title: C_Gingival tissue, microgrooves combined with CGF

city: 济南

first: 之涵

last: 崔

address: 山东省济南市文化西路四十四号山东大学趵突泉校区

institute: 山东大学

description: Library name: SAMPLES C

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Ensembl-v107
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Canis lupus familiaris

source_name: gingival tissue

growth_protocol: Firstly, a beagle tooth loss model is constructed, followed by grouping and implanting implants. Grouping: Smooth neck ring implant, Micro groove neck ring implant, Micro groove neck ring combined with CGF implant.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). 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 (NEB, cat.m0280, USA) 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 NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: After one month of implantation, euthanize the beagle dogs and perform transcriptome analysis by ring cutting each group of gingiva.

value: gingival tissue

tag: implant type

value: microgrooves combined with CGF


title: DSP-1001660002557-B-G07_AH2G7CDSX7

status: Public on Mar 01 2026

type: SRA

city: Boston

first: Fangyuan

last: Chen

state: MA

address: 450 Brookline Avenue

country: USA

institute: Dana-Farber Cancer Institute

description: Library name: DSP-1001660002557-B-G07_AH2G7CDSX7

library_source: transcriptomic

data_processing:
The raw data were quantile normalized for epithelial sections (ER-Hi, ER-Lo, ER-Neg) and stromal segments (Stroma) separately.
Assembly: hg38
Supplementary files format and content: Data is distributed as raw files (DCC), pkc file provided
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer

extract_protocol: Following NanoString Digital Spatial Profiler protocol ((v1.0) Human NGS Whole Transcriptome Atlas)

tag: tissue

value: breast cancer

tag: sample group

value: ER-Lo


title: a sample of liver constituent cells from the endothelial cell-specific CTGF KO mouse after pIVCL

city: Suita

first: Seiya

last: Kato

state: Osaka

address: 2-2, Yamadaoka

department: Gastroenterology and Hepatology

country: Japan

institute: Osaka University

description:
Library name: WT
BD Rhapsody

library_source: transcriptomic single cell

data_processing:
To generate a fastq file for each sample, raw sequence reads were demultiplexed using splitBarcode v2.0.0 (MGI Tech). Primary quality control was performed in the Seven Bridge pipeline using FASTQ files and mouse genome annotation files (GRCm39).
Assembly: GRCm39
Supplementary files format and content: comma-separated values files containing cell barcodes and Gene Expression Counts

organism: Mus musculus

source_name: liver

extract_protocol:
After liver perfusion with pronase (#107433; Sigma‒Aldrich) and collagenase (#C5138; Sigma‒Aldrich), hepatocytes were removed via low-speed centrifugation (50 × g), and dead cells and erythrocytes were removed via density gradient centrifugation using Percoll PLUS (GE17-5445-02; Cytiva). The percentage of viable cells in the cell suspension was greater than 70%, and approximately 10,000 viable cells were used for library preparation.
For the construction of the scRNA-seq library, a cDNA Kit and Whole Transcriptome Analysis (WTA) Amplification Kit (Becton Dickinson and Co., Franklin Lakes, NJ) were used according to the manufacturer’s instructions. Rhapsody WTA libraries were sequenced on the DNBSEQ-G400RS platform (MGI Tech).

treatment_protocol: The endothelial cell-specific CTGF KO male mouse and  the control WT littermate were subjected to partial inferior vena cava ligation (pIVCL) (Simonetto DA, et al. Hepatology. 2015; 61:648-659).

value: liver

tag: cell type

value: liver constituent cells

tag: genotype

value: Ctgffl/fl

tag: treatment

value: pIVCL

tag: batch


title: ATAC-seq_Ws82_ZT24_1

city: Beijing

first: Hao

last: Tian

address: 105 West Third Ring Road North, Haidian District, Beijing,

country: China

institute: Capital normal university

library_source: genomic

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC and aligned to the glycine max v2.1 reference genome using Bowtie2, and sorted and indexed using samtool.
Model based analysis of ChIP-seq (MACS) used for peak calling.Or got the bigwig file afted downsample and merge.
Assembly: Ws82v2.1
Supplementary files format and content: narrowpeak and bigwig

molecule: genomic DNA

organism: Glycine max

source_name: first tri-foliate leaf

growth_protocol: Wild-type (WT) soybean (Glycine max (L.) Mer. Willimas82 (Ws82)) seedlings were grown under SD conditions (8 h light / 16 h dark) for about 18 days with temperature cycles of 24 °C (light) / 22 °C (dark), until the first tri-foliate leaf open.

extract_protocol:
Approximately 0.5 g of soybean mature leaves were used in each experiment. About 1 to 2g of the sample was ground into a fine powder in liquid nitrogen.
For ATAC-seq, 50 k Isolated soybean nuclei were prepared for chromatin digestion by Tn5 transposase (VAHTS; cat. no. TD501) for 30 min at 37 °C. Digested chromatin was purified using a 2xCTAB followed by PCR amplification, product purification (vazyme, N411) and paired- end sequencing (2 ×150 bp) using an Illumina Hiseq X-Ten.

treatment_protocol: On the nineteenth day, the plants were transferred into LL (constant light, 25°C). After one day under LL, first tri-foliate leaf were sampled every 4 h for 20 h starting at ZT0 on the 21th day for RNA-seq, ATAC-seq and ChIP-seq under free-running conditions. 3 biological replicates were obtained for each time point.

value: first tri-foliate leaf

tag: cultivar

value: free-running


title: pIVCL 1

description:
Library name: pIVCL 1
BD Rhapsody

source_name: sample 1 of liver constituent cells from a wild-type male mouse at 2 weeks after pIVCL

treatment_protocol: Nine-week-old wild-type male mice were subjected to partial inferior vena cava ligation (pIVCL) or sham surgery (Simonetto DA, et al. Hepatology. 2015; 61:648-659).

value: wild


title: DSP-1001660002557-B-G06_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-G06_AH2G7CDSX7

value: ER-Hi


title: DSP-1001660002557-B-G05_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-G05_AH2G7CDSX7

value: Stroma


title: sham 2

description:
Library name: sham 2
BD Rhapsody

source_name: sample 2 of liver constituent cells from a wild-type male mouse at 2 weeks after sham surgery

value: sham surgery


title: Germinal_center_B_cells_1Mek2_rep2

city: Québec

first: Jean

last: Charron

state: QC

address: 2260, boul. Henri-Bourassa

department: Biologie moléculaire, Biochimie médicale & Pathologie

country: Canada

institute: CRCHU de Québec-Université Laval

description:
Library name: 570_1Mek2_GC
100bp

data_processing:
Reads were trimmed with the software Trim Galore (v0.6.5;https://github.com/FelixKrueger/TrimGalore)
Trimmed reads were mapped to NCBI GRCm39 (mm39) with the software STAR (v2.7.11a) (Dobin et al., Bioinformatics 2013).
Read counts extraction were made with the mm39 genome with FeatureCounts (v2.0.3; Liao et al., Bioinformatics 2014).
Counts were normalized in TPM ( transcripts per million)
Assembly: NCBI GRCm39 (mm39)
Supplementary files format and content: Tab_delimited text file include raw counts for each Sample
Supplementary files format and content: Tab_delimited text file include TPM for each Sample

molecule: polyA RNA

source_name: Germinal center B cell

growth_protocol: 3 to 5 months mice were used to isolate the splenocytes

extract_protocol:
mRNA were isolated by polyA selection from 500ng to 1000 ng of total RNA. Library were made using Illumina TruSeq RNA prep kit
RNA-seq

treatment_protocol: The spleen was gently mashed on a 70-μm nylon strainer to generate a single cell suspension. Cell collection was performed in PBS 2% BSA and filtered through a 70-μm nylon strainer. Cell purification was performed by cell sorting after labeling with the fluorochrome-conjugated antibodies against B220, CD93, CD138, GL7, FAS, CD21 and CD23.

value: Germinal center B cell


title: DSP-1001660002557-B-G04_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-G04_AH2G7CDSX7

value: ER-Neg


title: Germinal_center_B_cells_1Mek2_rep4

description:
Library name: 405_1Mek2_GC
100bp


title: CONb8

city: Madison

last: Ortega

state: Wisconsin

address: 1675 Observatory Drive

department: Department of Animal and DairySciences

institute: University of Wisconsin

description: pool of 15 bovine embryos

data_processing:
The quality of fastq files of sequences data was checked with a FastQC tool
Illumina adapters were trimmed
Reads were mapped to the bovine reference genome using the Hisat2
Read counts were determined using FeatureCounts program
Differentially expressed genes (DEGs) between sample groups were determined by edgeR-robust
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: blastocyst stage bovine embryo

growth_protocol: in vitro embryo development

extract_protocol:
PicoPure™ RNA Isolation Kit (ThermoFisher)
Takara SMART-Seq v4 Ultra Low-input RNA Kit (Takara Bio)

treatment_protocol: addition of FGF2, LIF, and IGF1

value: blastocyst stage bovine embryo

tag: developmental stage

value: blastocyst

value: control


title: DSP-1001660002557-B-G03_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-G03_AH2G7CDSX7

value: breast cancer


title: Germinal_center_B_cells_1Mek2_rep3

description:
Library name: 636_1Mek2_GC
100bp


title: DSP-1001660002557-B-G02_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-G02_AH2G7CDSX7


title: pIVCL 2

description:
Library name: pIVCL 2
BD Rhapsody

source_name: sample 2 of liver constituent cells from a wild-type male mouse at 2 weeks after pIVCL


title: pIVCL 3

description:
Library name: pIVCL 3
BD Rhapsody

source_name: sample 3 of liver constituent cells from a wild-type male mouse at 2 weeks after pIVCL


title: Germinal_center_B_cells_wt_rep4

description:
Library name: 565_Mek1ff_GC
100bp

value: wt


title: sham 1

description:
Library name: sham 1
BD Rhapsody

source_name: sample 1 of liver constituent cells from a wild-type male mouse at 2 weeks after sham surgery

value: liver


title: muscle, gammadelta T cells of IL17A-/- mice infected with M.abscessus for 12h, rep3

city: Shanghai

first: Xiaoqian

last: Hu

address: No. 130, Dongan Road, Xuhui District, Shanghai

institute: Fudan University

description:
Library name: KO_gdT_NTM_3
muscle,γδT cells of IL17A-/- mice infected with M.abscessus for 12h,rep3

data_processing:
The data obtained from sequencing, referred to as raw reads or raw data, underwent quality control (QC) to determine whether the sequencing data were suitable for subsequent analysis. After QC, clean reads were obtained and aligned to the reference sequence. After alignment, the alignment results were subjected to a second QC, where alignment rate, distribution of reads on the reference sequence, and other metrics were assessed. If the results passed the second QC, gene quantification analysis and various analyses based on gene expression levels (such as principal component analysis, correlation analysis, differential gene selection, etc.) were conducted. Differential expression genes identified between samples were then subjected to Gene Ontology (GO) enrichment analysis, pathway enrichment analysis, clustering, protein-protein interaction network analysis, and transcription factor analysis for more in-depth exploration.
Assembly: Mus_musculus_10090.NCBI.GCF_000001635.26_GRCm38.p6.v2201
Supplementary files format and content: The table contains information about the RNA modification sites identified by each sample

source_name: gamma delta (gammadelta) T Cell

extract_protocol:
A total of 9 samples were tested using the DNBSEQ platform, with an average yield of 1.14G data per sample. The average alignment ratio of the sample comparison genome was 97.19%, which was comparative The average alignment of the gene set was 84.57%; a total of 17810 genes were detected.
For library construction, total RNA was processed using mRNA enrichment. The mRNA was enriched using magnetic beads with Oligo(dT) to capture mRNA with a polyA tail. The obtained RNA was fragmented using a breaking buffer, and random N6 primers were used for reverse transcription. Subsequently, double-stranded cDNA was synthesized. The ends of the synthesized double-stranded DNA were blunted and 5' end-phosphorylated. A single-base overhang "A" was added to the 3' end, and a bubble-shaped adapter with a protruding "T" at the 3' end was ligated. The ligated products were PCR-amplified using specific primers. The PCR products were denatured to form single-stranded DNA, and single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries underwent quality control, and after passing, they were subjected to sequencing.

