title: T1-NONTARGETplusIMA1-48H_S16

description:
Library name: T1-NONTARGETplusIMA1-48H_S16
Imatinib sensitive GIST-T1 cells


title: Vehicle_3

status: Public on Jul 17 2026

type: SRA

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

description: Sample 3342

library_source: transcriptomic

data_processing:
Raw reads were mapped to mouse genome GRCm39 using STAR 2.7.11b.
Counts were calculated while mapping applying STAR option --quantMode GeneCounts and the gencode.vM35 annotation.
Assembly: GRCm39
Supplementary files format and content: raw_counts.txt: tab-delimited text file includes gene expression raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: liver

growth_protocol: Forty male C57BL/6J mice were fed with standard chow diet (n=10) or with a choline-deficient amino-acid adapted high-fat diet (CDA-HFD) (n=30) for a total of 18 weeks.

extract_protocol:
All the mice were anesthetized and sacrificed after a total of 18 weeks. Liver pieces were  snap frozen and kept at -80 °C . A small fraction was processed using gentleMACS™ Dissociator (Miltenyi Biotec) and TRIzol®. Total RNA was purified using Direct-zol RNA Purification Kit (Zymo Research)
NovaSeq X Plus (Novogene)

treatment_protocol: After 12 weeks of diet, the mice fed with CDA-HFD were randomized in 2 groups, receiving daily IP injections of either SR9009 (100mg/kg/day) or vehicle control (Kolliphor ELP 15% in injectable NaCl) for 6 weeks (n=15 per group).

tag: tissue

value: liver

tag: treatment

value: CDA/HFD


city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

country: USA

institute: St. Jude Childrens Research Hospital

description: Library name: CMY_CIITA_KO.Miller-Plate106-D04-CGACATGATA-CTAGTC

library_source: genomic

data_processing:
samples were demultiplexed using index sequences
fastq files were generated
fastq riles were merged with Paired-End reAd mergeR (PEAR)
analysis using CRIS.py
Supplementary files format and content: .txt files; top exact read counts and indel sizes and matches to test_seqs

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line

extract_protocol:
crude lysis with QuickExtract buffer
targeted amplicon sequencing using 2-step PCR

treatment_protocol: nucleofection of RNPs

value: cell line

tag: cell line

value: CMY

tag: cell type

value: Myeloid leukemia of Down syndrome (ML-DS) cell line

tag: batch


title: Vehicle_2

description: Sample 3347


title: T1-ESRRA-KD1_S6

city: Philadelphia

first: Ronald

middle: P

last: DeMatteo

state: PA

address: 3400 Spruce Street

department: Surgery

institute: University of Pennsylvania Perelman School of Medicine

description:
Library name: T1-ESRRA-KD1_S6
Imatinib sensitive GIST-T1 cells

data_processing:
Reads were aligned to the human genome (GRCh38) using STAR aligner(v2.7.3a) with default parameters. Gene-count matrices were produced by featureCounts (v2.0.1).
Assembly: GRCh38
Supplementary files format and content: Sample by gene matrix of read counts

molecule: polyA RNA

growth_protocol: Cells grown in RPMI media + 10% FBS + 1% antibiotics. Media replaced with in anti-biotic free RPMI media with 10% FBS 24h prior to transfection

extract_protocol:
RNA isolated using Rneasy Plus Mini Kit (Qiagen)
Pooled libraries were then sequenced with paired-end 2x100 bp format

treatment_protocol: Lipofectamine and siRNA transfection reagents diluted in Opti-MEM medium and added to each well. Cells harvested 48h after transfection.

value: Human GIST

tag: genotype

value: KIT exon 11 del560-79

value: ESRRA knockdown


title: HK2 cells, DDX18_WT3

city: Guangzhou

first: Lijun

last: Dong

address: 1023-1063 Shatai South Road, Baiyun District

country: China

institute: Southern Medical University

description: Library name: Sample 3

data_processing:
Raw sequencing reads were assessed for quality using FastQC, and adapter sequences and low-quality bases were trimmed using Trimmomatic.
Clean reads were aligned to the human reference genome (GRCh38/hg38) using the splice-aware aligner STAR. Gene-level read counts were quantified using featureCounts based on the corresponding Ensembl gene annotation (GTF file).
To identify transcripts significantly enriched in DDX18 immunoprecipitates, differential enrichment analysis was performed by comparing IP samples with matched input (or IgG) controls using DESeq2.
Transcripts with an adjusted p-value < 0.05 and |log₂ fold-change| ≥ 1 were considered significant candidate interactors.
Downstream functional annotation, including Gene Ontology (GO) and KEGG pathway enrichment analysis, was performed to explore the biological relevance of the identified transcripts.
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig, narrowPeak(except for input sample)

source_name: kidney

extract_protocol:
Following lysis of HK-2 cells with lysis buffer, DDX18 was immunoprecipitated from the cell lysates using an anti-DDX18 antibody.Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: kidney

value: HK2 cells

value: renal tubular epithelial cells

value: hypoxia/reoxygenation


description: Library name: CMY_CIITA_KO.Miller-Plate106-D02-TGAAATATAC-CTAGTC


description: Library name: CMY_CIITA_KO.Miller-Plate106-D03-CTCAACTGAG-CTAGTC


title: SR9009_3

description: Sample 3369


title: T1-ESRRA-KD1_S4

description:
Library name: T1-ESRRA-KD1_S4
Imatinib sensitive GIST-T1 cells


title: HK2 cells, DDX18_WT2

description: Library name: Sample 2


title: SR9009_2

description: Sample 3361


title: T1-NONTARGET1_S3

description:
Library name: T1-NONTARGET1_S3
Imatinib sensitive GIST-T1 cells

value: Non-target control


description: Library name: CMY_CIITA_KO.Miller-Plate106-D01-GTCAGAAGGT-CTAGTC


title: HK2 cells, DDX18_WT1

description: Library name: Sample 1


title: SR9009_1

description: Sample 3370


description: Library name: CMK_STAG2_R305X_Het_project.Miller-Plate55-F07-CTCTAGAATG-GCATCA

value: CMK


title: Vehicle_1

description: Sample 3343


title: DMD

city: Milan

first: Mattia

last: Chiesa

address: Via Parea 4

department: Bioinformatics and Artificial Intelligence facility

country: Italy

institute: Centro Cardiologico Monzino IRCCS

library_source: transcriptomic single cell

data_processing:
Raw fastq files was processed by Cell Ranger software (Version 6.1.2, 10× genomics).
The sequencing reads were demultiplexed, mapped to the GRCh38 human reference genome, and counted by unique molecular identifier (UMI). Then, the UMI count matrix was analyzed using the Seurat R package (v5.0.3). Cells with 200-5000 detected genes and <5% mitochondrial UMIs were used for downstream analysis. The count matrix was next normalized for library size, log-transformed using Seurat’s default parameters. The percentage of mitochondrial UMIs was used to remove potential batch effects.
Individual sample data have been then integrated after finding 2000 anchor genes and scaled. Dimension reduction analysis has been performed by the 'Uniform Manifold Approximation and Projection' (UMAP) strategy, selecting the top 30 principal components. Cells has been clustered using FindNeighbors and FindClusters functions with default parameters.
To infer the cell type, we first performed a differential expression analysis, exploiting the DaMiRseq  (filtering and normalization) and LIMMA (statistical analysis) R packages, comparing the expression of each cluster against all the others and selecting as markers the top 25 significant up-regulated genes, sorted by t-statistics. The EnrichR  and CellXgene  repository have been used as reference databases to infer the cell-type for each set of markers.
To identify modulated pathways in each cell type across conditions, we first performed differential analyses by DamiRseq and LIMMA and, then, applied the Gene Set Enrichment Analysis (GSEA), using the Gene Ontology Biological Process (GOBP) and Reactome Pathways as reference databases. Each plot has been generated by 'ggplot2 (v.3.5.1)' or 'Seurat' R packages, while pathway networks have been generated by the 'EnrichmentMap' plugin of Cyscape (v.3.9.1). The cell-cell communication analysis has been performed by CellPhoneDB (v.5).
Supplementary files format and content: GRCh38
Supplementary files format and content: Tab-delimited files and matrix files

molecule: nuclear RNA

source_name: Engineered heart tissues

extract_protocol:
The single nuclei suspension was obtained using the GEXSCOPE® Single Nucleus RNA Library Kit V2 (Singleron Biotechnologies) following manufacturer’ instructions. Briefly, EHT tissues were placed in cold nucleus separation solution on ice and cut into small pieces using ophthalmic scissors. Further homogenization was achieved by performing 5 strokes with pestle A and 5 strokes with pestle B of the Kimble douncer (KIMBLE® KONTES® Dounce Tissue Grinder). The sample was incubated on ice for 15 minutes where the state of dissociation was monitored every 5 minutes under a light microscope. Following homogenization and digestion, the suspension was filtered using a 40-μm sterile strainer (Greiner). The nuclei suspension was centrifuged at 200 × g at 4°C for 2 minutes, after which the supernatant was centrifuged at 500 × g for 5 minutes at 4°C to collect the nuclei. The resulting pellet was gently resuspended in 250 μL of cold nuclei suspension buffer. The quality of the nuclei was assessed by Trypan Blue staining (0.4% w/v, Gibco) under a light microscope. The nuclei were counted using propidium iodine with a Luna FX7 automated cell counter (Logos Biosystems).
A total of 45,000 nuclei were loaded onto a microfluidic chip using the Singleron GEXSCOPE® Single Nucleus RNA Library Kit V2, targeting the capture of approximately 10,000 nuclei. Barcoded beads, each containing a unique cell barcode, were loaded into the chip alongside the nuclei, which were subsequently lysed to release cellular RNA. Following lysis, polyadenylated RNA molecules were captured by the poly(dT) sequence on the barcoded beads. The beads containing captured mRNA were then collected for reverse transcription to generate cDNA. The cDNA was amplified, followed by quality control (QC) checks. Illumina-compatible next-generation sequencing (NGS) libraries were generated and sequenced at Macrogen Europe BV facility (Amsterdam, The Netherlands) using a paired-end 150 bp read length Illumina™ Novaseq X Plus platform.

value: Engineered heart tissues

value: iPSCs

value: DMD del49-50


title: T1-NONTARGET1_S1

description:
Library name: T1-NONTARGET1_S1
Imatinib sensitive GIST-T1 cells


title: Healthy blood plasma cfDNA, Female 08

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description:
Library name: Healthy_Female_08
YNG.bw

data_processing:
Illumina cfDNA datasets were processed with Cutadapt in paired-end mode to remove Illumina adapters. Only reads at least 35 bp after removal of adapters were retained. Reads were trimmed down to a maximum of 130 bp using Cutadapt. Trimmed reads were aligned to the human reference genome (T2T CHM13v2.0/hs1) using bowtie2 (with parameters “--local --very-sensitive-local  --no-unal --no-mixed --no-discordant -I 10 -X 500”). Samtools and bedtools were used for processing aligned reads from SAM to BED files. Duplicate reads were discarded for further analysis if the reads had the same start and end coordinates. For Nanopore data, base-calling was performed with Dorado. Since P5/P7 adapters were ligated before ONT library preparation, we could use them as anchors to precisely define read lengths. Hence, we wrote custom python script to trim P5 and P7 adapters from ONT reads. Reads were also aligned to the CHM13 T2T hs1 v2 human reference genome using minimap2. Alignments with SAM flags of 0 and 16 were selected and used for constructing BigWig files.
For Illumina libraries, BigWig files were created using centers of fragments between 120 and 160 bp. Selected fragment centers were extended by 30 bp upstream and downstream, and coverage was calculated  at 10 bp windows genome-wide, which was calculated as the number of extended fragment centers that mapped at that window, normalized by the factor N: N = 3117275501/(Total number of mapped reads). 3117275501 was a number chosen arbitrarily. For Nanopore reads, BigWig files were created for fragments (with an upper limit of 100 kb in length). Coverage was calculated at 100 bp windows genome-wide, which is number of fragments that map at a window normalized by a factor N: 3117275501/(Total number of mapped reads). 3117275501 was a number chosen arbitrarily.
Assembly: Telomere to Telomere (T2T) CHM13 hs1 v2
Supplementary files format and content: bw

