title: HK2 cell transfected with circAASS-overexpression plasmids, repeat 3

city: guangzhou

first: peng

last: wang

address: 1838 North Guangzhou Avenue

institute: Southern Medical University

description:
Library name: Sample6
with PE150 model

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome of Homo_sapiens.GRCh38 using STRA software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: EXCEL file include FPKM values for each sample

growth_protocol: HK2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/Ham’s F12 medium (Invitrogen), which contained (supplemented with) 10% FBS (Invitrogen).

extract_protocol:
Total RNA was extracted from tissues and cells by Trizol reagent (Invitrogen). RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit（Life Technologies, Q10210）.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: HK2 cells were transfected with either empty vector plasmids or circAASS-OE plasmids. After the validation of the overexpression of circAASS, HK2 cell transfected with empty-vector plasmids or circAASS-OE plasmids were subjected to 1% hypoxia treatment for 24 hours followed by 12-hour reoxygenation.

value: Proximal tubular epithleial cell

value: circAASS-overexpressed

value: 1% oxygen for 24 hours followed by 12-hour reoxygenation


title: Overex High Rep1

status: Public on Mar 01 2026

type: SRA

city: NY

first: Robert

last: Schneider

address: 550 1ST AVE

country: USA

institute: NYU Langone Health

library_source: transcriptomic

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

molecule: cytoplasmic RNA

organism: Mus musculus

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

tag: cell line

tag: cell type

value: mousemyoblastcell line

tag: genotype

value: AUF1 overexpression


title: HeartWt1

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

country: France

institute: ENSL

description: Library name: H1

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

molecule: total RNA

source_name: Heart

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: Heart

value: Euthyroid

value: Wild-type

tag: treatment

value: Untreated


title: RNA Seq of BMMs: IGF2BP2_KO2_IL4

city: Saarbruecken

first: Jessica

last: Hoppstaedter

address: Campus C2 3

department: Pharmacy

country: Germany

institute: Saarland University

description: Library name: IGF2BP2_KO2_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


title: WT Total Rep 1

value: WT


title: HK2 cell transfected with circAASS-overexpression plasmids, repeat 2

country: China

description:
Library name: Sample5
with PE150 model

organism: Homo sapiens


title: ChIP-seq_input_ZT0biol rep1

city: Beijing

first: Hao

last: Tian

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

institute: Capital normal university

description: input_ZT_0_replicate_123_PE_sorted_sampled_merged_reheader.bw

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 samtools.All 3 repeats were merged into bigwig
Assembly: Ws82v2.1
Supplementary files format and content: 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.
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.

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.

tag: tissue

value: first tri-foliate leaf

tag: chip antibody

value: none (input)

tag: cultivar

value: free-running


title: WT High Rep1


title: HK2 cell transfected with circAASS-overexpression plasmids, repeat 1

description:
Library name: Sample4
with PE150 model


title: Cis3

city: nanjing

first: Wenli

last: Hao

address: No. 22 Hankou Road, Gulou District, Nanjing City, Jiangsu Province

institute: Nanjing University

description:
Library name: Sample 9
C3

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: cell line

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

value: cell line

value: Hair cell-like cell line


title: RNA Seq of BMMs: IGF2BP2_KO1_IL4

description: Library name: IGF2BP2_KO1_IL4


title: HK2 cell transfected with empty-vector plasmids, repeat 3

description:
Library name: Sample3
with PE150 model

value: Proximal tubular epithleial cell


title: ChIP-seq_H3K27ac_ZT20biol rep3

description: k27_ZT_20_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: ChIP-seq_H3K27ac_ZT20biol rep1


title: ChIP-seq_H3K27ac_ZT20biol rep2


title: RNA Seq of BMMs: IGF2BP2_KO3

description: Library name: IGF2BP2_KO3


title: Cis2

description:
Library name: Sample 8
C2


title: HK2 cell transfected with empty-vector plasmids, repeat 2

description:
Library name: Sample2
with PE150 model


title: Cis1

description:
Library name: Sample 7
C1


title: RNA Seq of BMMs: IGF2BP2_KO1

description: Library name: IGF2BP2_KO1


title: ChIP-seq_H3K27ac_ZT16biol rep3

description: k27_ZT_16_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: RNA Seq of BMMs: IGF2BP2_KO2

description: Library name: IGF2BP2_KO2


title: M032, negative control

city: 广州

first: Zhou

last: Jiewen

address: 广东省广州市越秀区中山大学北校区

institute: 中山大学附属第一医院

description: Library name: M032CTRL

data_processing:
The RNA-sequencing data were processed through a series of quality control steps using FastQC (version 0.11.9).
Fastp (version 0.39) was employed to filter out low-quality reads and adapter sequences.
The clean reads were then aligned to the human reference genome (hg38) using the HISAT2 alignment tool (version 2.2.1).
Assembly: StringTie assembler (version 2.1.4)
Supplementary files format and content: tab-delimited text file includes raw counts

source_name: human nasal epithelium

extract_protocol:
RNA extraction from samples was accomplished using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA), following the manufacturer’s prescribed protocol.
RNA-sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA), following the recommended kit procedures.

value: human nasal epithelium

value: nasal epithelial cells


title: Neo3

description:
Library name: Sample 6
B3


title: ChIP-seq_H3K27ac_ZT16biol rep1


title: ChIP-seq_H3K27ac_ZT12biol rep3

description: k27_ZT_12_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: RNA Seq of BMMs: WT3_IL4

description: Library name: WT3_IL4


title: M032, SA7 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M032A7B


title: ChIP-seq_H3K27ac_ZT12biol rep2


title: Neo2

description:
Library name: Sample 5
B2


title: RNA Seq of BMMs: WT1_IL4

description: Library name: WT1_IL4


title: M032, SA7 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M032A7


title: M032, SA4 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M032A4B


title: Con2

description:
Library name: Sample 2
A2


title: HK2 cell transfected with empty-vector plasmids, repeat 1

description:
Library name: Sample1
with PE150 model

value: 1% oxygen for 24 hours followed by 12-hour reoxygenation


title: RNA Seq of BMMs: WT2_IL4

description: Library name: WT2_IL4


title: RNA Seq of BMMs: WT3

description: Library name: WT3


title: ChIP-seq_H3K27ac_ZT16biol rep2


title: Con1

description:
Library name: Sample 1
A1


title: ChIP-seq_H3K27ac_ZT8biol rep3

description: k27_ZT_8_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: M032, CS infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M032B


title: ChIP-seq_H3K27ac_ZT8biol rep2


title: ChIP-seq_H3K27ac_ZT12biol rep1


title: M032, SA4 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M032A4


title: nop2 mutant zebrafish (48 dpf) brain tissues  for bs-seq

city: Zhan Jiang

first: Xiaoyu

last: Li

state: Guangdong

address: 57 People's Avenue

institute: Affiliated Hospital of Guangdong Medical University

description:
Library name: sample4
dss_dmls_final.bed.txt
dss_dmrs_final.bed.txt

data_processing:
For ribo-seq: Low quality reads were filtered by fastp. Raw reads containing over 50% of low quality bases or over 10% of N bases were removed. Adapter sequences were trimmed. Reads with length between 20-40bp were retained for subsequent analysis. Short reads alignment tool Bowtie2 was used for mapping reads to ribosome RNA (rRNA) database, GenBank, Rfam database. The reads mapped to rRNAs, transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), and miRNA were removed. Processed RNA-seq reads were aligned to the genome using whole genome alignment by STAR with 2- pass setting enabled. The reads mapped to classical noncoding RNAs (including long noncoding RNAs, microRNA precursors) were abandoned. Then remaining RFs were assigned to different genomic features (5’UTR, CDS, 3’UTR and intron) based on the position of the 5’ end of the alignment. For BS-seq: Low quality bases and Adapter sequences were trimmed by using Trimmomatic V0.38. The parameter settings used was “ HEADCROP:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20”. The cleaned reads were mapped back to Petunia hybrida genome reference (v1.6.2). using BS-RNA V1.0. The parameter settinds used was default parameter recomanded by BS-RNA document , detailed data processing steps were listed as below:The first step is the pre-treatment of reference genome sequences, sequencing data, and gene annotation file: (1) the reference genome sequence is converted twice in parallel as follows: (A) cytosines are replaced by thymines and (B) guanines are replaced by adenines. This genome sequence conversion only need to be performed the first time one uses the reference genome sequence, which means it could be reused for all the following analysis which use the same reference genome sequence. (2) cytosines in reads of the T-rich sequencing read file are replaced by thymines, while guanines in reads of the A-rich sequencing read file are replaced by adenines. And (3) the gene annotation file in GTF format is revised to fit the converted reference genome sequences. Each annotation line is converted twice simultaneously: "C-T" and "G-A" are appended to the chromosome label in the gene annotation file, respectively. Next, the HISAT2 program is invoked by BS-RNA to build alternative splicing according to the modified annotation gene file and align pre-processed reads to the converted reference genome sequence. BS-RNA filters out two types of reads that are mapped to the reference genome sequence as follows: (1) reads mapped to multiple positions and (2) reads mapped to the wrong strands (T-rich reads mapped to reverse-complement of reference sequence converted C to T or to reference sequence converted G to A, A-rich reads mapped to reference sequence converted C to T or to reverse complements of reference sequence converted G to A). The original mapping file (SAM format), filtered mapping file (SAM format), and mapping report file will be provided by BS-RNA when the mapping step is finished.  Further, BS-RNA splits the filtered mapping file into two files: a Watson-strand SAM format file (mapped to reference converted C to T) and a Crick-strand SAM format file (mapped to reference converted G to A). SAMtools is embedded into BS-RNA to convert the Watson-strand and Crick-strand SAM format files to BAM format and then sort these two BAM files according to the chromosome coordination. Single-base coverage information is extracted using the mpileup command of SAMtools from the sorted BAM files. For each cytosine position in the genome, the read base (SAMtools mpileup output information) is deemed to support methylated cytosine sequencing if it matches a dot or a comma, otherwise it is deemed to support an unmethylated cytosine sequencing. We excluded the reference skips (which menas "<" or ">" is not counted). BS-RNA provides the annotation result for each covered cytosine in a BED (.bed.txt) file with information related to the methylation character: location of the covered cytosine in the reference, sequence context type (CG/CHG/CHH, H = A, T, or C), reference sequencing depth (total number of reads mapped to the cytosine site), cytosine sequencing depth (total number of reads that supported a methylated cytosine at this site), and methylation level (the ratio of cytosine sequencing depth to sequencing depth at the cytosine site) on the Watson strand and Crick strands for each chromosome to the users. Differentially methylated cytosine (DMCs) were detected using MethylKit [3] among CpG sites with at least 10x coverage. The parameter settings used was “--mincov 5 --m_cutoff 0.05 --q_cutoff 0.05”. Then detected DMCs were filtered according to the standard: (1) corrected q-value must be less than 0.05; (2) methylation level difference must be greater than 0.05.
Assembly: GRCz11
Supplementary files format and content: bed and xlsx format which contains m5c peaks of bs-seq and gene expression value of ribo-seq