value: gamma delta (gammadelta) T Cell

tag: genotype/treatment


title: CONb7

description: pool of 15 bovine embryos


title: A_Gingival tissue, smooth

address: 山东省济南市文化西路四十四号山东大学趵突泉校区

description: Library name: SAMPLES A

value: gingival tissue

value: smooth


title: muscle, gammadelta T cells of IL17A-/- mice infected with M.abscessus for 12h, rep2

description:
Library name: KO_gdT_NTM_2
muscle,γδT cells of IL17A-/- mice infected with M.abscessus for 12h,rep2


title: Germinal_center_B_cells_1Mek2_rep1

description:
Library name: 323_1Mek2_GC
100bp


title: CONb5

description: pool of 15 bovine embryos


title: CONb6

description: pool of 15 bovine embryos


title: DSP-1001660002557-B-F12_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-F12_AH2G7CDSX7


title: DSP-1001660002557-B-G01_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-G01_AH2G7CDSX7


title: Germinal_center_B_cells_wt_rep2

description:
Library name: 413_WT_GC
100bp


title: DSP-1001660002557-B-F11_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-F11_AH2G7CDSX7

value: ER-Lo


title: FLIb8

description: pool of 15 bovine embryos

value: FGF2, LIF, IGF1 treatment


title: muscle, gammadelta T cells of IL17A-/- mice infected with M.abscessus for 12h, rep1

description:
Library name: KO_gdT_NTM_1
muscle,γδT cells of IL17A-/- mice infected with M.abscessus for 12h,rep1


title: Germinal_center_B_cells_wt_rep1

description:
Library name: 358_WT_GC
100bp


title: DSP-1001660002557-B-F10_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-F10_AH2G7CDSX7


title: FLIb7

description: pool of 15 bovine embryos


title: muscle, gammadelta T cells of WT mice infected with M.abscessus for 12h, rep2

description:
Library name: WT_gdT_NTM_2
muscle,γδT cells of WT mice infected with M.abscessus for 12h,rep2


title: DSP-1001660002557-B-F09_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-F09_AH2G7CDSX7


title: Immature_B_cells_1Mek2_rep4

description:
Library name: 636_1Mek2_Immature
100bp

source_name: Immature B cell

value: Immature B cell


title: FLIb6

description: pool of 15 bovine embryos


title: Immature_B_cells_1Mek2_rep3

description:
Library name: 570_1Mek2_Immature
100bp


title: muscle, gammadelta T cells of WT mice, rep3

description:
Library name: WT_gdT_3
muscle,γδT cells of WT mice,rep3

value: WT mice


title: Germinal_center_B_cells_wt_rep3

description:
Library name: 487_WT_GC
100bp


title: CONm3

description: pool of 15 bovine embryos

source_name: morula stage bovine embryo

value: morula stage bovine embryo

value: morula


title: DSP-1001660002557-B-F08_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-F08_AH2G7CDSX7


title: DSP-1001660002557-B-F06_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-F06_AH2G7CDSX7

value: ER-Hi


title: Immature_B_cells_1Mek2_rep1

description:
Library name: 565_Mek1ff_Immature
100bp


title: DSP-1001660002557-B-F07_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-F07_AH2G7CDSX7


title: FLIb5

description: pool of 15 bovine embryos


title: muscle, gammadelta T cells of WT mice, rep2

description:
Library name: WT_gdT_2
muscle,γδT cells of WT mice,rep2


title: muscle, gammadelta T cells of WT mice, rep1

description:
Library name: WT_gdT_1
muscle,γδT cells of WT mice,rep1


title: CONm7

description: pool of 15 bovine embryos


title: Immature_B_cells_wt_rep2

description:
Library name: 413_WT_Immature
100bp


title: CONm1

description: pool of 15 bovine embryos


title: DSP-1001660002557-B-F05_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-F05_AH2G7CDSX7

value: Stroma


title: CONm4

description: pool of 15 bovine embryos


title: Immature_B_cells_wt_rep3

description:
Library name: 487_WT_Immature
100bp


title: DSP-1001660002557-B-F03_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-F03_AH2G7CDSX7


title: Immature_B_cells_wt_rep1

description:
Library name: 358_WT_Immature
100bp


title: Immature_B_cells_1Mek2_rep2

description:
Library name: 323_1Mek2_Immature
100bp


title: muscle, gammadelta T cells of WT mice infected with M.abscessus for 12h, rep3

description:
Library name: WT_gdT_NTM_3
muscle,γδT cells of WT mice infected with M.abscessus for 12h,rep3


title: muscle, gammadelta T cells of WT mice infected with M.abscessus for 12h, rep1

description:
Library name: WT_gdT_NTM_1
muscle,γδT cells of WT mice infected with M.abscessus for 12h,rep1


title: DSP-1001660002557-B-F04_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-F04_AH2G7CDSX7

value: ER-Neg


title: GSCMGG8 cells,shHERC5-2

city: Nanjing

first: zhiting

last: Li

address: Longmian Avenue No.101

institute: Nanjing Medical University

description: Library name: Sample11

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). Structure variation detection The clean reads were mapped to the reference genome using HISAT2. After that, Ericscript (v0.5.5) and rMATS (V4.1.2) were used to detect fusion genes and differential splicing genes (DSGs), respectively. 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 (v1.0.12) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.34.0) (or DEGseq (v1.48.0) 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: GRCh38
Supplementary files format and content: FPKM,TPM and raw count values for each Sample

growth_protocol: GSC lines were cultured in Neurobasal medium (Gibco) supplemented with B27 without vitamin A (Gibco), EGF and bFGF (20 ng/mL each; R&D Systems), sodium pyruvate (Cat# 11360070; Life Technologies), GlutaMAX (Cat# 35050061; Life Technologies), and recombinant human IFN-γ (200 ng/mL; Cat# RP01038; Abclonal), maintained at 37°C in an incubator with 20% oxygen and 5% carbon dioxide.

extract_protocol:
Add the equal volume of 70% ethanol to the collection tube, mix by pipetting.Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube.Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow.Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min.Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min.Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
RNA-Seq (Quantification) uses a new generation of high-throughput sequencing technology to study the gene expression pattern of eukaryotic cells and provide accurate digital expression profile detection by sequencing and comparing transcripts. Transcriptome research is the basis and starting point of gene function and structure research. Through the new generation of high-throughput sequencing, almost all transcripts of a specific tissue or organ of a species can be obtained comprehensively and quickly. Select the corresponding testing methods for quality inspection according to the requirements of samples and products. A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. The PCR reaction system and program are configured and set up to amplify the product. The corresponding library quality control protocol will be selected depending upon product requirements. Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: Lentiviral  particles of shRNA targeting HERC5 (designated shHERC5-1) were produced in 293FT cells cultured in Neurobasal complete medium (Life Technologies) via co-transfection with the packaging plasmids psPAX2 and pMD2.G (Addgene), using a standard calcium phosphate transfection protocol. Knockdown efficiency of all shRNAs was confirmed by quantitative RT-PCR prior to use in functional assays.

tag: cell line

value: WT


title: B_Gingival tissue, microgrooves

address: 山东省济南市文化西路四十四号山东大学趵突泉校区

description: Library name: SAMPLES B

value: microgrooves


title: FLIm7

description: pool of 15 bovine embryos


title: DSP-1001660002557-B-F02_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-F02_AH2G7CDSX7

value: breast cancer


title: GSCMGG8 cells,shCONT-2

description: Library name: Sample8

value: shCONT


title: GSCMGG8 cells,shHERC5-3

description: Library name: Sample12


title: DM, infected 1

city: Freiburg

first: Vitka

last: Gres

address: Breisacherstraße 115b

department: Institute for Infection Prevention and Control

country: Germany

institute: University of Freiburg

data_processing:
paired-end sequencing of the quality-controlled library was conducted using NovaSeq6000.
Demultiplexing of sequenced reads was achieved through Illumina bcl2fastq (version 2.19), and Cutadapt was employed for adapter trimming.
The raw reads were then mapped to the mm10 murine reference genome using STAR (Version 2.5.2b) and counted using feature counts.
The resulting count data underwent processing with the DESeq2 package.
Assembly: mm10
Supplementary files format and content: Excel sheet includes raw counts for all samples

source_name: dura mater

extract_protocol:
Brain and dura were separately dissected and incubated for 20 min at 37°C shanking in 2.5 mg/ml collagenase IV, after which they were filtered through 70 µm strainer and washed with PBS. The pellet was resuspended using 37% Percoll and centrifuged for 30 min at 300g RT, without the acceleration and brake. Samples were washed and stained with respective antibodies. FcγII/III receptors were blocked by prior 10 min incubation with Fc block (anti mouse CD16/32 antibody Clone 93, Biolegend) on ice.
Library Preparation Kit: SMART-Seq Stranded Kit (Takara) using manufacturer's protocol

treatment_protocol: Mice were treated with tamoxifen 8 weeks prior to infection. Mice were either infected with GBS (infected group) or injected with PBS (control group) and analysed two days later.

