title: Parse_Rat_SS_BAT

description: Library name: Sample 5

source_name: subscapular brown adipose tissue

value: subscapular brown adipose tissue

tag: tissue common_name_ontology

tag: strain

value: SS/HsdMcwiCrl

tag: strain ontology

tag: organism ontology

value: male

tag: sex ontology

tag: housing temperature

tag: temperature unit

value: degree celsius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: polycarbonate cage

tag: bedding

value: aspen chip

tag: water

value: tap water

tag: library kit

value: Parse Evercode WT v3

tag: library kit_ontology

value: normal

tag: disease ontology

tag: preservation method

value: Snap Frozen

tag: organism supplier

value: Charles River Laboratory

tag: euthanasia method

value: Pentobarbital

tag: euthanasia method_ontology


title: CAGE_L_00213.BC10,Rottweiler,Lung_alveoli_only

status: Public on Apr 01 2026

type: SRA

city: Stockholm

first: Carsten

last: Daub

address: Blickagången 16, 14152 Flemingsberg

department: Gastroenterology and Nutrition Unit (GUT)

country: Sweden

institute: Karolinska Institute

description: Library name: CAGE_L_00213.BC10

library_source: transcriptomic

data_processing:
Library strategy is RNA-seq (CAGE). Basecalls were performed using bcl2fastq v2.20.0 for HiSeq output.
The 3’ adapter (“TCGTATGCCGTCTTC”), EcoP15 (“CAGCAG”), and 5’G regions of the CAGE-seq reads and reads with quality score < 20 were removed using cutadapt version 3.4. rRNA filtering was performed using SortMeRNA version 4.3.4.
CAGE-seq reads were aligned to the canFam4 genome using STAR version 2.7.9a. CAGE tags were normalized (TPM: Tag Per Million). CAGE tag clustering was conducted using CAGEFightR version 1.10.0
The promoter regions were identified with CAGEfightR’s `clusterUnidirectional()` function, with parameters pooled CAGE tags expressed at more than 10 tpm for the comprehensive set and longer than 1 bp and above 10 tpm in at least one sample for the robust promoter set. Bidirectional clusters were identified with the default CAGEfightR parameters. Only candidates located in introns or intergenic regions were retained if they had at least 4 different CAGE tag locations on each strand, and robust enhancers had to have at least 6 different CAGE tags on each strand. Those overlapping with our robust promoter set were excluded. The tags present in the comprehensive set but absent in the robust set were evaluated. Tags with 98% bidirectionality were included in the robust enhancers. Each enhancer region was trimmed to the first and last CTSS within it.
Assembly: canFam4 (UU_Cfam_GSD_1.0, GCF_011100685.1)
Supplementary files format and content: csv file includes enhancer comprehensive expression matrix TPM (Tag Per Million) normalized
Supplementary files format and content: csv file includes enhancer robust expression matrix TPM( Tag Per Million) normalized
Supplementary files format and content: csv file include promoter comprehensive expression matrix TPM (Tag Per Million) normalized
Supplementary files format and content: csv file include promoter robust expression matrix TPM (Tag Per Million) normalized
Supplementary files format and content: csv file include enhancer comprehensive expression matrix raw counts
Supplementary files format and content: csv file include enhancer robust expression matrix raw counts
Supplementary files format and content: csv file include promoter comprehensive expression matrix raw counts
Supplementary files format and content: csv file include promoter robust expression matrix raw counts
Supplementary files format and content: csv file include promoter annotation file
Supplementary files format and content: csv file include enhancer annotation file
Supplementary files format and content: text file includes md5sum

molecule: total RNA

organism: Canis lupus familiaris

source_name: lung

extract_protocol:
CAGE libraries were prepared using 1 μg of total RNA from each sample.The CAGE experiment requires at least 10 μl of sample to proceed. Therefore, tissue pools were created for samples with insufficient volume. We begin with at least 10 μl of volume for each sample.
CAGE libraries were prepared following the previously described protocol by Takahashi et al. (Takahashi et al., 2012). In each library, we used eight barcodes (CTT, GAT, ACT, ATG, AGT, TGG, GTA, and GCC) for eight RNA samples. Single-strand cDNA was barcoded by adding a 5’ linker containing a 5’ barcode sequence and the EcoP15I sequence. A 3′ linker with Illumina primer sequence was added to the barcoded cDNA fragment. The size of the resulting CAGE libraries ranged between 97 and 103 bp. Libraries were single-read sequenced at 50 cycles using the HiSeq 2500 Illumina System. The HiSeq SR Rapid Cluster Kit v2 (Illumina) and the HiSeq Rapid Duo cBot Sample Loading Kit (Illumina) were used to sequence CAGE libraries in the rapid mode.

tag: tissue

value: lung

tag: breed

value: Rottweiler

tag: Sex

value: Male

tag: age (month)

tag: batch


title: H3K4me3_P1P6MLL_DKO_FGO_Rep2

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

description: Library name: Sample16

library_source: genomic

data_processing:
CATCH-seq and CUT&RUN sequencing reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.3.5) with the parameters “-q -N 1 -L 25”. After removing PCR duplicates and filtering out multiple mapping reads, uniquely mapped reads were used for the downstream analysis. Spike-in normalization of CATCH-seq reads was performed as previously described. The reads were aligned to the mouse (mm10) and D. melanogaster (dm6) reference genome. All the H2A.Z and histone modification peaks were called by MACS2 (version 2.1.2) with the parameters ‘-g mm –nomodel --nolambda’.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: ovary

extract_protocol:
After ZP of SN-type FGOs were removed by acid tyrodes’ solution, ZP-free oocytes were collected to 9 µL of Nuclei EZ lysis buffer (Sigma, NUC-101) supplemented with complete EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride. The samples were snap frozen in liquid nitrogen and stored at -80C until use. At the day of library construction, the samples were thawed on ice, and added with 1 µL of the lysis buffer containing a constant number of Drosophila melanogaster S2 cells (Thermo Fisher Scientific, R69007) for spike-in normalization purpose. Then, 1 µL of 1% Triton X-100 (Merck 93443) and 1% deoxycholate (Nacalai, 10712-54) mixture solution was added to the samples, and sit on ice for 5 min. The chromatin was fragmented by 2 U/µl MNase (M0247S, NEB) in 1xMNase buffer supplemented with 1% PEG6000 (HAMPTON RESEARCH, HR2-533) and 2 mM DTT (Nacalai) at 21C or 37C for 7.5 min. The digestion temperature was dependent on the experimental condition, including the lot of MNase and the freshness of PEG6000, which had been determined by fragment sizes of input libraries in a preliminary test. The MNase reaction was stopped by adding 1/10 volume of 100 mM EDTA and 1/12 volume of the 1% Triton X-100 and 1% deoxycholate mixture, and the samples were rest on ice for 15 min. The chromatin lysates were then added with freshly prepared immunoprecipitation buffer (Brind’Amour et al. 2015), and 5% volume was kept for input library construction. To the rest of the lysate, 30 ng of annealed I-SceI carrier DNA was added (Zhu et al. 2021).
CATCH-seq is an improved method of the ultra-low-input native ChIP-seq (ULI-NChIP). The original protocol of CATCH-seq was described in Zhu et al., and we have made some modifications to improve its usability. For each immunoprecipitation reaction, 0.25 µL of rabbit anti-H3K4me3 (Active Motif 39159, 70 oocytes/library), 500 ng of rabbit anti-H3K27me3 (Diagenode C15410069, 50-80 oocytes/library), 1.0 µg of mouse anti-H3K36me2 (MBL, MABI0332, 100 oocytes/library) or 1.0 µL of rabbit anti-H3K36me3 antibody (Active Motif 61022, MABI0333, 100 oocytes/library) conjugated to precleared Dynabeads Protein A (Thermo Fisher Scientific, 10006D) and G (Thermo Fisher Scientific, 10007D) mixture was used. CUT&RUN libraries were prepared as previously described (Hayashi, R. & Inoue, A). The antibodies used were rabbit anti-H3K27me3 (1/100, Diagenode C15410069, 150-170 oocytes/library). Protein A-MNase was provided by Dr. Steven Henikoff’s laboratory (Skene et al.). CUT&RUN libraries were sequenced on a NextSeq500 or Nextseq2000 with paired-end or single-end reads (Illumina).

value: ovary

tag: developmental stage

value: Full-grown oocyte

tag: genotype

value: Pcgf1/6 double knockout


title: Parse_Rat_taPVAT_BAT

city: East Lansing

first: Leah

last: Terrian

state: MI

address: 775 Woodlot Dr.

country: USA

institute: Michigan State University

description: Library name: Sample 4

library_source: transcriptomic single cell

data_processing:
The quality of the raw sequencing files was first checked using FastQC. Reads were then split by species using the fastq_sep_groups_v0.5.py script from Parse (v0.5, Parse Biosciences, Seattle, WA, USA). Rat and cattle reads were aligned to their respective reference genomes (GRCr8, ARS-UCD1.3) using the Parse Biosciences split-pipe pipeline (v1.5.1, Parse Biosciences, Seattle, WA, USA). Alignment quality was assessed, and the resulting filtered features, genes, and matrix files (DGE_filtered) were further processed and analyzed using Python.
First, the aligned reads were preprocessed with scDblFinder (Germain et al., 2021) to identify doublets. Then individual samples were further preprocessed using the scanpy Python package (Wolf et al., 2018). Quality control cut-offs were similar to those recommend in “Single Cell Best Practices” manual (Heumos et al., 2023). Genes found in 3 or fewer cells were removed, as were cells with fewer than 100 measured transcripts. Nuclei that had greater than 15000 reads or 4500 measured genes were also discarded. A mitochondrial read percentage cut-off of 3% was used since single-nuclei RNAseq is expected to capture far fewer mitochondrial reads than single-cell RNAseq.
After individual preprocessing, the anndata objects for each sample were combined and additional preprocessing was performed. Nuclei that were outside of 5 median absolute deviations from the medians of the number of detected genes (log1p_n_genes_by_counts)  and number of detected RNA molecules (log1p_total_counts) were labeled outliers and discarded. The high-dimensional data was then visualized using principal component analysis (PCA) and Uniform Approximation and Projection (UMAP). Batch integration was performed with scvi-tools (Gayoso et al., 2022) to remove technical noise from the reduced-dimension plots. Clustering was done using the Leiden algorithm. Previously published marker genes and cluster-specific genes identified by differential expression analysis were used to manually annotate each cluster.
Assembly: GRCr8 (GCA_036323735.1), ARS-UCD1.3
Supplementary files format and content: Matrix, tab-delimited, and comma-delimited files

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: thoracic aorta perivascular adipose tissue

extract_protocol:
Nuclei from Dahl SS rat and Holstein dairy cow adipose tissue were isolated and processed using a custom protocol outlined in the associated publication. The protocol is similar to the protocol found here: Whytock, K. L. et. al. (2023). Isolation of nuclei from frozen human subcutaneous adipose tissue for full-length single-nuclei transcriptional profiling. STAR Protocols, 4(1), 102054. https://doi.org/10.1016/j.xpro.2023.102054
The 10X Chromium Next GEM Single Cell 3’ Reagent Kit v 3.1 (Dual Index) was used with a targeted cell recovery of 10,000 according to manufacturer’s recommended protocol (CG000315, Rev D).

