title: WYpol32-100R

type: genomic

first: Daoqiong

last: Zheng

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

description: genotype of sectors

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio.

organism: Saccharomyces cerevisiae

source_name: cell culture of WYpol32-100R

label_protocol: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain WYpol32 labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were grown in YPD medium at 30 degree.

extract_protocol: Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)

treatment_protocol: After culturing WYpol32 at 30°C to obtain fresh single colonies, the cells were spontaneously diluted and plated onto YPD medium. Red and white sectored colonies were selected and purified, and the red and white fractions were subjected to chromosome IV microarray analysis.

source_name: cell culture of WYpol32


title: WYpol32-103R

status: Public on Mar 11 2025

city: Hangzhou

state: Zhejiang

country: China

description: genotype of sectors

molecule: genomic DNA

source_name: cell culture of WYpol32-103R

tag: strain


title: MEF_IP-WT-VSV-INF-2-A

type: SRA

city: Houston

first: Eric

last: Van Nostrand

state: Tx

address: 1 Baylor Plaza

department: Biochemistry and Molecular Pharmacology

country: USA

institute: Baylor College of Medicine

description: Library name: EV228_IP

library_source: other

data_processing:
Standard processing of eCLIP data was performed as previously described (Blue SB, et al. Nature Protocols 2022), with mapping performed to a custom genome index that included both the VSV genome and either hg19 (for 293T experiments) or mm10 (for MEF experiments) as described below.
UMI removal and cut adapt:  umi_tools extract   --random-seed 1   --bc-pattern NNNNNNNNNN   --stdin 23145FL-08-01-37_S37_L001_R1_001.fastq.gz   --log /dev/null | cutadapt   -j 8   --match-read-wildcards   --times 1   -e 0.1   --quality-cutoff 6   -m 18   -a a_adapters.fasta   -O 1   -   --report minimal   2> EV225_IP.cut.adapt.log | cutadapt   -j 8  --match-read-wildcards   --times 1   -e 0.1   --quality-cutoff 6   -m 18   -a a_adapters.fasta   -O 5   -   -o EV225_IP.trim.gz   --report minimal   >>EV225_IP.cut.adapt.log
Repeat mapping (takes adapter-trimmed fastq files, and maps to a repeat database to filter repeat elements prior to genome mapping:     STAR     --runMode alignReads     --runThreadN 8     --alignEndsType EndToEnd     --genomeDir  [mus_musculus_repbase_v2 or homo_sapiens_repbase_v2]   --genomeLoad NoSharedMemory     --outBAMcompression 10     --outFileNamePrefix EV225_IP.repeat.map     --outFilterMultimapNmax 100     --outFilterMultimapScoreRange 1     --outFilterScoreMin 10     --outFilterType BySJout     --outReadsUnmapped Fastx    --outSAMattrRGline ID:foo     --outSAMattributes All     --outSAMmode Full     --outSAMtype BAM Unsorted     --outSAMunmapped None     --outStd Log     --readFilesCommand zcat     --readFilesIn EV225_IP.trim.gz
Unique genomic mapping (takes repeat-removed reads and maps to the reference genome: STAR   --runMode alignReads   --runThreadN 8   --alignEndsType EndToEnd   --genomeDir [hg19+VSV or mm10+VSV] --genomeLoad NoSharedMemory   --outBAMcompression 10   --outFileNamePrefix EV225_IP.genome.map   --outFilterMultimapNmax 1   --outFilterMultimapScoreRange 1   --outFilterScoreMin 10   --outFilterType BySJout   --outReadsUnmapped Fastx   --outSAMattrRGline ID:foo   --outSAMattributes All   --outSAMmode Full   --outSAMtype BAM Unsorted   --outSAMunmapped None   --outStd Log   --readFilesIn EV225_IP.repeat.mapUnmapped.out.mate1
Sort mapped reads: samtools sort -@ 8 -m 2G -o EV225_IP.genome.map.bam *Aligned.out.bam
Remove PCR duplicate reads: samtools index EV225_IP.genome.map.bam umi_tools dedup   --random-seed 1   --stdin EV225_IP.genome.map.bam   --method unique   --stdout EV225_IP.bam
Make bigwigs: samtools index EV225_IP.bam b2bw EV225_IP.bam  --cpus 1
Isolate VSV-mapped reads only: bigWigToWig EV225.pos.bw -chrom=chrVSV EV225.pos.bw.chrVSV.wig
wigToBigWig EV225.pos.bw.chrVSV.wig /path/to/hg19_and_vsv.chrom.sizes EV242.pos.bw.chrVSV.wig.bw
Assembly: hg19 (for 293T) or mm10 (for MEF) with the addition of VSV (using accession NC_001560.1 with GFP was inserted between G and L as described in PMID 10400792)
Supplementary files format and content: bw files contain read density (in bigwig format) for the VSV genome (positive or negative strand as indicated in filename). Bigwig files are not included for datasets with zero reads

molecule: other

organism: Mus musculus

source_name: Mouse Embryonic Fibroblast

growth_protocol: HEK293T cells were obtained from ATCC (catalog # CRL-3216) and grown in complete medium containing DMEM (Gibco, Carlsbad, CA), 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco, Carlsbad, CA). For transient transfections, HEK293T cells were seeded the day prior to transfection in a 24-well plate (Genesee, El Cajon, CA) with 500 μL of complete media. Cells were transiently transfected with 500 ng of total DNA and 1.5 μL of TransIT-X2 (Mirus Bio, Madison, WI) following the manufacturer’s protocol.  For generation of inducible cell lines, sequences for mCherry, IFIT2, IFIT3, or IFIT2 and IFIT3 separated by a P2A site were cloned into the Flp-In vector pcDNA5/FRT/TO. Flp-In T-REx HEK293 cells (Invitrogen) maintained in 5 μg/mL of blasticidin were transfected at 70% confluency with mCherry or IFIT constructs and the vector containing the Flp recombinase pOG44 in a 1:10 molar ratio using TransIT-X2 (Mirus Bio). After one day, cells were transferred to new dishes, and on the following day, hygromycin (100 μg/mL) was added to cells. Following selection, cells were maintained in 5 μg/mL of blasticidin and 100 μg/mL of hygromycin. For induction of mCherry or IFIT proteins, cells were treated with 500 ng/mL of doxycycline for 24 h.   MEFs from Ifit2-/- and ΔIfit3a/b mice were prepared from day 13.5-14.5 embryos according to published protocols. Isolated MEFs were maintained in DMEM supplemented with 10% heat-inactivated, fetal bovine serum (FBS) (Cytiva), 100 U/mL penicillin-streptomycin (Invitrogen), non-essential amino acids (Cellgro), and Glutamax (Gibco). Passage 0 (P0 MEFs were frozen or split 1:4 when approximately 80% confluent (around 3 days). To generate transformed MEFs, 5x106 P1 primary MEFs were transfected with 10 μg of a plasmid (SV2) encoding the SV40 T antigen under control of a CMV promoter, using FuGene reagent (Promega) (3:1 μL FuGene to μg DNA ratio). Upon achieving confluence, MEF cultures were split 1:10. This process was repeated for approximately ten passages, at which time the transformed MEFs were frozen or used for experiments.

extract_protocol:
eCLIP was performed as previously described (Blue SB, et al. Nature Protocols 2022). Briefly, 10 million 293T or MEF cells were UV crosslinked (254 nM, 400 mJ/cm2), snap frozen, and lysed as previously described.
RNA fragmentation was performed, 2% of the sample was removed for size-matched input, and the remainder was subjected to immunoprecipitation of IFIT-bound RNA with antibodies against FLAG (M2 / F1804, Sigma) and HA (HA.11 / 901502, Biolegend) for 293T experiments, and IFIT2 (PA3-845, ThermoFisher) and IFIT3 (ABF1048, Millipore) for MEF experiments. Dephosphorylation, RNA adapter ligation, SDS-PAGE electrophoresis and nitrocellulose membrane transfer, RNA isolation, reverse transcription, and PCR amplification were performed as previously described (Blue, SM. et al, Nat Protocols 2022). Libraries are as previously described for eCLIP (Blue, SM. et al, Nat Protocols 2022), based on the Illumina RNA TruSeq HT adapter strategy.

treatment_protocol: Flp-In T-REx HEK293 cells expressing mCherry, IFIT2, IFIT3, or IFIT2 and IFIT3 in 10 cm culture dishes were induced with doxycycline for 24 h. Cells were then infected with VSV at an MOI of 3.0, and dishes were crosslinked using a UV cross-linker (254 nm; CL-1000 from UVP/Analytik Jena) at 400 mJ/cm2. Downstream sample processing and eCLIP were performed as previously described, using antibodies against FLAG (M2 / F1804, Sigma) and HA (HA.11 / 901502, Biolegend) for 293T experiments, and IFIT2 (PA3-845, ThermoFisher) and IFIT3 (ABF1048, Millipore) for MEF experiments. Most experiments were performed in biological duplicate, excepting the uninfected 293T samples (which were single replicates).

tag: cell type

value: Mouse Embryonic Fibroblast

tag: genotype

value: WT

tag: treatment

value: VSV infected

value: Interferon treated


title: MEF_INPUT-WT-VSV-INF-A

description: Library name: EV228_input


title: PM381_vc

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

description:
Library name: M20220
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

library_source: transcriptomic

data_processing:
Raw sequencing reads were trimmed to remove the UMI, Illumina TruSeq 3’ adapter sequence, and all nucleotides after the 3’ adapter. Pre-processed reads were aligned to the genome for seven small non-coding RNAs using the miRMaster2 online tool. Raw read counts were processed using R. Data was batch-corrected using COMBAT-seq. Low quality samples and sequences were removed, and data was normalized per sncRNA species separately using the Relative Log Expression (RLE) method and scaled by counts per million (CPM).
Assembly: hg38
Supplementary files format and content: Raw count matrix of all samples before quality control and normalization

molecule: total RNA

organism: Homo sapiens

source_name: placenta

extract_protocol:
Sorted cells were isolated from fresh chorionic villi using FACS as described in GSE159526. Sorted cells and chorionic villi samples were extracted using the ZYMO Quick-RNA MiniPrep kit according to manufacturer’s instructions or using TRIzol (ThermoFisher Scientific, USA).
5.8S rRNA was masked during adapter ligation by a complementary oligonucleotide, while miRNAs underwent 3′ adapter ligation, digestion of unligated adapters, and 5′ adapter ligation sequentially. The 5′ adapter contains a unique molecular identifier (UMI), followed by two nucleotides (CA) prior to the miRNA sequence. Upon conversion to cDNA by reverse transcription, the cDNA was amplified by PCR to include the sequences required for Illumina cluster generation and sample indexing developed by the GSC. The number of PCR cycles was dependent on the amount of input RNA; samples with low and high input were subjected to 20 and 15 cycles of PCR, respectively. Quality of libraries was assessed using the Agilent Bioanalyzer 2100 HS DNA chip Assay, (Agilent, USA)