organism: Danio rerio

source_name: brain

extract_protocol:
For ribo-seq: Tissues were immediately frozen in liquid nitrogen and ground to power in liquid nitrogen with a mortar and pestle, then dissolved in 400μL of lysis buffer. The resuspended extracts in lysis buffer were transferred to new microtubes, pipetted several times and incubated on ice for 10 min. Then cells were triturated ten times through a 26-G needle. The lysate was centrifuged at 20000g for 10min at 4℃, and the supernatant was collected. To prepare RFs , 10μL of RNase I (NEB, Ipswich, MA, USA) and 6μL of DNase I (NEB, Ipswich, MA, USA) were added to 400μL of lysate，which was then incubated for 45 min at room temperature with gentle mixing on a Nutator mixer. Nuclease digestion was stopped by adding 10μL of SUPERase·In RNase inhibitor (Ambion, Austin, TX, USA). Size exclusion columns (illustra MicroSpin S-400 HR Columns; GE Healthcare; catalog no. 27- 5140-01) were equilibrated with 3 mL of polysome buffer by gravity flow and centrifuged at 600g for 4 min at room temperature. 100μL of digested RFs were added to the column and centrifuged at 600g for 2 min. Next, 10μL 10% (wt/vol) SDS was added to the elution, and RFs with a size greater than 17nt was isolated according to the RNA Clean and Concentrator-25 kit (Zymo Research;R1017). rRNA was removed using the method reported previously[2]. Briefly, short (50–80 bases) antisense DNA probes complementary to rRNA sequences was added to solution containing RFs, then RNase H (NEB, Ipswich, MA, USA) and DNase I (NEB, Ipswich, MA, USA) was added to digest rRNA and residual DNA probes. Finally, RFs were further purified using magnet beads (Vazyme, Nanjing, Jiangsu, China) For BS-seq: Total RNA was extracted using Trizol reagent (Thermo Fisher Scientific) and the concentration and integrity of total RNA were measured by Qubit RNA BR Assay and 2% agarose gel electrophoresis, respectively.
For ribo-seq: After obtaining ribosome footprints above, Ribo-seq libraries were constructed using NEBNext® Multiple Small RNA Library Prep Set for Illumina® (catalog no.E7300S, E7300L). Briefly, adapters were added to both ends of RFs, followed by reverse transcription and PCR amplification. The 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina NovaSeq X plus Gene Denovo Biotechnology Co. (Guangzhou, China). For BS-seq: After quality testing, the RNA-Bis libraries were constructed by E-GENE Co. Ltd. as follows. Briefly, the extracted total RNA was firstly subjected to DNase I (NEB) treatment at 37℃ for 30min to remove residual DNA. After purification, mRNA was isolated using Dynabeads™ mRNA Purification Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. The isolated mRNA was quantified by Qubit RNA HS Assay and then 1/500 amount of artificial spike-in RNA about 700nt length from pUC19 plasmid was mixed in as control. RNA bisulfite conversion of the isolated RNA samples with spike-in control was conducted using EZ RNA Methylation Kit (Zymo Research) with two cycles of 70 ℃ for 5min followed by 54℃ for 45min incubation and then purified using the provided Zymo-Spin IC Column according to the manufacturer’s instructions. After purification, an UMI adapter was ligated to the 3’ end of the converted RNA using T4 RNA ligase (NEB). Seven bases of UMI were designed for PCR based duplication evaluation. Ligated RNA was reverse transcribed using SuperScript II (Invitrogen) and the cDNA was subjected to a 3′ ligation with a second adaptor using T4 ligase. The strand-specific libraries were finally amplified for about 10 cycles in a PCR reaction. After analyzed by Agilent Bioanalyzer (Agilent Technologies，USA) and quantified by real time PCR, RNA-Bis libraries were sequenced using Illumina sequencer platform (Illumina，USA).

value: brain

value: primary cells

value: whole brain cells

value: nop2 mutant


title: Con3

description:
Library name: Sample 3
A3


title: Neo1

description:
Library name: Sample 4
B1


title: RK_ribominus_293T_shNC

city: Hefei

first: Ruikun

last: Wu

state: Anhui

address: No.443 Huangshan Road

institute: University of Science and Technology of China

description: Library name: sample18

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)

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.


title: ChIP-seq_H3K27ac_ZT8biol rep1


title: M032, SA2 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M032A2B


title: RNA Seq of BMMs: WT2

description: Library name: WT2


title: Apc-knockout_IGF2BP3 OE_rep3

city: Kyoto

first: Masahiro

last: Inoue

address: Shimoadachi-cho 46, Sakyou-ku

country: Japan

institute: Kyoto University, Graduate School of Medicine

description: Library name: DK24015_03

data_processing:
The poly (A) tail and adapter sequences were removed using BBDuk (BBMap version 38.96, https://sourceforge.net/projects/bbmap/) with the following parameters: k=13, ktrim=r, useshortkmers=t, mink=5, qtrim=r, trimq=10, and minlength=20.
Trimmed reads were mapped to the mm10 genome (Ensembl GRCm38 release 102) using STAR version 2.7.10a14 with the following parameters: outFilterType=BySJout, outFilterMultimapNmax=20, alignSJoverhangMin=8, alignSJDBoverhangMin=1, outFilterMismatchNmax=999, outFilterMismatchNoverLmax=0.1, alignIntronMin=20, alignIntronMax=1,000,000, and alignMatesGapMax=1,000,000.
Read counts for each gene were obtained using HTSeq-count version 1.99.215 with the following parameters: m=intersection-nonempty and s=yes.
Assembly: mm10
Supplementary files format and content: tab-delimitated text file includes raw counts, gene symbols, and Ensembl Gene IDs for each samples

source_name: mouse intestinal organoids

extract_protocol:
Total RNA was extracted with the RNeasy mini kit (Qiagen, 74106) plus on-column DNAse I digestion (Qiagen, 79254) according to the manufacturer's instructions.
RNA sequencing libraries were prepared from 500 ng of total RNA using a Quant Seq 3′ mRNA-Seq Library Preparation Kit FWD (Lexogen, Vienna, Austria)

value: mouse intestinal organoids

value: Apc-knockout, IGF2BP3 overexpression


title: nop2 sibling zebrafish (48 dpf) brain tissues for bs-seq

description:
Library name: sample3
dss_dmls_final.bed.txt
dss_dmrs_final.bed.txt

value: nop2 sibling


title: RNA Seq of BMMs: WT1

description: Library name: WT1

value: bone-marrow derived macrophages

value: WT


title: Apc-knockout_IGF2BP3 OE_rep2

description: Library name: DK24015_02


title: M032, SA1 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M032A1B


title: M032, SA2 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M032A2


title: mutant-riboseq

description: Library name: Sample4

data_processing:
The clean data were mapped to the reference genome using Hisat2 software. Guiding by the Ensembl GTF gene annotation file, featureCounts was used to obtain the gene level FPKM as the expression profiles of mRNA, fold change and p-value were calculated based on FPKM.
Assembly: GRCg11
Supplementary files format and content: excel format. Gene expression values (TPM and Counts)
Library strategy: Ribo-Seq

source_name: head

extract_protocol:
Total RNA was isolated from the head using TRIZOL reagent (Invitrogen, 15596018CN), 2 ug of total RNA was used for the construction of sequencing libraries.
Eukaryotic mRNA with polyA tail was enriched by magnetic beads with Oligo(dT), and the mRNA was interrupted by buffer solution. Using fragmented mRNA as template and random oligonucleotides as primer, the first cDNA strand was synthesized in M-MuLV reverse transcriptase system, then the RNA strand was degraded by RNaseH, and the second cDNA strand was synthesized in DNA polymerase I system using dNTPs as raw material. The purified double-stranded cDNA was end-repaired, A-tail was added, and sequencing joints were connected. cDNA of about 200bp was screened by AMPure XP beads for PCR amplification, and PCR products were purified by AMPure XP beads again. Finally, A library was obtained. The construction principle of the database is shown below.

