title: Kras G12R c2 + doxy rep2 R2021-000578

description: Kras G12R c2 + doxy rep2


title: S8_2

status: Public on Apr 01 2026

type: SRA

city: Yangzhou

first: Guoqing

last: Wang

state: Jiangsu province

address: 48 East Wenhui Road

country: China

institute: yangzhou university

description: Library name: Exprimental group 5

library_source: transcriptomic

data_processing:
After sequencing, the raw reads that were generated by sequencers were saved in the fastq format. Then, clean reads were obtained by removing reads containing rRNA sequences, poly-N, adapter sequences, and low-quality reads from the dirty raw reads. All high-quality clean reads were used for downstream analyses.
Clean reads were aligned to the mouse mm10 reference genome using HISAT2 v2.2.0.
Aligned clean reads were assembled into transcripts using StringTie v2.1.5.
Gene expression levels were quantified using FPKM values, which were calculated through StringTie v2.1.5 to normalize transcriptional abundance. Differential expression analysis for lncRNAs and mRNAs between the infected and the mock groups was performed using the edgeR package. The p value and false discovery rate (FDR) for each gene were determined based on the negative binomial distribution model.
Assembly: mouse mm10 reference genome
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: lung

growth_protocol: Mice were housed in negative-pressure isolators with HEPA filters in bio-safety level 3 (BSL3) animal facilities

extract_protocol:
Total RNAs from mouse lung samples were extracted using TRIzolTM reagent (Invitrogen, USA) according to the manufacturer’s instructions. The concentration and RNA integrity number (RIN) of the purified RNAs were assessed using Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit), and the purity of total RNAs was detected by NanoDropTM.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Six-week-old female BALB/c mice (n = 3 per group) were intranasally inoculated with S8 or SDL124 virus, respectively. Mice inoculated with PBS were served as the mock group.Mice lung samples were collected at 2 days post infection (dpi) and frozen immediately in liquid nitrogen.

tag: tissue

value: lung


title: Kras G12R c2 -doxy rep1 R2021-000575

city: Milwaukee

first: Michael

middle: T

last: Zimmermann

state: WI

address: 8701 Watertown Plank Road

department: Mellowes Center

country: USA

institute: Medical College of Wisconsin

description: Kras G12R c2 -doxy rep1

data_processing:
Reads were aligned to GRCh38.p13 and Gencode v32 (based on Ensembl v98) transcript reference using the STAR aligner and MAPR-Seq3 workflow.
Assembly: GRCh38.p13

organism: Homo sapiens

source_name: human embryonic kidney cells

growth_protocol: HEK 293 KRAS mutant isogenic cell lines were created by co-transfecting KRAS mutant pcDNA5/FRT/TO plasmid containing KRAS variants with pOG44 plasmid into the human Flp-In™ T-REx™ 293 Cell Line (Invitrogen) and selecting for hygromycin-resistant clones.

extract_protocol:
RNA extraction was done following the miRNeasy Mini Kit protocol (Qiagen), with cells lysed and collected in 700µL QIAzol lysis reagent (Qiagen) per well.
RNA libraries were prepared with the Illumina TruSeq RNA v2 kit

treatment_protocol: Mutant cells were plated at 200,000 cells/well in 6-well plates and induced to express KRAS with 1µg/mL doxycycline the following morning. Twenty-four hours after adding doxycycline, the cells were harvested.

tag: cell type

value: Flp-In T-REx HEK 293

tag: kras variant

tag: treatment

value: control no doxycycline

tag: biological replicate


title: hiPSC-CMs, OGPs, hypoxia, biological replicate2

city: Cincinnati

first: JIALIANG

last: LIANG

address: 231 Albert Sabin Way

department: Department of Pathology and Laboratory Medicine

institute: University of Cincinnati

description: Library name: C2

data_processing:
Raw reads were quality-filtered and aligned to the human reference genome using Salmon. Differential gene expression analysis was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: .tsv format files (DESeq2 normalized counts)

source_name: ipsc

growth_protocol: Human induced pluripotent stem cell (hiPSC) lines (ATCC#CYS0105) were maintained under standard pluripotent culture conditions in mTeSR Plus basal medium (Stemcell Technologies) and passaged at ~70% confluency. Six-well plates were coated with extracellular matrix by diluting 50 µL of ATCC basement membrane gel (ACS-3035) in 5 mL cold serum-free DMEM/F-12 and incubating at 37°C for 1 h. For CM differentiation, hiPSCs were dissociated into a single-cell suspension using 0.5 mM EDTA and replated onto matrix-coated plates (either Matrigel or ATCC basement membrane gel) at ~70% confluency. Mesoderm induction was initiated by treating cells with 10 µM CHIR99021 in RPMI 1640 supplemented with B-27 minus insulin for 24 h, followed by 2 µM CHIR99021 for an additional 24 h. At ~48 h, due to observed cell loss, Wnt inhibition was performed using 4 µM ZAV939 in RPMI/B-27 minus insulin for 24-48 h. Subsequently, cultures were maintained in RPMI 1640 supplemented with B-27 with insulin, with medium changes every 24-48 h. Spontaneous beating was observed between days 7--10, consistent with cardiomyocyte differentiation. Thereafter, cells were maintained with medium changes every 1-2 days. Metabolic selection of hiPSC-CMs was performed using RPMI 1640 without glucose, supplemented with B-27 with insulin and 4 µM L-lactate. Cells were used for experiments once stable contractility and CM-like morphology were established.

extract_protocol:
PureLink RNA Mini Kit, according to
Approximately 200ng of total RNA for each sample was prepared for conventional sequencing libraries using the TruSeq RNA Library Prep Kit (Illumina) as per the manufacturer’s instructions, with mRNA enriched via poly-A-selection using oligoDT beads. RNA was then thermally fragmented with random priming, converted to cDNA, and PCR amplified.

treatment_protocol: Oxygen-generating PLGA microparticles were fabricated using a modified oil-in-water (O/W) emulsion-solvent evaporation method. PLGA was dissolved in dichloromethane (DCM) at a concentration of 100mg/mL, after which sodium percarbonate (20% w/w relative to PLGA) and β-carotene (1-2% w/w relative to PLGA) were added and dispersed using probe sonication (30-second pulse in an ice bath) to ensure homogeneous suspension of oxygen-generating components. The organic phase was then emulsified into a 1% (w/v) polyvinyl alcohol (PVA) aqueous solution using high-speed homogenization at 12,000 rpm for 2 minutes to produce an O/W emulsion targeting a final microparticle size of 5-20µm. After emulsification, the mixture was stirred magnetically at room temperature for 4 hours to allow solvent diffusion and evaporation, leading to particle solidification. Microparticles were collected by centrifugation at 5,000 × g for 5 minutes, washed 3 times with sterile deionized water to remove residual PVA, and frozen at -80°C overnight, then lyophilized for 48 hours. The dry OGPs were stored at -80°C until use. Hypoxic chamber (INVIVO2-500) condition: 1% O2, 5% CO2, 94% N2.

tag: cell line

value: ipsc

value: CMs

value: differentiatiated, hypoxia, OGP


title: S8_1

description: Library name: Exprimental group 4


title: 188 ileum CTR 2H,rep1

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

country: France

institute: Parean Biotechnologies

description: Library name: 1-188_I_1

data_processing:
FastQC (version 0.11.9) and MultiQC (version 1.12) were used for quality control of raw paired-end fastq files.
Illumina's adaptors as well as low quality reads were trimmed out using TrimGalore (version 0.6.7)
Transcript quantification was performed using Salmon (version 1.10.0) on trimmed fastqs against GENCODE V44 transcript reference database (assembly GRCh38)
Quantified transcripts were imported in R (version 4.3.9) using the package tximport (version 1.30.0)
Count data handling and differential analysis were performed using the package EBSeq (version 2.0.0)
Genes were pre-filtered out if they expressed (count > 0) in less than 60% of samples of 1 group.
Assembly: GENCODE 44/GRCh38
Supplementary files format and content: tab delimited transcript quantification (Salmon output)

source_name: ileum

extract_protocol:
RNA was extracted using Qiagen RNeasay kit following manufacturer instruction
mRNA library preparation were realized following manufacturer’s recommendations (Stranded Total RNA Prep Ligation with Ribo-Zero Plus from ILLUMINA). Final samples pooled library prep were sequenced on Novaseq 6000 ILLUMINA with S1-200 cycles cartridge (2x1600Millions of 100 bases reads) corresponding to 2x33Millions of reads per sample after demultiplexing.