value: dura mater

value: macrophage

value: tamoxifen + GBS


title: FLIm2

description: pool of 15 bovine embryos


title: GSCMGG8 cells,shCONT-3

description: Library name: Sample9


title: DSP-1001660002557-B-F01_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-F01_AH2G7CDSX7


title: DSP-1001660002557-B-E12_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-E12_AH2G7CDSX7


title: DM, control 3

value: tamoxifen + PBS


title: FLIm4

description: pool of 15 bovine embryos


title: DM infected 3


title: DSP-1001660002557-B-E11_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-E11_AH2G7CDSX7

value: ER-Lo


title: DM, infected 2


title: FLIm6

description: pool of 15 bovine embryos

value: FGF2, LIF, IGF1 treatment


title: GSC3028 cells,shHERC5-3

description: Library name: Sample6


title: CON10

description: pool of 15 bovine embryos

source_name: 9-16 cell stage bovine embryo

value: 9-16 cell stage bovine embryo

value: 9-16 cell embryo

value: control


title: GSCMGG8 cells,shCONT-1

description: Library name: Sample7


title: DM, control 2


title: GSCMGG8 cells,shHERC5-1

description: Library name: Sample10


title: DSP-1001660002557-B-E10_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-E10_AH2G7CDSX7


title: CON11

description: pool of 15 bovine embryos


title: GSC3028 cells,shHERC5-2

description: Library name: Sample5


title: DM, control 1


title: CON13

description: pool of 15 bovine embryos


title: GSC3028 cells,shHERC5-1

description: Library name: Sample4


title: DSP-1001660002557-B-E08_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-E08_AH2G7CDSX7


title: CON12

description: pool of 15 bovine embryos


title: MG, infected 3

source_name: brain

value: brain


title: MG, infected 2


title: DSP-1001660002557-B-E07_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-E07_AH2G7CDSX7


title: FLI13

description: pool of 15 bovine embryos


title: GSC3028 cells,shCONT-2

description: Library name: Sample2


title: DSP-1001660002557-B-E09_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-E09_AH2G7CDSX7


title: GSC3028 cells,shCONT-3

description: Library name: Sample3


title: GSC3028 cells,shCONT-1

description: Library name: Sample1


title: DSP-1001660002557-B-E06_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-E06_AH2G7CDSX7

value: ER-Hi


title: FLI11

description: pool of 15 bovine embryos


title: DSP-1001660002557-B-E05_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-E05_AH2G7CDSX7

value: Stroma


title: FLI12

description: pool of 15 bovine embryos


title: MG, control 3


title: MG, infected 1


title: MG, control 1


title: FLI10

description: pool of 15 bovine embryos


title: MG, control 2


title: DSP-1001660002557-B-E04_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-E04_AH2G7CDSX7

value: ER-Neg


title: CON8

description: pool of 15 bovine embryos

source_name: 4-6 cell stage bovine embryo

value: 4-6 cell stage bovine embryo

value: 4-6 cell embryo


title: standard chow, cage 3 mouse 5

city: Iowa City

first: Samuel

last: Stephens

state: Iowa

address: 169 Newton Rd, 3400 PBDB

institute: University of Iowa

data_processing:
Raw reads were mapped to the Ensembl mouse (mm10/GRCm38) genomes using STAR (v2.5)
reads were quantified using HTSeq (v2_1.6.3)
Differential expression analysis was performed using the DESeq2 R package (2_1.6.3)
Assembly: mm10/GRCm38
Supplementary files format and content: .xls containing  raw counts, FPKM, log2 foldchange, pvalue, adjusted pvalue

source_name: pancreatic islet

growth_protocol: Mice 8-10 weeks of age were fed western diet or standard chow diet for 4 weeks

extract_protocol:
RNAeasy microkit
libraries were generated using NEBNext Ultra TM RNA Library Prep Kit

treatment_protocol: pancreatic islets were isolated and immediately processed

tag: strain

value: pancreatic islet

value: standard chow


title: DSP-1001660002557-B-E03_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-E03_AH2G7CDSX7

source_name: breast cancer

value: breast cancer


title: Tr_Mk_sh_2

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
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.
Differential expression analysis of two conditions/groups  was performed using the DESeq2Rpackage (1.20.0). Genes with an adjusted P-value <=0.05found by DESeq2 were assigned as differentially expressed.Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5).
Assembly: Arabidopsis thaliana
Supplementary files format and content: Excel, log2 transform count based Normalization

organism: Arabidopsis thaliana

source_name: 16 days old seedlings (shoot)

growth_protocol: Seedlings were grown for 5 days on 1/2 MS on plates with or without SA187

extract_protocol:
Total RNA extractions were performed using the NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer's recommendations
RNA-Seq was carried out using Illumina TruSeq standard mRNA Library Preparation protocol as per manufacturer’s instructions for 50-bp-end sequencing.
The pooled libraries were sequenced on Illumina HiSeq4000 platform

treatment_protocol: 5d old seedlings were transferred to 1/2 MS plates ± 100mM NaCl, and plug of S. indica was placed next to seedlings as needed

value: shoot

tag: age

value: 16 days old

tag: ecotype

tag: colonization

value: Mock colonized

value: 100mM NaCl


title: Tr_Mk_sh_3


title: Tr_Mk_sh_1


title: standard chow, cage 3 mouse 4


title: CON9

description: pool of 15 bovine embryos


title: DSP-1001660002557-B-E02_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-E02_AH2G7CDSX7


title: DSP-1001660002557-B-E01_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-E01_AH2G7CDSX7


title: Tr_Mk_rt_2

source_name: 16 days old seedlings (root)

value: root


title: CON6

description: pool of 15 bovine embryos


title: Tr_Mk_rt_3


title: CON7

description: pool of 15 bovine embryos


title: DSP-1001660002557-B-D12_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-D12_AH2G7CDSX7


title: DSP-1001660002557-B-D11_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-D11_AH2G7CDSX7

value: ER-Lo


title: Tr_Mk_rt_1


title: standard chow, cage 3 mouse 3


title: FLI8

description: pool of 15 bovine embryos

value: FGF2, LIF, IGF1 treatment


title: standard chow, cage 3 mouse 2


title: western diet, cage 2 mouse 5

value: western diet


title: standard chow, cage 3 mouse 1


title: DSP-1001660002557-B-D10_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-D10_AH2G7CDSX7


title: DSP-1001660002557-B-D09_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-D09_AH2G7CDSX7


title: Tr_C_sh_3

value: Sync. colonized


title: FLI7

description: pool of 15 bovine embryos


title: DSP-1001660002557-B-D08_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-D08_AH2G7CDSX7


title: western diet, cage 4 mouse 4


title: Tr_C_sh_1


title: FLI6

description: pool of 15 bovine embryos


title: DSP-1001660002557-B-D07_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-D07_AH2G7CDSX7


title: FLI9

description: pool of 15 bovine embryos


title: western diet, cage 4 mouse 5


title: 20170525

first: Zhe

last: Wang

state: Shanghai

address: Siping Road, Shanghai

institute: Tongji university

data_processing:
The fastq data were cleaned with the Fastx-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) with the default protocol by the manufacturer. The Blastn (http://blast.ncbi.nlm.nih.gov/) was used to annotated the miRNA. The Bowtie ( http://bowtie-bio.sourceforge.net/index.shtml ) was used to mapped the sequences to reference gennome.
Assembly: hg38
Supplementary files format and content: Raw counts

extract_protocol:
The peripheral blood samples from pregnant women with written informed consent were stored in EDTA tubes, then were centrifuged in 1,600g for 10 minutes to remove blood cells. The supernatant was transferred to a new EP tube and was centrifuged at 16,000g for another 10 minutes to obtain the purified plasma, which was stored at -80 °C. Then， total RNA was isolated by TRIzol® Reagent (Invitrogen)
then the construction of cDNA library was performed by Illumina TruSeq Small RNA sample prep kit. The target PCR products were purified through 6% Novex TBE PAGE gel and the quality was checked by TBS380 (Picogreen). Then PCR amplification was performed and the generated clusters were sequenced by Illumina HiSeq platform.

value: maternal peripheral blood

tag: Sex

value: female

tag: condition

value: preterm labor


title: western diet, cage 4 mouse 2


title: DSP-1001660002557-B-D06_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-D06_AH2G7CDSX7

value: ER-Hi


title: Tr_C_sh_2


title: A67506


title: western diet, cage 4, mouse 1


title: A29080


title: DSP-1001660002557-B-D04_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-D04_AH2G7CDSX7

value: ER-Neg


title: low glucose, replicate 4

growth_protocol: mouse pancreatic islets were maintaining in RPMI 1640 (7.5 mM or 20 mM glucose), 10% FBS, 1 mM HEPES pH 7.2

treatment_protocol: Islets were cultured for 72 h in 20 mM glucose (HG) or 7.5 mM glucose (LG)

value: pancreatic islet

value: low glucose


title: Tr_C_rt_3


title: Tr_B_sh_3

value: S. indica colonized


title: Tr_C_rt_1


title: A28488


title: DSP-1001660002557-B-D05_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-D05_AH2G7CDSX7

value: breast cancer

value: Stroma


title: Tr_B_sh_2

value: shoot

value: 16 days old


title: Tr_C_rt_2

value: root

value: 100mM NaCl


title: Tr_B_sh_1


title: low glucose, replicate 3


title: DSP-1001660002557-B-D03_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-D03_AH2G7CDSX7

value: ER-Lo


title: A57521

value: term labor


title: low glucose, replicate 1


title: low glucose, replicate 2


title: DSP-1001660002557-B-D02_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-D02_AH2G7CDSX7


title: A21133


title: Tr_B_rt_3


title: A13256


title: high glucose, replicate 4

value: high glucose


title: Tr_B_rt_2


title: DSP-1001660002557-B-D01_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-D01_AH2G7CDSX7


title: DSP-1001660002557-B-C12_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-C12_AH2G7CDSX7


title: high glucose, replicate 3


title: DSP-1001660002557-B-C11_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-C11_AH2G7CDSX7


title: A13242

value: maternal peripheral blood


title: A63571

value: female

value: term not in labor


title: DSP-1001660002557-B-C10_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-C10_AH2G7CDSX7

value: ER-Hi


title: high glucose, replicate 2


title: A54506


title: Tr_B_rt_1


title: high glucose, replicate 1


title: Tr_A_sh_3

value: SA187 colonized


title: DSP-1001660002557-B-C09_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-C09_AH2G7CDSX7


title: DSP-1001660002557-B-C08_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-C08_AH2G7CDSX7

value: ER-Neg


title: A20923


title: DSP-1001660002557-B-C07_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-C07_AH2G7CDSX7


title: Trigeminal ganglion, Balb/c nude mouse, Rimegepant treatment2

first: mingtao

address: 180 Fenglin Road, Xuhui District, Shanghai

institute: Zhongshan Hospital, Fudan University

data_processing:
CLC Genomics Workbench v 11.0.1
Trimmed sequence reads were mapped to GrOMB8/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 lent
Read count extraction and normalization were perfarmed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: xlsx file includes raw counts for each Sample

source_name: Trigeminal ganglion

extract_protocol:
RNA was harvested using Rneasy mini plus kt (Qiagen). 13 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RINA-sed were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturers protocols

treatment_protocol: BALB/c nude mice (8 weeks old, weighing 20–25 g) were randomly divided into an experimental group and a control group (n=3 in each group). Unilateral tongue orthotopic transplantation models were established for each group. In the experimental group, Rimegepant (50mg/kg/day) was intraperitoneally injected every 24 h for 4 consecutive days, starting from the 5th day after tumor inoculation. The control group received an equal volume of physiological saline. After the final drug treatment, both groups of mice were euthanized, with the trigeminal ganglia on the side of the transplantation tumor carefully isolated.