source_name: plasma

extract_protocol:
Human plasma (1 to 10 ml) was thawed from −80°C storage. Plasma samples were spun at maximum speed [21,000 rcf (relative centrifugal force)] at 4°C for 5 to 10 min to pellet any cell debris. The blood plasma supernatant was transferred to new tubes. For 1 mL blood plasma cfDNA extractions the following steps were followed. 1 mL of blood plasma was transferred to a 5 mL conical and 10 µL of proteinase K (20 mg/mL) was added to each donor sample. 650 µL of Digestion Buffer (5M GITC, 25% Tween 20, 50 mM Tris pH 8.0, and 25 mM EDTA) was added to the blood plasma and mixed well by pipetting. The samples incubated at 56°C for 1 hour. 3.3 mL of Binding Buffer (3.5M GITC, 45% Isopropanol, 2.5% Tween 20, 10 mM Tris pH 8.0, and 1mM EDTA) was added to each sample. 40 µL of 400 nm SPHERO Silica Superparamagnetic beads were added to each blood plasma sample and mixed well by vortexing. The bead-plasma slurry incubated for 10 minutes at RT. The tubes were placed on a magnetic rack and when the supernatant was clear (~ 5 min) the blood plasma supernatant was discarded. The tubes were then removed from the magnetic rack, the beads were resuspended and washed with 500 µL of Wash Buffer 1 (3M GITC, 30% Isopropanol, 5% Tween 20, 40 mM Bis-Tris pH 6.0, and 2 mM EDTA). The tubes were placed back on the magnetic rack and once the slurry was clear the supernatant was discarded. The tubes were removed again and were resuspended and washed with 500 µL of Wash Buffer 2 (50 mM Tris pH 8.0, 0.5 mM EDTA, and 80% EtOH). The tubes were placed back on the magnetic rack and once the slurry was clear the supernatant was discarded. The tubes were removed and resuspended with 100 µL of 100% EtOH. The new sample slurries were moved to 1.5 mL tubes. The tubes were then placed on a 1.5 mL magnetic rack and when the slurry cleared the supernatant was discarded. The tubes were spun down briefly and returned to the magnetic rack to remove the remaining EtOH. With the tube caps open they were air dried at 37°C for 2 minutes in a bead bath. 30 µL of nuclease free H2O were added to each sample and carefully mixed by pipetting. The tubes incubated at RT for 5 minutes and were returned to the magnetic rack. Once the supernatant was clear the DNA was eluted to a new tube for each sample. DNA fragments were then checked for quality using the Invitrogen Qubit dsDNA HS Assay kit.
UltraPrep cfDNA Isolation: cfDNA extraction was performed using the UltraPrep method. Briefly, human plasma (1 to 10 mL) was thawed from −80°C and spun at 21,000 rcf (relative centrifugal force), 4°C for 5 to 10 min to pellet any cell debris. The blood plasma supernatant was transferred to new tubes. 1 mL of blood plasma was transferred to a 5 mL conical tube, and 10 µL of proteinase K (20 mg/mL) was added to each donor sample. 650 µL of Digestion Buffer (5M guanidine thiocyanate (GITC), 25% Tween 20, 50 mM Tris pH 8.0, and 25 mM ethylenediaminetetraacetic acid (EDTA)) was added to the plasma and mixed well by pipetting. The samples were incubated at 56°C for 1 hour. 3.3 mL of Binding Buffer (3.5M GITC, 45% isopropanol, 2.5% Tween 20, 10 mM Tris pH 8.0, and 1 mM EDTA) was added to each sample. 40 µL of 400 nm SPHERO Silica Superparamagnetic beads (Spherotech) were added to each blood plasma sample and mixed well by vortexing. The bead-plasma slurry was incubated for 10 minutes at room temperature (RT). The tubes were placed on a magnetic rack, and when the supernatant was clear (~ 5 minutes), it was discarded. The tubes were then removed from the magnetic rack, the beads were resuspended and washed with 500 µL of Wash Buffer 1 (3M GITC, 30% isopropanol, 5% Tween 20, 40 mM bis-tris pH 6.0, and 2 mM EDTA). The tubes were placed back on the magnetic rack, and once the slurry was clear, the supernatant was discarded. The beads were resuspended and washed with 500 µL of Wash Buffer 2 (50 mM Tris pH 8.0, 0.5 mM EDTA, and 80% ethanol). The tubes were placed back on the magnetic rack, and once the slurry was clear, the supernatant was discarded. The beads were resuspended with 100 µL of 100% EtOH. The new sample slurries were moved to 1.5 mL tubes. The tubes were then placed on a 1.5 mL magnetic rack, and when the slurry cleared, the supernatant was discarded. The tubes were spun down briefly and returned to the magnetic rack to remove the remaining EtOH. With the tube caps open, they were air dried at 37°C for 2 minutes in a bead bath. 30 µL of nuclease-free H2O was added to each sample and carefully mixed by pipetting. The tubes were incubated at RT for 5 minutes and returned to the magnetic rack. Once the supernatant was clear, the DNA was eluted into a new tube for each sample. Extracted DNA was quantified using the Invitrogen Qubit dsDNA HS Assay. Sequencing Libraries: cfDNA libraries were generated using the SRSLY PicoPlus Base Kit (cat. CBS-K250B-96). 1 to 10 ng of cfDNA per sample was combined with Nuclease-Free (NF) H2O and SRSLY ss Enhancer in a 0.5 mL Axygen PCR tube (Fisher Scientific cat. 14-222-290) on ice. Following incubation on ice for 2 minutes, tubes were moved into a 0.5 mL PCR block for a heat shock at 98°C (lid 105°C) for 3 minutes to allow denaturation. The tubes were then incubated on ice for 2 minutes and the PCR block was set to 37°C (lid temp 45°C). A phosphorylation master mix was created by combining the SRSLY Master Mix, SRSLY Adapter A, and SRSLY Adapter B, all provided from the SRSLY Base Kit. To each sample, a phosphorylation master mix was added for a final volume of 50 μL. Once the tubes were mixed well via vortex, they were incubated for 1 hour in a PCR block at 37°C (lid temp 45°C). cfDNA was isolated after incubation using AMPure XP Beads (Beckman Coulter cat. A63881) at a ratio of 0.54x, mixed with 100% Isopropanol at a ratio of 0.24x, and NF-H2O.  A 0.5 mL magnetic rack was used to capture and wash cfDNA with 80% EtOH. cfDNA-beads were suspended in 15 μL of NF-H2O, and cfDNA was eluted into new 0.5 mL Axygen PCR Tubes. Purified cfDNA libraries were amplified via PCR with a master SRSLY PCR Mix (provided in the base kit) and NF-H2O. Uniquely barcoded primers, P5 and P7, with a final concentration of 0.25 μM each, were added to each sample. Samples were initially incubated at 98°C (lid 105°C) for 3 minutes, followed by 10 cycles of amplification [98°C for 20 seconds, 65°C for 30 seconds, 72°C for 30 seconds], 72°C for 1 minute, then a final hold at 12°C. After PCR, cfDNA libraries were captured and washed with AMPure XP beads at a ratio of 0.95x. The final elution was in 20 μL 0.1X TE buffer and transferred to 1.5 mL Eppendorf LoBind tubes (cat. 022431021).  Eluted libraries were quantified via Qubit (dsDNA Quantitation, High Sensitivity kit cat. Q32854) and quality checked using an Agilent Tapestation (D1000 tape cat. 5067-5582).  Sequencing libraries were stored at -20°C until shipped for sequencing on the Novaseq. All libraries contained dual barcodes and were subjected to 150 bp paired-end sequencing. PCR enrichment of telomere sequences from SRSLY cfDNA libraries: cfDNA libraries until the PCR amplification step were generated as described above. To enrich for telomeric sequences for long-read sequencing, the libraries were amplified using CloneAmp HiFi PCR premix, which accurately amplifies long amplicons. Either standard P5/P7 primers or primers that recognize the junction between Illumina adapters and telomeric repeats were used for amplification (primer sequences below). We used three primer sets: 1. P5 standard primer sequence and P7 standard primer sequence 2. P5 standard primer sequence and P7 + telomere repeat sequence 3. P7 standard primer sequence and P5 + telomere repeat sequence The PCR conditions were (lid temp 105°C), 98°C 10 seconds, 52°C 15 seconds, 72°C 5 seconds, repeated for 12 total cycles, and a 10°C holding temperature. The cfDNA PCR product was purified using a 2X AMPure bead clean. Eluted libraries were quantified using Qubit (dsDNA Quantitation, High Sensitivity kit cat. Q32854) and quality-checked using an Agilent Tapestation (D1000 tape cat. 5067-5582).  Sequencing libraries were stored at -20°C until utilized for Nanopore sequencing. P5 standard primer sequence: 5’ TTTCCCTACACGACGCTCTT 3’ P7 standard primer sequence: 5’ GTTCAGACGTGTGCTCTTCC 3’ P5 + telomere repeat sequence: 5’ TCTTCCGATCTCCCTAACCCTA 3’ P7 + telomere repeat sequence: 5’ CTCTTCCGATCTCCCTAACCC 3’ Oxford Nanopore Long Read Sequencing: The Nanopore Ligation Sequencing DNA SQK-LSK 110 and SQK-LSK 114 kits were used to generate cfDNA Nanopore sequencing libraries, which were sequenced on R9.4.1 MinION and R10.4.1 PromethION flow cells, respectively.

value: plasma

tag: age

value: 29 yo

tag: sample type

value: Blood plasma cfDNA


description: Library name: CMY_CIITA_KO.Miller-Plate106-D07-TCAATATGAT-CTAGTC

value: cell line

value: CMY


title: RNA-seq of SMAD4 knockout PANC-1 cellstransfected with SMAD4 R272K replicate 2

status: Public on Jul 16 2026

city: Wuhan

first: Yizhou

last: Liu

state: Hubei

address: 1277 Jiefang Ave

department: Department of Pancreatic Surgery

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology,

description: Library name: MT_SMAD4_2

data_processing:
1) Raw Data Preprocessing: Raw sequencing data (FASTQ) were subjected to quality control and filtering using the open-source software fastp (v0.23.0). Low-quality reads were removed according to the following criteria: (i) removal of adapter sequences; (ii) removal of reads containing ambiguous 'N' bases (default threshold: 5 bp); (iii) removal of reads in which the proportion of low-quality bases (quality value ≤ 20) exceeded 40%; (iv) sliding-window trimming (window size: 4 bp) where the average quality dropped below 20. This filtering was applied to both Read1 and Read2, yielding high-quality Clean Data for each sample.
(2) Reference Genome Alignment: The resulting Clean Reads were aligned to the reference genome using HISAT2 (v2.1.0), a splice-aware aligner. The alignment output was stored in SAM/BAM format. Samtools was subsequently used to sort the BAM files and remove duplicate reads to ensure accurate downstream quantification.
(3) Gene Expression Quantification (Reads Count): Gene-level read quantification was performed using HTSeq (v0.10.0) with the "union" counting model (as recommended by the software authors). For each sample, the number of reads unambiguously mapped to each gene was calculated, generating the raw Reads Count matrix for all genes across all samples.
(4) Normalization to TPM: To account for both gene length and sequencing depth, the raw Reads Counts were converted to TPM (Transcripts Per Kilobase of exon model per Million mapped reads). This normalization was performed by first dividing each read count by the gene length (in kilobases) to obtain reads per kilobase (RPK), and then dividing the RPK by the total number of RPK values across all genes, multiplied by 1,000,000.
Assembly: GRCh38
Supplementary files format and content: txt file include TPM values for each Sample
Supplementary files format and content: txt file includes raw counts for each Sample

source_name: Pancrea

extract_protocol:
Total RNA was extracted from PANC-1 cells using the RNeasy® Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer‘s protocol.  RNA purity was assessed using a NanoDrop™ One/OneC spectrophotometer (OD260/280 and OD260/230 ratios). RNA concentration was accurately quantified using a Qubit® 3.0 fluorometer with the Qubit™ RNA HS Assay Kit, and RNA integrity was evaluated using an Agilent 4200 TapeStation system (RIN value). Only qualified RNA samples were used for library construction.
Polyadenylated mRNA was enriched using oligo(dT)-coated magnetic beads. Captured mRNA was fragmented, and first-strand cDNA was synthesized with random hexamer primers and M-MuLV reverse transcriptase. Second-strand cDNA was synthesized using RNase H and DNA Polymerase I. The ds-cDNA was purified, end-repaired, A-tailed, and ligated to Illumina adapters. Fragments of ~200 bp were selected with AMPure XP beads, followed by PCR amplification and final purification with AMPure XP beads. Library quality was assessed by Kapa qPCR and Agilent 4200 TapeStation.