treatment_protocol: F. prausnitzii EXL01 strain was grown at 37°C in a Exeliom Bisociences’ proprietary medium according to an in-house production process based on the know-how of Exeliom Biosciences. The test material was prepared to be ready-to-use in PBS/glycerol, characterized by enumerating the number of morphologically intact bacteria i.e. the Total Cell Count (TCC). Total CD14+ isolated cells (1. 105) were treated with control medium, LPS (100 ng/ml) or EXL01 strain at 2 doses (MOI 10 and 100) for 6 or 16 h

value: ileum

value: CD14+ monocytes

value: CTR

tag: time


title: hiPSC-CMs, OGPs, hypoxia, biological replicate1

description: Library name: C1


title: Kras G12F c1 + doxy rep2 R2021-000574

description: Kras G12F c1 + doxy rep2

value: add doxycycline for 24hr


title: SDL124_3

description: Library name: Exprimental group 3


title: PC9,Osimertinib,rep 1

city: Jerusalem

first: Xue

last: Sun

address: Hebrew University, Givat Ram campus

department: Biochemistry department

country: Israel

institute: The Hebrew University of Jerusalem

description: Raw reads from all lanes are merged

library_source: transcriptomic single cell

data_processing:
The raw sequencing data were paired-end fastq files. In data QC, Read1 from all lanes was iterated through and filtered for reads possessing the correct barcode structure, and single-cell barcodes and UMIs were extracted. Barcodes that could be uniquely assigned to an accepted barcode with a Hamming distance of 2 nt or less were merged. UMI deduplication was performed by removing reads with duplicated UMIs under the same single-cell barcode. Unique UMI reads per barcode were counted and plotted in a histogram. Thresholds were determined based on the separation between the first and second peaks. This threshold was then applied in the filtering step, where a similar process was performed as in QC, but outputting reads with UMI counts greater than the threshold into barcode-specific fastq files. Single cell fastqs were then trimmed for Illumina adaptors, barcode spacers and repeated elements (20x A/T/G/C). Finally reads aligned to ribosomal RNA were removed. Raw data were then aligned in multiple rounds to exclusively map to total RNA. Reads were first mapped to the whole genome, then counted with different GTF files in each round. Only reads that failed to align proceeded to the next round. The alignment order was short RNA, long RNA exons, long RNA introns, and pseudogenes. Single cell matrix obtained from each round were combined in downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: sc-rDSeq; scRNAseq

growth_protocol: PC9 cells were grown in DMEM supplemented with 10% fetal bovine serum, 50 μg/ml penicillin-streptomycin, 2 mM L-glutamine, and 1 mM sodium pyruvate. HCC827 cells were grown in RPMI 1640 (+Glu) supplemented with 10% fetal bovine serum, 50 μg/ml penicillin-streptomycin and 10mM HEPES. All cells were maintained in 5% CO2 in a humidified incubator at 37 °C.

extract_protocol:
Cells were detached from culture dish with treatment of 2mL trypsin for 10cm2 dish. After counting and checking viability, single cell suspension were prepared at concentration of 300,000 cells/mL in PBS containing 10% Optiprep.
The total RNA library was prepared in two steps. First, total RNA was captured in nanodroplets, and single-cell barcodes were assigned to reversely transcribed cDNA. Subsequently, the cDNA was pooled for in vitro amplification and integration of Illumina adapters. Briefly, using a microfluidics device, single cells were encapsulated in water-in-oil droplets containing a lysis buffer with reverse transcription (RT) enzymes and hydrogel beads carrying primers. These primers included single-cell barcodes and rDS/polyT sequences, as well as the Illumina adapter PE1 and a T7 promoter for in vitro transcription (IVT). Following reverse transcription, the cDNA from all droplets was pooled, unused primers were removed, and the cDNA was cleaned. The second strand was then synthesized prior to IVT amplification. The amplified RNA was slightly fragmented, and the Illumina adapter PE2 was integrated via a random RT step. Finally, the library was amplified by PCR, during which Illumina indexes were incorporated.

treatment_protocol: For drug treatment experiments, stock solutions of Osimertinib and Gefitinib were first diluted in DMSO and then in culture medium, maintaining a final DMSO concentration of 1% across all dilutions. Untreated cells were given 1% DMSO as a control. As start, 1 x 106 PC9 or HCC827 cells were seeded to a 10 cm2 plate. 24h after seeding, 1μM Osimertinib and Gefitinib were given to cells. Every 3 days, medium was changed with fresh drugs. After 9 days, remained cells were collected for sc-rDSeq. Control groups were treated with DMSO for 3 days. Cell survival relative to the control was about 1% for all groups.

value: Osimertinib


title: Kras G12F c1 -doxy rep2 R2021-000572

description: Kras G12F c1 -doxy rep2


title: hiPSC-CMs, control vehicles, hypoxia, biological replicate3

description: Library name: B6

value: differentiatiated, hypoxia


title: hiPSC-CMs, control vehicles, hypoxia, biological replicate2

description: Library name: B5


title: PC9,Gefitinib,rep 2

description: Raw reads from all lanes are merged

value: Gefitinib


title: Kras G12F c1 -doxy rep1 R2021-000571

description: Kras G12F c1 -doxy rep1


title: PC9,Gefitinib,rep 1

description: Raw reads from all lanes are merged


title: NC_2

description: Library name: Control2


title: hiPSC-CMs, OGPs, biological replicate3

description: Library name: F3

value: differentiatiated, OGP


title: SDL124_1

description: Library name: Exprimental group 1


title: PC9,DMSO,rep 2

description: Raw reads from all lanes are merged

value: DMSO


title: hiPSC-CMs, control vehicles, hypoxia, biological replicate1

description: Library name: B4


title: PC9,DMSO,rep 1

description: Raw reads from all lanes are merged


title: Kras G12D c1 + doxy rep2 R2021-000570-002

description: Kras G12D c1 + doxy rep2

tag: technical replicate

value: tech rep3


title: Kras G12D c1 + doxy rep2 R2021-000570-001

description: Kras G12D c1 + doxy rep2

value: tech rep2


title: hiPSC-CMs, OGPs, biological replicate2

description: Library name: F2


title: SDL124_2

description: Library name: Exprimental group 2

value: lung


title: Kras G12F c1 + doxy rep1 R2021-000573

description: Kras G12F c1 + doxy rep1

value: Flp-In T-REx HEK 293


title: hiPSC-CMs, OGPs, biological replicate1

description: Library name: F1


title: COVID-4-2

city: Chicago

first: Luis

middle: B

last: Barreiro

state: Illinois

address: 5841 S Maryland Ave

department: Department of Medicine

institute: University of Chicago

description:
Illumina NovaSeq X
multiplexed 10X single-cell capture

data_processing:
Single-cell RNA-seq reads were mapped using the count function in cellranger (v6.0.2).
Assembly: GRCh38
Supplementary files format and content: .mtx files include count values for each multiplexed sample; .tsv files include the description of barcodes (cells) and features (genes)

molecule: polyA RNA

source_name: multiplexed PBMCs

extract_protocol:
PBMCs were unfrozen, rested overnight, washed, and prepared for single-cell capture using the 10X workflow. Immediately prior to the capture, cells from different individuals were combined into pools.
Single-cell GEMs were generated using a Chromium Controller instrument (10x Genomics). Sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kits (v3.1 Dual Index chemistry, 10x Genomics) according to the manufacturer’s instructions.

value: multiplexed PBMCs

value: primary immune cells

value: PBMCs


title: NC_1

description: Library name: Control1


title: NC_3

description: Library name: Control3


title: COVID-4-1


title: hiPSC-CMs, control vehicles, biological replicate3

description: Library name: D6

value: ipsc

value: CMs

value: differentiatiated


title: Kras G12D c1 + doxy rep2 R2021-000570

description: Kras G12D c1 + doxy rep2

value: tech rep1


title: siFAT4, 48h

city: San Antonio

first: Hanzhou

state: TX

address: 8403 Floyd Curl Drive, MSC 7784

department: GCCRI

institute: UT Health at San Antonio

description: Library name: siFAT4_48h

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
Gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count. Merged HTSeq file is similar to individual HTSeq file, first column is gene symbol, and first row is sample name, and each column with read counts from each sample.

growth_protocol: A673 cells were cultured in DMEM/10% fetal bovine serum.

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen/Thermo Fisher).
cDNA fragment libraries were synthesized using TruSeq stranded mRNA library preparation kit (Illumina).

treatment_protocol: siRNA transfection was performed using Lipofectamine™ RNAiMAX Transfection Reagent (Thermo Fisher).

value: Ewing sarcoma cell line


title: COVID-3-2


title: hiPSC-CMs, control vehicles, biological replicate2

description: Library name: D5


title: siFAT4, 24h

description: Library name: siFAT4_24h


title: COVID-3-1


title: Control_siRNA, 48h

description: Library name: Control_siRNA_48h


title: Kras G12D c1 + doxy rep1 R2021-000569-002

description: Kras G12D c1 + doxy rep1

value: add doxycycline for 24hr


title: COVID-2-2


title: COVID-2-1


title: Undifferentiated hiPSCs biological replicate2

description: Library name: A2

value: stem cells

value: undifferentiation medium


title: Kras G12D c1 + doxy rep1 R2021-000569-001

description: Kras G12D c1 + doxy rep1


title: Control_siRNA, 24h

description: Library name: Control_siRNA_24h


title: Undifferentiated hiPSCs biological replicate1

description: Library name: A1


title: hiPSC-CMs, control vehicles, biological replicate1

description: Library name: D4


title: COVID-1-1


title: ipsilateral-brain-tissue_VEH-treated_sham_rat6

type: RNA

city: Duarte

first: Margarita

last: Gutova

state: CA

address: 1500 E Duarte Rd

department: Stem Cell and Regenerative Medicine

institute: City of Hope

description: tissue lysates

hyb_protocol: RNA was hybridized with the Codeset from the the mouse nCounter® PanCancer Immune Profiling Panel for the Nanostring nCounter Platform (CAT#Catalog#XT-CSO-MIP1-12, Nanostring Technologies) gene panel at 65°C for 16 h. The post-hybridization probe-target mixture was quantified using the nCounter Digital Analyzer, and all data analyses were performed with ROSALIND (Version 3.39.28.7; https://rosalind.bio/).

scan_protocol: Scanning was done using NanoString nCounter system, following manufacturer's instructions.