tag: tissue common_name_ontology

tag: strain

value: SS/HsdMcwiCrl

tag: strain ontology

tag: organism ontology

value: male

tag: sex ontology

tag: housing temperature

tag: temperature unit

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

tag: humidity unit_ontology

tag: light cycle

tag: cage type

tag: disease


title: CAGE_L_00213.BC02,Swedish_Elkhound,Uterine_horn_only

description: Library name: CAGE_L_00213.BC02

source_name: uterus

tag: tissue

value: uterus

tag: breed

value: Swedish Elkhound

tag: Sex

value: Female

tag: age (month)

tag: batch


title: H3K4me3_P1P6MLL_WT_FGO_Rep2

description: Library name: Sample14

tag: developmental stage

tag: genotype

value: wild type


title: CAGE_L_00212.BC15,Swedish_Elkhound,Eye_pool

description: Library name: CAGE_L_00212.BC15

source_name: retina,optic II nerve

value: retina,optic II nerve


title: 105379-001-070

city: Leiden

first: Daan

last: van der Vliet

address: Einsteinweg 55

department: Molecular Physiology

country: Netherlands

institute: Leiden university

data_processing:
The workflow started with a quality control stage. In this stage checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw data set was determined using third-party (FastQC v0.11.9) and in-house (FastQA v3.1.27) QC tools. Sequence reads were trimmed to remove possible adapter sequences and filtered on low-quality bases using fastp v0.23.2. Presumed adapter sequences were removed from the read when the bases matched a sequence in the adapter sequence set (TruSeq adapters). To remove noise introduced by sequencing errors, the reads were filtered based on the base quality score. Reads of which more than 40% of the bases had an average phred score below Q15 or which had more than 5 unknown bases (N) were removed. If the resulting reads were shorter than 15 bp, they were removed altogether (both pairs in paired-end reads).  For each sample, the trimmed reads were mapped to the human GRCh38.p13 (Homo_sapiens.GRCh38.dna.primary_assembly.fa) reference provided in the References directory. The reads were mapped to the reference sequence using a short read aligner based on Burrows-Wheeler Transform (HISAT2 v2-2.2) with default settings. BAM files were generated as a result of this step. The alignment files (BAM files sorted on coordinates and indexed with the samtools v1.10 package) Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v2.0.2. The hit counts were summarised and reported in the .count files
Assembly: human GRCh38.p13 (Homo_sapiens.GRCh38.dna.primary_assembly.fa)
Supplementary files format and content: Based on the mapped locations in the alignment the frequency of how often a read was mapped on a transcript was determined with HTSeq v2.0.2. The hit counts were summarised and reported in the .count files

organism: Homo sapiens

source_name: white matter

extract_protocol:
Isolated tissues were dissolved in 500 µL Trisure (BIO-38032, Bioline). Subsequently, 100 µL CHCl3 was added to the tube and the solution was centrifuged (15 min, 11,000 rcf, 4 ⁰C). The aqueous layer was carefully removed and 500µL was added to the same tube for an additional extraction. After combining the two aqueous layers 1 equal volume 70% EtOH was added and the solution was added to an RNAeasy column (QIAgen). The RNA was washed with RW1 buffer, after which any DNA contamination was removed by incubation with DNase (15 min, RT). After this the column was washed in subsequent steps with RW1 buffer, then with RPE buffer and lastly with 80% EtOH. The column was air dried for 5 minutes before eluting the RNA in 16 µL RNAse free water. 1 µL of the extracted RNA was used for analysis on a Denovix DS-11 spectrofotometer to analyze the purity and concentration.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s).

value: Brain

value: white matter

tag: sample code

value: Multiple sclerosis

tag: lesion type


title: CAGE_L_00212.BC12,Rottweiler,Supraspinatus_only

description: Library name: CAGE_L_00212.BC12

source_name: skeletal muscle

value: skeletal muscle


title: H3K4me3_P1P6MLL_DKO_FGO_Rep1

description: Library name: Sample15


title: 105379-001-066


title: CAGE_L_00213.BC03,Rottweiler,Cerebral_cortex_pool

description: Library name: CAGE_L_00213.BC03

source_name: frontal cortex,parietal cortex,temporal cortex,occipital cortex


title: H3K4me3_P1P6MLL_WT_FGO_Rep1

description: Library name: Sample13


title: 105379-001-064


title: 10x_Rat_Mes_PVAT_WAT

description: Library name: Sample 1

source_name: mesenteric perivascular adipose tissue

value: mesenteric perivascular adipose tissue

tag: tissue common_name_ontology

tag: strain

tag: strain ontology

tag: organism ontology

tag: sex ontology

tag: housing temperature

tag: temperature unit

value: degree celsius

value: percent

value: polycarbonate cage

tag: bedding

value: aspen chip

tag: water

value: tap water

tag: library kit

tag: library kit_ontology

value: normal

tag: disease ontology

tag: preservation method

value: Snap Frozen

tag: organism supplier

value: Charles River Laboratory

tag: euthanasia method

value: Pentobarbital

tag: euthanasia method_ontology


title: Parse_Rat_RP_WAT

description: Library name: Sample 3

source_name: retroperitoneal adipose tissue

tag: tissue

value: retroperitoneal adipose tissue

value: SS/HsdMcwiCrl

tag: batch

tag: Sex

value: male

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Parse Evercode WT v3

tag: disease


title: f_standard_saline_oLN_390

city: Wuerzburg

first: Simon

last: Kloock

address: Oberduerrbacherstr. 6

department: Endocrinology

country: Germany

institute: University Hospital Wuerzburg

description: Library name: A390

data_processing:
Sequencing and data analysis was executed by Novogene Corp. The resulting data underwent QC before processed reads were aligned to the rat reference genome (mratbn7.2). Differential expression analysis was carried out with the DESeq2 R package (version 1.42.0). P-values were adjusted using the Benjamini–Hochberg method to control the false discovery rate, and genes were considered significantly differentially expressed when padj≤0.05 and |log2(fold change)|≥1. Downstream bioinformatic analyses included Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis using Novogene’s implementation of the clusterProfiler software.
Assembly: ensembl_110_rattus_norvegicus_mratbn7_2_toplevel
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

source_name: Femora

extract_protocol:
RNA was extracted from bone using PureLink RNA Mini Kit (#12183018A, Invitrogen, Carlsbad, CA, USA)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification

value: Femora

tag: strain

value: Wistar rat

value: female

tag: treatment

value: Healthy control


title: CAGE_L_00212.BC08,Rottweiler,Colon_only

description: Library name: CAGE_L_00212.BC08

source_name: colon

value: colon

tag: breed

value: Rottweiler

value: Male

tag: age (month)


title: H3K27me3_CR_P1P6MLL_TKO_FGO_Rep1

description: Library name: Sample11

data_processing:
CATCH-seq and CUT&RUN sequencing reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.3.5) with the parameters “-q -N 1 -L 25”. After removing PCR duplicates and filtering out multiple mapping reads, uniquely mapped reads were used for the downstream analysis. Spike-in normalization of CATCH-seq reads was performed as previously described. The reads were aligned to the mouse (mm10) and D. melanogaster (dm6) reference genome. All the H2A.Z and histone modification peaks were called by MACS2 (version 2.1.2) with the parameters ‘-g mm –nomodel --nolambda’.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Run

value: ovary

tag: developmental stage

value: Full-grown oocyte

tag: genotype

value: Pcgf1/6 & Mll2 triple knockout


title: 105379-001-071

value: Brain

value: white matter

tag: sample code

value: Multiple sclerosis

tag: lesion type

value: PLWM


title: CAGE_L_00214.BC03,Border_Collie,Kidney_pool

description: Library name: CAGE_L_00214.BC03

source_name: kidney

tag: tissue

value: kidney

value: Border Collie

tag: batch


title: f_standard_saline_oLN_389

description: Library name: A389

tag: Sex


title: 105379-001-062


title: CAGE_L_00212.BC05,German_pinscher,Stomach_fundus_only

description: Library name: CAGE_L_00212.BC05

source_name: stomach

value: stomach

value: German Pinscher

value: Female


title: 105379-001-061


title: f_standard_saline_oLN_392

description: Library name: A392

value: Femora

value: Wistar rat

value: female


title: f_hfd_lfd_pyy_sema_LN_320

description: Library name: A320

value: MetOP-Sema+PYY


title: f_hfd_lfd_pyy_sema_LN_318

description: Library name: A318


title: H3K27me3_CR_P1P6MLL_DKO_FGO_Rep1

description: Library name: Sample9

value: Pcgf1/6 double knockout


title: CAGE_L_00212.BC02,Rottweiler,Liver__only

description: Library name: CAGE_L_00212.BC02

source_name: liver

value: liver

value: Rottweiler

value: Male


title: H3K27me3_CR_P1P6MLL_WT_FGO_Rep1

description: Library name: Sample7

value: ovary

value: Full-grown oocyte

value: wild type


title: 105379-001-060

value: Brain

value: white matter

value: Multiple sclerosis


title: CAGE_L_00211.BC13,Swedish_Elkhound,Adrenal_gland_pool

description: Library name: CAGE_L_00211.BC13

source_name: adrenal gland

value: adrenal gland

value: Swedish Elkhound


title: f_standard_saline_oLN_387

description: Library name: A387

value: Healthy control


title: Input_H3K27me3_PRC1-CD_FGO

description: Library name: Sample6

value: PRC1 catalytic dead


title: 105379-001-057


title: Input_H3K27me3_PRC1-WT_FGO

description: Library name: Sample5


title: 105379-001-059


title: 105379-001-063

value: PLWM


title: CAGE_L_00211.BC15,Border_Collie,Parathyroid_only

description: Library name: CAGE_L_00211.BC15

source_name: thyroid gland

value: thyroid gland

value: Border Collie


title: CAGE_L_00212.BC10,Mixed_Breed,Embryos_(day_30)

description: Library name: CAGE_L_00212.BC10

source_name: embryo

value: embryo

value: Mixed Breed

value: not provided

value: Embryo. Age about 30 days.


title: 105379-001-058


title: H3K27me3_PRC1-CD_FGO_Rep2

description: Library name: Sample4

source_name: ovary

value: ovary


title: Parse_Rat_Mes_PVAT_WAT

description: Library name: Sample 2

value: mesenteric perivascular adipose tissue

tag: tissue common_name_ontology

value: SS/HsdMcwiCrl

tag: strain ontology

tag: organism ontology

value: male

tag: sex ontology

tag: housing temperature

tag: temperature unit

value: degree celsius

tag: temperature unit_ontology

tag: housing humidity

value: percent

value: polycarbonate cage

tag: bedding

value: aspen chip

tag: water

value: tap water

tag: library kit

value: Parse Evercode WT v3

tag: library kit_ontology

value: normal

tag: disease ontology

tag: preservation method

value: Snap Frozen

tag: organism supplier

value: Charles River Laboratory

tag: euthanasia method

value: Pentobarbital

tag: euthanasia method_ontology


title: f_hfd_lfd_saline_LN_265

description: Library name: A265

tag: tissue

value: Femora

tag: strain

value: Wistar rat

tag: Sex

value: female

tag: treatment

value: MetOP-Saline

tag: batch


title: CAGE_L_00211.BC12,Swedish_Elkhound,Kidney_pool

description: Library name: CAGE_L_00211.BC12

value: kidney

tag: breed

value: Swedish Elkhound

value: Female

tag: age (month)


title: H3K27me3_PRC1-CD_FGO_Rep1

description: Library name: Sample3

value: ovary

tag: developmental stage

value: Full-grown oocyte

tag: genotype

value: PRC1 catalytic dead


title: 105379-001-055

value: Brain

value: white matter

tag: sample code

tag: disease

value: Multiple sclerosis

tag: lesion type

value: NAWM


title: CAGE_L_00211.BC05,East-European_Shepherd,Heart_valve_pool

description: Library name: CAGE_L_00211.BC05

source_name: heart endocardium,heart valve

value: heart endocardium,heart valve

value: East-European Shepherd


title: f_hfd_lfd_pyy_sema_LN_251

description: Library name: A251

value: MetOP-Sema+PYY


title: H3K27me3_PRC1-WT_FGO_Rep2

description: Library name: Sample2

value: wild type


title: H3K27me3_PRC1-WT_FGO_Rep1

description: Library name: Sample1


title: 105379-001-054

value: Non-demented control

value: CWM


title: f_hfd_lfd_sema_LN_243

description: Library name: A243

value: Femora

value: Wistar rat

value: female

value: MetOP-Sema


title: P1P6MLL_matTKO_morula_embryos_Rep9

description:
Library name: Sample42
matTKO_rep9

data_processing:
For RNA-seq, all reads after trimming by Trim Galore (version 0.6.4) were mapped to the mouse reference genome (mm10) by STAR (version 2.7.3) with default parameters "--runMode alignReads --outSAMattributes NH NI NM MD --outSAMtype BAM Unsorted". The RPKM values of each gene were generated by RSEM (version 1.3.1). For allele-specific analysis of BDF1 x JF1 F1 hybrid embryos, The SNPs in BDF1 and JF1 were masked as ‘N’ in the reference genome (GRCm38) by the ‘Dual strain mode’ in SNPsplit_genome_preparation of SNPsplit (version 0.3.4). Then reads were aligned to the N-masked genome by STAR (version 2.7.6) with specific setting of parameters ‘--alignEndsType EndToEnd --outSAMattributes NH HI NM MD’. By filtering the alignment records with the ‘NH:i:1’ tag, uniquely aligned reads were assigned to its parental origins. SNPsplit was used to assign the SNP-containing reads to maternal and paternal genome. The number of allelic reads of each gene were calculated by featureCounts (version 1.6.0) to calculate the RPKM values.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include RPKM value for each sample
Supplementary files format and content: bigWig files for FGO sample

extract_protocol:
For bulk RNA-seq of PRC1-WT and -CD FGOs, ten oocytes were pooled to generate each RNA-seq library. The zona pellucida was removed by brief incubation in acidic Tyrode's solution. All samples for RNA-seq were washed three times in 0.2% BSA/PBS before being transferred into a 0.2-ml tube with ~0.5μl carryover.
For RNA-seq, libraries were prepared as previously described (Inoue et al., Genes Dev. 2018). Briefly, cDNA was prepared by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TAKARA, 634890) according to the manufacture's instructions. Two hundreds picograms of cDNA were used for the library construction by using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) according to the manufacture's instructions.