value: Trigeminal ganglion

value: BALB/c

value: 8 weeks old

value: Rimegepant treatment


title: Tr_A_sh_2

value: shoot


title: A09913


title: Tr_A_rt_3

value: 16 days old


title: Tr_A_sh_1


title: DSP-1001660002557-B-C06_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-C06_AH2G7CDSX7

value: breast cancer


title: Trigeminal ganglion, Balb/c nude mouse, Rimegepant treatment3


title: Trigeminal ganglion, Balb/c nude mouse, Rimegepant treatment1


title: Patient6, non-GVHD, scRNAseq

first: Guoju

last: You

state: Beijing

address: Shuangqing Road

institute: Tsinghua University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood

extract_protocol:
All patients enrolled were adult recipients who underwent haploidentical HSCT for acute leukemia and achieved stable engraftment without other severe transplant-related complications including infections, hemorrhagic cystitis. Cyclosporine A, mycophenolate mofetil, and short-term methotrexate were used for GVHD prophylaxis for all recipients. Uniform strategies for infection prevention and supportive care were given. Freshly collected  blood samples were placed into tubes containing EDTA (ethylenediamine tetraacetic acid) and then transferred for single-cell preparations within 10 minutes.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Peripheral blood cells

value: Peripheral blood

value: Male


title: Patient5, non-GVHD, scRNAseq

description: 10x Genomics


title: Trigeminal ganglion, Balb/c nude mouse, Control3

value: Control


title: Tr_A_rt_2

value: root

value: 100mM NaCl


title: Tr_A_rt_1


title: DSP-1001660002557-B-C05_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-C05_AH2G7CDSX7

value: Stroma


title: Trigeminal ganglion, Balb/c nude mouse, Control2


title: BN1470, Rep3 Dam::EMR-1

city: Seville

first: Peter

last: Askjaer

address: UPO Carretera de Utrera km 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

data_processing:
FASTQ files from the NextSeq2000 platform were processed in R Studio using the pipeline RDamIDSeq (https://github.com/damidseq/RDamIDSeq) (Sharma et al. 2016) for mapping of reads to GATC sites and to bins of fixed size (e.g. 2 kb, 10 kb or 100 kb). The pipeline includes a quality check where only reads that contain the DamID adapter (“CGCGGCCGAG”) and map to GATC sites in the C. elegans genome are retained for further analysis. The number of reads fulfilling these criteria ranged from 15.8 to 22.8 million. UCSC genome version ce11 (BSgenome.Celegans.UCSC.ce11) was used for alignment.
The DESeq2 package (Love et al. 2014) was used to identify bins or GATC site with significantly different read numbers for Dam::EMR-1  compared to GFP::Dam across the 3 replicas. Next, for each sample a pseudocount of 1 was added to each bin and the relative number of reads per bin was calculated followed by averaging across the replicas. The ratio of Dam::EMR-1  to GFP::Dam was calculated for each bin and log2-transformed. Normalization was done by subtracting the genome-wide average log2 ratio from the log2 ratio of each bin (Brueckner et al. 2020). Finally, bins or GATC sites with <10 reads across all six samples were discarded.
Assembly: ce11
Supplementary files format and content: Files contain columns for coordinates, log2(Dam::EMR-1/GFP::Dam) values (average and individual replicas), number of reads per bin (or GATC site), bin or GATC number and padj value.

organism: Caenorhabditis elegans

source_name: EMS

growth_protocol: Worms were grown asynchronically at 20C on NGM plates seeded with E. coli GM119 dam(-) for at least two generations before egg-prepping with hypochlorite. Hatched L1s were counted the day after and 1000 L1s were aliquoted onto 10 cm NGM plates seeded with E. coli GM119 dam(-). Worms were grown at 20C for 72 h. 4000 1 day-old adult nematodes per strain were washed twice with M9 with 0.01% Tween-20 and bleached to collect embryos. Then, embryos were washed 5 times with 15 ml of M9 with 0.01% Tween-20. Embryos were transferred to 1.5 ml tubes with M9 with 0.01% Tween-20 using Pasteur pipettes followed by two additional washes. Supernatants were aspirated and aliquots of 30 µl were snap frozen in liquid nitrogen and maintained at -80C until DNA extraction.

extract_protocol:
To purify genomic DNA, samples were lysed in 5 freeze/thaw cycles (1min in liquid nitrogen; 3min in 37C shaker) and processed with DNeasy Blood and Tissue Kit (QIAGEN #69504).
DamID was performed on 200 ng genomic DNA  extracted from embryos cultured and collected as indicated above. Three replicates were performed as described (de la Cruz Ruiz et al. 2022), using primer AdR (5'-NNNNGTGGTCGCGGCCGAGGATC) and 24 PCR cycles. Successful amplification of Dam-methylated genomic DNA yielded a smear of ~400-~1500 bp fragments when analyzed on Agilent Bioanalyzer. 50 ng of PCR amplified fragments were used for library preparation as described (de la Cruz Ruiz et al. 2022), using E7370 NEBNext® Ultra™ DNA Library Prep Kit for Illumina. Library amplicons’ size distribution was checked to be maintained as for PCR fragments indicated above followed by pooling, repurification and sequencing on a Illumina NextSeq2000 platform at EMBL GeneCore.

value: EMS

value: WT


title: Patient4, GVHD, scRNAseq

description: 10x Genomics


title: Patient3, GVHD, scRNAseq

description: 10x Genomics

value: Female


title: BN1470, Rep2, Dam::EMR-1


title: Patient2, GVHD, scRNAseq

description: 10x Genomics


title: DSP-1001660002557-B-C03_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-C03_AH2G7CDSX7

value: ER-Lo


title: BN1470, Rep1, Dam::EMR-1


title: M5_5, A and B treatment for 40 days

first: Shilin

last: Ma

address: No.5, Yard 1, Beichen West Road, Chaoyang District, Beijing

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
CLC Genomics Workbench v11.0.1
Seguence reads were trimmed for adaptor sequencellow-quality sequence using CLC genomic benchwork (parameter- Quality limit. 0.05)
Trimmed sequence reads were maped to GrcM38/mm0 using CLc genomic benchwoank (parameters-mismath cost. 2 insertion cost: 3 deletion cost:3 engthfaction. .8 similanity faction. 0.8
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include FPKM values for each Sample

source_name: Muscle

growth_protocol: 4-week-old male Lepob/Lepob mice (n=30) were fed with AMLN diet (40% calories from fat, including 18.5% from trans-fat, 20% calories from fructose, and 2% (wt/wt) cholesterol) for 20 weeks to generate NASH model. Mice were housed with free access to water and diet. The light was on from 08.00 to 20.00, with the temperature kept at 21 to 24°C and humidity at 40–70%.

extract_protocol:
RNA is extracted from tissues or cells using standard extraction methods (Trizol), followed by rigorous quality control of RNA samples through Agilent 2100 bioanalyzer.
RNA libraryis for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® according to the manufacturer's instructions.

treatment_protocol: All experimental animals were divided into groups and received daily treatment while maintaining their previous diets. Animals were intraperitoneally injected with A (acetylsalicylate) 3.0mg/kg/day, B (trimetazidine) 5.0mg/kg/day, or the combination of A+B and vehicle control animals are intraperitoneally injected with same volume of solvent.

value: Muscle

value: Lepob/Lepob C57BL/6J

value: aspirin and trimetazidine treatment for 40 days


title: Trigeminal ganglion, Balb/c nude mouse, Control1

value: Trigeminal ganglion

value: BALB/c

value: 8 weeks old


title: DSP-1001660002557-B-C02_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-C02_AH2G7CDSX7

value: breast cancer

value: ER-Hi


title: Patient1, GVHD, scRNAseq

description: 10x Genomics

value: Peripheral blood cells

value: Peripheral blood

value: Male


title: DSP-1001660002557-B-C01_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-C01_AH2G7CDSX7


title: DSP-1001660002557-B-B12_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-B12_AH2G7CDSX7

value: ER-Neg


title: M5_4, A and B treatment for 40 days


title: M5_3, A and B treatment for 40 days


title: BN1465, Rep3, GFP::Dam


title: BN1465, Rep2, GFP::Dam


title: DSP-1001660002557-B-B11_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-B11_AH2G7CDSX7


title: CHP-134/sgTRIM24_2

first: Haizhong

last: Feng

address: Pujian Road 160

department: Ren Ji Hospital

institute: Shanghai Jiao Tong University

description:
CHP-134 cells knockout of TRIM24 using CRISPR/Cas9
FN-5

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2.
Read count extraction using featureCounts
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Trapnell et al., Nat Biotechnol, 2010.
Assembly: hg19
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using Illumina Truseq strand mRNA following manufacturer's protocols.

value: neuroblastoma cell

value: TRIM24 knockout


title: DSP-1001660002557-B-C04_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-C04_AH2G7CDSX7


title: CHP-134/sgTRIM24_1

description:
CHP-134 cells knockout of TRIM24 using CRISPR/Cas9
FN-4


title: M5_1, A and B treatment for 40 days


title: BN1465, Rep1, GFP::Dam

value: EMS

value: WT


title: M4_5, A and B treatment for 40 days


title: CHP-134/sgControl_3

description:
CHP-134 control cells
FN-3


title: DSP-1001660002557-B-B09_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-B09_AH2G7CDSX7

value: Stroma


title: DSP-1001660002557-B-B10_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-B10_AH2G7CDSX7


title: DSP-1001660002557-B-B08_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-B08_AH2G7CDSX7


title: M6_1, vehicle control for 40 days

value: Muscle

value: vehicle control treatment for 40 days


title: CHP-134/sgTRIM24_3

description:
CHP-134 cells knockout of TRIM24 using CRISPR/Cas9
FN-6


title: CHP-134/sgControl_1

description:
CHP-134 control cells
FN-1


title: M3_2, vehicle control for 40 days

value: Lepob/Lepob C57BL/6J


title: DSP-1001660002557-B-B07_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-B07_AH2G7CDSX7

value: ER-Lo


title: brainstem_TG_HFD_Bis_18

type: other

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

hyb_protocol: 200 g of bisulfite- and oxidative bisulfite-converted DNA per sample were run on Infinium Mouse Methylation BeadChip arrays (Illumina, San Diego, CA, USA).

