title: LN229 control-2


title: LN229 with HSD52 overexpression-2

status: Public on May 29 2025

type: SRA

city: Harbin

first: Xiangqi

last: Meng

address: No. 157, Baojian Road

country: China

institute: Harbin Medical University

library_source: transcriptomic

data_processing:
Quality control-The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome-Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level-featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include transcript expression for each sample

molecule: total RNA

organism: Homo sapiens

source_name: glioblastoma cell line

extract_protocol:
Total RNA was isolated using TRIzol reagent (Cat. 15596018, Invitrogen, USA) according to the manufacturer’s instructions. Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.

tag: tissue

value: glioblastoma cell line

tag: cell line

tag: cell type

value: glioblastoma

tag: genotype

value: HSD52 overexpression


title: LN229 with HSD52 overexpression-3


title: LN229 control-1

value: WT


title: SYSU335, high abundance

city: Guangzhou

first: Liu

state: GuangDong

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

data_processing:
RNA-Seq reads were adaptor trimmed and the data quality was assessed with the fastp (v 0.23.2) software.
Cleaned data were aligned to human reference genome (GRCh38 release 106 version) by STAR software (v 2.7.10).
RNA expression quantification with RSEM (v 1.3.3) for further quantification were calculated by rsem-calculate-expression.
Assembly: GRCh38 release 106 version
Supplementary files format and content: processed_data.txt represents Counts and FPKMs

source_name: NPC

extract_protocol:
We extracted RNA from tissue samples using the AllPrep DNA/RNA Micro Kit (QIAGEN GmbH).
Sequencing libraries were constructed using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations.

value: NPC

tag: risk bacteria abundance

value: high abundance


title: LN229 with HSD52 overexpression-1


title: SYSU341, high abundance


title: SYSU330, high abundance


title: SYSU329, high abundance


title: SYSU312, high abundance


title: SYSU324, high abundance


title: SYSU325, high abundance


title: Small RNA Sugar beet leaves, drought stress DR3

city: Taigu

first: Chunlei

last: Zou

address: No.1 Mingxian Road

institute: Shanxi Agricultural University

description: Sugar beet leaves, drought stress

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly
The Small RNAs were detected and identified using find_circ
MiRNA expression levels were estimated  by TPM
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.24.0)
Gene Ontology (GO) enrichment analysis for target genes of differentially expressed miRNAs were implemented by the GOseq R package, in which gene length bias was corrected
Assembly: beta_vulgaris_Ensembl_44

organism: Beta vulgaris

source_name: leaves

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The Small RNA libraries were generated by NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: leaves

tag: treatment

value: Drought stress


title: SYSU297, high abundance


title: SYSU317, high abundance


title: Small RNA Sugar beet leaves, drought stress DR2

description: Sugar beet leaves, drought stress


title: SYSU303, low abundance

value: low abundance


title: MM13 primary  tumor GFP negative M4

city: Milano

first: Marine

last: Melixetian

address: via Adamello 16

country: Italy

institute: European Institute of Oncology

library_source: transcriptomic single cell

data_processing:
After demultiplexing and barcode processing gene counting and aggregation was performed using  Cell Ranger Software v7.0.0
Assembly: GRCH38
Supplementary files format and content: Tab separated files and matrix files

source_name: melanoma PDX primary

extract_protocol:
Frozen vital pieces of primary and metastatic melanoma MM13 and MM27 H2B-GFP collected from NSG mice were defrost and mechanically and enzymatically digest with collagenase typeIII in a shaking incubator at 37C for the time necessary to reach single cell suspension. Digestion was stopped with medium supplemented with 10% serum and washed with PBS.  Sorting was performed using fluorescence-associated cell sorters (Aria and Melody, BD Bioscience) to isolate GFP positive and GFP negative populations from primary tumors after DAPI staining for live cells and from mice metastatic organs after labeling with human CD298-PE and DAPI for human melanoma and live cells. Sorted cell populations were resuspended in PBS-0.04%BSA for Chromium Next GEM Single Cell protocol.
Library was prepared with   10x Chromium  protocol according manufacturer recpommendation(10X Genomics 3′ v3 Single Cell Gene Expression Solution).Briefly, cell suspension was loaded onto each channels of the 10x Chromium Single Cell Chip tand single cells were then captured in GEMs. Captured polyA-mRNAs were reverse transcribed into cDNAs and amplified to generate amplified full-length cDNA tagged with CB and UMI (PCR1).

value: melanoma PDX primary

value: melanoma


title: SYSU270, low abundance


title: CircRNA Sugar beet leaves, drought stress DR3

description: Sugar beet leaves, drought stress

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly
The circRNAs were detected and identified using find_circ
The raw counts were first normalized using TPM
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.24.0)
Gene Ontology (GO) enrichment analysis for target genes of differentially expressed circRNAs were implemented by the GOseq R package, in which gene length bias was corrected
Assembly: beta_vulgaris_Ensembl_44

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The circRNA libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.


title: SYSU272, low abundance


title: Small RNA Sugar beet leaves, well-watered CK2

description: Sugar beet leaves, well-watered

value: Well-watered


title: CircRNA Sugar beet leaves, drought stress DR2

description: Sugar beet leaves, drought stress


title: clone-271, wt, ctrl 23d, rep1

city: Uppsala

first: Bengt

last: Westermark

address: Dag Hammarskjölds väg 20

country: Sweden

institute: Uppsala University

description: Sen#6_C271_CTL_DMSO_day 23

data_processing:
Nextflow (v 22.04.0) nf-core/rnaseq using reference genome  Ensembl GRCh37
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes tpm for all samples

molecule: polyA RNA

source_name: Glioblastoma cell line

growth_protocol: Cells were grown adherently on laminin (Sigma-Aldrich)-coated Primaria cell culture dishes (BD Biosciences) in serum-free neural stem cell media (Neurobasal and DMEM/F12 media (1:1) supplemented with N2, B27 w/o retinoic acid (Thermo Fisher Scientific), EGF (10 ng/ml) and bFGF (10 ng/ml) (Peprotech)). For cell detachment, TrypLE Select or TrypLE Express (Thermo Fisher Scientific) was used.

extract_protocol:
Total RNA was extracted using the RNeasy Plus kit (Qiagen)
llumina Stranded mRNA Library Prep

value: Glioblastoma cell line

value: wt

value: ctrl 23d


title: SYSU268, high abundance


title: Small RNA Sugar beet leaves, well-watered CK3

description: Sugar beet leaves, well-watered


title: SYSU263, high abundance


title: SYSU266, high abundance


title: CircRNA Sugar beet leaves, drought stress DR1

description: Sugar beet leaves, drought stress


title: CircRNA Sugar beet leaves, well-watered CK3

description: Sugar beet leaves, well-watered


title: CircRNA Sugar beet leaves, well-watered CK2

description: Sugar beet leaves, well-watered


title: SYSU249, high abundance


title: Small RNA Sugar beet leaves, drought stress DR1

description: Sugar beet leaves, drought stress


title: SYSU250, low abundance


title: SYSU248, low abundance


title: ΔnsdD, Conidia 2 days [FdC_5]

city: Madison

first: Heungyun

middle: Harrison

last: Moon

state: WI

address: 1550 Linden drive

department: Bacteriology

country: USA

institute: University of Wisconsin-Madison

data_processing:
Mapping of the clean reads to the genome was carried out using Tophat2 (version 2.0.12, Veg and Asex samples) and hisat2 (version 2.1, conidia samples).
Gene expression level was processed using HTSeq (version 0.6.1, Veg and Asex samples) and FeatureCounts (version 1.5.0, conidia samples).
Assembly: GCF_000006275.2
Supplementary files format and content: tab-delimited text files include associated peak information for each sample

organism: Aspergillus flavus

source_name: Conidia

growth_protocol: The fungal strains were inoculated into liquid or solid 1% glucose minimal medium (GMM) with appropriate supplements and incubated at 30 °C for 2 days. The conidia were collected in phosphate-buffered saline (PBS) from the entire plate and counted using a hemocytometer. To collect vegetatively growing cells, 5×105 conidia·ml-1 were inoculated into 100 ml liquid GMM and incubated for 36 hr at 30 °C, 220 rpm. To obtain asexually developing cells, postdevelopmental induction was performed as previously described in Seo et al. (2003). Briefly, 2×106 conidia·ml-1 were inoculated into 100 ml liquid GMM and cultured for 18 hr at 30 °C. Cultured mycelia were harvested and transferred on fresh solid GMM. The plates were air exposed and grown for 24 hr for asexual developmental induction.

extract_protocol:
Total RNA isolation and Northern blot analyses were carried out as described (Seo et al., 2003; Han et al., 2004).
DNA libraries were prepared using TruSeq ChIP library Preparation Kit (Illumina) and sequenced using an Illumina NovaSeq 6000 platform.

tag: time

value: 2 days

value: Conidia

value: {delta}nsdD


title: ΔnsdD, Conidia 2 days [FdC_7]


title: Small RNA Sugar beet leaves, well-watered CK1

description: Sugar beet leaves, well-watered


title: SYSU244, low abundance


title: wild-type, Conidia 2 days [FWC_4]

value: wild-type


title: SYSU274, low abundance


title: SYSU243, high abundance


title: wild-type, Conidia 2 days [FWC_3]


title: SYSU237, high abundance


title: ΔnsdD, Asex 24 hr [FdA_3]

source_name: Asexually developing cells

value: 24 hours

value: Asexually developing cells


title: wild-type, Conidia 2 days [FWC_1]


title: SYSU233, low abundance

value: NPC


title: ΔnsdD, Asex 24 hr [FdA_1]


title: ΔnsdD, Asex 24 hr [FdA_2]


title: SYSU236, low abundance


title: wild-type, Asex 24 hr [FWA_3]


title: SYSU229, low abundance


title: SYSU260, high abundance

value: high abundance


title: SYSU228, high abundance


title: SYSU216, low abundance


title: CircRNA Sugar beet leaves, well-watered CK1

description: Sugar beet leaves, well-watered

value: leaves


title: wild-type, Asex 24 hr [FWA_1]


title: ΔnsdD, Conidia 2 days [FdC_8]


title: SYSU208, low abundance


title: SYSU205, low abundance


title: ΔnsdD, Vege 36 hr [FdV_2]

source_name: vegetatively grown cells

value: 36 hours

value: vegetatively grown cells


title: ΔnsdD, Vege 36 hr [FdV_3]


title: wild-type, Vege 36 hr [FWV_1]


title: SYSU176, low abundance

value: low abundance


title: wild-type, Vege 36 hr [FWV_2]


title: SYSU166, low abundance


title: NsdD-FLAG strain, anti-FLAG antibody, 2 days [NsdD ChIP biol rep 4]

library_source: genomic

data_processing:
Read sequences were mapped to the genome using BWA (version 0.7.12) and MACS2 (version 2.1.0) was utilized to call peaks.
Identification of NsdD direct targets was done by selecting genes, in which NsdD peaks are found in their promoter regions within the 1.5kb upstream range from the translation start site (TSS).
Assembly: GCF_000006275.2
Supplementary files format and content: tab-delimited text files include associated peak information for each sample

molecule: genomic DNA

source_name: spores

growth_protocol: The fungal strains were inoculated into liquid or solid 1% glucose minimal medium (GMM) with appropriate supplements and incubated at 30 °C for 2 days. The conidia were collected in phosphate-buffered saline (PBS) from the entire plate and counted using a hemocytometer.

