 15th Street

department: Department of Neuroscience & Regenerative Medicine

institute: Augusta University

data_processing:
The Trimmomatic software was used to filter and trim minority low quality sequencing reads from the data set
The quality of sequence reads in the FASTQ files was evaluated using the FastQC analysis
High quality sequence reads were aligned to the mouse mm10 reference transcriptome using the HISAT2
The HISAT2 outputs were transformed with SAMtools and then fed into StringTie for transcript quantification
The count tables or matrices were input into the DESeq2 statistical package for determination of differential transcript expression between samples (cutoff fold change ≥ 2 and adjusted P value ≤ 0.05)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Retina

extract_protocol:
RNA extraction and sample QC were conducted at Azenta Life Sciences (South Plainfield, NJ, USA) as follows: Total RNA was extracted from fresh frozen tissues using Trizol following manufacturer’s instructions (ThermoFisher Scientific, Waltham, MA, USA). RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).
Library Preparations and sequencing reactions were conducted at Azenta Life Sciences (South Plainfield, NJ, USA) as follows: Strand-specific RNA sequencing library was prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, the enriched RNAs were fragmented for 8 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library enrichment. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded onto the Illumina HiSeq 4000 or equivalent instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the control software. Raw sequence data (.bcl files) generated from the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.

value: Retina

value: knock-in homozygous retinas

tag: time

tag: strain background


title: XCV3-3h-1

value: WT

tag: timepoint


title: sig-SA-3h-2


title: XCV1-48h-3


title: Tc+Tc (fresh medium) biological replicate 4


title: sig-SA-3h-1


title: Retina, Rbpms-CreERT2/CreERT2, rep2


title: Tc+Tc (fresh medium) biological replicate 3


title: XCV1-48h-1


title: XCV1-48h-2


title: sig-SA-1h-2


title: sig-SA-3h-3


title: sig-SA-1h-1


title: Retina, Rbpms-CreERT2/+, rep3

value: knock-in heterozygous retinas


title: sig-ET-24h-3

value: ET


title: XCV1-24h-3


title: Retina, Rbpms-CreERT2/+, rep1


title: Retina, Rbpms-CreERT2/+, rep2


title: XCV1-24h-2


title: XCV1-24h-1


title: sig-ET-24h-2


title: Retina, wt, rep2

value: control retinas


title: sig-ET-24h-1


title: Tc+Tc (fresh medium) biological replicate 1

value: murine CD8+ T cells

value: spleen

value: wildtype


title: Retina, Rbpms-CreERT2/CreERT2, rep1


title: Tc+Tc (fresh medium) biological replicate 2


title: XCV1-12h-2


title: Tc+medium[DC] biological replicate 7

source_name: Primary murine CD8+ T cells, after 48 hr culture in supernatant of BMDCs


title: Tc+medium[DC] biological replicate 6


title: Tc+medium[DC] biological replicate 5


title: sig-SA-1h-3


title: Tc+medium[DC] biological replicate 4


title: sig-ET-12h-3


title: Retina, wt, rep3


title: sig-ET-12h-2


title: Curio_ovary_11hr_hCG

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

data_processing:
The sequencing data were aligned to the mouse genome (assembly: GRCm38) using the STAR Solo (version=2.7.9a) pipeline with a bead barcode whitelist to derive a feature x bead barcode expression matrix.
Bead barcode location files for the corresponding tiles were provided by Curio Bioscience.
Assembly: GRCm38
Supplementary files format and content: HDF5 file containing raw gene expression count matrix (UMI counts) with spatial locations for every barcode
Library strategy: Spatial transcriptomics

source_name: Ovary

growth_protocol: C57BL/6J mice were bred in-house for all experiments in the study.

extract_protocol:
Slide-seq spatial transcriptomics experiments were performed using the Curio Seeker Kit (Curio Bioscience) according to the manufacturer's instructions. Briefly, tissue sections from fresh-frozen murine ovaries were mounted on a 3mm x 3mm spatially indexed bead surface (Curio Seeker Platform, Curio Bioscience). After RNA hybridization and reverse transcription, the tissue section was digested, and the beads were removed from the glass tile and resuspended. Second-strand synthesis was then performed by semi-random priming followed by cDNA amplification.
Sequencing libraries were then prepared using the Nextera XT DNA sample preparation kit. The libraries were pooled and sequenced on an Illumina NextSeq 2K (P3 flow cell) using the 100-cycle kit (Read 1 = 50 bp, Read 2 = 72 bp , Index 1 = 8 bp, and Index 2 = 8 bp).

treatment_protocol: 21-23 days old female mice with body weight over 11 grams were treated with pregnant mare serum gonadotropin (PMSG) and human chorionic gonadotropin (hCG) to induce ovulation. Untreated mice of the same age were used as immature controls. Mice were first administered 5 IU PMSG in 100ul 0.1% bovine serum albumin (BSA)-PBS per mouse via intraperitoneal injection. 48 hours after PMSG treatment, mice were administered 5 IU hCG in 100ul 0.1% BSA-PBS per mouse via intraperitoneal injection using a 27G insulin syringe. Three immature and seven preovulatory mice across eight different time points, namely Immature, 0hr, 1hr, 4hr, 6hr, 8hr, 11hr, and 12hr post-hCG treatment, were used for spatial transcriptomics experiments. To evaluate the response of mice to hormone treatment, RNA extraction followed by reverse transcription (RT) and quantitative polymerase chain reaction (qPCR) was performed on one ovary from every mouse for a panel of selected genes. Second ovaries from the mice selected based on RT-qPCR results were used for spatial transcriptomics experiments.

value: Ovary

value: PMSG+hCG


title: Curio_ovary_12hr_hCG


title: XCV1-12h-1

value: Leaves


title: Celecoxib 60mpk QD Mouse 2

city: South San Francisco

first: Brian

last: Francica

state: CA

address: 2000 Sierra Point Hwy

institute: Tempest Therapeutics

data_processing: log2TPM data

source_name: small intestine hyperplasia

extract_protocol:
After 3 weeks of treatment, small intestines were removed and polyps were resected and frozen at -80°C until seqencing.
polyA, NEBNext Ultra II RNA Library Prep

treatment_protocol: Animals were treated starting at 13 weeks of age for 3 weeks with TPST-1495 (100mg/kg BID, orally), E7046 (150mg/kg QD, orally), PF04418948 (100mg/kg QD, orally), or Celecoxib (60mg/kg QD, orally).

