title: dual-CAR dual-Switch rep1 [single cell]

first: Scott

middle: Edward

last: James

state: NY

address: 408 E 69th Street

institute: Memorial Sloan Kettering Cancer Center

data_processing:
FASTQ files were processed using the 10x Cell Ranger package (v7.0.0)
Assembly: mm10-2020-A
Supplementary files format and content: *.H5AD - H5AD files containing raw and normalized read counts and cell annotation (after bad quality cell filtering)
Supplementary files format and content: filtered_feature_bc_matrix files (barcodes, features, matrix): contain only detected cell-associated barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: filtered_feature_bc_matrix.h5: same information as filtered_feature_bc_matrix in HDF5 format
Supplementary files format and content: raw_feature_bc_matrix files (barcodes, features, matrix): contain all detected barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: raw_feature_bc_matrix.h5: same information as raw_feature_bc_matrix in HDF5 format
Supplementary files format and content: metrics_summary.csv: metrics for quality assessment in CSV format
Supplementary files format and content: molecule_info.h5: contains per-molecule information for all molecules that contain a valid barcode, valid UMI, and were assigned with high confidence to a gene or Feature Barcode; this file is a required input to run cellranger aggr

source_name: T cell culture

growth_protocol: T cells were maintained in 50 IU/mL rhIL-2 prior to stimulation. During stimulation with BM185-CD19 target, no exogenous IL-2 was provided exogenously.

extract_protocol:
Following stimulation, T cells were stained for CD4 and CD8 and hash-tagged according to CAR/switch-receptor configuration (TotalSeq-B anti-mouse hashtag antibodies B0301, B0302, B0303; Biolegend 155831, 155833, and 155835) and sorted for viable, DAPI-negative, CD4+ and CD8+ T cells using a BD FACSAriaII. T cells were sorted into PBS + 2% BSA and were then washed twice in PBS 0.04% BSA and resuspended at ~ 1000 cells/μL. Sorted hash-tagged CD4+ and CD8+ T cells were combined at 1:1 ratios for each CAR/switch-receptor configuration sample. Each combined CD4+/CD8+ hash-tagged CAR T cell configuration was pooled 1:1:1 (dual-CAR, dual-CAR dual-Switch, dual-CAR triple-Switch) and approximately 30,000 cells were submitted for single-cell sequencing per combined biological replicate sample.
Following quality control (QC) steps, the single cell suspension was introduced into the Chromium Next GEM Chip G (10X Genomics PN 1000120) and gel bead in emulsion generation, cDNA synthesis, cDNA amplification, and library preparation of 30,000 cells were carried out using the Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics PN 1000268) according to the manufacturer’s instructions. cDNA amplification included 11 cycles and 138-159 ng of the material were used to prepare sequencing libraries with 10-12 cycles of PCR. Equimolar quantities of indexed libraries were pooled and sequenced on a NovaSeq X in a PE28/88 paired-end run using the NovaSeq X 10B Reagent Kit (100 cycles) (Illumina).  Average reads generated per cell were 23,000. cDNA and feature barcodes tagged with cell barcodes and unique molecular identifiers were generated using methods described above. Smaller feature barcode fragments were separated from longer amplified cDNA using a 0.6X cleanup using AMPure XP beads (Beckman Coulter catalog # A63882). A 3’ Feature Barcode Kit (10X Genomics PN 1000276) was used to construct libraries according to the manufacturer’s protocol with 10 cycles of PCR. Equimolar quantities of indexed libraries were pooled and sequenced on a NovaSeq X in a PE28/88 run using the NovaSeq X 10B Reagent Kit (100 cycles) (Illumina). An average of 335 million paired reads was generated per sample.

treatment_protocol: CAR T cells were stimulated for 24h at 1:1 effector:target ratio with BM185-CD19 in 12-well plates.

value: T cell culture

value: T cell line

value: T cell

value: wild type

value: BM185-CD19 stimulation


title: dual-CAR triple-Switch rep2 [single cell]

status: Public on Nov 24 2024

type: SRA

city: New York

country: USA

description: Chromium Next GEM Single Cell 3’ Kit v3.1

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: dual-CAR dual-Switch rep2 [single cell]


title: dual-CAR triple-Switch rep1 [single cell]


title: dual-CAR rep1 [single cell]


title: dual-CAR rep2 [single cell]


title: Brd4 KO, IFNg, rep1

city: Chuo-ku

first: Haruna

last: Takeda

state: Tokyo

address: 5-1-1 Tsukiji,

country: Japan

institute: National Cancer Center Japan

library_source: transcriptomic

data_processing:
Reference sequences for mapping were prepared using rsem-prepare-reference of RSEM version 1.3.1 and STAR version 2.7.7a.
Reads were trimmed using trim_galore of Trim Galore version 0.6.7 and Cutadapt version 3.5.
The processed reads were mapped to the reference sequences and CPM (Counts Per Million) were calculated using rsem-calculate-expression of RSEM version 1.3.1 and STAR version 2.7.10a.
Gene CPM values were extracted from CPM columns of RSEM result files.
Assembly: GRCm39
Supplementary files format and content: tab-deliminted text files include CPM values for each sample.

molecule: total RNA

source_name: colon

extract_protocol:
Organoids embedded in Matrigel were dissolved in ISOGEN, and RNA was extracted following the protocol.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (Cat No. 7770)  following manufacturer's protocols.

treatment_protocol: Cas9 was intraduced by lenti-virus, then gRNA targeting Brd4 or non-targeting gRNA were introduced by lenti-virus.

value: colon

value: organoid epithelial cells

tag: strain

value: Brd4 gRNA, IFNg


title: control, IFNg, rep3

value: non-target gRNA, IFNg


title: control, IFNg, rep1


title: Brd4 KO, rep1

value: Brd4 gRNA


title: Brd4 KO, IFNg, rep3


title: CAR T cell stimulation rep1


title: control, IFNg, rep2


title: Brd4 KO, rep3


title: Brd4 KO, IFNg, rep2


title: mice without treatment rep3

city: Erlangen

first: Yewei

last: Jia

address: Werner-von-Siemens-Straße 7

department: Department of Internal Medicine 3

country: Germany

institute: Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen

data_processing:
Raw reads of FASTQ format were processed through fastp. Clean reads were obtained by removing reads containing adapter and poly-N sequences and reads with low quality. Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl). Paired-end clean reads were aligned to the reference genome using theSTAR (v2.5) software. STAR used the method of Maximal Mappable Prefix (MMP), which can generate a precise maping result forjunction reads.
HTSeq v0.6.1 was used to count the read numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and read counts mapped to this gene.
Supplementary files format and content: Excel file (xlsx) contains raw counts for each sample
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: long bone without bone marrow

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries
Sequencing libraries were generated using  NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA), and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina).

value: long bone without bone marrow


title: control, non-target gRNA rep4

value: non-target gRNA


title: Brd4 KO, rep2


title: control, non-target gRNA rep3


title: control, non-target gRNA rep2


title: GC cells cocultured with CNO-activited DRG, n=2

first: Timothy

middle: Cragin

last: Wang

state: New York

address: 1130 St Nicholas Ave

department: Dept Med Digestive & Liver Dis

institute: Columbia University

data_processing:
Illumina RTA
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
We perform a pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Human:GRCh38.p12) using kallisto (0.44.0).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include estimated transcript count values for each Sample

source_name: ACKP

growth_protocol: ACKP cells were resuspended in Matrigel (1:1, Corning), and 5000 cells in 30 μL Matrigel per droplet were seeded into a prewarmed 24-well plate. Cells were cultured in DMEM containing 10% FBS, B27 and N2 supplements. The medium was replaced every other day.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 200 ng of total RNA was used for the construction of sequencing libraries.
Libraries were constructed using Illumina TruSeq  RNA Library Prep Kit v2 following manufacturer's instructions

value: ACKP

value: gastric cancer cell

value: Atp4b-Cre; Cdh1fl/fl; KrasG12D; Trp53 fl/fl; YFP

value: cocultured with CNO-activited DRG


title: GC cells cocultured with DRG, n=2

value: cocultured with DRG


title: GC cells cocultured with DRG, n=1


title: GC cells alone, n=3

value: PBS (vehicle)


title: GC cells cocultured with CNO-activited DRG, n=1


title: GC cells cocultured with DRG, n=3


title: GC cells alone, n=2


title: GC cells alone, n=1


title: CAR T cell stimulation rep2

value: T cell culture

value: T cell line


title: GC cells cocultured with CNO-activited DRG, n=3


title: control, non-target gRNA rep1


title: blood-CDI_883582_0wk

type: RNA

city: Liverpool

first: Maria

last: Tsakiroglou

address: Block A, Waterhouse Building, 1-5 Brownlow Street,

department: Department of Pharmacology and Therapeutics

country: United Kingdom

institute: University of Liverpool

hyb_protocol: Fragmented and labelled ssDNA were incubate with rotation at 60 rpm for 16 hours at 45°C on Clariom D Human Array. Cartridge arrays were washed and stained in the GeneChip™ Fluidics Station 450 (GeneChip™ WT PLUS Reagent Kit USER GUIDE, 2018, Applied Biosystems).

scan_protocol: Cartridge arrays were scanned using the  GCS3000 scanner (GeneChip™ Command Console™ User Guide).

data_processing: All processing was performed in R (v4.4.1). CEL files were imported using the oligo package (v1.68.2) and converted to an AnnotatedDataFrame with Biobase (v2.64.0). RMA transformation was performed with the oligo package using default settings, summarised at the 'core' target level. Transcript clusters (TCs) were filtered to those with a transformed probe-intensity greater than 3 in at least 37 samples. The remaining TCs were annotated with Entrez gene IDs using the AnnotationDbi package (v1.66.0) with data obtained from the clariomdhumantranscriptcluster.db package (v8.8.0). TCs assigned to multiple gene IDs were removed, and where gene IDs were assigned to multiple TCs the TC with greatest mean abundance across samples was chosen.

label: Biotin

organism: Homo sapiens

source_name: Whole blood

label_protocol: cRNA were prepared according to the standard GeneChip protocol from a minimum of 50 ng total RNA (GeneChip™ WT PLUS Reagent Kit USER GUIDE, 2018, Applied Biosystems). Following synthesisation of ss-cDNA from 15 μg of cRNA, the fragmented cDNA (5.5 μg) is labeled by terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent that is covalently linked to biotin.

extract_protocol: Performed using a Tempus Spin RNA Isolation kit according to the manufacturer's instructions.