data_processing: Normalization, Differential gene expression to calculate fold changes, and p-values were calculated using default parameters provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library (Perkins et al., 2012). P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library2 that takes into consideration the direction and type of all signals on a pathway, the position, role and type of every gene, etc. The significant differential gene lists were further filtered by using |fold change| ≥1.5 and p-value <0.05 for downstream heretical cluster analysis. Downstream pathway and network analysis were performed by using Qiagen IPA software.

label: RNA

organism: Rattus norvegicus

source_name: ipsilateral brain tissue, vehicle treated, sham injury

label_protocol: Brain tissue isolated from TBI site were labeled as follows: LMNSC01 treated, CCI surgery (MSTNCR1 to MSTNCR5), LMNSC01 treated, sham surgery (MSTNSR1 to MSTNSR6), vehicle treated, CCI surgery (MSTVCR1 to MSTVCR5) and vehicle treated sham surgery (MSTVSR1 to MSTVSR6). Similarly brain tissue from contralateral site were labeled as follows:  LMNSC01 treated, CCI surgery (MSCNCR1 to MSCNCR5), LMNSC01 treated, sham surgery (MSCNSR1 to MSCNSR6), vehicle treated, CCI surgery (MSCVCR1 to MSCVCR5) and vehicle treated sham surgery (MSCVSR1 to MSCVSR6).

growth_protocol: Adult male Sprague–Dawley rats (N = 41) (Envigo RMS, Inc., Indianapolis, IN) were pair-housed in ventilated polycarbonate micro-isolator rat cages and maintained in a temperature (21 ± 1 °C) and light (0700–1900 h) controlled vivarium with ad libitum food and water access. The rats were allowed to acclimate for 1 week before undergoing experimental procedures. After the acclimatization period, the rats were randomly assigned to injury groups (CCI + LMNSC01 [n = 12] and CCI + vehicle [VEH, n = 11]) and control groups (Sham + LMNSC01 [n = 9] and Sham + VEH [n = 9]) to assess experimental differences among the surgery groups ± LMNSC01 cells. All experimental manipulations were conducted during the lights-on phase.

extract_protocol: RNA was isolated from snap frozen tissues according to a diagram in figure 1 and half was used for Nanostring analysis and half for protein ELISA assays.

treatment_protocol: Anesthesia was induced with 4% isoflurane in 2:1 N2O:O2, which was followed by endotracheal intubation, placement on a stereotaxic frame, and mechanical ventilation. Anesthesia was maintained with 2% isoflurane and the same volume of carrier gases. Core temperature was monitored and maintained at 37 ± 0.5 °C with a rectal thermistor and heating pad, respectively. Utilizing aseptic procedures, a CCI injury was produced as previously described (Kline et al., 2004, 2016). Specifically, a midline scalp incision was made, the skin and fascia were reflected, and a 10 mm craniectomy was made above the right parietal-hemisphere with a high-speed dental drill. The bone flap was removed and the craniotomy was enlarged using bone rongeurs to ensure consistent placement of the impact tip (6 mm, flat). Following the craniectomy, the impact tip was lowered until contact with the dura mater (zero point). The impact tip was then retracted into a ready position and set to impact 2.8 mm below the surface of the dura. Impact speed was set to 4 m/s with a dwell time of 100 ms. Following impact, Isoflurane was discontinued to reduce neuroprotective confounds, and the rats were rapidly sutured. Sham rats were not subjected to the impact but received all other surgical manipulations to control the potential effects of anesthesia and craniectomy. After the injury procedures, the anesthesia was discontinued and rats were extubated and assessed for acute neurological outcomes to ensure injury equivalence across all groups. To facilitate the engraftment of LMNSC01 cells, an immunosuppressive regimen of cyclosporin A (CsA; 10 mg/kg; subcutaneously [s.c].) was provided to all rats beginning 2 days before the first IN administration of NSCs or VEH and continuing once per day until the brains were harvested. Human LMNSC01 cells from our Master Cell Bank were prepared for intranasal (IN) administration according to established SOPs (Balyasnikova et al., 2014; Gutova et al., 2021; Li et al., 2016; Rockne et al., 2018). Briefly, LMNSC01 cells were thawed, washed, and re-suspended in PBS (6 × 106 cells in 24 μL for a single bolus dose administration). Prior to infusion, rats were anesthetized using Isoflurane and placed on a nose cone in the supine position. The nasal epithelium was disrupted via hyaluronidase infusions at 6 μL per nostril at 2 min intervals for a total volume of 24 μL. After 20 min of disruption exposure, rats then received IN infusions of LMNSC01 cells or the same volume of VEH (6 μL per nostril drop at 2 min intervals for a total volume of 24 μL).  VEH consisted of 2% HSA in PBS. IN dosing occurred on day 7 after CCI or SHAM injury.

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

value: ipsilateral brain

value: VEH

tag: surgery

value: sham


title: T47D-YA cells overexpressing 22.5 kDa FGF2 isoforms 2

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

description: Library name: T47D-YA-FGF2-22_2

data_processing:
Quality control and alignment to the human reference genome (hg19) were performed with the ShortRead and Rsubread R/Bioconductor packages, respectively.
Gene-level read counts per gene were obtained using the UCSC.hg19. KnownGene database and annotated using GenomicFeatures, GenomicAlignments, and org.Hs.eg.db. Differential expression between FGF2 isoform-overexpressing and control groups was analyzed with edgeR on normalized counts.
Assembly: Hg19
Supplementary files format and content: raw counts per sample
Supplementary files format and content: counts_matrix.csv

source_name: breast cancer cell line

extract_protocol:
Total RNA was extracted using TriReagent. RNA concentration and integrity were measured on an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA samples with RNA integrity number (RIN) over 5 were considered for RNA sequencing.
mRNA from T47D-YA cells overexpressing -18 or -22.5 kDa FGF2 isoforms, and from empty vector controls (MOCK), was processed for directional library preparation with the TruSeq RNA Sample Preparation Kit v2 (Illumina). Paired-end sequencing (101-nt) was performed on an Illumina HiSeq2500 platform at Macrogen Core Facility, yielding ~30 million reads per sample.

value: breast cancer cell line

tag: genotype

value: overexpressing 22.5 kDa FGF2 isoforms


title: pl21

description: multiplexed 10X single-cell capture

value: multiplexed PBMCs

value: primary immune cells


title: Kras G12D c1 -doxy rep1 R2021-000567-002

description: Kras G12D c1 -doxy rep1

value: Flp-In T-REx HEK 293

value: control no doxycycline

value: tech rep3


title: Kras G12D c1 -doxy rep2 R2021-000568-001

description: Kras G12D c1 -doxy rep2

value: tech rep2


title: ipsilateral-brain-tissue_VEH-treated_sham_rat4

description: tissue lysates


title: Kras G12D c1 + doxy rep1 R2021-000569

description: Kras G12D c1 + doxy rep1

value: tech rep1


title: ipsilateral-brain-tissue_VEH-treated_sham_rat5

description: tissue lysates


title: ipsilateral-brain-tissue_VEH-treated_sham_rat3

description: tissue lysates


title: COVID-1-2

value: PBMCs


title: T47D-YA cells overexpressing 18 kDa FGF2 isoforms 2

description: Library name: T47D-YA-FGF2-18_2

value: overexpressing 18 kDa FGF2 isoforms


title: Kras G12D c1 -doxy rep2 R2021-000568

description: Kras G12D c1 -doxy rep2


title: T47D-YA cells overexpressing 22.5 kDa FGF2 isoforms 1

description: Library name: T47D-YA-FGF2-22_1


title: Kras G12D c1 -doxy rep1 R2021-000567-001

description: Kras G12D c1 -doxy rep1


title: pl20

description: multiplexed 10X single-cell capture


title: T47D-YA cells overexpressing 18 kDa FGF2 isoforms 1

description: Library name: T47D-YA-FGF2-18_1


title: pl19

description: multiplexed 10X single-cell capture


title: Kras G12C c1 -doxy rep2 R2021-000564

description: Kras G12C c1 -doxy rep2


title: T47D-YA cells with the empty vector control 1

description: Library name: T47D-YA-MOCK_1

value: empty vector control


title: Kras G12C c1 + doxy rep2 R2021-000566

description: Kras G12C c1 + doxy rep2

value: add doxycycline for 24hr


title: pl18

description: multiplexed 10X single-cell capture


title: Kras G12C c1 + doxy rep1 R2021-000565

description: Kras G12C c1 + doxy rep1


title: Kras G12D c1 -doxy rep1 R2021-000567

description: Kras G12D c1 -doxy rep1


title: pl16

description: multiplexed 10X single-cell capture


title: T47D-YA cells with the empty vector control 2

description: Library name: T47D-YA-MOCK_2


title: ipsilateral-brain-tissue_VEH-treated_sham_rat2

description: tissue lysates

value: Sprague-Dawley

value: male


title: ipsilateral-brain-tissue_VEH-treated_CCI_rat4

description: tissue lysates

source_name: ipsilateral brain tissue, vehicle treated, controlled coritcal impact injury

value: ipsilateral brain

value: VEH

value: CCI


title: ipsilateral-brain-tissue_VEH-treated_sham_rat1

description: tissue lysates

value: sham


title: Kras G12C c1 -doxy rep1 R2021-000563

description: Kras G12C c1 -doxy rep1


title: Kras G12A c1 + doxy rep2 R2021-000562

description: Kras G12A c1 + doxy rep2


title: ipsilateral-brain-tissue_VEH-treated_CCI_rat3

description: tissue lysates


title: pl14

description: multiplexed 10X single-cell capture

value: multiplexed PBMCs


title: ipsilateral-brain-tissue_VEH-treated_CCI_rat5

description: tissue lysates


title: ipsilateral-brain-tissue_VEH-treated_CCI_rat2

description: tissue lysates


title: pl15

description: multiplexed 10X single-cell capture

value: primary immune cells


title: Prdm16-overexpressing BOECs rep3

city: LEUVEN

first: Aernout

last: Luttun

state: België

address: Herestraat 49 box 911

department: Cardiovascular Sciences; Centre for Molecular and Vascular Biology

country: Belgium

institute: KU Leuven

description: Gene Expression data of Prdm16-overexpressing BOECs

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450  (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.