value: head

value: mutant


title: Apc-knockout_IGF2BP3 OE_rep1

description: Library name: DK24015_01


title: M032, SA1 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M032A1


title: ChIP-seq_H3K27ac_ZT4biol rep1

description: k27_ZT_4_replicate_123_PE_sorted_sampled_merged_reheader.bw

value: first tri-foliate leaf

value: free-running


title: ChIP-seq_H3K27ac_ZT4biol rep2


title: Apc-knockout_rep3

description: Library name: DK24138_03

value: Apc-knockout


title: mutant-RNAsseq

description: Library name: Sample2

data_processing:
The clean data were mapped to the reference genome using Hisat2 software. Guiding by the Ensembl GTF gene annotation file, featureCounts was used to obtain the gene level FPKM as the expression profiles of mRNA, fold change and p-value were calculated based on FPKM.
Assembly: GRCg11
Supplementary files format and content: excel format. Gene expression values (TPM and Counts)


title: Apc-knockout_rep1

description: Library name: DK24138_01


title: M031, CS infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M031B

value: human nasal epithelium


title: ChIP-seq_H3K27ac_ZT0biol rep2

description: k27_ZT_0_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: ChIP-seq_H3K27ac_ZT4biol rep3


title: M031, negative control

address: 广东省广州市越秀区中山大学北校区

description: Library name: M031CTRL

value: nasal epithelial cells


title: Ctrl-6m_3

city: Winnipeg

first: Athanasios

last: Zovoilis

state: MB

address: 745 Bannatyne Ave

department: Biochemistry and Medical Genetics

country: Canada

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

tag: age

value: 6 months

value: Hippocampus L+R


title: Ctrl-6m_2

description: Total RNA (Native)


title: ChIP-seq_H3K27ac_ZT0biol rep3


title: Female RPC-ERαKO mouse, scRNAseq

city: Firenze

first: Giulia

last: Carangelo

address: Viale Pieraccini 6

country: Italy

institute: University of Florence

description: C57Bl/6 mice, 10x Genomics data

library_source: transcriptomic single cell

data_processing:
Basecall performed with cellranger mkfastq v6.1.2
Single cell feature counts performed with cellranger count v6.1.2
Reference genome alignment performed with STAR v2.7.5a_2020-06-29
Assembly: mm10
Supplementary files format and content: All tab-separated values files

source_name: kidney

extract_protocol:
The single cell suspension with 95% viability was run on a 10x Chromium Single Cell instrument (10x Genomics, Pleasanton, CA) following Manufacturer’s instructions
3’ gene expression libraries were constructed following 10x Genomics's instructions
Libraries were sequenced on an Illumina NextSeq500 (Illumina Inc., San Diego, CA).

treatment_protocol: Mice received doxycycline induction at 20 days of age and were traced until 90 days of age

value: kidney

value: Total cells from glomerulus kidney

tag: Sex

value: female

tag: disease state

value: healthy


title: M031, SA7 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M031A7B


title: M031, SA7 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M031A7


title: ChIP-seq_H3K27ac_ZT0biol rep1


title: M031, SA4 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M031A4B


title: ChIP-seq_H3K9ac_ZT20biol rep3

description: k9_ZT_20_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: APP-6m_3

description: Total RNA (Native)

value: APP NL-G-F


title: Male mouse, scRNAseq

description: C57Bl/6 mice, 10x Genomics data

value: male


title: Apc-knockout_rep2

description: Library name: DK24138_02

value: mouse intestinal organoids


title: APP-6m_2

description: Total RNA (Native)


title: Male_SW_MGO_rfp_rep4

city: Madison

first: Zachary

middle: T

last: Campbell

state: WI

address: 1111 Highland Avenue

department: Anesthesiology

institute: University of Wisconsin - Madison

data_processing:
Raw files were downloaded from Illumina BaseSpace and subjected to quality assessment with FastQC 0.11.5 (Babraham Bioinformatics)
Sequence reads were trimmed for adaptor sequence
Strand specific mapping was conducted with TopHat 2.1.1 (with Bowtie 2.2.9) to the mouse reference genome (NCBI reference assembly GRCm38.p4) and reference transcriptome (Gencode vM10).
Processed bam files were quantified for each gene using Cufflinks 2.2.1 with gencode.vM10 genome annotation. Read counts were not normalized by length by the using the Cufflinks option -- no–length–correction.
Relative abundance was calculated using TPM
Assembly: mm10
Supplementary files format and content: excel file containing TPM values for processed data

source_name: DRG

extract_protocol:
MicroSpin S-400 columns (GE Healthcare) were used to isolate ribosome bound RNAs. After rRNA was removed using RiboCop rRNA depletion kit (Lexogen), footprints were dephosphorylated then size selected (28-34nt) by PAGE on 15% TBE-Urea gels (Bio-Rad). Footprints were generated by SMARTer smRNA-Seq kit for Illumina (TaKaRa).
RNA abundance was quantified using the Quantseq 3ʹ mRNA-Seq library kit (Lexogen). The concentrations of purified libraries were quantified using Qubit (Invitrogen)

treatment_protocol: Treatment with saline as a control measurement

value: DRG

tag: strain

value: SW

value: WT

value: Male

value: Methylglyoxal (MGO) at 2 mg/kg, i.p; for 6 days


title: sibling-riboseq

description: Library name: Sample3

value: head


title: Male_SW_MGO_rfp_rep3


title: ChIP-seq_H3K9ac_ZT20biol rep1

value: first tri-foliate leaf

value: free-running


title: Male_SW_MGO_rfp_rep2


title: Female mouse, scRNAseq

description: C57Bl/6 mice, 10x Genomics data


title: leaves, Spore Infection + DHEA Rep4

city: Jena

first: Emanuel

last: Barth

address: Leutragraben 1

department: Bioinformatics Core Facility FSU Jena

institute: Friedrich Schiller University Jena

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
Raw sequencing reads were assessed for quality using FastQC (version 0.11.9).
Adaptor trimming, quality filtering, and read preprocessing were performed using fastp (version 0.23.2). In detail, 5' and 3' bases with a Phred quality score below 28 were cut, and reads were removed if they had more than one ambiguous base, an average quality score below 28, or a length of fewer than 15 bases.
Processed reads were aligned to the current A. thaliana genome (tair10.1) using Hisat2 (version 2.2.1) with standard parameters. The aligned reads were sorted and indexed using SAMtools (version 1.11).
Read counting was performed using featureCounts (version 2.0.1) with the tair10.1 annotation as reference.
Assembly: tair10.1
Supplementary files format and content: semicolon-delimited csv file includes raw counts for each sample

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: 10-day-old seedlings ofA. thalianaCol. 0 (A. thaliana) cultivated on MS-medium (Murashige and Skoog, 1962) were transferred to poor nutrient medium (PNM; Camehl et al., 2011) consisting of 5 mM KNO3, 2 mM MgSO4, 2 mM Ca(NO3)2, 0.01 µM FeSO4, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0,2 µM Na2MoO4, 0.01 µM CoCl2, 10.5 g L−1 agar (pH 5.6).

extract_protocol:
RNA was isolated using TRIzol® Reagent (Invitrogen™ by Thermo Fisher Scientific, MA, USA), as described previously (Chomczynski, 1993;Shiko et al., 2023).
RNA sequencing library preparation was prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: 7 days oldA. thalianaplants were transferred to PNM medium. After 2 days of adaption to the new medium, plants were treated with 10 µM DHEA (dissolved in 0.12% DMSO), while 0.12% DMSO was used as a mock-treatment. Leaves were harvested after 1 h and immediately frozen in liquid nitrogen. Additionally,A. thalianaplants were infected withA. brassicicolaspore solution (in 0.12% DMSO) or spore solution supplemented with 10 µM DHEA (in 0.12% DMSO). Leaves were harvested after 24 h and immediately frozen in liquid nitrogen.

value: leaves

tag: ecotype

value: spore solution with 10 µM DHEA (in 0.12% DMSO)


title: leaves, Spore Infection + DHEA Rep3


title: sibling-RNAsseq

description: Library name: Sample1


title: M031, SA4 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M031A4

value: human nasal epithelium

value: nasal epithelial cells


title: APP-6m_1

description: Total RNA (Native)

value: 6 months

value: Hippocampus L+R


title: ChIP-seq_H3K9ac_ZT20biol rep2


title: leaves, Spore Infection + DHEA Rep2


title: M031, SA1 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M031A1


title: ChIP-seq_H3K9ac_ZT16biol rep3

description: k9_ZT_16_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: ChIP-seq_H3K9ac_ZT16biol rep2


title: M031, SA2 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M031A2


title: Male_SW_MGO_rna_rep4

extract_protocol:
Total RNA was isolated using TRIzol reagent and applied to a Phase Lock Gel-Heavy column. Eluted RNA was then rRNA depleted using the RiboCop  rRNA kit, according to the manufacturer’s protocols
Libraries were generated from 1mg of RNA using Lexogen’s QuantSeq 39mRNASeq library kit. The concentrations of purified  libraries were quantified using Qubit and the average size was determined by a fragment analyzer with a  high-sensitivity NGS fragment analysis kit

treatment_protocol: Methylglyoxal (MGO) at 2 mg/kg, i.p; for 6 days


title: ChIP-seq_H3K9ac_ZT16biol rep1


title: ChIP-seq_H3K9ac_ZT12biol rep2

description: k9_ZT_12_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: Male_SW_MGO_rfp_rep1


title: leaves, Spore Infection + DHEA Rep1


title: Male_SW_MGO_rna_rep3


title: M031, SA1 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M031A1B


title: M027, CS infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M027B


title: M031, SA2 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M031A2B


title: ChIP-seq_H3K9ac_ZT12biol rep3


title: M027, negative control

address: 广东省广州市越秀区中山大学北校区

description: Library name: M027CTRL


title: ChIP-seq_H3K9ac_ZT12biol rep1


title: Male_SW_MGO_rna_rep2


title: leaves, Spore Infection Rep3

value: spore solution (in 0.12% DMSO)


title: Male_SW_MGO_rna_rep1


title: leaves, Spore Infection Rep4


title: ChIP-seq_H3K9ac_ZT8biol rep1

description: k9_ZT_8_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: M027, SA7 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M027A7


title: leaves, Spore Infection Rep1


title: ChIP-seq_H3K9ac_ZT8biol rep2


title: leaves, Spore Infection Rep2


title: M027, SA4 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M027A4


title: M027, SA4 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M027A4B


title: ChIP-seq_H3K9ac_ZT4biol rep3

description: k9_ZT_4_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: HGSOC tissue, circASCOR high 2