tag: condition

value: CDI

tag: age

tag: Sex

value: Male


title: blood-CDI_470404_0wk

value: Female


title: blood-CDI_519568_0wk


title: blood-CDU_939385_0wk

value: DC


title: blood-CDI_851594_0wk


title: blood-CDI_156742_0wk


title: blood-CDI_450890_0wk


title: blood-CDU_486759_0wk


title: blood-CDU_661720_0wk


title: blood-CDI_511323_0wk


title: blood-CDU_633723_0wk


title: blood-CDU_339116_0wk


title: blood-CDU_586303_0wk


title: blood-CDU_475441_0wk


title: blood-CDU_988859_0wk


title: blood-CDI_555613_0wk


title: blood-CDU_378001_0wk


title: blood-CDU_568090_0wk


title: blood-CDU_118025_0wk


title: blood-CDU_377460_0wk


title: blood-CDU_727309_0wk


title: blood-CDU_936139_0wk


title: blood-CDU_368102_0wk


title: blood-CDU_976602_0wk


title: blood-CDU_802424_0wk


title: blood-CDU_717444_0wk


title: blood-CDU_781685_0wk


title: blood-CDU_555571_0wk


title: blood-CDU_386276_0wk


title: blood-CDU_399381_0wk


title: blood-CDI_950398_2wk


title: blood-CDI_451148_2wk


title: blood-CDI_762896_0wk


title: blood-CDI_797384_2wk


title: blood-CDI_154392_2wk


title: blood-CDI_705318_2wk


title: blood-CDI_731551_0wk


title: blood-CDI_729607_2wk


title: blood-CDI_632963_2wk


title: blood-CDI_162688_0wk


title: blood-CDI_202449_0wk


title: blood-CDI_611758_0wk


title: blood-CDI_335894_0wk


title: blood-CDI_862048_0wk


title: blood-CDI_687097_0wk


title: blood-CDI_809495_0wk


title: blood-CDI_388819_2wk


title: blood-CDI_124478_0wk


title: blood-CDI_929162_0wk


title: blood-CDI_341992_0wk


title: blood-CDI_753552_2wk


title: blood-CDI_451148_0wk


title: blood-CDI_867784_0wk


title: blood-CDI_797384_0wk


title: blood-CDI_577526_0wk


title: blood-CDI_632963_0wk


title: blood-CDI_894169_0wk


title: blood-CDI_416539_0wk


title: blood-CDI_220833_0wk


title: blood-CDI_711895_0wk


title: blood-CDI_426201_0wk


title: blood-CDI_390964_0wk


title: blood-CDI_753552_0wk


title: blood-CDH_146197_0wk

value: HC


title: blood-CDH_828214_0wk


title: blood-CDI_700705_0wk


title: blood-CDU_143167_0wk

value: GDH


title: blood-CDH_647862_0wk


title: blood-CDH_931701_0wk


title: blood-CDI_958056_0wk


title: blood-CDI_729607_0wk


title: blood-CDH_683738_0wk


title: blood-CDH_417316_0wk


title: blood-CDI_986987_0wk


title: blood-CDI_152012_0wk


title: blood-CDI_839330_0wk


title: blood-CDI_927240_0wk


title: blood-CDH_792397_0wk


title: blood-CDI_900323_0wk


title: blood-CDI_451385_0wk


title: blood-CDH_849318_0wk


title: blood-CDH_130684_0wk


title: blood-CDH_595309_0wk


title: blood-CDH_689009_0wk


title: blood-CDU_413229_0wk


title: blood-CDU_979254_0wk


title: blood-CDH_785388_0wk


title: blood-CDU_883358_0wk


title: blood-CDU_126458_0wk


title: blood-CDU_251797_0wk


title: blood-CDU_876955_0wk


title: blood-CDB_866141_0wk

value: IBD


title: blood-CDB_815858_0wk


title: blood-CDI_676632_2wk


title: blood-CDI_725486_0wk


title: blood-CDB_553481_0wk


title: blood-CDB_492390_0wk


title: blood-CDB_602306_0wk


title: blood-CDI_260502_0wk


title: blood-CDI_855533_0wk


title: blood-CDI_646322_2wk


title: blood-CDI_540454_0wk


title: blood-CDI_939945_2wk


title: blood-CDB_611256_0wk


title: blood-CDB_947332_0wk


title: blood-CDU_667401_0wk


title: blood-CDI_154392_0wk


title: blood-CDI_511323_2wk


title: blood-CDI_933485_0wk


title: blood-CDI_341992_2wk


title: blood-CDU_424901_0wk


title: blood-CDU_610381_0wk


title: blood-CDU_370678_0wk


title: blood-CDI_538843_2wk


title: blood-CDU_408609_0wk


title: blood-CDU_619979_0wk


title: blood-CDI_950398_0wk


title: blood-CDU_728184_0wk


title: blood-CDU_185009_0wk


title: blood-CDI_646322_0wk


title: blood-CDU_560140_0wk


title: blood-CDU_189873_0wk


title: blood-CDH_765123_0wk


title: blood-CDI_736273_2wk


title: blood-CDU_454488_0wk


title: blood-CDI_175117_0wk


title: blood-CDI_736273_0wk


title: blood-CDI_388819_0wk


title: blood-CDI_166984_0wk


title: blood-CDI_327250_0wk


title: blood-CDI_705318_0wk


title: blood-CDH_177895_0wk


title: blood-CDH_274615_0wk


title: blood-CDH_773224_0wk


title: blood-CDH_672774_0wk


title: blood-CDH_299378_0wk


title: blood-CDH_928877_0wk


title: blood-CDH_759370_0wk


title: blood-CDH_919043_0wk


title: blood-CDH_738351_0wk


title: blood-CDH_428105_0wk


title: blood-CDH_119709_0wk


title: blood-CDH_876868_0wk


title: blood-CDH_581887_0wk


title: blood-CDH_439039_0wk


title: blood-CDH_111565_0wk


title: blood-CDH_850048_0wk


title: blood-CDU_393998_0wk


title: blood-CDH_629566_0wk


title: blood-CDU_977535_0wk


title: blood-CDU_856228_0wk


title: blood-CDU_704447_0wk


title: blood-CDU_746882_0wk


title: blood-CDU_229261_0wk


title: blood-CDH_305869_0wk


title: blood-CDU_636169_0wk


title: blood-CDU_772535_0wk


title: blood-CDU_650004_0wk


title: blood-CDU_337611_0wk


title: blood-CDU_739110_0wk


title: blood-CDU_340808_0wk


title: blood-CDU_695932_0wk


title: blood-CDU_431961_0wk


title: blood-CDU_292094_0wk


title: blood-CDU_304699_0wk


title: blood-CDU_423335_0wk


title: blood-CDH_149002_0wk


title: blood-CDH_802085_0wk


title: blood-CDU_475164_0wk


title: blood-CDU_306392_0wk


title: blood-CDU_138402_0wk


title: blood-CDU_183805_0wk


title: blood-CDU_370516_0wk


title: blood-CDU_292189_0wk


title: blood-CDU_817627_0wk


title: blood-CDU_967277_0wk


title: blood-CDU_555492_0wk


title: blood-CDU_183803_0wk


title: blood-CDH_662077_0wk


title: blood-CDB_187373_0wk


title: blood-CDB_893435_0wk


title: blood-CDU_131294_0wk


title: blood-CDB_727847_0wk


title: blood-CDB_813365_0wk


title: blood-CDB_411020_0wk


title: blood-CDB_831693_0wk


title: blood-CDH_508447_0wk


title: blood-CDB_404305_0wk


title: blood-CDB_904729_0wk


title: blood-CDB_873553_0wk


title: blood-CDB_265166_0wk


title: blood-CDU_608427_0wk


title: blood-CDB_796339_0wk


title: blood-CDB_423244_0wk


title: blood-CDB_305527_0wk


title: blood-CDB_731372_0wk


title: blood-CDB_104369_0wk


title: blood-CDB_720223_0wk


title: blood-CDB_649482_0wk


title: blood-CDB_858243_0wk


title: blood-CDH_544839_0wk


title: blood-CDB_449897_0wk


title: blood-CDB_447571_0wk


title: blood-CDB_376429_0wk


title: blood-CDB_577305_0wk


title: blood-CDB_238581_0wk


title: blood-CDB_808513_0wk


title: blood-CDI_201157_0wk


title: blood-CDB_656930_0wk


title: blood-CDB_312111_0wk


title: miRNA Caenorhabditis elegans-cadmium exposure-rep3

city: Zhengzhou

first: Panpan

address: 郑州市高新区科学大道100号郑州大学

department: College of Public Health

country: China

institute: 郑州大学

data_processing:
After quality control by FastQC (0.11.9) and discarding 3’ and 5’ adapter by Cutadapt (3.4) and as well as short fragments (≤20bp) in reads, the trimmed data was aligned to reference genome (WBcel235) by Hisat2 (2.2.1) and then determined whether to use its results for further analysis according to the quality. The StringTie (2.1.5) software was applied to estimate transcription abundance and get the count data of genes and transcripts. The Fragments per kilobase of transcript per million mapped reads (FPKM) in gene and transcript level was calculated by “Ballgown” of the R package; while the average FPKM of gene and transcript in treat or control group less than 0.1 was excluded. After exclusion, the FPKM value in gene level was used to conduct the spearman correlation analysis for validation of the samplesconcordance, which the spearman correlation should greater than 0.9, according to the standard of ENCODE (https://www.encodeproject.org). Then, the count data of genes and transcripts were employed to explore the differentially expressed genes (DEGs) and differentially expressed transcripts using R package “DESeq2”, with the standards of P < 0.05 and |log2FC| > 0.585. According to the file of gene transfer format (Caenorhabditis_elegans.WBcel235.103.gtf, GTF file, http://www.ensembl.org/), the protein-coding RNA (mRNA) and lncRNA were identified. CircRNAs were identified and quantitated by the software of bowtie2 (2.4.2) and find_circ (1.2). Count data of circRNA were used to perform differentially expressed analysis for circRNA using “edgeR”of R package with the standards of P < 0.05 and |log2FC| > 0.585. The differentially expressed mRNAs (DEmRNAs), lncRNA (DElncRNAs) and circRNAs (DEcircRNAs) were prepared for further analysis.
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include count, CPM values for each Sample.

organism: Caenorhabditis elegans

source_name: whole individual

growth_protocol: Wild type N2 nematodes grew in standard NGM medium.

extract_protocol:
For per 50-100mg tissue sample, 1ml TRI REAGENT was added and an electric homogenizer used to mix it. After that, the sample was incubated for 5 minutes at 15 to 30℃ to completely dissociate the nucleic acid protein complex. Add 0.2ml chloroform to 0.2ml chloroform was added in per 1ml mixture, and close the tube cap tightly. After shaking the tube vigorously by hand for 15 seconds, it was incubated at 15 to 30℃ for 2 to 3 minutes. Centrifuge at 12000xg for 15 minutes at 4℃. After that, the mixture will be divided into the lower red phenol-chloroform phase, the middle layer and the upper colorless water phase. The RNA is all distributed in the water phase. The volume of the water phase is approximately 60% of the TRI REAGENT reagent added during the homogenization. Transfer the aqueous phase to a new centrifuge tube. The aqueous phase is mixed with 0.5ml isopropanol to precipitate the RNA. After mixing, it was incubated at 15 to 30°C for 10 minutes, and centrifuged at 12000xg at 4℃ for 10 minutes. Remove the supernatant, and add at least 1ml 75% ethanol to every 1ml mixture to wash the RNA precipitate. After shaking, centrifuge at 7500xg at 4℃ for 5 minutes. Remove the ethanol solution and dry the RNA pellet in the air for 5-10 minutes. When dissolving RNA, add RNase-free water and pipe repeatedly with a gun several times, and then incubate at 55 to 60°C for 10 minutes. The obtained RNA solution was stored at -70℃.
The library of miRNA of C. elegans was constructed using Multiplex Small RNA Library Prep Set for Illumina (E7508L, New England Biolabs, Netherlands). After degrading to ssDNA, it was captured in Illumina flow cell and conducted in situ amplification. According to the manufacturer’s operating manual, it was sequenced on the platform of Illumina NextSeq 500 (50 cycles). Other steps were similar to the mRNA sequencing.

treatment_protocol: CdCl2 was dissolved to 1000 μM as the standard solution and gradiently diluted to 60 μmol/L; and the L4-larvae of C. elegans was exposed to CdCl2 at this concentration mixed with NGM and then added with OP50 with the colony forming units (CFUs) of 4 × 106 at 20 °C.

