title: TT3

city: nanchang

first: zhao

middle: hai

last: wang

state: jiangxi

address: zhimin dadao 1101

institute: jiangxi agricultural university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10

organism: Oryza sativa

source_name: rice

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
Approximately 5ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero Gold rRNA Removal Kit (Illumina, cat.MRZG12324, San Diego, USA). After removing ribosomal RNAs, the left RNAs were fragmented (NEBNext® Magnesium RNA Fragmentation Module, cat.E6150S, USA) into short fragments using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection (300-600bp) was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: rice

value: heat-tolerant line XN0437T

value: high night temperature stress


title: Mini_screen_Lu65_end_DMSO_rep1

status: Public on Feb 20 2023

type: SRA

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

country: USA

institute: NYU Grossman School of Medicine

library_source: genomic

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
20bp sgRNA sequence was extracted from each read.
Each 20bp sequence was aligned to the mini CRISPR library with Bowtie.
Count table was generated through counting the frequency of each sgRNA.
Supplementary files format and content: tab-delimited counts file
Library strategy: CRISPR screen

molecule: genomic DNA

organism: Homo sapiens

source_name: Human lung giant cell carcinoma cell line

extract_protocol:
Cells were lysed with Tris/SDS buffer supplemented with protease inhibitor, and DNA was precipitated with 40% isopropanol
Region contatining sgRNA sequence was amplified with two sequenctial PCR and final product was gel purified--focused CRISPR mini-library was recovered

tag: tissue

value: Lung

tag: genotype

value: Parental

tag: cell line

tag: treatment

value: DMSO

tag: duration

value: 10 doublings


title: IAD21

city: Shanghai

first: Wei

last: Liu

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

country: China

institute: Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Raw reads were filtered using FastQC and Trimmomatic. Then, aligned to the GRCh38 human genome assembly using STAR.
Gene expression levels were calculated in size factor. Annotations of exlRNA in the human genome were retrieved from the Ensembl (V96).
Feature selection was performed by R package boruta to find all relevant variables for machine learning.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized values for each sample

molecule: total RNA

source_name: Extracellular vesicles

extract_protocol:
EVs were purified from 0.5-1 mL serum using the exoRNeasy Midi kit (Qiagen; Cat#77144) according to the manufacturer’s instructions. For RNA extraction, EVs were lysed on column with 1 mL Trizol reagent (Invitrogen; Cat#15596026) and the RNA pellet was dissolved in 11 μL of deionized water treated with DEPC (diethylpyrocarbonate).
EV long RNA libraries were constructed using poly(A) independent extracellular RNA sequencing . Briefly, 1 ng RNA was reverse transcribed with random primer by SMART technology. cDNA was purified twice using Ampure XP beads (Beckman Coulter, Cat# A63881) and amplified with indexed primers. 200–500 base-paired PCR products were size-selected using Ampure XP beads.

