title: Wild-boar-temporal-lobe

city: Wuhan

first: yi

last: huang

address: No.1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

library_source: other

data_processing:
We processed the original FASTQ files using cellranger-atac v2.0.0 with default parameters, aligning the data to the pig susScr11 reference genome, removing PCR duplicates, and identifying transposase cut sites. Reference genome (FASTA) and annotation (GTF) files were input into the “cellranger-atac mkref” command to create a reference package. Each sample library was processed separately using “cellranger-atac count,” and all samples were merged with “cellranger-atac aggr.” Mitochondrial-mapped reads were removed.
Assembly: susScr11
Supplementary files format and content: CellRanger-atac output files: barcodes.tsv, matrix.mtx, peaks.bed

molecule: other

organism: Sus scrofa

source_name: Temporal lobe

extract_protocol:
Following strict ethical guidelines, we dissected the cerebral cortex and cerebellum from one duroc pig and one wild boar. The cerebral cortex was further subdivided into the frontal, parietal, occipital, and temporal lobes. After dissection, the tissues were washed with cold phosphate-buffered saline (PBS), placed into cryovials, and immediately flash-frozen in liquid nitrogen to preserve their original state.
The scATAC-seq process was performed using the 10x Genomics single-cell ATAC reagent v1.1 kit, adhering strictly to the manufacturer’s instructions. Initially, the cell pellet was resuspended in 100 µL of lysis buffer, thoroughly mixed 10 times with a pipette, and incubated on ice for 3 minutes. Following this, 1 mL of wash buffer was added to the lysed cells, and the cell nuclei were centrifuged at 500×g for 5 minutes at 4 °C. The resulting nuclei pellet was then resuspended in 250 µL of 1x nuclei buffer. The cell nuclei were counted using Trypan blue to ensure accurate quantification. We utilized 10,000 to 15,000 resuspended cell nuclei for the transposition reaction, which were subsequently loaded into the 10x Genomics Chromium Single Cell system. The libraries were constructed and amplified through 10 cycles of PCR. Finally, the amplified libraries were sequenced on the Illumina NextSeq platform.

value: Temporal lobe


title: RENCA cells expressing empty vector, replicate 3

status: Public on May 12 2025

type: SRA

city: Nashville

first: w. Kimryn

middle: N.

last: Rathmell

state: TN

address: 1161 21st Avenue South

country: USA

institute: Vanderbilt University Medical Center

description: Library name: EVP_3

library_source: genomic

data_processing:
Nextera adaptor sequences were firstly trimmed form the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ≥ 13), non mitochondrial chromosome, and properly paired reads (longer than 18 nt).
All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel --keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
Assembly: mm10
Supplementary files format and content: BigWig (bw) files were generated using deepTools

molecule: genomic DNA

organism: Mus musculus

source_name: Kidney Tumor

growth_protocol: RENCA cells (ATCC CRL-2947) were grown in RPMI supplemented with 10% FBS, 1% penicillin/streptomycin, 1% l-glutamine, 1% HEPES, 1% sodium pyruvate, and 1% MEM amino acid.

extract_protocol:
ATAC-seq was performed as previously reported (Buenrostro et al. 2013;Corces et al. 2017; Bajic M et al. 2018). Briefly, nuclei was extracted from samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.

treatment_protocol: The following CRISPR guides were used for single-guide scaffold PX458. For NDUFA4L2: forward, CACCGAGATGGCAGGAACTAGTCTA; for reverse, aaacTAGACTAGTTCCTGCCATCTC. NDUFA4L2 KO clones were grown from single-cell colonies and screened for effective KO using qPCR. For re-expression, an NDUFA4L2 3rd-generation lentiviral expression vector were designed with a puromycin resistance cassette and purchased from Vectorbuilder Inc. Lentiviral supernatants were used immediately to infect target cells. 48-72hrs after transduction, cells were selected using 1.5ug/mL puromycin.

tag: tissue

value: Kidney Tumor

tag: cell line

value: RENCA

tag: cell type

value: Cancer Cell

tag: genotype

value: WT

tag: treatment

value: Empty Vector


title: Wild-boar-occipital-lobe

status: Public on May 11 2025

country: China

source_name: Occipital lobe

value: Occipital lobe


title: Wild-boar-parietal-lobe

source_name: Parietal lobe

value: Parietal lobe


title: Wild-boar-frontal-lobe-1

source_name: Frontal lobe

value: Frontal lobe


title: Wild-boar-frontal-lobe-2


title: Duroc-temporal-lobe


title: Wild-boar-cerebellum

source_name: Cerebellum

value: Cerebellum


title: RENCA cells expressing empty vector, replicate 1

description: Library name: EVP_1


title: Duroc-occipital-lobe


title: Duroc-frontal-lobe


title: Duroc-parietal-lobe


title: Duroc-cerebellum


title: supplemented with Wnt5a-overexpressing BMSC-Exos rep3

city: guangzhou

first: Dan

last: Luo

address: dade road Num.111

institute: The Second Affiliated Hospital of Guangzhou University of Chinese Medicine

description: Library name: wnt3

library_source: transcriptomic

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).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: GRCr8
Supplementary files format and content: tab-delimited text files include genecount values for each Sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat spinal cords

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: Rat spinal cords

value: Neural stem cells

tag: batch


title: supplemented with BMSC-Exos rep1

description: Library name: exo1

value: supplemented with BMSC-Exos rep1


title: supplemented with BMSC-Exos rep3

description: Library name: exo3

value: supplemented with BMSC-Exos rep3


title: supplemented with BMSC-Exos rep2

description: Library name: exo2

value: supplemented with BMSC-Exos rep2


title: cultured in differentiation medium rep3

description: Library name: con3

value: cultured in differentiation medium rep3


title: cultured in differentiation medium rep1

description: Library name: con1

value: cultured in differentiation medium rep1


title: supplemented with Wnt5a-overexpressing BMSC-Exos rep2

description: Library name: wnt2


title: cultured in differentiation medium rep2

description: Library name: con2

value: cultured in differentiation medium rep2


title: BiMOF3(Mg-ALN@Gel3)

first: Lei

last: Zhou

state: guangdong

address: 63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province

institute: The Third Affiliated Hospital of Guangzhou Medical University

description: Library name: BiMOF3

data_processing:
Clustering and sequencing (Novogene Experimental Department): The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Quality control: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Novel transcripts prediction The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed. (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Assembly: ensembl_97_rattus_norvegicus_rnor_6_0_toplevel
Supplementary files format and content: TXT files include FPKM values for each Sample

source_name: Femoral fracture middle end

extract_protocol:
RNA was hanvested using Rneasy mini plus kit (Qiagen). 1.3 μg oftotal RNA was used for the construction of sequencing libranes.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Femoral fracture middle end


title: BiMOF1(Mg-ALN@Gel1)

description: Library name: BiMOF1


title: ALN2(ALN+Gel2)

description: Library name: ALN2


title: ALN3(ALN+Gel3)

description: Library name: ALN3


title: r2_8_3

city: hangzhou

first: xiao

middle: chen

last: wen

address: desheng_road NO.298

institute: Zhejiang Academy of Agricultural Sciences

description: CDR3 gene complemented to mutant Magnaporthe grisea

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: ABySS_70bp_45k_152cov_v1（https://www.ncbi.nlm.nih.gov/genome/?term=txid523103[orgn]）
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Pyricularia grisea

source_name: mycelium

growth_protocol: SDA plates were prepared respectively. The fungi were inoculated on the medium and cultured for 10 days.

extract_protocol:
For extraction of total RNA, TRIzol Reagent (Invitrogen) was used per manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: sample type


title: pals-22rrf-3_mRNA_2

city: Tel Aviv

first: Hila

last: Gingold

address: 30 Haim Levanon Street

country: Israel

institute: Tel-Aviv University

description:
Library name: L16
kallisto_output_scaled_per_gene_pals22_WT_rrf-3.csv
297-3_S8_R1_merged

data_processing:
Adapter trimming - CutAdapt
Quality control - FastQC
Alignment - ShortStack (small RNA), Kallito (mRNA)
Feature counting - featureCounts
Differential expression - DESeq2
Downstream analysis - RNAlysis
Assembly: WS235/ce11
Supplementary files format and content: Raw count matrices (comma-separated values)

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: fed on E.coli OP-50 bacteria

extract_protocol:
TRIzol®
small RNA-seq and mRNA-seq; NEBNext® Small RNA Library Prep Set for Illumina®; NEBNext® Ultra II Directional RNA Library Prep Kit

value: Whole worm


title: Control3(Gel3)

description: Library name: Control3


title: Control2(Gel2)

description: Library name: Control2


title: pals-22rrf-3_mRNA_1

description:
Library name: L15
kallisto_output_scaled_per_gene_pals22_WT_rrf-3.csv
297-2_S7_R1_merged


title: r2_8_2

description: CDR2 gene complemented to mutant Magnaporthe grisea

treatment_protocol: SDA plates were prepared respectively. The fungi were inoculated on the medium and cultured for 10 days.


title: Control1(Gel1)

description: Library name: Control1


title: r2_8_1

description: CDR1 gene complemented to mutant Magnaporthe grisea


title: Shade , root, Root918, replication 3

city: Shanghai

first: Chuanwei

last: Yang

address: 2005 Songhu Road, Yangpu District

department: school of life sciences

institute: Fudan university

data_processing:
Raw sequence reads were initially processed by fastp for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filitered reads were then mapped to Tair10 using Hisat2
Differential gene expression analysis was done using R package DESeq2
Assembly: TAIR10
Supplementary files format and content: all_genes_expresson_TPM.csv

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Wild type Arabidopsis seedlings were cultured under white light for 5 days, then inoculated with Pseudomonas fluorescens and Root918 under white light for 4 days, and finally treated under white light and shade for 4 hours to extract RNA from shoot and root samples, respectively.