value: Pancrea

value: Pancreas Epithelioid Carcinoma


title: ISO-50

value: WT


title: RNA-seq of SMAD4 knockout PANC-1 cellstransfected with SMAD4 WT replicate 2

description: Library name: WT_SMAD4_2


title: RNA-seq of SMAD4 knockout PANC-1 cellstransfected with SMAD4 WT replicate 1

description: Library name: WT_SMAD4_1


description: Library name: CMK_STAG2_R305X_Het_project.Miller-Plate55-F03-CTCGGTACAC-GCATCA

value: Myeloid leukemia of Down syndrome (ML-DS) cell line


title: HK2 cells, DDX18A_1

description: Library name: Sample 4

value: kidney

value: HK2 cells


title: DU_Sp_WT_2

city: Houston

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

institute: MD Anderson Cancer Center

description: Library name: DU_Sp_WT_2

data_processing:
The reads were aligned to the human genome (hg38) using TopHat (version 2.0.10).
The number of reads for each gene from GENCODE (version 37) was quantified using htseq-count from the HTSeq package (version 0.6.0).
Assembly: hg38
Supplementary files format and content: Column 1: Ensembl gene IDs; column 2: the number of reads mapped to each gene.

growth_protocol: DU145 cells were cultured in the EMEM medium (ATCC, 30-2003) with 10% FBS (Gibco, 10082147) and 1% penicillin/streptomycin (Gibco, 15140163) and incubated at 37 °C under 5% CO2

extract_protocol:
Wild-type and mutant (F133V) SPOP DU145 cells were lysed with TRIzol (Invitrogen, 15596026), and total RNAs were extracted using the RNeasy Mini Kit (Qiagen, 74104).
Library preparation and sequencing were performed by MDACC Sequencing and the ncRNA Core at MD Anderson, using a 1x75 bases single-read protocol on a NextSeq500 instrument.

value: prostate cancer cell line

value: wild-type


title: DU_Sp_WT_1

description: Library name: DU_Sp_WT_1


title: Chow_1

description: Sample 3374

value: liver

value: chow diet


description: Library name: CMK_STAG2_R305X_Het_project.Miller-Plate55-F01-AAATACGCAG-GCATCA

value: CMK


title: T1-ESRRA-KD1_S5

description:
Library name: T1-ESRRA-KD1_S5
Imatinib sensitive GIST-T1 cells

value: Human GIST

value: KIT exon 11 del560-79

value: ESRRA knockdown


title: OCI-AML3 RAD21 - Single Cell CUT&Tag - All Cells

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8797 Watertown Plank Rd

department: Stem Cell Transriptional Regulation

institute: Versiti Blood Research Institte

description: Library name: OCIAML3_RAD21_allcells

data_processing:
For each of the human OCI-AML3 CUT&Tag samples, the adaptors and low-quality sequences (> 20 bp) were trimmed by Cutadapt using this criterion '-a CTGTCTCTTATACACATCT -m 20 -q 20'.
Then all the raw reads were aligned to the human genome using bowtie2. The PCR duplicate reads were removed using Picard. After removing PCR duplicates, files for each single cell were merged and sorted.
These merged alignment files were used to generate bigwig files (CPM normalization).
Assembly: hg38
Supplementary files format and content: .bw file of biological reads from all single cells for visualization
Library strategy: CUT&Tag

growth_protocol: Human OCI-AML3 cells were cultured in MEM alpha media supplemented with 20% FBS.

extract_protocol:
Single Cell CUT&Tag data generated according to the procol laid out by Jannsens et al. Nature Genetics, 2021.
scCUT&Tag libraries for RAD21 in human OCI-AML3 sequenced by Novogene (illumina Novaseq X).

treatment_protocol: Human OCI-AML3 cells were maintained at 0.2-0.8 x 10^6/mL in a 37C incubator before collecting cells for CUT&Tag experiment.

value: human acute meyloid leukemia OCIAML3


title: DU_Sp_133_1

description: Library name: DU_Sp_133_1


title: RNA-seq of SMAD4 knockout PANC-1 cellstransfected with SMAD4 R272K replicate 3

description: Library name: MT_SMAD4_3


title: MDA-MB-231HM cells with negative control rep 2

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

description: Library name: 231HMNegPre2

data_processing:
Adapter trimming was performed using cutadapt (v1.3) with the following parameters: --quality-cutoff=28 --adapter=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --error-rate=0.2 --overlap=5 --minimum-length=18, leaving 85-118 million reads per sample. Read quality was assessed using FASTQC (v0.11.2).
Trimmed reads were aligned to the human reference genome hg19 using TopHat2 (v2.0.13, Kim et al., 2013). Alignments were guided by gene annotation from GENCODE (v19), the strand-specific protocol was specified (--library-type fr-secondstrand), and otherwise default parameters were used.
Transcript-level quantification was guided by GENCODE v19 gene annotation, with bias correction enabled using the reference genome sequence (--frag-bias-correct) and correction for multi-mapping reads (--multi-read-correct). A transcript mask file was used to exclude reads overlapping mitochondrial, rRNA, and tRNA features.
Differential expression analysis was performed using Cufflinks (Trapnell et al., 2013) comparing expression in miR-342-3p and miR-342-5p mimic samples to negative control,
Assembly: hg19
Supplementary files format and content: Tab separated file of differential expression analysis results including expression, log fold change and p value

extract_protocol:
After 72 hours, cells were lysed in Trizol (Thermo Fisher) and total RNA extracted according to the manufacturer’s protocol.
Total RNA-seq was performed on two biological replicates by first conducting rRNA depletion using Ribo Zero Gold (Illumina) followed by library construction using the KAPA stranded RNA Library Prep kit (Roche). RNA-seq libraries were multiplexed and sequenced on the Illumina NextSeq 500 platform using the stranded 1 x 75 bp protocol by the Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility.

treatment_protocol: 231HM cells were transfected with 20 nM miRVana mimic (negative control, miR-342-3p or miR-342-5p, Ambion) 2 replicates of each using Lipofectamine RNAiMAX (Thermo Fisher).

value: breast

value: negative control miR transfection

tag: replicate


title: RNA-seq of SMAD4 knockout PANC-1 cellstransfected with SMAD4 R272K replicate 1

description: Library name: MT_SMAD4_1

value: Pancrea


title: DU_Sp_133_2

description: Library name: DU_Sp_133_2


title: HK2 cells, DDX18A_2

description: Library name: Sample 5

value: renal tubular epithelial cells

value: hypoxia/reoxygenation


title: RNA-seq of SMAD4 knockout PANC-1 cellstransfected with SMAD4 WT replicate 3

description: Library name: WT_SMAD4_3

value: Pancreas Epithelioid Carcinoma


title: MDA-MB-231HM cells with miR-342-5p rep 2

description: Library name: 231HM342_5p2

value: WT

value: miR-342-5p transfection


title: MDA-MB-231HM cells with miR-342-5p rep 1

description: Library name: 231HM342_5p1


title: MDA-MB-231HM cells with negative control rep 1

description: Library name: 231HMNegPre1


title: MDA-MB-231HM cells with miR-342-3p rep 2

description: Library name: 231HM342_3p2

value: miR-342-3p transfection


title: AGO HITS-CLIP of MDA-MB-231HM cells with neg miR rep 2

description: Library name: 231HM_neg_miR_R2

data_processing:
Barcodes were extracted and appended to read headers using custom python scripts. Adapters were trimmed and reads were filtered by read length using cutadapt (v1.13)
Trimmed reads were aligned to the human reference genome (hg19) using Tophat2 (v2.0.13, Kim et al., 2013)
alignments were deduplicated using UMI-tools dedup (Smith et al., 2017) with default parameters.
Peak calling was performed separately for each strand using MACS2 2.1.1.20160309 (Zhang et al., 2008) (callpeak program parameters: -t <experimental bam file> -c <control bam file> -f BAM -g hs --keep-dup all --nomodel --shift -15 --extsize 50 -B --call-summits --llocal 0 --slocal 0 --fe-cutoff 2 -q 0.05). The resulting peak files from each strand were merged prior to downstream analyses.
Downstream quality assessment of alignments and peaks was performed by manual inspection in IGV
Assembly: hg19
Supplementary files format and content: tab separated bed files of peak positions as called by MACS2

extract_protocol:
After 48 hours, cells were cross-linked using a UV Stratalinker-1800 (Agilent) and lysed in 500 mL of 1 X PXL (1 X PBS, 0.1% SDS, 0.5% deoxycholate, 0.5% Igepal) + EDTA-free Complete protease inhibitor cocktail (Roche).
Following DNA and partial RNA digestion, AGO-RNA complexes were immunoprecipitated using mouse IgA2 monoclonal anti-Ago2 antibody 4F970 conjugated to protein L Dynabeads (ThermoFisher) with a mouse IgA antibody (GeneTex S107) used as a control.
AGO-RNA complexes were ligated with RNA linkers on-bead, labelled with 32P-ATP, eluted in 1 X Bolt LDS sample buffer (ThermoFisher) + 1% β-mercaptoethanol. 3' adapter NEBNext 3’SR adaptor for Illumina; /5rApp/AGA TCG GAA GAG CAC ACG TCT /3AmMO/. 5' adapter; /5AmMC6/GUUCAGAGUUCUACAGUCCGACGAUCNNNNNNNNNN.
Ago-RNA complexes were separated on Bolt 8% Bis-tris Plus gels (ThermoFisher) then transferred to nitrocellulose and 120-180 kDa regions (corresponding to RNA tags 30-70 nt) were excised followed by proteinase K digestion and RNA extraction using acid phenol (ThermoFisher) with 1:1 isopropanol:ethanol precipitation.
AGO bound RNA was pelleted by centrifugation then separated on a 15% denaturing polyacrylamide gel where gel slices corresponding to the expected size of the cross-linked RNA were cut out and eluted by the ‘‘crush and soak’’ method.
Reverse transcription and amplification were performed essentially as previously described (Ngo et al 2024) using SR-RT primer for reverse transcription (IDT, AGACGTGTGCTCTTCCGATCT) with SuperScript IV. Products were amplified using a common forward primer (NEBNext SR primer for Illumina) and barcoded reverse primers for each sample (NEBNext Index primers for Illumina). PCR products were purified using 1.8 volumes of Axygen AxyPrep magneticbeads (MAG-PCR-CL), separated on an 8% acrylamide (29:1) TBE non- denaturing gel, stained with SYBR Gold nucleic acid gel stain (ThermoFisher) and imaged on a ChemiDoc (BioRad). Products corresponding to an insert size of ~30 – 70 nt were excised from the gel and extracted by the “crush and soak” method as previously described (Jensen and Darnell 2006). Library quality and quantity was assessed by Bioanalyzer (Agilent) and qPCR, pooled and sequenced on an Illumina NextSeq 500 (1 x 75bp).

treatment_protocol: 231HM cells were transfected with 20 nM miRVana mimic (negative control, miR-342-3p or miR-342-5p, Ambion) 3 replicates of each using Lipofectamine RNAiMAX (Thermo Fisher).