scan_protocol: Beta values were generated from raw intensity signals for 287050 CpG sites using GenomeStudio software (Illumina).

data_processing: Preprocessing with Minfi (v 1.50.0) with SWAN normalization. CpG probes with detection p-value below 0.05 and standard deviation value below 0.005 across samples were excluded.

label: Cy3 and Cy5

molecule: other

source_name: brainstem

label_protocol: Standard Illumina Protocol.

extract_protocol: DNA was isolated using the AllPrep DNA/RNA Mini Kit (Qiagen).

value: brainstem

value: TG

tag: diet

value: HFD

tag: method

value: Bis


title: M5_2, A and B treatment for 40 days

tag: tissue

value: aspirin and trimetazidine treatment for 40 days


title: CHP-134/sgControl_2

description:
CHP-134 control cells
FN-2

tag: cell type


title: M2_4, vehicle control for 40 days

tag: genotype


title: DSP-1001660002557-B-B06_AH2G7CDSX7

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description: Library name: DSP-1001660002557-B-B06_AH2G7CDSX7

data_processing:
The raw data were quantile normalized for epithelial sections (ER-Hi, ER-Lo, ER-Neg) and stromal segments (Stroma) separately.
Assembly: hg38
Supplementary files format and content: Data is distributed as raw files (DCC), pkc file provided
Library strategy: Spatial Transcriptomics

extract_protocol: Following NanoString Digital Spatial Profiler protocol ((v1.0) Human NGS Whole Transcriptome Atlas)

value: breast cancer

tag: sample group

value: ER-Hi


title: T-ALL cell_Control_biological rep2

type: RNA

city: Madrid

first: Javier

last: Redondo-Muñoz

address: C/ Ramiro de Maeztu 9

institute: Centro de Investigaciones Biológicas Margarita Salas - CSIC

description: Gene expression data from T-ALL cells cultured in suspension after 10 days 3D confinement

hyb_protocol: RNA was hybridized to Clariom™ S Human Array following manufacturer’s instructions in a GeneChip Hybridization Oven 645 at 45ºC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software Genechip Command Console Software (AGCC)

data_processing: The intensity cell files were then imported, normalized for background correction (used RMA for normalization) with Transcriptome Analysis Console (TAC)

label: Biotin

source_name: Jurkat cells cultured in suspension after 10 days 3D confinement (TR cells)

label_protocol: RNA was labeled using the GeneChip WT PLUS Reagent kit

growth_protocol: Jurkat cells were cultured in RPMI (supplemented with 10% FBS) at 37oC  and 5% CO2

extract_protocol: 10x106 cells were lysed using TRI reagent (Sigma) for 30 min. Then, chloroform was added, mixed and incubated for 30 min. After 15 min centrifugation at 13000 rpm, the soluble phase containing the RNA was collected and precipitated with isopropanol for 15 min on ice. The pellet obtained by 15 min 13000 rpm centrifugation at 4ºC, was washed with cold ethanol 80%, centrifugated at 8000 rpm for 5 min and allowed to dry. Total RNA was resuspended in RNAse-free H2O, and purity and concentration were determined by Nanodrop measurement.

treatment_protocol: Control cells are Jurkat cells cultured in normal conditions in suspension in RPMI supplememented with 10% FBS at 37ºC 5% CO2. TR cells were obtained upon long-term 3D confinement. For this, Jurkat cells were embedded in a solution of 3.3 mg/mL of collagen type I from bovine in complete medium and neutralized with 7.5% NaHCO3 and 25 mM Hepes. After 1 hour polymerization at 37ºC, additional complete medium was added at the top of the 3D collagen matrix. Jurkat cells were maintained in the 3D matrix for 10 days and complete medium was changed every 3-4 days. Then, cells were collected from the collagen gel mechanically, the collagen fragments were filtered, and cells were cultured, expanded, and kept in culture conditions as TR.

value: Jurkat


title: ALDH3B1 +/+, 2-HD5

city: Mannheim

first: Xin

last: Qian

state: Baden-Wuerttemberg

address: Ludolf-Krehl-Str. 13-17

department: Vascular Biology&Tumor Angiogenesis

institute: Medical Faculty Mannheim, Heidelberg University

data_processing:
QC with fq  nersion 0.11.9  Parameters:fq *.fastq
trimmed with trim_galore version 0.6.7. Parameters: trim_galore phred33 -q 30 --length 36 --stringency 3
alignment with hisat2  version 2.2.1 . Parameters: hisat2 -t -p 30 -x
Get raw counts with featureCounts Version 2.0.1. Parameters: featureCounts -T 5 -p -t exon -g gene_id -a
Assembly: GRCz11
Supplementary files format and content: Raw counts generated with featureCounts Version 2.0.1.

organism: Danio rerio

source_name: larvae

extract_protocol:
Total RNA was extracted using TRIzol method
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

value: larvae

tag: line

tag: treatment


title: brainstem_TG_HFD_Bis_21


title: ALDH3B1 +/+, 2-HD4


title: ALDH3B1 +/+, 2-HD3


title: brainstem_WT_SD_Bis_17

value: SD


title: T-ALL cell_Control_biological rep1


title: DSP-1001660002557-B-B04_AH2G7CDSX7

first: Fangyuan

last: Chen

description: Library name: DSP-1001660002557-B-B04_AH2G7CDSX7

value: ER-Neg


title: M2_3, vehicle control for 40 days


title: M2_1, vehicle control for 40 days


title: ALDH3B1 +/+, 2-HD2

value: WT


title: brainstem_WT_HFD_Bis_23


title: L5_5, A and B treatment for 40 days

source_name: Liver

value: Liver


title: ALDH3B1 -/- 3

value: KO

value: no


title: T-ALL cell_TR_biological rep1

description: Gene expression data from T-ALL cells control

source_name: Control Jurkat cells


title: M2_5, vehicle control for 40 days

value: Muscle

value: Lepob/Lepob C57BL/6J

value: vehicle control treatment for 40 days


title: DSP-1001660002557-B-B02_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-B02_AH2G7CDSX7


title: L5_4, A and B treatment for 40 days


title: brainstem_WT_HFD_Bis_20_1

value: brainstem


title: T-ALL cell_TR_biological rep2

description: Gene expression data from T-ALL cells cultured in 3D conditions for 1 hour


title: DSP-1001660002557-B-B05_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-B05_AH2G7CDSX7

value: Stroma


title: DSP-1001660002557-B-B01_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-B01_AH2G7CDSX7


title: DSP-1001660002557-B-B03_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-B03_AH2G7CDSX7

value: ER-Lo


title: ALDH3B1 +/+, 2-HD1


title: L5_3, A and B treatment for 40 days

value: aspirin and trimetazidine treatment for 40 days


title: ALDH3B1 -/- 2


title: L5_2, A and B treatment for 40 days


title: ALDH3B1 -/- 7


title: brainstem_TG_SD_Bis_22_2

value: TG

value: Bis


title: brainstem_TG_SD_Bis_22_1


title: L5_1, A and B treatment for 40 days


title: DSP-1001660002557-B-A11_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-A11_AH2G7CDSX7

value: breast cancer


title: ALDH3B1 +/+ 14

value: larvae


title: brainstem_WT_SD_Bis_19

value: SD


title: DSP-1001660002557-B-A10_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-A10_AH2G7CDSX7

value: ER-Hi


title: ALDH3B1 +/+ 13

value: WT


title: brainstem_TG_HFD_Bis_23

value: HFD


title: ALDH3B1 +/+ 10


title: DSP-1001660002557-B-A09_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-A09_AH2G7CDSX7


title: brainstem_WT_SD_Bis_18


title: L6_1, vehicle control for 40 days

value: Liver


title: DSP-1001660002557-B-A08_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-A08_AH2G7CDSX7

value: ER-Neg


title: brainstem_TG_SD_Bis_21


title: DSP-1001660002557-B-A12_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-A12_AH2G7CDSX7


title: ALDH3B1 +/+ 5

value: no


title: brainstem_WT_HFD_Bis_20


title: L2_5, vehicle control for 40 days

value: Lepob/Lepob C57BL/6J


title: DSP-1001660002557-B-A06_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-A06_AH2G7CDSX7


title: DSP-1001660002557-B-A07_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-A07_AH2G7CDSX7


title: Ctrl-6m_1

city: Winnipeg

first: Athanasios

last: Zovoilis

state: MB

address: 745 Bannatyne Ave

department: Biochemistry and Medical Genetics

institute: University of Manitoba

description: Total RNA (Native)

data_processing:
Base calling was performed using guppy version 3.0
Mapping nanopore reads to UCSC mm10 unique B2 sequences from RepeatMasker using minimap2-2.17 (PMID: 29750242), with sr option and default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: B2_RNAs_counts.txt contains the count numbers for mapped unique B2 sequences from RepeatMasker for each sample. Column one depicts the name of each sample while column two depicts the absolute count number.

source_name: Hippocampus L+R

extract_protocol:
Left and right hippocampus tissue was homogenized in 1.0mL Trizol reagent: 15 minute incubation and subsequent grinding using a pestle until nothing but insoluble connective tissue remained. The homogenized mix was pipetted up and down and the solution was stored at -80°C. 0.5mL of homogenized mixture was phase separate by the addition of 200mL of chloroform (Sigma, C2432) and mixed by inversion, incubated for three minutes and centrifuged at 12 500xg for fifteen minutes at 4°C. The top (aqueous) layer was transferred to a new tube and mixed with 500mL of isopropanol (Fisher, 67-63-0), followed by a 1 hour incubation at -20°C and centrifugation at 12 500xg for ten minutes at 4°C. The supernatant was removed and the pellet was washed and mixed with 1mL of 75% ethanol, followed by a centrifugation at 7 600xg for five minutes at 4°C. The supernatant was removed and the pellet was allowed to dry for 1 minute before eluting in 50mL of nuclease free H2O. The eluted RNA was heated at 55°C for fifteen minutes, and subsequently incubated with 1mL of DNaseI (NEB, M0303), 10mL of 10x DNaseI buffer (NEB, B0303), and 39mL of nuclease free H2O for 15 minutes at 37°C. The RNA was further cleaned using the Zymo Research RNA clean and concentrator kit -25 (R1017). The RNA was stored at -80°C.
1.5ug total RNA was size selected using the Invitrogen MirVana kit (AM1561). 90uL of the short elution was polyadenylated using 12uL 10x polyA polymerase buffer (NEB, B0276), 12uL 10mM ATP (NEB, B0756A), 6uL polyA polymerase (NEB, M0276) and incubated at 37C for 30min. The polyadenylated short fraction and the long fraction were combined and purified and concentrated using the RNeasy MinElute kit (Qiagen, 74204). 12uL of the RNA was adaptor ligated using 4uL NEBNext Quick ligation buffer (B6058), 0.66uL RNA CS (Nanopore), 1.3uL RTA adaptor (Nanopore), 2uL 2 000 000U T4 DNA ligase (NEB, M0202). The reaction was incubated at room temperature for 10 minutes. The sample was subsequently reverse transcribed using 1.5uL of the Lucigen OmniAmp polymerase (F831942-1), 10uL 10x OmniAmp buffer (Lucigen, F883707-1), 8uL dNTP (NEB, N0447), 6uL 100mM MgSO4 (Lucigen, F98695-1), 10uL Betaine (Lucigen, F881901-1), 5uL random primer mix (NEB, S1330), and 39.5uL RNase free H2O. The mixture was incubated for 50C – 10min, 70C – 2min. Samples were cleaned by 2.88x Omega Mag-BindÒ TotalPure NGS beads. The 20uL library was ligated to the Nanopore RMX adaptor using 6uL RMX adaptor (Nanopore), 8uL NEBNext quick ligation buffer, 3uL RNase free H2O, and 3uL 2 000 000U T4 DNA ligase and incubated for 10 minutes at room temperature. The adapted library was 1x bead cleaned using the Omega Mag-BindÒ TotalPure NGS beads, eluted in Nanopore elution buffer. Library was loaded onto Nanopore PromethION according to manufacturer’s instructions.