value: wild type

value: cadmium

value: cadmium exposure


title: miRNA Caenorhabditis elegans-cadmium exposure-rep2

address: 郑州市高新区科学大道100号郑州大学


title: miRNA Caenorhabditis elegans-cadmium exposure-rep1

address: 郑州市高新区科学大道100号郑州大学


title: blood-CDB_994153_0wk


title: blood-CDB_232906_0wk


title: blood-CDB_756696_0wk


title: blood-CDB_651333_0wk


title: miRNA Caenorhabditis elegans-control-rep3

address: 郑州市高新区科学大道100号郑州大学

value: untreated

value: control


title: blood-CDH_494862_0wk


title: blood-CDU_657683_0wk


title: blood-CDI_296520_0wk


title: blood-CDI_478048_0wk


title: miRNA Caenorhabditis elegans-control-rep2

address: 郑州市高新区科学大道100号郑州大学


title: blood-CDI_352868_0wk


title: blood-CDB_461815_0wk


title: blood-CDI_156742_2wk


title: blood-CDB_261850_0wk


title: blood-CDB_822500_0wk


title: blood-CDI_740376_0wk


title: blood-CDI_958056_2wk


title: blood-CDH_402955_0wk


title: blood-CDI_558602_2wk


title: miRNA Caenorhabditis elegans-control-rep1

address: 郑州市高新区科学大道100号郑州大学


title: 55175 0.5 uM TGN-1062, 24 hrs

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
NovaSeq Control Software 1.2.0.28691 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.
Assembly: GRCh38.p14 RNA sequences (Transcriptome)
Supplementary files format and content: comma-delimited csv file includes raw counts for each samples

source_name: Bone Marrow

extract_protocol:
RNA was harvested using miRNeasy Mini Kit (Qiagen). DNA digestion was conducted during RNA extraction. 10 ug of total RNA was prepared for the downstream processing for RNA-sequencing.
RNA libraries for RNA-seq were prepared using KAPA mRNA Hyperprep Kit following manufacturer's protocols.

value: Bone Marrow

value: Patient-drived primary CD34+CD38- blast

value: Acute Myeloid Leukemia


title: 55174 0.5 uM TGN-1062, 24 hrs


title: blood-CDI_558602_0wk


title: 55172 0.5 uM TGN-1062, 24 hrs


title: blood-CDI_314344_0wk


title: blood-CDI_326720_0wk


title: 55167 DMSO, 24 hrs


title: 55164 DMSO, 24 hrs


title: 55162 No Treatment


title: 55166 DMSO, 24 hrs


title: blood-CDI_855533_2wk


title: blood-CDI_700705_2wk


title: 55163 No Treatment


title: blood-CDI_265643_0wk


title: 55160 No Treatment


title: 55173 0.5 uM TGN-1062, 24 hrs


title: 55161 No Treatment


title: blood-CDH_880992_0wk


title: 55165 DMSO, 24 hrs


title: U937_4C_KRAB_3SNPs_THBS1_cQTL_rep1

city: London

first: Mikhail

last: Spivakov

address: Du Cane Road

institute: MRC London Institute of Medical Sciences

description: 4C-seq library amplified at the cQTL rs2033937

library_source: genomic

data_processing:
Read 1 of the paired end reads was used for all 4C-seq analyses. 4C-seq reads were mapped and filtered using the pipe4C tool from the de Laat lab.
Restriction digest files (rmap) were made for DpnII-AseI using the Digester script from HiCUP123 v0.9.2. These were used alongside the 4C BAM files as input to the coverageBed function from BEDtools141 v2.31.1,  to count the number of reads in each BAM file corresponding to restriction fragments.
Assembly: GRCh38
Supplementary files format and content: bedgraph files per replicate (raw counts).
Library strategy: 4C-seq

molecule: genomic DNA

growth_protocol: U-937 cells were cultured in RPMI media, supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol:
10 million cells were crosslinked for 10 minutes with 1% formaldehyde.
Crosslinked cells were lysed and digested with 200U DpnII at 37C overnight. The enzyme was heat inactivated (65oC for 20 minutes), the nuclei were spun down and then re-suspended in a ligation mixture containing 50 units of DNA ligase (Invitrogen 15224017). After an overnight incubation at 16oC, crosslinks were reversed by addition of Proteinase K (Sigma 3115879001) and incubation at 65oC overnight. Samples were purified using SPRI beads (AMPure XP, Beckman Coulter) and up to 60 μg of template was digested using 1U per μg template of the secondary restriction enzyme (AseI) at 37oC overnight. The enzyme was heat inactivated (65oC for 20 minutes), and ligation was performed at a final DNA concentration of 5 ng/uL, using 2U per μg of T4 DNA ligase, overnight at 16oC. Purification was performed the next day with Phenol Chloroform Isoamyl Alcohol (P:C:I) using MaXtract High Density tubes (Qiagen). A final purification was performed using SPRI beads, prior to library amplification, which followed the 2-step protocol described in Krijger et al. For the first PCR, four PCR reactions containing 200 ng of template were set up for each sample, and 16 cycles of PCR were performed using Expand Long Template Polymerase Mix (Roche), using a reading primer containing the sequence TGAGTGATTGCAAATGGAAA. The DNA was pooled and cleaned using 0.8X SPRI to remove long primers. For the second PCR (sequencing adapter addition), up to 100 ng of template was used per reaction for 12 cycles of PCR. Final library cleanup was done using 0.8X SPRI and the samples were sequenced using 150bp paired end reads on a NovaSeq platform (Novogene Europe).

treatment_protocol: To generate cell lines expressing dCas9 KRAB, the lentiviral puromycin resistance vector pLV-dCas9-KRAB (Addgene plasmid #99372) was used. For sgRNA expression, we further used the lentiviral hygromycin resistance vector pLV-sgRNA (Addgene plasmid #62205). We cloned the following sgRNA targeting cQTLs in the THBS1 locus separately into plasmid #62205: 1) TATGCTCTTCAGAACAAACC (targeting chr15:39607469-39607488); 2) AGCTGATGAATGCCCATACT (targeting chr15:39607555-39607574) and 3) AATTTAGGCCTCCTAATATG (targeting chr15:39602387-39602406). We combined the three plasmids containing each sgRNA in equimolar quantities, making a pool of cQTL sgRNA plasmids. As a control, we cloned a sgRNA with a scrambled, non-targeting sequence into plasmid #62205 (CTTAGTTACGCGTGGACGA). Lentivirus was produced for the pLV-dCas9-KRAB plasmid (#99372) and the cloned sgRNA plasmids (#62205) using a third generation system. HEK293 cells were seeded to 10 million cells  per vector in 15cm round plates in a 20 mL volume of complete media and incubated overnight. The media was replaced with 20 mL fresh media with FBS but without penicillin-streptomycin. Then, 6 μg of plasmid DNA was combined with 1.5 μg of REV packaging plasmid (Addgene # 12253), 3 μg pRRE packaging plasmid (Addgene # 12253) and 1.5 μg VSV-G envelope (Addgene # 12259) in 2 mL serum-free DMEM without phenol red in a sterile 15 mL tube. After filter sterilising, we added 72 μL of 1mg/ml Polyethyleneimine linear MW 25K (PEI; Fisher Scientific 11460630) to the tube, vortexed and left at room temperature for 10-15 minutes. The DNA/PEI mix was added to the cells in a dropwise fashion using a pasteur pipette. The cells were incubated overnight before a media change. After a 48 hour incubation, the media containing lentivirus was harvested and filtered (0.45 μm filter) before use.  The first round of transduction generated U-937 cells expressing dCas9-KRAB. Before transduction, 300,000 U-937 cells were seeded into 3mL media in a 6 well plate. The next day, cells were spun down and resuspended in a 2 mL of media with FBS but no penicillin-streptomycin. After 2 hours, 24 μL of polybrene was added (Hexadimethrine bromide, Sigma H9268-5G, prepared at 1 mg/mL in 0.9% NaCl), followed by 1mL of lentivirus. Cells were incubated overnight, before changing the media (RPMI media + 10% FBS and 1% penicillin-streptomycin). After a further 48 hours, the cells underwent selection with puromycin (250 μg/mL) for several days, until cells that had not integrated the plasmid had died and transduced cell viability returned to high levels. Subsequently, the cells were transduced with the sgRNA lentivirus (either the pool of cQTL-targeting sgRNA or the scrambled control sgRNA) in the same manner as for dCas9 KRAB. The cells were then selected with hygromycin (1 μg/mL) until viability returned to high levels. Three independent rounds of sgRNA transductions were performed to generate biological triplicates.

value: Expressing dCas9 KRAB and a sgRNA targeting cQTLs nearby THBS1 gene


title: U937_4C_KRAB_3SNPs_THBS1_cQTL_rep3


title: U937_4C_KRAB_3SNPs_THBS1_cQTL_rep2


title: blood-CDU_960845_0wk


title: blood-CDI_538843_0wk


title: blood-CDI_674850_0wk


title: blood-CDI_929162_2wk


title: U937_4C_scramControl_THBS1_cQTL_rep2

value: Expressing dCas9 KRAB and a non-targeting sgRNA


title: blood-CDU_134958_0wk


title: blood-CDU_543472_0wk


title: blood-CDU_283137_0wk


title: U937_4C_scramControl_THBS1_cQTL_rep1


title: U937_4C_scramControl_THBS1_cQTL_rep3


title: blood-CDU_209712_0wk


title: blood-CDH_101865_0wk


title: U937_ATAC_KRAB_THBS1_3SNPs_rep3

description: ATAC-seq library

data_processing:
Adapters were trimmed using fastp
Reads were aligned to GRCh38 using bowtie2 --very-sensitive --no-discordant -p 120 -X 2000
Aligned reads were filtered to mapQ30 using alignmentSieve --minMappingQuality 30 --samFlagInclude 2
Duplicate reads were removed using Picard
Mitochondrial reads were removed using Samtools
1kb windows were defined across chromosome 15 using bedtools makewindows. Counts were generated in these windows for all samples using bedtools multicov.
Assembly: GRCh38
Supplementary files format and content: Read counts (txt)

extract_protocol:
Cells were crosslinked for 10 minutes with 1% formaldehyde.
ATAC-seq libraries were generated following the omni-ATAC protocol, with modifications for crosslinked chromatin. Between 25 thousand and 100 thousand crosslinked, lysed nuclei (1-2 technical replicates per individual) were re-suspended in a tagmentation reaction mixture (10mM tris HCl [pH 8.4-9.0], 5 mM MgCl2, 10% DMF, 0.005% digitonin and 0.05% tween 20 and up to 5µL of homemade Tn5 enzyme) and incubated at 37°C for 2 hours with 1000 rpm mixing. Reverse crosslinking was performed using proteinase K overnight at 65°C and then samples were cleaned using minElute spin columns (Qiagen). Libraries were amplified using 5-7 cycles of PCR using KAPA HiFi DNA polymerase and purified with 1.1X SPRI (Beckman Coulter). Nucleosome profiles were manually inspected using a Tapestation with the D1000 Screen Tape system (Agilent).


title: U937_ATAC_KRAB_THBS1_3SNPs_rep2

description: ATAC-seq library


title: U937_ATAC_KRAB_THBS1_3SNPs_rep1

description: ATAC-seq library


title: blood-CDI_841314_0wk

value: CDI


title: blood-CDI_450890_2wk


title: blood-CDI_762909_0wk


title: U937_ATAC_KRAB_scramControl_rep3

description: ATAC-seq library


title: blood-CDI_555613_2wk


title: U937_ATAC_KRAB_scramControl_rep2

description: ATAC-seq library


title: U937_ATAC_KRAB_scramControl_rep1

description: ATAC-seq library


title: blood-CDI_395042_0wk

value: Male


title: blood-CDU_983274_0wk

value: Female


title: 12B_R1, CTL2, TNFa 10 ng/mL 6h, rep1

city: Paris

first: Quentin

last: Riller

address: 24 Boulevard du Montparnasse

country: France

institute: INSERM UMRS 1163, Imagine Institute

data_processing:
The oriented cDNA produced from the poly-A+ fraction was sequenced on a NovaSeq6000 from Illumina (Paired-End reads 100 bases + 100 bases). A total of ~50 million of passing-filters paired-end reads was produced per library. Paired-end RNA-seq reads were aligned to the human Ensembl genome GRCh38.91 using STAR (v2.7.5a) and counted using featureCounts from the Subread R package
Assembly: Ensembl genome GRCh38.91
Supplementary files format and content: CSV raw data count

growth_protocol: Cultivated in 12 well-plates overnight before stimulation, plated as 200 000 cells / well on D0

extract_protocol:
Extraction of total RNA with DNAseI digestion using the protocol from Zymo Quick-RNA 96™ Kit and following manufacturer instructions
RNaseq libraries were prepared starting from 500 ng of total RNA using the Universal Plus mRNA-Seq kit (Nugen) as recommended by the manufacturer.