extract_protocol:
Total RNA was extracted from tissue samples, and the concentration and purity of the extracted RNA were detected by Nanodrop2000. The integrity of RNA was detected by agarose gel, and the RIN value was determined by Agilent 2100. Using magnetic beads with Oligo (dT) and ployA for A-T base pairing, mRNA can be isolated from total RNA for analysis of transcriptome information. Under the action of reverse transcriptase, six random primers were added to reverse synthesize a single strand of cDNA using mRNA as a template, followed by a two-strand synthesis to form a stable double-stranded structure. The structure of double-stranded cDNA is sticky end. Add End Repair Mix to repair it into a flat end, and then add an "A" base at the 3 'end to connect the Y-shaped connector.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: With 4 h shade (R/FR=0.65) treatment

value: root

value: Wild type

value: shade

tag: inoculation


title: supplemented with Wnt5a-overexpressing BMSC-Exos rep1

description: Library name: wnt1


title: Shade , root, Root918, replication 2


title: m2_8_3

description: The CDR1 gene of Magnaporthe grisea was knocked out and replenished by ATMT technology


title: BiMOF2(Mg-ALN@Gel2)

description: Library name: BiMOF2


title: Shade , root, P. fluorescens, replication 2

value: P. fluorescens


title: pals-22_mRNA_1

description:
Library name: L12
kallisto_output_scaled_per_gene_pals22_WT_rrf-3.csv
144-1_S1_R1_merged


title: m2_8_1

value: The CDR1 gene of Magnaporthe grisea was knocked out and replenished by ATMT technology


title: Shade , root, P. fluorescens, replication 3


title: Shade , root, mock, replication 3

value: mock


title: rrf-3_mRNA_3

description:
Library name: L11
kallisto_output_scaled_per_gene_pals22_WT_rrf-3.csv
rrf-3_S6_R1_merged


title: m2_8_2


title: Guy11_3

description: Original strain of Magnaporthe grisea

value: Original strain of Magnaporthe grisea


title: Shade , root, mock, replication 2


title: Shade , root, mock, replication 1


title: White light, root, Root918, replication 2

value: white light


title: White light, root, Root918, replication 3


title: ALN1(ALN+Gel1)

description: Library name: ALN1


title: pals-22_mRNA_3

description:
Library name: L14
kallisto_output_scaled_per_gene_pals22_WT_rrf-3.csv
144-3_S3_R1_merged


title: White light, root, Root918, replication 1


title: rrf-3_mRNA_1

description:
Library name: L9
kallisto_output_scaled_per_gene_pals22_WT_rrf-3.csv
rrf-1_S4_R1_merged


title: Guy11_1

description: Original strain of Magnaporthe grisea


title: White light, root, P. fluorescens, replication 3


title: Guy11_2

description: Original strain of Magnaporthe grisea


title: White light, root, P. fluorescens, replication 2


title: pals-22_mRNA_2

description:
Library name: L13
kallisto_output_scaled_per_gene_pals22_WT_rrf-3.csv
144-2_S2_R1_merged


title: White light, root, P. fluorescens, replication 1


title: WT_mRNA_2

description:
Library name: L8
kallisto_output_scaled_per_gene_pals22_WT_rrf-3.csv
N2-3_S10_R1_merged


title: WT_mRNA_1

description:
Library name: L7
kallisto_output_scaled_per_gene_pals22_WT_rrf-3.csv
N2-2_S9_R1_merged


title: Shade , root, Root918, replication 1


title: Shade , root, P. fluorescens, replication 1


title: Pancreatic tumor, C3-/-, rep4

city: Gainesville

first: Andrew

middle: R

last: Judge

state: FL

address: 1275 Center Drive, Biomedical Sciences Building RM J303

institute: University of Florida

data_processing:
Reference genome and gene model annotation files were downloaded  from genome website (NCBI/UCSC/Ensembl) directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.) Differential expression analysis of groups was performed using the DESeq2 R package (1.20.0).
Assembly: mm39
Supplementary files format and content: xls file includes log2 fold changes, readcounts, fpkm and padj values

source_name: Pancreatic tumor

extract_protocol:
RNA isolation was performed by homogenization of the pancreatic tumor in Trizol followed by extraction with chloroform and precipitation with isopropanol. Isolated RNA was sent to Novogene Co., LTD (Sacramento, CA) for quality assessment, cDNA library construction, and Illumina transcriptome sequencing aligned to the mouse genome (mm39).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: The pancreas of male mice were surgically exposed, and 2.5 x 10E5 murine KPC pancreatic cancer cells diluted in 50 μl of sterile PBS were orthotopically injected.

value: Pancreatic tumor

value: KPC pancreatic tumor-bearing


title: pals-22_sRNA_3

description:
Library name: L6
featureCounts_counts_pals-22_WT_sRNA.csv
BFF144-3_S6_R1_merged


title: White light, root, mock, replication 2


title: Pancreatic tumor, C3-/-, rep3


title: pals-22_sRNA_2

description:
Library name: L5
featureCounts_counts_pals-22_WT_sRNA.csv
BFF144-2_S5_R1_merged


title: CX3CR1-EGFP and NG2DsRed cells

city: Portland

first: Xiaorui

last: Shi

state: OR

address: 3181 SW Sam Jackson Park Road, NRC04

department: Oregon Hearing Research Center

institute: Oregon Health & Science University

description:
Library name: Sample 1
10x Gemonics

library_source: transcriptomic single cell

data_processing:
Bcl conversion and demultiplexing was performed using bcl2fastq version 2.20.0.422.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tympanic membrane

extract_protocol:
CX3CR1EGFP; NG2DsRed mice at P15 were used for scRNA-seq. Temporal bones were harvested from 10 mice (20 capsules) and placed in ice-cold RPMI medium. Eardrums were dissected and transferred to 1.5 mL microcentrifuge tubes containing 1 mL of RPMI medium supplemented with 1.5 mg/mL collagenase IV (Gibco, Cat# 17104019) and 1 mg/mL DNase I (Roche, Cat# 10104159001). Tissues were minced with sterile micro scissors and digested at 37°C for 30 minutes with gentle shaking (100 rpm Following digestion, the mixture was centrifuged at 300 × g for 5 minutes at 4°C. The pellet was further dissociated in TrypLE Express (Gibco, Cat# 12604013) at 37°C for 10 minutes, with pipette trituration every 5 minutes using a 1000 μL tip to generate a single-cell suspension. The suspension was passed through a 70 μm cell strainer (Falcon), washed once with PBS, and resuspended in 0.04% BSA in PBS with DAPI. Alive cells were sorted using FACS (Influx-Kirk) according to the presence or absence of EGFP and DsRed signal using a C57BL6 mouse as negative control. Purified cells were resupspended in 0.04% BSA in PBS.
Libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics), following the manufacturer’s protocol. Briefly, 4,860 cells (87% viability; estimated recovery: 2,859 cells) were resuspended in the master mix and loaded onto a Chromium chip along with gel beads and partitioning oil to generate gel bead-in-emulsions (GEMs).  Within each GEM, cells were lysed and poly-A RNA transcripts were reverse transcribed into cDNA. Each cDNA molecule incorporated an Illumina R1 primer sequence, a Unique Molecular Identifier (UMI), and a 10x barcode during this step. Barcoded cDNA was then pooled, purified using Silane DynaBeads, and amplified by PCR. Size selection of the amplified products was performed using SPRIselect reagent. Approximately 50 ng of cDNA was obtained after 14 cycles of amplification, and 29 ng was used for library construction. During this process, the Illumina R2 primer sequence, paired-end adapters (P5 and P7), and a sample index were added.

value: tympanic membrane

value: primary

value: Macrophages; pericytes

value: CX3CR1-EGFP; NG2DsRed


title: White light, root, mock, replication 3


title: rrf-3_mRNA_2

description:
Library name: L10
kallisto_output_scaled_per_gene_pals22_WT_rrf-3.csv
rrf-2_S5_R1_merged


title: M CRM 2 R2

type: RNA

city: SAN ANTONIO

first: Sijia

last: He

state: Texas

address: 7703 Floyd Curl Dr.

institute: uthealth sa

description: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen, Canada, Cat. #: 25700). NanoString multiplex gene expression analysis was performed using the Mouse Neuroinflammation Panel on the nCounter® Max machine Profiler (NanoString Technologies, USA).

hyb_protocol: Hybridization reactions were performed in a 65°C thermal cycler for at least 16 hours

scan_protocol: Scan were performed with the nCounter Max Analysis System.

data_processing: Data were analyzed using nSolver 4.0 software. Basic analysis included the default Normalization Parameters which consisted of Positive Control Normalization Parameters and CodeSet Content.  Both parameters included a geometric mean calculation that flags samples if their normalization factor is outside of the 0.3-3.0 range or 0.1-1.0 range, respectively.  All pairwise ratios were selected for the Fold Change Estimation. Advanced analysis included custom analysis including pathway scoring and probe descriptive modules.  Default settings were used except selecting genotype as the selected predictor and pathway score annotation. P-value adjustments (Benjamini Hochberg) and “use all probes” were selected under the section of differential profiling and cell type profiling.

label: biotin

source_name: Cerebrum

label_protocol: RNA sample were not labeled as the NanoString panel contains labeled probes.

growth_protocol: Mice were housed in groups of ≤5 mice/cage in a temperature and humidity-controlled environment under a 12-h light /12-h dark cycle.

extract_protocol: Tissues were harvested at about 7 month of age post cardiac perfusion, snap-frozen, and homogenized for total RNA extraction.

treatment_protocol: Tamoxifen was administered to induce cGAS deletion at 2 month of age.

tag: species

tag: Sex

value: Male

value: cGAS mKO/5xFAD


title: M CRM 2 R3


title: pals-22_sRNA_1

description:
Library name: L4
featureCounts_counts_pals-22_WT_sRNA.csv
BFF144-1_S4_R1_merged

value: Whole worm


title: Pancreatic tumor, C3-/-, rep2


title: White light, root, mock, replication 1

value: root


title: M CRM 2 R1


title: M CRM 1 R3

value: cGAS Loxp/5xFAD


title: Shade , shoot, Root918, replication 3

source_name: shoot

value: shoot

value: Wild type

value: shade


title: WT_sRNA_3

description:
Library name: L3
featureCounts_counts_pals-22_WT_sRNA.csv
N2-3_S3_R1_merged


title: WT_sRNA_2

description:
Library name: L2
featureCounts_counts_pals-22_WT_sRNA.csv
N2-2_S2_R1_merged


title: Pancreatic tumor, WT, rep3


title: Shade , shoot, Root918, replication 1


title: WT_sRNA_1

description:
Library name: L1
featureCounts_counts_pals-22_WT_sRNA.csv
N2-1_S1_R1_merged


title: Pancreatic tumor, WT, rep2


title: Shade , shoot, P. fluorescens, replication 3

value: P. fluorescens


title: HT1080-siQ61K+poly(dA:dT)-3

city: Guangzhou

first: Jia-Lu

last: Shan

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

description:
Library name: sample12
TPM

data_processing:
Raw paired-end reads were aligned to the reference hg19 genome and gene counts were quantified with Salmon (version 0.8.0) using default settings.
Assembly: hg19 genome
Supplementary files format and content: csv files include TPM for each sample

organism: Homo sapiens

source_name: fibrosarcoma

extract_protocol:
Total RNA was extracted from HT1080 cells and purified with EZ-press RNA Purification Kit (Cat#B0004D, EZBioscience) according to the manufacturer’s instructions.
Whole transcriptome RNA sequencing (RNA-seq) was carried out by Novogene with a total amount of 1 µg RNA per sample. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and sequenced on an Illumina Novaseq 6000 platform.

value: fibrosarcoma


title: M CRM 1 R1


title: F CRM 2 R3

value: Female


title: HT1080-siQ61K+poly(dA:dT)-2

description:
Library name: sample11
TPM


title: Shade , shoot, P. fluorescens, replication 2


title: Pancreatic tumor, WT, rep1

value: Pancreatic tumor


title: Shade , shoot, P. fluorescens, replication 1


title: F CRM 2 R2


title: HT1080-siQ61K+poly(dA:dT)-1

description:
Library name: sample10
TPM


title: HT1080-siQ61K-3

description:
Library name: sample9
TPM

value: DMSO


title: Muscle, Control, rep3

data_processing:
Reference genome and gene model annotation files were downloaded  from genome website (NCBI/UCSC/Ensembl) directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5.) Differential expression analysis of groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: xls file includes log2 fold changes, readcounts, fpkm and padj values

source_name: Tibialis anterior

extract_protocol:
RNA isolation was performed by homogenization of tibialis anterior muscles in Trizol followed by extraction with chloroform and precipitation with isopropanol. Isolated RNA was sent to Novogene Co., LTD (Sacramento, CA) for quality assessment, cDNA library construction, and Illumina transcriptome sequencing aligned to the mouse genome (mm10).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: Tamoxifen was injected intraperitoneally at a concentration of 80 mg/kg of tamoxifen diluted in 100 μL of corn oil on 4 consecutive days to FoxP1flSTOPx HSA-MCM mice to enable overexpression of skeletal muscle FoxP1 (FoxP1iSkmTg) and to FoxP1flSTOP (Control) mice.