tag: background strain

value: 6 months

value: Hippocampus L+R


title: brainstem_TG_SD_Bis_23

value: brainstem


title: L2_4, vehicle control for 40 days

value: vehicle control treatment for 40 days


title: L2_3, vehicle control for 40 days


title: L3_2, vehicle control for 40 days


title: brainstem_WT_HFD_Bis_19_1


title: ALDH3B1 +/+ 1


title: L4_5, A and B treatment for 40 days

value: aspirin and trimetazidine treatment for 40 days


title: RRBS hippocampus, Mtr-cKO, biological replicate 6

city: Strasbourg

first: Karim

last: Matmat

address: 1 Rue Eugène Boeckel

department: Faculty of Medicine

country: France

institute: University of Strasbourg

description: Library name: beta_RRBS11

data_processing:
Raw sequencing quality was assessed using FastQC v0.11.5. Adapter trimming and removal of low-quality bases were performed using Trim Galore! v0.6.6. Reads were aligned to the mouse reference genome GRCm38/mm10 using Bismark v0.22.3 with Bowtie2 v2.4.4. CpG methylation calls were extracted using Bismark (--cytosine_report --comprehensive --merge_non_CpG). Differential methylation analysis was performed using methylKit v1.16.1 in R 4.1, including coverage filtering (minimum 10x), normalization, CpG and DMR calling with FDR correction, and genome annotation.
Assembly: GRCm38/mm10
Supplementary files format and content: Files are compressed using gzip (.gz) and correspond to per-sample CpG reports or group-level DMR tables.

source_name: Brain hipocampus

growth_protocol: Mice were maintained under standard housing conditions with ad libitum access to food and water. Hippocampal tissue was collected at postnatal day 21.

extract_protocol:
Hippocampal tissue was lysed at 56°C overnight and genomic DNA was extracted using the QIAamp DNA Kit (Qiagen) according to the manufacturer’s instructions. DNA was eluted in 50 µl elution buffer. DNA concentration was measured using the Quant-iT PicoGreen dsDNA Assay (Invitrogen) and DNA integrity was assessed with the Agilent TapeStation 4150 using the Genomic DNA ScreenTape assay.
Reduced Representation Bisulfite Sequencing (RRBS) libraries were prepared from 100 ng genomic DNA using the Diagenode Premium RRBS Kit following the manufacturer’s guidelines. The protocol included restriction digestion, size selection, bisulfite conversion, and PCR amplification. Methylated and unmethylated spike-in controls provided in the kit were used to estimate bisulfite conversion efficiency. Libraries were quantified using PicoGreen and fragment size distribution was assessed using the Agilent Bioanalyzer High Sensitivity DNA Kit. Libraries were denatured and diluted to 1.8 pM with 20% PhiX Control (Illumina) prior to sequencing.

treatment_protocol: No treatment was applied.

value: Brain hipocampus

value: Mtr KO


title: DSP-1001660002557-B-A05_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-A05_AH2G7CDSX7

value: breast cancer

value: Stroma


title: L2_1, vehicle control for 40 days


title: RRBS hippocampus, WT, biological replicate 6

description: Library name: beta_RRBS12

value: wild-type


title: DSP-1001660002557-B-A04_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-A04_AH2G7CDSX7


title: DSP-1001660002557-B-A03_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-A03_AH2G7CDSX7

value: ER-Lo


title: DSP-1001660002557-B-A02_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-A02_AH2G7CDSX7

value: ER-Hi


title: RRBS hippocampus, WT, biological replicate 5

description: Library name: beta_RRBS10


title: D1_D_M, 24h after vehicle control injection

value: Muscle

value: 24h after vehicle control injection


title: brainstem_WT_HFD_Bis_19

value: WT

value: HFD

value: Bis


title: brainstem_TG_SD_Bis_22

value: TG

value: SD


title: RRBS hippocampus, Mtr-cKO, biological replicate 5

description: Library name: beta_RRBS8


title: DSP-1001660002557-B-A01_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-A01_AH2G7CDSX7

value: No Template Control


title: brainstem_WT_SD_Bis_16

value: brainstem


title: D1_D_L, 24h after vehicle control injection

value: Liver

value: Lepob/Lepob C57BL/6J


title: brainstem_TG_HFD_OxBis_18

value: OxBis


title: U118_ZBTB7B

city: DaLian

first: YiDing

last: Liu

address: wwde

institute: Dalian Medical University

description:
Library name: ZBTB7B
Treated

data_processing:
Remove reads containing adapters
Remove reads containing N (where N represents undetermined base information)
Remove low-quality reads (reads where the number of bases with Qphred ≤ 5 accounts for more than 50% of the total read length)
Assembly: mm10,hg38
Supplementary files format and content: all_compare1.txt,all_compare2.txt
Supplementary files format and content: counts values for each Sample

extract_protocol:
To extract RNA from samples, the Trizol method was used. After successful extraction, the RNA was dissolved in 50 µL of DEPC-treated water. Subsequently, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of  the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
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: glioma cells

value: overexpression ZBTB7B

value: Treated

tag: batch


title: D1_AB_L, 24h after A and B injection

value: 24h after aspirin and trimetazidine injection


title: brainstem_TG_HFD_OxBis_21


title: D1_AB_M, 24h after A and B injection


title: RRBS hippocampus, WT, biological replicate 3

description: Library name: beta_RRBS7

value: Brain hipocampus

value: wild-type


title: RRBS hippocampus, WT, biological replicate 4

description: Library name: beta_RRBS9


title: RRBS hippocampus, WT, biological replicate 2

description: Library name: beta_RRBS6


title: EO771-ADAR1 p150, replicate 2

city: Guangzhou

first: Qidong

last: Xia

state: Guangdong

address: No.107, Yangjiangxi Road, Guangzhou

department: Breast Tumor Center

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm38.91
Supplementary files format and content: csv file includes count values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: ADAR1 p150 OE


title: brainstem_WT_SD_OxBis_17

value: WT


title: brainstem_TG_HFD_Bis_17

value: HFD


title: U118_Vector

description:
Library name: Vector
Control

value: Control


title: VPA-700 6

city: Melbourne

first: Alison

middle: May

last: Anderson

state: VIC

address: Commercial Road

department: Neuroscience

country: Australia

institute: Monash University

description: Library name: CR44

data_processing:
nf-core/rnaseq pipeline with STAR Salmon was used to produce an abundance matrix with scaled and normalised transcripts per million (TPM)  and a matrix with count-level data. The counts matrix was restricted to protein coding genes.
Data were processed using limma and edgeR and normalised with voom.
Assembly: human GRCh38 (hg38)
Supplementary files format and content: csv file includes raw counts for each Sample

source_name: hESC

extract_protocol:
RNA-seq was harvested using NEBNext® Ultra II
RNA-seq libraries for RNA-seq were prepared using Illumina® (NEBNext®, E7770)

value: hESC

value: valproate 700uM


title: VPA-700 5

description: Library name: C117


title: EO771-ADAR1 p150, replicate 1


title: RRBS hippocampus, Mtr-cKO, biological replicate 4

description: Library name: beta_RRBS5

value: Mtr KO


title: brainstem_WT_HFD_OxBis_23

value: brainstem


title: VPA-700 4

description: Library name: C115


title: VPA-700 3

description: Library name: C114


title: EO771-vector, replicate 2

value: vector


title: EO771-vector, replicate 1


title: brainstem_WT_SD_OxBis_19

value: SD


title: brainstem_WT_HFD_OxBis_20_2

value: OxBis


title: brainstem_WT_HFD_OxBis_20


title: RRBS hippocampus, Mtr-cKO, biological replicate 1

description: Library name: beta_RRBS1


title: RRBS hippocampus, Mtr-cKO, biological replicate 2

description: Library name: beta_RRBS2


title: EO771-12-HETE, replicate 5


title: VPA- 700 1

description: Library name: C112


title: StriatumMut-HypoTH4

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

institute: ENSL

description: Library name: 24

data_processing:
Read were trimmed at their 5'end (15 nucleotides)
Reads mapped on the mouse genome (Grcm39 assembly) using Bowtie2 to produce .bam files
.bam files were processed with Htseq-count to produce count tables
Assembly: Grcm39 mus musculus
Supplementary files format and content: Count files .tsv tables

source_name: Striatum

growth_protocol: Adult mice raised in standard condition.

extract_protocol:
Total RNA was extracted with RNAeasy mini kit (Qiagen). 1 ug of RNA was used /library
libraries were prepared with the CORRALL V2 kit (Lexogen, Vienna Austria)

treatment_protocol: 3 groups of mice per genotype: untreated. Fed for 15 days with low iodine food with propyl-thio-uracyl (PTU) to cause hypothyroidism. Fed with PTU and then with thyroid hormone (TH) for 24 hours to restore TH level.