treatment_protocol: Treatment with human TNFα 10 ng/mL for 6h or Poly I:C HMW 10 ug/mL for 6h as indicated or left unstimulated


title: blood-CDI_540454_2wk


title: 12C_R1, CTL2, poly I:C HMW 10 ug/mL 6h, rep1


title: 12Bbis_R1, CTL2, TNFa 10 ng/mL 6h, rep2


title: blood-CDI_738745_0wk


title: 9Cbis_R1, NFKB2 patient, poly I:C HMW 10 ug/mL, rep2


title: 9C_R1, NFKB2 patient, poly I:C HMW 10 ug/mL 6h, rep1


title: blood-CDI_250169_0wk


title: blood-CDI_674850_2wk


title: blood-CDI_255870_2wk


title: blood-CDI_799868_0wk


title: blood-CDI_255870_0wk


title: 12A_R1, CTL2, no stimulation, rep1


title: 12Cbis_R1, CTL2, poly I:C HMW 10 ug/mL, rep2


title: blood-CDI_788403_0wk


title: blood-CDH_407690_0wk


title: blood-CDI_546501_0wk


title: 9B_R1, NFKB2 patient, TNFa 10 ng/mL 6h, rep1


title: 9Abis_R1, NFKB2 patient, no stimulation, rep2


title: blood-CDU_434358_0wk

value: DC


title: blood-CDI_555629_0wk


title: 9A_R1, NFKB2 patient, no stimulation, rep1


title: blood-CDI_556083_0wk


title: 9Bbis_R1, NFKB2 patient, TNFa 10 ng/mL 6h, rep2


title: blood-CDI_575655_0wk


title: 8C_R1, CHUK patient, poly I:C HMW 10 ug/mL 6h, rep1


title: 12Abis_R1, CTL2, no stimulation, rep2


title: 8Bbis_R1, CHUK patient, TNFa 10 ng/mL 6h, rep2


title: blood-CDU_731031_0wk


title: 8Abis_R1, CHUK patient, no stimulation, rep2


title: blood-CDU_415483_0wk


title: blood-CDU_845124_0wk


title: 3C_R1, CTL1, poly I:C HMW 10 ug/mL 6h, rep1


title: 8Cbis_R1, CHUK patient, poly I:C HMW 10 ug/mL, rep2


title: 8B_R1, CHUK patient, TNFa 10 ng/mL 6h, rep1


title: 3Cbis_R1, CTL1, poly I:C HMW 10 ug/mL, rep2


title: 8A_R1, CHUK patient, no stimulation, rep1


title: blood-CDH_346908_0wk

value: HC


title: 3B_R1, CTL1, TNFa 10 ng/mL 6h, rep1


title: 3Bbis_R1, CTL1, TNFa 10 ng/mL 6h, rep2


title: blood-CDH_446298_0wk


title: blood-CDU_587393_0wk


title: blood-CDH_647386_0wk


title: blood-CDU_696889_0wk


title: 3Abis_R1, CTL1, no stimulation, rep2


title: blood-CDH_135248_0wk


title: 3A_R1, CTL1, no stimulation, rep1


title: blood-CDH_293965_0wk


title: blood-CDH_117276_0wk


title: THP-1 cells, HSV-1, shDUX4, repeat-3

city: Wuhan

first: Junjie

last: Zhang

state: Hubei

address: Donghu Road, No. 115

department: Medical Research Institute

institute: Wuhan University

data_processing:
The raw sequencing data were processed using SOAPnuke (v.1.5.2) to remove low-quality reads, and the clean reads were mapped to the reference genome using HISAT2 (v.2.0.4). Bowtie2 (v.2.2.5) was employed to align the clean reads to the reference coding gene set, and RSEM (v.1.2.12) was used to quantify gene expression levels. Differential gene expression analysis was conducted with DESeq2 (v.1.4.5).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: the difference expressed genes HSV-1 vs mock-infected group, and HSV-1_shDUX4 vs HSV-1_shControl

extract_protocol:
Total RNA was isolated with the TRIzol reagent (Takara)
Oligo(dT)-coupled magnetic beads were used to purify mRNA, and then a sequencing library was constructed

value: Monocytes

value: DUX4 knockdown

value: HSV-1 infection with DUX4 knockdown


title: fever-3

city: Shanghai

first: Haiyou

last: Gao

state: 上海市

address: State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai, China

institute: 华东师范大学

description: Library name: Sample 7

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: O_niloticus_UMD_NMBU
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Oreochromis niloticus

source_name: spleen

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

value: spleen

value: lymphocytes

value: primary cell


title: THP-1 cells, HSV-1, shDUX4, repeat-1


title: fever-2

description: Library name: Sample 6


title: 1Cbis_R1, NEMO_null, poly I:C HMW 10 ug/mL, rep2


title: blood-CDH_503294_0wk


title: blood-CDH_249849_0wk


title: fever-4

description: Library name: Sample 8


title: THP-1 cells, HSV-1, shDUX4, repeat-2


title: fever-1

description: Library name: Sample 5


title: blood-CDH_888066_0wk


title: ctrl-2

description: Library name: Sample 2


title: ctrl-3

description: Library name: Sample 3


title: 1Bbis_R1, NEMO_null, TNFa 10 ng/mL 6h, rep2


title: ctrl-4

description: Library name: Sample 4


title: 1B_R1, NEMO_null, TNFa 10 ng/mL 6h, rep1


title: THP-1 cells, HSV-1, shControl, repeat-2

value: WT

value: HSV-1 infection


title: THP-1 cells, HSV-1, shControl, repeat-3


title: ctrl-1

description: Library name: Sample 1


title: blood-CDH_639364_0wk


title: THP-1 cells, HSV-1, shControl, repeat-1


title: 1C_R1, NEMO_null, poly I:C HMW 10 ug/mL 6h, rep1


title: SiRNA-GLUT10-3-2

first: Zhipeng

last: Hu

address: 238 Jiefang Road

department: cardiovascular surgery

institute: Renmin hospital of Wuhan University

data_processing:
Bcl2fastq (v2.17.1.14)software used for base calling.
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or   fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data.
Mapping: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2(v2.0.1).
Alternative splicing analysis: Predicted transcripts of StringTie(V1.0.4) (Nature Biotechnology 2015; Pertea M, et al.) were classified and expressed by using  ASprofile（V1.0.4）software.
Put together the genome-wide comparisons of all the sequencing reads data, use StringTie (1.0.4) (Nature Biotechnology, 2015; Pertea M, et al.) for assembly, then use Cuffcompare compared with a known gene model (*.gtf).
By comparing the results of each sample with the reference genome, samTools (V0.1.18) software was used for MPileup processing, so as to obtain the possible SNV results of each sample, and then Annovar (V2013.02.11) software was used for annotation.
Gene expression was calculated using Htseq software (V 0.6.1), which used FPKM(Fragments Per Kilo bases Per Million reads)(Mortazavi, 2008) to calculate gene expression.
The software RSeQC resampled the total by comparing reads（jackknifing）, evaluating the RPKMs at the current sequencing depth, the Percent relative error rate was used to measure the accuracy of the assessed RPKM
Principal component analysis has been dealed with R language.
The expression levels of genes under different experimental conditions were compared by  distribution map and box map of FPKM of all genes.
GO and KEGG enrichment analysis: GO-TermFinder was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant p-value less than 0.05. We used scripts in house to enrich significant differential expression gene in KEGG pathways.
DEU analysis was performed using DEXSeq(V1.18.4) software to detected the differential gene expression at exon level.
Genome_build: SLC2A10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Rattus norvegicus

source_name: VSMCs

growth_protocol: SLC2A10 knock-down VSMCs were routinely inoculated generated in Dulbecco's modified Eagle's medium/F12 (DMEM/F12) medium supplemented with 20% fetal bovine serum (FBS)（Gibco; Thermo Fisher Scientific）and 1% penicillin streptomycin solution （both from Gibco).

extract_protocol:
Aorta were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: aorta

value: SD


title: 1A_R1, NEMO_null, no stimulation, rep1


title: 1Abis_R1, NEMO_null, no stimulation, rep2


title: PLC cells, high glucose

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
Gene annotated in NCBI were quantified using featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited csv file includes counts values for each sample
Supplementary files format and content: xls file include FPKM values for each sample

source_name: PLC

growth_protocol: Huh7 and PLC were cultured in glucose-freee Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, Carlsbad, CA, USA) containing 10% fetal bovine serum (FBS) (HyClone, Logan, UT, USA) and antibiotics (penicillin and streptomycin, Invitrogen) at 37 °C in 5% CO2.

extract_protocol:
RNA samples were extracted using TRIzol reagent (Invitrogen, CA, USA).
The RiboMinus Eukaryote Kit (Qiagen, CA, USA) was used to eliminate rRNAs, and the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, MA, USA) was used to build the RNA-seq library.

treatment_protocol: Cell culture medium was supplemented with 5 mM or 25mM glucose

value: PLC

value: human hepatocellular carcinoma cells

value: high glucose


title: SiRNA-GLUT10-2-2


title: PLC cells, low glucose

value: low glucose


title: THP-1 cells, mock-infected, shControl, repeat-3

value: mock infection


title: MycWT_ChIP

city: La Jolla

first: Chunyu

last: Jin

address: 9500 Gilman Dr. MC0648

institute: University of California, San Diego

data_processing:
The sequence tag returned by the Illumina Pipeline was adapter trimmed by Trim Galore and aligned to the hg38 assembly by Bowtie2. For subsequent visualization of ChIP-Seq signal, bigwig files were generated using the DeepTools “bamCoverage” script integrated in Galaxy server using “Normalized to reads per kilobase per million(RPKM)”. DeepTools “computeMatrix”, “plotHeatmap”, and “plotProfile” functions were used to generate heatmaps and profile plots.
Assembly: hg38
Supplementary files format and content: bamcoverage bigwig file for each sample, which can be visualized by UCSC genome browser or IGV

source_name: MIA PaCa-2

extract_protocol:
1-5 million cells were dual cross-linked with 2 mM disuccinimidyl glutarate (DSG, ProteoChem, #C1104-1GM) for 20min at room temperature and followed by 1% formaldehyde for 10 min for Mediator’s ChIP. For transcription factors’ ChIP, cells were only fixed in 1% formaldehyde for 10 min. In both situations, the cross-linking was quenched with 0.125M glycine for 5 min. Chromatin was fragmented using a Bioruptor to get 200-500bp fragments. Subsequently, the soluble chromatin was incubated with 1-3 mg antibodies at 4°C overnight. Immunoprecipitated complexes were collected using 20 ul Protein G Dynabeads (Life Technologies) per reaction. After washing, the protein-DNA complexes were eluted and de-crosslinked overnight at 65°C. and DNA was purified with QIAquick PCR Purification Kit (Qiagen, # 28104).
The ChIP-seq DNA library construction was performed using Illumina’s ChIP-seq Sample prep kit or ABclonal’s the Rapid DNA Lib Prep Kit (ABclonal, #RK20200). Library was usually amplified by 14 cycles of qPCR. Constructed libraries were further double size selected between 150-600 bp with AMPure XP (Beckman, #A63881) and sequenced on NovaSeq 6000 with 100 bp paired-end reads at the UCSD IGM Genomics Center.