value: Tibialis anterior

value: Tamoxifen


title: F CRM 2 R1


title: Shade , shoot, mock, replication 3

value: mock


title: Pancreatic tumor, C3-/-, rep1

value: KPC pancreatic tumor-bearing


title: Pancreatic tumor, WT, rep4


title: Shade , shoot, mock, replication 2


title: Shade , shoot, Root918, replication 2


title: HT1080-siQ61K-2

description:
Library name: sample8
TPM


title: F CRM 1 R2


title: M CRM 1 R2

value: Male


title: Muscle, Control, rep2


title: HT1080-siQ61K-1

description:
Library name: sample7
TPM


title: Shade , shoot, mock, replication 1


title: Muscle, Control, rep1


title: tgfb3

city: Birmingham

first: Adam

last: Croft

state: Please Select

address: Birmingham

country: United Kingdom

institute: University of Birmingham

data_processing:
Bowtie2, Samtools
Assembly: GRCh38
Supplementary files format and content: count matrix

source_name: synovial fibroblast

extract_protocol:
RNA extration
bulk RNAseq

value: synovial fibroblast

value: fibroblast

value: TGFb


title: White light, shoot, Root918, replication 3

value: white light


title: Muscle, Control, rep5


title: HT1080-siNC+poly(dA:dT)-3

description:
Library name: sample6
TPM


title: F CRM 1 R1

value: cGAS Loxp/5xFAD


title: tgfb2


title: Muscle, Control, rep4


title: White light, shoot, Root918, replication 2

value: shoot

value: Wild type


title: Muscle, FoxP1iSkmTg, rep5

value: FoxP1flSTOPx HSA-MerCreMer


title: HT1080-siNC+poly(dA:dT)-2

description:
Library name: sample5
TPM

value: fibrosarcoma


title: tgfb1


title: White light, shoot, Root918, replication 1


title: White light, shoot, P. fluorescens, replication 3

value: P. fluorescens


title: HT1080-siNC+poly(dA:dT)-1

description:
Library name: sample4
TPM


title: ctrl3


title: Muscle, FoxP1iSkmTg, rep3


title: ctrl2


title: F CRM 1 R3

value: Female


title: HT1080-siNC-2

description:
Library name: sample2
TPM

value: DMSO


title: White light, shoot, P. fluorescens, replication 2


title: Muscle, FoxP1iSkmTg, rep1

value: Tibialis anterior


title: ctrl1


title: Muscle, FoxP1iSkmTg, rep2

value: Tamoxifen


title: HT1080-siNC-1

description:
Library name: sample1
TPM


title: White light, shoot, P. fluorescens, replication 1


title: Muscle, KPC, FoxP1 skeletal muscle KO, 20:00/circadian time 38, rep2

description:
KM20_2
KPC_FP1_8pmvsSH_FP1_8pm_deg.xls
gene_fpkm.xls

data_processing:
Reference genome and gene model annotation files were downloaded  from genome website (NCBI/UCSC/Ensembl) directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5.) Differential expression analysis of groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm39
Supplementary files format and content: xls files include log2 fold changes, readcounts, fpkm and padj values
Supplementary files format and content: gene_fpkm file contains fpkm for all samples

extract_protocol:
RNA isolation was performed by homogenization of tibialis anterior muscles in Trizol followed by extraction with chloroform and precipitation with isopropanol. Isolated RNA was sent to Novogene Co., LTD (Sacramento, CA) for quality assessment, cDNA library construction, and Illumina transcriptome sequencing aligned to the mouse genome (mm39).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: The pancreas of 39- to 55-week-old male mice were surgically exposed, and 2.5 x 10E5 murine KPC pancreatic cancer cells diluted in 50 μl of sterile PBS (KPC group) or 50 μl of sterile PBS (Control group) were orthotopically injected.

value: Foxp1fl/fl; Acta1-cre

value: KPC tumor-bearing


title: Muscle, pooled input

data_processing:
ChIP DNA sequences generated by a standard Illumina ChIP-sequencing library were aligned to the mouse genome (mm10). Binding events were called and identified using MACS with the manufacturer default cutoff of P <1 × 10-7. De novo motifs were identified via HOMER.
Assembly: mm10
Supplementary files format and content: xlsx, merged peak regions is a table comparing peak region metrics between different samples.
Supplementary files format and content: BigWig

source_name: Gastrocnemius-plantaris complex

extract_protocol:
Isolated whole gastrocneumius-plantaris muscle complexes were sent to Active Motif (Carlsbad, CA) for ChIP-sequencing.
A ChIP reaction was carried out using 15 ug of skeletal muscle chromatin and anti-FoxP1 antibody (Millipore, ABE68, RRID:AB_10631734).

treatment_protocol: Cancer cachexia model: The pancreas of 12-week-old male C57BL/6J mice were surgically exposed, and 2.5 x 10E5 murine KPC pancreatic cancer cells diluted in 50 μl of sterile PBS (KPC group) or 50 μl of sterile PBS (Control group) were orthotopically injected.

value: Gastrocnemius-plantaris complex

tag: chip antibody

value: pooled


title: White light, shoot, mock, replication 3

value: mock


title: White light, shoot, mock, replication 2


title: 2519_9_Synovial Tissue_total RNA

description: 2519_9_T_total RNA

data_processing:
Cellranger (scRNAseq)
Assembly: scRNAseq: GRCh38

source_name: Synovial tissue

extract_protocol: 5' scRNAseq (10x genomics)

value: Synovial tissue


title: 2519_6_Synovial Tissue_total RNA

description: 2519_6_T_total RNA


title: Muscle, KPC, FoxP1 skeletal muscle KO, 20:00/circadian time 38, rep1

description:
KM20_1
KPC_FP1_8pmvsSH_FP1_8pm_deg.xls
gene_fpkm.xls


title: Muscle, FoxP1iSkmTg, rep4


title: Muscle, fasted, rep2

value: FOXP1 (Millipore, ABE68)

value: Non-tumor bearing and fasted


title: White light, shoot, mock, replication 1

value: shoot

value: white light


title: Muscle, KPC, FoxP1 skeletal muscle KO, 16:00/circadian time 34, rep1

description:
KM16_1
KPC_FP1_4pmvsSH_FP1_4pm_deg.xls
gene_fpkm.xls


title: HT1080-siNC-3

description:
Library name: sample3
TPM


title: 2519_10_Synovial Tissue_total RNA

description: 2519_10_T_total RNA


title: Muscle, KPC, FoxP1 skeletal muscle KO, 16:00/circadian time 34, rep2

description:
KM16_2
KPC_FP1_4pmvsSH_FP1_4pm_deg.xls
gene_fpkm.xls


title: MOCK-transduced 16DCRPC; Biological replicate 2

city: Vancouver

first: Yen-Yi

last: Lin

state: British Columbia

address: 2660 Oak St

country: Canada

institute: University of British Columbia

description:
Library name: V160_2
Column Name in 16D-CRPC_raw_counts.txt: V160_1

data_processing:
We map 2*100 bp reads using STAR 2.6.0a to the reference database built upon human genome sequences and gene annotations from Ensembl GRCh38 Release 90. Gene-level read counts were obtained using htseq-count 0.11.2 with the intersection-strict mode.
Assembly: GRCh38
Supplementary files format and content: tab-limited file includes raw read counts for each sample

source_name: Prostate

extract_protocol:
Total RNA was extracted with the Maxwell RSC SimplyRNA Cells kit (Promega).  QC was checked with the Agilent Tapestation high sensitivity RNA kit, and the Qubit high sensitivity RNA assay.
300ng of total RNA was used as input for MGIEasy rRNA Depletion Kit and the MGIEasy RNA Directional Library Prep Set (MGI) following manufacturer's instructions.  Library QC was checked with the Agilent Tapestation high sensitivity d1000 kit.  Single stranded circular libraries and DNA nanoballs were prepared following manufacturer's instructions prior to DNBSEQ-G50 sequencing (PE100).

value: Prostate


title: Muscle, KPC, rep2


title: Muscle, KPC, FoxP1 skeletal muscle KO, 12:00/circadian time 30, rep2

description:
KM12_2
KPC_FP1_12pmvsSH_FP1_12pm_deg.xls
gene_fpkm.xls


title: 2518_17_Synovial Fluid_protein

data_processing:
Cellranger (scRNAseq)
Assembly: scRNAseq: GRCh38
Library strategy: CITE-Seq

molecule: protein

source_name: Synovial Fluid

value: Synovial Fluid


title: MOCK-transduced 16DCRPC; Biological replicate 1

description:
Library name: V160_1
Column Name in 16D-CRPC_raw_counts.txt: V160_1


title: Muscle, sham/control, rep2

value: Non-tumor bearing


title: Muscle, KPC, FoxP1 skeletal muscle KO, 12:00/circadian time 30, rep1

description:
KM12_1
KPC_FP1_12pmvsSH_FP1_12pm_deg.xls
gene_fpkm.xls


title: Muscle, KPC, rep1


title: LASP1-OE-16DCRPC; Biological replicate 2

description:
Library name: 37854.4_2
Column Name in 16D-CRPC_raw_counts.txt: 37854.4_2


title: 2518_17_Synovial Fluid_total RNA

description: 2518_17_SF_total RNA


title: Muscle, sham/control, rep1


title: Muscle, KPC, FoxP1 skeletal muscle KO, 08:00/circadian time 26, rep2

description:
KM08_2
KPC_FP1_8amvsSH_FP1_8am_deg.xls
gene_fpkm.xls


title: 2518_17_Blood_protein

source_name: Peripheral blood

value: Peripheral blood


title: LASP1-OE-16DCRPC; Biological replicate 1

description:
Library name: 37854.4_1
Column Name in 16D-CRPC_raw_counts.txt: 37854.4_1


title: P18-Ex002-037

city: Suita

first: Hiroki

last: Ide

state: Osaka

address: 2-1 Yamadaoka

department: Engineering

country: Japan

institute: Osaka University

data_processing:
The adapter-sequences were trimmed off from Raw data (raw reads) of fastq format by flexbar 3.4.0.
The resulting reads were aligned to teh Ensemble mouse reference genome (GRCm38 ver.95) by hisat 2 2.1.0 with the default parameters.
StringTie (v1.3.5) was used for calculation of transcript per million(TPM) with a transcriptome reference obtained from Ensembl.
Numbers of reads assigned to genes are calculated by featureCounts v.1.6.4.
mm10
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: Spleen

extract_protocol:
Cells were collected in 0.2 mL microtubes containing 2.7 uL of hypotonic lysis buffer consisted of 0.2% (w/v) Triton X-100 (SIGMA) and RNase inhibitor (Thermofisher).
Cell-lysis solutions were processed to the construction of cDNA libraries according to the SMART-seq2 protocol with slight modification.