extract_protocol:
To collect samples for ChIP-seq analysis, two-day-old conidia (2×109) of THM5 were cross-linked with 1% formaldehyde, resuspended in lysis buffer, and homogenized by a mini-beadbeater with 0.5mm zirconia/silica beads. The lysates were then sonicated for five to seven cycles (60 s on, 60 s off) with a sonicator to achieve 150-200 bp size DNA fragments. After centrifugation, the lysates were diluted in the ChIP dilution buffer and applied for ChIP assays using the MAGnify Chromatin Immunoprecipitation System (Invitrogen) follwing the manufacturer’s instruction with a modest modification. The diluted chromatin extracts were incubated with 1 μg of mouse monoclonal Anti-FLAG antibody (Sigma-Aldrich). Initial input DNAs before immunoprecipitation were used as positive controls. The enriched DNA fragments were retrieved and used as a template for ChIP-seq.
DNA libraries were prepared using TruSeq ChIP library Preparation Kit (Illumina) and sequenced using an Illumina NovaSeq 6000 platform.

value: spores

value: NsdD::FLAG expressing strain

value: mouse monoclonal anti-FLAG antibody


title: wild-type, Vege 36 hr [FWV_3]


title: SYSU158, low abundance


title: SYSU195, high abundance


title: ΔnsdD, Vege 36 hr [FdV_1]


title: SYSU137, high abundance


title: SYSU136, high abundance


title: wild-type, Asex 24 hr [FWA_2]


title: SYSU144, low abundance


title: SYSU168, low abundance


title: Constitutive, tumor

city: Los Angeles

first: Peixiang

last: He

state: California

address: 1002 Childs Way

institute: USC

description:
Library name: scRNA_seq_Co_PGK
10X Genomics

data_processing:
Alignments and count aggregation of gene expression and sgRNA reads were completed using Cell Ranger (v.7.0.1). Gene expression and sgRNA reads were aligned using the cellranger count command with default settings. Gene expression reads were aligned to aligned to the human (hg38) reference genome using STAR 2.7.2a. A sample-specific approach was employed to identify the boundary between empty microwells and those containing a cell, based on log-scale barcode rank plots. Low-quality cells with <200 detected genes or >15% mitochondrial reads were discarded. Cells with fewer mRNA UMIs than the specified threshold were excluded from downstream analysis. Quality control criteria for unsupervised clustering involved retaining cells with gene expression counts between 1,000 and 6,500 genes. Subsequently, mRNA expression data were normalized using the 'SCTransform' function in Seurat (Choudhary and Satija, 2022), and batch effects related to experimental conditions were removed via the Seurat v3 anchor-based integration workflow using default parameters.
Assembly: human hg38
Supplementary files format and content: filtered gene expression counts for each feature and sample. Gene identifiers are gene symbols, aligned to the human genome build hg38.

source_name: T cells

extract_protocol:
T cell and glioblastoma cell line U87 cocultured were collected and resuspend in PBS for FACS. Constitutive GD2CAR T cells and EchoBack GD2CAR T cells were sorted for mCherry signal (maker of CAR-T cells) using SONY SH800. Sorted Cells were imediately frozen in cyropresrvation buffer (7.5% DMSO+92.5% FBS) until further use. Cells were thawed and washed in DPBS and finaly resuspended in DPBS for library construction.
Library was constructed by Molecular Genomics Core at USC Norris Comprehensive Cancer Center foloowing manufacturer's instructions (Chromium platform 10X Genomics and the Chromium Single Cell 3' HT v3.1 kit). cDNA libraries were separately prepared for EchoBack CAR-T cells and standard CAR-T cells.

value: T cells

value: PGK-GD2 CAR T cells

value: chronic couclture with glioblastoma


title: SYSU188, low abundance


title: NsdD-FLAG strain, anti-FLAG antibody, 2 days [NsdD ChIP biol rep 2]

value: 2 days


title: EchoBack, tumor+HS

description:
Library name: scRNA_seq_Co_HS_HI7HE_FB
10X Genomics

value: EchoBack-GD2 CAR T cells

value: chronic couclture with glioblastoma, heat shock


title: SYSU206, high abundance


title: SYSU135, low abundance


title: SYSU131, low abundance


title: APOE4_untreated_REP1

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: Library name: APOE4_untreated_REP1

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software used for basecalling and deplexing. Post deplexing, FASTQ files were quality inspected using the FastQC tool (available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and the MultiQC tool (Ewels et al., 2016). For reference mapping (hg38), the nf-core RNA-Seq Seq pipeline was used (version 3.10.1; available at https://nf-co.re/rnaseq) in conjunction with select parameters (--clip_r1 9, --clip_r2 9). Expression enumeration was accomplished within the pipeline instance using salmon (https://salmon.readthedocs.io/en/latest/salmon.html) with gene-length normalized counts returned per known gene.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files describing gene-length normalized counts for known genes.

source_name: iPSC

growth_protocol: Two sets of isogenic APOE3/APOE3 and APOE4/APOE4 iPSCs (from parental lines Coriell #AG09173 and #AG10788, obtained via MTA from MIT) were thawed in a 6-well plate coated with hESC-qualified Matrigel Matrix (Corning) in Essential 8 Medium (ThermoFisher Scientific) with 10 μM Y-27632 compound (StemCell Technologies). The media was replaced with Essential 8 Medium the following day and cultured until cells reached ∼90% confluence. Cells were passaged using ReLeSR (StemCell Technologies) for dissociation, as per manufacturer protocols. iPSC-derived microglia were differentiated using the StemCell Technologies recommended microglial differentiation workflow (unless otherwise noted), which is based on the published protocol for the differentiation process33, hESC-qualified Matrigel-coated cultureware was used. Briefly, hematopoietic progenitor cells were generated using the STEMdiff Hematopoietic kit (StemCell Technologies). In lieu of half media changes, 1 mL media additions were performed throughout the hematopoietic differentiation protocol. Hematopoietic progenitors were harvested and passaged for microglia differentiation using STEMdiff Microglia Differentiation Kit (StemCell Technologies). Cells were maintained in this media for 24 days, according to manufacturer’s guidelines. For the last 4 days, microglia progenitors were cultured in the STEMdiff Microglia Maturation Kit (StemCell Technologies) medium to mature the microglia. Flow cytometry (CD11+ APC,  Miltenyi Biotec ) and immunocytochemistry were used to assess purity.

extract_protocol:
Cells were seeded at a density of 5 x105 cells per well in a tissue culture-treated 12-well plate (NEST). Microglia were treated with LPS, DGAT inhibitors, or DMSO vehicle as described above. Cells were harvested after treatments in 300 μL of TRIzol Reagent (Invitrogen) and RNA was purified using Direct-zol RNA isolation kits (Zymo Research).
The Illumina RNA Stranded PolyA library kit was used followed by sequening using the NextSeq 2000.

treatment_protocol: Microglia were treated with 5 µg/mL LPS, E. Coli O111:B4 (Millipore Sigma) in spent medium for 16 hours at 37 °C. To assess the number of lipid droplets (LD) in microglia, cells were plated in an ibiTreated μ-Plate 96 square well plate (Ibidi) in STEMdiff Microglia Maturation Medium or iTF-Microglia Medium. To decrease LD accumulation cells were treated 16 hours  with a combination of inhibitors of 5 μM PF-04620110 (DGAT1 inhibitor, Sigma) and 5 μM PF-06424439 (DGAT2 inhibitor, Sigma) or 1 μM Triacsin C (ACSL inhibitor, Tocris Bio-Techne).  To inhibit LD lipase activity, cells were treated with either 1.3 nM KLH45 (DDHD2 inhibitor, Cayman Chemical) or 10 μM Atglistatin  (ATGL inhibitor, Sigma) for 6 hours.

value: iPSC

tag: type

value: untreated


title: APOE4_untreated_REP3

description: Library name: APOE4_untreated_REP3


title: SYSU134, low abundance

value: NPC


title: APOE4_LPS_REP3

description: Library name: APOE4_LPS_REP3

value: LPS


title: APOE4_untreated_REP2

description: Library name: APOE4_untreated_REP2


title: SYSU132, high abundance

value: high abundance


title: NsdD-FLAG strain, anti-FLAG antibody, 2 days [NsdD ChIP biol rep 1]


title: APOE4_LPS_REP4

description: Library name: APOE4_LPS_REP4


title: SYSU129, low abundance


title: SYSU122, high abundance


title: SYSU153, low abundance


title: glp-4, Day 7, Rep 2

city: Huddinge

first: Christian

middle: Günter

last: Riedel

state: Stockholm

address: Blickagången 16 (Neo Building, 6th floor)

department: Biosciences and Nutrition

institute: Karolinska Institute

data_processing:
The analysis of raw ATAC-seq and mRNA-seq data was conducted using Cactus v0.8.4 (Salignon et al, Genomics, 2024), using default parameters and the following custom parameters: species = 'worm', chromatin_state = 'iHMM.M1K16.worm_L3', use_input_control = true, diffbind__summits = 'TRUE', diffbind__design = 'FALSE', diffbind__edger_tagwise = 'FALSE', diffbind__min_count = 1, diffbind__background = 'FALSE', diffbind__library_size = 'DBA_LIBSIZE_FULL', diffbind__scale_control = 'FALSE', diffbind__score = 'DBA_SCORE_TMM_READS_FULL_CPM', split__peak_assignment = [ 'all', 'prom', 'distNC' , '3pUPR' ] and pwms_motifs = hughesCePWMSForHomerLO9.motif'. The latter custom motif file contained experimentally defined C. elegans TF binding motifs and was created by the Brunet lab and used in (Daugherty et al, Genome Research, 2017). Two replicates of a genomic DNA control, taken from the strain GR1373, were used in all analyses to remove peaks located in hotspot regions.
Assembly: ce11/WBcel235, Ensembl release 107
Supplementary files format and content: mrna_raw_counts.txt.gz: TSV file containing the raw count matrix. Counts estimated from Kallisto were rounded.
Supplementary files format and content: mrna_TPM.txt.gz: TSV file containing the Transcripts Per Million count matrix.

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: C. elegans were grown on the Escherichia coli strain OP-50 using standard methods (Stiernagle, 2006). In the case of RNAi experiments, animals were grown on the Escherichia coli strain HT115 transformed with L4440-based plasmids expressing double-stranded RNA targeting the genes of interest.

extract_protocol:
For each condition and timepoint, a minimum of 80 worms were collected in triplicate. Worms were washed twice with M9, resuspended in 100 µl Tri Reagent (Zymo Research, Cat. No.: R2050-1-200), and then immediately frozen in liquid nitrogen. RNA was extracted with the Direct-zolTM RNA MiniPrep kit (Zymo Research, Cat. No.: R2052) according to the manufacturer’s instructions, and RNA amount and quality were determined using a NanoDrop. mRNA was isolated and cDNA constructed by following the TruSeq RNA Library Preparation Kit v2 protocol (Illumina, Cat. No.: RS-122-2001/RS-122-2002).
mRNA-seq libraries were constructed using the TruSeq RNA Library Preparation Kit v2 (Illumina, Cat. No.: RS-122-2001/RS-122-2002) according to the manufacturer’s instructions.

treatment_protocol: C. elegans were synchronized at the L1 stage by bleaching and hedging in M9 and seeded onto plates pre-seeded with either OP-50 or RNAi bacteria (E. coli strain HT115 containing dsRNA-expressing plasmids that target a specific gene of interest). HT115 with the empty plasmid L4440 was used as the control. The RNAi clone targeting daf-16 was obtained from the Ahringer library (Kamath et al., Nature 2003), while the clone targeting lin-39 was obtained from the Vidal library (Reboul et al., Nature Genetics 2003). Plates were incubated at 15°C until the animals reached the late L4 stage. FUDR was added to a final concentration of 50 µM to prevent progeny production, and plates were shifted to 20°C (mRNA-seq) or 25°C (ATAC-seq) for the remainder of the assays. Worms were collected and harvested at indicated timepoints.