treatment_protocol: All samples were stored in RNAlater (ThermoFisher Scientific, USA) upon sampling and prior to extraction

tag: case id

tag: tissue

value: placenta

value: Villi

tag: gestational age

tag: trimester

value: Term

tag: fetal sex

value: Male

tag: batch

tag: plate

tag: extraction type

value: Villi:TRIzol; Operator 1


title: mCD8T:ODCKO,NCP,sp,7,1rep

city: Baltimore

first: Taekjip

last: Ha

state: Maryland

address: 3400 N. Charles Street

institute: Johns Hopkins University

description:
Library name: mCD8T:ODCKO_NCP_sp_7_1rep
Native nucleosome sample, Spermine used as condensing agent

library_source: genomic

data_processing:
Bowtie2 alignment
Coverage and read counts were computed using custom python scripts
Nucleosome peak calling using custom python scripts
Condensabilities for each genomic bins and each nucleosomes were computed
Assembly: hg38 (Human), mm10 (Mouse)
Supplementary files format and content: Condensability scores for 10kb, 1kb genomic bins and individual nucleosome resolution
Library strategy: Condense-seq

source_name: CD8+ T cell

extract_protocol:
DNA library were prepared using NEBNext Ultra II kit
Condense-seq

treatment_protocol: Native nuclesomes were purified from cells using HAP (hydroxy apartite purification) protocol and genomic DNA were purified by phenol chloroform extraction

tag: cell line

value: CD8+ T cell

value: Ornithine decarboxylase (ODC) knockout


title: PM381_troph

description:
Library name: M20218
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Cytotrophoblast

value: Sorted-cells:Zymo Quick-RNA Miniprep


title: WYpol32-106R

description: genotype of sectors

source_name: cell culture of WYpol32-106R


title: mCD8T:ODCKO,NCP,sp,6,1rep

description:
Library name: mCD8T:ODCKO_NCP_sp_6_1rep
Native nucleosome sample, Spermine used as condensing agent


title: MEF_IP-WT-VSV-2-A

description: Library name: EV227_IP

value: untreated


title: mCD8T:ODCKO,NCP,sp,5,1rep

description:
Library name: mCD8T:ODCKO_NCP_sp_5_1rep
Native nucleosome sample, Spermine used as condensing agent


title: WYpol32-99R

description: genotype of sectors

source_name: cell culture of WYpol32-99R


title: WYpol32-98R

description: genotype of sectors

source_name: cell culture of WYpol32-98R


title: PM381_hofb

description:
Library name: M20217
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Hofbauer


title: PM379_vc

description:
Library name: M20216
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Female


title: MEF_INPUT-WT-VSV-A

description: Library name: EV227_input


title: mCD8T:ODCKO,NCP,sp,4,1rep

description:
Library name: mCD8T:ODCKO_NCP_sp_4_1rep
Native nucleosome sample, Spermine used as condensing agent


title: MEF_IP-WT-INF-2-A

description: Library name: EV226_IP

value: uninfected


title: WYpol32-93R

description: genotype of sectors

source_name: cell culture of WYpol32-93R


title: WYpol32-89R

description: genotype of sectors

source_name: cell culture of WYpol32-89R


title: mCD8T:ODCKO,NCP,sp,3,1rep

description:
Library name: mCD8T:ODCKO_NCP_sp_3_1rep
Native nucleosome sample, Spermine used as condensing agent


title: WYpol32-90R

description: genotype of sectors

source_name: cell culture of WYpol32-90R


title: mCD8T:ODCKO,NCP,sp,2,1rep

description:
Library name: mCD8T:ODCKO_NCP_sp_2_1rep
Native nucleosome sample, Spermine used as condensing agent


title: WYpol32-82R

description: genotype of sectors

source_name: cell culture of WYpol32-82R


title: MEF_INPUT-WT-INF-A

description: Library name: EV226_input

value: Mouse Embryonic Fibroblast


title: PM379_strom

description:
Library name: M20215
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Stromal


title: PM379_hofb

description:
Library name: M20214
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: MEF_IP-WT-NO-INF-2-A

description: Library name: EV225_IP

value: WT


title: mCD8T:ODCKO,NCP,sp,1,1rep

description:
Library name: mCD8T:ODCKO_NCP_sp_1_1rep
Native nucleosome sample, Spermine used as condensing agent


title: PM378_vc

description:
Library name: M20213
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: MEF_INPUT-WT-NO-INF-A

description: Library name: EV225_input


title: mCD8T:ODCKO,NCP,sp,0,1rep

description:
Library name: mCD8T:ODCKO_NCP_sp_0_1rep
Native nucleosome sample, Spermine used as condensing agent


title: WYpol32-80R

description: genotype of sectors

source_name: cell culture of WYpol32-80R


title: PM378_strom

description:
Library name: M20212
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: PM378_hofb

description:
Library name: M20211
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: mCD8T:DFMO,NCP,sp,9,1rep

description:
Library name: mCD8T:DFMO_NCP_sp_9_1rep
Native nucleosome sample, Spermine used as condensing agent

value: Difluoromethylornithine (DFMO) treated


title: mCD8T:DFMO,NCP,sp,8,1rep

description:
Library name: mCD8T:DFMO_NCP_sp_8_1rep
Native nucleosome sample, Spermine used as condensing agent


title: 11_P42_Mut2

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

data_processing:
Basecalling was performed using RTA 1.18.61
bcl files were converted to fastq using CASAVA 1.8.2
fastq files were aligned to the mouse genome (Gencode M11) using the Star aligner (version STAR_2.5.2b)
Gene counts were generated using featureCounts from the Subread package (featureCounts v1.5.1)
Prior to differential gene expression analysis low gene counts were removed with the lowest 32% of genecounts (sums of all samples) being removed.
Count normalization and differential gene expression analysis was performed using the limma/voom pipeline (limma version 3.28.21).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files with raw transcript counts.

molecule: polyA RNA

source_name: microglia

extract_protocol:
Approximately 1000 FACS sorted microglia cells were homogenized in 170 µl Trizol reagent using Precellys CK14 ceramic beads (2 cycles of 10 seconds at 6500 rpm; 10 seconds break). After 5 minutes incubation at room temperature 34 µl of chloroform was added and the samples were again incubated at room temperature for 2 minutes. Phase separation was achieved by 15 minutes centrifugation at 12,000 x g at 4 °C. An equal amount of 70 % ethanol was added to the aqueous supernatant and the mixture was applied to RNeasy MinElute spin columns (RNeasy Micro Kit, QIAGEN, Hilden, Germany), followed by an on-column DNase digestion and several wash steps. Finally total RNA was eluted in 14 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 0.3 to 1.0 ng total-RNA. Double stranded cDNA was amplified by LD PCR (14 or 15 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3. The sequencing run was performed on an HiSeq 1000 instrument using the indexed, 50 cycles single-read (SR) protocol and the TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide.

value: microglia

value: Lyl1 KO

tag: age


title: PM377_vc

description:
Library name: M20209
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: placenta

value: Villi

value: Term


title: 09_P42_WT3

value: wildtype


title: 12_P42_Mut3


title: WYpol32-81R

description: genotype of sectors

source_name: cell culture of WYpol32-81R


title: WYpol32-60R

description: genotype of sectors

source_name: cell culture of WYpol32-60R


title: 10_P42_Mut1


title: WYpol32-59R

description: genotype of sectors

source_name: cell culture of WYpol32-59R


title: 08_P42_WT2


title: WYpol32-73R

description: genotype of sectors

source_name: cell culture of WYpol32-73R

source_name: cell culture of WYpol32


title: WYpol32-71R

description: genotype of sectors

source_name: cell culture of WYpol32-71R


title: mCD8T:DFMO,NCP,sp,7,1rep

description:
Library name: mCD8T:DFMO_NCP_sp_7_1rep
Native nucleosome sample, Spermine used as condensing agent

value: CD8+ T cell


title: WYpol32-58R

description: genotype of sectors

source_name: cell culture of WYpol32-58R


title: PM377_troph

description:
Library name: M20207
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

source_name: placenta

value: Cytotrophoblast


title: mCD8T:DFMO,NCP,sp,4,1rep

description:
Library name: mCD8T:DFMO_NCP_sp_4_1rep
Native nucleosome sample, Spermine used as condensing agent

source_name: CD8+ T cell


title: 07_P42_WT1


title: PM377_hofb

description:
Library name: M20206
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Sorted-cells:Zymo Quick-RNA Miniprep


title: Hcal_MicroC

city: Barcelona

first: Arnau

last: Sebé-Pedrós

address: C/ Dr. Aiguader, 88

department: Systems and Synthetic Biology

country: Spain

institute: Centre for Genomic Regulation (CRG)

data_processing:
Raw reads were mapped to the reference genome using bwa mem (version: 0.7.17-r1188) with the -SP5M option.
The mapped reads were sorted and filtered with pairtools (version 0.3.0). Pairs that mapped within 2 bp distance from each other were considered duplicates and removed. We also discarded reads mapping within the distance of 200 bp, which eliminates self-ligated pairs and reads mapping to adjacent nucleosomes.
Unique valid pair reads from biological and technical replicates were pooled to obtain final chromatin interaction matrices. Contact matrices were normalized with cooler (version 0.8.11) using ICE balancing method.
Insulation profiles were calculated using cooltools insulation module. Chromatin loops were identified using SIP (version 1.6.1).
Assembly: Cladtertia collaboinventa genome assembly HoiH23_v2, Hormiphora californensis genome assembly GCA_020137815.1; Nematostella vectensis genome assembly GCA_932526225.1; Sphaeroforma arctica genome assembly Sarc_v2, Salpingoeca rosetta genome assembly Sros_v2
Supplementary files format and content: pairs.gz contains a tsv table with valid chromatin contact detected in Micro-C experiments.
Supplementary files format and content: mcool contains chromatin contact matrices at different resolutions
Supplementary files format and content: insulation_score.bedgraph is a BedGraph file with insulation score values
Supplementary files format and content: boundary_strength.bedgraph is a BedGraph file with boundary strength values
Supplementary files format and content: loops.txt includes genomic coordinates of detected chromatin loops
Supplementary files format and content: domains.bed includes genomic coordinates of identified chromatin domains
Library strategy: Micro-C

organism: Hormiphora californensis

source_name: Hormiphora californensis

growth_protocol: Sphaeroforma arctica culture was grown in Marine Broth (37.4 g/L) at 12 ºC. Salpingoeca rosetta culture was kept in artificial sea water with salinity 33 ppt supplemented with 4 % CGM3 and 4 % SWC at 23 ºC. Nematostella vectensis specimens were grown in 1/3 artificial sea water with salinity 14 ppt at 25 ºC. Cladtertia collaboinventa colonies were grown in artificial sea water (Red Sea, R11055) with salinity 33 ppt at 21 ºC.