treatment_protocol: Splenocytes were isolated from OT-1 mice, treated wtih red blood cell lysis buffer, and the single-cell suspension was purified by a cell strainer.

tag: strain

value: Spleen

tag: cell population

value: Splenocyte

value: T cell

value: T-nothing-presenting APC interaction for 3h


title: Muscle, fasted, rep1


title: Muscle, KPC, FoxP1 skeletal muscle KO, 04:00/circadian time 22, rep2

description:
KM04_2
KPC_FP1_4amvsSH_FP1_4am_deg.xls
gene_fpkm.xls

value: Tibialis anterior

value: Foxp1fl/fl; Acta1-cre

value: KPC tumor-bearing


title: P18-Ex002-036


title: Muscle, KPC, FoxP1 skeletal muscle KO, 08:00/circadian time 26, rep1

description:
KM08_1
KPC_FP1_8amvsSH_FP1_8am_deg.xls
gene_fpkm.xls


title: 331R-2D; UNC6042 treatment; Biological replicate 1

description:
Library name: 331R-2D-UNC0642_1
Column Name in 331-2D_raw_counts.txt: 331R-2D-UNC0642_1

extract_protocol:
Total RNA was extracted with the Maxwell RSC SimplyRNA Cells kit (Promega).  QC was checked with the Agilent Tapestation high sensitivity RNA kit, and the Qubit high sensitivity RNA assay.
300ng of total RNA was used as input for polyA enrichment with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and the MGIEasy RNA Directional Library Prep Set (MGI) following manufacturer's instructions.  Library QC was checked with the Agilent Tapestation high sensitivity d1000 kit.  Single stranded circular libraries and DNA nanoballs were prepared following manufacturer's instructions prior to DNBSEQ-G50 sequencing (PE100).


title: 2518_17_Blood_total RNA

description: 2518_17_B_total RNA


title: 331R-2D; UNC6042 treatment; Biological replicate 2

description:
Library name: 331R-2D-UNC0642_2
Column Name in 331-2D_raw_counts.txt: 331R-2D-UNC0642_2


title: 2518_17_Synovial Tissue_total RNA

description: 2518_17_T_total RNA


title: 2518_14_Synovial Tissue_total RNA

description: 2518_14_T_total RNA


title: P18-Ex002-035


title: Muscle, KPC, FoxP1 skeletal muscle KO, 04:00/circadian time 22, rep1

description:
KM04_1
KPC_FP1_4amvsSH_FP1_4am_deg.xls
gene_fpkm.xls


title: 2518_14_Synovial Fluid_protein


title: Muscle, KPC, FoxP1 skeletal muscle KO, 00:00/circadian time 18, rep2

description:
KM00_2
KPC_FP1_midvsSH_FP1_mid_deg.xls
gene_fpkm.xls


title: 331R-2D; Biological replicate 1

description:
Library name: 331R-2D_1
Column Name in 331-2D_raw_counts.txt: 331R-2D_1


title: 2518_14_Synovial Fluid_total RNA

description: 2518_14_SF_total RNA


title: transcripts_2519_18

hyb_protocol: For gene detection, slides hybridized with probes from the predesigned Xenium Human Multi-Tissue and Cancer Gene Expression and hMulti_v1 design (chemistry v1: 10x Genomics), consisting of 377 genes was used

data_processing: Seurat (R)

source_name: synovial tissue

label_protocol: Slides were prepared, processed, imaged and underwent post-run staining according to Xenium (10X Genomics) protocols: “CG000580 Rev C”, “CG000582 Rev D”, “CG000584 Rev B” and “CG000613 Rev A”, according to manufacturer’s instructions.

extract_protocol: Xenium instructions

value: synovial tissue


title: 331R-2D; Biological replicate 2

description:
Library name: 331R-2D_2
Column Name in 331-2D_raw_counts.txt: 331R-2D_2


title: Muscle, KPC, FoxP1 skeletal muscle KO, 00:00/circadian time 18, rep1

description:
KM00_1
KPC_FP1_midvsSH_FP1_mid_deg.xls
gene_fpkm.xls


title: Muscle, sham/control, FoxP1 skeletal muscle KO, 20:00/circadian time 38, rep2

description:
SM20_2
KPC_FP1_8pmvsSH_FP1_8pm_deg.xls
gene_fpkm.xls


title: 2518_14_Blood_total RNA

description: 2518_14_B_total RNA


title: transcripts_2519_15


title: P18-Ex002-032


title: P18-Ex002-031


title: transcripts_2519_4


title: 2518_14_Blood_protein


title: 2519_08_Synovial Fluid_protein


title: Muscle, sham/control, FoxP1 skeletal muscle KO, 20:00/circadian time 38, rep1

description:
SM20_1
KPC_FP1_8pmvsSH_FP1_8pm_deg.xls
gene_fpkm.xls


title: P18-Ex002-030


title: transcripts_2518_40


title: Muscle, sham/control, FoxP1 skeletal muscle KO, 16:00/circadian time 34, rep2

description:
SM16_2
KPC_FP1_4pmvsSH_FP1_4pm_deg.xls
gene_fpkm.xls


title: P18-Ex002-029

value: T-OVA-presenting APC interaction for 3h


title: Muscle, sham/control, FoxP1 skeletal muscle KO, 16:00/circadian time 34, rep1

description:
SM16_1
KPC_FP1_4pmvsSH_FP1_4pm_deg.xls
gene_fpkm.xls


title: 2519_08_Blood_protein


title: transcripts_2518_36


title: P18-Ex002-034


title: transcripts_2518_28


title: 2519_08_Blood_total RNA

description: 2519_08_B_total RNA


title: 2519_08_Synovial Fluid_total RNA

description: 2519_08_SF_total RNA


title: P18-Ex002-028


title: P18-Ex002-027


title: Muscle, sham/control, FoxP1 skeletal muscle KO, 12:00/circadian time 30, rep1

description:
SM12_1
KPC_FP1_12pmvsSH_FP1_12pm_deg.xls
gene_fpkm.xls


title: 2519_08_Tissue_total RNA

description: 2519_08_T_total RNA

value: Synovial tissue


title: Muscle, sham/control, FoxP1 skeletal muscle KO, 12:00/circadian time 30, rep2

description:
SM12_2
KPC_FP1_12pmvsSH_FP1_12pm_deg.xls
gene_fpkm.xls


title: P18-Ex002-033


title: transcripts_2518_24


title: P18-Ex002-026


title: transcripts_2518_11


title: 2519_7_Synovial Fluid_protein


title: rab-3vsra-1pals-22_mRNA_3

description:
Library name: L44
kallisto_output_scaled_per_gene_pals22_WT_vsra-1.csv
BFF3443_S14_R1_001

value: Whole worm

value: vsra-1(tm1637); pals-22(pig26); otIs356 [rab-3p(prom1)::2xNLS::TagRFP]


title: Muscle, sham/control, FoxP1 skeletal muscle KO, 08:00/circadian time 26, rep1

description:
SM08_1
KPC_FP1_8amvsSH_FP1_8am_deg.xls
gene_fpkm.xls


title: 2519_7_Blood_protein


title: P18-Ex002-024


title: Muscle, sham/control, FoxP1 skeletal muscle KO, 04:00/circadian time 22, rep2

description:
SM04_2
KPC_FP1_4amvsSH_FP1_4am_deg.xls
gene_fpkm.xls


title: rab-3vsra-1pals-22_mRNA_2

description:
Library name: L43
kallisto_output_scaled_per_gene_pals22_WT_vsra-1.csv
BFF3442_S13_R1_001


title: 2519_7_Synovial Fluid_total RNA

description: 2519_7_SF_total RNA


title: Muscle, sham/control, FoxP1 skeletal muscle KO, 04:00/circadian time 22, rep1

description:
SM04_1
KPC_FP1_4amvsSH_FP1_4am_deg.xls
gene_fpkm.xls


title: rab-3vsra-1pals-22_mRNA_1

description:
Library name: L42
kallisto_output_scaled_per_gene_pals22_WT_vsra-1.csv
BFF3441_S12_R1_001


title: rab-3vsra-1_mRNA_4

description:
Library name: L41
kallisto_output_scaled_per_gene_pals22_WT_vsra-1.csv
BFF3434_S11_R1_001


title: Muscle, sham/control, FoxP1 skeletal muscle KO, 00:00/circadian time 18, rep2

description:
SM00_2
KPC_FP1_midvsSH_FP1_mid_deg.xls
gene_fpkm.xls


title: 2519_7_Blood_total RNA

description: 2519_7_B_total RNA


title: P18-Ex002-021


title: 2518_4_Tissue_total RNA

description: 2518_4_T_total RNA


title: P18-Ex002-022


title: rab-3vsra-1_mRNA_3

description:
Library name: L40
kallisto_output_scaled_per_gene_pals22_WT_vsra-1.csv
BFF3433_S10_R1_001


title: Muscle, sham/control, FoxP1 skeletal muscle KO, 00:00/circadian time 18, rep1

description:
SM00_1
KPC_FP1_midvsSH_FP1_mid_deg.xls
gene_fpkm.xls


title: P18-Ex002-020


title: Muscle, KPC, wild-type, 20:00/circadian time 38, rep2

description:
KW20_2
KPC_WT_8pmvsSH_WT_8pm_deg.xls
gene_fpkm.xls


title: 2519_5_Tissue_total RNA

description: 2519_5_T_total RNA


title: 2518_8_Synovial Fluid_protein


title: Muscle, sham/control, FoxP1 skeletal muscle KO, 08:00/circadian time 26, rep2

description:
SM08_2
KPC_FP1_8amvsSH_FP1_8am_deg.xls
gene_fpkm.xls


title: P18-Ex002-025


title: rab-3vsra-1_mRNA_2

description:
Library name: L39
kallisto_output_scaled_per_gene_pals22_WT_vsra-1.csv
BFF3432_S9_R1_001


title: P18-Ex002-019


title: 2518_8_Blood_protein


title: Muscle, KPC, wild-type, 20:00/circadian time 38, rep1

description:
KW20_1
KPC_WT_8pmvsSH_WT_8pm_deg.xls
gene_fpkm.xls


title: Muscle, KPC, wild-type, 16:00/circadian time 34, rep2

description:
KW16_2
KPC_WT_4pmvsSH_WT_4pm_deg.xls
gene_fpkm.xls


title: P18-Ex002-018


title: rab-3vsra-1_mRNA_1

description:
Library name: L38
kallisto_output_scaled_per_gene_pals22_WT_vsra-1.csv
BFF3431_S8_R1_001


title: rab-3pals-22_mRNA_3

description:
Library name: L37
kallisto_output_scaled_per_gene_pals22_WT_vsra-1.csv
BFF1513_S7_R1_001