first: Hanyuan

last: Liu

address: 443 Huangshan Road Hefei, Anhui Province

description: Library name: Sample7

data_processing:
Raw Sequencing Data Generation and Quality Filtering
Libraries were sequenced on an Illumina NovaSeq 6000 platform with a paired-end 150 bp (PE150) sequencing strategy. Raw sequencing reads were generated in FASTQ format. Adapter sequences, low-quality reads (Q-score < 20), reads containing >10% N bases, and reads shorter than 50 bp were filtered out using Cutadapt v2.10 and FastQC v0.11.9 to obtain clean reads.
Cell Barcode and UMI Processing
Clean reads were processed using the Cell Ranger v7.1.0 pipeline (10× Genomics) for single-nucleus RNA-seq data analysis. Reads were aligned to the human reference genome (GRCh38) using the STAR aligner integrated in Cell Ranger. Cell barcodes and unique molecular identifiers (UMIs) were extracted from the reads, and duplicate UMIs corresponding to the same gene and cell barcode were removed to eliminate PCR amplification bias.
Nucleus Calling and Gene Expression Matrix Construction
Empty droplets were distinguished from valid nuclei based on the number of detected genes and UMI counts using the emptyDrops function in the DropletUtils v1.18.1 R package. Nuclei with <200 detected genes or >10% mitochondrial gene reads were excluded to remove low-quality nuclei and potential cytoplasmic contamination. A gene-by-nucleus expression matrix was generated, where the value for each gene in each nucleus represented the UMI count.
Assembly: hg38
Supplementary files format and content: matrix files

source_name: HGSOC

extract_protocol:
Fresh ovarian cancer tissue samples (approximately 50–100 mg) were immediately dissected after surgical resection, rinsed 3 times with pre-chilled phosphate-buffered saline (PBS) containing 1% penicillin-streptomycin to remove residual blood and necrotic tissue, and cut into 1–2 mm³ pieces using sterile scalpels on ice. Tissue pieces were transferred into a 15 mL centrifuge tube containing 5 mL pre-chilled nucleus isolation buffer (NIB; 0.25 M sucrose, 25 mM KCl, 5 mM MgCl₂, 20 mM Tris-HCl pH 7.4, 1 mM DTT, 0.1% Triton X-100, 1× protease inhibitor cocktail). The mixture was gently pipetted 20–30 times with a 1 mL pipette tip to facilitate mechanical dissociation, followed by incubation on ice for 10 min. The homogenate was filtered sequentially through 70 μm and 40 μm cell strainers to remove undissociated tissue debris. The filtrate was centrifuged at 300 × g for 10 min at 4 °C. The supernatant was discarded, and the pellet was resuspended in 5 mL pre-chilled NIB, followed by a second centrifugation at 300 × g for 10 min at 4 °C. The pellet was resuspended in 1 mL pre-chilled NIB, and the nuclear suspension was layered onto a 30% sucrose cushion (prepared in NIB). After centrifugation at 1,500 × g for 20 min at 4 °C, the supernatant was discarded, and the purified nuclear pellet was resuspended in 500 μL pre-chilled PBS containing 0.1% BSA. Nuclear integrity was assessed using a hemocytometer under a phase-contrast microscope; only samples with >90% intact nuclei (round morphology, clear nuclear membrane, no obvious cytoplasmic contamination) were retained. The concentration of nuclei was adjusted to 1×10⁶ nuclei/mL for subsequent library construction.
Library construction was performed using the 10× Genomics Chromium Single Cell 3′ Reagent Kit v3.1 following the manufacturer’s standard protocols with minor modifications adapted for ovarian cancer nuclear samples:Single Nucleus Partitioning: Purified ovarian cancer nuclei (1×10⁴ nuclei per sample) were mixed with reverse transcription (RT) reagents and loaded onto the Chromium Chip G. The chip was processed on the Chromium Controller to generate Gel Bead-In-Emulsions (GEMs), where each GEM contained a single nucleus, a barcoded gel bead, and RT reaction mix.Reverse Transcription and cDNA Amplification:GEMs were incubated in a thermal cycler for RT reaction (53 °C for 45 min, 85 °C for 5 min, hold at 4 °C) to synthesize barcoded cDNA. Emulsions were then broken, and cDNA was recovered and purified using AMPure XP beads. Purified cDNA was amplified via PCR (98 °C for 3 min; 12–15 cycles of 98 °C for 15 s, 60 °C for 30 s, 72 °C for 30 s; 72 °C for 5 min; hold at 4 °C) to obtain sufficient cDNA yield.Library Fragmentation, End Repair and Adapter Ligation:Amplified cDNA was fragmented to 200–300 bp using a Covaris M220 Focused-ultrasonicator. Fragmented cDNA was subjected to end repair, A-tailing, and ligation with indexed adapters (Illumina) according to the kit instructions. Adapter-ligated DNA was purified using AMPure XP beads to remove excess adapters and small fragments.Final Library Amplification and QC:The ligated products were amplified by PCR (98 °C for 3 min; 6–8 cycles of 98 °C for 15 s, 60 °C for 30 s, 72 °C for 30 s; 72 °C for 5 min; hold at 4 °C). The final libraries were quantified using a Qubit 4 Fluorometer (Thermo Fisher Scientific) and their size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Only libraries with average fragment size of 250–350 bp and concentration >10 nM were used for sequencing.

value: HGSOC

tag: sample group

value: circASCOR high


title: leaves, DMSO Rep3


title: HGSOC tissue, circASCOR high 3

description: Library name: Sample8


title: HGSOC tissue, circASCOR high 4

description: Library name: Sample9


title: ChIP-seq_H3K9ac_ZT4biol rep2


title: M027, SA2 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M027A2B


title: HGSOC tissue, circASCOR high 1

description: Library name: Sample6


title: leaves, DMSO Rep1


title: ChIP-seq_H3K9ac_ZT0biol rep3

description: k9_ZT_0_replicate_123_PE_sorted_sampled_merged_reheader.bw


title: SAM24356486_HCI-003_Ser, GDC-9545, 80 mg/kg, #763

city: South San Francisco

first: Marc

last: Hafner

state: CA

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

data_processing:
RNA-seq was analyzed with HTSeqGenie R package.
Reads were trimmed to 75 bp, filtered for quality and rRNA/adapter contamination, and aligned to the reference genome GRCh38 using GSNAP.
Gene expression was quantified as Reads Per Kilobase exon model per Million mapped reads normalized by size factor (nRPKM), defined as number of reads aligning to a gene in a sample / (total number of uniquely mapped reads for that sample x gene length x size factor)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file that include gene counts for each sample

source_name: Breast

growth_protocol: Tumors were grown in immunocompromised mice in the presence of exogenous estrogen. Tumor-bearing mice were randomized into the treatment groups when tumors reached a volume of between 450 and 850 mm3.

extract_protocol:
Flash frozen tumors were pulverized to powder by mechanical force (Covaris cryoPREP).  Tumor powder was lysed by addition of TRIzol Reagent (Thermo Fisher Scientific) and homogenized by mechanical disruption (SPEX SamplePrep).  RNA was isolated from homogenized lysates by chloroform extraction and precipitated using the MagMAX-96 Total RNA Isolation Kit (Thermo Fisher Scientific), according to the manufacturer’s protocol.
Approximately 500 ng of total RNA was used as an input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). In addition, RNA input of 100 ng was used for library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina). The libraries were multiplexed.

treatment_protocol: Giredestrant was dosed orally once per day for 5 days, and tumors were harvested 4 hours following the last dose.

value: Breast

tag: xenograft model

value: Adenocarcinoma


title: HGSOC tissue, circASCOR low 5

description: Library name: Sample5

value: circASCOR low


title: M027, SA2 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M027A2

value: WT


title: leaves, DMSO Rep4


title: ChIP-seq_H3K9ac_ZT4biol rep1


title: M027, SA1 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M027A1B


title: M027, SA7 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M027A7B


title: leaves, DMSO Rep2


title: M027, SA1 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M027A1


title: HGSOC tissue, circASCOR high 5

description: Library name: Sample10


title: ChIP-seq_H3K9ac_ZT0biol rep2


title: HGSOC tissue, circASCOR low 3

description: Library name: Sample3


title: M024, negative control

address: 广东省广州市越秀区中山大学北校区

description: Library name: M024CTRL


title: ChIP-seq_H3K9ac_ZT8biol rep3


title: SAM24356484_HCI-003_Ser, GDC-9545, 80 mg/kg, #736


title: M024, SA7 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M024A7B


title: HGSOC tissue, circASCOR low 4

description: Library name: Sample4


title: SAM24356482_HCI-003_Ser, GDC-9545, 1 mg/kg, #771


title: RNA-seq_ZT20_L

data_processing:
remove adapter using Trimmonmati, mapping to soybean genome by HISAT2(V2.2.1), detecting the gene expression level by StringTie.
Assembly: Ws82v2.1
Supplementary files format and content: ReadsCount

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.
Total RNA was isolated from mature rice leaves using the RNeasy Plant Mini Kit according to the manufacturer’s recommendations (QIAGEN, 74904). Ribosome RNA was removed from 0.5 to 1.5 g of Total RNA using a kit TruSeq Stranded Total RNA with Ribo-Zero Plant for RNA-seq according to the manufacturer’s recommendations.


title: HGSOC tissue, circASCOR low 1

description: Library name: Sample1


title: SAM24356483_HCI-003_Ser, GDC-9545, 80 mg/kg, #733


title: HGSOC tissue, circASCOR low 2

description: Library name: Sample2


title: RNA-seq_ZT20_M


title: M024, SA4 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M024A4B


title: RNA-seq_ZT20_R


title: CB96_MLL_9_minusAF4_d74

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

description: Library name: s12

data_processing:
Raw fastq files were processed with the nfcore/rnaseq pipeline v3.10.1
Assembly: GRCh38 assembly, v113 Ensembl GTF
Supplementary files format and content: tab-separated raw counts per gene and sample

molecule: polyA RNA

source_name: Human cord blood-derived cells

growth_protocol: t(9;11) and t(4;11) cells derived from cord blood were maintained in StemMACS™ HSC Expansion Media (Miltenyi) supplemented with 10% FCS, 1% Penicillin/Streptomycin, human cytokines (IL-3, IL-6, SCF, FLT3L, SCF, G-CSF, 50 ng/ml each), SR-1 and UM-729 (0.75 µM each).