extract_protocol:
S. arctica and S. rosetta cells were double crosslinked with 1% formaldehyde and 3 mM DSG (Thermo Scientific, A35392). H.californensis specimens were flash-frozen in liquid nitrogen. Frozen tissues were then pulverized, cells and nuclei were collected by centrifugation for 15 min at 2,000 g. Collected cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG. N. vectensis 1.5-2 month old specimens were crosslinked with 1 % formaldehyde under vacuum. Crosslinked tissues were dissociated into single cells in Ca2+/Mg2+-free artificial sea water in the presence of Protease XIV (Sigma-Aldrich, P5147). Dissociated cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted to isolate mOrange-positive neuronal cells. FACS-sorted cells were additionally crosslinked with 3 mM DSG. C. collaboinventa specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG.
Micro-C libraries were prepared as previously described by Hsieh et al., 2020 (PMID: 32213323) and Krietenstein et al. 2020 (PMID: 32213324).

treatment_protocol: To synchronize cells in G1/early S phase, S. arctica cells were treated with 200 mM hydroxyurea (Sigma-Aldrich, H8627) for 18 hours, S. rosetta culture was treated with 0.05 mM aphidicolin for 18 hours.

value: Whole-organism

value: wild type


title: WYpol32-54R

description: genotype of sectors

source_name: cell culture of WYpol32-54R


title: WYpol32-57R

description: genotype of sectors

source_name: cell culture of WYpol32-57R


title: mCD8T:DFMO,NCP,sp,3,1rep

description:
Library name: mCD8T:DFMO_NCP_sp_3_1rep
Native nucleosome sample, Spermine used as condensing agent


title: PM376_vc

description:
Library name: M20205
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Female

value: Villi:TRIzol; Operator 1


title: WYpol32-51R

description: genotype of sectors

source_name: cell culture of WYpol32-51R


title: STING wildtype

city: Zurich

first: Michael

last: Herbst

address: Winterthurerstrasse 190

country: Switzerland

institute: UZH

library_source: transcriptomic single cell

data_processing:
read alignment, cell barcode demultiplexing, deduplication of reads, generation of expression matrices and quality report were done using the Rhapsody Sequence Analysis Pipeline v2.0 (https://www.bdbiosciences.com/en-us/products/software/rhapsody-sequence-analysis-pipeline)
Assembly: mm39
Supplementary files format and content: Tab-separated value files and matrix files

source_name: tumor

extract_protocol:
Tumors were collected in RPMI with 10% FCS and digested with 1 mg/ml collagenase IV (Thermo Fisher Scientific) and 50 µg/ml DNase I (Roche) for 45 minutes at 37°C using a rotating device. The cells were then washed in PBS with 2 mM EDTA and passed through a 70-µm filter (Biologix). Red blood cells were lysed with a buffer (17 mM Tris pH 7.2, 144 mM NH4Cl) for 2 minutes, followed by a PBS wash.
Library amplification was carried out following the BD Rhapsody System mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol (Doc ID: 23-24119 (02))

value: tumor

tag: Sex

value: female

value: 12 weeks old

value: CD8+ T-cells

tag: strain background


title: mCD8T:DFMO,NCP,sp,2,1rep

description:
Library name: mCD8T:DFMO_NCP_sp_2_1rep
Native nucleosome sample, Spermine used as condensing agent

value: WT

value: Difluoromethylornithine (DFMO) treated


title: PM377_strom

description:
Library name: M20208
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: placenta

value: Stromal


title: PM376_strom

description:
Library name: M20204
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Term


title: mCD8T:DFMO,NCP,sp,5,1rep

description:
Library name: mCD8T:DFMO_NCP_sp_5_1rep
Native nucleosome sample, Spermine used as condensing agent


title: PM376_troph

description:
Library name: M20203
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: PM376_hofb

description:
Library name: M20202
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Hofbauer


title: STING KO

value: KO


title: STING wildtype + induced cGAS expression

value: induced cGAS expression

value: WTDox


title: WYpol32-45R

description: genotype of sectors

source_name: cell culture of WYpol32-45R


title: mCD8T:DFMO,NCP,sp,6,1rep

description:
Library name: mCD8T:DFMO_NCP_sp_6_1rep
Native nucleosome sample, Spermine used as condensing agent

value: CD8+ T cell


title: WYpol32-46R

description: genotype of sectors

source_name: cell culture of WYpol32-46R


title: STING KO + induced cGAS expression

value: KODox


title: mCD8T:DFMO,NCP,sp,0,1rep

description:
Library name: mCD8T:DFMO_NCP_sp_0_1rep
Native nucleosome sample, Spermine used as condensing agent


title: PM376_endo

description:
Library name: M20201
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Endothelial

value: Female

value: Sorted-cells:Zymo Quick-RNA Miniprep


title: mCD8T:WT,NCP,sp,9,1rep

description:
Library name: mCD8T:WT_NCP_sp_9_1rep
Native nucleosome sample, Spermine used as condensing agent


title: WYpol32-39R

description: genotype of sectors

source_name: cell culture of WYpol32-39R


title: PM375_vc

description:
Library name: M20200
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Villi

value: Villi:TRIzol; Operator 1


title: mCD8T:WT,NCP,sp,7,1rep

description:
Library name: mCD8T:WT_NCP_sp_7_1rep
Native nucleosome sample, Spermine used as condensing agent


title: mCD8T:WT,NCP,sp,8,1rep

description:
Library name: mCD8T:WT_NCP_sp_8_1rep
Native nucleosome sample, Spermine used as condensing agent


title: WYpol32-25R

description: genotype of sectors

source_name: cell culture of WYpol32-25R


title: Embryo_TAK_11

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

description: Library name: Embryo_TAK_11

data_processing:
The sequencing reads were then aligned to mouse reference genome Mm10 using STAR (2.7.11b) and the annotation from Gencode (vM23). Alignments were filtered with samtools on MAPQ >= 30. The gene expression matrix was generated using featuresCount from the subread package (v2.0.6) and differentially expressed genes (DEGs) were identified using DESeq2 (v.1.44) Genes with adjusted P value <0.05 were considered to be DEGs.
Assembly: Mm10
Supplementary files format and content: bigwig files for each experiment.
Supplementary files format and content: counts_table.txt is a tabulated file. Rows are genes and columns are experiments.

source_name: Whole E13.5 Embryo

growth_protocol: C57BL/6 male and female mice were used, and all bred at the Pasteur Institute animal facility under specific pathogen-free conditions.

extract_protocol:
Total RNA was extracted from control and Tak-progeny embryos, collected at day E13.5 (n= 6 for control and n=12 for Tak-progeny) by guanidinium thiocyanate-phenol-chloroform extraction and DNAse treatment. Briefly, RNA was extracted and purified using a TRIzol-based protocol followed by acidic phenol/chloroform purification and DNase treatment to ensure RNA integrity and purity. Samples were homogenized in TRIzol (Invitrogen), followed by chloroform extraction and centrifugation to isolate the aqueous phase. RNA precipitation was achieved with isopropanol, followed by ethanol washes and air drying. Pellets were resuspended in RNase-free water. To enhance RNA quality, an acidic phenol/chloroform purification was performed twice, including Na-acetate addition and vortexing, with phases separated by centrifugation. Precipitation steps used isopropanol and ethanol, with overnight incubation at -20°C to enhance RNA recovery. DNAse treatment (DNAse I at concentration of 2u/µg of RNA) was conducted at 37°C for 30 minutes to remove residual DNA, followed by a final acidic phenol/chloroform purification and ethanol precipitation. Final RNA pellets were air-dried and dissolved in RNase-free water, with incubation at 50°C for optimal resuspension, ensuring RNA suitable for downstream applications.
The mRNA libraries were performed by BGI Genomics using Hieff NGS Ultima Dual-mode mRNA kit (#12308ES96, Yeasen).

treatment_protocol: Female mice aged 8-10 weeks were matted and administered intraperitoneally with vehicle (20 % HPBCD diluted in dH2O) at day E6.5, E7.5 and E8.5 of pregnancy, or 15mg/kg TAK981 on days E6.5, E7.5 and E8.5.

tag: developmental stage

value: Whole E13.5 Embryo

value: TAK981 injection on days E6.5, E7.5 and E8.5


title: PM375_strom

description:
Library name: M20199
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: WYpol32-22R

description: genotype of sectors

source_name: cell culture of WYpol32-22R

tag: strain


title: Embryo_TAK_10

description: Library name: Embryo_TAK_10

tag: cell type


title: mCD8T:DFMO,NCP,sp,1,1rep

description:
Library name: mCD8T:DFMO_NCP_sp_1_1rep
Native nucleosome sample, Spermine used as condensing agent

tag: genotype

value: WT

value: Difluoromethylornithine (DFMO) treated


title: PM375_troph

description:
Library name: M20198
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: placenta

value: Cytotrophoblast


title: mCD8T:WT,NCP,sp,6,1rep

description:
Library name: mCD8T:WT_NCP_sp_6_1rep
Native nucleosome sample, Spermine used as condensing agent

tag: treatment


title: Embryo_TAK_9

description: Library name: Embryo_TAK_9


title: mCD8T:WT,NCP,sp,5,1rep

description:
Library name: mCD8T:WT_NCP_sp_5_1rep
Native nucleosome sample, Spermine used as condensing agent


title: PM375_hofb

description:
Library name: M20197
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

tag: case id

value: Hofbauer

value: Term


title: mCD8T:WT,NCP,sp,4,1rep

description:
Library name: mCD8T:WT_NCP_sp_4_1rep
Native nucleosome sample, Spermine used as condensing agent


title: WYpol32-21R

description: genotype of sectors

source_name: cell culture of WYpol32-21R


title: PM375_endo

description:
Library name: M20196
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

tag: tissue


title: mCD8T:WT,NCP,sp,3,1rep

description:
Library name: mCD8T:WT_NCP_sp_3_1rep
Native nucleosome sample, Spermine used as condensing agent


title: WYpol32-44R

description: genotype of sectors

source_name: cell culture of WYpol32-44R

source_name: cell culture of WYpol32


title: WYpol32-17R

description: genotype of sectors

source_name: cell culture of WYpol32-17R


title: Embryo_TAK_12

description: Library name: Embryo_TAK_12


title: Embryo_TAK_6

description: Library name: Embryo_TAK_6


title: PM374_vc

description:
Library name: M20195
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