title: 2518_8_Synovial Fluid_total RNA

description: 2518_8_SF_total RNA


title: P18-Ex002-017


title: Muscle, KPC, wild-type, 16:00/circadian time 34, rep1

description:
KW16_1
KPC_WT_4pmvsSH_WT_4pm_deg.xls
gene_fpkm.xls


title: 2518_8_Blood_total RNA

description: 2518_8_B_total RNA


title: rab-3pals-22_mRNA_2

description:
Library name: L36
kallisto_output_scaled_per_gene_pals22_WT_vsra-1.csv
BFF1512_S6_R1_001


title: P18-Ex002-023


title: P18-Ex002-016


title: Muscle, KPC, wild-type, 12:00/circadian time 30, rep2

description:
KW12_2
KPC_WT_12pmvsSH_WT_12pm_deg.xls
gene_fpkm.xls


title: rab-3pals-22_mRNA_1

description:
Library name: L35
kallisto_output_scaled_per_gene_pals22_WT_vsra-1.csv
BFF1511_S5_R1_001


title: P18-Ex002-015


title: 2518_8_Tissue_total RNA

description: 2518_8_T_total RNA


title: rab-3WT_mRNA_4

description:
Library name: L34
kallisto_output_scaled_per_gene_pals22_WT_vsra-1.csv
BFF304_S4_R1_001

value: otIs356 [rab-3p(prom1)::2xNLS::TagRFP]


title: 2518_11_Synovial Fluid_protein


title: P18-Ex002-014


title: Muscle, KPC, wild-type, 12:00/circadian time 30, rep1

description:
KW12_1
KPC_WT_12pmvsSH_WT_12pm_deg.xls
gene_fpkm.xls


title: rab-3WT_mRNA_3

description:
Library name: L33
kallisto_output_scaled_per_gene_pals22_WT_vsra-1.csv
BFF303_S3_R1_001


title: rab-3WT_mRNA_2

description:
Library name: L32
kallisto_output_scaled_per_gene_pals22_WT_vsra-1.csv
BFF302_S2_R1_001


title: 2518_11_Blood_protein


title: P18-Ex002-013


title: 2518_11_Synovial Fluid_total RNA

description: 2518_11_SF_total RNA


title: P18-Ex002-012


title: Muscle, KPC, wild-type, 08:00/circadian time 26, rep1

description:
KW08_1
KPC_WT_8amvsSH_WT_8am_deg.xls
gene_fpkm.xls


title: rab-3WT_mRNA_1

description:
Library name: L31
kallisto_output_scaled_per_gene_pals22_WT_vsra-1.csv
BFF301_S1_R1_001


title: Muscle, KPC, wild-type, 04:00/circadian time 22, rep2

description:
KW04_2
KPC_WT_4amvsSH_WT_4am_deg.xls
gene_fpkm.xls


title: Muscle, KPC, wild-type, 04:00/circadian time 22, rep1

description:
KW04_1
KPC_WT_4amvsSH_WT_4am_deg.xls
gene_fpkm.xls


title: 2518_11_Blood_total RNA

description: 2518_11_B_total RNA


title: P18-Ex002-010


title: rab-3vsra-1pals-22_sRNA_3

description:
Library name: L30
featureCounts_counts_pals22_WT_vsra-1_sRNA.csv
BFF3443_S14_L001_R1_001


title: P18-Ex002-011


title: rab-3vsra-1pals-22_sRNA_2

description:
Library name: L29
featureCounts_counts_pals22_WT_vsra-1_sRNA.csv
BFF3442_S13_L001_R1_001


title: Muscle, KPC, wild-type, 00:00/circadian time 18, rep2

description:
KW00_2
KPC_WT_midvsSH_WT_mid_deg.xls
gene_fpkm.xls


title: P18-Ex002-009


title: 2519_05_Synovial Fluid_protein


title: 2519_05_Blood_protein


title: Muscle, KPC, wild-type, 00:00/circadian time 18, rep1

description:
KW00_1
KPC_WT_midvsSH_WT_mid_deg.xls
gene_fpkm.xls


title: rab-3vsra-1pals-22_sRNA_1

description:
Library name: L28
featureCounts_counts_pals22_WT_vsra-1_sRNA.csv
BFF3441_S12_L001_R1_001


title: Muscle, sham/control, wild-type, 20:00/circadian time 38, rep2

description:
SW20_2
KPC_WT_8pmvsSH_WT_8pm_deg.xls
gene_fpkm.xls


title: LTL331; Biological replicate 2

description:
Library name: LTL331_2
Column Name in LTL331_H3K9me3_spikeadj_intervals.txt: 4_s2

data_processing:
1. Sequence Analysis: The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
2. Determination of Fragment Density: Since the 5´-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended _in silico_ (using Active Motif software) at their 3´- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp). To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be visualized in genome browsers (see Section V.). bigWig files also provide the peak metrics in the Active Motif analysis program described below.
3. “Peak Finding”: The generic term “Interval” is used to describe genomic regions with local enrichments in tag numbers. Intervals are defined by the chromosome number and a start and end coordinate. The two main peak callers used at Active Motif are MACS (Zhang _et al._, Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009). MACS is suitable to identify the binding sites of transcription factors that bind to discrete sites (often containing a consensus DNA sequence), while SICER is used to study proteins that bind to extended regions in the genome (such as histones or RNA polymerase II). Methylated sites or regions can be identified with both algorithms. Both methods look for significant enrichments in the ChIP/IP data file when compared to the Input data file (~ random background). Peaks can also be called by simple thresholding of the bigWIG files described in the previous paragraph.
Assembly: hg19
Supplementary files format and content: tab-limited file includes H3K9me3 enriched peaks in LTL331R

source_name: prostate

extract_protocol:
We completed the H3K9me3 ChIP reactions using 30 μg of human prostate tissue chromatin and 5 μl of antibody (Active Motif, cat # 39161). The ChIP reactions also contained a drosophila chromatin spike-in for normalization of the sequencing data.
The sequencing was done by Active Motif using the protocols described in ChIP-IT qPCR Analysis Kit version A1, catalog Nos 53029.

value: prostate


title: LTL331; Biological replicate 1

description:
Library name: LTL331_1
Column Name in LTL331_H3K9me3_spikeadj_intervals.txt: 3_s1


title: rab-3vsra-1_sRNA_4

description:
Library name: L27
featureCounts_counts_pals22_WT_vsra-1_sRNA.csv
BFF3434_S11_L001_R1_001

source_name: Whole worm


title: 2519_05_Synovial Fluid_total RNA

description: 2519_05_SF_total RNA

value: Synovial Fluid


title: Muscle, sham/control, wild-type, 20:00/circadian time 38, rep1

description:
SW20_1
KPC_WT_8pmvsSH_WT_8pm_deg.xls
gene_fpkm.xls

value: Non-tumor bearing


title: Muscle, KPC, wild-type, 08:00/circadian time 26, rep2

description:
KW08_2
KPC_WT_8amvsSH_WT_8am_deg.xls
gene_fpkm.xls


title: rab-3vsra-1_sRNA_3

description:
Library name: L26
featureCounts_counts_pals22_WT_vsra-1_sRNA.csv
BFF3433_S10_L001_R1_001


title: 2519_05_Blood_total RNA

description: 2519_05_B_total RNA

value: Peripheral blood


title: LTL331R; Biological replicate

description:
Library name: LTL331R_2
Column Name in LTL331_H3K9me3_spikeadj_intervals.txt: 2_s2_H3K9me3


title: Muscle, sham/control, wild-type, 16:00/circadian time 34, rep2

description:
SW16_2
KPC_WT_4pmvsSH_WT_4pm_deg.xls
gene_fpkm.xls


title: rab-3vsra-1_sRNA_2

description:
Library name: L25
featureCounts_counts_pals22_WT_vsra-1_sRNA.csv
BFF3432_S9_L001_R1_001


title: 2519_04_Synovial Fluid_protein


title: 2518_11_Tissue_total RNA

description: 2518_11_T_total RNA


title: Muscle, sham/control, wild-type, 16:00/circadian time 34, rep1

description:
SW16_1
KPC_WT_4pmvsSH_WT_4pm_deg.xls
gene_fpkm.xls


title: rab-3vsra-1_sRNA_1

description:
Library name: L24
featureCounts_counts_pals22_WT_vsra-1_sRNA.csv
BFF3431_S8_L001_R1_001


title: 2519_04_Blood_protein


title: Muscle, sham/control, wild-type, 12:00/circadian time 30, rep2

description:
SW12_2
KPC_WT_12pmvsSH_WT_12pm_deg.xls
gene_fpkm.xls


title: PA-SMCs treated with control siRNA [S9_254_NT]

city: CHATENAY MALABRY

first: Emy

last: Ponsardin

address: rue JB Clément

country: France

institute: Université Paris Saclay

description:
ribodepleted RNA
PA-SMCs treated with control siRNA

data_processing:
bcl2fastq2-2.18.12 (demultiplex)
Cutadapt 1.15 (adapter trimming)
FastQC v0.11.5 (quality control)
Rsubread v2.8.1 align
Rsubread v2.8.1 featureCounts
edgeR v3.36.0 TMM (normalization)
limma 3.50.0 (linearization)
Assembly: GRCh38
Supplementary files format and content: normalized counts

source_name: pulmonary artery

growth_protocol: small pieces of freshly micro-dissected pulmonary arteries were cultured in Dulbecco modified Eagle medium supplemented

extract_protocol:
Trizol
TruSeq Stranded Total RNA library prep kit (Illumina)

treatment_protocol: 15% fetal calf serum (FCS), 2 mM L-glutamine, and antibiotics (100 unit/ml penicillin and 100 mg/ml streptomycin). The isolated pulmonary PA-SMCs were strongly positive for a-smooth muscle actin, smooth muscle–specific SM22 protein, and calponin, and negative for von Willebrand factor and CD31

value: pulmonary artery

value: Primary cultures

value: pulmonary artery smooth muscle cells (PA-SMCs)

value: NT


title: rab-3pals-22_sRNA_3

description:
Library name: L23
featureCounts_counts_pals22_WT_vsra-1_sRNA.csv
BFF1513_S7_L001_R1_001

data_processing:
Adapter trimming - CutAdapt
Quality control - FastQC
Alignment - ShortStack (small RNA), Kallito (mRNA)
Feature counting - featureCounts
Differential expression - DESeq2
Downstream analysis - RNAlysis
Assembly: WS235/ce11
Supplementary files format and content: Raw count matrices (comma-separated values)

extract_protocol:
TRIzol®
small RNA-seq and mRNA-seq; NEBNext® Small RNA Library Prep Set for Illumina®; NEBNext® Ultra II Directional RNA Library Prep Kit


title: PA-SMCs treated with Mineralocorticoid Receptor siRNA [S10_254_MR]

description:
ribodepleted RNA
PA-SMCs treated with Mineralocorticoid Receptor siRNA

value: Mineralocorticoid Receptor


title: Muscle, sham/control, wild-type, 12:00/circadian time 30, rep1

description:
SW12_1
KPC_WT_12pmvsSH_WT_12pm_deg.xls
gene_fpkm.xls

value: Tibialis anterior


title: rab-3pals-22_sRNA_2

description:
Library name: L22
featureCounts_counts_pals22_WT_vsra-1_sRNA.csv
BFF1512_S6_L001_R1_001