value: small intestine hyperplasia

value: APCmin/+

value: Celecoxib 60mpk QD


title: XCV1-6h-2


title: Curio_ovary_8hr_hCG


title: XCV1-6h-3


title: XCV1-12h-3


title: sig-ET-12h-1


title: Celecoxib 60mpk QD Mouse 4


title: Retina, wt, rep1


title: Tc+medium[DC] biological replicate 1


title: Celecoxib 60mpk QD Mouse 3


title: Celecoxib 60mpk QD Mouse 1


title: sig-ET-6h-3


title: XCV1-6h-1


title: PF04418948 100mpk QD Mouse 4


title: sig-ET-6h-2


title: XCV1-3h-3


title: Curio_ovary_4hr_hCG


title: Curio_ovary_1hr_hCG


title: sig-ET-6h-1


title: Tc+medium[DC] biological replicate 2


title: PF04418948 100mpk QD Mouse 3


title: Tc+medium[DC] biological replicate 3


title: XCV1-3h-2


title: sig-ET-3h-3


title: Curio_ovary_0hr_hCG

value: PMSG


title: PF04418948 100mpk QD Mouse 2


title: Curio_ovary_6hr_hCG


title: sig-ET-3h-2


title: mock-48h-3


title: XCV1-3h-1


title: E7046 150mpk QD Mouse 4


title: mock-48h-2


title: NMR, Heart, Igf1r, 13562, vl0438

source_name: Heart

value: Heart

value: wild-type

value: adult

value: male

tag: bait


title: PF04418948 100mpk QD Mouse 1


title: sig-ET-3h-1

value: WT


title: mock-48h-1


title: Heart, Female, Transgenic, Tamoxifen, 1 week, rep4

first: Mark

last: Sweeney

address: Du Cane Road

department: London Institute of Medical Science

institute: Imperial College London

description:
F_T1wk:Rosa6_84H
CPM_table_rosa_female.csv

data_processing:
Raw reads were aligned to the mouse reference genome GRCm39 (Ensembl release 106) using the STAR16 software v2.7.10a with default parameters.
Aligned reads were assigned to genes to give a gene-level count matrix using the featureCounts tool17 as part of the Rsubread package v2.10.4.
Differential gene expression analysis was performed using the edgeR18 software v3.38.1 following the author's recommended analysis pipeline utilising a quasi-likelihood negative binomial generalized log-linear model.
Assembly: GRCm39
Supplementary files format and content: Count per million data per sample

source_name: heart

extract_protocol:
The heart was dissected from the chest and washed in ice-cold PBS and snap-frozen in liquid nitrogen. Total RNA was extracted using TRIzol (Invitrogen, 15596026) in RNeasy columns (Qiagen, 74106).
RNASeq libraries prepared using the NEBNext Ultra II Directional RNA Library Prep Kit with NEBNext Poly(A) mRNA Magnetic Isolation Module following manufacturer’s instructions.