label: biotin

source_name: Blood outgrowth endothelial cells

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 90 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix).  All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: BOECs were isolated from peripheral blood from donors and are cultured on collagen-coated culture flasks supplemented with endothelial gowth factors under normal culture conditions (5% CO2 and 37°C).

extract_protocol: Total BOEC RNA was extracted six days after lentiviral transduction by using a TRIzol extraction protocol.

treatment_protocol: The day prior to lentiviral transduction, BOECs were seeded at 125 cells per mm2  in collagen-coated wells. Next, BOECs were transduced with Prdm16-overexpressing or Cherry-control lentivirus and two days after transduction, medium was replaced.

value: Blood outgrowth endothelial cells

tag: transduced with

value: Prdm16-overexpressing lentivirus


title: Kras G12D c1 -doxy rep2 R2021-000568-002

description: Kras G12D c1 -doxy rep2

value: Flp-In T-REx HEK 293

value: control no doxycycline

value: tech rep3


title: Cherry-overexpressing BOECs rep3

description: Gene Expression data of Cherry-overexpressing BOECs

value: Cherry-control lentivirus


title: Kras G12A c1 + doxy rep1 R2021-000561

description: Kras G12A c1 + doxy rep1


title: Kras G12A c1 -doxy rep2 R2021-000560

description: Kras G12A c1 -doxy rep2


title: pl13

description: multiplexed 10X single-cell capture

value: PBMCs


title: pl11

description: multiplexed 10X single-cell capture


title: pl12

description: multiplexed 10X single-cell capture


title: ipsilateral-brain-tissue_NSC-treated_sham_rat6

description: tissue lysates

source_name: ipsilateral brain tissue, NSC treated, sham injury

value: NSC


title: Prdm16-overexpressing BOECs rep2


title: pl10

description: multiplexed 10X single-cell capture


title: ipsilateral-brain-tissue_VEH-treated_CCI_rat1

description: tissue lysates


title: hFLT_2

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

country: Japan

institute: Yokohama City University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays ( G4845A,  G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner using one color scan setting for micro array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 12.1.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
The raw signal intensities of samples were log2-transformed and normalised by the quantile algorithm.

source_name: Hu FL

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Purification kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Fetal liver tissue


title: hFLT_1


title: Kras D38N c1 + doxy rep1 R2021-000557

description: Kras D38N c1 + doxy rep1

value: add doxycycline for 24hr


title: pl09

description: multiplexed 10X single-cell capture


title: ipsilateral-brain-tissue_NSC-treated_sham_rat4

description: tissue lysates

value: Sprague-Dawley

value: male


title: Kras G12A c1 -doxy rep1 R2021-000559

description: Kras G12A c1 -doxy rep1


title: ipsilateral-brain-tissue_NSC-treated_sham_rat5

description: tissue lysates

value: ipsilateral brain


title: Prdm16-overexpressing BOECs rep1


title: Cherry-overexpressing BOECs rep2


title: Cherry-overexpressing BOECs rep1


title: Kras D38N c1 + doxy rep2 R2021-000558

description: Kras D38N c1 + doxy rep2


title: Arabidopsis thaliana, Cvi, GS seed, H3K27me3 ChIP

city: Seoul

first: Jae-Wook

last: Yoon

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: Library name: H3K27me3_GS_Cvi

library_source: genomic

data_processing:
Raw reads were trimmed and quality-checked using Trimmomatic (v0.39; Bolger et al., 2014) with the following parameters: “PE -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”.
Trimmed reads were mapped to the nuclear genome of Arabidopsis using Bowtie2 (v2.5.1; Langmead and Salzberg, 2012) with the options “-p 40 -I 0 -X 500”.
Duplicate reads were removed using Picard MarkDuplicates (v2.18.29; McKenna et al., 2010) with the options “--REMOVE_DUPLICATES=true ASSUME_SORTED=true QUIET=true VALIDATION_STRINGENCY=LENIENT”. Only uniquely mapped reads were used for further analysis.
BigWig files were generated using deepTools bamCompare (v3.5.5; Ramirez et al., 2016) with the parameters “--scaleFactorsMethod None --operation subtract -bs 10 --normalizeUsing CPM -bl”, to produce input-subtracted signal tracks while excluding the Arabidopsis greenscreen regions (Klasfeld et al., 2022) to reduce background noise.
Assembly: Arabidopsis thaliana, Tair10.54 For Cvi, a pseudo-Cvi genome was generated by substituting Col SNPs in the TAIR10 with publicly available Cvi SNPs (ftp://ftp.Arabidopsis.org/home/tair/Sequences/Ecker_Cvi_snps.txt; https://1001genomes.org/data/MPIPZ/MPIPZJiao2020/releases/current/strains/Cvi/Cvi.syri.out.gz).
Supplementary files format and content: .bigwig (except for Input)

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Seed

growth_protocol: Arabidopsis thaliana accessions Columbia-0 (Col) and Cape Verde Islands (Cvi) were used in this study. Plants were grown under standard long-day conditions (16h light / 8h dark) at 22°C. Freshly harvest (FH) seeds were obtained from yellow-green siliques 14–16 days after pollination (DAP). After-ripened (AR) seeds were collected from yellow-brown dehiscent siliques, followed by the subsequent storage for two weeks (w) for Col and 60 days (d) for Cvi at room temperature. Germination-stimulated seed (GS) were prepared by plating AR seeds on 1/2 Murashige and Skoog (MS) medium, followed by a 3-d imbibition at 4℃, a 2-hour (hr) white-light exposure, and a 24-hr dark incubation at 22°C.

extract_protocol:
Seed chromatin was isolated for native-ChIP as previously described by Müller et al. (2012) with the following modifications. Whole seeds rather than isolated embryos were used for chromatin extraction. Chromatin was fragmented using MNase (NEB, MS247S) by incubating at 37°C for 20 minutes (min), extending the incubation time from the 8 min described in the original protocol. For immunoprecipitation of histone protein-DNA complexes, the following antibodies were used: α-H3K4me3 (Millipore, 07-473), α-H3K9me3 (Millipore, 07-442), and α-H3K27me3 (Millipore, 07-449). ChIPed DNAs were purified by the MinElute PCR Purification Kit (Qiagen, 28006), followed by Proteinase K (Roche, 03115828001) treatment.
ChIP-seq libraries were constructed using the TruSeq Library Preparation Kit (Illumina, IP-202-1012) and sequenced on the Illumina HiSeq4000 platform by Macrogen (Seoul, South Korea).

value: Seed

tag: ecotype

value: Cvi

tag: seed stage

value: GS

tag: chip antibody

value: a-H3K27me3 (Millipore, 07-449)


title: ipsilateral-brain-tissue_NSC-treated_sham_rat2

description: tissue lysates

value: sham


title: Kras D38N c1 -doxy rep2 R2021-000556

description: Kras D38N c1 -doxy rep2


title: pl08

description: multiplexed 10X single-cell capture

value: multiplexed PBMCs

value: primary immune cells


title: Arabidopsis thaliana, Cvi, AR seed, H3K27me3 ChIP

description: Library name: H3K27me3_AR_Cvi

value: AR


title: Kras D38N c1 -doxy rep1 R2021-000555

description: Kras D38N c1 -doxy rep1

value: Flp-In T-REx HEK 293

value: control no doxycycline


title: pl06

description: multiplexed 10X single-cell capture

value: PBMCs


title: Arabidopsis thaliana, Cvi, FH seed, H3K27me3 ChIP

description: Library name: H3K27me3_FH_Cvi

value: FH


title: Kras A146T c2 + doxy rep2 R2021-000554

description: Kras A146T c2 + doxy rep2


title: ipsilateral-brain-tissue_NSC-treated_sham_rat1

description: tissue lysates

value: NSC


title: Arabidopsis thaliana, Cvi, GS seed, H3K9me3 ChIP

description: Library name: H3K9me3_GS_Cvi

value: a-H3K9me3 (Millipore, 07-442)


title: ipsilateral-brain-tissue_NSC-treated_CCI_rat5

description: tissue lysates

source_name: ipsilateral brain tissue, NSC treated,controlled cortical impact injury

value: Sprague-Dawley

value: CCI


title: pl07

description: multiplexed 10X single-cell capture


title: ipsilateral-brain-tissue_NSC-treated_CCI_rat4

description: tissue lysates

value: male

value: ipsilateral brain


title: pl05

description: multiplexed 10X single-cell capture


title: Arabidopsis thaliana, Cvi, AR seed, H3K9me3 ChIP

description: Library name: H3K9me3_AR_Cvi

value: Seed

value: Cvi


title: Kras A146T c2 - doxy rep2 R2021-000552

description: Kras A146T c2 - doxy rep2


title: pl04

description: multiplexed 10X single-cell capture


title: Arabidopsis thaliana, Cvi, FH seed, H3K9me3 ChIP

description: Library name: H3K9me3_FH_Cvi


title: ipsilateral-brain-tissue_NSC-treated_CCI_rat2

description: tissue lysates


title: Kras A146T c2 - doxy rep1 R2021-000551

description: Kras A146T c2 - doxy rep1


title: pl01

description: multiplexed 10X single-cell capture


title: ipsilateral-brain-tissue_NSC-treated_CCI_rat3

description: tissue lysates


title: Arabidopsis thaliana, Cvi, GS seed, H3K4me3 ChIP

description: Library name: H3K4me3_GS_Cvi

value: GS

value: a-H3K4me3 (Millipore, 07-473)