title: MDA-MB-231HM cells with miR-342-3p rep 1

description: Library name: 231HM342_3p1


title: AGO HITS-CLIP of MDA-MB-231HM cells with miR-342-5p rep 3

description: Library name: 231HM_342_5p_R3


title: AGO HITS-CLIP of MDA-MB-231HM cells with neg miR rep 1

description: Library name: 231HM_neg_miR_R1


title: AGO HITS-CLIP of MDA-MB-231HM cells with miR-342-3p rep 3

description: Library name: 231HM_342_3p_R3


title: AGO HITS-CLIP of MDA-MB-231HM cells with neg miR rep 3

description: Library name: 231HM_neg_miR_R3


title: AGO HITS-CLIP of MDA-MB-231HM cells with miR-342-5p rep 1

description: Library name: 231HM_342_5p_R1


title: AGO HITS-CLIP of MDA-MB-231HM cells with miR-342-3p rep 2

description: Library name: 231HM_342_3p_R2


title: T1-NONTARGET1_S2

description:
Library name: T1-NONTARGET1_S2
Imatinib sensitive GIST-T1 cells

value: Non-target control


title: AGO HITS-CLIP of MDA-MB-231HM cells with miR-342-5p rep 2

description: Library name: 231HM_342_5p_R2


title: AGO HITS-CLIP of MDA-MB-231HM cells with miR-342-3p rep 1

description: Library name: 231HM_342_3p_R1


title: SMARCA4 in JVM2TRESOX11HA AU-15330

city: Barcelona

first: Virginia

middle: Amador

last: Espinosa

state: Barcelona

address: Carrer del Rosselló, 149

country: Spain

institute: FCRB - IDIBAPS

description: Library name: JVM2TRESOX11HA_SMARCA4_AU-15330

data_processing:
Read quality was assessed with FastQC (v0.11.9) and summarized with MultiQC (v1.10).
Reads were aligned to the human genome (GRCh38) using BWA (v0.7.17), sorted, and filtered with SAMtools (v1.10).
Peaks were called using MACS2 (v2.2.7.1) with p < 0.01, and only peaks present in 100% of biological replicates were retained.
Peak annotation (ChIPseeker), differential binding (DiffBind), and functional enrichment (clusterProfiler, rrvgo) were performed in R (v4.1.2).
Motif enrichment was performed with SEA and MEME (v5.5.5). Heatmaps were generated using DeepTools (v3.5.4).
NarrowPeak files of MACS2-called peaks for each condition and replicate.
Assembly: GRCh38 (GENCODE v42)
Supplementary files format and content: Processed data files include BigWig signal tracks representing genome-wide binding profiles of SOX11 and SMARCA4 in the tested cell lines and conditions.
Library strategy: CUT&RUN

source_name: lymphoid

growth_protocol: MCL cell lines (Z138 wild-type, Z138SOX11KO, Z138 treated with AU-15330, JVM2TRE, JVM2TRE-SOX11:HA, JVM2TRE-SOX11:HA treated with AU-15330, and Granta-519) were cultured in RPMI-1640 or DMEM supplemented with 10% fetal bovine serum, 2 mM L-glutamine, and 1% penicillin–streptomycin at 37°C in 5% CO₂

extract_protocol:
CUT&RUN was performed following the EpiCypher CUTANA™ protocol v2.0 with modifications. 5×10⁵ cells per condition were bound to ConA beads, incubated overnight at 4 °C with antibodies (anti-SOX11, anti-SMARCA4, or IgG), and digested with MNase. Chromatin was released, extracted with phenol-chloroform, precipitated with ethanol at −20 °C, and resuspended in nuclease-free water.
Libraries were prepared from extracted chromatin using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®, according to the manufacturer’s instructions. Libraries were pooled and sequenced as 75 bp paired-end reads on an Illumina NextSeq500 platform.

treatment_protocol: Z138 and JVM2TRE-SOX11:HA were treated with 0.5 μM AU-15330 for 24 h

value: lymphoid

value: lymphoblast cell line

tag: antibody


title: SMARCA4 in JVM2TRESOX11HA DMSO

description: Library name: JVM2TRESOX11HA_SMARCA4_DMSO

value: DMSO


title: Negative control IgG in JVM2TRE DMSO

description: Library name: JVM2TRE_IgG_DMSO

value: TRE

value: Negative control IgG


title: SMARCA4 in JVM2TRE DMSO

description: Library name: JVM2TRE_SMARCA4_DMSO


title: SOX11 in JVM2TRESOX11HA AU-15330

description: Library name: JVM2TRESOX11HA_SOX11_AU-15330


title: SMARCA4 in Granta-519

description: Library name: Granta-519_SMARCA4


title: SOX11 in JVM2TRESOX11HA DMSO

description: Library name: JVM2TRESOX11HA_SOX11_DMSO


title: SOX11 in JVM2TRE DMSO

description: Library name: JVM2TRE_SOX11_DMSO


title: SOX11 in Z138SOX11KO Replicate 3

description: Library name: Z138SOX11KO_SOX11_3

value: DMSO 24h


title: SOX11 in Z138SOX11KO Replicate 2

description: Library name: Z138SOX11KO_SOX11_2


title: IgG in Granta-519

description: Library name: Granta-519_IgG

value: IgG


title: SOX11 in Granta-519

description: Library name: Granta-519_SOX11


title: SOX11 in Z138SOX11KO Replicate 1

description: Library name: Z138SOX11KO_SOX11_1


title: Negative control IgG rabbit in Z138SOX11KO_2

description: Library name: Z138SOX11KO_IgG_2

value: Negative control IgG rabbit


title: SOX11 in Z138WT+ AU-15330 Replicate 3

description: Library name: Z138 AU-15330_SOX11_3


title: SOX11 in Z138WT+ AU-15330 Replicate 1

description: Library name: Z138 AU-15330_SOX11_1


title: SOX11 in Z138WT Replicate 3

description: Library name: Z138_SOX11_3


title: SOX11 in Z138WT Replicate 2

description: Library name: Z138_SOX11_2


title: SOX11 in Z138WT+ AU-15330 Replicate 2

description: Library name: Z138 AU-15330_SOX11_2


title: Negative control IgG rabbit in Z138WT_2

description: Library name: Z138_IgG_2


title: SOX11 in Z138WT Replicate 1

description: Library name: Z138_SOX11_1


title: SMARCA4 in Z138SOX11KO Replicate 2

description: Library name: Z138SOX11KO_SMARCA4_2


title: SMARCA4 in Z138SOX11KO Replicate 3

description: Library name: Z138SOX11KO_SMARCA4_3


title: Negative control IgG rabbit in Z138SOX11KO_1

description: Library name: Z138SOX11KO_IgG_1


title: SMARCA4 in Z138WT+ AU-15330 Replicate 2

description: Library name: Z138 AU-15330_SMARCA4_2


title: SMARCA4 in Z138WT+ AU-15330 Replicate 3

description: Library name: Z138 AU-15330_SMARCA4_3


title: SMARCA4 in Z138WT+ AU-15330 Replicate 1

description: Library name: Z138 AU-15330_SMARCA4_1


title: SMARCA4 in Z138WT Replicate 3

description: Library name: Z138_SMARCA4_3


title: SMARCA4 in Z138WT Replicate 2

description: Library name: Z138_SMARCA4_2


title: SMARCA4 in Z138SOX11KO Replicate 1

description: Library name: Z138SOX11KO_SMARCA4_1


title: SMARCA4 in Z138WT Replicate 1

description: Library name: Z138_SMARCA4_1


title: Negative control IgG rabbit in Z138WT

description: Library name: Z138_IgG_1


title: coch_IgG

city: New York

first: Xiaohui

last: Ma

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

description: Library name: Sample 3

data_processing:
Quality controls using FastQC (v0.11.2) were generated and raw sequencing reads were then aligned to the mouse mm10 genome using default settings of HISAT2.
Peak-calling was performed using MACS (v2.1.1) (Zhang et al., 2008) with various P-value cutoffs. The peak bed files were generated from peak calling against genomic input control or IgG control with the default setting (10-5 cutoff).
The common peaks from these two bed files were used for subsequent analyses. The overlapping peaks of bed files were identified using the bedtools
Assembly: mm10
Supplementary files format and content: bed

source_name: ear

extract_protocol:
30-40 cochleae were dissected from 4-5-week-old mice, fixed, homogenized, and lysed for chromatin preparation. The immunoprecipitation was performed using anti-Six1 and  anti-H3K27ac or IgG as a control.
The pull-down and input control sequencing libraries were generated using the ThruPLEX DNA-seq Kit (R400429, Rubicon Genomics).

value: ear


title: coch_Six1

description: Library name: Sample 4

value: IP


title: coch_H3K27ac

description: Library name: Sample 2


title: DREADD Pilo + CNO, Seizures and Silenced_2

city: San Antonio

first: Jenny

last: Hsieh

state: Texas

address: 1 UTSA Circle, SEB 4.166

department: Neuroscience, Developmental and Regenerative Biology

institute: University of Texas at San Antonio

description:
Library name: hm4Digfp2
DrREADD-silenced abGCs

data_processing:
Paired-end 150 bp RNA-seq reads (~35 million reads/sample) were generated on the Illumina HiSeq platform.
Raw reads were aligned to the mouse genome using Bowtie2, and gene-level counts were generated with the featureCounts function from the Subread package using Gencode vM4 annotations.
Differential expression analysis was performed in R (v4.1.1) using the EdgeR package.
Genes with a false discovery rate (FDR) < 0.05 were considered significantly differentially expressed.
Volcano plots were generated using the EnhancedVolcano R package (v1.13.2).
Assembly: hg38
Supplementary files format and content: Genecounts.csv contains raw read counts for all detected genes across all samples.

source_name: hippocampus

extract_protocol:
cDNA libraries were constructed using the following methods: cells were harvested using direct lysis and reverse transcription from sorted cells using the SMART-seq v4 kit. Approximately 800–1000 live GFP⁺ abGCs per sample were directly used for first-strand cDNA synthesis using the SMART-Seq v4 Ultra Low Input RNA kit (Takara), which accommodates ultra-low RNA inputs (10–1000 cells or ~100–1000 pg total RNA) without prior RNA extraction or quantification
RNA-seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA kit (Takara) according to the manufacturer’s protocol. Approximately 800–1000 live GFP⁺ abGCs per sample were directly used for first-strand cDNA synthesis using the SMART-Seq v4 Ultra Low Input RNA kit (Takara), which accommodates ultra-low RNA inputs (10–1000 cells or ~100–1000 pg total RNA) without prior RNA extraction or quantification

treatment_protocol: Status epilepticus (SE) was induced via i.p. injections of scopolamine methyl nitrate (2 mg/kg; Sigma-Aldrich, S2250) and terbutaline hemisulfate (2 mg/kg; Sigma-Aldrich, T2528) to reduce peripheral cholinergic effects and mitigate respiratory complications. Thirty minutes later, pilocarpine hydrochloride (Sigma-Aldrich, P6503) was administered (300 mg/kg, i.p.). Mice were placed in an incubated chamber (ThermoCare) at 31°C until SE onset (typically between 20 – 30 minutes), then transferred to a room-temperature cages. SE was terminated 3 hours later with diazepam (10 mg/kg; Sigma-Aldrich, D0899, i.p.).

value: hippocampus

value: DREADD Pilo + CNO_2


title: DREADD Pilo + CNO, Seizures and Silenced_3

description:
Library name: hm4Digfp3
DrREADD-silenced abGCs

value: DREADD Pilo + CNO_3


title: DREADD Pilo + CNO, Seizures and Silenced_1

description:
Library name: Hm4digfp1
DrREADD-silenced abGCs

value: WT

value: DREADD Pilo + CNO_1


title: DREADD Sham + CNO, No Seizures_4

description:
Library name: Dreadsc4
DREADD control abGCs

value: DREADD Sham + CNO_4


title: DREADD Sham + CNO, No Seizures_3

description:
Library name: Dreadsc3
DREADD control abGCs

value: DREADD Sham + CNO_3


title: DREADD Sham + CNO, No Seizures_1

description:
Library name: DREADSC1
DREADD control abGCs

value: DREADD Sham + CNO_1


title: DREADD Sham + CNO, No Seizures_2

description:
Library name: DREADSC2
DREADD control abGCs

value: DREADD Sham + CNO_2


title: CAG-GFP Sham + CNO, WT (No Seizure)_2

description:
Library name: CAGSC2
Control abGCs

value: CAG-GFP Sham + CNO_2


title: CAG-GFP Sham + CNO, WT (No Seizure)_3

description:
Library name: CAGSC3
Control abGCs

value: CAG-GFP Sham + CNO_3


title: CAG-GFP Pilo + CNO, Seizures_4

description:
Library name: CAGPC2
pilocaarpine-treated abGCs

value: CAG-GFP Pilo + CNO_4


title: CAG-GFP Sham + CNO, WT (No Seizure)_1

description:
Library name: CAGSC1
Control abGCs

value: CAG-GFP Sham + CNO_1


title: CAG-GFP Pilo + CNO, Seizures_3

description:
Library name: CAGPC1
pilocaarpine-treated abGCs

value: CAG-GFP Pilo + CNO_3


title: CAG-GFP Pilo + CNO, Seizures_1

description:
Library name: CAG_GFP1
pilocaarpine-treated abGCs

value: CAG-GFP Pilo + CNO_1


title: CAG-GFP Pilo + CNO, Seizures_2

description:
Library name: CAG_GFP2
pilocaarpine-treated abGCs

value: CAG-GFP Pilo + CNO_2


title: TAMposH3K27me3_rep4

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

description:
Library name: TAMposH3K27me3_rep4
TAMposH3K27me3.bw

data_processing:
Remove adapters and low quality reads with fastp version 0.21.0
Align to mouse mm10 reference genome with bowtie2 version 2.5.2
Convert sam files to position sorted bam files with picard tools version 2.25.0
Deduplicate bam files with picard tools
Create bigWig files with deeptools version 3.3.0
Assembly: mm10
Supplementary files format and content: reads per genomic content (RPGC) normalized bigwig files
Library strategy: CUT&Tag

extract_protocol:
DNA was purified using a MinElute PCR Purification Kit (Qiagen)
DNA was PCR amplified using barcoded primers and NEBNext HiFi 2x PCR master mix (NEB). Libraries were purified using AMPure XP beads (Beckman).