source_name: placenta

tag: gestational age

value: Male


title: WYpol32-18R

description: genotype of sectors

source_name: cell culture of WYpol32-18R


title: WYpol32-16R

description: genotype of sectors

source_name: cell culture of WYpol32-16R


title: WYpol32-15R

description: genotype of sectors

source_name: cell culture of WYpol32-15R


title: mCD8T:WT,NCP,sp,2,1rep

description:
Library name: mCD8T:WT_NCP_sp_2_1rep
Native nucleosome sample, Spermine used as condensing agent

source_name: CD8+ T cell


title: PM374_strom

description:
Library name: M20194
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Stromal

tag: trimester


title: mCD8T:WT,NCP,sp,1,1rep

description:
Library name: mCD8T:WT_NCP_sp_1_1rep
Native nucleosome sample, Spermine used as condensing agent

value: CD8+ T cell


title: WYpol32-14R

description: genotype of sectors

source_name: cell culture of WYpol32-14R


title: PM374_troph

description:
Library name: M20193
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

tag: fetal sex


title: Embryo_TAK_4

description: Library name: Embryo_TAK_4


title: mCD8T:WT,NCP,sp,0,1rep

description:
Library name: mCD8T:WT_NCP_sp_0_1rep
Native nucleosome sample, Spermine used as condensing agent


title: PM374_hofb

description:
Library name: M20192
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

tag: batch


title: Embryo_TAK_3

description: Library name: Embryo_TAK_3


title: Embryo_TAK_2

description: Library name: Embryo_TAK_2


title: PM374_endo

description:
Library name: M20191
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

tag: plate


title: KO_MII_3

first: Heng-yu

last: Fan

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
raw reads were trimmed by using trim-galore (v.0.6.10) and mapped to the mm10 genome (gencode, vM25) by using STAR (v.2.7.10a). Uniquely mapped reads were quantified by using FeatureCounts (v.2.0.2) and further calibrated with the ERCC spike-in as described before. Differential expression genes (DEG, adjusted P value < 0.01, average |log2 fold change| > 1) were analyzed by using DESeq2 R package for further analysis.
Assembly: mm10
Supplementary files format and content: Count_list.xlsx

source_name: oocytes

extract_protocol:
Harvested oocytes were washed three times with PBS with 0.2% (wt/vol) bovine serum albumin (BSA) and transferred into a 1.5 ml RNase/DNase free PCR tubes and the TRIzol-chloroform-isopropanol method were used to obtain the total RNA. In brief, 750 μl TRIzol Reagent and 1 μl 1:1000 ERCC were added to each sample and mix thoroughly, then lyse cells at room temperature (RT) for 5 minute before adding 500 μl chloroform. After chloroform being added, mix thoroughly on a vortex and centrifuge at 12000g at 4℃ for 15 minutes, then collect the top phase with leaving some for avoiding contamination, the volume of the top phase should be the same. Then, isopropanol with the equal volume and 1 μl LPA (GeneElute LPA, Sigma, Cat. no. 56575) was added, mixed up and frozen at -20℃ for overnight. Next, the mixture was centrifuged at 12000g at 4℃ for 30 minutes, and the liquid was taken out and the pellet was washed once with fresh 75% ethanol at 7500g at 4℃ for 5 min then re-suspended in 12 μl.
The extracted RNA was then be used for total RNA-seq(Figure S1A) with rRNA deletion (rRNA Depletion Module (H/M/R), ABclonal, Cat. no. RK20348) and library construction (Fast RNA-seq Lib Prep Kit V2, ABclonal, Cat# RK20306). In brief, rRNA was hybridized by probes and then digested by RNase H, the probes were then cleaned up by DNase I. The rRNA-depleted RNA were purified by beads (AFTMag NGS DNA Clean Beads, ABclonal, Cat. no. RK20257) and fragmented into 200-350 nt fragments with random primer hybridized onto the fragmented RNA. Then the fragmented RNA were reverse transcripted (RT) into cDNA with random primers in a first-second-strand synthesis strategy, and the truncated adapter will be ligated to the cDNA. After purifying the ligated cDNA with beads (AFTMag NGS DNA Clean Beads, ABclonal, Cat. no. RK20257), the i5 and i7 indexes were ligated onto the cDNA and the amplification (~11 cycles) was processed meanwhile.

value: oocytes


title: Embryo_TAK_8

description: Library name: Embryo_TAK_8


title: 926991

city: Munich

first: Thomas

last: Metzler

address: Trogerstr. 18

department: CEP

institute: TU Munich

data_processing:
*library strategy: Spatial Transcriptomics
Raw sequencing data were processed using bcl2fastq v2.20.0.422 to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: aligned_tissue_image.jpg: image of the aligned tissue
Supplementary files format and content: cytassist_image.tiff: image taken by the cytassist
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: spatial_enrichment.csv: table containing Moran's I value for each feature
Supplementary files format and content: tissue_hires_image.png: highres image of the tissue
Supplementary files format and content: tissue_lowres_image.png: lowres image of the tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene Ids
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: adata.h5ad: dataset containing megred spatial transcriptomic information, pathological annotations, clusters, pseudotime and scRNA integrated data of all datasets combined

source_name: pancreas

extract_protocol:
Pancreata were fixed in formalin, dehydrated and embedded in Paraffin (FFPE) and 5µm sections were cut on a microtome.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial for FFPE Gene Expression Slides & Reagent kit according to manufacterer's construction.

value: pancreas

value: female

value: 6 months


title: Embryo_TAK_7

description: Library name: Embryo_TAK_7


title: PM373_vc

description:
Library name: M20190
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Villi

tag: extraction type


title: WYpol32-12R

description: genotype of sectors

source_name: cell culture of WYpol32-12R


title: Embryo_TAK_1

description: Library name: Embryo_TAK_1


title: WYpol32-10R

description: genotype of sectors

source_name: cell culture of WYpol32-10R


title: WYpol32-11R

description: genotype of sectors

source_name: cell culture of WYpol32-11R


title: Embryo_TAK_5

description: Library name: Embryo_TAK_5

source_name: Whole E13.5 Embryo


title: KO_MII_2


title: PM373_troph

description:
Library name: M20188
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Sorted-cells:Zymo Quick-RNA Miniprep


title: WYpol32-8R

description: genotype of sectors

source_name: cell culture of WYpol32-8R


title: KO_GV_3


title: PM373_hofb

description:
Library name: M20187
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: KO_GV_2


title: Embryo_Ctrl_4

description: Library name: Embryo_Ctrl_4

value: Whole E13.5 Embryo

value: vehicle injection on days E6.5, E7.5 and E8.5


title: WYpol32-7R

description: genotype of sectors

source_name: cell culture of WYpol32-7R


title: PM373_endo

description:
Library name: M20186
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Endothelial


title: WYpol32-6R

description: genotype of sectors

source_name: cell culture of WYpol32-6R


title: WYpol32-4R

description: genotype of sectors

source_name: cell culture of WYpol32-4R

source_name: cell culture of WYpol32


title: Embryo_Ctrl_3

description: Library name: Embryo_Ctrl_3


title: Embryo_Ctrl_2

description: Library name: Embryo_Ctrl_2


title: PM372_vc

description:
Library name: M20185
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

source_name: placenta

value: Villi:TRIzol; Operator 1


title: WYpol32-2R

description: genotype of sectors

source_name: cell culture of WYpol32-2R


title: PM372_strom

description:
Library name: M20184
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: placenta


title: KO_GV_1


title: PM373_strom

description:
Library name: M20189
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: WT_MII_3


title: KO_MII_1


title: Embryo_Ctrl_6

description: Library name: Embryo_Ctrl_6


title: Embryo_Ctrl_1

description: Library name: Embryo_Ctrl_1


title: PM372_troph

description:
Library name: M20183
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Cytotrophoblast


title: WYpol32-1R

description: genotype of sectors

source_name: cell culture of WYpol32-1R


title: HPC-7, p42, LPS 12h, R3

city: Badalona

first: LUCIA

last: LORENZI

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute

data_processing:
RNA-seq raw sequencing reads were aligned to the human or mouse reference genome (hg38 and mm39 assemblies respectively) with bowtie2 v2.4.4 with the “--very-sensitive” tag
Quantification of gene expression for KO52 cells, macrophages and HSPC was performed with featureCounts from Subread v2.0.3 using uniquely mapping reads on NCBI RefSeq gene annotation for either human hg38 or mouse mm39. For HPC-7 samples, quantification was performed with htseq-count v0.11.12 (options ”--mode intersection-nonempty” and ”--supplementary-alignments ignore”) against GENCODE gene annotation for mm39 release M27.
Assembly: mm39, hg38
Supplementary files format and content: tab-delimited text files contain raw counts for each sample

growth_protocol:
To isolate bone marrow progenitors, total bone marrow cells were stained with a cocktail of biotin-conjugated lineage antibodies. Lineage positive cells were depleted using EasySep Mouse Streptavidin RapidSpheres (Stem Cell 5001), and lineage-negative cells were cultured in IMDM 20% FBS, 1% P/S, 1% L-Gln, 50µM b-mercaptoethanol supplemented with 100ng/mL SCF, 100ng/mL IL-6 (Peprotech 216-16), 100ng/mL Flt3 (Miltenyi biotec 130-094-038) and 10ng/mL IL-11 (Stem Cell 78026.1).
To generate bone marrow-derived macrophages, bone marrow cells were cultured in complete DMEM medium (10% FBS, 1% penicillin/streptomycin, 1% L-glutamine, 1mM sodium pyruvate) with 20% L929-conditioned media. To induce Cre nuclear translocation in lineage-negative cells or in macrophages, 400nM 4-OHT (Sigma, H7904) was added in the media where indicated.
HPC-7 cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) (Gibco 12440-053) supplemented with 10% FBS, 1% penicillin/streptomycin (Gibco 15140-122), 1% L-glutamine (Gibco 25030-024), 50μM b-mercaptoethanol (Gibco 31350-010), and 50 ng/mL murine SCF (Miltenyi Biotec, 130-101-697).
KO-52 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Dominique Dutscher, L0106-500) supplemented with 10% FBS, 1% penicillin/streptomycin and 2% L-glutamine.