title: pl03

description: multiplexed 10X single-cell capture

value: multiplexed PBMCs


title: pl02

description: multiplexed 10X single-cell capture

value: primary immune cells


title: Kras A146T c2 + doxy rep1 R2021-000553

description: Kras A146T c2 + doxy rep1

value: add doxycycline for 24hr


title: Arabidopsis thaliana, Cvi, AR seed, H3K4me3 ChIP

description: Library name: H3K4me3_AR_Cvi

value: AR


title: 105379-002-010

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

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

tag: disease

value: Multiple sclerosis

tag: lesion type

value: PLWM


title: FM79 Cells, siKLF2/KLF4 72h, Trametinib 5nM 48h, biol rep 2

city: Wuerzburg

first: Rupesh

last: Paudel

state: Bavaria

address: Josef-Schneider Straße 2

department: Department of Dermatology, Venerology und Allergology

country: Germany

institute: University Hospital Wuerzburg

description: Library name: Sample 2

data_processing:
quality/adapter trimming of FASTQ files with Cutadapt
Reads alignment to Human reference genome (GCF_000001405.39_GRCh38.p13) primary assembly and mitochondrion, read quantification on gene level based on annotated exons via featureCounts using both, uniquely and multimapping reads.
Differentially expressed genes between different groups were compared in two arms: Tram/siScr vs Tram/siKLF2/4 (=siKLF2/4-regulated genes) using DeSeq2 (Bioconductor)
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab delimited CSV file includes original and normalized FPKM values

growth_protocol: Cells were grown at 37°C with 5% CO2 in RPMI1640 GlutaMAX medium (ThermoFisher Scientific), supplemented with 10% fetal calf serum (Capricorn) and 30 µg/ml Gentamycin (Sigma Aldrich)

extract_protocol:
Toral RNA was extracted using RNAeasy Kit (Qiagen).
cDNA library preparation was done using TruSeq Kit, (Illumina) according to manufacturers protocol.

treatment_protocol: Day 0 : Cells seeded, Day 1:  cells were either transfected with siScr or siKLF2/4 Day 2:  Cells were either treated with vehicle or Trametinib 5nM Day 4: Cells were lysed.

tag: cell type

value: melanoma cell lines

value: KLF2/KLF4 knockdown

value: Trametinib 5nM 48h


title: FM79 Cells, siKLF2/KLF4 72h, Trametinib 5nM 48h, biol rep 3

description: Library name: Sample 3

tag: treatment


title: Arabidopsis thaliana, Col, GS seed, H3K27me3 ChIP

description: Library name: H3K27me3_GS_Col

tag: tissue

value: Col

value: a-H3K27me3 (Millipore, 07-449)


title: contralateral-brain-tissue_VEH-treated_sham_rat5

description: tissue lysates

source_name: contralateral brain tissue, vehicle treated, sham injury

value: Sprague-Dawley

value: male

value: contralateral brain

value: VEH

value: sham


title: FM79 Cells, siKLF2/KLF4 72h, Trametinib 5nM 48h, biol rep 1

description: Library name: Sample 1

tag: cell line


title: contralateral-brain-tissue_VEH-treated_sham_rat6

description: tissue lysates


title: ipsilateral-brain-tissue_NSC-treated_CCI_rat1

description: tissue lysates

value: ipsilateral brain

value: NSC

value: CCI


title: MYOC-A445V A- S3

city: Omaha

first: Iqbal

last: Ahmad

state: NE

address: 42nd St and Emile St

department: Ophthalmology and Visual Sciences

institute: University of Nebraska Medical Center

description: Library name: Sample6

data_processing:
FASTQ files were trimmed by Trim Galore to remove adapters, terminal unknown bases, and low quality 3' regions (Phred <20)
Quality control was performed using FastQC and MultiQC.
The trimmed FASTQ files were aligned using the STAR aligner and RSEM for annotation and quantification.
Genes with 0 or 1 counts were excluded.
Filtered counts were normalized using the median of ratios approach.
Assembly: hg38
Supplementary files format and content: xlsx files include raw counts, TPM, and FPKM values

source_name: MYOC-A445V A iPSC

growth_protocol: Cells were differentiated into RGCs then analyzed.

extract_protocol:
RNA was isolated using the miRNeasy kit (Qaigen). 50 ng per ssample was used to assemble the libraries.
Libraries were created the TruSeq mRNA V2 kit from Illumina.

value: MYOC-A445V A iPSC

value: retinal ganglion cell


title: contralateral-brain-tissue_VEH-treated_sham_rat4

description: tissue lysates


title: Arabidopsis thaliana, Cvi, FH seed, H3K4me3 ChIP

description: Library name: H3K4me3_FH_Cvi

value: Seed

value: Cvi

value: FH

value: a-H3K4me3 (Millipore, 07-473)


title: Arabidopsis thaliana, Col, AR seed, H3K27me3 ChIP

description: Library name: H3K27me3_AR_Col

value: AR


title: 105379-002-009

value: Brain

value: white matter

value: Multiple sclerosis


title: 105379-002-008

value: PLWM


title: MYOC-ISOGENIC G2- S3

description: Library name: Sample3

source_name: MYOC ISO-G2 iPSC

value: MYOC ISO-G2 iPSC

value: WT


title: contralateral-brain-tissue_VEH-treated_sham_rat3

description: tissue lysates

value: Sprague-Dawley

value: male

value: contralateral brain

value: VEH

value: sham


title: MYOC-A445V A- S1

description: Library name: Sample4

value: MYOC-A445V A iPSC

value: retinal ganglion cell


title: Arabidopsis thaliana, Col, AR seed, H3K9me3 ChIP

description: Library name: H3K9me3_AR_Col

value: Seed

value: Col

value: a-H3K9me3 (Millipore, 07-442)


title: 105379-002-007


title: MYOC-ISOGENIC G2- S2

description: Library name: Sample2


title: contralateral-brain-tissue_VEH-treated_CCI_rat5

description: tissue lysates

source_name: contralateral brain tissue, vehicle treated, controlled coritcal impact injury

value: CCI


title: contralateral-brain-tissue_VEH-treated_CCI_rat4

description: tissue lysates


title: contralateral-brain-tissue_VEH-treated_sham_rat1

description: tissue lysates


title: Arabidopsis thaliana, Col, FH seed, H3K9me3 ChIP

description: Library name: H3K9me3_FH_Col

value: FH


title: 105379-002-005

value: Brain

value: white matter


title: contralateral-brain-tissue_VEH-treated_sham_rat2

description: tissue lysates


title: ipsilateral-brain-tissue_NSC-treated_sham_rat3

description: tissue lysates

value: ipsilateral brain

value: NSC


title: 105379-002-004

value: Multiple sclerosis

value: NAWM


title: MYOC-ISOGENIC G2- S1

description: Library name: Sample1

value: MYOC ISO-G2 iPSC

value: WT


title: 105379-002-003


title: Arabidopsis thaliana, Col, GS seed, H3K4me3 ChIP

description: Library name: H3K4me3_GS_Col

value: GS

value: a-H3K4me3 (Millipore, 07-473)


title: Parse_Cow_Flank_sWAT

city: East Lansing

first: Leah

last: Terrian

state: MI

address: 775 Woodlot Dr.

institute: Michigan State University

description: Library name: Sample 6

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: Bos taurus

source_name: subcutaneous white 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).

value: subcutaneous white adipose tissue

tag: tissue common_name_ontology

value: Holstein

tag: batch

tag: organism ontology

value: female

tag: sex ontology

tag: cage type

value: tie-stalls

tag: bedding

value: sawdust

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


title: 105379-002-002

value: Brain

value: white matter

tag: sample code

tag: disease

value: PLWM


title: 105379-002-001

value: Non-demented control

tag: lesion type

value: CWM


title: P6_DMSO_rep2

first: Litao

last: Tao

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

description: Library name: Sample 13

data_processing:
Adaptor and quality trimming using TrimGalore v0.6.0 with Cutadapt v1.15
Alignment to the reference genome and counting reads per gen using STAR v2.7.0f
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw read counts assigned to each gene, in each sample

source_name: cochlea

growth_protocol: Cochleae were dissected from P0-P1 and P6 Lfng-EGFP mice and cultured for 24 hr in 24-well cell culture plates (Millicell™, PICM01250) in DMEM/F12 cell culture medium (Sigma-Aldrich, D6421) with the addition of Neuro-2 supplement (Gibco™, 17502048), Ciprofloxacin hydrochloride (Enzo Life Sciences, ALX-380-288G00) and conc FBS (, ALX-380-288G005).

extract_protocol:
GFP-positive supporting cells were collected into RLT Plus lysis buffer from the Qiagen RNeasy Plus Micro Kit (Cat. no. 74034) and RNA was extracted according to the manufacturer's instructions. RNA quality was assessed by TapeStation.
Libraries were prepared from approximately 0.5–1 ng of total RNA from sorted cells (RIN > 7) using the SMART-Seq® v4 PLUS Kit (Takara Bio).