value: tamoxifen


title: TAMposH3K27me3_rep3

description:
Library name: TAMposH3K27me3_rep3
TAMposH3K27me3.bw


title: TAMposH3K27me3_rep2

description:
Library name: TAMposH3K27me3_rep2
TAMposH3K27me3.bw


title: TAMnegH3K27me3_rep4

description:
Library name: TAMnegH3K27me3_rep4
TAMnegH3K27me3.bw

value: vehicle


title: TAMposH3K27me3_rep1

description:
Library name: TAMposH3K27me3_rep1
TAMposH3K27me3.bw


title: TAMnegH3K27me3_rep3

description:
Library name: TAMnegH3K27me3_rep3
TAMnegH3K27me3.bw


title: TAMnegH3K27me3_rep2

description:
Library name: TAMnegH3K27me3_rep2
TAMnegH3K27me3.bw


title: TAMnegH3K27me3_rep1

description:
Library name: TAMnegH3K27me3_rep1
TAMnegH3K27me3.bw


title: TAMposH3K27ac_rep4

description:
Library name: TAMposH3K27ac_rep4
TAMposH3K27ac.bw


title: TAMposH3K27ac_rep3

description:
Library name: TAMposH3K27ac_rep3
TAMposH3K27ac.bw


title: TAMposH3K27ac_rep2

description:
Library name: TAMposH3K27ac_rep2
TAMposH3K27ac.bw


title: TAMposH3K27ac_rep1

description:
Library name: TAMposH3K27ac_rep1
TAMposH3K27ac.bw


title: TAMnegH3K27ac_rep3

description:
Library name: TAMnegH3K27ac_rep3
TAMnegH3K27ac.bw


title: TAMnegH3K27ac_rep2

description:
Library name: TAMnegH3K27ac_rep2
TAMnegH3K27ac.bw


title: TAMposH3K4me3_rep4

description:
Library name: TAMposH3K4me3_rep4
TAMposH3K4me3.bw


title: TAMnegH3K27ac_rep4

description:
Library name: TAMnegH3K27ac_rep4
TAMnegH3K27ac.bw


title: TAMposH3K4me3_rep3

description:
Library name: TAMposH3K4me3_rep3
TAMposH3K4me3.bw


title: TAMposH3K4me3_rep1

description:
Library name: TAMposH3K4me3_rep1
TAMposH3K4me3.bw


title: TAMnegH3K27ac_rep1

description:
Library name: TAMnegH3K27ac_rep1
TAMnegH3K27ac.bw


title: TAMposH3K4me3_rep2

description:
Library name: TAMposH3K4me3_rep2
TAMposH3K4me3.bw


title: TAMnegH3K4me3_rep3

description:
Library name: TAMnegH3K4me3_rep3
TAMnegH3K4me3.bw


title: TAMnegH3K4me3_rep2

description:
Library name: TAMnegH3K4me3_rep2
TAMnegH3K4me3.bw


title: TAMnegH3K4me3_rep4

description:
Library name: TAMnegH3K4me3_rep4
TAMnegH3K4me3.bw


title: TAMposH3K4me1_rep4

description:
Library name: TAMposH3K4me1_rep4
TAMposH3K4me1.bw


title: TAMposH3K4me1_rep1

description:
Library name: TAMposH3K4me1_rep1
TAMposH3K4me1.bw


title: TAMnegH3K4me3_rep1

description:
Library name: TAMnegH3K4me3_rep1
TAMnegH3K4me3.bw


title: TAMposH3K4me1_rep3

description:
Library name: TAMposH3K4me1_rep3
TAMposH3K4me1.bw


title: TAMposH3K4me1_rep2

description:
Library name: TAMposH3K4me1_rep2
TAMposH3K4me1.bw


title: TAMnegH3K4me1_rep4

description:
Library name: TAMnegH3K4me1_rep4
TAMnegH3K4me1.bw


title: TAMnegH3K4me1_rep3

description:
Library name: TAMnegH3K4me1_rep3
TAMnegH3K4me1.bw


title: TAMnegH3K4me1_rep1

description:
Library name: TAMnegH3K4me1_rep1
TAMnegH3K4me1.bw


title: TAMnegH3K4me1_rep2

description:
Library name: TAMnegH3K4me1_rep2
TAMnegH3K4me1.bw


title: Endotome_SMC_lineage_d20

city: Hong Kong

first: Tianming

last: Wu

state: Hong Kong

address: LKS Int Biomed Sci Bldg

department: School of Biomedical Sciences

institute: Chinese University of Hong Kong

description:
Library name: scRNA_Sample14
scRNA-seq
endotome_vSMC_int_obj.qs

data_processing:
For CUT&Tag, raw single-indexed fastq reads were aligned to the human genome reference hg38 using STAR (v2.7.10a) with default settings. For scRNA-seq data generated using the Singleron platform, raw reads were processed with the SCOPE tools pipeline (https://github.com/SingleronBio/SCOPE-tools) and aligned to the GRCh38 reference genome (Ensembl v99).
Assembly: hg38
Supplementary files format and content: For CUT&Tag processed data, bigwig outputs and corresponding index files were generated for d6 somite and d8 endotome cells. For scRNA-seq processed data, the integrated objects (.qs format) for somite compartments, BAs of endotome, BAs of dermomyotome and vSMC of endotome were included. MSC-derived beige adipocyte object was not integrated with other samples.

source_name: Endotome vSMC lineage cultures

extract_protocol:
For CUT&Tag, Cells from day-6 somite and day-8 endotome cultures were dissociated into single-cell suspensions using Accutase. Then the cells were counted using a hemocytometer. 100,000 live cells were processed according to manufacturer’s instruction of CUT&Tag assay kit (CST, #77552).  For scRNA-seq, monolayered cells were dissociated from TC surface using Accutase at 37 °C for 5-10 minutes. For densely packed brown (endotome-derived BA at day24, dermomyotome-derived BAs at day 36 and 46) and beige adipocyte cultures, which were rich in extracellular matrix and lipids, cells were detached using 2.5 mg/ml collagenase IV (Thermo, 17104019) and 0.25% Trypsin-EDTA (Thermo, 25200056) at 37 °C for 10-15 minutes. The resulting brown and beige adipocyte suspensions were filtered through 100 µm strainers, centrifuged at 1,000 rpm for 4 minutes, and resuspended in DPBS at a density of 1 x 105 cells/ml in DPBS for single-cell capture using Singleron platform. The resulting brown and beige adipocyte suspensions were filtered through 100 µm strainers, centrifuged at 1,000 rpm for 4 minutes, and resuspended in DPBS at a density of 1 x 105 cells/ml in DPBS for single-cell capture using Singleron platform.
CUT&Tag libraries were amplified using i5 and i7 single-end index priemrs, and purified using 1.3x Mag-Bind TotalPure NGS beads. Final CUT&Tag libraries were sequenced on a Nextseq 2000 with pair-end mode. scRNA-seq was conducted using GEXSCOPE® Single‑Cell RNA Library Kit (Singleron Biotechnologies). Libraries were sequenced on a Hiseq Ten instrument with PE150 mode.

value: Endotome vSMC lineage cultures

value: female


title: MSC_derived_beige_adipocytes

description:
Library name: scRNA_Sample15
scRNA-seq
MSC_derived_beige_adipocyte_obj.qs

source_name: hESC derived, MSC derived, beige adipocytes


title: Dermomyotome_BA_lineage_d36

description:
Library name: scRNA_Sample11
scRNA-seq
dermomyotome_BA_time_course_int_obj.qs

source_name: Dermomyotome BA lineage cultures

value: Dermomyotome BA lineage cultures


title: Dermomyotome_BA_lineage_d46

description:
Library name: scRNA_Sample12
scRNA-seq
dermomyotome_BA_time_course_int_obj.qs


title: Dermomyotome_BA_lineage_d26

description:
Library name: scRNA_Sample10
scRNA-seq
dermomyotome_BA_time_course_int_obj.qs


title: Endotome_SMC_lineage_d13

description:
Library name: scRNA_Sample13
scRNA-seq
endotome_vSMC_int_obj.qs


title: Dermomyotome_BA_lineage_d20

description:
Library name: scRNA_Sample9
scRNA-seq
dermomyotome_BA_time_course_int_obj.qs


title: Dermomyotome_BA_lineage_d8

description:
Library name: scRNA_Sample7
scRNA-seq
dermomyotome_BA_time_course_int_obj.qs


title: Endotome_BA_lineage_d20

description:
Library name: scRNA_Sample5
scRNA-seq
endotome_BA_time_course_int_obj.qs

source_name: Endotome BA lineage cultures

value: Endotome BA lineage cultures


title: Endotome_BA_lineage_d12

description:
Library name: scRNA_Sample3
scRNA-seq
endotome_BA_time_course_int_obj.qs


title: Endotome_BA_lineage_d16

description:
Library name: scRNA_Sample4
scRNA-seq
endotome_BA_time_course_int_obj.qs


title: WT1

city: Beijing

first: Hanchi

last: Miao

state: Beijign

address: Datun Road No.15

institute: Institute of Biophysics，Chinese Academy of Sciences

description:
Library name: sample1
fpkm_wt1

data_processing:
Filter out reads with low quality, adapter contamination, and excessive unknown base N
Clean reads  were aligned to the reference genome using HISAT
Clean reads were aligned to the reference gene sequences using Bowtie2
Assembly: GCF_000409795.2_Chlorocebus_sabeus_1.1
Supplementary files format and content: xls files including fpkm values for each sample

organism: Chlorocebus sabaeus

growth_protocol: COS7 cells were maintained in DMEM with 10% fetal bovine serum (Viva cell) and 1% penicillin and streptomycin, under 5% CO2 at 37°C.

extract_protocol:
Colleted cells were homogenized in TRIzol reagent. Subsequently, add chloroform to the homogenate and shake the tube vigorously, centrifuge at 12,000 × g for 15 minutes at 4 °C, then carefully transfer the upper aqueous phase containing RNA into a new tube. After that, mix the collected aqueous phase with isopropanol and centrifuge at 12,000 × g for 10 minutes at 4 °C to precipitate the RNA pellet. Next, wash the obtained pellet with RNase-free 75% ethanol, centrifuge at 7,500 × g for 5 minutes at 4 °C, and air-dry the pellet briefly. Finally, dissolve the dried RNA pellet in RNase-free water and store at −80 °C.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China) following maufacture's protocols

value: WT


title: Vocal fold fibroblast, TGF-beta1, K-975, Replicate 3

first: Ryosuke

last: Nakamura

state: NY

address: 435 E 30th Street

institute: New York University School of Medicine

description:
Library name: TGF_K-975_3
Yap164-12_S12_L008

data_processing:
RNA-seq reads were aligned to the UCSC hg38 genome using STAR.
Reads were quantified using HTseq4 and normalized via Relative Log Expression using DESeq2 R library.
Assembly: hg38
Supplementary files format and content: csv

source_name: HVOX

growth_protocol: DMEM high glucose supplemented with 10% FBS and 1% antibiotic/antimicotic in humidified atomosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit.
ChIP-seq libraries were prepared using theTruSeq Stranded mRNA library prep Kit.

treatment_protocol: 10 ng/mL TGF-beta1 and 10 µM K-975, 12 hours

value: HVOX

value: Vocal fold fibroblast

value: TGF-beta-1, K-975


title: Vocal fold fibroblast, TGF-beta1, K-975, Replicate 2

description:
Library name: TGF_K-975_2
Yap164-11_S11_L008


title: Vocal fold fibroblast, TGF-beta1, K-975, Replicate 1

description:
Library name: TGF_K-975_1
Yap164-10_S10_L008


title: Vocal fold fibroblast, TGF-beta1, Replicate 2

description:
Library name: TGF_2
Yap164-8_S8_L008


title: Vocal fold fibroblast, K-975, Replicate 3

description:
Library name: K-975_3
Yap164-6_S6_L008


title: Vocal fold fibroblast, TGF-beta1, Replicate 1

description:
Library name: TGF_1
Yap164-7_S7_L008


title: Vocal fold fibroblast, K-975, Replicate 2

description:
Library name: K-975_2
Yap164-5_S5_L008


title: Vocal fold fibroblast, K-975, Replicate 1

description:
Library name: K-975_1
Yap164-4_S4_L008


title: Vocal fold fibroblast, Control, Replicate 3

description:
Library name: Cnt_3
Yap164-3_S3_L008


title: Vocal fold fibroblast, Control, Replicate 1

description:
Library name: Cnt_1
Yap164-1_S1_L008


title: Vocal fold fibroblast, TGF-beta1, SMAD2/3, YAP, TAZ, H3K27ac Replicate 3(Input)

description: Library name: TGF_Input_of_SMAD3_YAP3_TAZ3_H3K27ac3

data_processing:
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie.
Narrow peak files were generated using MACS2.
bigWig files were generated using deeptools after merging BAM files of replicates.
Assembly: hg38
Supplementary files format and content: narrowPeak, bw