value: Female

tag: time point

value: 1 week

tag: replicate

value: heart

value: Tamoxifen


title: mock-24h-3

tag: tissue


title: sig-ET-1h-3

value: ET


title: Heart, Female, Transgenic, Tamoxifen, 1 week, rep3

description:
F_T1wk:Rosa6_83H
CPM_table_rosa_female.csv


title: sig-ET-1h-2


title: E7046 150mpk QD Mouse 2


title: Heart, Female, Control, Tamoxifen, Baseline, rep4

description:
F_WT:Rosa6_82H
CPM_table_rosa_female.csv

value: Baseline


title: E7046 150mpk QD Mouse 3


title: E7046 150mpk QD Mouse 1


title: sig-ET-1h-1


title: sig-ABA-24h-3

value: ABA


title: Heart, Female, Control, Tamoxifen, Baseline, rep3

description:
F_WT:Rosa6_81H
CPM_table_rosa_female.csv


title: TPST-1495 100mpk QD Mouse 4

value: TPST-1495 100mpk QD


title: mock-24h-2

value: Leaves


title: mock-24h-1


title: Heart, Female, Transgenic, Tamoxifen, 6 weeks, rep4

description:
F_T6wk:Rosa6_68H
CPM_table_rosa_female.csv

value: 6 weeks


title: Curio_ovary_immature_untreated

value: Ovary

value: Immature

value: Untreated


title: sig-ABA-24h-2


title: TPST-1495 100mpk QD Mouse 3

value: small intestine hyperplasia

value: APCmin/+


title: mock-12h-3


title: sig-ABA-24h-1


title: Heart, Female, Transgenic, Tamoxifen, 6 weeks, rep3

description:
F_T6wk:Rosa6_51H
CPM_table_rosa_female.csv


title: mock-12h-2


title: TPST-1495 100mpk QD Mouse 2


title: mock-12h-1


title: TPST-1495 100mpk QD Mouse 1


title: Heart, Female, Trangenic, No tamoxifen, Baseline, rep4

description:
F_T0wk:Rosa6_46H
CPM_table_rosa_female.csv

value: No tamoxifen


title: Heart, Female, Transgenic, Tamoxifen, 1 week, rep2

description:
F_T1wk:Rosa6_47H
CPM_table_rosa_female.csv


title: sig-ABA-12h-3

value: WT


title: sig-ABA-12h-2


title: TPST-1495 100mpk BID Mouse 1

value: TPST-1495 100mpk BID


title: mock-6h-3


title: Vehicle mouse 4

value: Vehicle


title: sig-ABA-12h-1


title: mock-6h-2


title: Heart, Female, Transgenic, Tamoxifen, 1 week, rep1

description:
F_T1wk:Rosa6_42H
CPM_table_rosa_female.csv

value: Female

value: 1 week

value: heart


title: mock-6h-1


title: Vehicle mouse 3


title: Vehicle mouse 2


title: mock-3h-3


title: Heart, Female, Transgenic, Tamoxifen, 3 weeks, rep3

description:
F_T3wk:Rosa6_33H
CPM_table_rosa_female.csv

value: 3 weeks

value: Tamoxifen


title: Heart, Female, Trangenic, No tamoxifen, Baseline, rep3

description:
F_T0wk:Rosa6_43H
CPM_table_rosa_female.csv

value: Baseline


title: sig-ABA-6h-3

value: Leaves

value: ABA


title: Heart, Female, Transgenic, Tamoxifen, 3 weeks, rep4

description:
F_T3wk:Rosa6_34H
CPM_table_rosa_female.csv


title: sig-ABA-6h-1


title: mock-3h-2


title: Vehicle mouse 1


title: Heart, Female, Transgenic, Tamoxifen, 6 weeks, rep2

description:
F_T6wk:Rosa6_29H
CPM_table_rosa_female.csv

value: 6 weeks


title: sig-ABA-3h-3


title: mock-3h-1


title: Mouse, Heart, H3K27ac, 6837,  do8339

tag: strain

value: Heart

value: wild-type

value: adult

value: male


title: sig-ABA-3h-2


title: sig-ABA-3h-1


title: sig-ABA-6h-2


title: Mouse, Heart, H3K4me3, 6842,  do8334

tag: Sex


title: Heart, Female, Trangenic, No tamoxifen, Baseline, rep1

description:
F_T0wk:Rosa6_26H
CPM_table_rosa_female.csv

tag: treatment

value: No tamoxifen


title: mock-0h-1

value: WT


title: Mouse, Heart, H3K27ac, 6839,  do4441


title: sig-ABA-1h-3


title: Heart, Female, Transgenic, Tamoxifen, 3 weeks, rep2

description:
F_T3wk:Rosa6_22H
CPM_table_rosa_female.csv


title: sig-ABA-1h-2


title: Heart, Female, Trangenic, No tamoxifen, Baseline, rep2

description:
F_T0wk:Rosa6_25H
CPM_table_rosa_female.csv


title: Mouse, Heart, H3K4me3, 6837,  do8329


title: sig-ABA-1h-1


title: spinal cord, male, biol rep4

city: Northampton

first: Lisa

last: Mangiamele

address: Clark Science Center, 44 College Ln

department: Dept of Biological Sciences

institute: Smith College

data_processing:
We used data from all three tissue types (brain, leg muscle, spinal cord) to assemble a de novo transcriptome for S. parvus. First, we concatenated all of the reads into a single forward and reverse dataset composed of 60 million forward and 60 million reverse reads. We assembled a de novo transcriptome using the Oyster River Protocol using a minimum filter of TPM = 1. We then used TransDecoder to predict protein coding regions using the Uniprot database (The Uniprot Consortium 2019) and "blastp" as well as "hmmscan" and the Pfam database to identify known peptides..
Supplementary files format and content: tab-delimited CSV files provide raw gene counts for each sample
Supplementary files format and content: File "Staurois_parvus.annotations.csv" provides public accession numbers and annotations for each gene

organism: Staurois parvus

source_name: spinal cord

extract_protocol:
We completely disrupted the tissue using a homogenizer and extracted total RNA following the TRIzol protocol (Invitrogen). RNA precipitated overnight at -20 C. We pelleted the RNA by centrifugation, resuspended in 50 uL of nuclease-free water, and treated samples with TURBO DNAse (Invitrogen) to remove contaminating DNA. We cleaned up the RNA using 2x Ampure RNAclean beads (Beckman Coulter).
We used 100 ng of total RNA to generate CNDA libraries using the Illumina Stranded mRNA ligation kit according to the manufacturer's protocol.

value: spinal cord


title: Mouse, Heart, H3K27ac, 73317,  do4245

data_processing:
ChIP-seq peak files were generated my MACS2 callPeak function (default parameters).
4C data was processed with pipe4C (Krijger et al. 2020)
Supplementary files format and content: MACS2 peak files for each ChIP and input combination (.narrowPeak extension)
Supplementary files format and content: 4C wig files for each 4C experiment

extract_protocol:
Tissues were prepared by direct perfusion of the liver with PBS, followed by dicing the whole organs (liver and heart) in small pieces around 1cm3. Blood clots within the heart ventricles were removed. Cross-linking of the diced tissue was performed in 1% formaldehyde solution for 20 min, addition of 250 mM glycine and incubation for a further 10 min to neutralize the formaldehyde. After homogenization of cross-linked tissues in a dounce tissue grinder, samples were washed twice with PBS and lysed according to published protocols (SCHMIDT et al. 2009 for ChIP and Krijger et al. 2020 for 4C) to solubilize DNA-protein complexes. For ChIP, chromatin was fragmented to 300 bp average size by sonication on a Misonix sonicator 3000 with a 418 tip (1/16 inch diameter). Chromatin from 50-200 mg of dounced tissue was used for each ChIP experiment using antibodies against H3K4me3 (millipore 05-1339), H3K27ac (abcam ab4729), H3K4me1 (abcam ab8895), TBX5 (Insight bio sc-515536), RXRA (sc-553), FOXA1 (ab70382), HNF4A (ARP31946), CEBPA (sc-9314) and HNF6 (sc-13050). For 4C, locus-specific 4C templates were made using two rounds of enzyme digestion (primary and secondary) and ligation. Purified 4C templates were amplified by inverse PCR with bait-specific primers.
Illumina sequencing libraries were prepared from ChIP-enriched or 4C-enriched DNA using ThruPLEX DNA-seq library preparation kit (Takara Bio) or NEBNext Ultra II DNA Library Prep Kit for Illumina with up to 10ng of input DNA and 8-15 PCR cycles. After PCR, libraries were pooled in equimolar concentrations and sequenced on Illumina HiSeq 4000, NextSeq 500 or NovaSeq 6000 instruments.
ChIP-Seq, 4C-Seq


title: Mouse, Heart, H3K4me3, 6839,  do4436


title: Heart, Female, Transgenic, Tamoxifen, 3 weeks, rep1

description:
F_T3wk:Rosa6_17H
CPM_table_rosa_female.csv


title: sig-mock-24h-3


title: spinal cord, male, biol rep3


title: Heart, Female, Control, Tamoxifen, Baseline, rep2

description:
F_WT:Rosa6_12H
CPM_table_rosa_female.csv


title: spinal cord, male, biol rep2


title: Heart, Female, Control, Tamoxifen, Baseline, rep1

description:
F_WT:Rosa6_11H
CPM_table_rosa_female.csv


title: spinal cord, male, biol rep1


title: Mouse, Liver, H3K4me1, 85924,  do3169

source_name: Liver

value: Liver


title: Heart, Female, Transgenic, Tamoxifen, 6 weeks, rep1

description:
F_T6wk:Rosa6_28H
CPM_table_rosa_female.csv

value: Female


title: Mouse, Heart, input, 75191,  do4092

value: input


title: mock-0h-3

source_name: Leaves


title: sig-mock-24h-1


title: Heart, Male, Trangenic, No tamoxifen, Baseline, rep4

description:
M_T0wk:Heart66
CPM_table_male.csv

value: Male

value: heart


title: Mouse, Liver, H3K4me1, 85923,  do3168


title: mock-0h-2


title: leg muscle, male, biol rep5

source_name: leg muscle

value: leg muscle


title: Mouse, Liver, H3K4me1, 85921,  do3167


title: sig-mock-12h-3


title: sig-mock-12h-2


title: Heart, Male, Control, Tamoxifen, Baseline, rep3

description:
M_WT:Heart64
CPM_table_male.csv

value: Baseline

value: Tamoxifen


title: leg muscle, male, biol rep3


title: leg muscle, male, biol rep4


title: sig-mock-12h-1

value: Leaves


title: Mouse, Liver, H3K4me1, 85920,  do3166


title: Heart, Male, Trangenic, No tamoxifen, Baseline, rep3

description:
M_T0wk:Heart63
CPM_table_male.csv


title: sig-mock-24h-2


title: Mouse, Liver, input, 85923,  do3150


title: leg muscle, male, biol rep2


title: sig-mock-6h-3


title: leg muscle, male, biol rep1


title: Heart, Male, Trangenic, Tamoxifen, 3 week, rep4

description:
M_T3wk:Heart44
CPM_table_male.csv

tag: 3 week


title: Mouse, Liver, input, 85924,  do3151

tag: genotype


title: sig-mock-6h-2


title: brain, male, biol rep2

source_name: brain

value: brain


title: Mouse, Liver, input, 85920,  do3148

tag: developmental stage


title: sig-mock-6h-1


title: Heart, Male, Trangenic, Tamoxifen, 3 week, rep3

description:
M_T3wk:Heart43
CPM_table_male.csv


title: Mouse, Liver, input, 85921,  do3149

tag: age (months)