value: Striatum

value: Hypothyroid+Thyroid hormone

value: PTU+TH

tag: time

value: 15 days+24 hours TH


title: brainstem_TG_SD_OxBis_22_2

value: TG


title: VPA-300 6

description: Library name: BR42

value: valproate 300uM


title: brainstem_TG_HFD_OxBis_23


title: brainstem_WT_HFD_OxBis_20_1


title: EO771-12-HETE, replicate 4


title: EO771-vehicle, replicate 5

value: vehicle


title: VPA-700 2

description: Library name: C113


title: StriatumMut-HypoTH3

description: Library name: 23


title: brainstem_TG_SD_OxBis_21


title: StriatumMut-HypoTH2

description: Library name: 22


title: StriatumMut-HypoTH1

description: Library name: 21


title: EO771-12-HETE, replicate 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm38.91
Supplementary files format and content: csv files include count values for each Sample

value: tumor cells


title: VPA-300 5

description: Library name: B111


title: RRBS hippocampus, Mtr-cKO, biological replicate 3

description: Library name: beta_RRBS4

value: Brain hipocampus


title: EO771-12-HETE, replicate 2


title: VPA-300 4

description: Library name: B109


title: VPA-300 3

description: Library name: B108


title: StriatumMut-Hypo4

description: Library name: 20

value: Hypothyroid

value: PTU

value: 15 days


title: EO771-12-HETE, replicate 1


title: brainstem_WT_SD_OxBis_16

value: WT


title: EO771-vehicle, replicate 4


title: EO771-vehicle, replicate 3


title: StriatumMut-Hypo3

description: Library name: 19


title: brainstem_WT_SD_OxBis_18

value: brainstem


title: VPA-300 2

description: Library name: B107

value: hESC


title: brainstem_TG_SD_OxBis_23

value: SD


title: StriatumMut-Hypo2

description: Library name: 18


title: EO771-vehicle, replicate 2


title: brainstem_TG_SD_OxBis_22

value: OxBis


title: Control 6

description: Library name: A105


title: StriatumMut4

description: Library name: 16

value: Striatum

value: Euthyroid

value: Untreated


title: Control 4

description: Library name: A103


title: HECs, tumor, replicate 3

source_name: lymph node metastases

value: lymph node metastases

value: HECs


title: StriatumMut3

description: Library name: 15


title: brainstem_TG_HFD_OxBis_17

value: TG

value: HFD


title: Control 5

description: Library name: A104


title: HECs, tumor, replicate 2


title: EO771-vehicle, replicate 1

value: tumor cells

value: vehicle


title: StriatumMut-Hypo1

description: Library name: 17

value: Hypothyroid


title: StriatumMut2

description: Library name: 14


title: brainstem_WT_HFD_OxBis_19


title: hippocampus_TG_SD_Bis_4

source_name: hippocampus

value: hippocampus

value: Bis


title: Control 3

description: Library name: A102


title: brainstem_TG_SD_OxBis_22_1


title: hippocampus_TG_SD_OxBis_4


title: VPA-300 1

description: Library name: B106

value: valproate 300uM


title: HECs, tumor, replicate 1


title: StriatumWt-HypoTH4

description: Library name: 12

value: Hypothyroid+Thyroid hormone

value: Wild-type

value: PTU+TH

value: 15 days+24 hours TH


title: Lyso_ribominus_239T_Mock

city: Hefei

first: Ruikun

last: Wu

state: Anhui

address: No.443 Huangshan Road

institute: University of Science and Technology of China

description: Library name: sample53

data_processing:
For data processing, raw reads were first processed with fastp to obtain clean reads.
Clean Reads were then aligned to the reference genome (Human: hg19; Mouse: mm10; C. elegans: ce10) with BWA-MEM or Bowtie2. For circRNA prediction, backsplicing junctions (BSJs) were identified using both CIRI2 and Find_circ, and BSJ reads identified by CIRI2 were used to quantify circRNAs. For linear RNA, read counts were generated using BEDTools.
Assembly: hg19(human), mm10(mouse), ce11(C. elegans)

source_name: cell line

extract_protocol:
Total RNA from cells or C. elegans strains was extracted by TRIzol Reagent or TRIzol LS Reagent according to the manufacturer?s procedures.
The concentration of isolated RNAs was verified by Nanodrop, and RNA quality was checked with gel electrophoresis. For ribosomal RNA-depleted (Ribo-) RNA-seq, rRNA in total RNA was depleted with the Illumina Ribo-Zero Gold kit (Illumia) and subjected to library preparation with the TruSeq Ribo Profile Library Prep Kit (Illumina) according to the manufacturer?s instructions. For Ribo-/RNase R+ RNA-seq, total RNA was rRNA-depleted, RNase R-treated and subjected to library preparation according to the manufacturer?s instructions.

value: WT


title: hippocampus_TG_SD_Bis_3

value: SD


title: StriatumMut1

description: Library name: 13

value: Striatum

value: Euthyroid

value: Untreated


title: HECs, normal, replicate 3

source_name: lymph node

value: lymph node

value: HECs


title: StriatumWt-HypoTH3

description: Library name: 11


title: Control 1

description: Library name: A100

value: hESC


title: BECs, tumor, replicate 3

source_name: primary tumor

value: primary tumor

value: BECs


title: Lyso_ribominus_239T_CQ

description: Library name: sample52


title: HECs, normal, replicate 1


title: Control 2

description: Library name: A101


title: Lyso_ribominus_239T_BafA1

description: Library name: sample51


title: StriatumWt-HypoTH1

description: Library name: 9


title: HECs, normal, replicate 2


title: hippocampus_WT_SD_Bis_12

value: hippocampus


title: hippocampus_TG_SD_OxBis_3

value: TG

value: OxBis


title: StriatumWt-HypoTH2

description: Library name: 10

value: Hypothyroid+Thyroid hormone


title: Lyso_R+_hela_Mock

description: Library name: sample42

value: HeLa


title: BECs, tumor, replicate 2


title: BECs, tumor, replicate 1


title: StriatumWt-Hypo4

description: Library name: 8

value: Hypothyroid

value: Wild-type

value: PTU

value: 15 days


title: hippocampus_WT_HFD_Bis_16

value: WT

value: HFD

value: Bis


title: hippocampus_WT_HFD_OxBis_16


title: Lyso_R+_hela_CQ

description: Library name: sample41

value: CQ


title: Lyso_R+_hela_BafA1

description: Library name: sample40


title: StriatumWt-Hypo3

description: Library name: 7

value: Striatum


title: BECs, normal, replicate 2

source_name: fat pad

value: fat pad


title: BECs, normal, replicate 1


title: hippocampus_WT_SD_OxBis_12

value: SD


title: hippocampus_WT_SD_Bis_11


title: StriatumWt-Hypo2

description: Library name: 6


title: BECs, normal, replicate 3

value: BECs


title: StriatumWt-Hypo1

description: Library name: 5


title: hippocampus_WT_SD_OxBis_11

value: hippocampus


title: Lyso_R+_293T_Mock

description: Library name: sample39


title: StriatumWt4

description: Library name: 4

value: Euthyroid

value: Untreated


title: hippocampus_TG_HFD_Bis_8

value: TG


title: StriatumWt3

description: Library name: 3


title: hippocampus_WT_HFD_Bis_14


title: RNase_R+_293T_shRN6

description: Library name: sample36


title: StriatumWt2

description: Library name: 2


title: Lyso_R+_293T_BafA1

description: Library name: sample37


title: RNase_R+_293T_shNC_6

description: Library name: sample35


title: StriatumWt1

description: Library name: 1


title: Lyso_R+_293T_CQ

description: Library name: sample38


title: Primary tumor-EO771-HEVM3, replicate 1, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38.91
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Briefly, primary tumors and paired lymph nodes from six C57BL/6J mice were collected, washed with Hanks Balanced Salt Solution three times and minced into small pieces using surgical scissors. The tumor tissues were digested with DMEM medium containing 2 mg/ml collagenase I (Worthington, #LS004196), 2 mg/ml collagenase III (Worthington, #LS004182) and 2 mg/mL hyaluronidase (Sigma Aldrich, #H3506) for 2 h at 37 °C under constant shaking. The lymph node tissues were digested with RPMI-1640 medium containing 0.2 mg/ml collagenase P (Sigma Aldrich, #11213857001), 0.8 mg/ml dispase Ⅱ (Sigma Aldrich, #D4693) and 0.01 mg/ml DNase (Sigma Aldrich, #DN25) for 1 h at 37 °C under constant shaking. FBS (final concentration 30%) was added to stop the digestion. Dissociated cell suspensions were then passed through 100 μM and 40 μM filter. Cells were pelleted at 250 g for 5 min, and treated with 2ml of 1× RBC lysis buffer (Biolegend, #420301) on ice for 10 min. The washing buffer was then added and the cells were centrifuged at 1000 rpm for 5 min and was resuspended in PBS.
The single-cell suspension was converted to barcoded scRNA-seq libraries using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit and Chip Kit (10× Genomics) according to the manufacturer’s protocol. Briefly, the single-cell suspension was loaded into each reaction. The RNA transcripts were uniquely barcoded and reverse-transcribed. Complementary DNA (cDNA) was generated, amplified, fragmented, end repaired, and ligated with adaptors to generate sequencing libraries.

value: primary tumor


title: Lymph node-EO771-HEVM3, replicate 1, scRNAseq

description: 10x Genomics

source_name: lymph nodes

value: lymph nodes


title: hippocampus_WT_HFD_OxBis_14

value: OxBis


title: RNase_R+_293T_siRN2

description: Library name: sample34


title: HeartMut-HypoTH4

description: Library name: H22

source_name: Heart

value: Heart

value: Hypothyroid+Thyroid hormone

value: PTU+TH

value: 15 days+24 hours TH


title: HeartMut-HypoTH3

description: Library name: H21


title: hippocampus_TG_HFD_OxBis_7

value: HFD


title: HeartMut-HypoTH2

description: Library name: H20


title: hippocampus_TG_HFD_OxBis_8


title: RNase_R+_293T_siNC_2

description: Library name: sample33

value: WT


title: RNase_R+_293T_siRN1

description: Library name: sample31


title: hippocampus_TG_HFD_Bis_6

value: Bis


title: RNase_R+_293T_siRNT2

description: Library name: sample32


title: hippocampus_TG_HFD_Bis_7


title: HeartMut-HypoTH1

description: Library name: H19

value: 15 days


title: HeartMut-Hypo3

description: Library name: H18

value: Hypothyroid

value: PTU


title: RNase_R+_293T_siNC_1_T2

description: Library name: sample30


title: hippocampus_TG_HFD_OxBis_6

value: hippocampus


title: ChIP-seq_noab

city: Beijing

first: Hao

last: Tian

address: 105 West Third Ring Road North, Haidian District, Beijing,

institute: Capital normal university

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC and aligned to the glycine max v2.1 reference genome using Bowtie2, and sorted and indexed using samtools.All 3 repeats were merged into bigwig
Assembly: Ws82v2.1
Supplementary files format and content: bigwig

source_name: first tri-foliate leaf

extract_protocol:
Approximately 0.5 g of soybean mature leaves were used in each experiment. About 1 to 2g of the sample was ground into a fine powder in liquid nitrogen.
Soybean tissues were crosslinked with 1% formaldehyde and quenched with 0.2 M glycine. For each experiment, about 1 to 2g of the sample was ground into a fine powder in liquid nitrogen. The nuclei were lysed in Honda buffer (0.44 M sucrose, 1.25% Ficoll,2.5% Dextran T40,20mM Hepes,10mM MgCl2, 0.5% Triton X-100, 5mM DTT, and protease inhibitor cocktail) at 4°C , and then the chromatin was fragmented into 200–600 bp by ultrasound processing using a Bioruptor (Diagenode). The lysates were centrifuged at 16000 g at 4 °C for 20 min. Then 2-5μL antibody (H3K9ac,) and 40μL suspended protein G magnetic beads (Life Technologies) were incubated at 4°C for 8h and rotated. The protein-DNA complexes were subjected to immunoprecipitation by incubating the antibody-bead complexes with the fragmented chromatin. Then, the target protein-DNA complexes were eluted from the beads by adding 1mL of freshly prepared High salt buffer, low salt buffer, LiAc buffer, and TE buffer. After reverse cross-linking of DNA and protein by Chelex-100, ChIP-DNA was extracted using phenol: chloroform: isoamyl alcohol. ChIP-DNA libraries were prepared using a NEBNext ®Ultra ™II DNA Library Preparation Kit. DNA clean beads (vazyme, N411) were used to select 250–650 bp library fragments.