value: whole organism


title: SYSU118, low abundance


title: SYSU116, low abundance


title: glp-4, Day 7, Rep 1


title: APOE4_DGAT_1_2_inh_REP4

description: Library name: APOE4_DGAT_1_2_inh_REP4

value: DGAT1 and DGAT2 inhibitor


title: SYSU107, low abundance

value: low abundance


title: APOE4_LPS_REP1

description: Library name: APOE4_LPS_REP1


title: SYSU102, low abundance


title: glp-4, Day 3, Rep 2


title: APOE4_LPS_REP2

description: Library name: APOE4_LPS_REP2


title: SYSU090, high abundance


title: glp-4, Day 3, Rep 1


title: SYSU083, low abundance


title: SYSU092, high abundance


title: glp-4, Day 1, Rep 2


title: APOE4_DGAT_1_2_inh_REP2

description: Library name: APOE4_DGAT_1_2_inh_REP2


title: SYSU066, low abundance


title: APOE4_DGAT_1_2_inh_REP1

description: Library name: APOE4_DGAT_1_2_inh_REP1


title: SYSU060, high abundance


title: glp-4, Day 1, Rep 1


title: SYSU114, low abundance


title: APOE4_DGAT_1_2_inh_LPS_REP3

description: Library name: APOE4_DGAT_1_2_inh_LPS_REP3

value: DGAT1 and DGAT2 inhibitor and LPS


title: SYSU051, high abundance


title: APOE4_DGAT_1_2_inh_LPS_REP2

description: Library name: APOE4_DGAT_1_2_inh_LPS_REP2


title: APOE4_DGAT_1_2_inh_REP3

description: Library name: APOE4_DGAT_1_2_inh_REP3


title: NsdD-FLAG strain, anti-FLAG antibody, 2 days [NsdD ChIP biol rep 3]

value: spores

value: NsdD::FLAG expressing strain


title: SYSU041, high abundance


title: SYSU044, high abundance


title: scRNA-seq-organoids-human stomach-IX

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

description: scRNA-seq

data_processing:
Raw reads were aligned to the different species genome (Human: GRCh38/hg38, Mouse: GRCm38/mm10), and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers (UMIs).
Raw aligned features were loaded and processed using the Seurat package (v4.0.2)
Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes
Assembly: Human: GRCh38/hg38, Mouse: GRCm38/mm10
Supplementary files format and content: text files

source_name: Gastric organoids

growth_protocol: Organoids were embedded in Matrigel and seeded on 48- or 24- well plate. After Matrigel polymerization, the CM medium (Advanced DMEM/F12 supplemented with Penicillin/Streptomycin, GlutaMAX, N2, B27, and N-acetylcysteine containing 50 ng/mL EGF, 100 ng/mL Noggin, 500 ng/mL R-spondin1, 5 μM CHIR, 10 nM Gastrin, 10 μM SB431542, 100 ng/mL FGF10 and 10 μM Y27632) was added and refreshed every 2 days.

extract_protocol:
Gastric glands and organoids were isolated and digested with EDTA and Tryple, alive cells were sorted by flow cytometry. Single cell suspensions were captured using the 10X Genomics Chromium
ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000.

treatment_protocol: Organoids were treated with CM and differentiation medium for 2 days.

value: Gastric organoids

tag: group

value: Sleeve gastric surgery

value: Treated with Noggin Rspondin1 SB431542 IXA4 and CHIR 2 days


title: APOE3_Untreated_REP2

description: Library name: APOE3_Untreated_REP2


title: Schizosaccharomyces Pombe,E112Kclr6-1,repeat1

city: 南京

first: Ruifan

last: Zhu

address: 江苏省南京市栖霞区仙林街道南京师范大学生命科学学院

institute: 南京师范大学

description: Library name: Sample7

data_processing:
First, the descending raw reads was quality-controlled using the fastp
clean reads were aligned to the ribosome database of this species using the short reads alignment tool bowtie2[2], the reads on the upper ribosomes were removed without mismatch allowed, and the retained unmapped reads was used for subsequent transcriptome analysis.
Using the HISAT2 software, a reference genome-based alignment analysis was performed.
Based on the alignment results of the HISAT2, we reconstructed the transcripts using the Stringtie and calculated the expression levels of all the genes in each sample using the RSEM
Input data for gene differential expression analysis are the reads count data obtained from gene expression level analysis and were analyzed using DESeq2[6] software
Assembly: Using the STRING protein interaction database (http://string-db.org).
Supplementary files format and content: Ensembl_release45
Supplementary files format and content: Each Excel corresponds to the information of one sample, with a total of two tables, namely all gene expression and significant gene expression.

organism: Schizosaccharomyces pombe

source_name: whole cell

extract_protocol:
Total RNA was extracted using Trizol reagent kit.The RNA libraries of RNA-Seq were enriched for mRNA using Oligo (dT), reverse transcribed to cDNA, after PCR amplification, and then sequenced.
The RNA libraries of RNA-Seq were enriched for mRNA using Oligo (dT),following manufacturer's protocols.

value: whole cell

value: htb1-E112K clr6-1


title: SYSU043, high abundance


title: Schizosaccharomyces Pombe,E112Kclr6-1,repeat2

address: 江苏省南京市栖霞区仙林街道南京师范大学生命科学学院

description: Library name: Sample8


title: Schizosaccharomyces Pombe,H2BE112K,repeat3

address: 江苏省南京市栖霞区仙林街道南京师范大学生命科学学院

description: Library name: Sample6


title: scRNA-seq-organoids-human stomach-WT

description: scRNA-seq

value: Untreated


title: SYSU073, high abundance


title: APOE3_Untreated_REP3

description: Library name: APOE3_Untreated_REP3

value: iPSC


title: scRNA-seq-organoids-human stomach-BI

description: scRNA-seq

value: Treated with BMP4 Metformin DY131 PD0325901and ISX-9 2 days


title: scRNA-seq-organoids-human stomach-EB

description: scRNA-seq

value: Treated with EGF and BMP4 2 days


title: Schizosaccharomyces Pombe,H2BE112K,repeat2

address: 江苏省南京市栖霞区仙林街道南京师范大学生命科学学院

description: Library name: Sample5


title: APOE3_Untreated_REP1

description: Library name: APOE3_Untreated_REP1

value: untreated


title: scRNA-seq-tissue-human corpus-3

description: scRNA-seq

source_name: Corpus epithelium and stromal cells

value: Corpus epithelium and stromal cells


title: scRNA-seq-tissue-human corpus-2

description: scRNA-seq


title: SYSU056, low abundance

value: NPC


title: scRNA-seq-tissue-human corpus-1

description: scRNA-seq


title: SYSU047, high abundance

value: high abundance


title: APOE3_LPS_REP3

description: Library name: APOE3_LPS_REP3

value: LPS


title: Schizosaccharomyces Pombe,E112Kclr6-1,repeat3

address: 江苏省南京市栖霞区仙林街道南京师范大学生命科学学院

description: Library name: Sample9


title: RNA-seq-organoids-human IXA-2

description: RNA-Seq

data_processing:
RNA-seq reads were aligned to the human or mouse genome available in Ensembl (release 95) with HISAT2 (v2.1.0)
StringTie (v1.3.3b) for transcript assembly
The quantitative gene expression (FPKM) was obtained with Ballgown
Assembly: Human: hg38, Mouse: mm10
Supplementary files format and content: csv

extract_protocol:
Organoids were digested with Tryple and alive cells were sorted by flow cytometry. Total RNA was extracted with RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.
The library were prepared for sequecing using NEBNext Ultra RNA library Prep Kit for Illumina.

tag: strategy


title: RNA-seq-organoids-human IXA-1

description: RNA-Seq


title: Schizosaccharomyces Pombe,WT,repeat3

address: 江苏省南京市栖霞区仙林街道南京师范大学生命科学学院

description: Library name: Sample3

value: WT


title: APOE4_DGAT_1_2_inh_LPS_REP1

description: Library name: APOE4_DGAT_1_2_inh_LPS_REP1

value: DGAT1 and DGAT2 inhibitor and LPS


title: Schizosaccharomyces Pombe,WT,repeat2

address: 江苏省南京市栖霞区仙林街道南京师范大学生命科学学院

description: Library name: Sample2


title: APOE3_LPS_REP2

description: Library name: APOE3_LPS_REP2


title: RNA-seq-organoids-human EB-2

description: RNA-Seq


title: APOE3_LPS_REP1

description: Library name: APOE3_LPS_REP1


title: RNA-seq-organoids-human EB-1

description: RNA-Seq


title: Schizosaccharomyces Pombe,WT,repeat1

address: 江苏省南京市栖霞区仙林街道南京师范大学生命科学学院

description: Library name: Sample1


title: RNA-seq-organoids-human BIM-2

description: RNA-Seq


title: RNA-seq-organoids-human BIM-1

description: RNA-Seq


title: APOE3_DGAT_1_2_inh_REP2

description: Library name: APOE3_DGAT_1_2_inh_REP2

value: DGAT1 and DGAT2 inhibitor


title: RNA-seq-organoids-human con-1

description: RNA-Seq


title: APOE3_DGAT_1_2_inh_REP3

description: Library name: APOE3_DGAT_1_2_inh_REP3


title: RNA-seq-organoids-human con-2

description: RNA-Seq


title: Schizosaccharomyces Pombe,H2BE112K,repeat1

address: 江苏省南京市栖霞区仙林街道南京师范大学生命科学学院

description: Library name: Sample4


title: Whole adult Botrylloides diegensis colony including zooids and vasculature.

city: Dunedin

first: Megan

middle: J.

last: Wilson

state: Otago

address: 56 Hanover St

department: Anatomy

country: New Zealand

institute: University of Otago

description:
Library name: Sample 1
10X Genomics

data_processing:
Quality checks of the library were performed using FastQC. Raw sequencing reads were mapped to the reference B. diegensis genome using STARSolo. The genome file of B. diegensis (formerly B. leachii) was downloaded from the Aniseed Database. Gene models were identified using the StringTie software (Pertea et al., 2016). First, genome indices were created using STAR 2.7.9 (--genome SAindexNbases 12). The indices were then used to map the raw sequences to the B. diegensis genome using STAR 2.7.9, which masks the polyA tail during alignment;
therefore, no prior trimming was performed. These run options were selected for the default barcode lengths using a droplet-type algorithm (soloUMIlen 12, soloType Droplet). No barcode read length defined (--soloBarcodeReadLength  0).
The empty droplets were then filtered (soloCellFilter EmptyDrops_CR). Finally, sequences with barcodes present within the barcode whitelist were selected while mapping (soloCBwhitelist).
Assembly: The genome file of B. diegensis (formerly B. leachii) was downloaded from the Aniseed Database https://aniseed.fr/
Supplementary files format and content: Tab seperated value and matrix files.

organism: Botrylloides diegensis

source_name: whole adult colony

growth_protocol: Colonies of B. diegensis were sampled from Otago Harbor in New Zealand (45°52’18.1″’’S, 170°31’37.6’’″ E). The animals were attached to × 5x7 cm glass slides. The tanks were aerated, and the colonies were fed a shellfish diet (a blend of marine microalgae). The colonies were fed every two days, and the seawater was replaced. Colonies were confirmed to be B. diegensis by COI barcoding

extract_protocol:
A mature colony, in stage A of blastogenesis with active filtering, newly emerged primary buds, and no signs of secondary buds was processed using the ACME dissociation method García-Castro, H., et. al. (2021). ACME dissociation: A versatile cell fixation-dissociation method for single-cell transcriptomics. Genome Biology, 22(1), 89. https://doi.org/10.1186/s13059-021-02302-5
Library preparation was carried out according to the 10X Genomics protocol for 3’ Gene Expression (v3) user guide (10X Genomics CG000183 Rev C). The combined cDNA libraries were sequenced with a length of 150 bp on an Illumina NovaSeq 6000 sequencing platform.