extract_protocol:
RNA was isolated using the NucleoSpin RNA Kit (Macherey-Nagel, 740955.50) according to the manufacturer’s instructions.
Library preparation and sequencing was performed at GenXPro GmbH (Frankfurt/Main). MACE-seq was used to prepare 3'RNA sequencing libraries. The DNA-depleted RNA molecules underwent the library preparation, using the MACE-Seq Kit (GenXPro GmbH) according to the manual of the manufacturer. Fragmented RNA was reverse transcribed, followed by the template switching combined with the incorporation of the TrueQuant UMI. The cDNA fragments were PCR amplified and purified. Sequencing was performed on an Illumina NextSeq instrument with 1×76 bps.

treatment_protocol: No treatment

value: Human cord blood-derived cells

value: Cells derived from cord blood donor CB96 (Donor 1)

value: Differentiated human hematopoietic stem and progenitor cells


title: ChIP-seq_H3K9ac_ZT0biol rep1

value: first tri-foliate leaf

value: free-running


title: M024, CS infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M024B


title: CB96_MLL_11_minusAF9_d74

description: Library name: s11


title: RNA-seq_ZT16_R


title: SAM24356485_HCI-003_Ser, GDC-9545, 80 mg/kg, #759


title: SAM24356480_HCI-003_Ser, GDC-9545, 1 mg/kg, #732


title: M024, SA2 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M024A2B


title: CB96_MLL_9_minusAF9_d74

description: Library name: s13


title: M024, SA4 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M024A4


title: SAM24356479_HCI-003_Ser, GDC-9545, 1 mg/kg, #728


title: CB96_MLL_11_minusAF4_d74

description: Library name: s10


title: M024, SA2 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M024A2


title: SAM24356481_HCI-003_Ser, GDC-9545, 1 mg/kg, #738


title: RNA-seq_ZT16_M


title: SAM24356475_HCI-003_Ser, Vehicle, #755

value: Vehicle


title: CB126_wt_d78

description: Library name: s9

value: Cells derived from cord blood donor CB126 (Donor 3)

value: wildtype


title: M024, SA1 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M024A1B

value: human nasal epithelium

value: nasal epithelial cells


title: RNA-seq_ZT12_R


title: M024, SA1 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M024A1


title: RNA-seq_ZT12_L


title: RNA-seq_ZT16_L


title: RNA-seq_ZT12_M


title: M016, CS infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M016B


title: SAM24356473_HCI-003_Ser, Vehicle, #739


title: CB126_MLL_9_minusAF4_d78

description: Library name: s7


title: M016, negative control

address: 广东省广州市越秀区中山大学北校区

description: Library name: M016CTRL


title: CB126_MLL_11_minusAF4_d78

description: Library name: s6


title: SAM24356471_HCI-011_Ser, GDC-9545, 80 mg/kg, #693


title: SAM24356472_HCI-003_Ser, Vehicle, #731


title: M016, SA7 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M016A7B


title: CB102_wt_d72

description: Library name: s5

value: Cells derived from cord blood donor CB102 (Donor 2)


title: RNA-seq_ZT8_R


title: M016, SA4 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M016A4B


title: RNA-seq_ZT8_M


title: SAM24356470_HCI-011_Ser, GDC-9545, 80 mg/kg, #682


title: CB102_MLL_9_minusAF9_d79

description: Library name: s4


title: CB102_MLL_9_minusAF4_d79

description: Library name: s3


title: RNA-seq_ZT8_L


title: M016, SA2 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M016A2B


title: RNA-seq_ZT4_R


title: CB126_MLL_9_minusAF9_d78

description: Library name: s8


title: SAM24356474_HCI-003_Ser, Vehicle, #751


title: RNA-seq_ZT4_M


title: SAM24356468_HCI-011_Ser, GDC-9545, 80 mg/kg, #652


title: CB102_MLL_11_minusAF9_d79

description: Library name: s2


title: SAM24356467_HCI-011_Ser, GDC-9545, 1 mg/kg, #671


title: M016, SA1 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M016A1B


title: M016, SA1 infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M016A1


title: CB102_MLL_11_minusAF4_d79

description: Library name: s1


title: SAM24356466_HCI-011_Ser, GDC-9545, 1 mg/kg, #660


title: RNA-seq_ZT4_L


title: M012, negative control

address: 广东省广州市越秀区中山大学北校区

description: Library name: M012CTRL


title: M012, CS infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M012B


title: SAM24356465_HCI-011_Ser, GDC-9545, 1 mg/kg, #659


title: Pregnant1_hRPC, scRNAseq

description: Library name: hRPC_pregnant woman1

data_processing:
Basecall performed with cellranger mkfastq v8.0.1
Single cell feature counts performed with cellranger count v8.0.1
Reference genome alignment performed with STAR v2.7.11b
Assembly: GRCh38
Supplementary files format and content: All tab-separated values files

source_name: urine

extract_protocol:
The single cell suspension with 95% viability was run on a 10x Chromium Single Cell instrument (10x Genomics, Pleasanton, CA) following Manufacturer’s instructions
3’ gene expression libraries were constructed following 10x Genomics's instructions

value: urine

value: hRPC

value: Primary cell culture of renal progenitor from urine


title: RNA-seq_ZT0_M


title: M012, SA7 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M012A7B


title: RNA-seq_ZT0_R


title: Pregnant3_hRPC, scRNAseq

description: Library name: hRPC_pregnant woman3


title: Pregnant2_hRPC, scRNAseq

description: Library name: hRPC_pregnant woman2


title: M012, SA2 and CS co-infected

address: 广东省广州市越秀区中山大学北校区

description: Library name: M012A2B


title: SAM24356464_HCI-011_Ser, GDC-9545, 1 mg/kg, #653

value: Breast

value: Adenocarcinoma


title: Female1_hRPC, scRNAseq

description: Library name: hRPC_woman1

value: kidney

value: Primary cell culture of renal progenitor from kidney


title: SAM24356458_HCI-011_Ser, Vehicle, #663


title: SAM24356469_HCI-011_Ser, GDC-9545, 80 mg/kg, #680


title: ATAC-seq_ZT20_R

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

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.


title: SAM24356459_HCI-011_Ser, Vehicle, #674


title: ATAC-seq_ZT20_M


title: HC2

city: Chongqing

first: Yunfei

last: An

address: No. 136, Zhongshan 2nd Road, Yuzhong District

institute: Children's Hospital of Chongqing Medical University

data_processing:
The reads alignment and gene counting were processed with the Cell Ranger software (version 6.1.2)
Assembly: GRCh38
Supplementary files format and content: h5 file of gene expresion matrix

source_name: bone marrow

extract_protocol:
Fresh bone marrow was collected, and cells were used for single cell suspension after red blood cell lysis
Library was performed according to manufacter's instructions (Single Cell 3' v3, 10X genomics)

value: bone marrow


title: SAM24356457_HCI-011_Ser, Vehicle, #656


title: Male2_hRPC, scRNAseq

description: Library name: hRPC_man2


title: HC1


title: ATAC-seq_ZT16_R


title: SAM24356456_HCI-011_Ser, Vehicle, #655


title: MCF-7, H3K27ac, ChIP, GNE-858 rep 2

data_processing:
Fastqs were filtered for read quality (Phred scores 23+).
Reads were aligned to the human reference genome (NCBI Build 38) and the drosophila reference genome using GSNAP v2013-10-10, with maximum two mismatches per read (parameters: ‘-M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap’). Duplicate reads were removed.
BigWig files containing reads aligned to the human reference were drosophila spike-in adjusted, by rescaling the read coverage by a factor that resulted in the same number of spike-in drosophila reads for each sample.
Peaks of 200 bp width were individually identified in each sample relative to the respective input samples using MACS 2.1.0 with cutoffs of p=1e-7 and 3-fold increase over input control.
The level of chromatin binding within each peak was quantified as the number of pseudo-fragments overlapping the peak in question based on the spike-in adjusted BigWig files. Read counts for each sample were normalized based on the number of reads outside significant peaks across samples. Fold-change in chromatin binding is calculated as the ratio of the normalized reads in a treated sample versus reads in the vehicle-treated sample.
Assembly: GRCh38
Supplementary files format and content: narrowPeak
Supplementary files format and content: bigWig

source_name: breast

growth_protocol: Cell lines were cultured using standard aseptic tissue culture techniques at 37°C in RPMI medium supplemented with 10% FBS, 2mM L-Glutamine (Catalog 10440, Sigma), 1X Minimum Essential Media, Non-Essential Amino Acids (MEM NEAA, Catalog No. 11140-0500, Thermo Fisher) and 1X Antibiotic-Antimycotic (Catalog No.15240-112, Thermo Fisher).

extract_protocol:
Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp.
Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer.
An aliquot of chromatin (30 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using relevant antibodies against specified targets. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. The ChIP reactions also contained a drosophila chromatin spike in for the normalization of the sequencing data. ChIPseq was performed by Active Motif.

treatment_protocol: Treatments were done for a period of 24 hrs.

value: breast


title: RNA-seq_ZT0_L

value: first tri-foliate leaf


title: SAM24423305_MCF-7, RNP FoxA1, sgAC + 300nM GDC-9545 for 4 days, rep2

extract_protocol:
Total RNA was extracted from duplicates using Qiagen RNeasy kit as per manufacturer’s protocol. The concentration of RNA samples was determined using NanoDrop 8000 (Thermo Scientific) and the integrity of RNA was determined by Fragment Analyzer (Advanced Analytical Technologies).
Approximately 500 ng of total RNA was used as an input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). In addition, RNA input of 100 ng was used for library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina). The libraries were multiplexed.

treatment_protocol: Treatments were done for a period of 4 days.