extract_protocol:
RNA was isolated from 1-2 x 106 cells in 1mL of TRIzol Reagent (ABP Biosciences FP312) following the manufacturer’s instructions. For low starting cell number samples, RNA was extracted with Direct-zol RNA MicroPrep kit (Zymo R2060).
1) Oligo dT Selection to enrich the mRNA. 2) RNA fragment and reverse transcription (second-strand cDNA synthesis with dUTP instead of dTTP). 3) End repair, add A and adaptor ligation 4) PCR 5) Single strand separation and cyclization 6) DNA nanoball synthesis

treatment_protocol: For TLR4 stimulation, cells were exposed to LPS (Escherichia coli O111:B4, Sigma L2630) at a final concentration of 100 ng/mL

tag: cell line

value: LPS 12h


title: WT_MII_2


title: WT_MII_1


title: PM372_hofb

description:
Library name: M20182
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Hofbauer

value: Term


title: Embryo_Ctrl_5

description: Library name: Embryo_Ctrl_5


title: WYpol32-106W

description: genotype of sectors

source_name: cell culture of WYpol32-106W


title: HPC-7, p42, LPS 12h, R2


title: WT_GV_3


title: PM372_endo

description:
Library name: M20181
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Male


title: WT_GV_2


title: PM371_vc

description:
Library name: M20180
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Female


title: HPC-7, p42, LPS 12h, R1


title: HPC-7, p30, LPS 12h, R3


title: WT_GV_1

value: oocytes


title: PM371_strom

description:
Library name: M20179
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Stromal


title: PM371_troph

description:
Library name: M20178
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: WT, Mincle KO, Tag

city: Chikusa-ku

first: Hiro

last: Kohda

state: Nagoya

address: Furo-cho

department: Research Institute of Environmental Medicine

country: Japan

institute: Nagoya Univ.

description: Tas-seq

data_processing:
Pair-end Fastq files (R1: cell barcode reads, R2: RNA reads) were processed as follows. Adapter trimming of sequencing data was performed using cutadapt 3.4. Filtered reads were chunked into 16 parts for parallel processing by using Seqkit 0.15.0. Filtered cell barcode reads were annotated by Python script provided by BD Biosciences with minor modification for compatibility to Python 3.7. Reference RNA sequences were built by concatenating cDNA and ncRNA fasta files of the Ensembl database (build GRCm38 release-101). Associated cDNA reads were mapped to reference RNA using bowtie2-2.4.2. Then, cell barcode information of each read was added to the bowtie2-mapped BAM files, and read counts of each gene in each cell barcode were counted using mawk. Resultant count data was converted to a single-cell gene-expression matrix file by using R-3.6.3. The inflection point of the knee-plot (total read count versus the rank of the read count) was detected using DropletUtils package in R-4.1.2. Cells of which total read count was over inflection point were considered as valid cells.
There is no fastq for each sample because it is cell hashing data.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw tag-count values for each sample
Supplementary files format and content: The correspondence between HTO (cell hashing) and the sample is as follows: sample 1 (WT, rep1): A0309, sample 2(WT, rep2): A0310, sample 3 (Mincle KO, rep1): A0311, sample 4(Mincle KO, rep2): A0312.
Supplementary files format and content: The description rule of cell barcode is as follows: <hashtag ID>_<dataID>_<cell barcode>.
Supplementary files format and content: Please refer to “README_for_WTA3”.

source_name: visceral adipoe tissue

extract_protocol:
Epididymal white adipose tissue were minced and digested with Liberase solution at 37 ºC. Cell suspensions were centrifuged, and stromal vascular fraction was collected. Each single-cell suspension cell concentration was counted using Flow-count fluorospheres (Beckman Coulter) and a Gallios flow cytometer (Beckman Coulter). Cells were stained with 2.5 μg/ml of Totalseq anti-mouse Hashtag-A antibodies (BioLegend) at 4ºC for 30 minutes and washed thrice with Cell Staining Buffer (BioLegend) and pooled.
Pooled single-cell suspensions were subjected to a BD Rhapsody system with BD Rhapsody Targeted & Abseq Reagent kit (BD Biosciences) following the manufacturer’s instructions. 20000 cells were subjected to the BD Rhapsody workflow. After reverse transcription, Exonuclease I treatment of the resultant BD Rhapsody beads was performed at 37ºC for 60 minutes with 1,200 rpm on a Thermomixer C with Thermotop. Resultant beads were immediately chilled on ice; the supernatant was removed and washed with 1 mL of WTA wash buffer [10 mM Tris-HCl (pH 8.0), 50 mM NaCl, 1 mM EDTA, and 0.05% Tween-20], 200 μL of BD Rhapsody lysis buffer (for inactivation of enzyme), once with 1 ml of WTA wash buffer, twice with 500 μL of WTA wash buffer, resuspended with 200 μL of Beads resuspension buffer. During the washing step, beads-containing DNA LoBind tubes (Eppendorf Japan) were replaced twice. Exonuclease I-treated BD Rhapsody beads were subjected to TAS- Seq workflow for cDNA and/or hashtag library amplification (Shichino S., bioRxiv, 2021). 150 ng of amplified cDNA libraries was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina. Ligated products were purified by AmPure XP beads and 9 cycles of Barcoding PCR were performed. Resultant products were purified twice by double size selection with 0.5× → 0.3× (final 0.8×) AmPure XP beads and eluted with 30 μL of 10 mM Tris-HCl pH8.0. Size distribution of amplified products was analyzed by MultiNA system with appropriate dilutions. Resultant libraries and barcoded hashtag libraries were quantified using the KAPA Library Quantification Kit. Pooled libraries were sequenced by Illumina Novaseq 6000 sequencer.

treatment_protocol: Male wild-type and Mincle-deficient mice with a C57BL/6J background were fed a high-fat diet for 15 weeks.

value: visceral adipoe tissue

value: stromal vascular fraction

value: WT, Mincle KO

value: high-fat diet, 15 weeks


title: HPC-7, p30, LPS 12h, R2


title: WYpol32-98W

description: genotype of sectors

source_name: cell culture of WYpol32-98W


title: HPC-7, p30, LPS 12h, R1


title: WT, Mincle KO, WTA

description: Tas-seq


title: PM371_hofb

description:
Library name: M20177
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Sorted-cells:Zymo Quick-RNA Miniprep


title: HPC-7, p42, LPS 2h, R3

value: LPS 2h


title: HPC-7, p42, LPS 2h, R2


title: WYpol32-99W

description: genotype of sectors

source_name: cell culture of WYpol32-99W


title: SD, HFD8, HFD16, WTA

description: TAS-seq

data_processing:
Pair-end Fastq files (R1: cell barcode reads, R2: RNA reads) were processed as follows. Adapter trimming of sequencing data was performed using cutadapt 2.10. Filtered reads were chunked into 16 parts for parallel processing by using Seqkit 0.9.0. Filtered cell barcode reads were annotated by Python script provided by BD Biosciences with minor modification for compatibility to Python 3.7. Reference RNA sequences were built by concatenating cDNA and ncRNA fasta files of the Ensembl database (build GRCm38 release-101). Associated cDNA reads were mapped to reference RNA using bowtie2-2.4.2. Then, cell barcode information of each read was added to the bowtie2-mapped BAM files, and read counts of each gene in each cell barcode were counted using mawk. Resultant count data was converted to a single-cell gene-expression matrix file by using R-3.6.3. The inflection point of the knee-plot (total read count versus the rank of the read count) was detected using DropletUtils package in R-3.6.3. Cells of which total read count was over inflection point were considered as valid cells.
There is no fastq for each sample because it is cell hashing data.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw tag-count values for each sample
Supplementary files format and content: The correspondence between HTO (cell hashing) and the sample is as follows: sample 1 (SD, rep1): A0301, sample 2(SD, rep2): A0302, sample 3 (SD, rep3): A0303, sample 4(HFD8, rep1): A0304, sample 5 (HFD8, rep2): A0305, sample 6 (HFD8, rep3): A0307, sample 7(HFD16, rep1): A0308, sample 8(HFD16, rep2): A0309, sample 9 (HFD16, rep3): A0310.
Supplementary files format and content: The description rule of cell barcode is as follows: <hashtag ID>_<dataID>_<cell barcode>.
Supplementary files format and content: Please refer to “README_for_WTA2”.

treatment_protocol: Male C57BL/6J mice were fed a standard diet (SD) for 16 weeks and  a high-fat diet (HFD)  for 8 and 16 weeks.

value: WT

value: standard diet, 16 weeks, high-fat diet, 8 weeks, high-fat diet, 16 weeks


title: WYpol32-89W

description: genotype of sectors

source_name: cell culture of WYpol32-89W


title: WYpol32-90W

description: genotype of sectors

source_name: cell culture of WYpol32-90W


title: WYpol32-81W

description: genotype of sectors

source_name: cell culture of WYpol32-81W


title: PolyA enriched RNAseq from RPM

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

description: RPM

data_processing:
The analysis was performed with the Qiagen online software for RNA-seq analysis
Assembly: GRCm38
Supplementary files format and content: Tab-separated features and barcodes, and matrix of each sample

source_name: Primary RPM

extract_protocol:
Cells were sorted with the Flow cytometry (FC) before sequencing. Organs were smashed into small pieces and then incubated 15min at 37°C in agitation with a tissue digestion solution composed of 1 mL IMDM (Corning) supplemented with 0.35 mg/mL collagenase type IV (Sigma-Aldrich/ SCR103), 1 mg/ml dispase II (Gibco/ 17105041) and 0.2 mg/ml DNAse (Roche/ 11284932001). The tissue was then further dissociated by pipetting and filtered using 40 μm cell strainers (Corning/ 352340). Single cell solution was washed with 30 mL of autoMACS Running Buffer (Miltenyi Biotec/130-940 091-221) and pelleted for 5min 300g 4°C to remove excess enzymes. Samples were transferred to FACS tubes, stained with surface antibody. Cells were sorted according to GFP and cell marker positivity: B cells (CD45+CD19+), RPM (CD45+F4/80+), cDC1(CD45+CD11c+CD8a+), cDC2(CD45+CD11c+Cd11b+), LSEC(CD45-CD31+), KC(CD45+,F4/80+). Cells were sorted from nr=3 animals per pool, adding up to 500k-3mln cells per sample. After sorting, cells were pelleted 300g for 5min 4°C, resuspended in 700uL QIAzol buffer and total RNA was extracted with miRNeasy Mini kit(QIAgen/ 217004) following manifacturer instruction.
Libraries were prepared using QIAseq UPX 3' Transcriptome Kit (QIAgen/ 333068) following manifacturer instruction.