value: whole adult colony

value: wildtype


title: ScrPS5

city: La Jolla

first: Miguel

middle: Alejandro

last: Lopez Ramirez

state: CA

address: 9500 Gilman Dr

department: Medicine

institute: University of California, San Diego

description: Library name: Sample 30

data_processing:
Data was processed using the systempipeR workflow.
Sequencing analysis was conducted in the R environment, following quality assurance of the data using FastQC. Reads were aligned to the human genome (GRCh38) using RNAStar, and read counts were obtained using featureCounts.
Differential gene expression was calculated using DeSeq2
Assembly: GRCh38
Supplementary files format and content: DEG_Summary.xlsx
Supplementary files format and content: normalisedcounts.csv

source_name: HUVEC

growth_protocol: Human umbilical vein endothelial cells (HUVECs) purchased from Lonza (C2519A) were cultured according to the manufacturer’s protocol and recommended growth medium (CC-3162). Experiments described were performed using cells between passages 3 and 6. HUVECs were maintained by passaging 1:3 and grown to confluence in fibronectin-coated T-75 flasks using 2μg/mL human fibronectin (Sigma, F2006) dissolved in sterile PBS and incubated for 1 hour at 37°C.

extract_protocol:
Isolatedbrain endothelial cells were harvested from animals and homogenized in TRIzol solution for RNAseq analysis according to the manufacturer’s instructions.
Glass slides of HUVECs were removed from the flow chamber and cells were directly lysed in 400µl of TRIzol (Invitrogen, 15596026) per slide and stored in RNase-free microcentrifuge tubes, which were transferred to dry ice for storage until all samples were collected. Total RNA was extracted using the RNeasy mini kit (Qiagen, 74104) according to manufacturer’s directions.
RNA quality was confirmed using an Agilent Tapestation 4200, and high-quality RNA (RIN > 8.0) was used for RNA-seq library preparation with the Illumina® Stranded mRNA Prep kit (Illumina, San Diego, CA) RNA libraries were multiplexed and sequenced with 100‐bp paired reads (PE100) on an Illumina NovaSeq 6000 platform with a target depth of 30 million reads per sample. Samples were demultiplexed using bcl2fastq conversion software

treatment_protocol: Cells were transfected with 75nM SMARTpool siRNA against KRIT1 (Dharmacon, M-003825–01) or non-targeting control siRNA (Dharmacon, D-001206–13). Transfection mix was prepared in OptiMEM (Gibco) using lipofectamine3000 (Invitrogen), which was added dropwise to cells plated in complete growth medium. Following overnight (12-hour) incubation, cells were given fresh growth medium for 24 hours before replating onto fibronectin-coated glass slides for flow chamber experiments. HUVECs transfected with siRNA for 48 hours were replated using 0.05% Trypsin/EDTA (Thermo Fisher, 25300054) on 38 mm × 76 mm glass plates at 95% confluence. A subset of the glass plates were then assembled into a parallel-plate flow channel as previously described for each condition: siScr+PS, siKrit1+PS, siSCr+OS, and siKrit1+OS. The flow system was maintained at 37°C and ventilated with 95% humidified air with 5% CO2. HUVECs were exposed to pulsatile flow (PS) (12 ± 4 dyn/cm2, 1 Hz) or oscillatory flow (OS) (1 ± 4 dyn/cm2, 1 Hz) for 24 hours as described previously. Additional control plates of siScr- and siKrit1-transfected HUVECs were subject to static conditions (no flow) and maintained in the same culture medium and conditions described above in an adjacent incubator.

value: HUVEC

value: Endothelial cell

value: Krit1 WT

value: Pulsatory flow


title: ScrStat5

description: Library name: Sample 31

value: Static


title: TUMOR_TE57_97

type: RNA

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

data_processing: Data were quantified by relative threshold cycles (Crt) methods and normalized on miR-16-5p as per the manufacturer’s instructions (Thermo Fisher Scientific). To further compensate for variability, we added additional normalizers by selecting the two miRNAs most correlating with miR-16-5p, from the list of six miRNAs previously described as housekeeping (doi:10.1093/jnci/djv063). Normalization was performed using the following procedure: a scaling factor (SF) was calculated for each sample, by subtracting the average of the three normalizers to a constant value (K=19.079)(doi:10.1093/jnci/djv063). Data were then normalized using the formula: Crt normalized=miRNA Crt raw – SF. Normalization was skipped for Crt=40. Batch bias was investigated through analysis of the miRNAs expression distribution across centers (FC analysis, Wilcoxon Rank Sum test).

label: FAM

source_name: plasma

label_protocol: Total RNA was reverse transcribed using the custom RT Primers and components supplied with the TaqMan MicroRNA Reverse Transcription Kit. The pre-amplified samples were assembled with TaqMan OpenArray Real-Time PCR Master Mix and loaded to OpenArray plates using the OpenArray Accufill System

growth_protocol: not applicable

extract_protocol: Plasma samples were thawed on ice, and RNA was extracted with the commercial miRNeasy mini-Kit (QIAgen™, Hilden, Germany) using the QIAcube™ robot, following the manufacturer´s instructions.

treatment_protocol: not applicable

tag: age

tag: gender

value: F

tag: smocking status

value: CURRENT

tag: histology

value: adenocarcinoma

tag: Stage

value: IIIA

tag: nodule density

value: non-solid

tag: nodule size

tag: molecule subtype

value: microRNA

tag: center

value: HUM


title: TUMOR_TE57_95

value: FORMER

value: typical carcinoid

value: IA

value: solid

value: MUG


title: APOE3_DGAT_1_2_inh_REP1

description: Library name: APOE3_DGAT_1_2_inh_REP1

tag: tissue

value: iPSC

value: DGAT1 and DGAT2 inhibitor


title: ScrPS4

description: Library name: Sample 29

tag: cell line

value: HUVEC

tag: cell type

value: Endothelial cell

tag: genotype

value: Krit1 WT


title: APOE3_DGAT_1_2_inh_LPS_REP2

description: Library name: APOE3_DGAT_1_2_inh_LPS_REP2

tag: treatment

value: DGAT1 and DGAT2 inhibitor and LPS


title: ScrPS3

description: Library name: Sample 28

value: Pulsatory flow


title: CONTROL_TE57_94

value: M

value: CURRENT


title: TUMOR_TE57_93


title: APOE3_DGAT_1_2_inh_LPS_REP3

description: Library name: APOE3_DGAT_1_2_inh_LPS_REP3

tag: type


title: APOE3_DGAT_1_2_inh_LPS_REP1

description: Library name: APOE3_DGAT_1_2_inh_LPS_REP1


title: ScrOS5

description: Library name: Sample 27

value: Oscilatory flow


title: CONTROL_TE57_92

value: F

value: microRNA


title: CONTROL_TE57_91

value: FORMER

value: HUM


title: ScrOS4

description: Library name: Sample 26


title: ScrStat6

description: Library name: Sample 32

value: Static


title: ScrOS3

description: Library name: Sample 25


title: Total RNA, Fus d14/d14, biol rep 5

city: London

first: Pietro

last: Fratta

address: Queen Square

country: United Kingdom

institute: University College London

description: Library name: Input_HOM5

data_processing:
Raw sequences (in FASTQ format) were trimmed using Fastp  and aligned using STAR (v2.7.0f)  to the Mus musculus genome assembly GRCm38.
Counting the reads was performed using featureCounts v1.6.4
Assembly: GRCm38
Supplementary files format and content: Tab-separated files with raw counts for each sample

organism: Mus musculus

source_name: total spinal cord

extract_protocol:
3 month-old spinal cords were homogenized using TissueRuptor (Qiagen) in a buffer containing 50 mM tris-HCl (pH 7.4), 100 mM KCl, 12 mM MgCl2, and 1% NP-40,  cycloheximide (0.1 mg/ml), heparin (1 mg/ml), SuperaseIn RNase (Thermo Fisher Scientific). Lysates were cleared by centrifugation at 10,000 × g for 10 min, and 5% of the lysate was saved as input (total RNA samples). For RiboTag immunopurifications, to reduce nonspecific-binding protein G magnetic beads (Dynabeads, Thermo Fisher Scientific) were added to the lysate and incubated for 2 h at 4°C. Next, 5 μl of anti-HA antibody (Sigma-Aldrich) was added to the precleared lysate and incubated for 2 h at 4°C. 100 μl of beads slurry with 2 μl of SuperaseIn was added to the lysate followed by 2 h incubation at 4°C. Beads were then washed five times in washing buffer [300 mM KCl, 1% NP-40, 50 mM tris-HCl (pH 7.4), 12 mM MgCl2, and cycloheximide (0.1 mg/ml)]. Beads were eluted in Qiazol (Qiagen), and RNAs were isolated using the RNeasy Micro Kit (Qiagen). The quality control of RNA was performed using TapeStation (Agilent).
cDNA libraries were made using the KAPA mRNA HyperPrep Kit with RiboErase (Roche)

value: total spinal cord

value: Fus d14/d14


title: CONTROL_TE57_90


title: BENIGN_TE57_89

value: solid


title: BENIGN_TE57_87


title: Total RNA, Fus d14/d14, biol rep 3

description: Library name: Input_HOM3


title: Total RNA, Fus d14/d14, biol rep 4

description: Library name: Input_HOM4


title: CONTROL_TE57_96

value: MUG


title: CONTROL_TE57_83


title: TUMOR_TE57_85

value: adenocarcinoma

value: IA

value: part-solid


title: CONTROL_TE57_82


title: Total RNA, Fus d14/d14, biol rep 2

description: Library name: Input_HOM2


title: TUMOR_TE57_84


title: Total RNA, Fus+/+, biol rep 5

description: Library name: Input_WT5

value: Fus+/+


title: KRIT1Stat5

description: Library name: Sample 23

value: HUVEC

value: Endothelial cell

value: KRIT1 KD


title: Total RNA, Fus d14/d14, biol rep 1

description: Library name: Input_HOM1


title: TUMOR_TE57_81

value: CURRENT

value: large-cell neuroendocrine


title: CONTROL_TE57_8

value: M

value: microRNA


title: TUMOR_TE57_80

value: IIB


title: KRIT1PS4

description: Library name: Sample 21

value: Pulsatory flow


title: CONTROL_TE57_79

value: HUM


title: CONTROL_TE57_9

value: FORMER


title: BENIGN_TE57_88

value: F

value: solid


title: Total RNA, Fus+/+, biol rep 4

description: Library name: Input_WT4

value: total spinal cord


title: CONTROL_TE57_76


title: CONTROL_TE57_78


title: KRIT1OS5

description: Library name: Sample 19

value: Oscilatory flow


title: Total RNA, Fus+/+, biol rep 2

description: Library name: Input_WT2


title: BENIGN_TE57_74


title: KRIT1Stat6

description: Library name: Sample 24

value: Static


title: CONTROL_TE57_77


title: Total RNA, Fus+/+, biol rep 3

description: Library name: Input_WT3

value: Fus+/+


title: CONTROL_TE57_75


title: Total RNA, Fus+/+, biol rep 1

description: Library name: Input_WT1


title: BENIGN_TE57_73


title: KRIT1PS5

description: Library name: Sample 22

value: HUVEC


title: KRIT1OS4

description: Library name: Sample 18

value: Endothelial cell


title: CONTROL_TE57_71

value: MUG


title: ScrStat4

description: Library name: Sample 16

value: Krit1 WT


title: KRIT1OS3

description: Library name: Sample 17

value: KRIT1 KD


title: Cardiomyocyte_LPS_24h

city: Fukuoka

first: Masataka

last: Ikeda

state: Fukuoka

address: 3-1-1, Maidashi, Higashiku

country: Japan

institute: Kyushu University

description: Gene expression 24 h after LPS treatment

hyb_protocol: cRNA was hybridized to Affymetrix Clariom D Assay Rat array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

label: biotin

organism: Rattus norvegicus

source_name: Cardiomyocyte, 24h LPS

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using ISOSPIN Cell & Tissue RNA kit (314-08211, NIPPON GENE CO; https://www.nippongene.com/english/tds/tds_isospin-cell-tissue-rna-e.pdf) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: primary neonatal cardiomyocyte