value: adenocarcinoma


title: Male1_hRPC, scRNAseq

description: Library name: hRPC_man1


title: ATAC-seq_ZT20_L

value: free-running


title: Pt1


title: MCF-7, H3K27ac, ChIP, GNE-858 rep 1


title: Wistar Strain, Male Rat, 5

city: São Paulo

first: Victor

middle: Jardim

last: Duque

state: SP

address: Rua da Contagem, 273, Porta Madeira

country: Brazil

institute: Federal University of Sao Paulo

description: Library name: W5DM_S14

data_processing:
This preprocessing included adaptor clipping, quality-based filtering, and length selection, carried out with Trimmomatic, using a Phred score threshold of 30 (≈99.9% base call accuracy).
The resulting high-quality reads were then aligned to the Rattus norvegicus reference genome (Rn7) using the Spliced Transcripts Alignment to a Reference (STAR) aligner. The counts of aligned reads were calculated using FeatureCountsvia featureCounts
Assembly: Rattus Novergicus (Rn7)
Supplementary files format and content: Coma separeted values (CSV) include raw counts for each sample

source_name: Paraventricular Nucleus

extract_protocol:
Total RNA was extracted using a Directzol RNA MiniPrep extraction kit (Zymo Research)
Poly(A) enriched bulk RNA-sequencing libraries were constructed using Illumina TruSeq Stranded mRNA kits

value: Paraventricular Nucleus

value: Male

value: Wistar


title: SAM24423304_MCF-7, RNP FoxA1, sgAC + 300nM GDC-9545 for 4 days, rep1


title: ATAC-seq_ZT16_M

source_name: first tri-foliate leaf


title: Wistar Strain, Female Rat, 5

description: Library name: W5DF_S5

value: Female


title: MCF-7, H3K27ac, ChIP, GDC-9545 rep 1


title: Wistar Strain, Male Rat, 4

description: Library name: W4DM_S13


title: ATAC-seq_ZT12_R


title: SAM24423303_MCF-7, RNP FoxA1, sgAC 4 days, rep2

value: FoxA1 KO


title: MCF-7, H3K27ac, ChIP, GDC-9545 rep 2


title: SAM24423302_MCF-7, RNP FoxA1, sgAC 4 days, rep1


title: ATAC-seq_ZT12_M


title: Wistar Strain, Female Rat, 4

description: Library name: W4DF_S4


title: SAM24423301_MCF-7, RNP ESR1, sgAA 4 days, rep2

value: ER KO


title: ATAC-seq_ZT16_L


title: MCF-7, H3K27ac, ChIP, DMSO rep 2

value: DMSO


title: MCF-7, H3K27ac, ChIP, DMSO rep 1


title: Wistar Strain, Male Rat, 3

description: Library name: W3DM_S12


title: MCF-7, ERa, ChIP, GNE-858 rep 2

value: ERa


title: ATAC-seq_ZT12_L


title: Wistar Strain, Female Rat, 3

description: Library name: W3DF_S3


title: Wistar Strain, Male Rat, 2

description: Library name: W2DM_S11


title: SAM24423299_MCF-7, RNP NTC, sg2 + 300nM GDC-9545 for 4 days, rep2


title: SAM24423300_MCF-7, RNP ESR1, sgAA 4 days, rep1


title: ATAC-seq_ZT8_R


title: MCF-7, ERa, ChIP, GNE-858 rep 1


title: MCF-7, ERa, ChIP, GDC-9545 rep 2


title: ATAC-seq_ZT8_L


title: ATAC-seq_ZT8_M


title: SAM24423297_MCF-7, RNP NTC, sg2, 4 days, rep2

value: NTC


title: MCF-7, ERa, ChIP, GDC-9545 rep 1

value: Adenocarcinoma


title: Wistar Strain, Female Rat, 2

description: Library name: W2DF_S2


title: ATAC-seq_ZT4_R


title: SAM24423296_MCF-7, RNP NTC, sg2, 4 days, rep1


title: MCF-7, ERa, ChIP, DMSO rep 2


title: Wistar Strain, Female Rat, 1

description: Library name: W1DF_S1


title: SHR Strain, Male Rat, 5

description: Library name: S5DM_S19

value: SHR


title: SAM24423298_MCF-7, RNP NTC, sg2 + 300nM GDC-9545 for 4 days, rep1


title: SHR Strain, Female Rat, 5

description: Library name: S5DF_S10


title: SAM24399635_MCF-7 with 24hrs treatment of GNE-858, 300 nM, rep2

value: Breast


title: ATAC-seq_ZT4_L


title: MCF-7, ERa, ChIP, DMSO rep 1


title: ATAC-seq_ZT4_M


title: SHR Strain, Male Rat, 4

description: Library name: S4DM_S18


title: MCF-7, FOXA1, ChIP, GNE-858 rep 2


title: MCF-7, FOXA1, ChIP, GNE-858 rep 1


title: ATAC-seq_ZT0_R


title: ATAC-seq_ZT0_M


title: SAM24399634_MCF-7 with 24hrs treatment of GNE-858, 300 nM, rep1


title: SAM24399633_MCF-7 with 24hrs treatment of GDC-9545, 300 nM, rep2


title: MCF-7, FOXA1, ChIP, GDC-9545 rep 2


title: SHR Strain, Female Rat, 4

description: Library name: S4DF_S9


title: SAM24399632_MCF-7 with 24hrs treatment of GDC-9545, 300 nM, rep1


title: SHR Strain, Female Rat, 3

description: Library name: S3DF_S8


title: ATAC-seq_ZT0_L


title: SAM24399631_MCF-7 treated with DMSO, rep2


title: MCF-7, FOXA1, ChIP, GDC-9545 rep 1


title: MCF-7, FOXA1, ChIP, DMSO rep 2


title: SHR Strain, Female Rat, 2

description: Library name: S2DF_S7


title: Lyso_polyA_worms_Mock

description: Library name: sample55

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)

organism: Caenorhabditis elegans

source_name: strain

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: whole worm

value: WT


title: SHR Strain, Male Rat, 2

description: Library name: S2DM_S16


title: Y87_BM

city: Tianjin

first: xiaowei

last: xie

address: 288 Nanjing Road

institute: Institute of Hematology and Blood Diseases Hospital

data_processing:
The clean reads were aligned to human reference genome (hg38 from Ensembl) by Hisat2 (version 2.0.3-beta), followed by calculating uniquely mapped reads through htseq-count (version 0.9.1) based on the genome annotation file from Ensembl (hg38). Finally, the total number of different UMIs for each gene was quantified as the read count of that gene.
Genome_build: hg38
Supplementary_files_format_and_content: .mtx (UMI matrix of cells); .tsv (cell information); .tsv (gene information)

extract_protocol:
Samples were incubated on ice for 30 mins in the dark and washed with PBS + 2% FBS (Gibco), cell suspension of which were added with DAPI (1 ug/ml, Sigma-Aldrich) to deplete dead cells for FACS.
Smart-seq2
Single cell RNAseq

treatment_protocol: All samples were freshly prepared and immediately stained with human antibodies including Lineage cocktail.

tag: developmental stage

value: aging

value: bone marrow

value: HSPCs


title: MCF-7, FOXA1, ChIP, DMSO rep 1

value: breast


title: Lyso_polyA_worms_CQ

description: Library name: sample54

value: CQ


title: MCF-7, GATA3, ChIP, GNE-858 rep 2

data_processing:
Fastq sequencing files for all ChIP-seq samples were first filtered for read quality (Phred scores 23+).
Reads were then aligned to the human reference genome (NCBI Build 38) and the drosophila reference genome using GSNAP (Wu and Nacu, 2010) version ‘2013-10-10’, allowing a maximum of two mismatches per read sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap’), followed by removal of duplicate reads.
The BigWig files with the reads aligned to the human reference genome were drosophila spike-in adjusted, by rescaling the read coverage by a factor that resulted in the same number of spike-in drosophila reads for each sample.
Peaks of 200 bp width were identified in each sample individually relative to the respective input samples using MACS 2.1.0 (Zhang et al., 2008) with cutoffs of p=1e-7 and 3-fold increase over input control.
We quantified the level of chromatin binding within each peak as the number of pseudo-fragments overlapping the peak in question based on the spike-in adjusted BigWig files. Read counts for each sample were normalized based on the number of reads outside of the atlas for each sample. Fold-change in chromatin binding is calculated as the ratio of the normalized reads in a ligand-treated sample versus reads in the vehicle-treated sample.
Assembly: GRCh38
Supplementary files format and content: narrowPeak
Supplementary files format and content: bigWig

growth_protocol: MCF7 cells were cultured in standard RPMI media (10% serum).


title: SHR Strain, Male Rat, 1

description: Library name: S1DM_S15

value: Paraventricular Nucleus

value: Male


title: SHR Strain, Male Rat, 3

description: Library name: S3DM_S17


title: RK_ribominus_worms_RNAiF49

description: Library name: sample22


title: Lyso_R+_worms_CQ

description: Library name: sample49


title: Lyso_R+_worms_Mock

description: Library name: sample50


title: Y68_BM


title: MCF-7, GATA3, ChIP, GNE-858 rep 1


title: Y12_BM

value: child


title: MCF-7, GATA3, ChIP, GDC-9545 rep 2


title: SHR Strain, Female Rat, 1

description: Library name: S1DF_S6

value: Female


title: M7_BM

value: infant


title: Y11_BM


title: RNAseq MAs sample #6

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
Sample from INS-1 832/13 cells used for RNAseq, batch R, MAs-treated
RNAseq_INS1_DESeq_normalized_counts.csv

data_processing:
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq), aligned and quantified using STAR/Salmon (RNAseq), or aligned and quantified using the ChROseq pipeline (ChROseq).
All sequencing types were processed with DESeq2.
Assembly: rn6
Supplementary files format and content: Normalized counts

source_name: beta-cell line

growth_protocol: The INS-1 832/13 rat insulinoma beta-cell line was maintained at 5% CO2, 37oC in RPMI 1640 media supplemented with 2 mM L-glutamine media, 10% FBS, 10 mM HEPES media, 1 mM sodium pyruvate media, 100 U/mL penicillin media, 100 μg/mL streptomycin media, and 0.05 mM β-mercaptoethanol.