treatment_protocol: For Notch inhibition, the gamma secretase inhibitor CompoundE (ABCAM, 142164-1-B) dissolved in DMSO was added to the final concentration of 2uM. Control samples were supplemented with equal volumes of DMSO. After 24 hr, cochleae were dissociated in Trypsin-EDTA (Sigma-Aldrich, T4049-100ML) The resulting cell suspension was passed through a 40 µm cell strainer into FACS sorting tubes and sorted using BD FACSAria Flow Cytometer with a 100 µm nozzle.

value: cochlea

tag: age

tag: cell type

value: supporting cells (SC)

tag: genotype

value: Lfng-EGFP

tag: treatment

value: Control (DMSO)


title: contralateral-brain-tissue_VEH-treated_CCI_rat3

description: tissue lysates

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

tag: tissue

value: contralateral brain

value: VEH

tag: surgery

value: CCI


title: P6_DMSO_rep3

description: Library name: Sample 14

tag: batch


title: Arabidopsis thaliana, Col, AR seed, H3K4me3 ChIP

description: Library name: H3K4me3_AR_Col

value: Seed

tag: ecotype

value: Col

tag: seed stage

value: AR

tag: chip antibody

value: a-H3K4me3 (Millipore, 07-473)


title: Arabidopsis thaliana, Col, FH seed, H3K4me3 ChIP

description: Library name: H3K4me3_FH_Col

value: FH


title: 105379-001-109

value: Brain

value: white matter


title: Arabidopsis thaliana, Input mix

description: Library name: Input

value: Col & Cvi

value: Mixed


title: P6_DMSO_rep1

description: Library name: Sample 12

value: cochlea

value: supporting cells (SC)


title: 105379-001-108

value: Non-demented control

value: CWM


title: contralateral-brain-tissue_VEH-treated_CCI_rat1

description: tissue lysates

value: Sprague-Dawley

value: male


title: contralateral-brain-tissue_VEH-treated_CCI_rat2

description: tissue lysates

value: contralateral brain

value: VEH


title: contralateral-brain-tissue_NSC-treated_sham_rat6

description: tissue lysates

source_name: contralateral brain tissue, NSC treated, sham injury

value: NSC

value: sham


title: contralateral-brain-tissue_NSC-treated_sham_rat4

description: tissue lysates


title: contralateral-brain-tissue_NSC-treated_sham_rat5

description: tissue lysates


title: synovial tissue_21days_treat5

city: Changsha

first: Yuqi

last: Wen

address: Xiangya Road

institute: Xiangya Hospital Central South University

hyb_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: Synovial tissue, induced arthritis rats, 21days

label_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA.

growth_protocol: Under the same conditions (temperature 21±2℃, humidity 70%, light time 6:00-18:00, free food)

extract_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

treatment_protocol: Synovial tissues from CIA and normal rats promptly frozen in liquid nitrogen.

value: Synovial tissue

value: Male

value: 7-8 weeks

tag: sample group

value: collagen-induced arthritis (CIA)

tag: molecule subtype

value: circular RNA


title: P6_CompE_rep3

description: Library name: Sample 11

value: Lfng-EGFP

value: Notch inhibition (CompE)


title: 105379-001-107

value: Brain

value: white matter

tag: sample code


title: MYOC-A445V A- S2

description: Library name: Sample5

tag: cell line

value: MYOC-A445V A iPSC

value: retinal ganglion cell


title: P6_CompE_rep2

description: Library name: Sample 10

value: cochlea

value: supporting cells (SC)


title: Arabidopsis thaliana, Col, GS seed, H3K9me3 ChIP

description: Library name: H3K9me3_GS_Col

value: Seed

value: Col

value: GS

value: a-H3K9me3 (Millipore, 07-442)


title: Arabidopsis thaliana, Col, FH seed, H3K27me3 ChIP

description: Library name: H3K27me3_FH_Col

value: FH

value: a-H3K27me3 (Millipore, 07-449)


title: 105379-002-006

tag: disease

value: Non-demented control

tag: lesion type

value: CWM


title: 105379-001-104

value: Multiple sclerosis


title: contralateral-brain-tissue_NSC-treated_sham_rat3

description: tissue lysates

value: Sprague-Dawley

value: male

value: contralateral brain

value: NSC

value: sham


title: 105379-001-105

value: Brain

value: white matter

value: PLWM


title: P6_CompE_rep1

description: Library name: Sample 9

value: cochlea

tag: age

tag: cell type

value: supporting cells (SC)

value: Lfng-EGFP

value: Notch inhibition (CompE)


title: contralateral-brain-tissue_NSC-treated_sham_rat1

description: tissue lysates

tag: treatment


title: 105379-001-106

value: NAWM


title: P0_DMSO_rep4

description: Library name: Sample 8

tag: genotype

value: Control (DMSO)


title: synovial tissue_21days_treat3

value: Synovial tissue

tag: Sex

value: Male

value: 7-8 weeks

value: collagen-induced arthritis (CIA)

value: circular RNA


title: synovial tissue_21days_treat2

tag: tissue


title: P0_DMSO_rep3

description: Library name: Sample 7


title: contralateral-brain-tissue_NSC-treated_sham_rat2

description: tissue lysates

tag: strain

value: Sprague-Dawley

value: male

value: contralateral brain

tag: surgery


title: contralateral-brain-tissue_NSC-treated_CCI_rat5

description: tissue lysates

source_name: contralateral brain tissue, NSC treated,controlled cortical impact injury

value: NSC

value: CCI


title: 105379-001-103

value: Brain

value: white matter

value: Multiple sclerosis


title: synovial tissue_21days_treat1


title: P0_DMSO_rep2

description: Library name: Sample 6

value: cochlea

value: supporting cells (SC)

value: Lfng-EGFP

tag: batch


title: P0_DMSO_rep1

description: Library name: Sample 5

value: Control (DMSO)


title: 105379-001-102


title: 105379-001-101

value: PLWM


title: synovial tissue_21days_treat4

value: Synovial tissue

value: Male


title: synovial tissue_21days_control5

source_name: Synovial tissue, normal rats, 21days

value: 7-8 weeks

value: normal


title: P0_CompE_rep4

description: Library name: Sample 4

value: Notch inhibition (CompE)


title: contralateral-brain-tissue_NSC-treated_CCI_rat4

description: tissue lysates

value: Sprague-Dawley

value: male


title: contralateral-brain-tissue_NSC-treated_CCI_rat3

description: tissue lysates

value: contralateral brain

value: NSC


title: 105379-001-100

value: Brain


title: synovial tissue_21days_control3

value: circular RNA


title: contralateral-brain-tissue_NSC-treated_CCI_rat2

description: tissue lysates

value: CCI


title: synovial tissue_21days_control4


title: 105379-001-099

value: white matter

value: Multiple sclerosis


title: P0_CompE_rep2

description: Library name: Sample 2

value: cochlea

value: supporting cells (SC)

value: Lfng-EGFP


title: contralateral-brain-tissue_NSC-treated_CCI_rat1

description: tissue lysates


title: synovial tissue_21days_control2

value: Synovial tissue


title: heart of stone, zebrafish embryonic heart, mutant

city: Ulm

first: Deung-Dae

last: Park

address: Albert-Einstein-Allee 23

department: Internal Medicine II

institute: University Ulm

description: Active Motif ATAC-seq service

data_processing:
For comparative analysis, standard normalization is achieved by down-sampling the usable number of tags for each sample in a group to the level of the sample in the group with the fewest usable number of tags. This results in an equal number of tags within each group in the “Used number of tags” column.
Peaks were called using the MACS algorithm at a cutoff of p-value 1e-7, without control file, and with the -nomodel option. Peak filtering was performed by removing false peaks as defined within the ENCODE blacklist. FRIP (fraction of reads in peaks) values of 10% or higher indicate good data quality.
Peak calling algorithm: MACS 2.1.0
Assembly: danRer11
Supplementary files format and content: Tab-separated values files and matrix files (peaks, merged regions)

organism: Danio rerio

source_name: heart

extract_protocol:
60 hearts of hos mutants and siblings were dissected from hos/Tg(myl7:GFP), flash frozen and sent to Active Motif for ATACseq library preparation and sequencing
Libraries for ATAC-seq were prepared by Active Motif

value: heart

value: cardiomyocytes

value: mut

tag: time

value: 96 hours post fertilization


title: CAGE_L_00216.BC15,German_pinscher,Corpus_callosum_only

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_00216.BC15

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

organism: Canis lupus familiaris

source_name: corpus callosum

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: corpus callosum

tag: breed

value: German Pinscher

value: Female

tag: age (month)


title: P0_CompE_rep3

description: Library name: Sample 3

value: Notch inhibition (CompE)


title: CAGE_L_00216.BC13,Finnish_Lapphund,olfactory_bulb_only

description: Library name: CAGE_L_00216.BC13

source_name: olfactory bulb

value: olfactory bulb

value: Finnish Lapphund


title: P0_CompE_rep1

description: Library name: Sample 1


title: 105379-001-097

value: Brain


title: CAGE_L_00216.BC12,Finnish_Lapphund,Piriform_lobe_only

description: Library name: CAGE_L_00216.BC12

source_name: piriform lobe

value: piriform lobe


title: heart of stone, zebrafish embryonic heart, sibling

description: Active Motif ATAC-seq service

value: wt


title: CAGE_L_00216.BC10,Rottweiler,Skin_only

description: Library name: CAGE_L_00216.BC10

source_name: skin

value: skin

value: Rottweiler

value: Male


title: synovial tissue_21days_control1

value: Synovial tissue

value: 7-8 weeks

tag: sample group

value: normal

tag: molecule subtype

value: circular RNA


title: 105379-001-098

value: white matter

tag: sample code

value: Multiple sclerosis


title: 105379-001-096

tag: disease


title: 1 cell embryo CBR+SAM, rep2

city: Sendai

first: Yohei

last: Hayashi

state: Miyagi

address: 4-1 Seiryo-machi, Aobaku

department: Institute of Development, Aging and Cancer

institute: Tohoku University

description: Library name: sample6

data_processing:
Sequenced reads then were trimmed using fastp software.
For gene expression analysis, reads were mapped to the mouse genome (UCSC mm10 genome assembly and NCBI RefSeq database) using kallisto software with an estimated average fragment length of 50, followed by calculation of read counts and TPM (transcripts per million).
DESeq2 (Love et al., 2014) was employed to identify differentially expressed genes (DEGs), with statistical significance determined using the Wald test.
Functional enrichment analysis of DEGs was performed using the Metascape (https://metascape.org/gp/index.html#/main/step1) (Zhou et al, 2019).
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing TPM value for each sample.