value: Primary RPM


title: PM370_strom

description:
Library name: M20162
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: placenta


title: WYpol32-82W

description: genotype of sectors

source_name: cell culture of WYpol32-82W


title: WYpol32-100W

description: genotype of sectors

source_name: cell culture of WYpol32-100W


title: PolyA enriched RNAseq from LSECs

description: LSEC

source_name: Primary LSECs

value: Primary LSECs


title: HPC-7, p30, LPS 2h, R3


title: PolyA enriched RNAseq from KCs

description: KC

source_name: Primary KCs

value: Primary KCs


title: WYpol32-93W

description: genotype of sectors

source_name: cell culture of WYpol32-93W


title: HPC-7, p30, LPS 2h, R2


title: PM370_hofb

description:
Library name: M20160
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Hofbauer

value: Term


title: HPC-7, p30, LPS 2h, R1


title: SD, HFD8, HFD16, Tag

description: TAS-seq


title: WYpol32-103W

description: genotype of sectors

source_name: cell culture of WYpol32-103W

source_name: cell culture of WYpol32


title: WYpol32-80W

description: genotype of sectors

source_name: cell culture of WYpol32-80W


title: PM371_endo

description:
Library name: M20164
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

source_name: placenta

value: Endothelial

value: Female


title: PM370_endo

description:
Library name: M20159
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: PM378_endo

description:
Library name: M20210
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Male


title: HPC-7, EV, UT, R3


title: PM370_vc

description:
Library name: M20163
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Villi

value: Villi:TRIzol; Operator 1


title: WYpol32-60W

description: genotype of sectors

source_name: cell culture of WYpol32-60W


title: PolyA enriched RNAseq from cDC1

source_name: Primary cDC1

value: Primary cDC1


title: WYpol32-71W

description: genotype of sectors

source_name: cell culture of WYpol32-71W


title: PM369_vc

description:
Library name: M20158
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: HPC-7, p42, LPS 2h, R1


title: WYpol32-59W

description: genotype of sectors

source_name: cell culture of WYpol32-59W


title: HPC-7, EV, UT, R2


title: PolyA enriched RNAseq from splenic B cells

source_name: Primary B cells

value: Primary B cells


title: PM369_strom

description:
Library name: M20157
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Stromal

value: Sorted-cells:Zymo Quick-RNA Miniprep


title: PM370_troph

description:
Library name: M20161
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Cytotrophoblast


title: HPC-7, EV, UT, R1


title: WYpol32-73W

description: genotype of sectors

source_name: cell culture of WYpol32-73W


title: PolyA enriched RNAseq from cDC2

source_name: Primary cDC2

value: Primary cDC2


title: WYpol32-58W

description: genotype of sectors

source_name: cell culture of WYpol32-58W


title: small RNAseq from RPM

description: RPM

data_processing:
The analysis was performed with the Qiagen online software for smallRNA-seq analysis
Assembly: mirbase
Supplementary files format and content: Tab-separated features and barcodes, and matrix of each sample

source_name: Primary RPM

extract_protocol:
Cells were sorted with the Flow cytometry (FC) before sequencing. Organs were smashed into small pieces and then incubated 15min at 37°C in agitation with a tissue digestion solution composed of 1 mL IMDM (Corning) supplemented with 0.35 mg/mL collagenase type IV (Sigma-Aldrich/ SCR103), 1 mg/ml dispase II (Gibco/ 17105041) and 0.2 mg/ml DNAse (Roche/ 11284932001). The tissue was then further dissociated by pipetting and filtered using 40 μm cell strainers (Corning/ 352340). Single cell solution was washed with 30 mL of autoMACS Running Buffer (Miltenyi Biotec/130-940 091-221) and pelleted for 5min 300g 4°C to remove excess enzymes. Samples were transferred to FACS tubes, stained with surface antibody. Cells were sorted according to GFP and cell marker positivity: B cells (CD45+CD19+), RPM (CD45+F4/80+), cDC1(CD45+CD11c+CD8a+), cDC2(CD45+CD11c+Cd11b+), LSEC(CD45-CD31+), KC(CD45+,F4/80+). Cells were sorted from nr=3 animals per pool, adding up to 500k-3mln cells per sample. After sorting, cells were pelleted 300g for 5min 4°C, resuspended in 700uL QIAzol buffer and total RNA was extracted with miRNeasy Mini kit(QIAgen/ 217004) following manifacturer instruction.
Libraries were prepared using QIAseq miRNA library kit (QIAgen/ 331502) following manifacturer instruction.

value: Primary RPM


title: small RNAseq from LSEC

description: LSEC


title: PM368_vc

description:
Library name: M20156
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: placenta


title: HPC-7, p42, UT, R2


title: HPC-7, p42, UT, R3


title: WYpol32-57W

description: genotype of sectors

source_name: cell culture of WYpol32-57W


title: PM368_troph

description:
Library name: M20154
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: HPC-7, p42, UT, R1


title: small RNAseq from cDC2


title: PM368_endo

description:
Library name: M20153
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: HPC-7, p30, UT, R3


title: PM366_vc

description:
Library name: M20152
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Villi:TRIzol; Operator 2


title: small RNAseq from cDC1


title: HPC-7, p30, UT, R2


title: small RNAseq from splenic B cells


title: WYpol32-46W

description: genotype of sectors

source_name: cell culture of WYpol32-46W


title: HPC-7, p30, UT, R1


title: WYpol32-45W

description: genotype of sectors

source_name: cell culture of WYpol32-45W


title: miR-342-3p overexpression - biological replicate 3

data_processing:
Pre-processing of the input sequences was done with FastQC (v0.11.6) to assess reads quality and trimmomatic to get rid of low-quality sequences. Then, reads were aligned to the mouse genome assembly (GRCm38) using the STAR software (v2.7.6a) with standard parameters, and abundances were calculated using the Subread featureCounts function (v2.0.1).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: iKCs

extract_protocol:
Cells were sorted with the Flow cytometry (FC) before sequencing.Adherent cells were washed with PBS and incubated in 0,05% trypsin for 3min 37°C, then detached by pipetting and collected in FACS tubes. 500k-1mln cells/sample were sorted according to mOrange positivity and viability. After sorting, cells were pelleted 300g for 5min 4°C, resuspended in 700uL QIAzol buffer and total RNA was extracted with miRNeasy Micro kit (QIAgen/ 217084) following manifacturer instruction.
Libraries were prepared from total RNA as service by Genewiz-Azenta.

value: iKCs

value: miR-342-3p overexpression


title: PM366_troph

description:
Library name: M20150
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Term


title: WYpol32-51W

description: genotype of sectors

source_name: cell culture of WYpol32-51W


title: Prog, p30, LPS 2h, R2

source_name: Lineage negative bone marrow cells

value: Lineage negative bone marrow cells

value: LPS 2h


title: small RNAseq from KC

description: KC

source_name: Primary KCs

value: Primary KCs


title: miR-342-3p overexpression - biological replicate 2


title: PM366_hofb

description:
Library name: M20149
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

source_name: placenta

value: Hofbauer

value: Female


title: WYpol32-44W

description: genotype of sectors

source_name: cell culture of WYpol32-44W

source_name: cell culture of WYpol32


title: WYpol32-54W

description: genotype of sectors

source_name: cell culture of WYpol32-54W


title: PM366_endo

description:
Library name: M20148
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Endothelial


title: miR-342-3p overexpression - biological replicate 1


title: Prog, p30, LPS 2h, R1


title: Prog, p30, LPS 2h, R3


title: Mutated miR-342-3p control - biological replicate 2

value: Mutated miR-342-3p control


title: PM364_vc

description:
Library name: M20147
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Villi

value: Male


title: Prog, WT, LPS 2h, R3

value: WT


title: Mutated miR-342-3p control - biological replicate 1


title: PM364_strom

description:
Library name: M20146
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Stromal

value: Sorted-cells:Zymo Quick-RNA Miniprep


title: WYpol32-25W

description: genotype of sectors

source_name: cell culture of WYpol32-25W


title: PM366_strom

description:
Library name: M20151
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: placenta


title: WYpol32-18W

description: genotype of sectors

source_name: cell culture of WYpol32-18W


title: WYpol32-22W

description: genotype of sectors

source_name: cell culture of WYpol32-22W


title: Prog, WT, LPS 2h, R2


title: miR-342-3p sponge - biological replicate 3

value: miR-342-3p sponge


title: WYpol32-21W

description: genotype of sectors

source_name: cell culture of WYpol32-21W


title: PM368_strom

description:
Library name: M20155
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: Prog, WT, LPS 2h, R1


title: miR-342-3p sponge - biological replicate 2

value: iKCs


title: WYpol32-39W

description: genotype of sectors

source_name: cell culture of WYpol32-39W


title: Prog, p30, UT, R2


title: PM359_vc

description:
Library name: M20143
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Villi:TRIzol; Operator 2


title: WYpol32-17W

description: genotype of sectors

source_name: cell culture of WYpol32-17W


title: PM364_endo

description:
Library name: M20144
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Term


title: Prog, p30, UT, R1

value: Lineage negative bone marrow cells


title: PM359_strom

description:
Library name: M20142
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: Prog, p30, UT, R3


title: WYpol32-16W

description: genotype of sectors

source_name: cell culture of WYpol32-16W


title: Scramble control sponge - biological replicate 2

value: Scramble control sponge


title: WYpol32-15W

description: genotype of sectors

source_name: cell culture of WYpol32-15W


title: Scramble control sponge - biological replicate 1


title: PM359_troph

description:
Library name: M20141
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Cytotrophoblast


title: Prog, WT, UT, R3


title: WYpol32-14W

description: genotype of sectors

source_name: cell culture of WYpol32-14W


title: PM359_hofb

description:
Library name: M20140
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Hofbauer


title: WYpol32-12W

description: genotype of sectors

source_name: cell culture of WYpol32-12W


title: miR-342 mice - pool 2

description:
CB-4
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger v7.2.0 software (10X Genomics).
All samples were merged into a single object and processed to remove cells with a low sequencing quality, those with a feature count below 600 and above 9,000, as well as cells with a fraction of mitochondrial genes higher than 10%.
Samples were demultiplexed using the hashtag information using the Seurat function HTODemux, and cells classified as HTO doublets were filtered out. At the same time, the scDblFinder (v1.16.0) package was employed to annotate doublets of cells and exclude them from the following analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated features and barcodes, and matrix of each sample

source_name: Peritumoral liver

extract_protocol:
Cells were sorted with the Flow cytometry (FC) before sequencing. Organs were smashed into small pieces and then incubated 15min at 37°C in agitation with a tissue digestion solution composed of 1 mL IMDM (Corning) supplemented with 0.35 mg/mL collagenase type IV (Sigma-Aldrich/ SCR103), 1 mg/ml dispase II (Gibco/ 17105041) and 0.2 mg/ml DNAse (Roche/ 11284932001). The tissue was then further dissociated by pipetting and filtered using 40 μm cell strainers (Corning/ 352340). Single cell solution was washed with 30 mL of autoMACS Running Buffer (Miltenyi Biotec/130-940 091-221) and pelleted for 5min 300g 4°C to remove excess enzymes. Samples were transferred to FACS tubes, stained with surface antibody and hashtags for sample identification. Then mOrange+ cells were sorted.
Library was constructed using a microfluidics-based approach on Chromium Controller (10X Genomics) using the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) (10X Genomics) according to the manufacturer’s instructions. For each mouse, 50,000 mOrange+ cells were sorted.  We then loaded 15-20,000 cells belonging to 3 mice from the same group onto the Chromium Controller (10X Genomics).