extract_protocol:
Libraries were prepared according to the NEB Next Ultra II kit protocol
Libraries were prepared using the TriLink CleanTag Small RNA Ligation kit (small RNAseq), NEBNext Ultra II RNA kit (RNAseq), or according to the ChROseq protocol.

treatment_protocol: INS-1 832/13 cells were either untreated, treated with sodium arsenite (iAs), or with methylarsine oxide (Mas)

value: beta-cell line

value: MAs-treated


title: RNAseq MAs sample #5


title: SAM24399630_MCF-7 treated with DMSO, rep1

value: Adenocarcinoma

value: DMSO


title: RNAseq iAs sample #4

description:
Sample from INS-1 832/13 cells used for RNAseq, batch R, iAs-treated
RNAseq_INS1_DESeq_normalized_counts.csv

value: iAs-treated


title: RK_ribominus_worms_RNAiC46

description: Library name: sample21

value: whole worm


title: RK_R+_worms_RNAiC46

description: Library name: sample16


title: MCF-7, GATA3, ChIP, GDC-9545 rep 1


title: RK_ribominus_worms_L4440

description: Library name: sample20


title: RK_R+_worms_L4440

description: Library name: sample15


title: MCF-7, GATA3, ChIP, DMSO rep 2


title: D0_BM4

value: neonate


title: M4_BM


title: GNE858 rep2

data_processing:
ATAC-seq reads were analyzed using the ENCODE ATAC-seq pipeline v1.
Reads were trimmed of adapters by cutadapt v1.9.1 and mapped to hg38 by Bowtie2 v2.2.6.
Bam files were converted to tagAlign format, which was then adjusted for Tn5 by shifting +4 bp for positive strand and by −5bp for negative strand.
TagAlign files were used to call peaks using MACS2 v2.1.0.  Peaks with p<1e-6 were retained for differential analysis.
Assembly: hg38
Supplementary files format and content: narrowPeak
Supplementary files format and content: bigWig

extract_protocol:
Cells were detached using Accutase® Cell Detachment Solution (Catalog No. 25-058-CI, Corning), counted and resuspended in growth media containing 5% DMSO. Cells were aliquoted into cryovials, frozen, and shipped to Active Motif (Carlsbad, CA).
The cells were thawed in a 37 degree celsius water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al., 2013), with some modifications based on (Corces et al., 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina).

treatment_protocol: treatments were done for a period of 24 hrs.

value: Breast


title: RK_R+_worms_RNAiF49

description: Library name: sample17


title: MCF-7, GATA3, ChIP, DMSO rep 1


title: RNAseq iAs sample #3


title: D0_BM1

value: bone marrow


title: GNE858 rep1


title: RNAseq control sample #3

description:
Sample from INS-1 832/13 cells used for RNAseq, batch R, control
RNAseq_INS1_DESeq_normalized_counts.csv

value: control


title: NN4_D7

city: Gold coast

first: Jiaying

address: G40, parkland drive

country: Australia

institute: Griffith university

description:
Library name: Sample 34
read_count_NN4_D7

data_processing:
SOAPnuke
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
HISAT was used to align the clean reads to the reference genome
Bowtie2 was used to align the clean reads to the reference genes
Assembly: GCF_015227675.2_mRatBN7.2
Supplementary files format and content: csv files include count values for each sample

source_name: periodontal healing tissue

growth_protocol: Samples were collected from experimental animals at different time points.

extract_protocol:
RNA was harvest with PureLink RNA extraction kit (Thermofisher). A total of 55μl at concentration above 10ng/μl RNA for each sample was used for the construction of sequencing libraries.
Library construction was performed by BGI using the DNBSEQ platform. Sequencing libraries were generated using the BGI mRNA-seq Library Prep Kit following the manufacturer’s protocol.

value: periodontal healing tissue

value: Mixed cells

value: WT

value: periodontal bone defect and sensory denervation


title: GDC9545 rep2


title: RNAseq control sample #4


title: SAM24352883_MCF-7, siRNA ER, 72 hrs, rep2

value: siRNA ER, 72 hrs Amaxa transfection


title: RNAseq MAs sample #3

description:
Sample from INS-1 832/13 cells used for RNAseq, batch K, MAs-treated
RNAseq_INS1_DESeq_normalized_counts.csv


title: RNAseq MAs sample #4


title: GDC9545 rep1


title: SAM24352880_MCF-7, siRNA, NTC, 72 hrs, rep1

value: siRNA, NTC, 72 hrs Amaxa transfection


title: RNAseq MAs sample #2


title: NN3_D7

description:
Library name: Sample 33
read_count_NN3_D7


title: SAM24352881_MCF-7, siRNA, NTC, 72 hrs, rep2


title: NN4_D14

description:
Library name: Sample19
read_count_NN4_D14

tag: time

value: Day 14


title: DMSO rep1

tag: cell line


title: SAM24352882_MCF-7, siRNA ER, 72 hrs , rep1

tag: cell type


title: NN2_D7

description:
Library name: Sample 32
read_count_NN2_D7

tag: genotype


title: RNAseq iAs sample #2

description:
Sample from INS-1 832/13 cells used for RNAseq, batch K, iAs-treated
RNAseq_INS1_DESeq_normalized_counts.csv

value: beta-cell line

tag: treatment


title: SAM24352879_MCF-7, siRNA ER, 48 hrs, rep2

tag: tissue

value: siRNA ER, 48 hrs Amaxa transfection


title: RNAseq iAs sample #1


title: NN4_D3

description:
Library name: Sample18
read_count_NN4_D3

value: Day 3


title: HCI-003 GDC9545 rep2

data_processing:
ATAC-seq reads were analyzed using the ENCODE ATAC-seq pipeline v1.
Reads were trimmed of adapters by cutadapt v1.9.1 and mapped to hg38 by Bowtie2 v2.2.6.
Bam files were converted to tagAlign format, which was then adjusted for Tn5 by shifting +4 bp for positive strand and by −5bp for negative strand.
TagAlign files were used to call peaks using MACS2 v2.1.0.  Peaks with p<1e-6 were retained for differential analysis.
Assembly: GRCh38
Supplementary files format and content: narrow Peak
Supplementary files format and content: bigWig

extract_protocol:
Flash frozen tumors were pulverized to powder by mechanical force (Covaris cryoPREP).  Tumor powder was lysed by addition of TRIzol Reagent (Thermo Fisher Scientific) and homogenized by mechanical disruption (SPEX SamplePrep).  RNA was isolated from homogenized lysates by chloroform extraction and precipitated using the MagMAX-96 Total RNA Isolation Kit (Thermo Fisher Scientific), according to the manufacturer’s protocol.
The cells were thawed in a 37 degree celsius water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al., 2013), with some modifications based on (Corces et al., 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina).


title: NN3_D14

description:
Library name: Sample17
read_count_NN3_D14


title: SAM24352875_MCF-7, mock, GDC-0927, rep2

value: Adenocarcinoma

value: mock, GDC-0927 (100 nM), 48 hrs Amaxa transfection


title: SAM24352876_MCF-7, siRNA, NTC, 48 hrs, rep1

value: siRNA, NTC, 48 hrs Amaxa transfection


title: DMSO rep2

value: DMSO


title: NN1_D7

description:
Library name: Sample 31
read_count_NN1_D7


title: HCI-003 GDC9545 rep1

value: Breast


title: SAM24352874_MCF-7, mock, GDC-0927, rep1


title: RNAseq control sample #1

description:
Sample from INS-1 832/13 cells used for RNAseq, batch K, control
RNAseq_INS1_DESeq_normalized_counts.csv


title: RNAseq MAs sample #1

value: MAs-treated


title: HCI-003 Vehicle rep3

value: Vehicle


title: NN3_D3

description:
Library name: Sample16
read_count_NN3_D3

value: periodontal healing tissue


title: SAM24352878_MCF-7, siRNA ER, 48 hrs, rep1


title: HCI-003 GDC9545 rep3


title: NN2_D3

description:
Library name: Sample14
read_count_NN2_D3

value: Mixed cells


title: HCI-003 Vehicle rep2


title: RRBS hippocampus, WT, biological replicate 1

city: Strasbourg

first: Karim

last: Matmat

address: 1 Rue Eugène Boeckel

department: Faculty of Medicine

institute: University of Strasbourg

description: Library name: beta_RRBS3

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: wild-type


title: NN2_D14

description:
Library name: Sample15
read_count_NN2_D14

value: WT

value: periodontal bone defect and sensory denervation


title: SAM24352877_MCF-7, siRNA, NTC, 48 hrs, rep2


title: SAM24352873_MCF-7, mock, GDC-9545, rep2

value: mock, GDC-9545 (100 nM), 48 hrs Amaxa transfection


title: RNAseq control sample #2

value: beta-cell line

value: control


title: HCI-003 Vehicle rep1


title: ChROseq iAs sample #4

description:
Sample from INS-1 832/13 cells used for ChROseq, batch R, iAs-treated
INS1arsenic_ChROseq_DESeq_normalized_counts.csv

extract_protocol:
Libraries were prepared according to the ChROseq protocol
Libraries were prepared using the TriLink CleanTag Small RNA Ligation kit (small RNAseq), NEBNext Ultra II RNA kit (RNAseq), or according to the ChROseq protocol.