value: embryo

value: Morula

value: maternal Pcgf1/6 & Mll2 triple knockout


title: f_hfd_lfd_sema_LN_242

description: Library name: A242


title: CAGE_L_00211.BC03,Rottweiler,Thyroid_gland_only

description: Library name: CAGE_L_00211.BC03

value: thyroid gland

value: Rottweiler

value: Male


title: 105379-001-049

value: Brain

value: white matter

value: Multiple sclerosis

value: NAWM


title: P1P6MLL_matTKO_morula_embryos_Rep10

description:
Library name: Sample43
matTKO_rep10


title: 105379-001-052


title: f_hfd_lfd_pyy_sema_LN_253

description: Library name: A253

value: MetOP-Sema+PYY


title: CAGE_L_00211.BC02,Rottweiler,DRG_only

description: Library name: CAGE_L_00211.BC02

source_name: spinal ganglion

value: spinal ganglion


title: P1P6MLL_matTKO_morula_embryos_Rep8

description:
Library name: Sample41
matTKO_rep8


title: CAGE_L_00210.BC15,Rottweiler,Adrenal_gland_pool

description: Library name: CAGE_L_00210.BC15

value: adrenal gland


title: 105379-001-050

value: PLWM


title: P1P6MLL_matTKO_morula_embryos_Rep7

description:
Library name: Sample40
matTKO_rep7


title: CAGE_L_00210.BC13,Border_Collie,Spinal_Cord_only

description: Library name: CAGE_L_00210.BC13

source_name: spinal cord

value: spinal cord

value: Border Collie


title: f_hfd_lfd_sema_LN_240

description: Library name: A240

value: Femora

value: Wistar rat

value: female

value: MetOP-Sema


title: f_hfd_lfd_pyy_sema_LN_248

description: Library name: A248


title: 105379-001-051

source_name: white matter


title: 105379-001-048


title: f_hfd_lfd_sema_LN_241

description: Library name: A241


title: CAGE_L_00210.BC12,Rottweiler,Prostate_only

description: Library name: CAGE_L_00210.BC12

source_name: prostate gland

value: prostate gland


title: P1P6MLL_matTKO_morula_embryos_Rep6

description:
Library name: Sample39
matTKO_rep6

value: embryo

value: Morula

value: maternal Pcgf1/6 & Mll2 triple knockout


title: 105379-001-047

value: Brain

value: white matter


title: P1P6MLL_matTKO_morula_embryos_Rep4

description:
Library name: Sample37
matTKO_rep4


title: CAGE_L_00210.BC08,Rottweiler,Blood_vessel_pool

description: Library name: CAGE_L_00210.BC08

source_name: artery,vena cava

value: artery,vena cava

value: Rottweiler

value: Male


title: CAGE_L_00210.BC02,German_pinscher,Kidney_pool

description: Library name: CAGE_L_00210.BC02

value: kidney

value: German Pinscher

value: Female


title: f_hfd_lfd_sema_LN_238

description: Library name: A238


title: f_hfd_lfd_saline_LN_226

description: Library name: A226

value: MetOP-Saline


title: CAGE_L_00209.BC15,Rottweiler,Lower_respiratory_tract_pool

description: Library name: CAGE_L_00209.BC15

source_name: trachea,bronchus

value: trachea,bronchus


title: 105379-001-041

value: Multiple sclerosis


title: 105379-001-044

value: PLWM


title: 105379-001-042


title: P1P6MLL_matTKO_morula_embryos_Rep3

description:
Library name: Sample36
matTKO_rep3


title: P1P6MLL_matTKO_morula_embryos_Rep1

description:
Library name: Sample34
matTKO_rep1


title: P1P6MLL_matTKO_morula_embryos_Rep5

description:
Library name: Sample38
matTKO_rep5


title: f_hfd_lfd_saline_LN_229

description: Library name: A229

value: Femora

value: Wistar rat

value: female


title: f_hfd_lfd_pyy_saline_LN_220

description: Library name: A220


title: P1P6MLL_matDKO_morula_embryos_Rep10

description:
Library name: Sample33
matDKO_rep10

value: embryo

value: Morula

value: maternal Pcgf1/6 double knockout


title: 105379-001-046

value: Brain

value: white matter


title: f_hfd_lfd_saline_LN_224

description: Library name: A224


title: CAGE_L_00209.BC12,Swedish_Elkhound,Lung_alveoli_only

description: Library name: CAGE_L_00209.BC12

source_name: lung

value: lung

value: Swedish Elkhound


title: 105379-001-043


title: CAGE_L_00209.BC10,Swedish_Elkhound,Supraspinatus_only

description: Library name: CAGE_L_00209.BC10

source_name: skeletal muscle

value: skeletal muscle


title: CAGE_L_00210.BC10,Collie,Lower_respiratory_tract_pool

description: Library name: CAGE_L_00210.BC10

value: Collie

value: Male


title: P1P6MLL_matTKO_morula_embryos_Rep2

description:
Library name: Sample35
matTKO_rep2

value: maternal Pcgf1/6 & Mll2 triple knockout


title: CAGE_L_00209.BC08,Rottweiler,Piriform_lobe_only

description: Library name: CAGE_L_00209.BC08

source_name: piriform lobe

value: piriform lobe

value: Rottweiler


title: f_hfd_lfd_pyy_saline_LN_219

description: Library name: A219

source_name: Femora


title: P1P6MLL_matDKO_morula_embryos_Rep9

description:
Library name: Sample32
matDKO_rep9


title: P1P6MLL_matDKO_morula_embryos_Rep7

description:
Library name: Sample30
matDKO_rep7


title: 105379-001-035

value: Multiple sclerosis


title: P1P6MLL_matDKO_morula_embryos_Rep8

description:
Library name: Sample31
matDKO_rep8


title: Col-0 roots, SiBs, day3, rep2

city: Köln

first: Natalie

last: Peltz

address: Bonner Str. 45

institute: University of Cologne

description:
Library name: Sample_50
Column name in count_table_col0.txt: 037-059

data_processing:
fastp v0.20.0, FastQC v0.11.9, MultiQC v1.19, STAR v2.7.10a
Raw paired-end RNA-Seq reads were processed with fastp v0.20.0 (Chen et al., 2018a) to remove adapter sequences and low-quality bases, discarding reads shorter than 98 bp.
Quality control of trimmed reads was conducted using FastQC v0.11.9 (Andrews, 2010) and summarized across samples with MultiQC v1.19 (Ewels et al., 2016).
Reads were aligned to the reference genomes using STAR v2.7.10a (Dobin et al., 2013) against the At TAIR10 genome (Lamesch et al., 2012)
Gene-level counts were obtained and imported into R for differential expression analysis using DESeq2 (Love et al., 2014). Genes <10 counts in all samples of the smallest condition group were excluded. Normalization and dispersion estimation were performed with DESeq2. For visualization, variance-stabilizing and regularized log transformations were computed. Differential expression was assessed separately for each genotype using appropriate models depending on the number of treatment groups. Log2 fold changes were shrunk using the apeglm method (Zhu et al., 2019)
Supplementary files format and content: tab-delimited file contains DESeq2 normalized counts for each sample

organism: Arabidopsis thaliana

source_name: whole root

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) and treated with DNase I (Thermo Fisher Scientific) following the manufacturers’ protocols.  Samples submitted for sequencing contained 2 µg of total RNA
mRNA-Sequencing libraries were prepared using the Illumina TruSeq stranded protocol (NEB, Frankfurt am Main, Germany) according to the manufacturer’s instructions (Illumina Inc., San Diego, CA, USA).

value: whole root

value: SiBs


title: Col-0 roots, SiBs, day3, rep1

description:
Library name: Sample_49
Column name in count_table_col0.txt: 037-058


title: P1P6MLL_matDKO_morula_embryos_Rep4

description:
Library name: Sample27
matDKO_rep4


title: f_hfd_lfd_pyy_saline_LN_216

description: Library name: A216

value: Femora

value: Wistar rat

value: female


title: 105379-001-039


title: 105379-001-040

value: PLWM


title: P1P6MLL_matDKO_morula_embryos_Rep6

description:
Library name: Sample29
matDKO_rep6

value: embryo

value: Morula

value: maternal Pcgf1/6 double knockout


title: CAGE_L_00209.BC03,Swedish_Elkhound,Bone_marrow_only

description: Library name: CAGE_L_00209.BC03

source_name: bone marrow

value: bone marrow

value: Swedish Elkhound

value: Female


title: CAGE_L_00208.BC05,Collie,Testis_only

description: Library name: CAGE_L_00208.BC05

source_name: testis

value: testis

value: Collie

value: Male


title: CAGE_L_00209.BC05,Rottweiler,Skin_only

description: Library name: CAGE_L_00209.BC05

source_name: skin

value: skin

value: Rottweiler


title: Col-0 roots, SiBs, day3, rep3

description:
Library name: Sample_51
Column name in count_table_col0.txt: 037-060

value: whole root


title: 105379-001-038

value: Brain

value: white matter

value: Multiple sclerosis


title: CAGE_L_00208.BC08,Finnish_Lapphund,Lower_respiratory_tract_pool

description: Library name: CAGE_L_00208.BC08

value: trachea,bronchus

value: Finnish Lapphund


title: P1P6MLL_matDKO_morula_embryos_Rep5

description:
Library name: Sample28
matDKO_rep5

source_name: embryo

value: embryo


title: f_hfd_lfd_pyy_saline_LN_215

description: Library name: A215

value: Femora

value: Wistar rat

value: female


title: CAGE_L_00208.BC03,German_pinscher,Skin_only

description: Library name: CAGE_L_00208.BC03

value: German Pinscher


title: 105379-001-034


title: Col-0 roots, Mock, day3, rep3

description:
Library name: Sample_48
Column name in count_table_col0.txt: 037-051

value: Mock


title: CAGE_L_00208.BC13,Rottweiler,Neurohypophysis_only

description: Library name: CAGE_L_00208.BC13

source_name: neurohypophysis

value: neurohypophysis


title: 105379-001-037


title: 105379-001-033

value: PLWM


title: 105379-001-032


title: P1P6MLL_matDKO_morula_embryos_Rep3

description:
Library name: Sample26
matDKO_rep3

value: Morula

value: maternal Pcgf1/6 double knockout


title: CAGE_L_00207.BC15,Swedish_Elkhound,Neurohypophysis_only

description: Library name: CAGE_L_00207.BC15

value: Swedish Elkhound

value: Female


title: CAGE_L_00207.BC13,Rottweiler,Eye_pool

description: Library name: CAGE_L_00207.BC13

source_name: retina,optic II nerve

value: retina,optic II nerve

value: Rottweiler

value: Male


title: 105379-001-029

value: Brain

value: white matter

value: Multiple sclerosis


title: Col-0 roots, Mock, day3, rep2

description:
Library name: Sample_47
Column name in count_table_col0.txt: 037-050

value: whole root


title: T530 roots, Si, day6, rep3

description:
Library name: Sample_43
Column name in count_table_col0.txt: 037-042

value: Si


title: 105379-001-031


title: CAGE_L_00207.BC05,Mixed_Breed,Embryos_(day_30)

description: Library name: CAGE_L_00207.BC05

value: embryo

value: Mixed Breed

value: not provided

value: Embryo. Age about 30 days.