tag: chip antibody

value: HA-Tag (CST #3724)

value: MIA PaCa-2

value: human pancreatic cancer

value: Dox-induced MycWT-3xHA

value: Dox


title: Huh7 cells, high glucose


first: William

last: Coetzee

state: United States

address: 550 First Ave

department: Pathology

institute: NYU School of Medicine

description:
Library name: Splenic NK cells, CD27-/CD27b-, KO, replicate 2
KO2_3

data_processing:
Data analysis was performed on BigPurple, a high-performance computing cluster available through NYU Langone’s High Performance Computing (HPC) Core.  Quality control of the paired RNA fastq files was performed with fastqc. No end-trimming was needed. Reads were aligned to the mm10 mouse genome using STAR and index files were produced with Samtools. The GeneCounts option of STAR was used to count number reads per gene while mapping. Off-line analysis was performed with R. Individual “ReadsPerGene.out.tab” files were combined. Gene expression analysis was performed with the DESeq2 package (version 1.44.0), which included filtering low expressing genes, calculating normalized gene counts, calculating the between-sample distance matrix, principal component analysis, and performing a differential expression analysis.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet containing normalized reads

source_name: Spleen

extract_protocol:
Splenocytes were isolated from wild-type mice, and Kir6.1flx/flx x NKp46-CreERT2 mice immediately following 4 days of tamoxifen induction (n=2 each). Cells were first gated for NK cell markers NK1.1 and NKp46, then sorted into four pools (CD27-/CD27b-, CD27+/CD27b-, CD27+/CD27b+, and CD27-/CD27b+). RNA was isolated with the RNeasy Mini Kit (Qiagen).  RNA extractions were quantified using RNA Pico Chips (Agilent, Cat. 5067-1513) on an Agilent 2100 BioAnalyzer.
cDNA was synthesized using the Takara SMART-Seq HT kit (Cat. 634438) with 0.5 ng of RNA input and 14 amplification cycles.  The Nextera XT DNA library Kit (Illumina, Cat. FC-131-1096) was used to construct sequencing libraries with 0.25 ng cDNA input and 11 cycles amplification.  Final libraries were visualized using High Sensitivity DNA ScreenTape (Agilent, Cat. #5067-5584) on the Agilent Tapestation 2200 instrument.  Quant-It (Invitrogen, Cat. P11495) was used for final concentration determination and libraries were pooled equimolar.  Paired-end 50 cycle RNA sequencing was performed by NYU Langone's Genome Technology Center (RRID: SCR_017929) using a single lane of a 10B 100 Cycle Flowcell using an Illumina NovaSeq X-Plus instrument.

value: Spleen

value: NK cells

value: NK-cell Kcnj8 KO


title: THP-1 cells, mock-infected, shControl, repeat-2

value: Monocytes

value: WT


title: SiRNA-GLUT10-3-1

value: aorta


title: THP-1 cells, mock-infected, shControl, repeat-1


title: MycWT(off)_ChIP

value: Dox-induced MycWT3xHA

value: NonDox


title: Huh7 cells, low glucose

value: human hepatocellular carcinoma cells


title: Control-1

value: SD

value: wild type


description:
Library name: Splenic NK cells, CD27+/CD27b-, KO, replicate 2
KO2_2


title: TH112

city: Ann Arbor

first: Thanh

last: Hoang

state: MI

address: 1000 Wall St, Brehm Building , Room 7426

department: Ophthalmology

institute: University of Michigan

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters.
Assembly: Rattus_norvegicus mRatBN7
Supplementary files format and content: TH112_barcodes.tsv.gz, TH112_features.tsv.gz, TH112_matrix.mtx.gz

source_name: Optic Nerve Head

extract_protocol:
scRNA-Seq following 10x V3.1 guideline, scMultiome using 10xGenomics Multiome
Illumina NovaSeq 6000

value: Optic Nerve Head

value: Optic Nerve Head cells


title: Mycdel348-377aa_ChIP

value: HA-Tag (CST #3724)

value: MIA PaCa-2

value: Dox-induced Mycdel348-377aa-3xHA


title: Mycdel210-310aa_ChIP

value: human pancreatic cancer

value: Dox-induced Mycdel210-310aa-3xHA

value: Dox


title: primary cervical cancer-RS_3

city: Changchun

first: Shun-Qing

last: Zhou

address: No. 218 Ziqiang Street, Changchun City, Jilin Province, China

institute: Jilin University

data_processing:
each from the RR and RS groups were selected, and eukaryotic mRNA was enriched using mRNA capture beads. The mRNA was fragmented by heating and used as a template for cDNA synthesis. Single-stranded cDNA was synthesized using random six-base primers (random hexamers), followed by the addition of buffer and deoxynucleotide triphosphates (dNTPs).
The double-stranded cDNA synthesized was purified using VAHTS DNA Clean Beads . The purified double-stranded cDNA was end-repaired, A-tailed, sequencing adaptor-ligated, and subjected to fragment size sorting using VAHTS DNA Clean Beads.
After library construction, the preliminary concentration was determined using Qubit 3.0 , and library insert fragments were then detected using Agilent 2100 Bioanalyzer. The different libraries were adjusted to the effective concentration and the demand of the on-target off-machine data, and Illumina HiSeq sequencing was performed after cooling.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: primary cervical cancer-RS

growth_protocol: The samples were collected from 10 patients with primary squamous-cell cervical cancer who were admitted to the Second Hospital of Jilin University between 2014 and 2016. These patients had not received other anti-tumor treatments before radiotherapy and did not undergo surgery after radiotherapy. The 29 patients were divided into two groups: (1) the radiotherapy-sensitive (RS) group, with patients who had no local recurrence or distant metastasis within 2–3 years after initial therapy; and (2) the radiotherapy-resistant (RR) group, with patients with conditions uncontrolled by radiotherapy, local recurrence, or distant metastasis within 2–3 years after the initial treatment.

extract_protocol:
Cervical cancer tissue specimens were homogenized and total RNA was extracted with TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cervical cancer tissue

tag: pathological

value: squamous cell carcinoma

tag: group

value: radiotherapy-sensitive (RS)


title: primary cervical cancer-RS_5


title: primary cervical cancer-RS_4


title: mycinTetonsh30Mia_ChIP

value: Dox-induced shMED30


title: MDA-MB-231-BrM3, shNAT10, Replicate 2

city: New Haven

first: Qin

last: Yan

state: CT

address: 310 Cedar Street

institute: Yale University

description: TruSeq stranded RNA-seq

data_processing:
Basecalls performed using CASAVA version 1.8.2 Raw reads were aligned using STAR 2.7.0 to hg38 using standard parameters Counts were obtained to GENCODEv96 transcripts DEseq2 was used to determine differential expression using counts.
Assembly: hg38
Supplementary files format and content: xlsx (DESeq2 results comparing shNAT10 and shControl)

source_name: breast

extract_protocol:
Cells from knockdown control or shNAT10 group were harvested with QIAzol Lysis Reagent (Qiagen) and homogenized using QIAshredder tubes (Qiagen). For each cell line, shRNA expression was induced with doxycycline (1 ug/mL) for 3 days and 3 biological replicates were harvested at different passages. RNA isolation was performed using miRNeasy with on-column DNase digestion. ERCC spike-in RNA was added in proportion to the number of cells obtained during cell counts.
Library generation was performed using TruSeq stranded mRNA library prep kit (Illumina). Paired-end sequencing was performed using an Illumina HiSeq4000 sequencer.

value: breast

value: mammary gland/breast epithelial cell

value: NAT10 knockdown


description:
Library name: Splenic NK cells, CD27-/CD27b+, KO, replicate 2
KO2_0

value: Spleen

value: NK cells

value: NK-cell Kcnj8 KO


title: SiRNA-GLUT10-2-1

value: aorta

value: SD


description:
Library name: Splenic NK cells, CD27+/CD27b+, KO, replicate 2
KO2_1


title: Control-2

value: wild type


title: primary cervical cancer-RS_2


title: MDA-MB-231-BrM3, shNAT10, Replicate 3

description: TruSeq stranded RNA-seq


description:
Library name: Splenic NK cells, CD27-/CD27b-, KO, replicate 1
KO1_3


title: MDA-MB-231-BrM3, shNAT10, Replicate 1

description: TruSeq stranded RNA-seq


title: primary cervical cancer-RS_1


title: mycMia_ChIP

value: MIA PaCa-2

value: NonDox


title: Mycdel393-430aa_ChIP

value: HA-Tag (CST #3724)

value: human pancreatic cancer

value: Dox-induced Mycdel393-430aa-3xHA


title: primary cervical cancer-RR_5

source_name: primary cervical cancer-RR

value: cervical cancer tissue

value: squamous cell carcinoma

value: radiotherapy-resistant (RR)


title: MDA-MB-231-BrM3, shCtrl, Replicate 3

description: TruSeq stranded RNA-seq

value: breast

value: WT


description:
Library name: Splenic NK cells, CD27+/CD27b+, KO, replicate 1
KO1_1


title: Myc_ChIP


title: primary cervical cancer-RR_4


title: MED30_ChIP

value: MED30 (from Dr. Thomas G. Boyer, UT health San Antonio, homemade)


title: MDA-MB-231-BrM3, shCtrl, Replicate 2

description: TruSeq stranded RNA-seq

value: mammary gland/breast epithelial cell


description:
Library name: Splenic NK cells, CD27-/CD27b+, KO, replicate 1
KO1_0

value: Spleen

value: NK cells


title: primary cervical cancer-RR_3


title: MED17_ChIP

value: MED17 (invitrogen PA5-30314)


title: MDA-MB-231-BrM3, shCtrl, Replicate 1

description: TruSeq stranded RNA-seq


title: primary cervical cancer-RR_2


title: shMED30_2

data_processing:
Following sequencing, quality control with FastQC and trimming of adaptor sequence and poly-A tails with Trim Galore, reads were mapped and assigned to the human transcripts using HISAT2. The counts file was generated by “featureCounts” on Galaxy (usegalaxy.org) with build-in genome hg38. Differential expression gene (DEG) analysis was performed using the DESeq2 package in Galaxy
Assembly: hg38
Supplementary files format and content: gene expression alteration for whole transcriptiome calculated by Deseq2.

extract_protocol:
RNA was extracted by Trizol (Life Technologies) RNA concentration and quality was quantified by Qubit and Agilent 2100 Bioanalyzer system, respectively.
Libraries were generated using illunima PolyA RNA library kit and sequenced by HiSeq4000 with single-end reads or NovaSeq 6000 with 100 bp paired-end reads. Each condition contains two replicates.

value: MED30 knockdown


description:
Library name: Splenic NK cells, CD27+/CD27b-, Wild-type, replicate 2
WT2_2

value: Wild-type


description:
Library name: Splenic NK cells, CD27-/CD27b-, Wild-type, replicate 2
WT2_3


title: primary cervical cancer-RR_1


title: Tet-on_Med30_73A74A_1

description: Med30wtHA_7374A[Normalized_counts].tabular.txt

value: MIA PaCa-2

value: Dox-induced Med30_73A74A

value: Dox


title: Tet-off_Med30_73A74A_2

value: human pancreatic cancer

value: non-Dox


description:
Library name: Splenic NK cells, CD27+/CD27b+, Wild-type, replicate 2
WT2_1


title: shMED20_2

value: MED20 knockdown


description:
Library name: Splenic NK cells, CD27-/CD27b+, Wild-type, replicate 2
WT2_0


title: shMED20_1

description: DESeq2_result_siMed20_vs_siCtrl].tabular.txt


title: shMED30_1

description: DESeq2_result_siMed30_vs_siCtrl].tabular.txt


title: Tet-off_Med30_73A74A_1

description: Med30wtHA_7374A[DESeq2_result].tabular.txt


description:
Library name: Splenic NK cells, CD27+/CD27b-, KO, replicate 1
KO1_2

value: NK-cell Kcnj8 KO


title: Tet-on_Med30WT-HA_2

value: Dox-induced Med30WT-HA


title: shMED1_2

value: MED1 knockdown


description:
Library name: Splenic NK cells, CD27+/CD27b-, Wild-type, replicate 1
WT1_2


title: shMED1_1

description: DESeq2_result_siMed1_vs_siCtrl.tabular.txt


title: Tet-on_Med30_73A74A_2


description:
Library name: Splenic NK cells, CD27-/CD27b-, Wild-type, replicate 1
WT1_3


description:
Library name: Splenic NK cells, CD27+/CD27b+, Wild-type, replicate 1
WT1_1


title: Tet-off_Med30WT-HA_2


title: CnKO_12h

city: Suita

first: Daisuke

last: Motooka

address: Yamadaoka

institute: Osaka University

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.1.1 in combination with Bowtie2.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 100000000.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Bone marrow

growth_protocol: For obtaining bone marrow-derived dendritic cells, mouse bone marrow cells were cultured in RPMI1640 medium containing FBS and GM-CSF for 15 days.