title: CONTROL_TE57_72

value: M

value: microRNA


title: RiboTag, Fus d14/d14, biol rep 4

description: Library name: IP_HOM4

source_name: spinal cord

value: spinal cord

value: motor neuron

value: ribosome associated RNAs

value: Fus d14/d14


title: CONTROL_TE57_70

value: F

value: CURRENT

value: solid


title: TUMOR_TE57_69

value: FORMER

value: adenocarcinoma

value: IA


title: RiboTag, Fus d14/d14, biol rep 5

description: Library name: IP_HOM5


title: Cardiomyocyte_vehicle_24h

description: Gene expression 24 h after vehicle treatment

source_name: Cardiomyocyte, 24h vehicle


title: ScrStat3

description: Library name: Sample 15

value: HUVEC

value: Endothelial cell

value: Static


title: CONTROL_TE57_7

value: MUG


title: TUMOR_TE57_61

value: IB

value: HUM


title: KRIT1PS3

description: Library name: Sample 20

value: KRIT1 KD

value: Pulsatory flow


title: CONTROL_TE57_67

value: microRNA


title: CONTROL_TE57_60

value: M


title: RiboTag, Fus d14/d14, biol rep 2

description: Library name: IP_HOM2

value: spinal cord

value: motor neuron

value: ribosome associated RNAs

value: Fus d14/d14


title: ScrStat1

description: Library name: Sample 13

value: Krit1 WT


title: RiboTag, Fus d14/d14, biol rep 1

description: Library name: IP_HOM1


title: CONTROL_TE57_6

value: FORMER

value: solid


title: CONTROL_TE57_68

value: CURRENT


title: RiboTag, Fus d14/d14, biol rep 3

description: Library name: IP_HOM3


title: TUMOR_TE57_56

value: carcinoma planoepitheliale

value: IIB


title: ScrPS1

description: Library name: Sample 11

value: HUVEC

value: Endothelial cell


title: ScrStat2

description: Library name: Sample 14

value: Static


title: RiboTag, Fus+/+, biol rep 4

description: Library name: IP_WT4

value: Fus+/+


title: ScrPS2

description: Library name: Sample 12

value: Pulsatory flow


title: CONTROL_TE57_59

value: F

value: microRNA

value: MUG


title: TUMOR_TE57_55

value: M

value: adenocarcinoma

value: IA


title: CONTROL_TE57_54

value: non-solid


title: CONTROL_TE57_58


title: CONTROL_TE57_57

value: FORMER


title: ScrOS2

description: Library name: Sample 9

value: Krit1 WT

value: Oscilatory flow


title: CONTROL_TE57_53

value: CURRENT

value: HUM


title: CONTROL_TE57_52


title: BENIGN_TE57_51

value: solid


title: RiboTag, Fus+/+, biol rep 1

description: Library name: IP_WT1

value: spinal cord

value: motor neuron

value: ribosome associated RNAs


title: CONTROL_TE57_48_I


title: RiboTag, Fus+/+, biol rep 3

description: Library name: IP_WT3

value: Fus+/+


title: RiboTag, Fus+/+, biol rep 5

description: Library name: IP_WT5


title: CONTROL_TE57_46


title: KRIT1Stat2

description: Library name: Sample 6

value: HUVEC

value: Endothelial cell

value: KRIT1 KD

value: Static


title: RiboTag, Fus+/+, biol rep 2

description: Library name: IP_WT2


title: TUMOR_TE57_45

value: M

value: carcinoma planoepitheliale

value: IIA

value: microRNA

value: MUG


title: TUMOR_TE57_5

value: IA


title: KRIT1Stat1

description: Library name: Sample 5


title: KRIT1Stat3

description: Library name: Sample 7


title: KRIT1Stat4

description: Library name: Sample 8


title: TUMOR_TE57_43

value: F

value: CURRENT

value: typical carcinoid


title: snRNAseq_Den_Gastrocnemius_skeletal_muscle

city: Dallas

first: Matthieu

last: Dos Santos

state: Texas

address: 5323 Harry Hines Blvd

institute: UtSouthwestern

description:
Library name: SnRNAseq_Den
Chromium Next GEM Single Cell Multiome Gene Expression

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software 2.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Gastrocnemius Skeletal muscle

extract_protocol:
Muscles were dissected, snap-frozen, and stored at -80°C. For each condition 3-4 muscles were pooled together. Muscles were thawed for 5 min on ice and minced with scissors in 1 ml cold lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NonidetTM P40, 1 mM DTT, 1 U/μl RNase inhibitor in Nuclease-Free Water). After 2 min, 4 ml of cold lysis buffer was added, and muscles were lysed for 5 min at 4 °C. 10 ml of cold wash buffer (PBS, BSA 2%, and 0.2 U/μl RNase inhibitor from Roche) was added, and the lysate was dounced with 20 strokes of a loose pestle. The homogenate was filtered with 70 μm and 40 μm cell strainers. Nuclei were pelleted by centrifugation for 5 min at 500 × g at 4 °C. Nuclei were resuspended in 0.5 ml of wash buffer and 2 μl of anti-Nuclear Pore Complex conjugated antibody (Biolegend, 682203) to stain all nuclei. After 15 min, nuclei were pelleted by centrifugation for 5 min at 500 × g at 4 °C. Then the nuclei were resuspended in 300 μl of wash buffer and filtered with 30μm cell strainers. More than 200,000 nuclei were FACS sorted with a BD FACSAria III and the BD FACSDIVA and FlowJo v10.8.1 software. Nuclei were pelleted by centrifugation for 10 min at 500 × g at 4 °C and then resuspended in 200 μl of ATAC lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, 0.01% NonidetTM P40, 0.001% Digitonin, 1% BSA, 1 mM DTT, 1U/ul RNase inhibitor in Nuclease-Free Water). After 2 min, 1.3 ml of ATAC wash buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1 mM DTT, 1% BSA, 1U/μl RNase inhibitor in Nuclease-Free Water) was added. Nuclei were pelleted by centrifugation for 10 min at 500 × g at 4 °C and resuspended in 20 μl of diluted nuclei buffer from 10X genomics.
Library was performed according to the manufacter’s instructions (Next GEM single-cell Multiome ATAC+ Gene expression kit). Briefly, Post GEM-incubation Cleanup using DynaBeads MyOne Silane Beads was followed by Pre-Amplification PCR (72 °C for 5 min, 98 °C for 3 min, cycled 7 × 98 °C for 20 s, 63 °C for 30 s, 72 °C for 1 min). After cleanup with SPRIselect Reagent Kit, ATAC library was generated (98 °C for 45 s, cycled 8 × 98 °C for 20 s, 67 °C for 30 s, 72 °C for 20 s) and purified with SPRIselect Reagent Kit. The fragment size estimation of the resulting ATAC libraries was assessed with Agilent TapeStation D1000 HS (Agilent) and quantified using the QubitTM double stranded DNA (dsDNA) High-Sensitivity HS assay (ThermoFisher Scientific). SnATAC-seq libraries were then sequenced by pair with a HighOutput flowcel using an Illumina Nextseq 500 with the following mode: Read 1N - 63 cycles, i7 index – 8 cycles, i5 index - 24 cycles *(8 dark cycles and 16 cycles on i5), Read 2N - 63 cycles. SnRNA-seq libraries were constructed by performing the following steps: cDNA Amplification, SPRIselect cleanup, Fragmentation, End reair and A tailing, SPRIselect cleanup, and Adaptor ligation, SPRIselect cleanup, Samplex index PCR and SPRIselect cleanup size selection. The fragment size estimation of the resulting libraries was assessed with Agilent TapeStation D1000 (Agilent) and quantified using the QubitTM double stranded DNA (dsDNA) High-Sensitivity HS assay (ThermoFisher Scientific).

value: Gastrocnemius Skeletal muscle

value: Skeletal muscle myofibers

value: WT

value: 7 days denervation

tag: library type

value: mRNA


title: KRIT1PS1

description: Library name: Sample 3

value: HUVEC

value: Endothelial cell

value: Pulsatory flow


title: CONTROL_TE57_47

value: solid


title: KRIT1OS2

description: Library name: Sample 2

value: KRIT1 KD

value: Oscilatory flow


title: TUMOR_TE57_44

value: M

value: FORMER

value: carcinoma planoepitheliale

value: microRNA


title: BENIGN_TE57_410

value: F

value: CURRENT

value: HUM


title: snRNAseq_WT_Gastrocnemius_skeletal_muscle

description:
Library name: SnRNAseq_WT
Chromium Next GEM Single Cell Multiome Gene Expression

value: Gastrocnemius Skeletal muscle

value: Skeletal muscle myofibers


title: KRIT1PS2

description: Library name: Sample 4


title: BENIGN_TE57_41


title: Multiome_Den_Maf2_SnATACseq

description:
Library name: Multiome_Den_Maf2_SnATACseq
Chromium Next GEM Single Cell Multiome ATAC

library_source: genomic single cell

value: WT

value: 7 days denervation

value: ATAC


title: CONTROL_TE57_42


title: CONTROL_TE57_408

value: MUG


title: CONTROL_TE57_407


title: Multiome_Den_Maf2_SnRNAseq

description:
Library name: Multiome_Den_Maf2_SnRNAseq
Chromium Next GEM Single Cell Multiome Gene Expression

value: mRNA


title: TUMOR_TE57_405

value: adenosquamous

value: IA

value: part-solid


title: CONTROL_TE57_404


title: CONTROL_TE57_413

value: M


title: CONTROL_TE57_412

value: FORMER


title: Multiome_Den_Maf1_SnATACseq

description:
Library name: Multiome_Den_Maf1_SnATACseq
Chromium Next GEM Single Cell Multiome ATAC


title: BENIGN_TE57_411

value: solid


title: CONTROL_TE57_402

value: microRNA


title: Multiome_Den_Maf1_SnRNAseq

description:
Library name: Multiome_Den_Maf1_SnRNAseq
Chromium Next GEM Single Cell Multiome Gene Expression


title: Bladder, CYP induced, rep1

first: Jialiang

address: Tianhe Road 600

department: Urology

institute: Third Affiliated Hospital of Sun Yat-Sen University

description: Library name: N11

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: rn6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: bladder

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: bladder


title: Bladder, CYP induced, rep2

description: Library name: N12


title: Bladder, normal, rep3

description: Library name: C23


title: Multiome_WT2_SnATACseq

description:
Library name: Multiome_WT2_SnATACseq
Chromium Next GEM Single Cell Multiome ATAC


title: BENIGN_TE57_409

value: F

value: CURRENT


title: BENIGN_TE57_40

value: HUM


title: KRIT1OS1

description: Library name: Sample 1

value: HUVEC

value: Endothelial cell

value: KRIT1 KD

value: Oscilatory flow


title: Multiome_Den_GFP2_SnATACseq

description:
Library name: Multiome_Den_GFP2_SnATACseq
Chromium Next GEM Single Cell Multiome ATAC

value: Gastrocnemius Skeletal muscle

value: Skeletal muscle myofibers

value: WT

value: 7 days denervation

value: ATAC


title: Bladder, CYP induced, rep3

description: Library name: N13


title: Multiome_WT2_SnRNAseq

description:
Library name: Multiome_WT2_SnRNAseq
Chromium Next GEM Single Cell Multiome Gene Expression

value: mRNA


title: TUMOR_TE57_406

value: adenocarcinoma

value: IA

value: MUG


title: Multiome_Den_GFP2_SnRNAseq

description:
Library name: Multiome_Den_GFP2_SnRNAseq
Chromium Next GEM Single Cell Multiome Gene Expression


title: CONTROL_TE57_396

value: microRNA


title: CONTROL_TE57_403

value: F


title: CONTROL_TE57_393

value: M

value: CURRENT

value: solid


title: ScrOS1

description: Library name: Sample 10

value: HUVEC

value: Endothelial cell

value: Krit1 WT


title: Multiome_Den_GFP1_SnATACseq

description:
Library name: Multiome_Den_GFP1_SnATACseq
Chromium Next GEM Single Cell Multiome ATAC

value: Gastrocnemius Skeletal muscle


title: BENIGN_TE57_390

value: FORMER

value: part-solid

value: HUM


title: Saline one-month mouse 302

city: Little Rock

first: Michael

middle: S

last: Robeson

state: Arkansas

address: 4301 W. Markham St., Slot 782

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description:
Library name: Saline.1M.302
Column name in ACT_combined_count_matrix_v02.csv file: RNASeqReport10026_Allen_ACTGolgi_3.csv

data_processing:
Dragen (v 4.3.6) was used for binary base call conversion and FastQC (v 0.11.9) was used for quality control.
Quantification was done using Salmon (v 1.9.0).
Fastq files were uploaded into Qiagen Ingenuity Pathway Analysis (IPA) via the RNA-Seq Analysis Portal (https://digitalinsights.qiagen.com/IPA).
Assembly: GRCm39
Supplementary files format and content: csv file contains raw count values per sample

source_name: Hippocampal bain tissue

growth_protocol: Mice were housed 4 per cage in a climate-controlled facility on a 12hr light/dark cycle (lights on 6:00-18:00). Water and standard lab chow was provided ad libitum

extract_protocol:
Whole brains were harvested and flash frozen in 2-methylbutane. Hippocampal samples were collected from coronal slices using a 0.2mm tissue punch and were sent to the RNA Sequencing Core for processing. RNA was extracted from samples using the Zymo Quick-DNA/RNA miniprep Plus Kit (Cat # D7003).
mRNA Library was constructed using the Illumina TruSeq Stranded mRNA Library Prep kit (Cat # 20020594). Samples were run on a 200-cycle NextSeq 2000 P2 flow cell.