title: Col-0 roots, Mock, day3, rep1

description:
Library name: Sample_46
Column name in count_table_col0.txt: 037-049

value: Mock


title: P1P6MLL_WT_morula_embryos_Rep10

description:
Library name: Sample23
CTR_rep10

value: Morula

value: wild type


title: T530 roots, SiBs, day6, rep1

description:
Library name: Sample_44
Column name in count_table_col0.txt: 037-046

value: SiBs


title: T530 roots, SiBs, day6, rep2

description:
Library name: Sample_45
Column name in count_table_col0.txt: 037-047


title: CAGE_L_00207.BC02,Collie,Heart_valve_pool

description: Library name: CAGE_L_00207.BC02

source_name: heart endocardium,heart valve

value: heart endocardium,heart valve

value: Collie


title: P1P6MLL_WT_morula_embryos_Rep9

description:
Library name: Sample22
CTR_rep9


title: CAGE_L_00207.BC03,German_pinscher,Colon_only

description: Library name: CAGE_L_00207.BC03

source_name: colon

value: colon

value: German Pinscher

value: Female


title: P1P6MLL_matDKO_morula_embryos_Rep2

description:
Library name: Sample25
matDKO_rep2

value: maternal Pcgf1/6 double knockout


title: CAGE_L_00207.BC10,Alaskan_Malamute,Ovary_only

description: Library name: CAGE_L_00207.BC10

source_name: ovary

value: ovary

value: Alaskan Malamute


title: 105379-001-028

source_name: white matter

value: Brain

value: white matter

value: Multiple sclerosis

value: PLWM


title: f_hfd_lfd_saline_LN_232

description: Library name: A232

value: Femora

value: Wistar rat

value: female

value: MetOP-Saline


title: 105379-001-030


title: P1P6MLL_matDKO_morula_embryos_Rep1

description:
Library name: Sample24
matDKO rep1

value: embryo

value: Morula


title: T530 roots, Si, day6, rep2

description:
Library name: Sample_42
Column name in count_table_col0.txt: 037-041

value: whole root

value: Si


title: P1P6MLL_WT_morula_embryos_Rep8

description:
Library name: Sample21
CTR_rep8

value: wild type


title: P1P6MLL_WT_morula_embryos_Rep7

description:
Library name: Sample20
CTR_rep7


title: 105379-001-027


title: P1P6MLL_WT_morula_embryos_Rep6

description:
Library name: Sample19
CTR_rep6


title: T530 roots, Si, day6, rep1, run2

description:
Library name: Sample_41
Column name in count_table_col0.txt: 037-040


title: CAGE_L_00206.BC12,Border_Collie,nucleus_reuniens-_LGN_pool

description: Library name: CAGE_L_00206.BC12

source_name: diencephalon (ent nucleus reuniens), lateral geniculate nucleus

value: Border Collie

value: Male


title: 105379-001-025


title: 105379-001-026


title: P1P6MLL_WT_morula_embryos_Rep5

description:
Library name: Sample18
CTR_rep5


title: T530 roots, Mock, day6, rep3

description:
Library name: Sample_39
Column name in count_table_col0.txt: 037-039

value: Mock


title: CAGE_L_00206.BC13,Swedish_Elkhound,Thyroid_gland_only

description: Library name: CAGE_L_00206.BC13

source_name: thyroid gland

value: thyroid gland

value: Swedish Elkhound

value: Female


title: CAGE_L_00206.BC03,Mixed_Breed,Embryos_(day_30)

description: Library name: CAGE_L_00206.BC03

value: Mixed Breed

value: not provided

value: Embryo. Age about 30 days.


title: 105379-001-022

value: Brain

value: white matter

value: Multiple sclerosis

value: PLWM


title: T530 roots, Mock, day6, rep2

description:
Library name: Sample_38
Column name in count_table_col0.txt: 037-038


title: 105379-001-024


title: P1P6MLL_WT_morula_embryos_Rep4

description:
Library name: Sample17
CTR_rep4

value: embryo

value: Morula


title: P1P6MLL_WT_morula_embryos_Rep2

description:
Library name: Sample15
CTR_rep2


title: CAGE_L_00206.BC05,German_pinscher,Eye_pool

description: Library name: CAGE_L_00206.BC05

value: retina,optic II nerve

value: German Pinscher


title: CAGE_L_00206.BC02,Alaskan_Malamute,Blood_vessel_pool

description: Library name: CAGE_L_00206.BC02

source_name: artery,vena cava

value: artery,vena cava

value: Alaskan Malamute


title: CAGE_L_00206.BC15,East-European_Shepherd,Uterine_horn_only

description: Library name: CAGE_L_00206.BC15

source_name: uterus

value: uterus

value: East-European Shepherd


title: T530 roots, Si, day6, rep1, run1

description:
Library name: Sample_40
Column name in count_table_col0.txt: 037-040

value: whole root

value: Si


title: 105379-001-021


title: P1P6MLL_WT_morula_embryos_Rep3

description:
Library name: Sample16
CTR_rep3

value: wild type


title: T530 roots, Mock, day6, rep1, run1

description:
Library name: Sample_36
Column name in count_table_col0.txt: 037-037

value: Mock


title: T530 roots, Mock, day6, rep1, run2

description:
Library name: Sample_37
Column name in count_table_col0.txt: 037-037


title: P1P6MLL_WT_morula_embryos_Rep1

description:
Library name: Sample14
CTR_rep1


title: CAGE_L_00205.BC13,Swedish_Elkhound,Liver__only

description: Library name: CAGE_L_00205.BC13

source_name: liver

value: liver

value: Swedish Elkhound

value: Female


title: 105379-001-023

value: Brain

value: white matter

value: Multiple sclerosis

value: NAWM


title: T530 roots, SiBs, day3, rep3

description:
Library name: Sample_35
Column name in count_table_col0.txt: 037-036

value: SiBs


title: 105379-001-020


title: CAGE_L_00205.BC08,Rottweiler,Prostate_only

description: Library name: CAGE_L_00205.BC08

source_name: prostate gland

value: prostate gland

value: Rottweiler

value: Male


title: PRC1-WT_FGO_Rep1

description:
Library name: Sample10
PRC1-WT rep1

value: ovary

value: Full-grown oocyte


title: CAGE_L_00204.BC15,German_pinscher,Ovary_only

description: Library name: CAGE_L_00204.BC15

value: German Pinscher


title: CAGE_L_00205.BC03,Rottweiler,nucleus_reuniens-_LGN_pool

description: Library name: CAGE_L_00205.BC03

value: diencephalon (ent nucleus reuniens), lateral geniculate nucleus


title: T530 roots, SiBs, day3, rep1

description:
Library name: Sample_33
Column name in count_table_col0.txt: 037-034

source_name: whole root

value: whole root


title: CAGE_L_00205.BC12,German_pinscher,Thyroid_gland_only

description: Library name: CAGE_L_00205.BC12

value: thyroid gland


title: PRC1-CD_FGO_Rep1

description:
Library name: Sample12
PRC1-CD rep1

value: PRC1 catalytic dead


title: 105379-001-018


title: P1P6MLL_TKO_FGO_Rep3

description:
Library name: Sample9
TKO_rep3

value: Pcgf1/6 & Mll2 triple knockout


title: T530 roots, Bs, day3, rep3

description:
Library name: Sample_32
Column name in count_table_col0.txt: 037-033

value: Bs


title: PRC1-CD_FGO_Rep2

description:
Library name: Sample13
PRC1-CD rep2

value: embryo

value: Morula


title: 105379-001-017

value: Brain

value: white matter

value: Multiple sclerosis

value: PLWM


title: 105379-001-016

value: NAWM


title: 105379-001-019


title: CAGE_L_00205.BC05,Rottweiler,Supraspinatus_only

description: Library name: CAGE_L_00205.BC05

source_name: skeletal muscle

value: skeletal muscle

value: Rottweiler

value: Male


title: PRC1-WT_FGO_Rep2

description:
Library name: Sample11
PRC1-WT rep2

value: ovary

value: Full-grown oocyte

value: wild type


title: T530 roots, Bs, day3, rep1

description:
Library name: Sample_30
Column name in count_table_col0.txt: 037-031

value: whole root


title: T530 roots, SiBs, day3, rep2

description:
Library name: Sample_34
Column name in count_table_col0.txt: 037-035

value: SiBs


title: 105379-001-015


title: CAGE_L_00205.BC02,Mixed_Breed,Embryos_(day_20-25)

description: Library name: CAGE_L_00205.BC02

value: Mixed Breed

value: not provided

value: Embryo. Age about 20-25 days.


title: T530 roots, Bs, day3, rep2

description:
Library name: Sample_31
Column name in count_table_col0.txt: 037-032

value: Bs


title: 105379-001-014

value: Brain


title: P1P6MLL_TKO_FGO_Rep2

description:
Library name: Sample8
TKO_rep2

value: Pcgf1/6 & Mll2 triple knockout


title: P1P6MLL_TKO_FGO_Rep1

description:
Library name: Sample7
TKO_rep1


title: T530 roots, Si, day3, rep3

description:
Library name: Sample_29
Column name in count_table_col0.txt: 037-030

value: Si


title: 105379-001-013

value: white matter

value: Multiple sclerosis

value: PLWM


title: CAGE_L_00204.BC05,Rottweiler,Ventricular_heart_muscle_pool

description: Library name: CAGE_L_00204.BC05

source_name: cardiac muscle tissue

value: cardiac muscle tissue

value: Rottweiler


title: CAGE_L_00204.BC13,Border_Collie,Corpus_callosum_only

description: Library name: CAGE_L_00204.BC13

source_name: corpus callosum

value: corpus callosum

value: Border Collie

value: Male


title: P1P6MLL_DKO_FGO_Rep2

description:
Library name: Sample5
DKO_rep2

value: ovary

value: Full-grown oocyte

value: Pcgf1/6 double knockout


title: P1P6MLL_DKO_FGO_Rep3

description:
Library name: Sample6
DKO_rep3


title: 105379-001-011


title: P1P6MLL_WT_FGO_Rep2

description:
Library name: Sample2
CTR_rep2

value: wild type


title: CAGE_L_00204.BC03,Swedish_Elkhound,Spinal_Cord_only

description: Library name: CAGE_L_00204.BC03

source_name: spinal cord

value: spinal cord

value: Swedish Elkhound

value: Female


title: T530 roots, Si, day3, rep1

description:
Library name: Sample_26
Column name in count_table_col0.txt: 037-028

value: whole root


title: P1P6MLL_DKO_FGO_Rep1

description:
Library name: Sample4
DKO_rep1


title: T530 roots, Mock, day3, rep2

description:
Library name: Sample_24
Column name in count_table_col0.txt: 037-026

value: Mock


title: T530 roots, Mock, day3, rep3

description:
Library name: Sample_25
Column name in count_table_col0.txt: 037-027


title: P1P6MLL_WT_FGO_Rep1

description:
Library name: Sample1
CTR_rep1


title: CAGE_L_00204.BC02,Finnish_Lapphund,nucleus_reuniens-_LGN_pool

description: Library name: CAGE_L_00204.BC02

value: diencephalon (ent nucleus reuniens), lateral geniculate nucleus

value: Finnish Lapphund


title: T530 roots, Si, day3, rep2, run1

description:
Library name: Sample_27
Column name in count_table_col0.txt: 037-029

value: Si


title: T530 roots, Si, day3, rep2, run2

description:
Library name: Sample_28
Column name in count_table_col0.txt: 037-029


title: 105379-001-010

value: Brain

value: white matter

value: Multiple sclerosis


title: T530 roots, Mock, day3, rep1

description:
Library name: Sample_23
Column name in count_table_col0.txt: 037-025


title: CAGE_L_00204.BC10,German_pinscher,Liver__only

description: Library name: CAGE_L_00204.BC10

value: liver

value: German Pinscher


title: CAGE_L_00203.BC15,Mixed_Breed,Embryos_(day_20-25)

description: Library name: CAGE_L_00203.BC15

source_name: embryo

value: embryo

value: Mixed Breed

value: not provided

value: Embryo. Age about 20-25 days.


title: CAGE_L_00204.BC08,Swedish_Elkhound,Adenohypophysis_only

description: Library name: CAGE_L_00204.BC08

source_name: adenohypophysis

value: adenohypophysis


title: P1P6MLL_WT_FGO_Rep3

description:
Library name: Sample3
CTR_rep3

value: ovary

value: Full-grown oocyte

value: wild type


title: 105379-001-009


title: 105379-001-007


title: T510 roots, SiBs, day6, rep3

description:
Library name: Sample_22
Column name in count_table_col0.txt: 037-024

value: whole root

value: SiBs


title: High_3

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

country: China

institute: Yangtze University

description: Library name: Sample9

data_processing:
A data filtration process was implemented to obtain high-quality, clean reads, and to remove low-quality reads present in the raw reads, as recommended by the manufacturer. The Hisat2 (Kim, Paggi et al. 2019) software was employed to map clean reads to the reference genome (Sus Scrofa 11.1), which was extracted from the NCBI ge-nome database (O'Leary, Cox et al. 2024). The calculated reads count per gene was estimated by Htseq-count (Putri, Anders et al. 2022) and used for comparing the difference in gene expression among samples. The library was nor-malized using median of ratios method and the DEseq2 R package [31] was utilized for the identification of differ-entially expressed genes.
Assembly: Sus Scrofa 11.1
Supplementary files format and content: Reads count

organism: Sus scrofa

source_name: Lung

growth_protocol: The lung tissue samples of the pigs utilized in this study were obtained from an ASFV-restored pig farm in Jingzhou, Hubei Province, where ASFV outbreak was first detected in August 2019.