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min. DNA was sheared by sonication using Diagenode Bioruptor Pico.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: 10 ng/mL TGF-beta1, 12 hours

tag: chip antibody


title: Vocal fold fibroblast, TGF-beta1, SMAD2/3, YAP, TAZ, H3K27ac Replicate 2(Input)

description: Library name: TGF_Input_of_SMAD2_YAP2_TAZ2_H3K27ac2


title: Vocal fold fibroblast, TGF-beta1, H3K27ac, Replicate 3 (ChIP)

description: Library name: TGF_H3K27ac_ChIP3


title: Dermomyotome_BA_lineage_d13

description:
Library name: scRNA_Sample8
scRNA-seq
dermomyotome_BA_time_course_int_obj.qs


title: DKO3

description:
Library name: sample6
fpkm_dko3

value: ATL2/3 knockout


title: Vocal fold fibroblast, TGF-beta1, YAP, TAZ, H3K27ac Replicate 1 (Input)

description: Library name: TGF_Input_of_YAP1_TAZ1_H3K27ac1


title: Vocal fold fibroblast, TGF-beta1, Replicate 3

description:
Library name: TGF_3
Yap164-9_S9_L008


title: Vocal fold fibroblast, TGF-beta1 SMAD2/3, Replicate 1 (Input)

description: Library name: TGF_Input_of_SMAD1


title: Vocal fold fibroblast, Control, Replicate 2

description:
Library name: Cnt_2
Yap164-2_S2_L008


title: WT3

description:
Library name: sample3
fpkm_wt3


title: Somite_d6

description:
Library name: scRNA_Sample1
scRNA-seq
endotome_BA_time_course_int_obj.qs

source_name: Somite cultures

value: Somite cultures


title: Endotome_BA_lineage_d24

description:
Library name: scRNA_Sample6
scRNA-seq
endotome_BA_time_course_int_obj.qs


title: Vocal fold fibroblast, TGF-beta1, TAZ, Replicate 3 (ChIP)

description: Library name: TGF_TAZ_ChIP3

value: TAZ (Atlas, HPA007415)


title: DKO2

description:
Library name: sample5
fpkm_dko2


title: Vocal fold fibroblast, TGF-beta1, H3K27ac, Replicate 1 (ChIP)

description: Library name: TGF_H3K27ac_ChIP1


title: Vocal fold fibroblast, TGF-beta1, H3K27ac, Replicate 2 (ChIP)

description: Library name: TGF_H3K27ac_ChIP2


title: WT2

description:
Library name: sample2
fpkm_wt2


title: Vocal fold fibroblast, TGF-beta1, TAZ, Replicate 1 (ChIP)

description: Library name: TGF_TAZ_ChIP1


title: Vocal fold fibroblast, TGF-beta1, YAP, Replicate 3 (ChIP)

description: Library name: TGF_YAP_ChIP3


title: Vocal fold fibroblast, TGF-beta1, YAP, Replicate 2(ChIP)

description: Library name: TGF_YAP_ChIP2


title: DKO1

description:
Library name: sample4
fpkm_dko1


title: Vocal fold fibroblast, TGF-beta1, SMAD2/3, Replicate 3 (ChIP)

description: Library name: TGF_SMAD_ChIP3


title: Vocal fold fibroblast, TGF-beta1, TAZ, Replicate 2(ChIP)

description: Library name: TGF_TAZ_ChIP2


title: Vocal fold fibroblast, TGF-beta1, SMAD2/3, Replicate 1 (ChIP)

description: Library name: TGF_SMAD_ChIP1


title: Vocal fold fibroblast, TGF-beta1, SMAD2/3, Replicate 2 (ChIP)

description: Library name: TGF_SMAD_ChIP2


title: Endotome_BA_lineage_d8

description:
Library name: scRNA_Sample2
scRNA-seq
endotome_BA_time_course_int_obj.qs


title: Vocal fold fibroblast, Control, SMAD2/3, YAP, TAZ, H3K27ac Replicate 3(Input)

description: Library name: Cnt_Input_of_SMAD3_YAP3_TAZ3_H3K27ac3


title: Vocal fold fibroblast, Control, SMAD2/3, YAP, TAZ, H3K27ac Replicate 2(Input)

description: Library name: Cnt_Input_of_SMAD2_YAP2_TAZ2_H3K27ac2


title: Vocal fold fibroblast, Control, YAP, TAZ, H3K27ac Replicate 1 (Input)

description: Library name: Cnt_Input_of_YAP1_TAZ1_H3K27ac1


title: Vocal fold fibroblast, Control, H3K27ac, Replicate 2 (ChIP)

description: Library name: Cnt_H3K27ac_ChIP2


title: Vocal fold fibroblast, Control, TAZ, Replicate 3 (ChIP)

description: Library name: Cnt_TAZ_ChIP3


title: Vocal fold fibroblast, Control, H3K27ac, Replicate 1 (ChIP)

description: Library name: Cnt_H3K27ac_ChIP1


title: Vocal fold fibroblast, Control, TAZ, Replicate 2(ChIP)

description: Library name: Cnt_TAZ_ChIP2


title: Vocal fold fibroblast, Control, H3K27ac, Replicate 3 (ChIP)

description: Library name: Cnt_H3K27ac_ChIP3


title: Vocal fold fibroblast, Control, SMAD2/3, Replicate 1 (Input)

description: Library name: Cnt_Input_of_SMAD1


title: Vocal fold fibroblast, Control, TAZ, Replicate 1 (ChIP)

description: Library name: Cnt_TAZ_ChIP1


title: Vocal fold fibroblast, Control, YAP, Replicate 3 (ChIP)

description: Library name: Cnt_YAP_ChIP3


title: Vocal fold fibroblast, Control, YAP, Replicate 2(ChIP)

description: Library name: Cnt_YAP_ChIP2


title: Vocal fold fibroblast, Control, YAP, Replicate 1 (ChIP)

description: Library name: Cnt_YAP_ChIP1


title: Vocal fold fibroblast, Control, SMAD2/3, Replicate 2 (ChIP)

description: Library name: Cnt_SMAD_ChIP2


title: Vocal fold fibroblast, Control, SMAD2/3, Replicate 3 (ChIP)

description: Library name: Cnt_SMAD_ChIP3


title: RNA seq of shNC-4

first: Dong

last: Han

address: 28 Fuxing street

institute: Chinese PLA general hospital

description: Library name: shNC-4

data_processing:
Bioinformatics data analysis was provided by NewCore BioTech. (Shanghai, China). Briefly, fastp software (v0.23.2) was used to trim adaptor and remove low quality reads to get high quality clean reads. STAR software (v2.7.9a) was used to align the high-quality clean reads to the human reference genome (hg38). featureCounts software (v2.0) was used to get the raw gene level mRNA read counts as the mRNA expression profile.  DESeq2 software (v1.30.1) was used to normalize the raw counts and get normalized counts.
Assembly: GRCh38/hg38
Supplementary files format and content: raw and normalized count in excel by Deseq2

source_name: Primary human valve interstitial cells

extract_protocol:
mRNA high throughput sequencing was performed by NewCore Biotech. (Shanghai, China). Briefly, total RNA was extracted using Trizol Reagent (ThermoFisher, 15596026). The mRNAs were purified using a NEBNext Poly(A) mRNA Magnetic Isolation Module Kit (NEB, E7490) according to the user manual.
mRNA libraries were constructed by using Illumina TrueSeq mRNA sample preparation kit (Cat. No. RS-122-2101) according to the manufacturer’s instructions. Library sequencing was performed on an Illumina X plus instrument with 150 bp paired end reads.

value: human aortic valve

value: human valve interstitial cells

value: osteogenic differentiation


title: Vocal fold fibroblast, TGF-beta1, YAP, Replicate 1 (ChIP)

description: Library name: TGF_YAP_ChIP1


title: Vocal fold fibroblast, Control, SMAD2/3, Replicate 1 (ChIP)

description: Library name: Cnt_SMAD_ChIP1


title: RNA seq of shNC-3

description: Library name: shNC-3


title: RNA seq of shNC-2

description: Library name: shNC-2


title: RNA seq of shNAT10-4

description: Library name: shNAT10-4

value: NAT10 knockdown


title: RNA seq of shNC-1

description: Library name: shNC-1


title: RNA seq of shNAT10-3

description: Library name: shNAT10-3


title: RNA seq of shNAT10-2

description: Library name: shNAT10-2


title: B cells, Whole transcriptome + TCR + BCR, patient 10 24 weeks after BTKi treatment_R

city: Palo Alto

first: Saurabh

last: Gawde

state: CA

address: 269 Campus Drive, CCSR 2220

institute: Stanford University

description: Library name: P10_Wk24_Bcells_R

data_processing:
Demultiplexing, barcode processing, VDJ annotation, gene counting and aggregation were performed using the BD Rhapsody Sequence Analysis Pipeline (v1.2) run on the Seven Bridges platform (https://www.sevenbridges.com/platform/)
Generation of Seurat rds files and contig_annotations.csv files for each sample from fastq.gz files can be facilitated by specifying the number of cells given in description of SAMPLES list as Exact Cell Count when running the BD Rhapsody Sequence Analysis Pipeline on Seven Bridges platform.
Assembly: Human hg38
Supplementary files format and content: rds files and csv files

source_name: Peripheral blood

extract_protocol:
PBMCs were isolated using Ficoll density gradient centrifugation and were cryopreserved at -80C for 24 hours before storage in liquid nitrogen. Cells were rapidly thawed at 37 °C, treated for 15 min with DNase I and MgCl2 in complete RPMI, and washed. PBMCs were labeled with oligonucleotide barcodes (sample tags) using the BD Human Single Cell Sample Multiplexing Kit (Waters Biosciences). B cells were enriched from remaining PBMCs using the EasySep Human Pan-B Cell Enrichment Kit (StemCell Technologies).
Single-cell capture and library preparation were performed using the microwell-based BD Rhapsody platform (Waters Biosciences) using the BD RhapsodyTM Enhanced Cartridge Reagent Kit v3. cDNA amplification and library preparation for whole transcriptome analysis (WTA), T cell receptors (TCR), B cell receptors (BCR), and sample tags were performed using BD Rhapsody kits according to manufacturer instructions.

value: Peripheral blood

value: B cells

value: Week 24

tag: exact cell_count


title: RNA seq of shNAT10-1

description: Library name: shNAT10-1


title: B cells, Whole transcriptome + TCR + BCR, patient 10 24 weeks after BTKi treatment

description: Library name: P10_Wk24_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 10 24 weeks after BTKi treatment_R

description: Library name: P10_Wk24_PBMCs_R

value: PBMCs


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 10 24 weeks after BTKi treatment

description: Library name: P10_Wk24_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, patient 10 12 weeks after BTKi treatment_R

description: Library name: P10_Wk12_Bcells_R


title: B cells, Whole transcriptome + TCR + BCR, patient 10 12 weeks after BTKi treatment

description: Library name: P10_Wk12_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 10 12 weeks after BTKi treatment_R

description: Library name: P10_Wk12_PBMCs_R


title: B cells, Whole transcriptome + TCR + BCR, patient 10 baseline

description: Library name: P10_Baseline_Bcells

value: Baseline


title: B cells, Whole transcriptome + TCR + BCR, patient 10 baseline_R

description: Library name: P10_Baseline_Bcells_R

value: 1650 (P10_Baseline_Bcells_R)