treatment_protocol: 12-week-old female C57/BL6 mice were treated with 8 once weekly intraperitoneal injections (IP) of the following chemotherapeutic treatment groups: 1) Saline, or 2) AC-T. AC-T entails  4 once weekly IP injections of Doxorubicin (Dox), and Cyclophosphamide (CYP), followed by 4 once weekly IP injections of Paclitaxel (PTX).

value: Hippocampal bain tissue

value: Hippocampal cells

value: saline (0.9% sodium chloride)


title: RASMC, NCshRNA, pol II, rep1(Cut&Tag)

city: Xiamen

first: Wei

last: Shen

state: Fujian

address: 2999 Jinshan Rd, Huli District

institute: Xiamen University

description:
Library name: RASMC_NCshRNA_pol II_rep1, Cut_Tag
rat aortic smooth muscle cell

data_processing:
raw reads was cleaned by fastp with default parameters
cleaned reads were mapped to rn7 genome downloaded from ensembl by bowtie2
duplicated reads were further removed by picard
narrowpeak files were generated by macs2
bigwig files were generated by deeptools
Assembly: rn7
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: aortic smooth muscle cell

extract_protocol:
cells were lysed and nucleus were extracted to incubate with primiary antibody, secondary antibody and pAG-Tn5
library was contructed by using CUT&TAG 3.0 High-Sensitivity Kit for Illumina (Novoprotein N259-YH01)

value: aortic smooth muscle cell

value: WT

value: control shRNA

tag: batch

value: pol II


title: CONTROL_TE57_383

tag: age

value: M

value: microRNA

value: MUG


title: CONTROL_TE57_382

tag: gender


title: Saline one-month mouse 300

description:
Library name: Saline.1M.300
Column name in ACT_combined_count_matrix_v02.csv file: RNASeqReport10024_Allen_ACTGolgi_3.csv


title: BENIGN_TE57_401

value: F

tag: smocking status

value: CURRENT


title: CONTROL_TE57_394

value: solid


title: Multiome_Den_GFP1_SnRNAseq

description:
Library name: Multiome_Den_GFP1_SnRNAseq
Chromium Next GEM Single Cell Multiome Gene Expression

value: Gastrocnemius Skeletal muscle

value: Skeletal muscle myofibers

value: 7 days denervation

value: mRNA


title: TUMOR_TE57_4

tag: histology

value: adenocarcinoma

value: IA


title: Bladder, normal, rep2

city: Guangzhou

description: Library name: C22

value: bladder


title: TUMOR_TE57_397

value: small cell neuroendocrine

tag: Stage

value: HUM


title: Bladder, normal, rep1

description: Library name: C21


title: Multiome_WT1_SnATACseq

description:
Library name: Multiome_WT1_SnATACseq
Chromium Next GEM Single Cell Multiome ATAC

value: WT

value: ATAC


title: CONTROL_TE57_395


title: CONTROL_TE57_380

value: M


title: RASMC, NCshRNA, H3K4me3, rep1(Cut&Tag)

description:
Library name: RASMC_NCshRNA_H3K4me3_rep1, Cut_Tag
rat aortic smooth muscle cell

value: aortic smooth muscle cell

value: control shRNA


title: RASMC, NCshRNA, cholesterol, pol II, rep2(Cut&Tag)

description:
Library name: RASMC_NCshRNA_cholesterol_pol II_rep2, Cut_Tag
rat aortic smooth muscle cell

value: pol II


title: Multiome_WT1_SnRNAseq

description:
Library name: Multiome_WT1_SnRNAseq
Chromium Next GEM Single Cell Multiome Gene Expression


title: CONTROL_TE57_392

value: F

value: CURRENT

value: microRNA

value: MUG


title: RASMC, NCshRNA, cholesterol, pol II, rep1(Cut&Tag)

description:
Library name: RASMC_NCshRNA_cholesterol_pol II_rep1, Cut_Tag
rat aortic smooth muscle cell


title: CONTROL_TE57_391


title: RASMC, NCshRNA, pol II, rep2(Cut&Tag)

description:
Library name: RASMC_NCshRNA_pol II_rep2, Cut_Tag
rat aortic smooth muscle cell


title: TUMOR_TE57_385

value: IIB

tag: nodule density

value: solid


title: RASMC, NCshRNA, H3K27ac, rep2(Cut&Tag)

description:
Library name: RASMC_NCshRNA_H3K27ac_rep2, Cut_Tag
rat aortic smooth muscle cell


title: Saline one-month mouse 301

description:
Library name: Saline.1M.301
Column name in ACT_combined_count_matrix_v02.csv file: RNASeqReport10025_Allen_ACTGolgi_3.csv

value: Hippocampal bain tissue

value: Hippocampal cells

value: saline (0.9% sodium chloride)


title: CONTROL_TE57_384

tag: nodule size


title: Saline one-month mouse 203

description:
Library name: Saline.1M.203
Column name in ACT_combined_count_matrix_v02.csv file: RNASeqReport10023_Allen_ACTGolgi_2.csv


title: RASMC, NCshRNA, H3K4me3, rep2(Cut&Tag)

description:
Library name: RASMC_NCshRNA_H3K4me3_rep2, Cut_Tag
rat aortic smooth muscle cell


title: CONTROL_TE57_381

tag: molecule subtype


title: CONTROL_TE57_376

tag: center


title: TUMOR_TE57_379

value: carcinoma planoepitheliale

value: IIA


title: TUMOR_TE57_378

value: adenocarcinoma

value: IA


title: BENIGN_TE57_374

value: M

value: HUM


title: AC-T one-month mouse 600

description:
Library name: ACT.1M.600
Column name in ACT_combined_count_matrix_v02.csv file: RNASeqReport10030_Allen_ACTGolgi_6.csv

tag: tissue

value: 2 mg/kg doxorubicin (A), 50 mg/kg cyclophosphamide (C), 5 mg/kg paclitaxel (T)


title: CONTROL_TE57_377


title: AC-T one-month mouse 602

description:
Library name: ACT.1M.602
Column name in ACT_combined_count_matrix_v02.csv file: RNASeqReport10032_Allen_ACTGolgi_6.csv

tag: cell line


title: CONTROL_TE57_372


title: CONTROL_TE57_371

value: FORMER


title: BENIGN_TE57_375


title: RASMC, H3K9me3, rep2(Cut&Tag)

description:
Library name: RASMC_H3K9me3_rep2, Cut_Tag
rat aortic smooth muscle cell

tag: cell type

value: aortic smooth muscle cell

value: WT


title: RASMC, NCshRNA, H3K27ac, rep1(Cut&Tag)

description:
Library name: RASMC_NCshRNA_H3K27ac_rep1, Cut_Tag
rat aortic smooth muscle cell

tag: genotype

value: control shRNA


title: AC-T one-month mouse 503

description:
Library name: ACT.1M.503
Column name in ACT_combined_count_matrix_v02.csv file: RNASeqReport10029_Allen_ACTGolgi_5.csv

tag: treatment


title: Saline one-month mouse 202

description:
Library name: Saline.1M.202
Column name in ACT_combined_count_matrix_v02.csv file: RNASeqReport10022_Allen_ACTGolgi_2.csv


title: CONTROL_TE57_369

value: F

value: CURRENT

value: microRNA

value: MUG


title: RASMC, H3K9me3, rep1(Cut&Tag)

description:
Library name: RASMC_H3K9me3_rep1, Cut_Tag
rat aortic smooth muscle cell


title: TUMOR_TE57_37

value: IIIA

value: part-solid


title: CONTROL_TE57_370

value: solid


title: Saline one-month mouse 201

description:
Library name: Saline.1M.201
Column name in ACT_combined_count_matrix_v02.csv file: RNASeqReport10021_Allen_ACTGolgi_2.csv

value: Hippocampal bain tissue

value: Hippocampal cells

value: saline (0.9% sodium chloride)


title: CONTROL_TE57_368

value: M


title: AC-T one-month mouse 502

description:
Library name: ACT.1M.502
Column name in ACT_combined_count_matrix_v02.csv file: RNASeqReport10028_Allen_ACTGolgi_5.csv


title: RASMC, H2a.z_KD_cholesterol, RNA-seq rep2

description:
Library name: RASMC_H2a.z_KD_cholesterol_rep2
rat aortic smooth muscle cell

data_processing:
raw reads was cleaned by fastp with default parameters
cleaned reads were mapped to Rn7 genome downloaded from ensembl by STAR
Raw counts were generated by using htseq-count with default parameters
Assembly: rn7
Supplementary files format and content: raw counts

extract_protocol:
The mRNA were purified, fragmented and amplified for RNA-Seq
Library was constructed by using Hieff NGS MaxUp Dual-mode mRNA Library Prep Kit for Illumina (Yeasen, 12301ES96)

value: H2a.z knockdown

value: cholesterol treatment


title: RASMC, H2a.z_KD_cholesterol, RNA-seq rep3

description:
Library name: RASMC_H2a.z_KD_cholesterol_rep3
rat aortic smooth muscle cell


title: CONTROL_TE57_365

value: HUM


title: TUMOR_TE57_367

value: FORMER

value: adenocarcinoma

value: IIB


title: CONTROL_TE57_366

value: F


title: RASMC, H2a.z_KD_cholesterol, RNA-seq rep1

description:
Library name: RASMC_H2a.z_KD_cholesterol_rep1
rat aortic smooth muscle cell

value: aortic smooth muscle cell


title: RASMC, H3K9me3, rep3(Cut&Tag)

description:
Library name: RASMC_H3K9me3_rep3, Cut_Tag
rat aortic smooth muscle cell

value: WT


title: anti-CD40+Delta24-RGD_6

city: Pamplona

first: Javier

last: Marco Sanz

state: Navarra

address: Av. Pio XII

country: Spain

institute: Centro de Investigacion Medica Aplicada

description: Library name: SL24

data_processing:
Quality assessment of the raw sequencing reads was performed using FastQC (v0.11.8) to evaluate data integrity.
Trimming of low-quality bases and adapter sequences removal were achieved through Trimmomatic (v0.38)
The alignment of the high-quality reads to the Mus musculus reference genome (GRC39, version 27) was conducted using STAR (v2.7.0)
Transcript quantification was executed with the featureCounts function from the Subread (v1.6.3). Differential expression analysis was implemented utilizing the edgeR (v3.40.2) R package
Assembly: Mus musculus GRC39
Supplementary files format and content: excel file with count per sample and gene

source_name: Brainstem Tumor

growth_protocol: XFM cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% streptomycin/penicillin.