title: PA-SMCs treated with control siRNA [S7_248_NT]


title: rab-3pals-22_sRNA_1

description:
Library name: L21
featureCounts_counts_pals22_WT_vsra-1_sRNA.csv
BFF1511_S5_L001_R1_001


title: Muscle, sham/control, wild-type, 08:00/circadian time 26, rep2

description:
SW08_2
KPC_WT_8amvsSH_WT_8am_deg.xls
gene_fpkm.xls


title: PA-SMCs treated with Mineralocorticoid Receptor siRNA [S8_248_MR]


title: 2519_01_Synovial Fluid_protein


title: Muscle, sham/control, wild-type, 08:00/circadian time 26, rep1

description:
SW08_1
KPC_WT_8amvsSH_WT_8am_deg.xls
gene_fpkm.xls


title: PA-SMCs treated with control siRNA [S3_229_NT]


title: rab-3WT_sRNA_4

description:
Library name: L20
featureCounts_counts_pals22_WT_vsra-1_sRNA.csv
BFF304_S4_L001_R1_001


title: 2519_01_Synovial Fluid_total RNA

description: 2519_01_SF_total RNA


title: 2519_01_Blood_protein


title: rab-3WT_sRNA_3

description:
Library name: L19
featureCounts_counts_pals22_WT_vsra-1_sRNA.csv
BFF303_S3_L001_R1_001


title: Muscle, sham/control, wild-type, 04:00/circadian time 22, rep1

description:
SW04_1
KPC_WT_4amvsSH_WT_4am_deg.xls
gene_fpkm.xls


title: rab-3WT_sRNA_2

description:
Library name: L18
featureCounts_counts_pals22_WT_vsra-1_sRNA.csv
BFF302_S2_L001_R1_001


title: PA-SMCs treated with Mineralocorticoid Receptor siRNA [S4_229_MR]


title: LTL331R; Biological replicate 1

description:
Library name: LTL331R_1
Column Name in LTL331_H3K9me3_spikeadj_intervals.txt: 1_s1_H3K9me3


title: Muscle, sham/control, wild-type, 00:00/circadian time 18, rep2

description:
SW00_2
KPC_WT_midvsSH_WT_mid_deg.xls
gene_fpkm.xls


title: 2519_01_Blood_total RNA

description: 2519_01_B_total RNA


title: PA-SMCs treated with control siRNA [S1_227_NT]


title: 2519_04_Synovial Fluid_total RNA

description: 2518_04_SF_total RNA


title: iPSCs (SSCW)

type: other

city: Kyoto

first: Yoshiki

last: Nakashima

state: Kyoto

address: Kyoto Research Park KISTIC Building Room 501, 5th floor, KISTIC building,  134 Chudoji Minami-cho, Shimogyo-ku

department: Research and Development Center

institute: Kyoto University Center for iPS Cell Research and Application Foundation (CiRA Foundation)

description: total DNA and RNA

hyb_protocol: Arrays were washed and stained using a GeneChip Fluidics Station 450 (Thermo Fisher Scientific) and scanned using a GeneChip Scanner 3000 7G (Thermo Fisher Scientific).

scan_protocol: Scanned data files were generated using the GeneChip Command Console software program and analyzed using the Chromosome Analysis Suite v4.3 (ChAS), considering 1-2 MB for gains/losses and 5 MB for LOH(heterozygosity)/AOH(absence of heterozygosity).

data_processing: We used the KaryoStat™ assay service provided by Life Technologies Corporation (Carlsbad, CA, USA) [Regen Med 14, 505-524 (2019)]. We used the PluriTest™ analysis service from Life Technologies Corporation (Carlsbad, CA, USA)[Regen Med 14, 505-524 (2019)]. This assay assesses 36,000 transcripts and variants against a reference set of >450 samples for gene expression analysis.   The transcriptomes of all samples were analyzed and processed in the PluriTest™ algorithm to generate pluripotency and novelty scores. The pluripotency score is based on many samples (pluripotent, somatic, and tissue) in the stem cell model matrix, which consists of an extensive reference set of >450 cell/tissue types, including 223 hESC lines (Stem Cell Matrix-2’ (SCM2) database)[Nat Methods 8, 315-317 (2011)] lines, 41 iPSC lines, somatic cells, and tissues.

source_name: iPSCs (CFiS-S01)

label_protocol: gDNA was processed according to the manufacturer's protocol. Briefly, 250 ng of gDNA was digested with the restriction enzyme NspI. The digested DNA was then ligated to the NspI adapter and amplified by PCR. The PCR products were purified and fragmented with DNase I. The fragmented products were end-labeled with biotin and hybridized overnight to KaryoStat arrays (Thermo Fisher Scientific) in a GeneChip Hybridization Oven 645 (Thermo Fisher Scientific).

growth_protocol: iMatrix-511 was added to the SSCW® cell culture dish at a concentration of 1.38 μL/ml in StemFitAK03 medium (Ajinomoto) while the plate was maintained at 37°C.

extract_protocol: RNA purification with this system involves cell preparation using a PureLink™ RNA Mini Kit (Catalog #12183025;(Thermo Fisher Scientific, Waltham, MA, USA) and quantification using the NanoDrop™2 (Thermo Fisher Scientific, Waltham, MA, USA). The GeneChip® for the PluriTest™ is prepared using 100 ng of total RNA. Genomic DNA (gDNA) was prepared using the Genomic DNA Purification Kit (Catalog K 0512;(Qiagen, Hilden, Germany) and quantified using the Qubit™ dsDNA BR Assay Kit (Catalog Q 32850GeneChip® Preparation;(Thermo Fisher Scientific, Waltham, MA, USA). A total of 250 ng of gDNA was used to prepare the GeneChip® for KaryoStat™ according to the instructions, which is an array that looks for copy number variants and single nucleotide polymorphisms across the genome.

treatment_protocol: When the temperature was lowered to 25°C after 7-day seeding period, the iPSCs became cell sheet-like and detached significantly from the plate.

value: iPSCs


title: rab-3WT_sRNA_1

description:
Library name: L17
featureCounts_counts_pals22_WT_vsra-1_sRNA.csv
BFF301_S1_L001_R1_001


title: PA-SMCs treated with Mineralocorticoid Receptor siRNA [S2_227_MR]


title: 2519_04_Blood_total RNA

description: 2518_04_B_total RNA


title: Muscle, sham/control, wild-type, 00:00/circadian time 18, rep1

description:
SW00_1
KPC_WT_midvsSH_WT_mid_deg.xls
gene_fpkm.xls


title: CUT&Run (NFYA) of sorted pachytene/diplotene  cells from adult testis,replicate 2

status: Public on May 10 2025

city: Stockholm

first: Masomeh

last: Askari

address: Svante Arrhenius väg 20C

country: Sweden

institute: Stockholm University

description: Library name: CUT_RUN_PD_NFYA_rep2

data_processing:
Adapter sequences were trimmed and low-quality reads were removed from the raw paired-end CUT&RUN reads using Fastp (v0.24.0; {Chen et al., 2018, #251424}). Reads were then aligned to the mouse reference genome (mm10) using Bowtie2 (v2.5.4; {Langmead and Salzberg, 2012, #21255}) with parameters —local —very-sensitive —no-unal —no-mixed —no-discordant -|10 -X700. Subsequently, SAM files were converted to BAM format using SAMtools (v1.20; {Danecek et al., 2021, #260227}), and alignments whose quality is less than 20 were removed. BAM files were then sorted and indexed, and multiple aligning read pairs were removed. Thereafter, duplicate reads were removed using MarkDuplicates function from picard-tools (v.3.3.0; {Toolkit, 2019, #210533}). Bigwig files were generated using bamCoverage function from deepTools (v3.3.2; {Ramírez et al., 2016, #143661}) and normalized to reads per million (RPM).
Assembly: mm10
Supplementary files format and content: Bigwig normalized by RPM
Library strategy: CUT&Run

source_name: Testis

extract_protocol:
FACS purified spermatogonia (SpG), leptotene & zygotene (L/Z), and pachytene & diplotene (P/D) cells.
CUT&RUN libraries were prepared using the Active Motif kit according to the manufacturer's protocol.

value: Testis

value: WT


title: CUT&Run (NFYA) of sorted Spermatogonia cells from adult testis, replicate 2

description: Library name: CUT_RUN_SPG_NFYA_rep2


title: CUT&Run (NFYA) of sorted Spermatogonia cells from adult testis, replicate 3

description: Library name: CUT_RUN_SPG_NFYA_rep3


title: CUT&Run (NFYA) of sorted Spermatogonia cells from adult testis, replicate 1

description: Library name: CUT_RUN_SPG_NFYA_rep1


title: CUT&Run (NFYA) of sorted pachytene/diplotene  cells from adult testis,replicate 3

description: Library name: CUT_RUN_PD_NFYA_rep3


title: CUT&Run (NFYA) of sorted pachytene/diplotene  cells from adult testis,replicate 1

description: Library name: CUT_RUN_PD_NFYA_rep1


title: CUT&Run (NFYA) of sorted leptotene/zygotene  cells from adult testis,replicate 2

description: Library name: CUT_RUN_NFYA_Lep_Zyg_rep2.bw


title: Muscle, sham/control, wild-type, 04:00/circadian time 22, rep2

description:
SW04_2
KPC_WT_4amvsSH_WT_4am_deg.xls
gene_fpkm.xls


title: CUT&Run (NFYA) of sorted leptotene/zygotene  cells from adult testis,replicate 1

description: Library name: CUT_RUN_NFYA_Lep_Zyg_rep1.bw


title: CUT&Run (NFYA) of sorted leptotene/zygotene  cells from adult testis,replicate 3

description: Library name: CUT_RUN_NFYA_Lep_Zyg_rep3.bw


title: CUT&Run (IgG) of sorted Spermatogonia cells from adult testis

description: Library name: CUT_RUN_IgG_SPG


title: CUT&Run (IgG) of sorted leptotene/zygotene  cells from adult testis

description: Library name: CUT_RUN_IgG_Lep_Zyg


title: CUT&Run (IgG) of sorted pachytene/diplotene cells from adult testis

description: Library name: CUT_RUN_IgG_PD


title: CUT&Run(H3K4me3) of sorted pachytene/diplotene cells from adult testis

description: Library name: CUT_RUN_H3K4me3_PD


title: FGC_E18.5_0531

city: Beijing

first: Jiansen

last: Lu

address: No. 5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

institute: Peking University

data_processing:
*library strategy: scNanoHi-C2
The detailed scNanoHi-C2 data analysis pipeline was referenced from scNanoHi-C with some modification. Specifically, we modified Pore-C-Snakemake pipeline (https://github.com/nanoporetech/Pore-C-Snakemake/) to align demultiplexed reads from each single cell to mm10 using minimap2 (v2.26-r1175) with the following parameters: "minimap2 -ax map-ont -r 500,500 -N 0". Here, "-ax map-ont" denotes the optimized alignment parameters for Nanopore sequencing data, "-r 500,500" is used to force split chimeric alignments into independent supplementary alignments, and "-N 0" is applied to remove secondary alignments. Subsequently, samtools (v1.15.1) was used to remove alignments with alignment scores less than 0 and to re-tag all supplementary alignments as primary alignments with the command “samtools view -h -e '[AS]>0' --remove-flags 2048 -”; the resulted bam files were further reformatted with pore_c software package with “pore_c alignments reformat-bam - -”, then sorted and indexed by samtools. The heterozygous single nucleotide polymorphism (SNP) sites between C57BL/6J and DBA/2N using for haplotype tags were derived from the Mouse Genome Project (MGP v5) at https://www.sanger.ac.uk/data/mouse-genomes-project/.
Assembly: mm10 or GRCh38
Supplementary files format and content: .parquet: filtered pair-wise contacts file of scNanoHi-C2 single cells with metadata
Supplementary files format and content: .mcool scNanoHi-C2 pair-wise multi-resolution cooler contacts matrcies