extract_protocol:
The samples were transferred to the designated DNA facility with dry ice for RNA-seq analysis.
The preparation of sequencing libraries was carried out in accordance with the protocol stipulated by the Illumina Truseq RNA sample preparation kit (Illumina Inc., USA). Approximately 10 μg of total RNA from each sample was utilized for library construction and RNA sequencing. The Sequencing was performed on an Illumina HiSeq 2500 sequencer (Illumina Inc., USA) using a single read of 50bp sequencing method.

treatment_protocol: Following the implementation of PCR detection and p72 antibody assay, we selected three groups of animals each have three individuals for sample collection: (i) p72-antibody-negative animals that were PCR-negative for ASFV, Elisa-negative for p72 antibody, and exhibited no symptoms of infection; (ii) low-p72-antibody animals that were PCR-negative for ASFV and low levels for p72-antibody (25% percentile); (iii) high-p72-antibody animals that were PCR-negative for ASFV and high levels of p72-antibody (95% percentile).

value: Lung

tag: disease state

value: antibody high


title: CAGE_L_00203.BC13,German_pinscher,Hippocampal_formation_only

description: Library name: CAGE_L_00203.BC13

source_name: hippocampal formation

value: hippocampal formation

value: Female


title: High_1

description: Library name: Sample7


title: High_2

description: Library name: Sample8


title: CAGE_L_00203.BC10,Border_Collie,Brain_stem_pool

description: Library name: CAGE_L_00203.BC10

source_name: substantia nigra,pons,medulla oblongata

value: substantia nigra,pons,medulla oblongata

value: Border Collie

value: Male


title: 105379-001-005

source_name: white matter

value: Brain

value: white matter

value: Multiple sclerosis


title: 105379-001-004

value: PLWM


title: T510 roots, SiBs, day6, rep1

description:
Library name: Sample_20
Column name in count_table_col0.txt: 037-022


title: T510 roots, SiBs, day6, rep2

description:
Library name: Sample_21
Column name in count_table_col0.txt: 037-023


title: T510 roots, Si, day6, rep3

description:
Library name: Sample_19
Column name in count_table_col0.txt: 037-018

value: Si


title: 105379-001-006


title: CAGE_L_00203.BC02,Finnish_Lapphund,Colon_only

description: Library name: CAGE_L_00203.BC02

source_name: colon

value: colon

value: Finnish Lapphund


title: 105379-001-003


title: CAGE_L_00203.BC03,Finnish_Lapphund,Spleen_only

description: Library name: CAGE_L_00203.BC03

source_name: spleen

value: spleen


title: Low_3

description: Library name: Sample6

value: antibody low


title: 105379-001-002


title: T510 roots, Si, day6, rep2

description:
Library name: Sample_18
Column name in count_table_col0.txt: 037-017

value: whole root


title: CAGE_L_00203.BC05,Rottweiler,Olfactory_pool

description: Library name: CAGE_L_00203.BC05

source_name: olfactory bulb,vomeronasal organ,nasal cavity olfactory mucosa

value: Rottweiler


title: Low_2

description: Library name: Sample5

value: Lung


title: T510 roots, Si, day6, rep1

description:
Library name: Sample_17
Column name in count_table_col0.txt: 037-016


title: T510 roots, Mock, day6, rep3, run2

description:
Library name: Sample_16
Column name in count_table_col0.txt: 037-015

value: Mock


title: siRNA RIPK3 #2_TZB

city: tokyo

first: tomohiro

last: koiwa

state: tokyo

address: 1-3-7 Hongo, Bunkyo-ku,

department: Respiratory medicine

institute: tokyo university

data_processing:
CLC Genomics Workbench v 24.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork.
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: lung

growth_protocol: NCI-H441 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
NCI-H441 cells were treated with 20 nM of siRNA NTC, RIPK3 siRNA #1, and RIPK3 siRNA #2 for 48 hours.
After the treatment, the cells were either stimulated with 10 ng/mL of TNFα or exposed to necroptosis-inducing stimuli consisting of 20 µM of zVAD-fmk and 100 nM of Birinapant, followed one hour later by 10 ng/mL of TNFα.

value: lung

tag: cell line

tag: cell type

value: Adenocarcinoma

value: siRNA RIPK3 KD

value: TNFalpha+zVAD-fmk+Brinapant


title: CAGE_L_00202.BC15,German_pinscher,Lung_alveoli_only

description: Library name: CAGE_L_00202.BC15

value: German Pinscher

value: Female


title: Low_1

description: Library name: Sample4


title: siRNA RIPK3 #2_TNFα

value: TNFalpha


title: Negative_3

description: Library name: Sample3

value: antibody negative


title: Negative_1

description: Library name: Sample1


title: CAGE_L_00202.BC10,Finnish_Lapphund,Pancreas_left_lobe_only

description: Library name: CAGE_L_00202.BC10

source_name: pancreas

value: pancreas


title: T510 roots, Mock, day6, rep3, run1

description:
Library name: Sample_15
Column name in count_table_col0.txt: 037-015


title: siRNA RIPK3 #1_no stimulation

value: no stimulation


title: T510 roots, Mock, day6, rep2

description:
Library name: Sample_14
Column name in count_table_col0.txt: 037-014


title: CAGE_L_00202.BC12,Rottweiler,Cerebellum_pool

description: Library name: CAGE_L_00202.BC12

source_name: cerebellum hemisphere,cerebellum vermis

value: cerebellum hemisphere,cerebellum vermis

value: Male


title: siRNA RIPK3 #2_no stimulation


title: T510 roots, Mock, day6, rep1

description:
Library name: Sample_13
Column name in count_table_col0.txt: 037-013

source_name: whole root


title: T510 roots, SiBs, day3, rep2

description:
Library name: Sample_11
Column name in count_table_col0.txt: 037-011

value: SiBs


title: siRNA RIPK3 #1_TNFα


title: siRNA RIPK3 #1_TZB


title: CAGE_L_00202.BC08,Mixed_Breed,Embryos_(day_20-25)

description: Library name: CAGE_L_00202.BC08

value: embryo

value: Mixed Breed

value: not provided

value: Embryo. Age about 20-25 days.


title: T510 roots, SiBs, day3, rep3

description:
Library name: Sample_12
Column name in count_table_col0.txt: 037-012

value: whole root


title: Negative_2

description: Library name: Sample2

value: Lung


title: CAGE_L_00202.BC05,German_pinscher,Neurohypophysis_only

description: Library name: CAGE_L_00202.BC05

source_name: neurohypophysis

value: neurohypophysis


title: CAGE_L_00202.BC13,German_pinscher,Blood_vessel_pool

description: Library name: CAGE_L_00202.BC13

source_name: artery,vena cava

value: artery,vena cava


title: MSC, Pros, P12

city: Guangzhou

first: Guang

last: Shi

state: Guangdong

address: 135 Xingang Xi Road, Haizhu District

department: School of Life Sciences

institute: Sun Yat-sen University

description:
Library name: Sample2
counts_of_sample_1_and_2.csv

data_processing:
Raw RNA-seq paired-end reads were processed following a standard workflow:
Raw reads were trimmed using Trim Galore! (v0.6.7) to remove low-quality bases, sequencing adapters, and short reads, quality control was assessed using FastQC (v0.11.9) and summarized with MultiQC (v1.14)
Cleaned reads were aligned to the hg38 human reference genome using STAR (v2.7.10a), Aligned reads were sorted and indexed using SAMtools (v1.17)
Gene-level read counts were generated using featureCounts (v2.0.3) with GRCh38 RefSeq gene annotation GTF file
Raw count matrix was imported into R (v4.2.3). Duplicate gene symbols were merged by sum. Count matrice was generated for downstream analysis
Assembly: hg38
Supplementary files format and content: CSV file including Reads count for ucMSC-Pros,ucMSC-GFP

source_name: Umbilical

growth_protocol: WJMSCs were routinely maintained in F12 medium supplemented with 15% fetal calf serum (FBS), 100 U/ml penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Pre Kit following manufacturer's protocal.

treatment_protocol: hMSCs were continuously cultured in the presence of GAPDH/S100A9/S100A8 at each concentrations of 200 nM for 20 days.

value: Umbilical

value: mesenchymal stem cells

value: wjmsc

value: wild type

value: Pros


title: MSC, EGFP, P12

description:
Library name: Sample3
counts_of_sample_1_and_2.csv

value: EGFP


title: MSC, Blank, P12

description: Library name: Sample1

value: Blank


title: T510 roots, SiBs, day3, rep1

description:
Library name: Sample_10
Column name in count_table_col0.txt: 037-010


title: siRNA NC_TZB

value: lung

value: Adenocarcinoma

value: siRNA nagative control

value: TNFalpha+zVAD-fmk+Brinapant


title: CAGE_L_00202.BC03,Rottweiler,Hippocampal_formation_only

description: Library name: CAGE_L_00202.BC03

value: hippocampal formation

value: Rottweiler

value: Male


title: WM115+IFN MHC-II- screen Rep 1

city: Beijing

first: Zexian

last: Zeng

address: No.5 Yiheyuan Road, Haidian District, Beijing

institute: Peking University

description:
Library name: WM115+IFN MHC-II- screen Rep 1
r1L
WM115-IFN.count.txt

data_processing:
Adapters ligated to the 5' end were removed using cutadapt (v4.1) with other default parameters.
Trimmed reads were processed using the count subcommand of MaGeCK (v0.5.9.5) to generate the count matrix.
The MAGeCK test subcommand with default setting was used to calculate log2 fold changes and p-values of the genes.
Custom R (v4.4.1) scripts were used to visualize the data.
Assembly: hg38
Supplementary files format and content: Tab-delimited txt files include row counts of each gRNA for each sample.
Library strategy: CRISPR Screen

source_name: Skin

extract_protocol:
The genomic DNA of each sample was extracted using the NucleoSpin Blood XL kit following the manufacturer’s instructions.
Amplification of the sgRNA cassettes by PCR was performed according to the broad GPP protocol (https://portals.broadinstitute.org/gpp/public/resources/protocols).

value: Skin

value: 100 ng/mL IFNγ for 72 h


title: T510 roots, Bs, day3, rep3

description:
Library name: Sample_9
Column name in count_table_col0.txt: 037-009

value: whole root

value: Bs


title: HMEC-1 cells, untreated, 24h-5

city: Guangzhou 510275

first: Weiyang

last: Fan

address: School of Life Sciences, Sun Yat-sen University, No. 135 Xingang West Road, Guangzhou

data_processing:
The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads, according to the manufacturer’s instructions.
The raw reads were further processed with a bioinformatic pipelinetool, BMKCloud(www.biocloud.net) online platform.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Assembly: human NCBI genome bulid 36
Supplementary files format and content: tab-delimited excel file includes raw counts for each Sample
Supplementary files format and content: tab-delimited excel files include RPKM values for each Sample

growth_protocol: HMEC-1 (ATCC, USA) were cultured in ECM supplemented with 5% foetal bovine se-rum, 1% penicillin/streptomycin, and 1% endothelial cell growth supplement (Scien-Cell, Carlsbad, USA) in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol:
The animal total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
RNA-seq. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: After cell adhesion, the medium was replaced by ECM complete medium containing LPS (200 ng/ml), Ctl-Exo (5 μg/mL) or NXT-Exo (5 μg/mL) for 24 hours.