title: brain, male, biol rep1


title: Heart, Male, Control, Tamoxifen, Baseline, rep4

description:
M_WT:Heart65
CPM_table_male.csv


title: Heart, Male, Trangenic, Tamoxifen, 6 week, rep2

description:
M_WT:Heart35
CPM_table_male.csv

tag: 6 week


title: Mouse, Liver, H3K4me3, 85924,  do3137

tag: individual

tag: antibody


city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
WT WIBR3 human naïve stem-cells, maintained in RCL medium for 3 days, to induce Primitive Endoderm/Extraembryonic Mesoderm lineages
filtered_feature_bc_matrix.tgz

data_processing:
Demultiplexing was done with bcl2fastq2
Alignment and quantification of single cell features was done with cellranger/7.1.0 counts
Aggregation of the two samples was done using  cellranger aggr
Cells with under 1000 expressing genes, over 8000 expressing genes or over 15% mitochondrial gene expression were filtered out for the rest of the analysis.
Seurat integrated analysis and anchoring of 2 individual samples was performed and then normalized by log-normalization using a scale-factor of 10,000. The top 2,000 variable genes were identified by the variance stabilizing transformation method, and subsequently scaled and centered.
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.tgz includes CellRanger output files that were used in the analysis process.  The order of the samples in filtered_feature_bc_matrix.tgz is: 1 - Human Naive Stem Cells, RCL medium, maintained for 3 days, 2 - Human Naive Stem Cells, BAP(J) medium, maintained for 3 days.

growth_protocol: Human naïve pluripotent stem-cells were expanded in human HENSM conditions for at least 3 passages.

extract_protocol:
RNA extracted according to 10x Genomics Chromium v3.1 Dual Index system kit instructions
10x Genomics Chromium v3.1 Dual Index system (5000 cell target cell recovery)

treatment_protocol: For induction HENSM cells were plated on gelatin-MEF coated plates the day before induction with 10 µM ROCKi Y27632, next day medium was changed to RCL for 72h. RCL is composed of: 480 ml RPMI media (GIBCO 21875-03), 10 ml B27 minus insulin supplement (Invitrogen A18956-01), 1 mM GlutaMAX (Invitrogen), 1 % penicillin-streptomycin (Invitrogen), 3 µM CHIR (Axon Medchem 1386) and 10 ng/ml LIF (Peprotech 300-05). RCL medium contains the same composition as RACL but without adding recombinant Activin.  Please see paper's Methods for further details.

tag: cell line

tag: cell type

value: PrE/ExEM

value: RCL (3 days)


title: Heart, Male, Control, Tamoxifen, Baseline, rep2

description:
M_T6wk:Heart31
CPM_table_male.csv


title: sig-mock-3h-3

tag: timepoint


title: Heart, Male, Trangenic, Tamoxifen, 1 week, rep4

description:
M_T1wk:Heart48
CPM_table_male.csv

tag: 1 week


title: Mouse, Liver, H3K4me3, 85923,  do3136

first: Diego

last: Villar

address: 4 Newark Street, Blizard Institute

institute: Queen Mary University of London

value: wild-type

value: adult


title: Human Naive Stem Cells, BAP(J) medium, maintained for 3 days

description:
WT WIBR3 human naïve stem-cells, maintained in BAP(J) medium for 3 days, to induce Trophoectoderm lineage
filtered_feature_bc_matrix.tgz

treatment_protocol: 24 hours before the induction, cells were plated in HENSM on 1% Matrigel (corning 356231) -coated plates supplemented with 10 µM ROCKi Y27632 (Axon 1683), next day the protocol was started. The 3-day protocol for human TE induction/priming: : BAP(J) media was used for 72 hours. This medium consisted on 2 µM TGFRi A83-01 and 2 µM MEKi/ERKi PD0325901 base, which was complemented the first 24h with 10ng/ml Human recombinant BMP4 (Peprotech) and then substituted with for 1µM JAK inhibitor I (Calbiochem 420099) on day 2 and 3.  Please see paper's Methods for further details

value: Trophoectoderm

value: BAP(J) (3 days)


title: Heart, Male, Trangenic, Tamoxifen, 6 week, rep3

description:
M_T6wk:Heart30
CPM_table_male.csv


title: sig-mock-3h-2

value: WT


title: Heart, Male, Control, Tamoxifen, Baseline, rep1

description:
M_WT:Heart25
CPM_table_male.csv

tag: time point


title: Mouse, Liver, H3K4me3, 85920,  do3134

value: Liver

value: male


title: Heart, Male, Trangenic, Tamoxifen, 1 week, rep3

description:
M_T1wk:Heart24
CPM_table_male.csv

tag: replicate


title: WT 1

city: Suzhou

first: Sai

last: Ma

state: Jiangsu

address: 242 guangji road

institute: The Affiliated Suzhou Hospital of Nanjing Medical University

data_processing:
none provided
Supplementary files format and content: counts

source_name: CASKI

extract_protocol: none providided

value: CASKI

value: cervical squamous cell carcinoma

value: MUC1 knockout


title: sig-mock-1h-2

tag: tissue


title: Mouse, Liver, H3K27ac, 85924,  do3131

city: London

tag: strain


title: sig-mock-1h-1


title: MUC1 knockout 2


title: WT 2


title: Heart, Male, Trangenic, Tamoxifen, 3 week, rep2

description:
M_T3wk:Heart16
CPM_table_male.csv

tag: Sex

value: Male

value: heart


title: Mouse, Liver, H3K27ac, 85923,  do3130


title: Heart, Male, Trangenic, Tamoxifen, 1 week, rep2

description:
M_T1wk:Heart23
CPM_table_male.csv

tag: treatment

value: Tamoxifen


title: Mouse, Liver, H3K27ac, 85921,  do3129


title: Heart, Male, Trangenic, Tamoxifen, 3 week, rep1

description:
M_T3wk:Heart15
CPM_table_male.csv

tag: 3 week


title: MUC1 knockout 1

tag: genotype


title: sig-mock-3h-1

value: Leaves


title: Mouse, Liver, H3K27ac, 85920,  do3128

tag: developmental stage


title: sig-mock-0h-1


title: sig-mock-1h-3


title: rCHOP 2

city: Boston

first: Matthew

middle: Ryan

last: Sullivan

state: Massachusetts

address: 140 The Fenway

department: Pharmaceutical Sciences

institute: Northeastern University

data_processing:
Unknown, performed by Novogene
Assembly: hg18
Supplementary files format and content: raw gene counts of all samples in excel format, along with basic gene information