source_name: embryo

extract_protocol:
cDNA was prepared using a SMART-Seq v4 Ultra-Low-Input RNA kit for Sequencing (Takara).
Each library was constructed using Nextera XT DNA library Prep Kit (Illumina)

value: embryo

value: WT

value: in vitro culture


title: OVX-AS-IV-High-2

city: jinzhong

first: xianying

last: yao

address: No. 121, Daxue Street, Yuci District, Jinzhong City, Shanxi Province,

department: The First Clinical College

institute: Shanxi University of Chinese Medicine

description:
Library name: OVX-AS-IV-High-2
PMOP+AS-IV 80 mg/kg

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mRatBN7.2  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes fpkm value and gene count for each sample

source_name: bone

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, tissue were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: bone

value: PMOP+AS-IV 80 mg/kg


title: 105379-001-095

source_name: white matter

value: Brain

tag: lesion type

value: PLWM


title: OVX-AS-IV-High-3

description:
Library name: OVX-AS-IV-High-3
PMOP+AS-IV 80 mg/kg


title: 1 cell embryo CBR, rep2

description: Library name: sample4


title: 1 cell embryo CBR, rep1

description: Library name: sample3


title: 105379-001-093


title: OVX-2

description:
Library name: OVX-2
PMOP+1% sodium carboxymethyl cellulose, CMC-Na


title: pl17

first: Luis

institute: University of Chicago

description: multiplexed 10X single-cell capture

data_processing:
Single-cell RNA-seq reads were mapped using the count function in cellranger (v6.0.2).
Assembly: GRCh38
Supplementary files format and content: .mtx files include count values for each multiplexed sample; .tsv files include the description of barcodes (cells) and features (genes)

source_name: multiplexed PBMCs

extract_protocol:
PBMCs were unfrozen, rested overnight, washed, and prepared for single-cell capture using the 10X workflow. Immediately prior to the capture, cells from different individuals were combined into pools.
Single-cell GEMs were generated using a Chromium Controller instrument (10x Genomics). Sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kits (v3.1 Dual Index chemistry, 10x Genomics) according to the manufacturer’s instructions.

value: multiplexed PBMCs

tag: cell line

value: primary immune cells

value: PBMCs


title: CAGE_L_00216.BC02,Swedish_Elkhound,olfactory_bulb_only

description: Library name: CAGE_L_00216.BC02

value: olfactory bulb

value: Swedish Elkhound

value: Female


title: OVX-AS-IV-High-1

description:
Library name: OVX-AS-IV-High-1
PMOP+AS-IV 80 mg/kg


title: 1 cell embryo CBR+SAM, rep1

description: Library name: sample5

tag: cell type


title: CAGE_L_00216.BC05,Swedish_Elkhound,Brain_stem_pool

description: Library name: CAGE_L_00216.BC05

source_name: substantia nigra,pons,medulla oblongata

value: substantia nigra,pons,medulla oblongata


title: 105379-001-094


title: Sham-3

description:
Library name: Sham-3
Removing the same amount of adipose tissue adjacent to the ovary+3% sodium carboxymethyl cellulose, CMC-Na

tag: treatment


title: OVX-3

description:
Library name: OVX-3
PMOP+1% sodium carboxymethyl cellulose, CMC-Na


title: CAGE_L_00216.BC08,German_pinscher,Spleen_only

description: Library name: CAGE_L_00216.BC08

source_name: spleen

value: spleen

value: German Pinscher


title: ADAR-ko, Input RNA, rep 3

city: Vienna

first: Alina

middle: F

last: Leuchtenberger

address: Dr. Bohr Gasse 9

department: Max Perutz Labs

country: Austria

institute: Medical University of Vienna and University of Vienna

description: Library name: Sample 18

data_processing:
Reads were preprocessed using Trim Galore (version 0.6.6) to trim Illumina adapters, remove low-quality ends (quality score below 20), and discard reads shorter than 20 bp. Processed reads were aligned using NextGenMap version 0.5.5. Genrich version 0.6.1 49 was used to call peaks for the "no MDA5, but RNase" and "MDA5 & RNase" libraries, using the corresponding "no MDA5 & no RNase" libraries as controls. Additionally, peaks were called for the "no MDA5 & no RNase" libraries. The peak calling parameters included a maximum adjusted p-value of 0.01, a minimum area under the curve (AUC) of 500, and a maximum gap of 20 bp between significant sites. Blacklisted regions from ENCODE (mm10_blacklist.bed, available at ENCODE Blacklist 50 and rRNA entries from RepeatMasker 51 were excluded from the analysis. For strand-specific peak detection, each chromosome's strands were treated as separate chromosomes.
Assembly: GRCm38
Supplementary files format and content: Peaks called with Genrich

source_name: Liver

extract_protocol:
Liver tissues from 8-9 days old WT and Adar1-/-/Mavs-/- mutant mice were extracted and weighed, with 100 mg used for total RNA isolation. Briefly, 1 mL of homemade TRIzol and 1.4 mm zirconium oxide beads were added to 100 mg of liver tissue in 2 mL screw cap tubes. The tissues were homogenized using a tissue homogenizer (MP Biomedicals). Following homogenization, 200 μL of chloroform was added and mixed well. Samples were centrifuged at 4°C, 15,000 rpm for 15 minutes to separate into layers. The aqueous layer was collected, and an equal volume of PCI (phenol:chloroform:isoamyl alcohol) was added, followed by another centrifugation at 4°C, 15,000 rpm for 10 minutes. The aqueous layer was again collected, and an equal volume of chloroform was added, followed by centrifugation at 4°C, 15,000 rpm for 10 minutes. To the final aqueous layer, 2x the volume of 96% ethanol and 1/10 volume of 3M sodium acetate (pH 5.3) were added. The tubes were kept at -20°C for a minimum of 2 hours or overnight for RNA precipitation. Afterwards, the samples were centrifuged at 4°C, 15,000 rpm for 15 minutes. The supernatant was discarded, and 1 mL of 70% ethanol was added to the tubes, which were centrifuged again under the same conditions. The supernatant was discarded, and the pellets were dried at 37°C for approximately 5 minutes. Finally, the pellets were resuspended in the desired volume of nuclease-free DEPC-treated ddH2O. The RNA samples were treated with DNase I (NEB) to remove genomic DNA contamination. For each sample, 10 μL of 10X DNase I Reaction Buffer, 15 μL DNase I (DNase-free), 1 μL RNase Inhibitor, and 74 μL nuclease-free ddH2O were added. The mixture was incubated at 37°C for 2 hours. After DNase I treatment, samples were extracted with 2x PCI, 1x chloroform, and 96% ethanol. RNA was quantified by Qubit fluorimetry (Thermo Fisher, Waltham, MA).
Total RNA isolated from the liver tissue of ADAR1 WT and ADAR1 deficient mice was kept at 70°C for 5 minutes and allowed to refold in a buffer containing 20 mM HEPES (pH 7.5), 50 mM NaCl, 2 mM MgCl₂ at room temperature for 15 minutes. The RNA was then incubated with recombinant purified MDA5Δ2CARD protein in a buffer containing 20 mM HEPES (pH 7.5), 50 mM NaCl, 2 mM MgCl₂, and 2 mM DTT. Next, 2 μg of total RNA from WT and ADAR1 deficient mice was incubated with increasing amounts of recombinant MDA5Δ2CARD protein (100 μM-400 μM) in the presence of 1 mM ATP at 25°C for 10 minutes. The samples were then treated with a 1:100 dilution of RNase A/T1 mix (Thermo Scientific) for 5 minutes to digest unbound RNAs. Untreated samples and samples treated with only RNA and RNase served as controls. RNase A/T1 digestion was quenched by adding five volumes of TRIzol reagent, and RNA was isolated using the 2x PCI, 1x CI, and 96% ethanol precipitation method. The samples were then loaded onto an 8M Urea PAGE (6% acrylamide) gel to check for protected RNA species. Protected RNA was purified using the RNAeasy Mini Kit (QIAGEN) to remove small digestion products. rRNA was depleted with the NEBNext rRNA Depletion Kit (E6310, E6350). Using the manufacturer's protocol, cDNA libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760, E7765). Libraries from control samples (no MDA5 and no RNase) and MDA5-protected samples from both WT and ADAR1 mutant groups were diluted to 0.5 nmol. For the final library pool, 2 µl of each library was used. Sequencing was performed on an Illumina NextSeq instrument with single-ended 75 bp reads.