value: endothelial cells

value: untreated


title: CAGE_L_00201.BC13,Rottweiler,Bone_marrow_only

description: Library name: CAGE_L_00201.BC13

source_name: bone marrow

value: bone marrow


title: T510 roots, Si, day3, rep3

description:
Library name: Sample_6
Column name in count_table_col0.txt: 037-006

value: Si


title: WM115+IFN MHC-II- screen Rep 2

description:
Library name: WM115+IFN MHC-II- screen Rep 2
r2L
WM115-IFN.count.txt


title: HMEC-1 cells, untreated, 24h-4


title: siRNA NC_TNFα

value: TNFalpha


title: WM115+IFN MHC-II+ screen Rep 1

description:
Library name: WM115+IFN MHC-II+ screen Rep 1
r1H
WM115-IFN.count.txt


title: siRNA NC_no stimulation

value: no stimulation


title: A375 MHC-II- screen Rep 3

description:
Library name: A375 MHC-II- screen Rep 3
r3L
A375.count.txt


title: CAGE_L_00202.BC02,Rottweiler,Testis_only

description: Library name: CAGE_L_00202.BC02

source_name: testis

value: testis


title: CAGE_L_00201.BC12,Finnish_Lapphund,Adrenal_gland_pool

description: Library name: CAGE_L_00201.BC12

source_name: adrenal gland

value: adrenal gland

value: Finnish Lapphund

value: Female


title: WM115+IFN MHC-II+ screen Rep 2

description:
Library name: WM115+IFN MHC-II+ screen Rep 2
r2H
WM115-IFN.count.txt


title: T510 roots, Bs, day3, rep1

description:
Library name: Sample_7
Column name in count_table_col0.txt: 037-007


title: CAGE_L_00201.BC08,Finnish_Lapphund,DRG_only

description: Library name: CAGE_L_00201.BC08

source_name: spinal ganglion

value: spinal ganglion


title: HMEC-1 cells, untreated, 24h-3


title: CAGE_L_00201.BC05,Swedish_Elkhound,caudate_nucleus-_amygdala_pool

description: Library name: CAGE_L_00201.BC05

source_name: caudate nucleus,amygdala

value: caudate nucleus,amygdala

value: Swedish Elkhound


title: T510 roots, Bs, day3, rep2

description:
Library name: Sample_8
Column name in count_table_col0.txt: 037-008


title: A375 MHC-II- screen Rep 2

description:
Library name: A375 MHC-II- screen Rep 2
r2L
A375.count.txt

value: Skin


title: T510 roots, Mock, day3, rep1

description:
Library name: Sample_1
Column name in count_table_col0.txt: 037-001

value: Mock


title: A375 MHC-II+ screen Rep 1

description:
Library name: A375 MHC-II+ screen Rep 1
r1H
A375.count.txt


title: T510 roots, Mock, day3, rep3

description:
Library name: Sample_3
Column name in count_table_col0.txt: 037-003

value: whole root


title: A375 MHC-II- screen Rep 1

description:
Library name: A375 MHC-II- screen Rep 1
r1L
A375.count.txt


title: HMEC-1 cells, untreated, 24h-1


title: HMEC-1 cells, LPS+NXT-EXO, 24h-4

value: LPS+NXT-EXO, 24h


title: T510 roots, Si, day3, rep2

description:
Library name: Sample_5
Column name in count_table_col0.txt: 037-005


title: CAGE_L_00201.BC02,Rottweiler,Spleen_only

description: Library name: CAGE_L_00201.BC02

value: spleen

value: Rottweiler

value: Male


title: CAGE_L_00201.BC03,German_pinscher,Adenohypophysis_only

description: Library name: CAGE_L_00201.BC03

source_name: adenohypophysis

value: adenohypophysis

value: German Pinscher


title: T510 roots, Si, day3, rep1

description:
Library name: Sample_4
Column name in count_table_col0.txt: 037-004

value: Si


title: QA19_HNSCC

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

description: Library name: QA19

library_source: other

data_processing:
Raw Nanopore signals were basecalled with Dorado in high-accuracy mode without trimming and demultiplexed to generate per-sample reads.
Sequencing data were processed through the FLARE pipeline, integrating read alignment, fragment size stratification, genome-wide copy number profiling, and tumor fraction estimation using both CNV-based (ichorCNA) and methylation-based models. Fragmentomic features were further characterized through 5′ end-motif analysis and unsupervised pattern discovery using non-negative matrix factorization. Longitudinal comparisons were performed to evaluate changes in tumor fraction, fragment size distribution, and fragmentation signatures over time.
Assembly: hg38.p13
Supplementary files format and content: normalized_motifs_matrix; txt file

molecule: other

source_name: HNSCC

extract_protocol:
ctDNA was extracted from liquid biopsies following QIAamp MinElute cfDNA Mini protocol (QIAGEN)
ONT libraries were made starting from 6 ng of cfDNA with native barcoding kit 24 v14 (SQK-NBD114.24) following the manufacturer’s protocol. Ten samples were multiplexed and sequenced on PromethION with flow cell FLO-PROM114M for 72h.

value: HNSCC

value: Nivolumab


title: T510 roots, Mock, day3, rep2

description:
Library name: Sample_2
Column name in count_table_col0.txt: 037-002


title: A375 MHC-II+ screen Rep 2

description:
Library name: A375 MHC-II+ screen Rep 2
r2H
A375.count.txt


title: CAGE_L_00142.BC01,Swedish_Elkhound,Cerebellum_pool

description: Library name: CAGE_L_00142.BC01

value: cerebellum hemisphere,cerebellum vermis


title: HMEC-1 cells, LPS+NXT-EXO, 24h-5

value: endothelial cells


title: A375 MHC-II+ screen Rep 3

description:
Library name: A375 MHC-II+ screen Rep 3
r3H
A375.count.txt


title: CAGE_L_00146.BC04,Rottweiler,Cerebral_cortex_pool

description: Library name: CAGE_L_00146.BC04

source_name: frontal cortex,parietal cortex,temporal cortex,occipital cortex


title: nSyb_AB42-yip7_S-3

city: hunan province

first: yang

last: meng

address: lusan

institute: hunan normal university

description:
Library name: nSyb_AB42-yip7_S-3
The brain were dissected from 10d flies

data_processing:
All raw sequencing data were quality controlled by fastqc. Adapters, reads with more than 10% unknown nucleotide (N) content,  and reads with more than half low quality (Q-value <20) bases were removed.
For RNA-seq data, the sequencing data after quality control was firstly mapped to ribosome RNA (rRNA) and transfer RNA(tRNA) database using  HISAT2(version 2.1.0) to remove rRNA and tRNA reads and get the clean sequencing data.
For RNA-seq data, The clean sequencing data were mapped to the Drosophila melanogaster reference genome (dm6) using HISAT2 (version 2.1.0) with default parameters after index building of the transcriptome.
For RNA-seq data, The mapped reads of each sample were assembled and quantified by StringTie (version 1.3.1) in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated.
For RNA-seq data, RNA differential expression analyses among groups were performed by DESeq2 (version 1.36.0). The genes/transcripts with the a false discovery rate (FDR) < 0.05 and absolute fold change >2 were considered as differentially expressed genes/transcripts and used for downstream analyses.
Assembly: dm6
Supplementary files format and content: Tab-delimited text files (.txt) include raw reads of RNA-seq data from all AD flies and Control flies.

organism: Drosophila melanogaster

source_name: head

growth_protocol: Flies were feeding with standard food

extract_protocol:
Total RNA of RNA-seq samples were homogenized in 500 μl TRIzol (TaKaRa) and precipitaed by isopropyl alcohol.
After total RNAs of each samples were extracted, the mRNAs enriched by Oligo(dT) beads were fragmented using fragmenta-tion buffer and reverse transcripted into cDNAs with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP, and buffer. The cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen), and were end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina NovaSeq 6000 by Berry Genomics.

treatment_protocol: Flies were reared at 29℃

value: head


title: HMEC-1 cells, LPS+NXT-EXO, 24h-2


title: CAGE_L_00144.BC04,Finnish_Lapphund,Cerebral_cortex_pool

description: Library name: CAGE_L_00144.BC04

value: frontal cortex,parietal cortex,temporal cortex,occipital cortex

value: Finnish Lapphund

value: Female


title: 105379-001-012

source_name: white matter

value: Brain

value: white matter

value: Multiple sclerosis


title: CAGE_L_00141.BC01,Swedish_Elkhound,Piriform_lobe_only

description: Library name: CAGE_L_00141.BC01

source_name: piriform lobe

value: piriform lobe

value: Swedish Elkhound


title: HMEC-1 cells, LPS+NXT-EXO, 24h-3

value: LPS+NXT-EXO, 24h


title: QA18_HNSCC

description: Library name: QA18


title: nSyb_AB42-yip7-3

description:
Library name: nSyb_AB42-yip7-3
The brain were dissected from 10d flies


title: QA17_HNSCC

description: Library name: QA17


title: HMEC-1 cells, LPS, 24h-1

value: LPS, 24h


title: nSyb_AB42-yip7-2

description:
Library name: nSyb_AB42-yip7-2
The brain were dissected from 10d flies


title: CAGE_L_00118.BC02,German_pinscher,Uterine_horn_only

description: Library name: CAGE_L_00118.BC02

source_name: uterus

value: uterus

value: German Pinscher


title: nSyb_AB42-yip7_S-2

description:
Library name: nSyb_AB42-yip7_S-2
The brain were dissected from 10d flies


title: QA13_HNSCC

description: Library name: QA13

value: HNSCC


title: QA14_HNSCC

description: Library name: QA14

value: Nivolumab


title: nSyb_AB42-yip7-1

description:
Library name: nSyb_AB42-yip7-1
The brain were dissected from 10d flies


title: CAGE_L_00118.BC01,Swedish_Elkhound,Ventricular_heart_muscle_pool

description: Library name: CAGE_L_00118.BC01

source_name: cardiac muscle tissue

value: cardiac muscle tissue


title: HMEC-1 cells, LPS, 24h-5

value: endothelial cells


title: HMEC-1 cells, LPS+NXT-EXO, 24h-1


title: HMEC-1 cells, LPS, 24h-3


title: HMEC-1 cells, untreated, 24h-2

value: untreated


title: nSyb_w1118-2

description:
Library name: nSyb_w1118-2
The brain were dissected from 10d flies

value: head


title: CAGE_L_00117.BC01,Rottweiler,Skin_only

description: Library name: CAGE_L_00117.BC01

source_name: skin

value: skin

value: Rottweiler

value: Male


title: QA10_HNSCC

description: Library name: QA10


title: nSyb_AB42-3

description:
Library name: nSyb_AB42-3
The brain were dissected from 10d flies


title: QA09_HNSCC

description: Library name: QA09


title: HMEC-1 cells, LPS+Ctl-EXO, 24h-4

value: LPS+Ctl-EXO, 24h


title: QA11_HNSCC

description: Library name: QA11


title: HMEC-1 cells, LPS, 24h-2


title: QA15_HNSCC

description: Library name: QA15


title: QA12_HNSCC

description: Library name: QA12


title: HMEC-1 cells, LPS+Ctl-EXO, 24h-5


title: nSyb_w1118-3

description:
Library name: nSyb_w1118-3
The brain were dissected from two-week-old flies


title: HMEC-1 cells, LPS+Ctl-EXO, 24h-3


title: nSyb_w1118-1

description:
Library name: nSyb_w1118-1
The brain were dissected from 10d flies


title: HMEC-1 cells, LPS+Ctl-EXO, 24h-2


title: NSCLC patient1_OAA captured miRNA_post nivolumab treatment_PD

type: RNA

city: Maebashi

first: EIJI

last: Narusawa

address: Showa-machi, Maebashi, Gunma 371-8511,

institute: Department of General Surgical Science, Gunma University Graduate School of Medicine

hyb_protocol: Following labeling, the biotin-labeled sample were hybridized for 16 hr at 48ºC on GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix GeneChips Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip™ Scanner 3000 7G with AutoLoader

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) Software.

label: biotin

source_name: NSCLC patient1_OAA captured miRNA from blood

label_protocol: Biotinylated cRNA were preprared according to the standard Affymetrix protocol from 8 µL micro RNA solution(FlashTag™ Biotin HRS RNA Labeling Kit - Thermo Fisher Scientific, Walthmam, MA, USA).

extract_protocol: RNA extraction from plasma was performed using the OAA-lectin column and the QIAzol® Lysis Reagent (Qiagen) followed by purification in the NucleoSpin® miRNA Plasma (MACHEREY-NAGEL GmbH & Co.).  All steps were performed as recommended by the manufacturers.

treatment_protocol: Peripheral blood was collected and plasma samples were obtained before RNA extraction.