source_name: Blood

extract_protocol:
Rneasy mini kit
Novogene ultra-low input

value: Blood

value: Primary cells

value: Cancer and immune cells

value: rCHOP


title: rCHOP 1


title: Heart, Male, Trangenic, Tamoxifen, 6 week, rep1

description:
M_T6wk:Heart13
CPM_table_male.csv


title: sig-mock-0h-2


title: Mouse, Liver, H3K4me3, 85921,  do3135

value: wild-type

value: adult

tag: age (months)


title: sig-mock-0h-3


title: Man-72h-3

value: Man


title: Heart, Male, Trangenic, No tamoxifen, Baseline, rep2

description:
M_T0wk:Heart12
CPM_table_male.csv

value: Baseline

value: No tamoxifen


title: Mouse, Heart, H3K4me1, 45884_45885_45886,  do17728

value: Heart

value: male


title: Heart, Male, Trangenic, No tamoxifen, Baseline, rep1

description:
M_T0wk:Heart11
CPM_table_male.csv


title: Rituximab 1

value: Rituximab


title: Mouse, Heart, input, 45884_45885_45886,  do17732

value: input


title: Rituximab 2


title: Mouse, Heart, H3K4me3, 45884_45885_45886,  do17726


title: Man-72h-2

value: WT


title: Mouse, Heart, H3K27ac, 45884_45885_45886,  do17727


title: Heart, Male, Trangenic, Tamoxifen, 1 week, rep1

description:
M_T1wk:Heart10
CPM_table_male.csv

value: Male

value: heart


title: HUVEC, No sera [Blank2_HUVEC_S57]

first: Chisato

last: Shimizu

address: 9500 Gilman Dr.

institute: UCSD

description: Additional information not provided

data_processing:
The RNA-Seq analysis pipeline consisted of: quality control using fastp and MultiQC and alignment and read counting using Salmon, DESeq2 and ensembl hg38 genome and annotation. Normalisation was performed using the DESeq2 method for estimating scale factors with a subsequent log transformation. P-values were adjusted using Benjamini-Hochberg method
Assembly: Genome_build: hg38
Supplementary files format and content: GEO_submitted_HUVEC_MIS-C_KD_rawdata062923.csv, Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: GEO_submitted_HUVEC_MIS-C_KD_normalizeddata062923.csv, Matrix table with raw gene counts for every gene and every sample

source_name: HUVEC

extract_protocol:
Total RNA from HUVECs was isolated using miRVana (ThermoFisher) for RNA-seq.
RNA sequencing libraries were generated using the Illumina Ribo-Zero Plus rRNA Depletion Kit with IDT for Illumina RNA UD Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) reads to a depth of approximately 25 per million reads on an Illumina NovaSeq 6000. Samples were demultiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

value: HUVEC

value: 24h incubation

value: not done

value: without sera


title: HUVEC, No sera [Blank3_HUVEC_S58]

description: Additional information not provided


title: Man-24h-3

value: Leaves


title: HUVEC, No sera [Blank1_HUVEC_S56]

description: Additional information not provided


title: Mouse, Heart, H3K27ac, 17_36584,  do17628

value: wild-type


title: WT_ON_701297

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

data_processing:
Raw sequencing reads were processed withkallisto using the mm10 reference transcriptome downloaded from Ensembl. The resulting counts for different isoforms were summed up to obtain counts at the gene level for each sample.
Assembly: mm10
Supplementary files format and content: matrix of raw counts with samples in columns and genes in rows

source_name: optic nerve

extract_protocol:
RNA was extracted from samples using the Total RNA Purification Micro Kit (Cat. 35300, Norgen Biotek Corp) following the supplied protocol.
Sample quality control wasperformed using the Agilent 2100 Bioanalyzer or the Agilent 4200 Tapestation. Qualifying samples were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina)

treatment_protocol: Mice were anesthetized under isoflurane (5%, 1.5L/min), and decapitated. Brains and optic nerves were dissected, and flash frozen in pre-chilled isopentane at -52°C for 30 seconds. Brains were then stored at -80°C until sectioning. The corpus callosum (Bregma 0.98mm – Bregma 0.62mm) was sectioned coronally at 100μm on a cryostat and mounted onto glass slides. Slides were then stored at -80°C until used. Corpus callosum samples were then dissected from frozen brain sections, while being cooled on dry ice.

value: optic nerve

value: wild type


title: Man-72h-1

value: Man


title: Mouse, Heart, H3K4me3, 17_36584,  do17627

value: adult


title: WT_ON_717652


title: Heart, Male, Trangenic, Tamoxifen, 6 week, rep4

description:
M_T6wk:Heart8
CPM_table_male.csv

tag: 6 week

value: Tamoxifen


title: HUVEC, MIS-C [203063A_HUVEC_S50]

description: Additional information not provided

value: 10percent pre-treatment sera from KD


title: WT_ON_719857


title: Man-24h-1


title: HUVEC, MIS-C [203064A_HUVEC_S51]

description: Additional information not provided


title: Man-24h-2


title: Man-12h-3


title: Mouse, Heart, H3K4me1, 33017,  do14467

value: Heart

value: male

tag: individual


title: HUVEC, MIS-C [203060A_HUVEC_S49]

description: Additional information not provided


title: Man-12h-2

value: WT


title: WT_ON_700858


title: WT_CCg_7198587

source_name: corpus callosum

value: corpus callosum


title: Mouse, Heart, H3K27ac, 33018,  do14468

tag: antibody


title: Man-12h-1


title: HUVEC, MIS-C [203055A_HUVEC_S48]

description: Additional information not provided

tag: cell line


title: Man-6h-3


title: HUVEC, MIS-C [203041A_HUVEC_S46]

description: Additional information not provided

tag: cell type

value: 10percent pre-treatment sera from MIS-C


title: WT_CCg_30


title: HUVEC, MIS-C [203040A_HUVEC_S45]

description: Additional information not provided

value: HUVEC


title: WT_CCg_28


title: HUVEC, Healthy control [193006C_HUVEC_S54]

description: Additional information not provided

value: 24h incubation

value: 10percent sera from healthy control


title: HUVEC, KD [183082A_HUVEC_S42]

description: Additional information not provided

value: not done


title: Man-6h-1

value: Leaves

tag: timepoint


title: Man-3h-2


title: WT_CCg_685232


title: HUVEC, KD [173062A_HUVEC_S44]