extract_protocol:
RNA was harvested using QIAzol Lysis Reagent (Qiagen).
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit.

treatment_protocol: Bone marrow-derived dendritic cells were stimulated with LAM for 0, 2, 4, 8, or 12 hours

value: Bone marrow-derived dendritic cells

value: calcineurin-deficient

value: LAM

tag: time point


title: shCtl_2

value: WT


title: Tet-off_Med30WT-HA_1


title: WT_12h

value: wild type


title: shCtl_1


title: human_lymph_node_EXP505

city: Seattle

first: Peiyao

middle: A

last: Zhao

state: WA

address: 615 Westlake Ave N

institute: Allen Institute

scan_protocol: MERSCOPE was used to image target RNA positions and cell boundaries. Proprietary software was used to decode and return RNA positions along with raw images of cell nucleus and boundary stainings.

data_processing: Cell segmentation was performed on merFISH instrument using CellPose algorithm with cell-boundary stain 3 staining as input. Cell type inference and microenvironment zone delineation were performed using SPARROW (Zhao et al., 2024).

source_name: lymph node

extract_protocol: 5 um sections were cut from human tonsil and lymph node Formalin-Fixed Paraffin-Embedded (FFPE) blocks. Sections were floated in an RNAseq free, 41°C water bath and adhered to proprietary MERSCOPE slides. Sectioned tonsil and lymph node samples were processed in accordance with the Vizgen Formalin-Fixed Paraffin-Embedded Tissue Sample preparation protocol.

value: lymph node

tag: tissue type

value: FFPE block


title: iTDP#2-C:HB9::GFP

city: Taipei

first: Yi-Ying

last: Wu

address: No. 128, Sec. 2, Academia Road, Nankang

department: ICOB

country: Taiwan

institute: Academia Sinica

description: noncoding and coding gene expression data from iPSC derived motor neuron

hyb_protocol: 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scaned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: HB9::GFP+ motor neuron from iTDP#2-C

label_protocol: cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit.

growth_protocol: iPSCs induced with MN basal medium for the first 6 days, cells were supplied with SB431542 ,DMH1, and CHIR99021 fro another 6 days. Cells were supplemented with retinoic acid and purmorphamine for another 6 days.

extract_protocol: Total RNA were extracted from cells with Trizol.

treatment_protocol: The MN were dissociated with Dispase and sorted the GFP+ cells for RNA extraction

value: isogenic ALS-iPSC derived motor neuron


title: iTDP#3-C:HB9::GFP

source_name: HB9::GFP+ motor neuron from iTDP#3-C


title: iTDP#2:HB9::GFP

source_name: HB9::GFP+ motor neuron from iTDP#2

value: ALS-iPSC derived motor neuron


title: CnKO_8h


title: WT_8h


city: New York

description:
Library name: Splenic NK cells, CD27-/CD27b+, Wild-type, replicate 1
WT1_0

value: Spleen

value: NK cells

value: Wild-type


title: iTDP#3:HB9::GFP

source_name: HB9::GFP+ motor neuron from iTDP#3


title: Tet-on_shMed30_1

value: MIA PaCa-2

value: human pancreatic cancer

value: Dox-induced shMED30

value: Dox


title: rnaseq_lncRNA_ siRNA_rep3

first: Lu

last: Zang

address: No.197, Ruijin 2nd rd. Shanghai, China

department: Department of General Surgery

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description: processed data file: mRNA_Expression_Profiling_FPKM.xlsx

data_processing:
RNA-seq:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
The high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
CUT&Tag:
Paired-end raw reads were aligned to hg19 using Bowtie2 (v2.3.0).
Next, filtering alignment reads with sambamba (v0.7.1) and samtools (v1.9), and MACS2 (v2.2.6) was used for calling peaks with cut off FDR (q-value) at 0.05.
Tracks were generated by deepTools (v3.3.0) Bamcoverage with normalized counts as bins per million (BPM) and visualized with IGV.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene FPKM for every gene and every sample
Supplementary_files_format_and_content: bigWig file of each sample

source_name: rnaseq_lncRNA_ siRNA

growth_protocol: The human MGC803 gastric cancer cell were cultured in RPMI-1640 medium (Basalmedia, Shanghai, China) supplemented with 10 % fetal bovine serum (Sigma-Aldrich, USA) at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Life Technologies, Carlsbad, CA, USA). Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). These libraries were sequenced on an Illumina HiSeq 4000 sequencer (Illumina, USA) and 150 bp paired-end reads were generated according to the instructions of manufacturer.

treatment_protocol: The lncRNA LOC105378662 siRNA were introduced into the MGC803 cells, while nonspecific siRNA was used as negative controls.

value: MGC803 cells

value: human gastric cancer cells


title: human_lymph_node_EXP621


title: CnKO_4h

value: Bone marrow-derived dendritic cells

value: calcineurin-deficient


title: rnaseq_lncRNA_ siRNA_rep1


title: Tet-on_Med30WT-HA_1

description: Med30wtHA[Normalized_counts].tabular.txt

value: Dox-induced Med30WT-HA


title: WT_4h

value: wild type

value: LAM


title: rnaseq_lncRNA_ siRNA_rep2


title: human_tonsil_EXP558

source_name: tonsil

value: tonsil

value: FFPE block


title: Tet-on_shMed30_2


title: Tet-off_shMed30_1

value: non-Dox


title: rnaseq_control_ siRNA_rep2

source_name: rnaseq_control_ siRNA

value: control siRNA


title: human_tonsil_EXP501


title: rnaseq_control_ siRNA_rep3


title: human_tonsil_EXP409


title: shMed30_2_PRO

library_source: other

data_processing:
Data were aligned to human genome hg38 and Drosophila genome dm3 by Bowtie2. Gene expression counts were calculated by analyzeRepeats.pl (http://homer.ucsd.edu/homer/ngs/analyzeRNA.html), and subjected to Deseq2 analysis for identifying different expressed genes and size factor.
Assembly: hg38
Supplementary files format and content: human and Drosophila reads for each sample
Library strategy: PRO-seq

molecule: other

extract_protocol:
For nuclei isolation, cells were incubated with swelling buffer (10 mM Tris-Cl pH 7.5, 2 mM MgCl2 and 3 mM CaCl2) for 5 min on ice and then incubated with lysis buffer (swelling buffer with 0.5% NP-40 and 10% glycerol) for 5 min on ice, before being re-suspended in 100 μl of freezing buffer (50 mM Tris-Cl pH 8.0, 40% glycerol, 5 mM MgCl2 and 0.1 mM EDTA).
For the run-on assay, an equal volume of reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 300 mM KCl, 1 mM dithiothreitol, 20 units of SUPERase•In, 1% sarkosyl, and 500 μM ATP, GTP, bio-UTP and bio-CTP) was added into each sample before incubation at 30 °C for 5 min. The nuclear run-on RNA was then extracted with TRIzol LS reagent (10296010, Invitrogen) and subjected to hydrolysis, buffer exchange and purification by streptavidin beads (88816, Thermo Fisher). Purified RNA was treated with PNK before being used for complementary DNA synthesis by using the NEBNext Multiplex Small RNA Library Prep Set for Illumina Kit (E7300S, NEB). Obtained complementary DNA template was amplified by PCR using the Phusion High-Fidelity enzyme (M0530L, NEB) for deep sequencing.


title: WT_2h


title: CnKO_2h


title: rnaseq_control_ siRNA_rep1


title: RNA Caenorhabditis elegans-cadmium exposure-rep3

first: Panpan

last: Wang

address: 郑州市高新区科学大道100号郑州大学

institute: 郑州大学

data_processing:
After quality control by FastQC (0.11.9) and discarding 3’ and 5’ adapter by Cutadapt (3.4) and as well as short fragments (≤20bp) in reads, the trimmed data was aligned to reference genome (WBcel235) by Hisat2 (2.2.1) and then determined whether to use its results for further analysis according to the quality. The StringTie (2.1.5) software was applied to estimate transcription abundance and get the count data of genes and transcripts. The Fragments per kilobase of transcript per million mapped reads (FPKM) in gene and transcript level was calculated by “Ballgown” of the R package; while the average FPKM of gene and transcript in treat or control group less than 0.1 was excluded. After exclusion, the FPKM value in gene level was used to conduct the spearman correlation analysis for validation of the samplesconcordance, which the spearman correlation should greater than 0.9, according to the standard of ENCODE (https://www.encodeproject.org). Then, the count data of genes and transcripts were employed to explore the differentially expressed genes (DEGs) and differentially expressed transcripts using R package “DESeq2”, with the standards of P < 0.05 and |log2FC| > 0.585. According to the file of gene transfer format (Caenorhabditis_elegans.WBcel235.103.gtf, GTF file, http://www.ensembl.org/), the protein-coding RNA (mRNA) and lncRNA were identified. CircRNAs were identified and quantitated by the software of bowtie2 (2.4.2) and find_circ (1.2). Count data of circRNA were used to perform differentially expressed analysis for circRNA using “edgeR”of R package with the standards of P < 0.05 and |log2FC| > 0.585. The differentially expressed mRNAs (DEmRNAs), lncRNA (DElncRNAs) and circRNAs (DEcircRNAs) were prepared for further analysis.
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include count, FPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: whole individual

extract_protocol:
For per 50-100mg tissue sample, 1ml TRI REAGENT was added and an electric homogenizer used to mix it. After that, the sample was incubated for 5 minutes at 15 to 30℃ to completely dissociate the nucleic acid protein complex. Add 0.2ml chloroform to 0.2ml chloroform was added in per 1ml mixture, and close the tube cap tightly. After shaking the tube vigorously by hand for 15 seconds, it was incubated at 15 to 30℃ for 2 to 3 minutes. Centrifuge at 12000xg for 15 minutes at 4℃. After that, the mixture will be divided into the lower red phenol-chloroform phase, the middle layer and the upper colorless water phase. The RNA is all distributed in the water phase. The volume of the water phase is approximately 60% of the TRI REAGENT reagent added during the homogenization. Transfer the aqueous phase to a new centrifuge tube. The aqueous phase is mixed with 0.5ml isopropanol to precipitate the RNA. After mixing, it was incubated at 15 to 30°C for 10 minutes, and centrifuged at 12000xg at 4℃ for 10 minutes. Remove the supernatant, and add at least 1ml 75% ethanol to every 1ml mixture to wash the RNA precipitate. After shaking, centrifuge at 7500xg at 4℃ for 5 minutes. Remove the ethanol solution and dry the RNA pellet in the air for 5-10 minutes. When dissolving RNA, add RNase-free water and pipe repeatedly with a gun several times, and then incubate at 55 to 60°C for 10 minutes. The obtained RNA solution was stored at -70℃.
1~2 μg total RNA of C. elegans was roughly extracted in each sample and prepared for library construction. The integrity of the total RNA of the samples was determined by agarose gel electrophoresis, and quantification and further quality control were performed using NanoDrop® (ND-1000, Thermo-Fisher, USA). The total RNA was firstly enriched by NEB Next® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Netherlands); and then, the library was constructed by using of KAPA stranded RNA-Seq library prep kit (Illumina, USA). Bioanalyzer (G2938C, Agilent, USA) was applied to control the quality of the library. The library was degraded to single-strand DNA (ssDNA) by 0.1mol/L NaOH and diluted to 8 pmol/L. Subsequently, they were conducted in situ amplification by NovaSeq 6000 S4 reagent kit (300 cycles) (15057934, illumina, USA). The product was sequenced by Illumina NovaSeq 6000.