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 10 12 weeks after BTKi treatment

description: Library name: P10_Wk12_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, patient 9 24 weeks after BTKi treatment

description: Library name: P9_Wk24_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, patient 10 baseline

description: Library name: P10_Baseline_PBMCs


title: PBMCs, Whole transcriptome + TCR + BCR, patient 10 baseline_R

description: Library name: P10_Baseline_PBMCs_R

value: 2101 (P10_Baseline_PBMCs_R)


title: B cells, Whole transcriptome + TCR + BCR, patient 9 12 weeks after BTKi treatment

description: Library name: P9_Wk12_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 9 12 weeks after BTKi treatment

description: Library name: P9_Wk12_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, patient 9 baseline

description: Library name: P9_Baseline_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 9 24 weeks after BTKi treatment

description: Library name: P9_Wk24_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, patient 78 12 weeks after BTKi treatment

description: Library name: P8_Wk12_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, patient 9 baseline

description: Library name: P9_Baseline_PBMCs


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 8 12 weeks after BTKi treatment

description: Library name: P8_Wk12_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, patient 8 baseline

description: Library name: P8_Baseline_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, patient 8 baseline

description: Library name: P8_Baseline_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, patient 7 24 weeks after BTKi treatment

description: Library name: P7_Wk24_Bcells


title: B cells, Whole transcriptome + TCR + BCR, patient 7 12 weeks after BTKi treatment

description: Library name: P7_Wk12_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 7 24 weeks after BTKi treatment

description: Library name: P7_Wk24_PBMCs


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 7 12 weeks after BTKi treatment

description: Library name: P7_Wk12_PBMCs


title: PBMCs, Whole transcriptome + TCR + BCR, patient 7 baseline

description: Library name: P7_Baseline_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, patient 5 24 weeks after BTKi treatment

description: Library name: P5_Wk24_Bcells


title: B cells, Whole transcriptome + TCR + BCR, patient 7 baseline

description: Library name: P7_Baseline_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 5 24 weeks after BTKi treatment

description: Library name: P5_Wk24_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, patient 5 12 weeks after BTKi treatment

description: Library name: P5_Wk12_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 5 12 weeks after BTKi treatment

description: Library name: P5_Wk12_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, patient 5 baseline

description: Library name: P5_Baseline_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, patient 5 baseline

description: Library name: P5_Baseline_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, patient 4 24 weeks after BTKi treatment

description: Library name: P4_Wk24_Bcells


title: B cells, Whole transcriptome + TCR + BCR, patient 4 baseline

description: Library name: P4_Baseline_Bcells


title: B cells, Whole transcriptome + TCR + BCR, patient 3 24 weeks after BTKi treatment

description: Library name: P3_Wk24_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, patient 4 baseline

description: Library name: P4_Baseline_PBMCs


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 4 24 weeks after BTKi treatment

description: Library name: P4_Wk24_PBMCs


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 3 24 weeks after BTKi treatment

description: Library name: P3_Wk24_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, patient 3 12 weeks after BTKi treatment

description: Library name: P3_Wk12_Bcells


title: B cells, Whole transcriptome + TCR + BCR, patient 4 12 weeks after BTKi treatment

description: Library name: P4_Wk12_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 3 12 weeks after BTKi treatment

description: Library name: P3_Wk12_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, patient 3 12 weeks after BTKi treatment_R

description: Library name: P3_Wk12_Bcells_R


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 4 12 weeks after BTKi treatment

description: Library name: P4_Wk12_PBMCs


title: PBMCs, Whole transcriptome + TCR + BCR, patiient 3 12 weeks after BTKi treatment_R

description: Library name: P3_Wk12_PBMCs_R


title: B cells, Whole transcriptome + TCR + BCR, patient 3 baseline

description: Library name: P3_Baseline_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, patient 3 baseline

description: Library name: P3_Baseline_PBMCs


title: PBMCs, Whole transcriptome + TCR + BCR, healthy control 10

description: Library name: HC10_PBMCs

value: Healthy control


title: B cells, Whole transcriptome + TCR + BCR, healthy control 10

description: Library name: HC10_Bcells


title: B cells, Whole transcriptome + TCR + BCR, healthy control 8

description: Library name: HC8_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, healthy control 8

description: Library name: HC8_PBMCs


title: PBMCs, Whole transcriptome + TCR + BCR, healthy control 9

description: Library name: HC9_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, healthy control 9

description: Library name: HC9_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, healthy control 7

description: Library name: HC7_PBMCs


title: PBMCs, Whole transcriptome + TCR + BCR, healthy control 5

description: Library name: HC5_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, healthy control 5

description: Library name: HC5_Bcells


title: B cells, Whole transcriptome + TCR + BCR, healthy control 7

description: Library name: HC7_Bcells


title: B cells, Whole transcriptome + TCR + BCR, healthy control 4

description: Library name: HC4_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, healthy control 4

description: Library name: HC4_PBMCs


title: B cells, Whole transcriptome + TCR + BCR, healthy control 3

description: Library name: HC3_Bcells


title: PBMCs, Whole transcriptome + TCR + BCR, healthy control 3

description: Library name: HC3_PBMCs


title: OCI-AML3 RAD21 - Replicate2

description: Library name: OCIAML3_RAD21_R2

data_processing:
For each of the mESCs and OCIAML3 CUT&Tag samples, the adaptors and low-quality sequences (> 20 bp) were trimmed by Cutadapt using this criterion ‘-a CTGTCTCTTATACACATCT -m 20 -q 20 ’.
Then all the raw reads were aligned to their respective genome (mm10 for mESC samples, and hg38 for OCI-AML3 samples) using bowtie2 --end-to-end --very-sensitive --no-mixed --no-discordant. The PCR duplicate reads were removed using Picard. After removing PCR duplicates, replicate alignment files for each sample were merged and sorted by using $PICARD MergeSamFiles.
These merged alignment files were used for peak calling by MACS2 (2.2.9.1). We called the ‘broad’ Peak for H3K9me3, and H3K36me3 and for RAD21, H3K27Ac, and H3K4me3 ‘narrow’ peaks were called.
These merged alignment files were used to generate bigwig files (CPM normalization)
Assembly: mm10 and hg38
Supplementary files format and content: .bw file for normalized signal files for visualization
Library strategy: CUT&Tag

growth_protocol: mESC cells were cultured in mouse ES cell media and OCIAML3 were cultured in MEM Alpha, both media supplemented with 15% and 20% FBS, respectively

extract_protocol:
Genomic DNA of mESCs and OCIAML3 was extracted to perform CUT&Tag using CUT&Tag-direct with CUTAC V.3 (Steven Henikoff, Jorja Henikoff, Kami Ahmad 2021. CUT&Tag-direct with CUTAC. protocols.io https://dx.doi.org/10.17504/protocols.io.bqwvmxe6)
CUT&Tag libraries for H3K4me3, H3K27ac, H3K9me3, H3K36me3, RAD21, and IgG were then prepared based on the before-mentioned protocol and sent all mESCs and OCIAML3 samples to the Novogene (illumina Novaseq 6000) for seuencing.

treatment_protocol: Both mESC and OCIAML3 cells were grown up to ~80% confluency before collecting cells for CUT&Tag experiment

value: Ontario Cancer Institute - Acute Myeloid Leukemia-3

value: WT


title: OCI-AML3 RAD21 - Replicate3

description: Library name: OCIAML3_RAD21_R3


title: OCI-AML3 RAD21 - Replicate4

description: Library name: OCIAML3_RAD21_R4


title: OCI-AML3 RAD21 - Replicate1

description: Library name: OCIAML3_RAD21_R1


title: smallRNA-Seq, Blood neutrophils, 0h,  Healthy Control replicate 9

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

description: Library name: 20_5015

data_processing:
Reads were mapped to the human genome (hg38) using Bowtie 2 (v2.5.4) using default parameters and specifying --sensitive
GTF file was filtered to only include small RNA genes, i.e. miRNA, Mt_tRNA, scaRNA, snoRNA, snRNA and sRNA entries, and piRNA annotation was downloaded from pirnadb.org (https://www.pirnadb.org/download/archive/gff_gtf)
miRNAs and tRNA fragments were processed with miRge3.0 and mapped to the miRBase reference
Read count data were generated using HTSeq-count
Assembly: hg38
Assembly: miRBase v22
Supplementary files format and content: Raw gene counts

source_name: Neutrophil

growth_protocol: Neutrophils (purity >99%) were isolated from whole blood using HetaSep followed by negative selection with the Stem Cell human neutrophil isilation kit.

extract_protocol:
Trizol:chloroform extraction followed by Qiagen miRNAeasy cleanup including on-column DNase digest
Total RNA was size selected (60-300nt) and de-capped using Cap-Clip™ acid pyrophosphatase
Libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (16 cycles)

treatment_protocol: Neutrophils were suspended in RPMI 1640 media and processed immediately

value: Neutrophil

value: 0h no treatment


title: smallRNA-Seq, Blood neutrophils, 0h,  Healthy Control replicate 10

description: Library name: 21_5016


title: smallRNA-Seq, Blood neutrophils, 0h,  Healthy Control replicate 7

description: Library name: 18_5013


title: smallRNA-Seq, Blood neutrophils, 0h,  SLE replicate 11

description: Library name: 17_6013

value: SLE


title: smallRNA-Seq, Blood neutrophils, 0h,  SLE replicate 10

description: Library name: 16_6012


title: smallRNA-Seq, Blood neutrophils, 0h,  SLE replicate 8

description: Library name: 14_6010


title: smallRNA-Seq, Blood neutrophils, 0h,  Healthy Control replicate 8

description: Library name: 19_5014


title: smallRNA-Seq, Blood neutrophils, 0h,  SLE replicate 9

description: Library name: 15_6011


title: RA 3

city: Cincinnati

first: Theresa

last: Alenghat

state: Ohio

address: 3333 Burnet Avenue

department: Division of Immunobiology

institute: Cincinnati Children's Hospital Medical Center

description: Library name: sample 6

data_processing:
Sequence reads were aligned to the mm10 genome using the Illumina sequence analysis pipeline.
Differentially expressed genes between Vehicle control and RA-treated stem cell orgnaoids were identified using DSeq2.
Assembly: mm10
Supplementary files format and content: text files with Dseq2 output for each sample

source_name: stem cell enteroid

growth_protocol: Organoids were dervied from the ileum (enteroids) of WT C57Bl/6 and maintained at 37C, 5% CO2, in organoid growth media.

extract_protocol:
Organoids were harvested and RNA was isolated using the RNeasy Kit (Qiagen) according to manufacturer's instructions
Directional polyA RNAseq according to standard Illumina protocols

treatment_protocol: Stem cell-enriched organoids were cultured in organoid growth media supplemented with 10 μM CHIR99021 for 96 hours, followed by treatment with 10 μM retinoic acid or vehicle control for 24 hours

value: stem cell enteroid

value: organoid

value: intestinal stem cells

value: 10 µM all-trans retinoic acid


title: smallRNA-Seq, Blood neutrophils, 0h,  SLE replicate 7

description: Library name: 13_6009


title: smallRNA-Seq, Blood neutrophils, 0h,  Healthy Control replicate 6

description: Library name: 11_5012


title: smallRNA-Seq, Blood neutrophils, 0h,  SLE replicate 6

description: Library name: 12_6008


title: smallRNA-Seq, Blood neutrophils, 0h,  Healthy Control replicate 5

description: Library name: 10_5011


title: smallRNA-Seq, Blood neutrophils, 0h,  Healthy Control replicate 3

description: Library name: 8_5009


title: smallRNA-Seq, Blood neutrophils, 0h,  Healthy Control replicate 4

description: Library name: 9_5010


title: smallRNA-Seq, Blood neutrophils, 0h,  Healthy Control replicate 2

description: Library name: 7_5006


title: smallRNA-Seq, Blood neutrophils, 0h,  Healthy Control replicate 1

description: Library name: 6_5008


title: smallRNA-Seq, Blood neutrophils, 0h,  SLE replicate 4

description: Library name: 4_6017


title: smallRNA-Seq, Blood neutrophils, 0h,  SLE replicate 3

description: Library name: 3_6016


title: smallRNA-Seq, Blood neutrophils, 0h,  SLE replicate 2

description: Library name: 2_6015


title: smallRNA-Seq, Blood neutrophils, 0h,  SLE replicate 1

description: Library name: 1_6014


title: OCI-AML3 CTCF - 0.5mM EGS and 0.1Percent Formaldehdye - Replicate 2

description: Library name: OCI_CTCF_0.5mMEGS-01pF_R2

data_processing:
For each of the human OCI-AML3 CUT&Tag samples, the adaptors and low-quality sequences (> 20 bp) were trimmed by Cutadapt using this criterion ‘-a CTGTCTCTTATACACATCT -m 20 -q 20’.
Then all the raw reads were aligned to the human genome using bowtie2 --end-to-end --very-sensitive --no-mixed --no-discordant. The PCR duplicate reads were removed using Picard. After removing PCR duplicates, replicate alignment files for each sample were merged and sorted by using $PICARD MergeSamFiles.
These merged alignment files were used to generate bigwig files (CPM normalization).
Assembly: hg38
Supplementary files format and content: bw file for normalized signal files for visualization
Library strategy: CUT&Tag

extract_protocol:
Genomic DNA of human OCI-AML3 cells was extracted to perform CUT&Tag using CUT&Tag-direct with CUTAC V.3 (Steven Henikoff, Jorja Henikoff, Kami Ahmad 2021. CUT&Tag-direct with CUTAC. protocols.io https://dx.doi.org/10.17504/protocols.io.bqwvmxe6).
CUT&Tag libraries for CTCF, and IgG then prepared based on the before-mentioned protocol and sent all human OCI-AML3 samples to the Novogene (illumina Novaseq X) for sequencing.