value: iAs-treated


title: NN1_D3

description:
Library name: Sample12
read_count_NN1_D3

value: Day 3


title: ChROseq MAs sample #4

description:
Sample from INS-1 832/13 cells used for ChROseq, batch R, MAs-treated
INS1arsenic_ChROseq_DESeq_normalized_counts.csv


title: SAM24352871_MCF-7, mock, DMSO, rep2

value: Adenocarcinoma

value: mock, DMSO, 48 hrs Amaxa transfection


title: ChROseq control sample #4

description:
Sample from INS-1 832/13 cells used for ChROseq, batch R, control
INS1arsenic_ChROseq_DESeq_normalized_counts.csv


title: HCI-011 GDC9545 rep1


title: Con4_D14

description:
Library name: Sample11
read_count_Con4_D14

value: peridontal bone defect

value: Day 14


title: SAM24352872_MCF-7, mock, GDC-9545, rep1

value: Breast


title: ChROseq MAs sample #3

value: MAs-treated


title: NN1_D14

description:
Library name: Sample13
read_count_NN1_D14

value: periodontal healing tissue


title: HCI-011 Vehicle rep2

value: Vehicle


title: AGS cells, 43C+SAHA, rep3

city: Shanghai

first: Fang

last: Guo

state: Shanghai

address: 800 Dongchuan RD. Minhang District

institute: Shanghai Jiao Tong University

data_processing:
Quality control of raw data(.fastq) was performed by fastqc
HISAT2 was used to align the reads to the reference genome hg38
HTSeq-count was used to quantify the gene expression
Assembly: hg38
Supplementary files format and content: counts

source_name: AGS

growth_protocol: AGS cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNAs were extracted from AGS cells using TRIzol .
Samples were outsourced to Tsingke Biotechnology (Beijing, China)

treatment_protocol:
AGS cells were subjected to heat shock at 43℃ for 1 hour
AGS cells were treated with 0.02μM SAHA for 1 hour and simultaneously subjected to heat shock at 43°C for 1 hour.

value: AGS

value: gastric tumor cells

value: Day 0


title: ChROseq Mas sample #2

description:
Sample from INS-1 832/13 cells used for ChROseq, batch K, MAs-treated
INS1arsenic_ChROseq_DESeq_normalized_counts.csv


title: HCI-011 Vehicle rep1


title: HCI-011 GDC9545 rep2


title: Con4_D7

description:
Library name: Sample10
read_count_Con4_D7

value: Mixed cells

value: WT

value: Day 7


title: Con3_D3

description:
Library name: Sample7
read_count_Con3_D3


title: SAM24352870_MCF-7, mock, DMSO, rep1

data_processing:
RNA-seq was analyzed with HTSeqGenie R package.
Reads were trimmed to 75 bp, filtered for quality and rRNA/adapter contamination, and aligned to the reference genome GRCh38 using GSNAP.
Gene expression was quantified as Reads Per Kilobase exon model per Million mapped reads normalized by size factor (nRPKM), defined as number of reads aligning to a gene in a sample / (total number of uniquely mapped reads for that sample x gene length x size factor)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file that include gene counts for each sample


title: HCI-011 GDC9545 rep3


title: HCI-011 Vehicle rep3


title: ChROseq control sample #3

value: beta-cell line

value: control


title: ChROseq iAs sample #2

description:
Sample from INS-1 832/13 cells used for ChROseq, batch K, iAs-treated
INS1arsenic_ChROseq_DESeq_normalized_counts.csv

value: iAs-treated


title: Con3_D14

description:
Library name: Sample9
read_count_Con3_D14


title: AGS cells, 43C, rep2


title: Con3_D7

description:
Library name: Sample8
read_count_Con3_D7


title: AGS cells, 43C+SAHA, rep2


title: Con2_D14

description:
Library name: Sample6
read_count_Con2_D14


title: AGS cells, 43C, rep3


title: PP3

first: Wenjun

last: Wang

address: No.130, Dong'an Road, Xuhui District

institute: FDU

description: Library name: Sample6

data_processing:
(1) data quality control;
(2) Sequence alignment: align the sequencing sequence to the reference genome downloaded from the genome database (including the gene model annotation file);
(3) Gene quantification: calculate the mapping reads of each gene through “featureCounts”to determine the gene expression level;
(4) Differential expression analysis: we used “DESeq2” software (version 1.16.1) to analyze the differences between the two groups, with the corrected P value and |log2foldchange| as the thresholds for significant differences;
Assembly: mm10
Supplementary files format and content: matrix files

extract_protocol:
RNA was isolated from cells using a standard extraction method, followed by stringent quality control of the RNA samples. The quality control was primarily performed using an Agilent 2100 Bioanalyzer to accurately assess RNA integrity.
Two main approaches are commonly used to obtain mRNA: First, taking advantage of the structural feature that most mRNAs of eukaryotes possess a poly(A) tail, mRNA with a poly(A) tail is enriched using Oligo(dT) magnetic beads. Second, ribosomal RNA (rRNA) is removed from total RNA, thereby obtaining mRNA. Subsequently, the mRNA is randomly fragmented with divalent cations in Fragmentation Buffer, and library construction is performed following either a conventional library construction method or a strand-specific library construction method. Conventional Library Construction mRNA is enriched from total RNA using Oligo(dT) magnetic beads. After fragmentation, first-strand cDNA is synthesized with random hexamer primers, followed by the synthesis of second-strand cDNA. Through end repair, A-tailing, adapter ligation, fragment selection, amplification, and purification, the library is ready for use. Strand-Specific Library Construction mRNA is enriched from total RNA using Oligo(dT) magnetic beads. After fragmentation, first-strand cDNA is synthesized with random hexamer primers. Then, second-strand cDNA is synthesized using dUTP instead of dTTP. Following end repair, A-tailing, adapter ligation, fragment selection, amplification, and purification, the strand-specific library is prepared. After library construction, preliminary quantification is first performed using a Qubit 2.0 Fluorometer, and the library is diluted to a concentration of 1.5 ng/μl. Subsequently, the insert size of the library is detected with an Agilent 2100 Bioanalyzer. Once the insert size meets the expected range, accurate quantification of the effective concentration of the library is conducted via qRT-PCR (with the effective concentration of the library required to be above 1.5 nM) to ensure library quality.

value: parenchymal hepatic cells

value: PP, 24 h


title: Con2_D7

description:
Library name: Sample5
read_count_Con2_D7

value: peridontal bone defect


title: ChROseq iAs sample #1


title: AGS cells, 43C, rep1


title: ChROseq Mas sample #1


title: AGS cells, 43C+SAHA, rep1


title: ChROseq control sample #2

description:
Sample from INS-1 832/13 cells used for ChROseq, batch K, control
INS1arsenic_ChROseq_DESeq_normalized_counts.csv


title: PP2

description: Library name: Sample5


title: P3

description: Library name: Sample3

value: PA/OA, 24 h


title: PP1

description: Library name: Sample4


title: AGS cells, 37C, rep3


title: ChROseq control sample #1


title: Con1_D14

description:
Library name: Sample3
read_count_Con1_D14

value: Day 14


title: AGS cells, 37C, rep2


title: Con2_D3

description:
Library name: Sample4
read_count_Con2_D3

value: Day 3


title: CD45+ cells, 6C5 Ab treatment, Day15

city: Beijing

first: Zuming

last: Yang

address: No. 30 Shuangqing Road Haidian District

institute: Tsinghua University

description:
Library name: B6C5
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: Mouse mm10
Supplementary files format and content: Helicobacter pylori ASM2599845v1
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Tumor tissues were harvested, minced into small fragments, and digested in RPMI 1640 containing 1 mg/mL collagenase type IV (Sigma-Aldrich) and 0.5 mg/mL DNase I (Roche) at 37 °C for 30 minutes. The resulting cell suspensions were passed through a 70 μm cell strainer to obtain single-cell suspensions. Cells were resuspended in FACS buffer (PBS supplemented with 2% FBS and 0.05% NaN₃), blocked with anti-mouse CD16/32 antibody (clone 2.4G2) for 20 minutes, and then stained with fluorophore-conjugated antibodies for 30 minutes at 4 °C. Target cell subsets for sequencing were subsequently sorted by flow cytometry.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell Reagent Kits v3 (10x Genomics), in accordance with the manufacturer’s instructions. Cells were captured in droplets to target a specific cell recovery rate. Following the reverse transcription step, emulsions were broken and barcoded cDNA was purified with Dynabeads, followed by PCR amplification. The amplified cDNA was then used for constructing the gene expression library. For this construction, 50 ng of amplified cDNA was fragmented and end-repaired, double-size selected with SPRIselect beads, and sequenced on a NovaSeq platform (Illumina) to generate 150 bp paired-end reads, as per the manufacturer’s instructions.

value: Tumor

value: CD45+ cells

value: immune cell

value: i.p. anti-AXL  Ab(6C5)


title: AGS cells, 37C, rep1

value: AGS

value: gastric tumor cells

value: Day 0


title: P1

description: Library name: Sample1

value: WT


title: ChROseq iAs sample #3

description:
Sample from INS-1 832/13 cells used for ChROseq, batch R, iAs-treated
INS1arsenic_ChROseq_DESeq_normalized_counts.csv

value: beta-cell line


title: P2

description: Library name: Sample2


title: CD45+ cells, PBS  treatment, Day15

description:
Library name: PBS
10x Genomics

value: i.p. PBS


title: DNase-seq from Kasumi-1 (ENCLB353QCI)

status: Public on Feb 28 2026

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR599KVP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR599KVP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB353QCI

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens Kasumi-1 cell line

tag: line

value: cell line

tag: biosample encode accession

tag: encode accession

value: male

tag: dev stage

value: child

value: 7 week

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: ATCC

tag: link

value: ENCBS225HWQ at ENCODE; https://www.encodeproject.org/ENCBS225HWQ/


title: DNase-seq from globus pallidus (ENCLB586ZHI)

description:
https://www.encodeproject.org/experiments/ENCSR599MFU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR599MFU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB586ZHI

source_name: Homo sapiens female adult (90 or above years) globus pallidus tissue

value: globus pallidus

value: tissue

tag: Sex

value: female

value: adult

tag: age

value: 90 or above year

value: Thomas Montine

value: ENCBS412TQU at ENCODE; https://www.encodeproject.org/ENCBS412TQU/


title: DNase-seq from suppressor macrophage (ENCLB051VZH)

description:
https://www.encodeproject.org/experiments/ENCSR377SES/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR377SES
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB051VZH

source_name: Homo sapiens male adult (40 years) suppressor macrophage primary cell treated with 0.1% dmso for 24 hours

value: suppressor macrophage

value: primary cell

value: 40 year

value: Shelly Heimfeld

tag: treatments

value: treatment_term_id:CHEBI:28262; treatment_term_name:dmso; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS414DZH at ENCODE; https://www.encodeproject.org/ENCBS414DZH/