value: cadmium


title: WT_0h

value: Untreated


title: Ctl_2_PRO

value: MIA PaCa-2


title: CnKO_0h


title: Tet-off_shMed30_2

value: human pancreatic cancer


title: Ctl_1_PRO

value: Dox-induced shMED30


title: paf1△ yeast, replicate 2

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

institute: University of Alabama at Birmingham

description: PAFB

data_processing:
After sequencing, bcl2fastq software (version 2.20.00) was used for base-calling the reads.
Quality control of reads was performed with FastQC (version 0.11.7).
Deduplication of reads was performed based on the UMI sequence with fqtrim (version 0.9.7) and the "-C" option.
Using cutadapt (version 3.4), the 5' adapter (5'-AGNNNNNNNNTG-3') was removed from reads with the "-g -no-indels" parameters.
Cutadapt (version 3.4) was used to removed the 3' adapter sequence (5'-CTGTAGGCACCAT-3') with the parameters "-a -no-indels".
Reads were aligned to the Saccharomyces cerevisiae genome with STAR (version 2.7.1a). The STAR alignIntronMax parameter was set to 1.
SAMtools (version 1.6) was used to sort and index BAM files.
Files were converted from BAM to BED format using BEDTools (version 2.28.0).
Genome coverage files were generated using BEDTools (version 2.28.0) with the genomecov function and parameters "-strand" and "+strand"
Data processing and visualization was performed using R (version 4.3.2) and RStudio (2024.04.1+748).
Assembly: S. cerevisiae R64-1-1
Supplementary files format and content: Three processed data files are included in a .csv format. For all three files, the content is organized in the same way. The header/column names specify which strain and replicate that the values in the table represent.

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: All strains of yeast included in this study were grown at 30ºC with nutation.

extract_protocol:
Extraction methods were exactly the same as described in previous publications from our lab. To summarize, yeast cells were rapidly harvested via filtration and lysed under cryogenic conditions. Pol I was isolated by immunoprecipitation. Finally, a total RNA extraction was performed with an acidic phenol/chloroform extraction.
NET-seq libraries were constructed exactly as described in previous publications by our lab. In summary, after the phenol/chloroform extraction, a DNA linker containing a UMI sequence was ligated onto the 3' end of resulting RNAs. Next, cDNAs were synthesized via reverse transcription. Finally, cDNA was circularized and amplified. Resulting libraries were purified with PCRClean DX beads and reads were sequenced.

value: yeast cells


title: paf1△ yeast, replicate 1

description: PAFA


title: ATCC.K562

city: Charlestown

first: Timothy

last: Graubert

state: Massachusetts

address: 149, 13th Street, Navy Yard

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
Fastp version 0.20.0 was invoked with default parameters to trim adapter reads.
RSEM version 1.3.1 using Bowtie1 with parameters --bowtie-m 100, --bowtie-chunkmbs 500, --calc-ci --output-genome-bam was invoked to align the reads to the transcriptome.
Aligned reads were filtered by requiring splice junction overhangs of at least 6 nucleotides. Reads with MAPQ scores of 0 where removed.
Unaligned reads from RSEM were mapped using Tophat v2.1.1 to the splice junctions with arguments --bowtie1 --read-mismatches 2 --read-edit-distance 2 --no-mixed --no-discordant --min-anchor-length 6 --splice-mismatches 0 --min-intron-length 10 --max-intron-length 1000000 --min-isoform-fraction 0.0 --no-novel-juncs --no-novel-indels --raw-juncs
Aligned reads from Tophat again were subject to filteration with splice junction overhangs of atleast 6 nucleotides as well as reads with MAPQ scores of 0
Aligned and subsequently filtered reads from RSEM and Tophat were merged for the final bam file
MISO v2.0 output was used to derive percent splice in (PSI) for alternative isoforms.
Assembly: Homo_sapiens.GRCh37.87 was used as reference build
Supplementary files format and content: Tab limited text files with Percent Spliced In (PSI) for isoform ratios

growth_protocol: K562 cell lines were cultured in IMDM medium. Media were supplemented with 10% fetal bovine serum, 5000 IU Penicillin/Streptomycin, and glutamate.

extract_protocol:
RNA was extracted from K562 cells using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). Samples SRSF2.P95R.Clone3.Batch2 and K562.Batch2 were extracted and sequenced as a different batch on different days than the rest of the cohort.
Poly(A)-selected, unstranded Illumina sequencing libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA). 150 million 150 bp paired-end reads per sample were sequenced using the NovaSeq 6000 (Illumina San Diego, CA).

treatment_protocol: SRSF2 P95H/L/R mutations were introduced into the endogenous locus by homology-directed CRISPR/Cas9 editing. Clonal lines were expanded by limiting dilution and confirmed to harbor the desired substitution and zygosity by amplicon-based next-generation sequencing. Matching clones with unedited SRSF2 were selected from the same population and used as wild type controls.

value: Chronic Myelogenous Leukaemia

value: No Treatment (Wild Type)


title: RNA Caenorhabditis elegans-cadmium exposure-rep1

address: 郑州市高新区科学大道100号郑州大学


title: RNA Caenorhabditis elegans-control-rep3

address: 郑州市高新区科学大道100号郑州大学

value: untreated


title: U2af1.S34F.Clone33

data_processing:
fastp version 0.20.0 was invoked with default parameters to trim adapter reads
RSEM version 1.3.1 using Bowtie1 with parameters --bowtie-m 100, --bowtie-chunkmbs 500, --calc-ci --output-genome-bam was invoked to align the reads to the transcriptome
Aligned reads were subject to filtered with splice junction overhangs of atleast 6 nucleotides as well as reads with MAPQ scores of 0
Unaligned reads from RSEM were used to map using Tophat v2.1.1 with arguments --bowtie1 --read-mismatches 2 --read-edit-distance 2 --no-mixed --no-discordant --min-anchor-length 6 --splice-mismatches 0 --min-intron-length 10 --max-intron-length 1000000 --min-isoform-fraction 0.0 --no-novel-juncs --no-novel-indels --raw-juncs on the splice junction file
Aligned reads from Tophat again were subject to filteration with splice junction overhangs of atleast 6 nucleotides as well as reads with MAPQ scores of 0
Aligned reads from RSEM and Tophat were merged
Isoform ratios were calculated using MISO v2.0
Assembly: Homo_sapiens.GRCh37.87 was used as reference build
Supplementary files format and content: Tab delimited format evaluated for Percent Splice In of alternative MISO isoforms.

growth_protocol: Clones were cultured in complete media (IMDM+10%FBS+1X Glutamax+1%Pen/Strep) at a density of 1 X 105 cells/ml with media changes every two days.

extract_protocol:
RNA was extracted from the cell lines using RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion)
Library was prepared as per manufacturer's guidelines using Kapa mRNA Hyper Prep Kit (polyA selection) from Roche

value: CRISPR targeted mutation


title: cdc73△ yeast, replicate 2


title: cdc73△ yeast, replicate 1


title: K562.Batch2


title: U2af1.S34F.Clone62


title: RNA Caenorhabditis elegans-control-rep2

address: 郑州市高新区科学大道100号郑州大学


title: SRSF2.P95R.Clone3.Batch2


title: RNA Caenorhabditis elegans-control-rep1

address: 郑州市高新区科学大道100号郑州大学


title: shMed30_1_PRO

source_name: MIA PaCa-2

value: Dox


title: WT yeast, replicate 2

description: WTB

value: WT


title: U2af1.S34.Clone25


title: U2af1.S34Y.Clone64


title: DescendantOfFounderB_H11_Round30

first: Chiara

last: Furusawa

state: Osaka

address: Furuedai

institute: RIKEN Quantitative Biology Center

description: Transcriptome of E. coli at exponential growth phase

hyb_protocol: Microarray experiment was performed using a custom-designed Agilent 8 × 60 K array (E.coli_K12_Expression_Ver.1), which was designed for the E. coli W3110 strain comprising 12 probes for each gene. The Cy3-labelled cRNA (600 ng) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent according to the manufacturer's instructions. Subsequently, 25 ul of 2x GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to the custom-designed arrays, for 17 hours while rotating at 10 rpm at 65°C in a hybridization oven (Agilent). The hybridized microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: The hybridixed microarrays were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (AgilentG3_GX_1Color, Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The microarray images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: ExternalFullGEML_043017_D_F_20120907) to obtain background-subtracted and spatially-detrended Processed Signal intensities. Expression level was calculated by median value of all probes corresponding to each ORF.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Isolate of MA experiment, Round 30, Descendant of Founder B, H11

label_protocol: The purified total RNA samples (100 ng) were labeled with Cyanine3 (Cy3) using the Low Input Quick Amp WT labeling kit (Agilent Technologies) according to the manufacture's instruction. The Cy3-labeled cRNA samples were quality-checked for amount (>5 µg) and specific activity (>25 pmol/µg) using NanoDrop ND-2000 (Thermo Scientific).

growth_protocol: A mutator strain of E. coli (MG1655, delta-dnaQ::kan) was used to conduct mutation accumulation (MA) experiments. Two independent colonies were used as founder strains, designated as founder A and B, respectively. Three independent MA lineages were established for each founder. The MA experiments were conducted for each lineage by propagating randomly chosen single colonies to fresh LB agar plates every day for 30 rounds (1 round/day). The plates were incubated at 32°C until next round. The founder strains and their descendants at round 10 and 30 were stored at –80°C until transcriptome analysis.

extract_protocol: An equal volume of ice-cold ethanol containing 10% (w/v) phenol was added directly to the exponentially growing cultures to stabilize cellular RNA. The cells were harvested by centrifugation at 20,000 × g at 4°C for 5 min. The pellets were stored at –80°C prior to RNA extraction. Total RNA was extracted using the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion for 15 min. The purified RNA samples were stored at – 80°C before microarray experiments. The quality of the purified RNA samples was quantified using Agilent 2100 Bioanalyzer with an RNA 6000 Nano kit (Agilent Technologies). The purified RNA samples were stored at −80°C prior to labeling.

treatment_protocol: Cells were inoculated into 96-well microplates containing 200 µl/well of LB and grown at 32°C  at 800 rpm. Cell density of the cultures was monitored during cultivation by a microplate reader. Cell cultures were sampled at exponential phase, where OD600 reached in the 0.072–0.135 range.