value: first tri-foliate leaf

tag: chip antibody

value: none (input)

tag: cultivar

value: free-running


title: HeartMut-Hypo2

description: Library name: H17


title: C1032-3

city: 北京

first: 何玥

middle: 玥

last: 何

address: 东城区骑河楼街17号

institute: 首都医科大学附属北京妇产医院

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45C on PrimeView Human Gene Expression Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 .

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: Normal siha cells were treated with the drug paclitaxel and then CRISPR-Cas9 technology was used to construct the virus and knock out the KCP gene-3

label_protocol: Affymetrix

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000.

value: Cervical cancer tissue


title: C1042-3

institute: 首都医科大学附属北京妇产医院

source_name: Normal siha cells plus sgRNA negative control group of drug-treated cells with viral infection-3


title: C1032-1

institute: 首都医科大学附属北京妇产医院

source_name: Normal siha cells were treated with the drug paclitaxel and then CRISPR-Cas9 technology was used to construct the virus and knock out the KCP gene-1


title: hippocampus_TG_SD_OxBis_2

value: TG

value: SD


title: HeartMut-Hypo1

description: Library name: H16

value: Heart


title: ChIP-seq_input_ZT20biol rep3

description: input_ZT_20_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: hippocampus_TG_SD_Bis_2


title: RN1_ribominus_293T_MutRN1

description: Library name: sample28


title: RN1_ribominus_293T_WTRN1

description: Library name: sample29


title: ChIP-seq_input_ZT20biol rep2


title: C1032-2

institute: 首都医科大学附属北京妇产医院

source_name: Normal siha cells were treated with the drug paclitaxel and then CRISPR-Cas9 technology was used to construct the virus and knock out the KCP gene-2


title: C1042-1

institute: 首都医科大学附属北京妇产医院

source_name: Normal siha cells plus sgRNA negative control group of drug-treated cells with viral infection-1


title: C1042-2

institute: 首都医科大学附属北京妇产医院

source_name: Normal siha cells plus sgRNA negative control group of drug-treated cells with viral infection-2


title: hippocampus_WT_HFD_OxBis_15

value: OxBis


title: RK_nascentRNA_IP_shRK

description: Library name: sample26


title: hippocampus_WT_HFD_Bis_15


title: RN1_ribominus_293T_EV

description: Library name: sample27


title: hippocampus_WT_SD_Bis_10


title: ChIP-seq_input_ZT20biol rep1


title: HeartMut3

description: Library name: H15

value: Euthyroid

value: Untreated


title: ChIP-seq_input_ZT16biol rep3

description: input_ZT_16_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: ChIP-seq_input_ZT16biol rep2


title: RK_nascentRNA_IP_shNC

description: Library name: sample25


title: HeartMut1

description: Library name: H13


title: hippocampus_WT_SD_OxBis_10


title: HeartWt-HypoTH4

description: Library name: H12

value: Hypothyroid+Thyroid hormone

value: Wild-type

value: PTU+TH

value: 15 days+24 hours TH


title: hippocampus_TG_HFD_OxBis_5

value: HFD


title: RK_ribonimus_293T_EV

description: Library name: sample23

value: WT


title: RK_ribonimus_293T_OERK

description: Library name: sample24


title: ChIP-seq_input_ZT12biol rep2

description: input_ZT_12_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: ChIP-seq_input_ZT16biol rep1


title: hippocampus_TG_HFD_Bis_5

value: hippocampus

value: Bis


title: HeartMut2

description: Library name: H14


title: HeartWt-HypoTH2

description: Library name: H10


title: RK_ribominus_293T_shRK

description: Library name: sample19


title: hippocampus_TG_SD_OxBis_1


title: ChIP-seq_input_ZT12biol rep1

value: first tri-foliate leaf

value: none (input)


title: hippocampus_WT_HFD_Bis_13


title: ChIP-seq_input_ZT12biol rep3

value: free-running


title: HeartWt-HypoTH1

description: Library name: H9


title: hippocampus_TG_SD_Bis_1

value: TG


title: RK_R+_hela_shRK

description: Library name: sample10

value: HeLa


title: hippocampus_WT_HFD_OxBis_13


title: RK_R+_hela_shNC

description: Library name: sample9


title: ChIP-seq_input_ZT8biol rep3

description: input_ZT_8_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: HeartWt-Hypo4

description: Library name: H8

value: Heart

value: Hypothyroid

value: PTU

value: 15 days


title: HeartWt-HypoTH3

description: Library name: H11

value: Hypothyroid+Thyroid hormone


title: HeartWt-Hypo3

description: Library name: H7

value: Wild-type


title: ChIP-seq_input_ZT8biol rep2


title: HeartWt-Hypo2

description: Library name: H6


title: ChIP-seq_input_ZT8biol rep1


title: RK_R+_293T_shRK_rep3

description: Library name: sample8


title: RK_R+_293T_shRK_rep2

description: Library name: sample7


title: Overex Total Rep2

city: NY

first: Robert

last: Schneider

address: 550 1ST AVE

institute: NYU Langone Health

data_processing:
Cutadapt to remove linker and polyA tail
BowTie to remove rRNA and alignment to rRNA library
Low quality reads were trimmed with Trimmomatic
sequences were aligned wih STAR;alignment results were sorted with SAMtools
RIVET was used to analyse translationally differentially expressed genes
Assembly: mm10
Supplementary files format and content: tab delimited text fileincludes raw counts for each file

growth_protocol: c2c12 were grown in DMEM with 10% FBS

extract_protocol:
Qiagen Rneasy MiniElute Cleanup Kit
500ngRNA used; NEBNext® Ultra DNA Library Prep

treatment_protocol: differentiation medium: DMEM with 2% HS for 48hrs

value: mousemyoblastcell line

value: AUF1 overexpression


title: HeartWt4

description: Library name: H4

value: Euthyroid

value: Untreated


title: ChIP-seq_input_ZT4biol rep3

description: input_ZT_4_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: HeartWt-Hypo1

description: Library name: H5


title: WT Total Rep 2

value: WT


title: ChIP-seq_input_ZT4biol rep1


title: RK_R+_293T_shNC_rep3

description: Library name: sample5


title: HeartWt3

description: Library name: H3


title: Overex High Rep2

molecule: cytoplasmic RNA


title: RK_R+_293T_shRK_rep1

description: Library name: sample6


title: ChIP-seq_input_ZT0biol rep3

description: input_ZT_0_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: RK_R+_293T_shNC_rep1

description: Library name: sample3


title: RK_R+_293T_shNC_rep2

description: Library name: sample4


title: ChIP-seq_input_ZT4biol rep2


title: Overex Total Rep1


title: WT High Rep2


title: HeartWt2

description: Library name: H2


title: ChIP-seq_input_ZT0biol rep2


title: RNA Seq of BMMs: IGF2BP2_KO3_IL4

city: Saarbruecken

first: Jessica

last: Hoppstaedter

address: Campus C2 3

department: Pharmacy

description: Library name: IGF2BP2_KO3_IL4

data_processing:
Raw sequencing reads were demultiplexed and assessed for quality control using FastQC (v0.11.2). Read processing was performed using the grape-nf pipeline (v1.1.3) with Nextflow (v20.10.0), and reads were mapped to the GRCm38/mm10 genome assembly. Following alignment, gene counts were obtained and used for differential expression analysis with DESeq2 (v1.40.2) in the R programming language. Differentially expressed genes (DEGs, p < 0.05) were identified by comparing IGF2BP2 KO vs. WT under both untreated and IL-4-treated conditions.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text-files include TPM values for each sample.
Supplementary files format and content: tab-delimited text-files include DESeq2 data for all comparisons.

source_name: bone-marrow derived macrophages

growth_protocol: Bone marrow from the femur and tibia was flushed out with media and passed through a 100 µm cell strainer before undergoing erythrocyte lysis in a hypotonic buffer (155 mM NH₄Cl, 10 mM KHCO₃, 1 mM Na₂EDTA) at 37°C for 3 minutes. Cells were then cultured for differentiation into BMMs for 6 days in a humidified incubator at 37°C with 5% CO₂ in RPMI-1640 cell culture medium, supplemented with 10% FBS, 1% 200 mM L-glutamine, 100 U/ml penicillin/streptomycin, and 50 ng/ml murine M-CSF (BMM medium). All experiments were conducted in BMM medium.

extract_protocol:
Total RNA was extracted using the High Pure RNA Isolation Kit (Roche, #11828665001) following the manufacturer’s protocol. The isolated RNA was immediately stored at −80°C. RNA integrity was assessed using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Kit (Agilent, #5067-1513), and only samples with an RNA Integrity Number (RIN) > 9 were used for further analysis.
RNA libraries were prepared from 500 ng of total RNA. Poly(A) enrichment was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, #E7490) following the manufacturer’s protocol. cDNA library preparation was carried out with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7420) as per the supplier’s recommendations. Briefly, first- and second-strand cDNA synthesis was performed, followed by adapter ligation and PCR amplification (12 cycles). PCR cleanup was conducted using Agencourt AMPure XP beads (Beckman Coulter, #A63881). The libraries were then sequenced (1 × 75 nt) on a NextSeq 500 (Illumina) platform.

treatment_protocol: 500,000 BMMs (1ml/well) were seeded in a 12-well plate and treated for 8 h with IL-4 (20ng/ml) on the next day.

value: bone-marrow derived macrophages

value: KO