value: human acute meyloid leukemia OCIAML3


title: OCI-AML3 IgG - 0.5mM EGS and 0.1Percent Formaldehdye - Replicate 1

description: Library name: OCI_IgG_0.5mMEGS-01pF_R1


title: smallRNA-Seq, Blood neutrophils, 0h,  SLE replicate 5

description: Library name: 5_6018


title: OCI-AML3 IgG - 0.2mM EGS - Replicate 4

description: Library name: OCI_IgG_0.2mMEGS_R4


title: OCI-AML3 CTCF - 0.5mM EGS and 0.1Percent Formaldehdye - Replicate 1

description: Library name: OCI_CTCF_0.5mMEGS-01pF_R1


title: OCI-AML3 IgG - 0.5mM EGS and 0.1Percent Formaldehdye - Replicate 2

description: Library name: OCI_IgG_0.5mMEGS-01pF_R2


title: OCI-AML3 IgG - 0.2mM EGS and 0.1Percent Formaldehdye - Replicate 2

description: Library name: OCI_IgG_0.2mMEGS-01pF_R2


title: rGlut2KO_kidney_WGBS_rep3

city: Lexington

first: Kavaljit

middle: H

last: Chhabra

state: KY

address: 760 Press Avenue

institute: University of Kentucky

description:
Library name: zr24946_6
WGBS of kidney from 12-week-old male rGlut2 KO mouse, biological replicate 3.

data_processing:
Raw FASTQ files were quality trimmed using Trim Galore (paired-end mode).
Trimmed reads were aligned to the mouse reference genome mm10 (GRCm38) using Bismark with Bowtie2.
CpG methylation levels were extracted using the Bismark methylation extractor.
Assembly: mm10 (GRCm38)
Supplementary files format and content: _CpG.bedGraph: Tab-separated bedGraph file containing per-CpG methylation levels. Columns: chromosome, start position, end position, methylation percentage.

source_name: Kidney

extract_protocol:
Genomic DNA was extracted from flash-frozen mouse kidney tissue.
Whole genome bisulfite sequencing libraries were prepared and sequenced by ZymoResearch (project ID: zr24946). Libraries were constructed using the Zymo-Seq WGBS Library Kit.

value: Kidney

tag: Sex

value: male

value: 12 weeks

value: rGlut2 KO (kidney-specific Glut2 knockout)


title: OCI-AML3 IgG - 0.2mM EGS and 0.1Percent Formaldehdye - Replicate 1

description: Library name: OCI_IgG_0.2mMEGS-01pF_R1


title: rGlut2KO_kidney_WGBS_rep2

description:
Library name: zr24946_5
WGBS of kidney from 12-week-old male rGlut2 KO mouse, biological replicate 2.


title: OCI-AML3 CTCF - 0.2mM EGS and 0.1Percent Formaldehdye - Replicate 2

description: Library name: OCI_CTCF_0.2mMEGS-01pF_R2


title: rGlut2KO_kidney_WGBS_rep1

description:
Library name: zr24946_4
WGBS of kidney from 12-week-old male rGlut2 KO mouse, biological replicate 1.


title: OCI-AML3 CTCF - 0.2mM EGS and 0.1Percent Formaldehdye - Replicate 1

description: Library name: OCI_CTCF_0.2mMEGS-01pF_R1


title: Control_kidney_WGBS_rep3

description:
Library name: zr24946_3
WGBS of kidney from 12-week-old male wild-type control mouse, biological replicate 3.

value: Wild-type


title: OCI-AML3 IgG - 0.2mM EGS - Replicate 3

description: Library name: OCI_IgG_0.2mMEGS_R3


title: OCI-AML3 CTCF - 0.2mM EGS - Replicate 4

description: Library name: OCI_CTCF_0.2mMEGS_R4


title: Control_kidney_WGBS_rep2

description:
Library name: zr24946_2
WGBS of kidney from 12-week-old male wild-type control mouse, biological replicate 2.


title: rGlut2KO_kidney_snMultiome_ATAC

description:
Library name: Exp_kidney_multiome_atac
Single-nucleus multiome (RNA + ATAC) sequencing of kidney nuclei pooled from three 12-week-old male rGlut2 KO mice. Estimated 6,088 nuclei captured.

library_source: genomic single cell

data_processing:
Raw FASTQ files were processed using Cell Ranger ARC 2.0.2 (10x Genomics) with the mouse reference genome mm10 (2020-A) using the Cell Ranger ARC count function.
Aggregate analysis was performed using Cell Ranger ARC aggr.
Downstream analysis used Seurat v5.1.0 and Signac v1.13.0 to construct multiomic Seurat objects with paired RNA and ATAC profiles per nucleus.
Assembly: mm10 (GRCm38, 2020-A build)
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format count matrix containing gene expression and ATAC peak counts per cell barcode
Supplementary files format and content: atac_fragments.tsv.gz: Tab-separated fragment file (tabix-indexed with .tbi file) containing ATAC-seq fragment coordinates per cell barcode. atac_peaks.bed: BED format file containing called ATAC-seq peaks.

extract_protocol:
Nuclei were isolated from flash-frozen mouse kidney tissue. Nuclei from three mice per group were pooled prior to library preparation.
Single-nucleus gene expression and ATAC-seq libraries were prepared using the 10x Genomics Chromium Multiome ATAC + Gene Expression kit according to the manufacturer protocol (Singulomics Corporation).


title: Control_kidney_WGBS_rep1

description:
Library name: zr24946_1
WGBS of kidney from 12-week-old male wild-type control mouse, biological replicate 1.


title: OCI-AML3 CTCF - 0.2mM EGS - Replicate 3

description: Library name: OCI_CTCF_0.2mMEGS_R3


title: OCI-AML3 IgG - 0.2mM EGS - Replicate 2

description: Library name: OCI_IgG_0.2mMEGS_R2


title: OCI-AML3 CTCF - 0.2mM EGS - Replicate 2

description: Library name: OCI_CTCF_0.2mMEGS_R2


title: rGlut2KO_kidney_snMultiome_GEX

description:
Library name: Exp_kidney_multiome_gex
Single-nucleus multiome (RNA + ATAC) sequencing of kidney nuclei pooled from three 12-week-old male rGlut2 KO mice. Estimated 6,088 nuclei captured.


title: OCI-AML3 CTCF - 0.2mM EGS - Replicate 1

description: Library name: OCI_CTCF_0.2mMEGS_R1


title: Control_kidney_snMultiome_GEX

description:
Library name: Con_kidney_multiome_gex
Single-nucleus multiome (RNA + ATAC) sequencing of kidney nuclei pooled from three 12-week-old male wild-type control mice. Estimated 5,723 nuclei captured.

value: wild type


title: Control_kidney_snMultiome_ATAC

description:
Library name: Con_kidney_multiome_atac
Single-nucleus multiome (RNA + ATAC) sequencing of kidney nuclei pooled from three 12-week-old male wild-type control mice. Estimated 5,723 nuclei captured.


title: OCI-AML3 IgG - 0mM EGS - Replicate 4

description: Library name: OCI_IgG_0mMEGS_R4


title: LT3

city: Guangzhou

first: Xiaojun

last: Ouyang

address: No. 58 Zhongshan Er Road

institute: the First Affiliated Hospital of Sun Yat-sen University

description:
Library name: SAMPLE 9
FPKM.LT3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: kidney

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: kidney


title: LT2

description:
Library name: SAMPLE 8
FPKM.LT2


title: OCI-AML3 IgG - 0mM EGS - Replicate 3

description: Library name: OCI_IgG_0mMEGS_R3


title: OCI-AML3 IgG - 0mM EGS - Replicate 2

description: Library name: OCI_IgG_0mMEGS_R2


title: LPS3

description:
Library name: SAMPLE 6
FPKM.LPS3

value: LPS


title: LT1

description:
Library name: SAMPLE 7
FPKM.LT1


title: OCI-AML3 IgG - 0mM EGS - Replicate 1

description: Library name: OCI_IgG_0mMEGS_R1

value: WT


title: OCI-AML3 CTCF - 0mM EGS - Replicate 3

description: Library name: OCI_CTCF_0mMEGS_R3


title: LPS1

description:
Library name: SAMPLE 4
FPKM.LPS1


title: OCI-AML3 CTCF - 0mM EGS - Replicate 4

description: Library name: OCI_CTCF_0mMEGS_R4


title: LPS2

description:
Library name: SAMPLE 5
FPKM.LPS2


title: OCI-AML3 CTCF - 0mM EGS - Replicate 2

description: Library name: OCI_CTCF_0mMEGS_R2


title: CTRL3

description:
Library name: SAMPLE 3
FPKM.CTRL3

value: saline


title: OCI-AML3 CTCF - 0mM EGS - Replicate 1

description: Library name: OCI_CTCF_0mMEGS_R1


title: CTRL2

description:
Library name: SAMPLE 2
FPKM.CTRL2


title: CTRL1

description:
Library name: SAMPLE 1
FPKM.CTRL1


title: OCI-AML3 IgG - 0.1Percent Formaldehdye - Replicate 4

description: Library name: OCI_IgG_01pF_R4


title: OCI-AML3 IgG - 0.1Percent Formaldehdye - Replicate 3

description: Library name: OCI_IgG_01pF_R3


title: MIA_Acu_5

first: Tang

last: Tianran

address: Chinese PLA General Hospital, No. 28, Fu Xing Road, Haidian District, Beijing 100853, China

institute: Chinese PLA General Hospital

description: Library name: MIA_Acu_5

data_processing:
Raw sequencing reads were quality‑checked using FastQC and trimmed using Trimmomatic to remove adapters and low‑quality bases.
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tab-delimited text file containing raw read counts and FPKM values for all genes across MIA, and MIA_Acu samples.

source_name: dorsal root ganglia (DRG)

extract_protocol:
Total RNA was extracted from L3‑L5 dorsal root ganglia (DRG) using TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA integrity and concentration were verified using an Agilent 2100 Bioanalyzer with RIN ≥ 8.0.
RNA‑seq libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina. Poly(A) mRNA was purified from total RNA, fragmented, and reverse‑transcribed into cDNA. Double‑stranded cDNA was ligated with adaptors, amplified, and purified to generate the final library.

value: dorsal root ganglia (DRG)


title: OCI-AML3 IgG - 0.1Percent Formaldehdye - Replicate 2

description: Library name: OCI_IgG_01pF_R2


title: MIA_Acu_4

description: Library name: MIA_Acu_4


title: MIA_Acu_2

description: Library name: MIA_Acu_2


title: OCI-AML3 CTCF - 0.1Percent Formaldehdye - Replicate 4

description: Library name: OCI_CTCF_01pF_R4


title: OCI-AML3 IgG - 0.1Percent Formaldehdye - Replicate 1

description: Library name: OCI_IgG_01pF_R1


title: OCI-AML3 CTCF - 0.1Percent Formaldehdye - Replicate 3

description: Library name: OCI_CTCF_01pF_R3


title: OCI-AML3 CTCF - 0.1Percent Formaldehdye - Replicate 2

description: Library name: OCI_CTCF_01pF_R2


title: MIA_5

description: Library name: MIA_5


title: MIA_Acu_1

description: Library name: MIA_Acu_1


title: OCI-AML3 CTCF - 0.1Percent Formaldehdye - Replicate 1

description: Library name: OCI_CTCF_01pF_R1


title: MIA_3

description: Library name: MIA_3