value: Peritumoral liver


title: Prog, WT, UT, R2

source_name: Lineage negative bone marrow cells


title: PM364_troph

description:
Library name: M20145
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: Prog, WT, UT, R1


title: P131_troph

description:
Library name: M20139
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Female


title: miR-342 mice - pool 1

description:
CB-3
10X Genomics


title: WYpol32-11W

description: genotype of sectors

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio.

source_name: cell culture of WYpol32-11W


title: Macroph, p30, 8h, R3

source_name: macrophages

value: macrophages

value: LPS 8h


title: miR-342-3p sponge - biological replicate 1

source_name: iKCs


title: P128_strom

description:
Library name: M20137
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

source_name: placenta


title: P131_strom

description:
Library name: M20138
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: miR-mut mice - pool

description:
CB-1
10X Genomics

value: miR mut


title: WYpol32-10W

description: genotype of sectors

source_name: cell culture of WYpol32-10W

source_name: cell culture of WYpol32


title: Mouse_Day1_Rep2_scRNAseq

city: Leioa

first: Fernando

last: García-Moreno

state: Bizkaia

address: Barrio Sarriena s/n Edificio Sede

institute: Achucarro BCN

description: 10X Chronium v3.2

data_processing:
For both species, 10X CellRangerv6.0.2 was employed for alignment and demultiplexing of FASTQ files to obtain feature-barcode matrices. The genomes used as reference for each species alignment were mm10-2020-A for mouse and Gallus_gallus6_98for chicken. The quality control statistics related to this alignment steps and others are summarized in Supplementary Table S4. Afterwards, data matrices were imported to R(v4.1.0), where Seurat (v4.1.0) (60)was employed to further analysis, as describe in their vignettes (https://satijalab.org/seurat/).
Assembly: mm10-2020-Afor mouse and Gallus_gallus6_98for chicken
Supplementary files format and content: Output folder of 10X CellRanger v6.0.2 (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

source_name: Brain

extract_protocol:
Isolation of birthdated cells for scRNAseq was performed as previously described(28). Briefly, chick and mouse embryos were birthdated at early neurogenic timepoints (E4 or E12, respectively) and sacrificed either two or eleven days after EdU injection. P3 postnatal mouse pups and E15 chick embryos were anesthetized by hypothermia after immersion of either pup or the chick egg in ice. Brains were extracted in ice-cold HBSS. Then, the pallial region was microdissected under a stereomicroscope, collected in ice-cold HBSS, pooled and cut into small pieces. Tissue was dissociated in a species and stage specific manner, according to Supplementary Table S3.Following enzymatic digestion, chick (both E6 and E15) and mouse P3 tissue was manually homogenized by carefully pipetting and tissue clogs were removed by filtering the cell suspension through a 40 μm nylon strainer to a 15 ml Falcon tube containing 4 mlof 25% fetal bovine serum (FBS) in HBSS. After mouse E14 tissue digestion, FBS was added to the mix, cells were manually dissociated by pipetting and tissue clogs were removed by filtering the cell suspension though a 40 μm nylon strainer. Dissociated cells were then centrifuged at 200g for 10 min at room temperature (RT) and EdU molecule was detected in the pelleted cells. Following reaction, cells were washed thrice by centrifugation at 200g for 10 min and suspended in 1 ml of HBSS then passed on a 50 μm cell strainer. PI-/EdU+ cells, gated to include only the top 10% brightest cells, were finally FAC-sorted: for the E6 chick E6 a Synergy 3200 2L sorter (Sony) was used; for the E15 chick sample a FACSAria (BD Biosciences) was used; and for both mice samples a FACS Jazz (BD Biosciences) was used.
Cells were processed for single cell GEM formation following the standard Chromium Single Cell 3’ v3.1. Briefly cells were placed at the Chromium chip with the beads and reagents for the RNA capture and cDNA amplification. After the emulsion were obtained, the cDNA was amplificated in a thermocycler. Post amplificated cDNA, now marked with individual cell barcode, were fragmented, ligated the sequencing adapters and amplified. After that, the PCR product were purified and quantified.
Single cell library was prepared using “Chromium Next GEM Chip G Single Cell Kit”, 16 rxns PN-1000127, “Chromium Next GEM Single Cell 3ʹ Kit v3.1”, 4 rxns PN-1000269 and “Dual Index Kit TT Set A”, 96 rxns PN-1000215, following “Chromium Next GEM Single Cell 3’ Reagent Kits v3.1(Dual Index) User Guide” (Document number CG000315). Resulting libraries were sequenced on a Novaseq 6000 for an approximated 50.000 reads per cell.

value: Brain

value: Wild-type

tag: Stage


title: Mouse_Day1_Rep1_scRNAseq

description: 10X Chronium v3.1


title: WYpol32-8W

description: genotype of sectors

source_name: cell culture of WYpol32-8W

extract_protocol: Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)


title: P128_troph

description:
Library name: M20136
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

data_processing:
Raw sequencing reads were trimmed to remove the UMI, Illumina TruSeq 3’ adapter sequence, and all nucleotides after the 3’ adapter. Pre-processed reads were aligned to the genome for seven small non-coding RNAs using the miRMaster2 online tool. Raw read counts were processed using R. Data was batch-corrected using COMBAT-seq. Low quality samples and sequences were removed, and data was normalized per sncRNA species separately using the Relative Log Expression (RLE) method and scaled by counts per million (CPM).
Assembly: hg38
Supplementary files format and content: Raw count matrix of all samples before quality control and normalization

value: Sorted-cells:Zymo Quick-RNA Miniprep


title: Macroph, p30, 8h, R1


title: Macroph, p30, 2h, R3

value: LPS 2h


title: WYpol32-7W

description: genotype of sectors

source_name: cell culture of WYpol32-7W


title: B16F1 - Nontreated

city: Stanford

first: Sirimuvva

last: Tadepalli

state: CA

address: 299 Campus Drive

institute: Stanford University

data_processing:
Processed using 10x CellRanger pipeline version 3.1.0 in the Stanford Functional Genomics Facility. Reads were aligned using the mm10 genome.
Downstream analysis was performed using Seurat V3. Cells were selected for number of genes between 50-7000, and % of mitochondrial genes less than 10%. Data was normalized using the “LogNormalize” method (scale factor 10000) of Seurat’s NormalizeData function.
Assembly: mm10
Supplementary files format and content: Counts matrix post quality control

source_name: Tumor

extract_protocol:
Cells were extracted from B16F1 tumors at day 0 or 5 post radiation and sorted
Constructed by Stanford Functional Genomics Facility using Single Cell 3' V3 kit from 10x Genomics per manufacturer's protocols.

value: Sorted myeloid cells from tumor

value: Tumor

value: WT

value: No radiation


title: P128_endo

description:
Library name: M20135
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

extract_protocol:
Sorted cells were isolated from fresh chorionic villi using FACS as described in GSE159526. Sorted cells and chorionic villi samples were extracted using the ZYMO Quick-RNA MiniPrep kit according to manufacturer’s instructions or using TRIzol (ThermoFisher Scientific, USA).
5.8S rRNA was masked during adapter ligation by a complementary oligonucleotide, while miRNAs underwent 3′ adapter ligation, digestion of unligated adapters, and 5′ adapter ligation sequentially. The 5′ adapter contains a unique molecular identifier (UMI), followed by two nucleotides (CA) prior to the miRNA sequence. Upon conversion to cDNA by reverse transcription, the cDNA was amplified by PCR to include the sequences required for Illumina cluster generation and sample indexing developed by the GSC. The number of PCR cycles was dependent on the amount of input RNA; samples with low and high input were subjected to 20 and 15 cycles of PCR, respectively. Quality of libraries was assessed using the Agilent Bioanalyzer 2100 HS DNA chip Assay, (Agilent, USA)

value: placenta

value: Endothelial


title: B16F1 - Treated

value: Radiation (20Gy) treated


title: WYpol32-6W

description: genotype of sectors

source_name: cell culture of WYpol32-6W


title: littermate control mouse, PBS 6hr treated BMDM, RNA-seq, replicate 3

city: Seoul

first: Su Min

last: Kim

state: Gangnam-gu

address: Dogok-ro 237

country: South Korea

institute: Severance Hospital

description: Library name: WT_UT_6h-3

data_processing:
RNA-seq : Sequencing yielded paired-end reads with a read length of 101 bp. Prepared bulk RNA-seq library quality was checked using FastQC (v0.11.9). Reads were aligned to the GRCm38 reference genome using HISAT2 (v2.1.0). The resulting SAM files were converted to BAM files and indexed using SAMtools (v1.17). A count matrix was constructed using featureCounts (v2.0.0) .
Assembly: mm10 (GRCm38)
Supplementary files format and content: RNA-seq : count matrix

source_name: Bone Marrow Derived Macrophages

growth_protocol: BMs were extracted from the femur and tibia of mice. To generate BMDMs, BM cells were cultured in Dulbecco’s Modified Eagle’s Medium (HyClone, SH30243.01) supplemented with 10% fetal bovine serum (FBS; Gibco, 10099141) and 20% L929-conditioned media. After 6 d in culture, cells were seeded and treated under the indicated conditions.

extract_protocol:
RNA-seq : Total RNA was extracted from samples using TRIzol reagent (Invitrogen, 15596018) following the manufacturer’s protocol. 500 ng of total RNA was used for library preparation.
RNA-seq : Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Globin Kit, following the manufacturer’s instructions.