tag: subject

value: NSCLC patient

value: plasma

tag: purification method

value: OAA lectin column

tag: response

value: PD


title: NSCLC patient2_OAA captured miRNA_post nivolumab treatment_PD

source_name: NSCLC patient2_OAA captured miRNA from blood

tag: tissue


title: QA16_HNSCC

description: Library name: QA16


title: HMEC-1 cells, LPS, 24h-4

value: LPS, 24h


title: nSyb_AB42-yip7_S-1

description:
Library name: nSyb_AB42-yip7_S-1
The brain were dissected from 10d flies


title: CAGE_L_00119.BC04,German_pinscher,Ventricular_heart_muscle_pool

description: Library name: CAGE_L_00119.BC04

tag: Sex

value: Female


title: HMEC-1 cells, LPS+Ctl-EXO, 24h-1

tag: treatment


title: QA08_HNSCC

description: Library name: QA08


title: Yeast cells, control, Day1

status: Public on Mar 31 2026

city: Turku

first: Mikko

last: Metsä-Ketelä

address: Tykistökatu 6A

department: Department of Life Technologies

country: Finland

institute: University of Turku

data_processing:
Chipster (CSC)
Reads were trimmed using TRIMMOMATIC (default parameters)
Trimmed reads were mapped using BowTie2 (default parameters)
Mapped reads were counted using HTSeq
Differential expression was done using edgeR
Assembly: Streptomyces lavendulae genome (GCA_008016805.1) / Saccharomyces cerevisiae genome (GCA_000146045.2)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Cells were grown in SC medium (Samples 17-20 contained autoclaved yeast 26 g/l)

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen).
Illumina PCR-free library

treatment_protocol: Co-cultures with live or dead yeast

value: yeast cells

tag: strain

value: ::mCherry

value: axenic culture

tag: time

value: Day 1


city: Kunming

first: Liangliang

last: Wang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

institute: Yunnan University

description: Library name: 1_1.5h_WT_PolII_ChIPseq_for_RescueExperiment_replicate_2

data_processing:
Paired-end reads were trimmed by trimmomatic (v0.39).
Clean reads were mapped to mapped to Drosophila melanogaster (dm6) using bowtie2 (v2.2.5).
PCR duplicates were marked using sambamba (v0.8.2).Non-uniquely mapped reads, low-quality reads (quality scores less than 30) were removed using samtools (v1.18).
Peaks were calculated using macs2 (v2.2.7.1)
Bigwig files were generated from resulting deduplicated and filtered bam files using deeptools (v3.5.1).
Assembly: dm6
Supplementary files format and content: BigWig, narrowPeak (except for Input sample)

source_name: embryo

extract_protocol:
The embryos of indicated genotypes were harvested and subjected to cross-linking by fixation buffer (50 mM HEPES, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl and 1.8% formaldehyde).  They were cross-linked for 20 minutes and then quenched with 125 mM glycine (final concentration) for 5 minutes at room temperature.  Chromatin immunoprecipitation (ChIP) reactions were carried out in duplicate using the Pierce Magnetic ChIP Kit.
Sequencing libraries were generated using the VAHTS Universal DNA Library Prep Kit for MGI.

value: embryo

tag: sample group


title: Yeast cells, control, Day3

value: Day 3


description: Library name: 2.5_3h_IntS11_mislocalized_IntS11_ChIPseq_replicate_1


description: Library name: 2.5_3h_IntS11_mislocalized_IntS11_ChIPseq_replicate_2


description: Library name: 2.5_3h_KD_for_IntS11_KD_PolII_ChIPseq_replicate_1


description: Library name: 2.5_3h_WT_for_IntS11_KD_PolII_ChIPseq_replicate_2


description: Library name: 2.5_3h_KD_for_IntS11_KD_PolII_ChIPseq_replicate_2


description: Library name: 1_1.5h_Mutant_IntS11_mislocalized_PolII_ChIPseq_for_RescueExperiment_replicate_2


title: NSCLC patient2_OAA captured miRNA_pre nivolumab treatment_PD


title: Yeast cells, control, Day7

value: Day 7


title: CAGE_L_00117.BC02,Collie,Parathyroid_only

description: Library name: CAGE_L_00117.BC02

data_processing:
Library strategy is RNA-seq (CAGE). Basecalls were performed using bcl2fastq v2.20.0 for HiSeq output.
The 3’ adapter (“TCGTATGCCGTCTTC”), EcoP15 (“CAGCAG”), and 5’G regions of the CAGE-seq reads and reads with quality score < 20 were removed using cutadapt version 3.4. rRNA filtering was performed using SortMeRNA version 4.3.4.
CAGE-seq reads were aligned to the canFam4 genome using STAR version 2.7.9a. CAGE tags were normalized (TPM: Tag Per Million). CAGE tag clustering was conducted using CAGEFightR version 1.10.0
The promoter regions were identified with CAGEfightR’s `clusterUnidirectional()` function, with parameters pooled CAGE tags expressed at more than 10 tpm for the comprehensive set and longer than 1 bp and above 10 tpm in at least one sample for the robust promoter set. Bidirectional clusters were identified with the default CAGEfightR parameters. Only candidates located in introns or intergenic regions were retained if they had at least 4 different CAGE tag locations on each strand, and robust enhancers had to have at least 6 different CAGE tags on each strand. Those overlapping with our robust promoter set were excluded. The tags present in the comprehensive set but absent in the robust set were evaluated. Tags with 98% bidirectionality were included in the robust enhancers. Each enhancer region was trimmed to the first and last CTSS within it.
Assembly: canFam4 (UU_Cfam_GSD_1.0, GCF_011100685.1)
Supplementary files format and content: csv file includes enhancer comprehensive expression matrix TPM (Tag Per Million) normalized
Supplementary files format and content: csv file includes enhancer robust expression matrix TPM( Tag Per Million) normalized
Supplementary files format and content: csv file include promoter comprehensive expression matrix TPM (Tag Per Million) normalized
Supplementary files format and content: csv file include promoter robust expression matrix TPM (Tag Per Million) normalized
Supplementary files format and content: csv file include enhancer comprehensive expression matrix raw counts
Supplementary files format and content: csv file include enhancer robust expression matrix raw counts
Supplementary files format and content: csv file include promoter comprehensive expression matrix raw counts
Supplementary files format and content: csv file include promoter robust expression matrix raw counts
Supplementary files format and content: csv file include promoter annotation file
Supplementary files format and content: csv file include enhancer annotation file
Supplementary files format and content: text file includes md5sum

source_name: parathyroid gland

extract_protocol:
CAGE libraries were prepared using 1 μg of total RNA from each sample.The CAGE experiment requires at least 10 μl of sample to proceed. Therefore, tissue pools were created for samples with insufficient volume. We begin with at least 10 μl of volume for each sample.
CAGE libraries were prepared following the previously described protocol by Takahashi et al. (Takahashi et al., 2012). In each library, we used eight barcodes (CTT, GAT, ACT, ATG, AGT, TGG, GTA, and GCC) for eight RNA samples. Single-strand cDNA was barcoded by adding a 5’ linker containing a 5’ barcode sequence and the EcoP15I sequence. A 3′ linker with Illumina primer sequence was added to the barcoded cDNA fragment. The size of the resulting CAGE libraries ranged between 97 and 103 bp. Libraries were single-read sequenced at 50 cycles using the HiSeq 2500 Illumina System. The HiSeq SR Rapid Cluster Kit v2 (Illumina) and the HiSeq Rapid Duo cBot Sample Loading Kit (Illumina) were used to sequence CAGE libraries in the rapid mode.

value: parathyroid gland

tag: breed

value: Collie

tag: age (month)

tag: batch


title: nSyb_AB42-2

description:
Library name: nSyb_AB42-2
The brain were dissected from 10d flies

value: head

tag: genotype


title: nSyb_AB42-1

description:
Library name: nSyb_AB42-1
The brain were dissected from 10d flies


title: Yeast cells, control, Day5

value: Day 5


title: NSCLC patient1_OAA captured miRNA_pre nivolumab treatment_PD

value: NSCLC patient


description: Library name: 1_1.5h_WT_PolII_ChIPseq_for_RescueExperiment_replicate_1


description: Library name: 2.5_3h_WT_for_IntS11_KD_PolII_ChIPseq_replicate_1


description: Library name: 1_1.5h_IntS11_mislocalized_IntS11_ChIPseq_replicate_2


description: Library name: 1_1.5h_Mutant_IntS11_mislocalized_PolII_ChIPseq_for_RescueExperiment_replicate_1


description: Library name: 2.5_3h_WT_for_IntS11KD_RNAseq_replicate_2

data_processing:
Sequence reads were trimmed by trimmomatic (v0.39)
Clean reads were mapped to dm6 using STAR (v2.7.10a)
Read count extraction were performed using RSEM (v1.3.1)
Reads normalization and differentially-expressed gene calling were performed using DESeq2 (v1.40.2)
Assembly: dm6
Supplementary files format and content: tab-delimited text files include gene expression for each Sample

extract_protocol:
Total RNAs were extracted from embryos at specific stages utilizing TRIzol reagent.  Each RNA sample (0.5 µg total RNA) underwent rRNA depletion.
Strand-specific libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for MGI, following the manufacturer's instructions.


description: Library name: 0_0.5h_KD_for_IntS11KD_RNAseq_replicate_2


description: Library name: 1_1.5h_KD_for_IntS11KD_RNAseq_replicate_1


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_PolII_ChIPseq_for_RescueExperiment_replicate_2


description: Library name: 1_1.5h_IntS11_mislocalized_IntS11_ChIPseq_replicate_1


description: Library name: 1_1.5h_WT_for_IntS11KD_RNAseq_replicate_2


description: Library name: 2.5_3h_WT_PolII_ChIPseq_for_RescueExperiment_replicate_2


description: Library name: 2.5_3h_KD_for_IntS11KD_RNAseq_replicate_2


description: Library name: 0_0.5h_WT_for_IntS11KD_RNAseq_replicate_2


description: Library name: 1_1.5h_E203Q_Rescue_PolII_ChIPseq_for_RescueExperiment_replicate_2


description: Library name: 1_1.5h_E203Q_Rescue_PolII_ChIPseq_for_RescueExperiment_replicate_1


description: Library name: 2.5_3h_KD_for_IntS11KD_RNAseq_replicate_1


description: Library name: 2.5_3h_WT_for_IntS11KD_RNAseq_replicate_1


description: Library name: 0_0.5h_KD_for_IntS11KD_RNAseq_replicate_1


description: Library name: 2.5_3h_E203Q_Rescue_PolII_ChIPseq_for_RescueExperiment_replicate_2


description: Library name: 0_0.5h_WT_for_IntS11KD_RNAseq_replicate_1


description: Library name: 1_1.5h_KD_for_IntS11KD_RNAseq_replicate_2


description: Library name: 1_1.5h_WT_for_IntS11KD_RNAseq_replicate_1


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_PolII_ChIPseq_for_RescueExperiment_replicate_1


description: Library name: 2.5_3h_FlagIntS11E203Q_Rescue_RNAseq_replicate_2


description: Library name: 2.5_3h_FlagIntS11E203Q_Rescue_RNAseq_replicate_1


description: Library name: 2.5_3h_E203Q_Rescue_PolII_ChIPseq_for_RescueExperiment_replicate_1


title: CAGE_L_00120.BC02,Rottweiler,Corpus_callosum_only

description: Library name: CAGE_L_00120.BC02

source_name: corpus callosum

value: corpus callosum

value: Rottweiler

value: Male


description: Library name: 1_1.5h_FlagIntS11E203Q_Rescue_RNAseq_replicate_1


description: Library name: 1_1.5h_FlagIntS11WT_Rescue_RNAseq_replicate_1


description: Library name: 2.5_3h_IntS11mislocalized_for_Rescue_RNAseq_replicate_2


description: Library name: 2.5_3h_FlagIntS11WT_Rescue_RNAseq_replicate_1


description: Library name: 2.5_3h_IntS11mislocalized_for_Rescue_RNAseq_replicate_1


title: 1_1.5h_WT_for_Rescue_RNAseq_replicate_2

description: Library name: 1_1.5h_WT_for_Rescue_RNAseq_replicate_2


description: Library name: 1_1.5h_Ctrl_for_a_amanitin_RNAseq_replicate_1


title: 2.5_3h_WT_for_Rescue_RNAseq_replicate_1

description: Library name: 2.5_3h_WT_for_Rescue_RNAseq_replicate_1


description: Library name: 1_1.5h_IntS11mislocalized_for_Rescue_RNAseq_replicate_2


title: 1_1.5h_WT_for_Rescue_RNAseq_replicate_1

description: Library name: 1_1.5h_WT_for_Rescue_RNAseq_replicate_1


title: 2.5_3h_a_amanitin_RNAseq_replicate_2

description: Library name: 2.5_3h_a_amanitin_RNAseq_replicate_2


title: CAGE_L_00120.BC04,German_pinscher,Parathyroid_only

description: Library name: CAGE_L_00120.BC04

value: German Pinscher


description: Library name: 1_1.5h_FlagIntS11E203Q_Rescue_RNAseq_replicate_2


description: Library name: 2.5_3h_FlagIntS11WT_Rescue_RNAseq_replicate_2


description: Library name: 1_1.5h_FlagIntS11WT_Rescue_RNAseq_replicate_2


title: 2.5_3h_WT_for_Rescue_RNAseq_replicate_2

description: Library name: 2.5_3h_WT_for_Rescue_RNAseq_replicate_2


title: 1_1.5h_a_amanitin_RNAseq_replicate_2

description: Library name: 1_1.5h_a_amanitin_RNAseq_replicate_2


description: Library name: 2.5_3h_Ctrl_for_a_amanitin_RNAseq_replicate_2


description: Library name: 1_1.5h_Ctrl_for_a_amanitin_RNAseq_replicate_2


description: Library name: 2.5_3h_Ctrl_for_a_amanitin_RNAseq_replicate_1


description: Library name: 1_1.5h_IntS11mislocalized_for_Rescue_RNAseq_replicate_1