source_name: embryonic stage germ cells

extract_protocol:
Eight- to ten-week-old wild-type female DBA/2N mice in natural estrus were mated with male C57BL/6J (Oct4-EGFP) transgenic mice. When female mice with evident vaginal plug around noon, the day was set as E0.5. Oct4 positive FGCs were isolated from E11.5, E13.5, E14.5, E15.5, E16.5, E17.5 and E18.5 fetal gonads by FACS. At E13.5-E18.5, male and female gonads could be distinguished from morphology which based on whether the testicular cords were presence or not, and gonads cells were collected with male or female respectively. Whole gonads at different stages were digested using the 0.25% trypsin-EDTA for 30 min at 37 °C, and then added 0.25% BSA to stop digestion. Gonads cells were centrifuged at 2,000×g.
A total amount of 0.5μg to 2 μg  DNA per library was used as input material for the DNA library preparations. SQK-LSK109 Kit (Nanopore, UK) was used to construct 1D library. The DNA library was constructed by standard ligation method without DNA fragmentation, after end repaired, added the sequencing adaptor, motor protein and tether protein were connected to prepare the DNA library. After that, each amplicon fragment library was loaded into one R9.4.1 or R10.4.1 flow cell and sequenced on PromethION 48 model.

value: embryonic stage germ cells

tag: Stage

value: female

tag: strain background

value: male C57BL/6J x female DBA/2N


title: FGC_E17.5m_0420

value: male


title: FGC_E18.5m_0601


title: ATAC-seq of sorted leptotene/zygotene cells from adult testis, replicate 2

description: Library name: ATAC_Seq_Lep_Zyg_rep2

data_processing:
Adapter sequences and low-quality reads were removed from the raw ATAC-seq reads using Fastp (v. 0.24.0; {Chen et al., 2018, #251424}). Subsequently, reads were aligned to the mouse reference genome (mm10) using Bowtie2 (v2.5.4; {Langmead and Salzberg, 2012, #21255}) with the parameters —very-sensitive —no —unal —no-mixed —no-discordant. Multiple aligning read pairs were removed using SAMtools (v1.20; {Danecek et al., 2021, #260227}). We then identified and removed duplicate reads using MarkDuplicates function from picard-tools (v.3.3.0; {Toolkit, 2019, #210533}). BAM alignments were then converted to bigwig format using deepTools (v.3.3.2; {Ramírez et al., 2016, #143661}) and normalized to reads per million mapped reads (RPM) accounting for differences in sequencing depth. ATAC-seq peaks were called in each biological replicates from spermatogonia (SpG), leptotene/zygotene (L/Z), and pachytene/diplotene (P/D) using MACS3 (v3.0.2; {Zhang et al., 2008, #38962}; FDR < 0.01).
Assembly: mm10
Supplementary files format and content: Bigwig normalized by RPM

extract_protocol:
FACS purified spermatogonia (SpG), leptotene & zygotene (L/Z), and pachytene & diplotene (P/D) cells.
ATAC-seq libraries were prepared using the Active Motif kit according to the manufacturer's protocol.


title: ATAC-seq of sorted spermatogonia cells from adult testis, replicate 3

description: Library name: ATAC_Seq_SPG_rep3


title: ATAC-seq of sorted spermatogonia cells from adult testis, replicate 2

description: Library name: ATAC_Seq_SPG_rep2


title: ATAC-seq of sorted leptotene/zygotene cells from adult testis, replicate 3

description: Library name: ATAC_Seq_Lep_Zyg_rep3


title: ATAC-seq of sorted spermatogonia cells from adult testis, replicate 1

description: Library name: ATAC_Seq_SPG_rep1


title: FGC_E17.5_0513


title: FGC_E18.5_0707


title: ATAC-seq of sorted pachytene/diplotene cells from adult testis, replicate 1

description: Library name: ATAC_Seq_PD_rep1


title: ATAC-seq of sorted pachytene/diplotene cells from adult testis, replicate 3

description: Library name: ATAC_Seq_PD_rep3


title: FGC_E16.5_0413


title: ATAC-seq of sorted leptotene/zygotene cells from adult testis, replicate 1

description: Library name: ATAC_Seq_Lep_Zyg_rep1


title: FGC_E15.5m_0331


title: FGC_E15.5_0304


title: FGC_E17.5_0409


title: FGC_E15.5_0420


title: FGC_E14.5m_0603


title: FGC_E14.5m_0331


title: FGC_E14.5_0227


title: ATAC-seq of sorted pachytene/diplotene cells from adult testis, replicate 2

description: Library name: ATAC_Seq_PD_rep2


title: FGC_E13.5_0227


title: FGC_E13.5m_0331


title: FGC_E15.5_0513


title: FGC_E11.5_0706


title: FGC_E11.5_0513


title: FGC_E16.5_0304


title: K562 scNanoHi-C2

description:
Library name: K562
scNanoHi-C2

data_processing:
The detailed scNanoHi-C2 data analysis pipeline was referenced from scNanoHi-C with some modification. Specifically, we modified Pore-C-Snakemake pipeline (https://github.com/nanoporetech/Pore-C-Snakemake/) to align demultiplexed reads from each single cell to mm10 using minimap2 (v2.26-r1175) with the following parameters: "minimap2 -ax map-ont -r 500,500 -N 0". Here, "-ax map-ont" denotes the optimized alignment parameters for Nanopore sequencing data, "-r 500,500" is used to force split chimeric alignments into independent supplementary alignments, and "-N 0" is applied to remove secondary alignments. Subsequently, samtools (v1.15.1) was used to remove alignments with alignment scores less than 0 and to re-tag all supplementary alignments as primary alignments with the command “samtools view -h -e '[AS]>0' --remove-flags 2048 -”; the resulted bam files were further reformatted with pore_c software package with “pore_c alignments reformat-bam - -”, then sorted and indexed by samtools. The heterozygous single nucleotide polymorphism (SNP) sites between C57BL/6J and DBA/2N using for haplotype tags were derived from the Mouse Genome Project (MGP v5) at https://www.sanger.ac.uk/data/mouse-genomes-project/.
Assembly: mm10 or GRCh38
Supplementary files format and content: .parquet: filtered pair-wise contacts file of scNanoHi-C2 single cells with metadata
Supplementary files format and content: .mcool scNanoHi-C2 pair-wise multi-resolution cooler contacts matrcies
Library strategy: scNanoHi-C2

extract_protocol:
Eight- to ten-week-old wild-type female DBA/2N mice in natural estrus were mated with male C57BL/6J (Oct4-EGFP) transgenic mice. When female mice with evident vaginal plug around noon, the day was set as E0.5. Oct4 positive EGCs were isolated from E11.5, E13.5, E14.5, E15.5, E16.5, E17.5 and E18.5 embryonic gonads by FACS. At E13.5-E18.5, male and female gonads could be distinguished from morphology which based on whether the testicular cords were presence or not, and gonads cells were collected with male or female respectively. Whole gonads at different stages were digested using the 0.25% trypsin-EDTA for 30 min at 37 °C, and then added 0.25% BSA to stop digestion. Gonads cells were centrifuged at 2,000×g.
A total amount of 0.5μg to 2 μg  DNA per library was used as input material for the DNA library preparations. SQK-LSK109 Kit (Nanopore, UK) was used to construct 1D library. The DNA library was constructed by standard ligation method without DNA fragmentation, after end repaired, added the sequencing adaptor, motor protein and tether protein were connected to prepare the DNA library. After that, each amplicon fragment library was loaded into one R9.4.1 or R10.4.1 flow cell and sequenced on PromethION 48 model.

value: chronic myelogenous leukemia


title: FGC_E16.5m_0331


title: GM12878

tag: biomaterial provider


title: GM12878_rep2

description:
Library name: GM12878_rep2
scNanoHi-C2

value: lymphoblast cell


title: GM12878_rep3

description:
Library name: GM12878_rep3
scNanoHi-C2


title: ZH11-Mi-ATAC-2

city: wuhan

first: zhu

last: bo

state: beijing

address: shi zi shan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

description: Library name: ZH11-Mi-ATAC-2

data_processing:
RNA-seq raw reads were filtered by fastp (v.0.23.4) to remove low quality reads and adapter. Clean reads were aligned to the MSU7.0 rice reference genome (Rice Genome Annotation Project, http://rice.plantbiology.msu.edu/) by hisat2 (v.2.1.0). FeatureCounts (v.2.0.1) were used for quantitative analysis and the differentially expressed genes were calculated by DESeq2. For the single-cell RNA seq data of hybrid (SY63), fastp (v.0.23.4) was used to remove duplicate and low-quality reads, and then clean reads were matched with the reference genomes of parents ZS97 and MH63 (ZS97RS3 and MH63RS3, Rice Information GateWay [RIGW], http://rice.hzau.edu.cn/rice_rs3/) using hisat2 (v.2.1.0). Further use PP2PG65 software to isolate parental reads through SNPs of ZS97 and MH63.
Fastp (v.0.23.4) was used to remove low-quality reads and adapter from the CUT&Tag raw data. Clean reads were mapped to the MSU7.0 genome by Bowtie2 (v.2.4.1). SAMtools (v.1.20)  is used to convert between SAM and BAM formats, sort and deduplicate BAM files, and merge two biological replicates. MACS2 (v.2.2.7.1) was used to call histone modification peaks with the parameters (-f BAMPE -g 3.8e8 --broad -q 0.01 for H3K27me3, H3K36me3 and H3K9me2; -f BAMPE -g 3.8e8 -q 0.01 for H3K4me3), and H3 sample was used as control. The bigwig files were generated using bamCoverage with the parameters (-bam -binSize 10 –normalize Using BPM) in deepTools (v.2.5.3), which were visualized in the Integrated Genome Browser, draw heatmaps and metaplots.
BS-seq low-quality reads were filtered out from the raw data by TrimGalore (v.0.6.6; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Clean reads were mapped to the MSU7.0 rice genome. Bismark (v.0.23.1) was used to match, deduplicate and extract methylation sites. To obtain more loci for analysis, we combined the two biological replicates. Duplicates were removed and uniquely mapped reads were retained and each cytosine covered by at least five reads for further analysis. Density plots show the frequency distribution of DNA methylation differences between 50-bp window of two samples with at least 20 informative sequenced cytosines in both samples and 70% CG, 30% CHG, or 10% CHH methylation in either of the samples as previously described.
Assembly: MSU7.0
Supplementary files format and content: bigwig file
Supplementary files format and content: RNA-seq normalized counts file

organism: Oryza sativa Japonica Group

source_name: Earl stage microspore

growth_protocol: For field cultivation, the plants were grown in Wuhan during summer seasons under standard agricultural practices. Seedlings were transplanted to the field in early May and harvested in October. For greenhouse experiments, germinated rice seedlings were planted in soil-filled containers and grown under controlled conditions with a 14-h light/10-h dark cycle at 32°C (light) and 26°C (dark). Tillers of rice plants at an appropriate developmental stage were harvested for collection of spikelets. The collected spikelets were used for phenotypic analysis and isolation of male germ cells.