extract_protocol:
After six days of treatment, total RNA was isolated from XFM tumors using the RNeasy® Mini Kit (Qiagen) according to the manufacturer’s instructions. The RNA concentration and quality were measured using a Qubit HS RNA Assay Kit (Thermo Fisher Scientific) and 4200 TapeStation with High Sensitivity RNA ScreenTape (Agilent Technologies). RNA samples showed good quality, with RIN values ranging from 7.6 to 8.2.
Library preparation was performed with 100 ng of total RNA using the Illumina Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: Mice were injected with 1,000 XFM tumor cells in the infratentorial area using the guide screw system as described previously. Three days after, animals were intratumorally treated with 10 7 pfu of the adenovirus Delta-24-RGD and 24µg of an antibody against CD40 (clone FGK4.5; Bioxcell) resuspended in 3µL of PBS.

value: Brainstem Tumor

value: XFM

value: DMG

value: PDGFR-B overexpression, INK4a-/-, ARF-/-


title: anti-CD40+Delta24-RGD_5

description: Library name: SL23


title: RASMC, RNA-seq rep3

description:
Library name: RASMC_rep3
rat aortic smooth muscle cell


title: TUMOR_TE57_361

value: CURRENT

value: IA

value: non-solid

value: microRNA


title: CONTROL_TE57_360

value: solid

value: MUG


title: anti-CD40+Delta24-RGD_4

description: Library name: SL22


title: CONTROL_TE57_36

value: M


title: anti-CD40+Delta24-RGD_3

description: Library name: SL21


title: CONTROL_TE57_358


title: RASMC, RNA-seq rep2

description:
Library name: RASMC_rep2
rat aortic smooth muscle cell


title: TUMOR_TE57_359

value: FORMER


title: anti-CD40+Delta24-RGD_2

description: Library name: SL20


title: CONTROL_TE57_356

value: part-solid


title: CONTROL_TE57_357


title: RASMC, H2a.z_KD_cholesterol, pol II, rep3(Cut&Tag)

description: Library name: RASMC_H2a.z_KD_cholesterol_pol II_rep3, CUTnTag

extract_protocol:
cells were lysed and nucleus were extracted to incubate with primiary antibody, secondary antibody and pAG-Tn5
library was contructed by usingCUT&TAG 3.0 High-Sensitivity Kit for Illumina (Novoprotein N259-YH01)

value: H2a.z knock down

value: H2a.z knock down plus cholesterol treatment

value: pol II


title: AC-T one-month mouse 501

description:
Library name: ACT.1M.501
Column name in ACT_combined_count_matrix_v02.csv file: RNASeqReport10027_Allen_ACTGolgi_5.csv

value: Hippocampal bain tissue

value: Hippocampal cells

value: 2 mg/kg doxorubicin (A), 50 mg/kg cyclophosphamide (C), 5 mg/kg paclitaxel (T)


title: CONTROL_TE57_355


title: anti-CD40+Delta24-RGD_1

description: Library name: SL19

value: Brainstem Tumor

value: XFM

value: DMG


title: CONTROL_TE57_354

value: CURRENT

value: HUM


title: CONTROL_TE57_364

value: F

value: microRNA


title: Delta24-RGD_6

description: Library name: SL18

value: PDGFR-B overexpression, INK4a-/-, ARF-/-


title: CONTROL_TE57_353

value: M


title: BENIGN_TE57_352

value: FORMER


title: BENIGN_TE57_363

value: solid


title: RASMC, H2a.z_KD_cholesterol, pol II, rep1(Cut&Tag)

description: Library name: RASMC_H2a.z_KD_cholesterol_pol II_rep1, CUTnTag

value: aortic smooth muscle cell

value: H2a.z knock down


title: CONTROL_TE57_35

value: MUG


title: Delta24-RGD_5

description: Library name: SL17


title: RASMC, H2a.z_KD, pol II, rep3(Cut&Tag)

description: Library name: RASMC_H2a.z_KD_pol II_rep3, CUTnTag

value: pol II


title: CONTROL_TE57_346


title: RASMC, H2a.z_KD, pol II, rep2(Cut&Tag)

description: Library name: RASMC_H2a.z_KD_pol II_rep2, CUTnTag


title: Delta24-RGD_4

description: Library name: SL16


title: Delta24-RGD_3

description: Library name: SL15


title: RASMC, RNA-seq rep1

description:
Library name: RASMC_rep1
rat aortic smooth muscle cell

value: WT


title: CONTROL_TE57_345


title: RASMC, H2a.z_KD, pol II, rep1(Cut&Tag)

description: Library name: RASMC_H2a.z_KD_pol II_rep1, CUTnTag


title: CONTROL_TE57_343


title: Delta24-RGD_2

description: Library name: SL14


title: RASMC, H2a.z_KD, H3K4me3, rep3(Cut&Tag)

description: Library name: RASMC_H2a.z_KD_H3K4me3_rep3, CUTnTag


title: TUMOR_TE57_342

value: adenocarcinoma

value: IA


title: CONTROL_TE57_341


title: RASMC, H2a.z_KD_cholesterol, pol II, rep2(Cut&Tag)

description: Library name: RASMC_H2a.z_KD_cholesterol_pol II_rep2, CUTnTag

value: H2a.z knock down plus cholesterol treatment


title: CONTROL_TE57_34


title: Delta24-RGD_1

description: Library name: SL13

value: Brainstem Tumor

value: XFM

value: DMG


title: RASMC, H2a.z_KD, H3K4me3, rep2(Cut&Tag)

description: Library name: RASMC_H2a.z_KD_H3K4me3_rep2, CUTnTag


title: CONTROL_TE57_336

value: CURRENT


title: CONTROL_TE57_335

value: microRNA


title: RASMC, H2a.z_KD, H3K4me3, rep1(Cut&Tag)

description: Library name: RASMC_H2a.z_KD_H3K4me3_rep1, CUTnTag


title: anti-CD40_5

description: Library name: SL11

value: PDGFR-B overexpression, INK4a-/-, ARF-/-


title: CONTROL_TE57_334

value: F


title: RASMC, H2a.z_KD, H3K27ac, rep3(Cut&Tag)

description: Library name: RASMC_H2a.z_KD_H3K27ac_rep3, CUTnTag


title: CONTROL_TE57_348

value: M

value: FORMER


title: CONTROL_TE57_347

value: solid


title: CONTROL_TE57_333


title: CONTROL_TE57_332

value: HUM


title: anti-CD40_4

description: Library name: SL10


title: RASMC, H2a.z_KD, H3K27ac, rep2(Cut&Tag)

description: Library name: RASMC_H2a.z_KD_H3K27ac_rep2, CUTnTag

value: aortic smooth muscle cell

value: H2a.z knock down


title: CONTROL_TE57_344

value: MUG


title: BENIGN_TE57_330


title: CONTROL_TE57_33


title: RASMC, H2a.z_KD, H3K27ac, rep1(Cut&Tag)

description: Library name: RASMC_H2a.z_KD_H3K27ac_rep1, CUTnTag


title: anti-CD40_2

description: Library name: SL8


title: TUMOR_TE57_327

value: carcinoma poorly differentiated

value: IV


title: CONTROL_TE57_331


title: RASMC, H2a.z, rep3(Cut&Tag)

description: Library name: RASMC_H2a.z_rep3, CUTnTag

value: WT


title: TUMOR_TE57_326

value: squamous cell carcinoma

value: IB


title: anti-CD40_3

description: Library name: SL9

value: Brainstem Tumor

value: XFM

value: DMG


title: TUMOR_TE57_325

value: adenocarcinoma

value: IA

value: part-solid

value: microRNA


title: CONTROL_TE57_324

value: M

value: FORMER

value: solid


title: anti-CD40_1

description: Library name: SL7

value: PDGFR-B overexpression, INK4a-/-, ARF-/-

value: IgG


title: anti-CD40_6

description: Library name: SL12


title: RASMC, H2a.z, rep2(Cut&Tag)

description: Library name: RASMC_H2a.z_rep2, CUTnTag

value: aortic smooth muscle cell


title: IgG_6

description: Library name: SL6


title: RASMC, H2a.z, rep1(Cut&Tag)

description: Library name: RASMC_H2a.z_rep1, CUTnTag


title: CONTROL_TE57_321

value: CURRENT

value: MUG


title: CONTROL_TE57_322


title: TUMOR_TE57_319

value: typical carcinoid


title: TUMOR_TE57_32

value: F


title: IgG_4

description: Library name: SL4

value: Brainstem Tumor


title: TUMOR_TE57_318

value: IIB


title: IgG_3

description: Library name: SL3

value: XFM

value: DMG


title: RASMC, H3K27me3, rep1(Cut&Tag)

description: Library name: RASMC_H3K27me3_rep1, CUTnTag

value: WT


title: RASMC, H3K27me3, rep2(Cut&Tag)

description: Library name: RASMC_H3K27me3_rep2, CUTnTag


title: CONTROL_TE57_317

value: HUM


title: BENIGN_TE57_316

value: microRNA


title: IgG_2

description: Library name: SL2


title: TUMOR_TE57_314

value: M

value: squamous cell carcinoma

value: IIA


title: CONTROL_TE57_323

value: FORMER


title: TUMOR_TE57_313

value: adenocarcinoma

value: IIIA

value: part-solid


title: RASMC_cholesterol_rep3

description:
Library name: RASMC_cholesterol_rep3
Rat aortic smooth muscle cell

data_processing:
raw reads was cleaned by fastp with default parameters
cleaned reads were mapped to GRCh38.p14 or Rn7 genome downloaded from ensembl by STAR
Raw counts were generated by using htseq-count with default parameters
Assembly: GRCh38.p14, Rn7
Supplementary files format and content: raw counts

value: aortic smooth muscle cell

value: cholesterol


title: RASMC_cholesterol_rep2

description:
Library name: RASMC_cholesterol_rep2
Rat aortic smooth muscle cell


title: TUMOR_TE57_311

value: CURRENT

value: IA

value: solid

value: MUG


title: RASMC_cholesterol_rep1

description:
Library name: RASMC_cholesterol_rep1
Rat aortic smooth muscle cell


title: CONTROL_TE57_310


title: IgG_5

description: Library name: SL5

value: Brainstem Tumor

value: XFM

value: DMG

value: PDGFR-B overexpression, INK4a-/-, ARF-/-

value: IgG


title: WT_SUMO2-3_Day1_1

city: Oslo

first: Pierre

last: Chymkowitch

address: Blindernveien 31

department: Biosciences

country: Norway

institute: University of Oslo

data_processing:
Image analysis and base calling were performed using RTA and bcl2fastq.
Bowtie2 was used to map reads to the Mus musculus genome (assembly mm10)  with default parameters. Then, samtools view v1.9 (Li et al. 2009) was used to remove reads (unmapped, mate unmapped, not primary alignment reads, reads failing platform, low quality reads (MAQ <30)) with the following parameters “samtools view -F 1804 -q 30”. Then, duplicated reads are marked with Picard MarkDuplicates v2.20.7 (“Picard Tools - By Broad Institute” n.d.) and removed with samtools with the following parameter “-F 1804”.
BigWig files were generated using Deeptools bamCoverage (Ramírez et al. 2016) v3.5.4 with the following parameters “-bs 10 -p 10 –normalizeUsing CPM –effectiveGenomeSize 2652783500 –skipNonCoveredRegions –extendReads –ignoreDuplicates”.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: ME3 cells

extract_protocol:
Same as in Zhao et al., Nucl. Acid Res., 2022
ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: ME3 cells