description: Additional information not provided


title: Man-3h-1


title: KO_ON_717651

value: Zdhhc9 knockout


title: Man-3h-3


title: KO_ON_693452

value: optic nerve


title: HUVEC, KD [173007A_HUVEC_S41]

description: Additional information not provided


title: KO_ON_48118A4


title: KO_ON_719856


title: Mouse, Heart, H3K4me3, 33016,  do14466

value: wild-type


title: HUVEC, MIS-C [203046A_HUVEC_S47]

description: Additional information not provided


title: HUVEC, Healthy control [163096C_HUVEC_S53]

description: Additional information not provided


title: KO_CCg_719856


title: HUVEC, KD [163048A_HUVEC_S174]

description: Additional information not provided


title: NaCl-72h-1

value: NaCl


title: KO_ON_48038A7


title: Man-6h-2

value: Man


title: WT_CCg_717652

value: wild type


title: NaCl-72h-3


title: NaCl-24h-3


title: KO_CCg_693452


title: HUVEC, KD [153003A_HUVEC_S173]

description: Additional information not provided


title: NaCl-24h-2


title: KO_CCg_717651


title: NaCl-12h-3


title: KO_CCg_29


title: NaCl-72h-2


title: HUVEC, Healthy control [163048C_HUVEC_S55]

description: Additional information not provided


title: KO_CCg_693451


title: NaCl-24h-1


title: KO_CCg_27


title: NaCl-6h-3


title: NaCl-12h-1


title: NaCl-12h-2


title: NaCl-6h-2


title: Skin, excised, cultured, expanded, for myogenic induction for 7 days, Rep3

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

data_processing:
RNA-seq reads were filtered to remove low-quality reads using fastp (v 0.23.2).
Expression of transcripts was quantified using Salmon package36 (v1.7.0) and Ensembl GRCh38.p13 (release 108).
Transcript abundance values were imported into R and summarized with tximport (v1.28.0 ) .DESeq2 (v1.36.0) as implemented in SARTools  was then used to normalize raw counts and apply exploratory analysis.

source_name: Skin

growth_protocol:
Immortalized fibroblasts were cultured in DMEM, 4.5 g/l glucose, 10% fetal bovine serum and 0.1% Penicillin-Streptomycin.
Immortalized myoblasts were cultured in DMEM (Invitrogen) supplemented with 16% M199 (Invitrogen), 4.5 g/l glucose, 20% fetal bovine serum, 0.1% Penicillin-Streptomycin, 5 µg/ml insulin (Sigma-Aldrich), 25 µg/ml fetuin (Life Technologies), 5 ng/ml human Epidermal Growth Factor (Life Technologies), 0.5 ng/ml basic fibroblast growth factor (Life Technologies) and 0.2 µg/ml dexamethasone (Sigma-Aldrich).

extract_protocol:
Total RNA was extracted with TRIzol (Thermo Fisher Scientific), eluted in 20 µl RNase-free water and concentration estimated by A260. RNA integrity number was assessed with an Agilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano kit
Libraries were prepared using the KAPA mRNA HyperPrep kit (Roche)

treatment_protocol:
For myo-conversion, immortalized fibroblasts were transduced with a Tet-on inducible lentiviral vector encoding mouse Myod with a multiplicity of injection of 10 in presence of 4 μg/ml of polybrene (Sigma-Aldrich). Cells were cultured in DMEM, 4.5 g/l glucose, 10% fetal bovine serum and 0.1% Penicil-lin-Streptomycin. Cells were then plated on dishes coated with 1% Matrigel (Sig-ma-Aldrich) at high density and cultured in DMEM, 10 µg/ml insulin and 4 µg/ml doxycycline (Sigma-Aldrich). After 5 days, myo-converted fibroblasts (McF) were harvest-ed for follow-up assays.
For myogenic differentiation, cells were plated on dishes coated with 1% Matrigel (Sigma-Aldrich) at high density in differentiating medium (DMEM, 10 µg/ml insulin, 50 µg/ml Penicillin-Streptomycin). After 5 days, myotubes (MT) were harvested for follow-up assays.

value: Skin

value: fibroblast

tag: treatment 1

value: hTRET-immorttalized

tag: treatment 2

value: Myogenic induction

tag: time

value: 7 days

value: rep 3


title: Paravertebral muscle, excised,  cultured, expanded, for myogenic induction, Rep3

source_name: Muscle

tag: tissue

value: Muscle

value: myoblast

value: WT

value: myogenic differentiation

value: 5 days

tag: replicate


title: NaCl-3h-2

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

institute: Gyeongsang National University

data_processing:
A quality control application for high throughput sequence data using FastQC Version 0.11.8
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt  Version 1.15
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using Trimmomatic Version 0.38
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Assembly: Capsicum annuum v1.6
Supplementary files format and content: tab-delimited text files include the values of read count for each sample

extract_protocol:
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols

value: Leaves


title: Paravertebral muscle, excised,  cultured, expanded, for Rep1

value: untreated

value: rep 1


title: Skin, excised, cultured, expanded, for myogenic induction for 7 days, Rep1


title: Skin, excised, cultured, expanded, for myogenic induction for 7 days, Rep2

value: rep 2


title: NaCl-6h-1

value: NaCl


title: Skin, excised, cultured, expanded, for myogenic induction, Rep3


title: Paravertebral muscle, excised,  cultured, expanded, for Rep3


title: Paravertebral muscle, excised,  cultured, expanded, for myogenic induction, Rep2


title: Paravertebral muscle, excised,  cultured, expanded, for Rep2


title: NaCl-3h-3


title: Paravertebral muscle, excised,  cultured, expanded, for myogenic induction, Rep1


title: NaCl-3h-1


title: lineage-ckit-Sca1-_miR-221/222-deficient

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

description: 1 mouse, non-hashtagged

data_processing:
Raw data were processed using cellranger-3.1.0 with refdata-gex-mm10-2020-A and refdata-cellranger-vdj_GRCm38_alts_ensembl-mouse-2.2.0 as reference.   .Mkfastq, count and vdj were used in default parameter settings with 3000 expected cells for demultiplexing, detection of intact cells, quantification of gene expression, antibody capture as well as assembly and quantification of T cell receptor sequences.
Assembly: mm10
Supplementary files format and content: h5: aggregated gene count matrix in hdf5 format including antibody counts for CD127,  AntiAPC, CD279, CD197, CD39, CD185, CD31, KLRG1, CD183, CD49d, CD73, FQPQNGQFI, KAVYNFATC, SGVENPGGYCL, CSANNSHHYI, ISHNFCNL as well as hashtag counts for different biological replicates. feature_reference.csv: ADT/HTO reference file, fasta: high-confidence contig sequences of immune receptors with the corresponding cellular barcode and contig-id; csv: results from single cell immune profiling, comprising the annotation of the immune receptor, cellular barcode and contig-id.