tag: genetic background

value: MG1655 delta-dnaQ::kan

tag: founder/descendant in ma

value: Descendant of Founder B

tag: ma lineage

tag: round of ma

tag: bio^sample


title: SRSF2.P95R.Clone69

tag: cell line

tag: cell type


title: SRSF2.P95R.Clone63

tag: genotype

tag: treatment


title: U2af1.S34F.Clone3


title: WT  yeast, replicate 1

description: WTA


title: Mussel gill tissues, long time period, deep-sea, 10 days, rep4

city: Qingdao

first: Luyang

last: Sun

state: Shandong

address: Songling Road 189#

department: Single-Cell Center

institute: Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences

description:
musselgilltissuseinsitucollectedfromcoldseepinlong-termreplicate4
LT-4

data_processing:
Raw reads were conducted quality control by fastp version 0.12.4 with default parameters.
de novo assembly of the reference transcriptome using Trinity version 2.13.260 with default parameters, except for both “--min_kmer_cov” and “--min_glue” of 3 options to remove the low abundance transcripts. These transcripts were then clustered to elimination redundancy using CD-HIT version 4.8.1 with sequence identity threshold of 0.9, resulting in the generation of the reference transcriptome, named unigenes.
The clean data were aligned to unigenes using bowtie version 1.3.171, abundance estimation was quantified by Salmon version 1.7.0, and the genes expression levels were measured in transcripts per million (TPM).
Assembly: de novo assembly ; unigenes.fasta
Supplementary files format and content: tab-delimied text files include Length, EffectiveLength, TPM, and NumReads for each gene of each Sample
Supplementary files format and content: tab-delimied text files include TPM values for each Sample

organism: Mytilus galloprovincialis

source_name: Gill tissues

extract_protocol:
Total RNA from gill tissues was extracted using TRIzol and sent to Novogene (Beijing, China) for sequencing. RNA integrity was assessed using the Fragment Analyzer 5400 (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: tissue

value: Gill tissues

value: not collected

value: Wildtype

value: Cold seep in situ exposure, 10 days


title: U2af1.S34.Clone38


title: DescendantOfFounderB_H08_Round30

source_name: Isolate of MA experiment, Round 30, Descendant of Founder B, H08


title: SRSF2.P95L.Clone52


title: Mussel gill tissues, long time period, deep-sea, 10 days, rep3

description:
musselgilltissuseinsitucollectedfromcoldseepinlong-termreplicate3
LT-3


title: U2af1.S34.Clone34


title: SRSF2.P95L.Clone25


title: SRSF2.P95R.Clone72


title: DescendantOfFounderA_H04_Round30

source_name: Isolate of MA experiment, Round 30, Descendant of Founder A, H04

value: Descendant of Founder A


title: Mussel gill tissues, long time period, deep-sea, 10 days, rep2

description:
musselgilltissuseinsitucollectedfromcoldseepinlong-termreplicate2
LT-2


title: U2af1.S34.Clone28


title: SRSF2.P95L.Clone17


title: DescendantOfFounderA_H06_Round30

source_name: Isolate of MA experiment, Round 30, Descendant of Founder A, H06


title: SRSF2.P95L.Clone11


title: Mussel gill tissues, short time period, deep-sea, 6 hours, rep5

description:
musselgilltissuseinsitucollectedfromcoldseepinshort-termreplicate5
ST-5

value: Cold seep in situ exposure, 6 hours


title: DescendantOfFounderB_H11_Round10

source_name: Isolate of MA experiment, Round 10, Descendant of Founder B, H11


title: U2af1.S34Y.Clone26


title: Mussel gill tissues, long time period, deep-sea, 10 days, rep5

description:
musselgilltissuseinsitucollectedfromcoldseepinlong-termreplicate5
LT-5


title: Mussel gill tissues, long time period, deep-sea, 10 days, rep1

description:
musselgilltissuseinsitucollectedfromcoldseepinlong-termreplicate1
LT-1


title: Mussel gill tissues, short time period, deep-sea, 6 hours, rep4

description:
musselgilltissuseinsitucollectedfromcoldseepinshort-termreplicate4
ST-4


title: SRSF2.P95.Clone79


title: U2af1.Q157R.Clone20


title: DescendantOfFounderB_H10_Round30

source_name: Isolate of MA experiment, Round 30, Descendant of Founder B, H10


title: Mussel gill tissues, short time period, deep-sea, 6 hours, rep3

description:
musselgilltissuseinsitucollectedfromcoldseepinshort-termreplicate3
ST-3


title: DescendantOfFounderA_H03_Round30

source_name: Isolate of MA experiment, Round 30, Descendant of Founder A, H03


title: DescendantOfFounderA_H06_Round10

source_name: Isolate of MA experiment, Round 10, Descendant of Founder A, H06


title: Mussel gill tissues, short time period, deep-sea, 6 hours, rep2

description:
musselgilltissuseinsitucollectedfromcoldseepinshort-termreplicate2
ST-2


title: U2af1.Q157.Clone11


title: U2af1.S34Y.Clone56


title: Mussel gill tissues, short time period, deep-sea, 6 hours, rep1

description:
musselgilltissuseinsitucollectedfromcoldseepinshort-termreplicate1
ST-1


title: SRSF2.P95H.Clone29


title: RNA Caenorhabditis elegans-cadmium exposure-rep2

city: Zhengzhou

address: 郑州市高新区科学大道100号郑州大学

value: wild type

value: cadmium


title: U2af1.Q157R.Clone21


title: SRSF2.P95.Clone40


title: DescendantOfFounderA_H03_Round10

source_name: Isolate of MA experiment, Round 10, Descendant of Founder A, H03


title: U2af1.Q157R.Clone6


title: U2af1.Q157R.Clone1


title: DescendantOfFounderB_H08_Round10

source_name: Isolate of MA experiment, Round 10, Descendant of Founder B, H08


title: DescendantOfFounderB_H10_Round10

source_name: Isolate of MA experiment, Round 10, Descendant of Founder B, H10


title: SRSF2.P95L.Clone19


title: SRSF2.P95R.Clone78


title: Mussel gill tissues, control, onboard, 6 hours, rep4

description:
musselgilltissusecollectedonboardreplicate4
Con-4

value: Onboard rearing, 6 hours


title: Mussel gill tissues, control, onboard, 6 hours, rep3

description:
musselgilltissusecollectedonboardreplicate3
Con-3


title: SRSF2.P95.Clone18

value: Chronic Myelogenous Leukaemia


title: FounderB_Round0_rep1

source_name: Founder B of MA experiment, biological replicate 1

value: Founder B

value: AncHb


title: FounderB_Round0_rep2

source_name: Founder B of MA experiment, biological replicate 2


title: U2af1.Q157P.Clone7

value: CRISPR targeted mutation


title: tonsillar cells and PBMCs

city: Guangzhou

first: Yifang

last: Gao

address: NO.58 zhongshan 2nd road, YueXiu district

institute: sun yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 40%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each cell

source_name: tonsillar cells and PBMCs

extract_protocol:
N/A
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.One sequenced sample is a mix of four experimental samples.

treatment_protocol: IgAN patient Post Tonsillectomy

value: mixed sample (non-demultiplexed)


title: U2af1.Q157R.Clone17


title: cuttag_lncRNA_ siRNA_BRD7Ab

data_processing:
library strategy: CUT&TAG
RNA-seq:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
The high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
CUT&Tag:
Paired-end raw reads were aligned to hg19 using Bowtie2 (v2.3.0).
Next, filtering alignment reads with sambamba (v0.7.1) and samtools (v1.9), and MACS2 (v2.2.6) was used for calling peaks with cut off FDR (q-value) at 0.05.
Tracks were generated by deepTools (v3.3.0) Bamcoverage with normalized counts as bins per million (BPM) and visualized with IGV.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene FPKM for every gene and every sample
Supplementary_files_format_and_content: bigWig file of each sample

source_name: cuttag_lncRNA_ siRNA_BRD7Ab

extract_protocol:
Genomic DNA after immunoprecipitation was extracted by NovoNGS CUT&Tag High-Sensitivity Kit (Novoprotein, N259-YH01, Shanghai, China) following manufacturer's protocol. 100,000 cells were used for CUT&Tag assay. After binding with Concanavalin A beads, cells were incubated with primary antibody targeting BRD7 (abeam, ab56036). Samples were then incubated with Goat anti-Rabbit antibody, CUT&Tag Assembled pA-Tn5 Transposomes. After tagmentation, released DNA was extracted by TIANSeq Size Selection DNA Beads (TIANGEN, NG316, China).
DNA library was perpared by illumina primers provided with NovoNGS CUT&Tag High-Sensitivity Kit.

value: MGC803 cells

value: human gastric cancer cells

tag: cut&tag ab

value: BRD7 (abcam, ab56036)


title: FounderA_Round0_rep2

source_name: Founder A of MA experiment, biological replicate 2

value: MG1655 delta-dnaQ::kan

value: Founder A

value: AncHa


title: DescendantOfFounderA_H04_Round10

source_name: Isolate of MA experiment, Round 10, Descendant of Founder A, H04


title: Mussel gill tissues, control, onboard, 6 hours, rep2

description:
musselgilltissusecollectedonboardreplicate2
Con-2

source_name: Gill tissues

value: Gill tissues

value: not collected

value: Wildtype


title: U2af1.Q157.Clone3


title: cuttag_control_ siRNA_BRD7Ab

source_name: cuttag_control_ siRNA_BRD7Ab

value: control siRNA


title: U2af1.Q157.Clone2


title: U2af1.Q157P.Clone1


title: Mussel gill tissues, control, onboard, 6 hours, rep5

description:
musselgilltissusecollectedonboardreplicate5
Con-5


title: Mussel gill tissues, control, onboard, 6 hours, rep1

description:
musselgilltissusecollectedonboardreplicate1
Con-1


title: EBV(-) exosome Tx, rep5

status: Public on Nov 23 2024

city: Taoyuan

first: Tzu-Tung

last: Liu

address: Zhongda Rd,. Zhongli District

institute: National central university

description:
Library name: sample35
MD_LTT_DKDL202004129-1a-3_HHMHLDSXY_cell_11

data_processing:
Exosome-mediated effects on macrophages were evaluated using bulk RNA sequencing.
Quality control excluded genes detected in fewer than half of the samples with at least one UMI.  The expression matrix for the remaining cells was then normalized using the Relative Log Expression (RLE) method implemented in the DESeq2 R package (version 1.30.1)
Assembly: GRCh38
Supplementary files format and content: Matrix table with normalized counts for each gene of all individual cell

source_name: macrophage

extract_protocol:
Total RNA was extracted using Qiagen RNA purification kit  following manufacturer’s instructions.
QIAseq UPX 3' transcriptome kit (Qiagen, catalog# 333088) was used for library construction.

value: macrophage

tag: phenotype

value: EBV(-) exosome Tx, rep1


title: M2d, rep5

description:
Library name: sample33
MD_LTT_DKDL202004129-1a-3_HHMHLDSXY_cell_5


title: EBV(+) exosome Tx, rep5

description:
Library name: sample34
MD_LTT_DKDL202004129-1a-3_HHMHLDSXY_cell_6

value: EBV(+) exosome Tx


title: M2c, rep5

description:
Library name: sample32
MD_LTT_DKDL202004129-1a-3_HHMHLDSXY_cell_4


title: EnE, rep4

description:
Library name: sample28
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_64


title: M2a, rep4

description:
Library name: sample24
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_60


title: M1, rep4

description:
Library name: sample23
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_59


title: EpE, rep4

description:
Library name: sample27
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_63


title: M1, rep5

description:
Library name: sample30
MD_LTT_DKDL202004129-1a-3_HHMHLDSXY_cell_2


title: EBV(+) exosome Tx, rep3

description:
Library name: sample20
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_56


title: EBV(-) exosome Tx, rep3

description:
Library name: sample21
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_57


title: M0, rep4

description:
Library name: sample22
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_58


title: M0, rep5

description:
Library name: sample29
MD_LTT_DKDL202004129-1a-3_HHMHLDSXY_cell_1


title: M2d, rep4

description:
Library name: sample26
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_62


title: M2d, rep3

description:
Library name: sample19
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_55


title: M2c, rep3

description:
Library name: sample18
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_54


title: M2a, rep3

description:
Library name: sample17
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_53


title: M0, rep3

description:
Library name: sample15
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_51


title: M2c, rep4

description:
Library name: sample25
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_61


title: EBV(-) exosome Tx, rep2

description:
Library name: sample14
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_50


title: FounderA_Round0_rep1

description: Transcriptome of E. coli at exponential growth phase

source_name: Founder A of MA experiment, biological replicate 1


title: EBV(+) exosome Tx, rep2

description:
Library name: sample13
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_49


title: M2c, rep2

description:
Library name: sample11
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_47


title: M2a, rep2

description:
Library name: sample10
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_46


title: M1, rep3

description:
Library name: sample16
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_52


title: M2a, rep5

description:
Library name: sample31
MD_LTT_DKDL202004129-1a-3_HHMHLDSXY_cell_3


title: M2d, rep2

description:
Library name: sample12
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_48


title: M0, rep2

description:
Library name: sample8
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_44


title: EBV(+) exosome Tx, rep1

description:
Library name: sample6
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_42