value: pre-adipocytes

tag: time

value: adipogenic induction medium

tag: chip antibody


title: CONTROL_TE57_320

value: M

value: microRNA


title: RASMC, H3K27me3, rep3(Cut&Tag)

description: Library name: RASMC_H3K27me3_rep3, CUTnTag

value: WT

tag: batch


title: RASMC_rep3

description:
Library name: RASMC_rep3
Rat aortic smooth muscle cell

value: aortic smooth muscle cell


title: WT_SUMO2-3_Day1_2


title: WT_SUMO2-3_Day-1_2

value: proliferation medium


title: BENIGN_TE57_307

tag: age

value: FORMER

value: HUM


title: CONTROL_TE57_309

tag: gender

value: CURRENT


title: RASMC_rep2

description:
Library name: RASMC_rep2
Rat aortic smooth muscle cell


title: WT_SUMO2-3_Day-1_1


title: BENIGN_TE57_306

tag: smocking status

value: solid


title: RASMC_rep1

description:
Library name: RASMC_rep1
Rat aortic smooth muscle cell


title: BENIGN_TE57_305


title: CONTROL_TE57_300

value: MUG


title: WT_Input_Day-1


title: IgG_1

description: Library name: SL1

value: Brainstem Tumor

value: XFM


title: RASMC, DAPT_plus_Cholesterol_treatment, H3K27ac, rep3(Cut&Tag)

description:
Library name: RASMC_DAPT_Cholesterol_H3K27ac_rep3, Cut_Tag
rat aortic smooth muscle cell

data_processing:
raw reads was cleaned by fastp with default parameters
cleaned reads were mapped to rn7 genome downloaded from ensembl by bowtie2
duplicated reads were further removed by picard
narrowpeak files were generated by macs2
bigwig files were generated by deeptools
Assembly: rn7
Supplementary files format and content: narrowpeak
Supplementary files format and content: bigwig
Library strategy: CUT&Tag


title: CONTROL_TE57_30


title: CONTROL_TE57_312

value: F


title: CONTROL_TE57_299


title: CONTROL_TE57_31


title: CONTROL_TE57_298


title: CONTROL_TE57_297


title: RASMC, DAPT_plus_Cholesterol_treatment, H3K27ac, rep2(Cut&Tag)

description:
Library name: RASMC_DAPT_Cholesterol_H3K27ac_rep2, Cut_Tag
rat aortic smooth muscle cell


title: Irx3-KO_SUMO2-3_Day1_2


title: CONTROL_TE57_296


title: Irx3-KO_SUMO2-3_Day1_1


title: TUMOR_TE57_295

tag: histology

value: adenocarcinoma

value: IA


title: Irx3-KO_SUMO2-3_Day-1_2

value: ME3 cells

value: pre-adipocytes


title: CONTROL_TE57_308


title: RASMC, DAPT_plus_Cholesterol_treatment, H3K27ac, rep1(Cut&Tag)

description:
Library name: RASMC_DAPT_Cholesterol_H3K27ac_rep1, Cut_Tag
rat aortic smooth muscle cell


title: TUMOR_TE57_294

value: M

tag: Stage


title: RASMC, DAPT_treatment, H3K27ac, rep3(Cut&Tag)

description:
Library name: RASMC_DAPT_H3K27ac_rep3, Cut_Tag
rat aortic smooth muscle cell


title: CONTROL_TE57_292_II

value: microRNA


title: Irx3-KO_SUMO2-3_Day-1_1


title: RASMC, DAPT_treatment, H3K27ac, rep2(Cut&Tag)

description:
Library name: RASMC_DAPT_H3K27ac_rep2, Cut_Tag
rat aortic smooth muscle cell

value: WT


title: Irx3-KO_Input_Day1

value: adipogenic induction medium


title: RASMC, DAPT_treatment, H3K27ac, rep1(Cut&Tag)

description:
Library name: RASMC_DAPT_H3K27ac_rep1, Cut_Tag
rat aortic smooth muscle cell

value: aortic smooth muscle cell


title: BENIGN_TE57_29

tag: nodule density

value: part-solid


title: CONTROL_TE57_288

value: FORMER


title: RASMC, Cholesterol_treatment, H3K27ac, rep3(Cut&Tag)

description:
Library name: RASMC_Cholesterol_H3K27ac_rep3, Cut_Tag
rat aortic smooth muscle cell


title: CONTROL_TE57_287

value: CURRENT

tag: nodule size


title: iSLK-WT Cells, Uninduced Latent infection, cytoplasmic RNA fraction Bio Rep 2

city: Lausanne

first: Mandy

last: Muller

address: Rue du Bugnon 48

department: Institute of Microbiology

country: Switzerland

institute: University Hospital of Lausanne

description: Library name: URBC

data_processing:
Samples were sequenced using the Illumina PE150 sequencing platform. Raw data generated on the sequencing platform contained a small percentage of low-quality data. The base quality score is an important indicator of sequencing quality. Base quality (Q) is closely related to the sequencing error rate (P) and is influenced by factors such as the status of the sequencer, the quality of sequencing reagents, and the characteristics of the samples. The formula for calculating the quality score is as follows. Q=-10log(10)P
The raw data then filtered to get high-quality data. The raw data were processed as the following steps: a. Start searching for poly(A) sequences in the reads from the right side, with a length of 6A and a mismatch rate of 0.2. b. Search for poly(A) sequences from the left side, with a length of 9A and a mismatch rate of 0.1. c. Truncate the part of the poly(A) sequence that contains 4 consecutive non-A bases, keeping the longest portion of the poly(A) sequence. d. If the remaining part of the reads after truncating the poly(A) sequence has a length of at least 20, then such reads are classified as poly(A) clean reads, and the corresponding poly(A) length is equal to the length of poly(A) in the reads.
The retained poly(A) sequence lengths are greater than or equal to 11 nt, and the alignment was performed using Bowtie2. In the end, only one type of read was obtained, meaning that the length of the front part of the sequence is not less than 20 nt, and the length of the back part poly(A) sequence is not less than 11 nt.
RPKM (Reads per kilobase of a gene per million reads) indicates the number of reads from a specific gene per kilobase length among every million reads, and it characterizes the expression abundance of the gene (Mortazavi, Williams et al. 2008). By normalizing for mRNA length and sequencing depth (RPKM), the expression abundance between different sequencing samples can be compared, eliminating biases that may arise from variations in mRNA length and sequencing depth between different samples. RPKM = total exon reads / (uniquely mapped reads * exon length) - total exon reads: The number of reads mapped to all exons of a gene, counted in units. - uniquely mapped reads: The number of reads in a sample that have a unique mapping in the genome, counted in millions. - exon length: The length of the exon, measured in Kb. - RPKM indicates the number of reads falling within the range of every kilobase length of a specific gene among every million uniquely mapped reads. In this part of the analysis, we will statistically analyze the number of genes detected in this project with RPKM > 0 and RPKM ≥ 1.
Assembly: Hg38  and  AF148805.2 HHV8
Supplementary files format and content: Obtain_the_high_quality_clean_reads.xls - xls file containign the number of detected reads, polyA containing reads, and cleaned polyA reads
Supplementary files format and content: Tab-delimited text files containing the RPKM for each experimental condtion, lists of number of transcripts or genes associated with polyA tail length, lists of comparisons looking at the change of polyA tail length between experimental conditions, list of the differential statistics between conditions and polyA tail change

molecule: cytoplasmic RNA

source_name: iSLK-WT (BAC16)

growth_protocol: iSLK-WT cells were grown in DMEM supplimented with 10% fetal bovine serum (FBS) and antibiotics (Penn/Strep) with humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cell pellets were washed with cold PBS, then resuspended and incubated in fractionation buffer A (50mM Tris pH8, 140mM NaCl, 1.5mM MgCl2, 0.2% NP40, 1mM DTT, and 200units RNAsin) for 5 minutes on ice. Solution was spun at 3000 x g. Supernatant was collected on ice as cytoplasmic fraction and pellet was kept as nuclear fraction. 1ml of TRIzol (invitrogen) reagent was added to each sample.
Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% agarose gel electrophoresis. For each sample, ~5μg of total RNA was used for poly(A)-seq library preparation. Total RNA was digested by RNase T1 (Thermo, EN0541), polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Vazyme, N401-01) before directional poly(A)-seq library preparation. After 3' adaptor (Gnomegen, K02420-L) ligation, purified mRNAs were reverse transcripted to cDNA with RT primer that was complemented with the 3' adaptor. Then DNA was synthesized with Terminal-Tagging oligo cDNA and SMARTer® Stranded RNA-Seq Kit (TAKARA, 634837). Followed by purification and amplification, PCR products corresponding to 200-500 bps were purified, quantified, and stored at -80 °C before sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Novaseq Xplus for 150 nt paired-end sequencing.

treatment_protocol: Lytic infection was induced by adding 0.2ug/ml doxycycline and 110ug/ml sodium butyrate for 24 hours

value: iSLK-WT (BAC16)

value: Epithelial/renal carcinoma


title: CONTROL_TE57_286

tag: molecule subtype

value: MUG


title: iSLK-WT Cells, Uninduced Latent infection, cytoplasmic RNA fraction Bio Rep 1

description: Library name: URAC


title: CONTROL_TE57_285

tag: center


title: CONTROL_TE57_284


title: TUMOR_TE57_283

value: IIIA

value: solid


title: iSLK-WT Cells, 24 hour lytic induction, cytoplasmic RNA fraction, Bio Rep 1

description: Library name: 24AC

value: Doxycycline induced lytic reactivation


title: CONTROL_TE57_293

value: HUM


title: TUMOR_TE57_282

value: F

value: adenocarcinoma

value: IA

value: non-solid


title: iSLK-WT Cells, Uninduced Latent infection, nuclear RNA fraction Bio Rep 2

description: Library name: URBN

value: WT


title: TUMOR_TE57_277

value: large-cell neuroendocrine

value: IIIB

value: microRNA


title: PBMCs of SPF chicken 21 days after vaccination of inactivated AIV vaccine

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://github.com/10XGenomics/cellranger)
Assembly: GRCg6a
Supplementary files format and content: Matrix file containing the transcription profiles of all single cells could be loaded to Seurat for further analysis.

organism: Gallus gallus

source_name: blood

extract_protocol:
Seperated single_cell samples were treated by Smart_Seq2 protocol to get amplified cDNA.
RNA libraries were prepared for sequencing using standard Illumina scRNA-seq and 10 × Chromium platform protocols (single cell 3’ v3 protocol, 10x Genomics).

tag: tissue

value: blood

tag: Sex

value: male

value: peripheral blood mononuclear cells

value: 35-day old

value: inactivated AIV vaccine


title: iSLK-WT Cells, Uninduced Latent infection, nuclear RNA fraction Bio Rep 1

description: Library name: URAN

tag: cell line

value: iSLK-WT (BAC16)

tag: cell type

value: Epithelial/renal carcinoma


title: RASMC, DMSO_treatment, H3K27ac, rep2(Cut&Tag)

description:
Library name: RASMC_DMSO_H3K27ac_rep2, Cut_Tag
rat aortic smooth muscle cell

value: aortic smooth muscle cell

tag: genotype

tag: treatment

value: DMSO


title: PBMCs of SPF chicken 14 days after vaccination of live AIV vaccine

description: 10x Genomics

value: live AIV vaccine


title: CONTROL_TE57_276

value: M

value: CURRENT

value: solid

value: MUG


title: RASMC, DMSO_treatment, H3K27ac, rep1(Cut&Tag)

description:
Library name: RASMC_DMSO_H3K27ac_rep1, Cut_Tag
rat aortic smooth muscle cell

value: WT


title: iSLK-WT Cells, 24 hour lytic induction, nuclear RNA fraction, Bio Rep 2

description: Library name: 24BN

value: Doxycycline induced lytic reactivation


title: CONTROL_TE57_291

value: microRNA

value: HUM


title: TUMOR_TE57_275

value: carcinoma planoepitheliale

value: IIB