value: Liver

tag: genotype

value: Adar-/-; Mavs-/-

tag: incubation with_mda5

value: no

tag: treatment with_rnase


title: CAGE_L_00216.BC03,Rottweiler,Brain_stem_pool

description: Library name: CAGE_L_00216.BC03

tag: tissue

value: Rottweiler

tag: Sex

value: Male


title: 1 cell embryo DMSO, rep2

description: Library name: sample2

value: embryo

value: WT

value: in vitro culture


title: CAGE_L_00215.BC12,German_pinscher,Skin_only

description: Library name: CAGE_L_00215.BC12

value: skin

tag: batch


title: ADAR-ko, MDA5-protected, rep 3

description: Library name: Sample 16

value: yes


title: Sham-1

description:
Library name: Sham-1
Removing the same amount of adipose tissue adjacent to the ovary+1% sodium carboxymethyl cellulose, CMC-Na

value: bone


title: 105379-001-092

value: Brain

value: white matter

value: Multiple sclerosis

value: PLWM


title: OVX-1

description:
Library name: OVX-1
PMOP+1% sodium carboxymethyl cellulose, CMC-Na


title: 1 cell embryo DMSO, rep1

description: Library name: sample1


title: CAGE_L_00215.BC13,German_pinscher,Heart_valve_pool

description: Library name: CAGE_L_00215.BC13

source_name: heart endocardium,heart valve

value: heart endocardium,heart valve

value: Female


title: CAGE_L_00215.BC15,Swedish_Elkhound,Piriform_lobe_only

description: Library name: CAGE_L_00215.BC15

value: piriform lobe

value: Swedish Elkhound


title: 105379-001-091


title: 105379-001-090


title: ADAR-ko, RNase only, rep 3

description: Library name: Sample 17

value: Liver

value: Adar-/-; Mavs-/-

value: no


title: ADAR-ko, Input RNA, rep 2

description: Library name: Sample 15


title: CAGE_L_00215.BC10,Rottweiler,Hippocampal_formation_only

description: Library name: CAGE_L_00215.BC10

source_name: hippocampal formation

value: hippocampal formation

value: Rottweiler

value: Male


title: 105379-001-087


title: ADAR-ko, RNase only, rep 2

description: Library name: Sample 14


title: Sham-2

description:
Library name: Sham-2
Removing the same amount of adipose tissue adjacent to the ovary+2% sodium carboxymethyl cellulose, CMC-Na


title: 105379-001-089


title: 105379-001-085


title: rat brain tissue, ICH_MA_4

city: Guiyang

first: Ke

last: Zhang

address: No.28, Guiyi Road, Liuguangmen

institute: Gui zhou Medical University

description: Library name: ICH_MA_4

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include genecount values for each Sample

source_name: Brain

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: basal ganglia cells

value: Mithramycin A treatment after ICH rep4


title: CAGE_L_00215.BC05,Border_Collie,Prostate_only

description: Library name: CAGE_L_00215.BC05

source_name: prostate gland

value: prostate gland

value: Border Collie


title: rat brain tissue, ICH_MA_5

description: Library name: ICH_MA_5

value: Brain

value: Mithramycin A treatment after ICH rep5


title: 105379-001-088

value: white matter

value: Multiple sclerosis

value: NAWM


title: 105379-001-086


title: ADAR-ko, Input RNA, rep 1

description: Library name: Sample 12


title: CAGE_L_00215.BC08,Finnish_Lapphund,Cerebellum_pool

description: Library name: CAGE_L_00215.BC08

source_name: cerebellum hemisphere,cerebellum vermis

value: cerebellum hemisphere,cerebellum vermis

value: Finnish Lapphund

value: Female


title: rat brain tissue, ICH_MA_2

description: Library name: ICH_MA_2

value: Mithramycin A treatment after ICH rep2


title: ADAR-ko, MDA5-protected, rep 2

description: Library name: Sample 13

value: Liver

value: Adar-/-; Mavs-/-

value: yes


title: rat brain tissue, ICH_MA_3

description: Library name: ICH_MA_3

value: Mithramycin A treatment after ICH rep3


title: CAGE_L_00215.BC03,Border_Collie,olfactory_bulb_only

description: Library name: CAGE_L_00215.BC03

value: olfactory bulb

value: Male


title: ADAR-ko, RNase only, rep 1

description: Library name: Sample 11

value: no


title: 105379-001-083


title: ADAR-ko, MDA5-protected, rep 1

description: Library name: Sample 10


title: 105379-001-082

value: Non-demented control

value: CWM


title: 105379-001-084

value: Brain

value: PLWM


title: rat brain tissue, ICH_4

description: Library name: ICH_4

value: basal ganglia cells

value: intracerebral hemorrhage rep4


title: 105379-001-080

value: white matter

value: Multiple sclerosis


title: CAGE_L_00214.BC12,Rottweiler,Testis_only

description: Library name: CAGE_L_00214.BC12

source_name: testis

value: testis

value: Rottweiler


title: CAGE_L_00214.BC10,Border_Collie,Stomach_fundus_only

description: Library name: CAGE_L_00214.BC10

source_name: stomach

value: stomach

value: Border Collie


title: wild-type, RNase only, rep 3

description: Library name: Sample 8

value: Liver

value: Mavs-/-

value: yes


title: CAGE_L_00215.BC02,Swedish_Elkhound,Stomach_fundus_only

description: Library name: CAGE_L_00215.BC02

value: Swedish Elkhound

value: Female


title: 105379-001-079


title: wild-type, Input RNA, rep 3

description: Library name: Sample 9

value: no


title: rat brain tissue, ICH_MA_1

description: Library name: ICH_MA_1

value: Mithramycin A treatment after ICH rep1


title: rat brain tissue, ICH_5

description: Library name: ICH_5

value: Brain

value: intracerebral hemorrhage rep5


title: 105379-001-081

value: Non-demented control

value: CWM


title: CAGE_L_00214.BC15,Rottweiler,Pancreas_left_lobe_only

description: Library name: CAGE_L_00214.BC15

source_name: pancreas

value: pancreas

value: Male


title: 105379-001-078

value: white matter

value: Multiple sclerosis


title: rat brain tissue, ICH_3

description: Library name: ICH_3

value: basal ganglia cells

value: intracerebral hemorrhage rep3


title: wild-type, RNase only, rep 2

description: Library name: Sample 5

value: Liver


title: wild-type, MDA5-protected, rep 3

description: Library name: Sample 7

value: Mavs-/-


title: CAGE_L_00214.BC08,Rottweiler,Skin_only

description: Library name: CAGE_L_00214.BC08

value: skin

value: Rottweiler


title: rat brain tissue, Sham_5

description: Library name: NC_5

value: sham operation rep5


title: rat brain tissue, ICH_2

description: Library name: ICH_2

value: intracerebral hemorrhage rep2


title: 105379-001-077

value: PLWM


title: rat brain tissue, Sham_4

description: Library name: NC_4

value: Brain

value: sham operation rep4


title: wild-type, Input RNA, rep 1

description: Library name: Sample 3

value: no


title: CAGE_L_00214.BC02,German_pinscher,Spinal_Cord_only

description: Library name: CAGE_L_00214.BC02

source_name: spinal cord

value: spinal cord

value: German Pinscher

value: Female


title: CAGE_L_00214.BC05,Finnish_Lapphund,Bone_marrow_only

description: Library name: CAGE_L_00214.BC05

source_name: bone marrow

value: bone marrow

value: Finnish Lapphund


title: 105379-001-076

value: white matter

value: Multiple sclerosis


title: wild-type, Input RNA, rep 2

description: Library name: Sample 6

value: Liver


title: CAGE_L_00213.BC13,Rottweiler,Adenohypophysis_only

description: Library name: CAGE_L_00213.BC13

source_name: adenohypophysis

value: adenohypophysis

value: Male


title: 105379-001-075


title: CAGE_L_00213.BC12,Border_Collie,Pancreas_left_lobe_only

description: Library name: CAGE_L_00213.BC12

value: pancreas

value: Border Collie


title: wild-type, MDA5-protected, rep 1

description: Library name: Sample 1

value: Mavs-/-

value: yes


title: wild-type, MDA5-protected, rep 2

description: Library name: Sample 4


title: rat brain tissue, Sham_2

description: Library name: NC_2

value: Brain

value: basal ganglia cells

value: sham operation rep2


title: rat brain tissue, ICH_1

description: Library name: ICH_1

value: intracerebral hemorrhage rep1


title: rat brain tissue, Sham_1

description: Library name: NC_1

value: sham operation rep1


title: 105379-001-074

value: Non-demented control

value: CWM


title: wild-type, RNase only, rep 1

description: Library name: Sample 2

value: no


title: CAGE_L_00213.BC15,Border_Collie,DRG_only

description: Library name: CAGE_L_00213.BC15

source_name: spinal ganglion

value: spinal ganglion


title: rat brain tissue, Sham_3

description: Library name: NC_3

value: sham operation rep3


title: 105379-001-073

source_name: white matter

value: white matter


title: 105379-001-072

value: Multiple sclerosis


title: H3K4me3_P1P6MLL_TKO_FGO_Rep1

city: Yokohama

first: Azusa

last: Inoue

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

department: Center for Integrative Medical Sciences

institute: RIKEN

description: Library name: Sample17

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

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

value: Pcgf1/6 & Mll2 triple knockout


title: H3K4me3_P1P6MLL_TKO_FGO_Rep2

description: Library name: Sample18


title: CAGE_L_00213.BC05,Swedish_Elkhound,Ovary_only

description: Library name: CAGE_L_00213.BC05

tag: breed

value: Swedish Elkhound

value: Female