source_name: Bone marrow

extract_protocol:
Single cell BM suspensions of unperturbed miR‑221/222 proficient and deficient mice were stained for FACS and MPP(3-4), CLP, lin-c-kit+Sca1- and lin-c-kit-Sca1- cells were sorted.
MPPs were sorted as pools of MPP3+MPP4 populations as ineage-ckit+Sca1+CD150-CD48+ population. CLP was sorted as lineage-ckitloSca1loFlk2+IL7R+ population. Cells from lineage- population were sorted as ckit+Sca1- and ckit-Sca1- populations.
Single cell BM suspensions of unperturbed miR‑221/222 proficient and deficient mice were stained for FACS and MPP(3-4), CLP, lin-c-kit+Sca1- and lin-c-kit-Sca1- cells were applied to the 10x Genomics workflow for cell capturing and generation of scRNA gene expression (GEX) library using the Chromium Single Cell 3′ Library & Gel Bead Kit.
Chromium Single Cell 3′ Library & Gel Bead Kit from 10x Genomics was used.

tag: strain

value: C57BL/6J background

tag: genotypes

value: miR-221/222fl/y- Tg(Vav1-icre)J

tag: sorting strategy

value: live lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)- Ly6a/e(Sca1)- cells


title: Skin, excised, cultured, expanded, for myogenic induction, Rep2

value: Skin

value: fibroblast

tag: genotype

value: hTRET-immorttalized


title: lineage-ckit-Sca1-_miR-221/222-proficient

description: 1 mouse, non-hashtagged


title: Skin, excised, cultured, expanded, for myogenic induction, Rep1

value: Myogenic induction


title: lineage-ckit+Sca1-_miR-221/222-deficient

description: 1 mouse, non-hashtagged

value: live lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)- cells


title: Heat-72h-3

tag: treatment

value: Heat


title: Heat-72h-1

value: WT


title: Skin, excised, cultured, expanded, for Rep2


title: Heat-72h-2


title: lineage-ckit+Sca1-_miR-221/222-proficient

description: 1 mouse, non-hashtagged


title: MPP_miR-221/222-deficient

description: 1 mouse, non-hashtagged

value: live lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)lo Ly6a/e(Sca1)lo CD127(IL7R)+ CD135(Flk2)+ CLP cells


title: Skin, excised, cultured, expanded, for Rep1


title: Skin, excised, cultured, expanded, for Rep3

value: rep 3


title: sws2_bluecone, scRNAseq

city: SHANGHAI

first: Shuguang

last: Yu

address: 320 Yueyang Road

institute: Institute of Neuroscience, Chinese Academy of Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Retina

extract_protocol:
To perform single-cell RNA sequencing (scRNA-seq), FACS-isolated cells were loaded onto the Chromium Single Cell Chip (10x Genomics, USA) according to the manufacturer’s protocol. The scRNA-seq libraries were generated using the GemCode Single-Cell Instrument and Single Cell 3’ Library and Gel Bread kit v2 and v3 Chip kit (10x Genomics, 120237). Library quantification and quality assessments were performed by Qubit fluorometric assay (Invitrogen) and dsDNA High Sensitivity Assay Kit (AATI, DNF-474-0500). The fragment analyser was performed using the High Sensitivity Large Fragment -50kb Analysis Kit (AATI, DNF-464). The indexed library was tested for quality, and sequenced by the Illumina NovaSeq 6000 sequencer with the S2 flow cell using paired-end 150 x 150 base pairs as the sequencing mode. Sequencing depth was 60K reads per cell.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, sorted cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Retina

tag: age

value: 9 dpf


title: MPP_miR-221/222-proficient

description: 1 mouse, non-hashtagged


title: lws2_redcone, scRNAseq

description: 10x Genomics


title: Paravertebral muscle, excised,  cultured, expanded, for input sample

data_processing:
Reads were mapped to the hg38 genome with Bowtie2 v2.4.1.
Bigwig tracks were generated from Log2(ChIP/input) ratios in 1 kilobase (kb) bins using bamCompare from Deeptools v3.5.1
Mapped reads were used to call Lamin A/C and H3K9me3 peaks using 10 runs of Enriched Domain Detector with auto-estimation of GapPenalty and BinSize parameters, and mean GapPenalty and BinSize outputs from these runs were used for a final EDD run.
Supplementary files format and content: peaks.bed
Supplementary files format and content: bw

extract_protocol:
Cells were fixed in 1% formaldehyde, lysed in 50 mM Tris-HCl, pH 8, 10 mM EDTA, 1% SDS, protease inhibitors and Na-butyrate, and sonicated into ~200 bp fragments using a Picorupter (Diagenode). After sedimentation,  chromatin was incubated with anti-lamin A/C antibodies at 10 µg/5x10e6 cells or with anti-H3K9me3 antibodies at 2.5 µg/10e6 cells. Cross-links were reversed, DNA purified, eluted in H2= and processed for library preparation.
Libraries were prepared using the Microplex kit (Diagenode)

value: Muscle

value: myoblast

value: myogenic differentiation

value: 5 days

tag: chip antibody

value: Input

value: rep 1


title: Skin, excised, cultured, expanded, for input sample

value: Skin


title: gfap_intact, scRNAseq

description: 10x Genomics


title: Paravertebral muscle, excised,  cultured, expanded, for H3K9me3 ChIP

value: H3K9me3 (Diagenode C15410056)


title: CLP_miR-221/222-deficient

description: 1 mouse, non-hashtagged

value: C57BL/6J background

value: miR-221/222fl/y- Tg(Vav1-icre)J

value: live lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD150- CD48+ MPP cells


title: MPP2_CITE_Pert

description:
4 mice, hashtagged (#1) miR-221/222-proficient, 4 mice, hashtagged (#2) miR-221/222-deficient,
MPP2_no3.h5

library_source: other

molecule: protein

extract_protocol:
Bone marrow derived lineage positive (B220+, CD3+, CD4+, CD8+, CD11b+, CD11c+,CD19+, Gr1+, NK1.1+, TER119+) cells from perturbed or unperturbed miR‑221/222 proficient and deficient mice were first depleted on magnetic column (LS from Miltenyi) using 4 mice in each condition. The BM single cell suspensions were labeled separately for preparative FACS, followed by staining with TotalSeq™-C anti-mouse antibodies: Hashtag‑1 for miR‑221/222 proficient and perturbed, Hashtag‑4 for miR‑221/222 proficient and unperturbed, Hashtag-2 for miR‑221/222 deficient and perturbed and Hashtag-5 miR‑221/222 deficient and unperturbed (BioLegned, #1: 155861, #2: 155863, #4: 155867, #5 155869). The unperturbed or perturbed miR221/222-proficient samples were pooled with deficient samples for scRNAseq.
HSC was sorted as live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34- Flk2- CD150+ CD48- cells; MPP1 was sorted as live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34+ Flk2- CD150+ CD48- cells; MPP2 was sorted as live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34+ Flk2- CD150+ CD48+ cells.
The samples were then applied to 10x Genomics workflow for cell capturing and scRNA gene expression (GEX) library preparation using the Chromium Single Cell 5′ Library & Gel Bead Kit as well as the Single Cell 5′ Feature Barcode Library Kit (10x Genomics). After cDNA amplification the CiteSeq libraries were prepared separately using the Single Index Kit N Set A while final GEX libraries were obtained after fragmentation, adapter ligation, and final Index PCR using the Single Index Kit T Set A.
Chromium Single Cell 5′ Library & Gel Bead Kit as well as the Single Cell 5′ Feature Barcode Library Kit (10x Genomics).