extract_protocol:
For collection of tetrads and microspores, when tillers flag leaf collar and penultimate leaf collar aligned spikelets of 0.4-0.6 cm length were taken. Like extracting meiocytes, anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with tetrad shapes were collected as tetrads. Cells with single, free-floating state and have not formed cell walls were collected as microspores.For collection of mature unicellular microspores, when tillers flag leaf auricle was about 5 cm above the auricle of the penultimate leaf, fresh spikelets > 0.6 cm were collected. At this stage the color of the spikelets is still white. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with distinct germination pores and having formed cell walls are collected as unicellular microspores.For collection of bicellular microspores, spikelets turning greener in color were taken. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with distinct large vacuoles, two nuclei, and thickened pollen walls are collected as bicellular microspores.For collection of mature pollen, tillers green spikelets were taken. At this point, the anthers have developed into yellow color. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. The cells that are distinctly filled with starch are collected as pollen.A differential centrifugation isolation method was used to separate sperm from whole rice anthers.
Isolation and purification of mRNA from different types of cells were performed using the Single Cell Full Length mRNA Amplification Kit (Vazyme, Cat. # N712). The RNA-seq libraries were prepared using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat. # TD502) and sequenced on Illumina HiSeq 6000. For rice in SY63 backgrounds, we used single male germ cell to construct the transcriptome library. We used approximately 100-200 male germ cells to construct the transcriptome library.BS-seq libraries were constructed using reported protocol Clark et al (2017). About 400–500 male germ cells were pooled for each replicate bisulfite seq library construction.The CUT&Tag libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, Cat. # TD903) and sequenced on Illumina HiSeq 6000. We used approximately 10,000 male germ cells to construct the CUT&Tag library by male germ cell isolation technology. The male germ cells were lysed with 200 µL Nuclear extraction buffer 2 (NEB2) (0.25 M sucrose, 10 mM Tris-HCl pH 8.0, 10 mM MgCl2, 1% Triton X-100, 1× protease inhibitor), and the nuclei pellet was resuspended in 100 µL wash buffer (from the TD903 kit) for library construction. About 100,000 sperm cells were pooled for each replicate CUT&Tag library construction. About 100,000–200,000 seedling cell nuclei were pooled for each replicate CUT&Tag library construction.For ATAC-seq library construction, the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, Cat. # TD711) was used to prepare libraries for different types of cells. Using the same number of cells as for CUT&Tag, we isolated approximately 10,000 male germ cells to construct the ATAC-seq library. Approximately 100,000 sperm cells and 100,000–200,000 seedling cell nuclei were pooled for each replicate ATAC-seq library construction.

value: Earl stage microspore


title: ZH11-Sp-ATAC-2

description: Library name: ZH11-Sp-ATAC-2

source_name: Sperm

value: Sperm


title: ZH11-UM-ATAC-1

description: Library name: ZH11-UM-ATAC-1

source_name: Unicellular microspore

value: Unicellular microspore


title: ZH11-Sp-ATAC-1

description: Library name: ZH11-Sp-ATAC-1


title: ZH11-Me-ATAC-1

description: Library name: ZH11-Me-ATAC-1

source_name: Meiocyte

value: Meiocyte


title: BS-ZH11-UM-2.

description: Library name: BS-ZH11-UM-2


title: ZH11-BM-ATAC-1

description: Library name: ZH11-BM-ATAC-1

source_name: Bicellular microspore

value: Bicellular microspore


title: FGC_E14.5_0513


title: ZH11-UM-ATAC-2

description: Library name: ZH11-UM-ATAC-2


title: BS-ZH11-UM-1.

description: Library name: BS-ZH11-UM-1


title: BS-ZH11-Mi-2

description: Library name: BS-ZH11-Mi-2


title: FGC_E13.5m_0601


title: FGC_E13.5_0513


title: BS-ZH11-Mi-1

description: Library name: BS-ZH11-Mi-1


title: BS-ZH11-Sp-1

description: Library name: BS-ZH11-Sp-1


title: BS-ZH11-Me-2

description: Library name: BS-ZH11-Me-2


title: ZH11-Me-ATAC-2

description: Library name: ZH11-Me-ATAC-2


title: BS-ZH11-Sp-2

description: Library name: BS-ZH11-Sp-2


title: BS-ZH11-Me-1

description: Library name: BS-ZH11-Me-1


title: Huh7 cells, shPPIL1#1

city: Tianjin

first: 佳仪

last: 吴

address: No.94 Weijin Road

institute: Nankai University

description:
Library name: Sample2
Column name in raw_counts.txt:sh1

data_processing:
After library preparation and pooling of different samples, the samples were subjected for NGS platform by Berry Genomics Co., Ltd
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

growth_protocol: Huh7 cells were maintained in DMEM suppleented with 10% fetal bovine serum and antibiotics inhumidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library

value: Hepatocellular carcinoma cells

value: PPIL1 knockdown


title: ZH11-Mi-ATAC-1

description: Library name: ZH11-Mi-ATAC-1


title: ZH11-BM-ATAC-2

description: Library name: ZH11-BM-ATAC-2


title: sdg725-Mi-H3K36me3-2

description: Library name: sdg725-Mi-H3K36me3-2

data_processing:
RNA-seq raw reads were filtered by fastp (v.0.23.4) to remove low quality reads and adapter. Clean reads were aligned to the MSU7.0 rice reference genome (Rice Genome Annotation Project, http://rice.plantbiology.msu.edu/) by hisat2 (v.2.1.0). FeatureCounts (v.2.0.1) were used for quantitative analysis and the differentially expressed genes were calculated by DESeq2. For the single-cell RNA seq data of hybrid (SY63), fastp (v.0.23.4) was used to remove duplicate and low-quality reads, and then clean reads were matched with the reference genomes of parents ZS97 and MH63 (ZS97RS3 and MH63RS3, Rice Information GateWay [RIGW], http://rice.hzau.edu.cn/rice_rs3/) using hisat2 (v.2.1.0). Further use PP2PG65 software to isolate parental reads through SNPs of ZS97 and MH63.
Fastp (v.0.23.4) was used to remove low-quality reads and adapter from the CUT&Tag raw data. Clean reads were mapped to the MSU7.0 genome by Bowtie2 (v.2.4.1). SAMtools (v.1.20)  is used to convert between SAM and BAM formats, sort and deduplicate BAM files, and merge two biological replicates. MACS2 (v.2.2.7.1) was used to call histone modification peaks with the parameters (-f BAMPE -g 3.8e8 --broad -q 0.01 for H3K27me3, H3K36me3 and H3K9me2; -f BAMPE -g 3.8e8 -q 0.01 for H3K4me3), and H3 sample was used as control. The bigwig files were generated using bamCoverage with the parameters (-bam -binSize 10 –normalize Using BPM) in deepTools (v.2.5.3), which were visualized in the Integrated Genome Browser, draw heatmaps and metaplots.
BS-seq low-quality reads were filtered out from the raw data by TrimGalore (v.0.6.6; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Clean reads were mapped to the MSU7.0 rice genome. Bismark (v.0.23.1) was used to match, deduplicate and extract methylation sites. To obtain more loci for analysis, we combined the two biological replicates. Duplicates were removed and uniquely mapped reads were retained and each cytosine covered by at least five reads for further analysis. Density plots show the frequency distribution of DNA methylation differences between 50-bp window of two samples with at least 20 informative sequenced cytosines in both samples and 70% CG, 30% CHG, or 10% CHH methylation in either of the samples as previously described.
Assembly: MSU7.0
Supplementary files format and content: bigwig file
Supplementary files format and content: RNA-seq normalized counts file
Library strategy: CUT&Tag


title: EYE treated with 75% oxygen Postnatal day13(P13), VLDLR deletion

city: shantou

first: xiaoqiang

last: xiao

state: Guangdong

address: North dongxia road

institute: Joint Shantou International Eye Center,Shantou University and the Chinese University of Hong Kong

description: No

data_processing:
raw reads quality control by Q30,Q20 and GC Content analysis, filtered the adaptor -polluted reads and low quality reads
The filtered reads then were further mapped to the rRNAs database with SOAP2 (Li R, 2009) to eradicate the rRNA pollution. rRNA-free clean reads were then mapped to reference genome with BWA –MEM software
Using de novo circRNA prediction softeware CITI, basing on Back-spliced junctions, identified circRNA candidates
DEseq2 software was used to screen differentially expressed circRNAs.
CIRI-AS software was used for the identification of alternative splicing events and exon position of circRNAs.
Supplementary files format and content: CIRI identified circular RNA reads
Supplementary files format and content: text files include circular Back splice reads  and SRPBM values for each Sample

organism: Mus

source_name: Ocular tissue

extract_protocol:
new birth mice (postnatal day 7,P7 treated with 75% oxygen for five days P12,then placed into air feed, Ocular tissues were then taken at P12(immediately after put back into the air) and P13.Total RNAs were extracted from the tissues and send to company for high-throughput circular RNA sequencing
Total RNA was removed the rRNA,and linear RNA ,the resultant was then fragmented and used to sequencing
The modified cDNAs fragments with length ranging from 150 bp to 200 bp were used for library construction.  Following cluster generation, the paired-end sequencing was conducted on an Illumina Hiseq 4000 platform.

value: Ocular tissue

value: VLDLR deletion

value: 75percent high oyxgen treatment through postnatal day 7 to postnatal day 12


title: sdg725-Mi-H3K36me3-1

description: Library name: sdg725-Mi-H3K36me3-1


title: sdg723-Mi-H3K4me3-1

description: Library name: sdg723-Mi-H3K4me3-1

value: mutant


title: sdg723-Mi-H3K4me3-2

description: Library name: sdg723-Mi-H3K4me3-2


title: EYE treated with 75% oxygen Postnatal day12(P12), VLDLR deletion

description: No

growth_protocol: new birth mice (postnatal day 7,P7 treated with 75% oxygen for five days P12,then placed into air feed


title: EYE treated with 75% oxygen Postnatal day13(P13), Wild type

description: No

treatment_protocol: new birth mice (postnatal day 7,P7 treated with 75% oxygen for five days P12,then placed into air feed

value: Wild type


title: sdg708-Mi-H3K36me3-2

description: Library name: sdg708-Mi-H3K36me3-2


title: sdg708-Mi-H3K36me3-1

description: Library name: sdg708-Mi-H3K36me3-1