title: 2.5_3h_a_amanitin_RNAseq_replicate_1

description: Library name: 2.5_3h_a_amanitin_RNAseq_replicate_1


description: Library name: 2.5_3h_WT_PolII_ChIPseq_for_RescueExperiment_replicate_1


title: 1_1.5h_a_amanitin_RNAseq_replicate_1

description: Library name: 1_1.5h_a_amanitin_RNAseq_replicate_1


description: Library name: 2.5_3h_Mutant_IntS9_mislocalized_RNAseq_replicate_1


description: Library name: 2.5_3h_WT_IntS9_mislocalized_RNAseq_replicate_2


description: Library name: 2.5_3h_Mutant_IntS9_mislocalized_RNAseq_replicate_2


description: Library name: 0_0.5h_Mutant_IntS9_mislocalized_RNAseq_replicate_2


description: Library name: 1_1.5h_WT_IntS11_mislocalized_RNAseq_replicate_2


description: Library name: 2.5_3h_WT_IntS11_mislocalized_RNAseq_replicate_2


description: Library name: 0_0.5h_Mutant_IntS9_mislocalized_RNAseq_replicate_1


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_RNAseq_replicate_2


description: Library name: 1_1.5h_Mutant_IntS9_mislocalized_RNAseq_replicate_1


description: Library name: 1_1.5h_WT_IntS9_mislocalized_RNAseq_replicate_2


description: Library name: 1_1.5h_WT_IntS9_mislocalized_RNAseq_replicate_1


description: Library name: 2.5_3h_WT_IntS9_mislocalized_RNAseq_replicate_1


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_RNAseq_replicate_1


description: Library name: 0_0.5h_WT_IntS9_mislocalized_RNAseq_replicate_1


description: Library name: 1_1.5h_WT_IntS11_mislocalized_RNAseq_replicate_1


description: Library name: 1_1.5h_Mutant_IntS11_mislocalized_RNAseq_replicate_1


description: Library name: 1_1.5h_Mutant_IntS11_mislocalized_RNAseq_replicate_2


description: Library name: 0_0.5h_Mutant_IntS11_mislocalized_RNAseq_replicate_2


description: Library name: 0_0.5h_Mutant_IntS11_mislocalized_RNAseq_replicate_1


description: Library name: 1_1.5h_Mutant_IntS9_mislocalized_RNAseq_replicate_2


description: Library name: 0_0.5h_WT_IntS9_mislocalized_RNAseq_replicate_2


description: Library name: 0_0.5h_WT_IntS11_mislocalized_RNAseq_replicate_2


description: Library name: 0_0.5h_WT_IntS11_mislocalized_RNAseq_replicate_1


title: 72hAEL_ZygoticMutant_RNAseq_replicate_2

description: Library name: 72hAEL_ZygoticMutant_RNAseq_replicate_2

source_name: larva

value: larva


description: Library name: 2.5_3h_WT_IntS11_mislocalized_RNAseq_replicate_1


title: 24hAEL_ZygoticMutant_RNAseq_replicate_1

description: Library name: 24hAEL_ZygoticMutant_RNAseq_replicate_1


title: 72hAEL_ZygoticMutant_RNAseq_replicate_1

description: Library name: 72hAEL_ZygoticMutant_RNAseq_replicate_1


title: WT_ECT_1

status: Public on Apr 02 2026

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.7.8a was used to align the reads to the GRCh38 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in GRCh38 version 108
Assembly: GRCh38 version 108
Supplementary files format and content: Tab-delimited gene counts

source_name: Engineered conncetive tissue

extract_protocol:
Total RNA isolation using the NucleoSpin RNA kit (Macheray-Nagel)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Engineered conncetive tissue

value: iPSC-cardiac fibroblasts

value: WT

value: untreated


title: 48hAEL_ZygoticMutant_RNAseq_replicate_1

description: Library name: 48hAEL_ZygoticMutant_RNAseq_replicate_1


title: 24hAEL_WT_RNAseq_replicate_1

description: Library name: 24hAEL_WT_RNAseq_replicate_1


description: Library name: Mutant_a_amanitin_GAF_ChIPseq_replicate_1

value: embryo


title: 48hAEL_WT_RNAseq_replicate_2

description: Library name: 48hAEL_WT_RNAseq_replicate_2


title: 48hAEL_WT_RNAseq_replicate_1

description: Library name: 48hAEL_WT_RNAseq_replicate_1


title: 48AEL_WT_PolII_ChIPseq_replicate_2

description: Library name: 48AEL_WT_PolII_ChIPseq_replicate_2


title: 48hAEL_ZygoticMutant_RNAseq_replicate_2

description: Library name: 48hAEL_ZygoticMutant_RNAseq_replicate_2


description: Library name: 48AEL_ZygoticMutant_PolII_ChIPseq_replicate_2


title: 72hAEL_WT_RNAseq_replicate_2

description: Library name: 72hAEL_WT_RNAseq_replicate_2


title: 24hAEL_WT_RNAseq_replicate_2

description: Library name: 24hAEL_WT_RNAseq_replicate_2


title: 48AEL_WT_PolII_ChIPseq_replicate_1

description: Library name: 48AEL_WT_PolII_ChIPseq_replicate_1


title: 72hAEL_WT_RNAseq_replicate_1

description: Library name: 72hAEL_WT_RNAseq_replicate_1


title: 2.5_3h_WT_IntS11_mislocalized_Micro-C

description: Library name: 2.5_3h_WT_IntS11_mislocalized_Micro-C

data_processing:
Raw FASTQ files were aligned to the reference genome (dm6) using BWA-MEM.
Reads were filtered, deduplicated, and only valid pairs are retained using pairtools.
Hi-C matrices at multiple resolutions were built using Juicer.
Assembly: dm6
Supplementary files format and content: a binary, compressed format for storing Hi-C data, particularly interaction matrices

extract_protocol:
Embryos were dechorionated for 5 min in 50% bleach and rinsed with PBS. The embryos were resuspended in PBST (PBS with 0.1% Triton X-100) and fixed with 3 mM DSG for 15 min at room temperature. The embryos were then subjected to a second crosslinking step using freshly prepared 1% formaldehyde at room temperature for 30 minutes, followed by washing with wash buffer. Subsequently, the embryos were resuspended in wash buffer and homogenized with a loose stroke 100 times, followed by centrifugation at 2000 g for 5 minutes at 4℃ to collect the pellet. The cell pellet was digested with MNase and subsequent steps were carried out according to the kit’s protocol.
Micro-C was performed using a Dovetail Micro-C kit (Cantata Bio) according to the manufacturer’s protocol.


title: 24hAEL_ZygoticMutant_RNAseq_replicate_2

description: Library name: 24hAEL_ZygoticMutant_RNAseq_replicate_2


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_Micro-C


description: Library name: 48AEL_ZygoticMutant_PolII_ChIPseq_replicate_1


description: Library name: Mutant_a_amanitin_Zelda_ChIPseq_replicate_2


description: Library name: Mutant_a_amanitin_Zelda_ChIPseq_replicate_1


title: WT_a_amanitin_GAF_ChIPseq_replicate_1

description: Library name: WT_a_amanitin_GAF_ChIPseq_replicate_1


description: Library name: Mutant_a_amanitin_GAF_ChIPseq_replicate_2


title: WT_a_amanitin_Zelda_ChIPseq_replicate_2

description: Library name: WT_a_amanitin_Zelda_ChIPseq_replicate_2


title: WT_a_amanitin_Zelda_ChIPseq_replicate_1

description: Library name: WT_a_amanitin_Zelda_ChIPseq_replicate_1


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_pSer5_ChIPseq_replicate_2


description: Library name: 1_1.5h_Mutant_IntS11_mislocalized_pSer5_ChIPseq_replicate_2


description: Library name: 1_1.5h_Mutant_IntS11_mislocalized_pSer5_ChIPseq_replicate_1


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_pSer5_ChIPseq_replicate_1


title: WT_a_amanitin_GAF_ChIPseq_replicate_2

description: Library name: WT_a_amanitin_GAF_ChIPseq_replicate_2


description: Library name: 2.5_3h_WT_IntS11_mislocalized_pSer5_ChIPseq_replicate_1


description: Library name: 2.5_3h_WT_IntS11_mislocalized_pSer5_ChIPseq_replicate_2


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_PolII_ChIPseq_replicate_2


description: Library name: 1_1.5h_WT_IntS11_mislocalized_pSer5_ChIPseq_replicate_1


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_GAF_ChIPseq_replicate_1


description: Library name: 1_1.5h_WT_IntS11_mislocalized_PolII_ChIPseq_replicate_1


description: Library name: 1_1.5h_WT_IntS11_mislocalized_PolII_ChIPseq_replicate_2


description: Library name: 2.5_3h_WT_IntS11_mislocalized_PolII_ChIPseq_replicate_2


description: Library name: 2.5_3h_WT_IntS11_mislocalized_GAF_ChIPseq_replicate_2


description: Library name: 2.5_3h_WT_IntS11_mislocalized_PolII_ChIPseq_replicate_1


description: Library name: 1_1.5h_Mutant_IntS11_mislocalized_PolII_ChIPseq_replicate_2


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_GAF_ChIPseq_replicate_2


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_PolII_ChIPseq_replicate_1


description: Library name: 1_1.5h_Mutant_IntS11_mislocalized_GAF_ChIPseq_replicate_1


description: Library name: 1_1.5h_Mutant_IntS11_mislocalized_GAF_ChIPseq_replicate_2


description: Library name: 1_1.5h_WT_IntS11_mislocalized_pSer5_ChIPseq_replicate_2


description: Library name: 2.5_3h_WT_IntS11_mislocalized_GAF_ChIPseq_replicate_1


description: Library name: 1_1.5h_WT_IntS11_mislocalized_GAF_ChIPseq_replicate_1


description: Library name: 1_1.5h_Mutant_IntS11_mislocalized_PolII_ChIPseq_replicate_1


description: Library name: 1_1.5h_WT_IntS11_mislocalized_GAF_ChIPseq_replicate_2


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_Zelda_ChIPseq_replicate_2


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_Zelda_ChIPseq_replicate_1


description: Library name: 1_1.5h_Mutant_IntS11_mislocalized_Zelda_ChIPseq_replicate_2


description: Library name: 2.5_3h_WT_IntS11_mislocalized_Zelda_ChIPseq_replicate_2


description: Library name: 1_1.5h_WT_IntS11_mislocalized_Zelda_ChIPseq_replicate_1


title: Streptomyces and yeast cells, co-culture, Day5

organism:
Streptomyces lavendulae
Saccharomyces cerevisiae

source_name: bacterial and yeast cells

value: bacterial and yeast cells

value: YAKB-15 and BY25610

value: WT and ::mCherry

value: co-culture


title: Streptomyces cells, co-culture, Hour6

organism: Streptomyces lavendulae

source_name: bacterial cells

value: bacterial cells

value: Hour 6


title: Streptomyces and yeast cells, co-culture, Day3

value: Day 3


title: Streptomyces and yeast cells, co-culture, Day7

value: Day 7


title: Streptomyces cells, co-culture, Hour48

value: Hour 48


description: Library name: 1_1.5h_WT_IntS11_mislocalized_Zelda_ChIPseq_replicate_2


description: Library name: 1_1.5h_Mutant_IntS11_mislocalized_Zelda_ChIPseq_replicate_1


description: Library name: 2.5_3h_WT_IntS11_mislocalized_Zelda_ChIPseq_replicate_1


title: Streptomyces cells, control, Hour12

value: axenic culture

value: Hour 12


title: 1_1.5h_WT_IntS11_ChIPseq_replicate_1

description: Library name: 1_1.5h_WT_IntS11_ChIPseq_replicate_1


title: 2.5_3h_WT_IntS11_ChIPseq_replicate_2

description: Library name: 2.5_3h_WT_IntS11_ChIPseq_replicate_2