value: live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34+ Flk2- CD150+ CD48+ MPP2 cells


title: Heat-12h-2

city: Jinju

value: Leaves

value: WT

value: Heat


title: Heat-12h-3


title: CLP_miR-221/222-proficient

description: 1 mouse, non-hashtagged


title: Heat-24h-2


title: BS_wt-DMSO_rep2

first: Jincong

last: Zhou

address: Tsinghua Yuan

institute: Tsinghua University

data_processing:
Whole-genome bisulfite-seq: Reads were trimed using trim_galore. Bismark v0.19.0 was used to map the trimmed reads and extract methylation level as described previously. The UCSC application tool wigToBigWig was used to get the bigwig file.
ChIP-seq: Reads were trimed using trim_galore.  Trimmed reads were aligned to the TAIR10 genome with Bowtie 2 version 2.3.0 using the default settings, and samtools 1.3.1 was used to remove reads with more than three mismatches and non-uniquely mapped reads. Then total mapped reads were further divided into forward and reverse reads. MACS2 was used to identify peaks and normalized coverage files (bigWig) with 5 bp bin sizes were obtained using bamCoverage from deeptools v2.26.0 to visualize on the Integrative Genomics Viewer. Furthermore, bamCompare or bigwigCompare from deeptools were used to compare immunoprecipitated and input samples for ChIP-seq analysis.
Assembly: TAIR10
Supplementary files format and content: ChIP-seq: bigwig files were generated using the bamCoverage from deeptools. Whole-genome bisulfite-seq: The UCSC application tool wigToBigWig was used to get the bigwig file.

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
Whole-genome bisulfite-seq: Nuclear DNA was extracted from 12 days old seedlings as described in DRIP/DRIP-seq section and sonicated to 250bp with COVARIS. After that Bisulfite conversion and DNA recovery was performed with EZ DNA Methylation-Gold Kit (ZYMO Research) by following the manufacturer instructions. Finally, the sequencing library is made using the EpiArt DNA Methylation Library Kit for Illumina V3 (Vazyme, NE103) by following the manufacturer instructions.
ChIP-seq: To gain the nucleosome resolution, native H3K9me2 ChIP without crosslink and sonication was performed as described in (Bernatavichute et al., 2008), with some modifications. In brief, nuclei were extracted from 12 days old seedlings with Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextran T40, 20 mM HEPES–KOH [pH 7.4], 10 mM MgCl2, 0.5% Triton X-100, 5 mM DTT, and protease inhibitors [Roche]). Nuclei were suspended in 1X MNAse buffer (50mM TriHCl pH 7.6, 5mM CaCl2, 0.1mM PMSF) containing 1X proteinase inhibitor cocktail (Roche). After RNase A (Thermo Scientific™) treatment at 37C for 30 minutes, chromatin was digested with MNase enzyme (NEB) for 6 minutes and the reaction was stopped with EDTA (10mM). Then, the nucleosomes were released with the addition of 0.005% SDS while rotating at 4C for 2-3 hours. After that the supernatant was separated and diluted with dilution buffer (0.1% triton, 50mM NaCl, 0.1mM PMSF, 17mM trisHCl, 3.33mM EDTA, 1x Cocktail inhibitor). Chromatin was pre-cleaned with Protein G beads, and immnoprecipitated with anti-H3K9me2 (Abcam, ab1220) antibodies at 4C overnight. The complexes were incubated with protein G beads (Millipore) at 4C for 3 hours with rotation, and washed three times with ChIP wash buffer having different concentration of NaCl in each wash (50mM TrisHCl pH 7.6, 10mM EDTA, 50/100/150 mM NaCl, 0.1mM PMSF, and 1x Cocktail inhibitor). Then DNA was eluted with elution buffer (0.1%SDS and 0.1M NaHCO3) at 65C for 15 minutes. Proteinase K treatment was performed at 55 C for 2 hour. DNA was recovered after phenol:chloroform extraction. Finally, the sequencing library is made using the TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme, TD502) by following the manufacturer instructions.

value: seedlings

tag: ecotype

value: Columbia


title: Heat-24h-3


title: Skin, excised, cultured, expanded, for H3K9me3 ChIP

value: fibroblast

value: hTRET-immorttalized

value: Myogenic induction


title: BS_wt-DMSO_rep1


title: Heat-12h-1


title: Paravertebral muscle, excised,  cultured, expanded, for lamin A/C ChIP Rep3

value: Muscle

value: myoblast

value: myogenic differentiation

value: 5 days

value: Lamin A/C (Santa Cruz sc7292x)

value: rep 3


title: Heat-6h-3


title: BS_ddm1-FLA_rep2


title: Paravertebral muscle, excised,  cultured, expanded, for lamin A/C ChIP Rep2

value: rep 2


title: Heat-6h-2


title: Heat-24h-1


title: Paravertebral muscle, excised,  cultured, expanded, for lamin A/C ChIP Rep1

value: rep 1


title: BS_ddm1-FLA_rep1


title: BS_ddm1-DMSO_rep2


title: MPP2_CITE_Unpert

description:
4 mice, hashtagged (#4) miR-221/222-proficient, 4 mice, hashtagged (#5) miR-221/222-deficient,
MPP2.h5

value: C57BL/6J background

value: live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34+ Flk2- CD150+ CD48+ MPP2 cells


title: Heat-6h-1

value: Leaves

value: WT


title: Skin, excised, cultured, expanded, for lamin A/C ChIP Rep3

value: Skin


title: BS_ddm1-DMSO_rep1

value: seedlings

value: Columbia


title: HSC_CITE_Unpert

description:
4 mice, hashtagged (#4) miR-221/222-proficient, 4 mice, hashtagged (#5) miR-221/222-deficient,
HSC.h5

value: live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34- Flk2- CD150+ CD48- HSC cells


title: Heat-3h-3

value: Heat