value: Bone Marrow Derived Macrophages

value: HSS9+/+ littermate controls

value: PBS


title: WYpol32-4W

description: genotype of sectors

source_name: cell culture of WYpol32-4W


title: WYpol32-2W

description: genotype of sectors

source_name: cell culture of WYpol32-2W


title: Macroph, p30, 2h, R1

value: macrophages


title: Nvec_ChIP_H3K4me3

data_processing:
Raw reads were filtered and trimmed with Trimmomtic (version 0.39) before mapping to the genome with bwa mem (version 0.7.17).
Duplicated reads were marked with bamsormadup from biobambam2 (https://github.com/gt1/biobambam2)
ATAC peaks were called with MACS2.
Assembly: Cladtertia collaboinventa genome assembly HoiH23_v2, Hormiphora californensis genome assembly GCA_020137815.1; Nematostella vectensis genome assembly GCA_932526225.1; Sphaeroforma arctica genome assembly Sarc_v2, Salpingoeca rosetta genome assembly Sros_v2
Supplementary files format and content: BigWig

organism: Nematostella vectensis

source_name: Nematostella vectensis

extract_protocol:
S. arctica and S. rosetta cells were double crosslinked with 1% formaldehyde and 3 mM DSG (Thermo Scientific, A35392). H.californensis specimens were flash-frozen in liquid nitrogen. Frozen tissues were then pulverized, cells and nuclei were collected by centrifugation for 15 min at 2,000 g. Collected cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG. N. vectensis 1.5-2 month old specimens were crosslinked with 1 % formaldehyde under vacuum. Crosslinked tissues were dissociated into single cells in Ca2+/Mg2+-free artificial sea water in the presence of Protease XIV (Sigma-Aldrich, P5147). Dissociated cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted to isolate mOrange-positive neuronal cells. FACS-sorted cells were additionally crosslinked with 3 mM DSG. C. collaboinventa specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG.
Chromatin immunoprecipitation was performed as previously described by Lara-Astiaso et al. (PMID: 25103404) with following modifications. For each species, 100 ng chromatin was used for immunoprecipitation.

value: neuronal ELAV+ cells

tag: chip antibody

value: H3K4me3, Millipore, 07-473


title: littermate control mouse, PBS 6hr treated BMDM, RNA-seq, replicate 2

description: Library name: WT_UT_6h-2


title: PL296_v

description:
Library name: M20134
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Villi

value: Male

value: Villi:TRIzol; Operator 1


title: scRNA-seq of wild-type border zone cells of regenerating hearts at 7 dpci

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description: 10x Genomics

data_processing:
Reads were aligned against the zebrafish genome (DanRer11) and counted by StarSolo.
Preprocessed counts were further analysed using Scanpy.
Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 23 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 40%. Furthermore, we filtered 9874 genes if they were detected in less than 30 cells (<0.01%).
Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding and cell clustering via community detection, were based on the initial PCA.
Final data visualization was done by scanpy and cellxgene packages.
Assembly: danRer11
Supplementary files format and content: starsolo outputs

organism: Danio rerio

source_name: Heart

extract_protocol:
Border zone cells from 8 hearts were pooled and tissue dissociation was performed using the Pierce Primary Cardiomyocyte Isolation kit according to manufacturer's instructions.  Cells were resuspended in DMEM with 10% FBS and 1x glutamate.
The cell suspensions were depleted for dead cells using LeviCell 1.0 device (Levitas Bio),counted with MOX Z cell counter and diluted according to manufacturer’s protocol to obtain 10.000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10xGenomics). Single cell RNAseq library preparation was done using standard protocol.

treatment_protocol: Zebrafish hearts were cryoinjured and extracted at 7 dpci.

value: Heart

value: Wild-type

value: Hearts were cryoinjured and border zone cells were microdissected at 7 dpci and pooled for scRNA-seq


title: PL295_vc

description:
Library name: M20132
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Female


title: Macroph, p30, UT, R3


title: Macroph, p30, 8h, R2

value: LPS 8h


title: Macroph, p30, UT, R2


title: WYpol32-1W

first: Daoqiong

last: Zheng

address: 866 Yuhangtang Road

institute: College of Life Sciences, Zhejiang University

description: genotype of sectors

source_name: cell culture of WYpol32-1W


title: littermate control mouse, PBS 6hr treated BMDM, RNA-seq, replicate 1

description: Library name: WT_UT_6h-1


title: PL295_strom

description:
Library name: M20131
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: placenta

value: Stromal

value: Sorted-cells:Zymo Quick-RNA Miniprep


title: littermate control mouse, LPS 6hr treated BMDM, RNA-seq, replicate 3

description: Library name: WT_LPS_6h-3

value: Bone Marrow Derived Macrophages

value: LPS


title: Nvec_ChIP_H3K4me2

value: H3K4me2, Abcam ab32356


title: Nvec_ChIP_input


title: Nvec_ChIP_H3K4me1

value: H3K4me1, Cell Signaling, 5326S


title: Macroph, p30, UT, R1

value: macrophages


title: PL295_troph

description:
Library name: M20130
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Cytotrophoblast


title: Macroph, WT, 8h, R3

value: WT


title: PL295_hofb

description:
Library name: M20129
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Hofbauer


title: PL296_strom

description:
Library name: M20133
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Male


title: Macroph, WT, 8h, R2


title: Macroph, p30, 2h, R2

value: LPS 2h


title: PL295_endo

description:
Library name: M20128
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Endothelial


title: littermate control mouse, LPS 6hr treated BMDM, RNA-seq, replicate 2

description: Library name: WT_LPS_6h-2

value: HSS9+/+ littermate controls


title: littermate control mouse, LPS 6hr treated BMDM, RNA-seq, replicate 1

description: Library name: WT_LPS_6h-1


title: PL294_v

description:
Library name: M20127
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Villi

value: Female

value: Villi:TRIzol; Operator 1


title: HSS9 KO mouse, PBS 6hr treated BMDM, RNA-seq, replicate 3

description: Library name: 9KO_UT_6h-3

value: HSS9 KO, homozygotes

value: PBS


title: Macroph, WT, 8h, R1

value: LPS 8h


title: Sorted-TAM_0dpRT_2

type: RNA

data_processing: Data was analyzed by ROSALIND® with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Normalization, fold changes and p-values were calculated using criteria provided by NanoSTRING ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual

source_name: Sorted Myeloid cells

growth_protocol: B16F1 tumor cells were implanted into C57BL/6J mice and treated with radiationtherapy (20Gy) once the tumor reached 40-100 mm3.

extract_protocol: Cells were washed and resuspended in 1/3 RNeasy Lysis Buffer RLT (Qiagen) at a concentration of 1,000-5,000 cells/μL. Samples were analyzed on the NanoSting nCounter® Mouse Myeloid Innate Immunity V2 Panel Standard Platform according to the manufacturer’s instructions.

treatment_protocol: Tumors were digested with collogenase and Dnase into a single cell suspension. Cells were stained with primary antibody, enriched with CD45-biotin and anti-biotin beads, and sorted for DC2s or TAMs

value: TAM

tag: treatement

value: nontreated control

tag: timepoint


title: Sorted-TAM_0dpRT_3


title: HSS9 KO mouse, PBS 6hr treated BMDM, RNA-seq, replicate 2

description: Library name: 9KO_UT_6h-2

value: Bone Marrow Derived Macrophages


title: PL294_strom

description:
Library name: M20126
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: placenta

value: Stromal

value: Sorted-cells:Zymo Quick-RNA Miniprep


title: Macroph, WT, 2h, R3

source_name: macrophages

value: macrophages

value: WT


title: HSS9 KO mouse, PBS 6hr treated BMDM, RNA-seq, replicate 1

description: Library name: 9KO_UT_6h-1


title: Macroph, WT, 2h, R1

value: LPS 2h


title: PL294_hofb

description:
Library name: M20125
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Hofbauer


title: PL294_endo

description:
Library name: M20124
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Endothelial


title: Sorted-TAM_0dpRT_1


title: PL290_strom

description:
Library name: M20122
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: PL290_v

description:
Library name: M20123
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Villi

value: Villi:TRIzol; Operator 2


title: Sorted-TAM_5dpRT_2

value: Radiation (20Gy)


title: HSS9 KO mouse, LPS 6hr treated BMDM, RNA-seq, replicate 2

description: Library name: 9KO_LPS_6h-2

value: HSS9 KO, homozygotes

value: LPS


title: Macroph, WT, UT, R2


title: Macroph, WT, 2h, R2


title: Sorted-TAM_5dpRT_3


title: Sorted-DC2_0dpRT_3


title: Macroph, WT, UT, R3


title: Sorted-TAM_5dpRT_1


title: HSS9 KO mouse, LPS 6hr treated BMDM, RNA-seq, replicate 1

description: Library name: 9KO_LPS_6h-1


title: PL290_troph

description:
Library name: M20121
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Cytotrophoblast

value: Female


title: Macroph, WT, UT, R1


title: LPS 1hr treated BMDM, RNA-seq, replicate 2

description: Library name: WT_LPS_R2


title: HPC-7, p42, UT, H3K27Ac, HiChIP, R2

data_processing:
HiChIP reads were mapped to the mm39 genome with the BWA-MEM software (v. 0.7.17) with specific settings to allow mapping of ligation events (bwa mem -5SP).
Alignment files were further processed with the ‘pairtools’ software to identify and record valid ligation events (pairtools parse) and to remove PCR duplicates (pairtools dedup).
Loop calling and differential loop analysis were performed with FitHiChIP.
Assembly: mm39
Supplementary files format and content: tab-delimited text files in bedpe format include predicted loops for each condition and common and condition-specific loops derived from differential loop analysis.
Library strategy: HiChIP

growth_protocol: HPC-7 cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) (Gibco 12440-053) supplemented with 10% FBS, 1% penicillin/streptomycin (Gibco 15140-122), 1% L-glutamine (Gibco 25030-024), 50μM b-mercaptoethanol (Gibco 31350-010), and 50 ng/mL murine SCF (Miltenyi Biotec, 130-101-697).

extract_protocol:
HiChIP was performed in duplicates using Dovetail Genomics’ HiChIP MNase kit and following manufacturer’s instructions. Briefly, 5x10^6 cells were pelleted to then be crosslinked, digested with MNase and lysed. After quality control, 1000ng of lysate were incubated with H3K27ac antibody.
Samples were then proximity ligated and DNA was purified for library preparation, followed by ligation capture and amplification.

value: H3K27ac antibody (Cell Signaling, 8173)


title: HPC-7, p42, UT, H3K27Ac, HiChIP, R1


title: LPS 1hr treated BMDM, RNA-seq, replicate 1

description: Library name: WT_LPS_R1

value: Bone Marrow Derived Macrophages


title: HSS9 KO mouse, LPS 6hr treated BMDM, RNA-seq, replicate 3

description: Library name: 9KO_LPS_6h-3


title: PL290_endo

description:
Library name: M20120
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: placenta


title: PL281_v

description:
Library name: M20119
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: PL281_strom

description:
Library name: M20118
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Stromal


title: HPC-7, p42, LPS 2h, H3K27Ac, HiChIP, R2


title: PBS 1hr treated BMDM, RNA-seq, replicate 3

description: Library name: WT_Control_R3

value: PBS


title: PL281_hofb

description:
Library name: M20117
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: LPS 1hr treated BMDM, RNA-seq, replicate 3

description: Library name: WT_LPS_R3


title: Sorted-DC2_0dpRT_2

value: nontreated control