value: Blood serum

tag: disease state

value: invasive adenocarcinoma


title: TT2


title: IAD20


title: IAD18


title: IAD22


title: TT1


title: IAD16


title: IAD17


title: IAD15


title: TC3

value: control


title: TC2


title: IAD13


title: IAD12


title: Mini_screen_KYSE520_start_rep2

source_name: Human esophageal adenocarcinoma cell line

value: Esophagus


title: Mini_screen_KYSE520_start_rep1


title: ST3

value: heat-sensitive line XN0437S


title: IAD11


title: TC1


title: Mini_screen_KYSE520_end_DMSO_rep2


title: IAD19


title: ST2


title: Mini_screen_KYSE520_end_DMSO_rep1


title: IAD8


title: IAD7


title: Mini_screen_Lu65_end_099_rep2

value: 10uM SHP099


title: Mini_screen_KYSE520_end_099_rep2


title: Mini_screen_Lu65_end_099_rep1


title: SC3


title: ST1


title: IAD4


title: IAD6


title: Mini_screen_KYSE520_end_099_rep1


title: IAD5


title: IAD2


title: IAD14


title: SC2


title: IAD1


title: Mini_screen_HCC827_start_rep2

source_name: Human lung adenocarcinoma cell line


title: MIA34

value: minimally invasive adenocarcinoma


title: Mini_screen_HCC827_start_rep1


title: IAD9


title: MIA33


title: IAD10


title: Mini_screen_HCC827_end_DMSO_rep2


title: Mini_screen_HCC827_end_DMSO_rep1


title: MIA29


title: Mini_screen_HCC827_end_099_rep2


title: IAD3


title: MIA27


title: MIA26


title: MIA28


title: MIA24


title: Mini_screen_H1975_start_rep2

source_name: Human non-small cell lung cancer cell line


title: MIA25


title: MIA22


title: MIA32


title: SC1


title: MIA23


title: Mini_screen_H1975_start_rep1


title: MIA21


title: MIA31


title: Mini_screen_HCC827_end_099_rep1


title: Mini_screen_H1975_end_DMSO_rep2


title: MIA30


title: 10 uM cadmium replicate 2

city: Aurora

first: Gregory

last: Wright

state: CO

address: 12800 East 19th Ave

institute: University of Colorado Anschutz Medical Campus

data_processing:
FASTQs were adaptor trimmed using Bbtools bbduk (v 38.87) using supplied adaptor reference file adaptors.fa with parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo
FASTQs were aligned to hg38 reference genome using Bowtie2 *v 2.3.4.1) sam files were converted to bam files and biological replicates were merged using samtools v. 1.8
bigwig files were generated for merged bam files using deeptools Bamcoverage
Peak calling performed using Epic2 v. 0.0.50 using default parameters with merged bam files as --treatment using --genome hg38
Assembly: hg38
Supplementary files format and content: bigwig files contain coverage tracks using  CPM
Supplementary files format and content: peak calling bed files for both control and cadmium treated samles
Library strategy: CUT&RUN

extract_protocol:
Epicypher CUT&RUN protocol (version 1.6, August 2020)
Illumina NEBNext Ultra II ChIP-Seq sample kit, according to the manufacturer’s protocol.

tag: cell type

value: breast

tag: chip antibody

value: cadmium


title: MIA20


title: blood_KD4_rep1

type: RNA

city: Suzhou

first: Yunjia

last: Tang

address: No 92, Zhongnan Street

institute: Children's Hospital of Soochow University

description: Neutrophilic gene expression in acute KD blood

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression (8*60 k) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, 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 by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent G2505C) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (version10.7.1.1, Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data.  Raw data were normalized in quantile algorithm with Genespring 13.0 (Agilent). Probes that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Peripheral Blood, KD4, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The total RNA was extracted using Total RNA Isolation Reagent (SuperfecTRI, Shanghai, China) according to the manufacturer’s instructions. It was quantified using a NanoDropTM 2000/2000C Spectrophotometer (Thermo, USA).

value: Kawasaki disease (KD)

value: whole blood

value: neutrophils


title: MIA19


title: blood_control3_rep1

description: Neutrophilic gene expression in healthy control blood

source_name: Peripheral Blood, control3, replicate 1

value: Healthy control


title: blood_control2_rep1

source_name: Peripheral Blood, control2, replicate 1


title: blood_KD3_rep1

source_name: Peripheral Blood, KD3, replicate 1


title: MIA18


title: blood_control1_rep1

source_name: Peripheral Blood, control1, replicate 1


title: 10 uM cadmium replicate 1


title: MIA16


title: MIA17


title: blood_KD2_rep1

source_name: Peripheral Blood, KD2, replicate 1


title: control biological replicate 2


title: Mini_screen_H1975_end_099_rep2

value: Lung


title: MIA15


title: Mini_screen_H1975_end_099_rep1

value: Parental


title: Mini_screen_H1975_end_DMSO_rep1

value: DMSO


title: blood_KD1_rep1

source_name: Peripheral Blood, KD1, replicate 1


title: MIA13


title: MIA14


title: control biological replicate 1


title: MIA12


title: MDA-MB-231 10 uM cadmium replicate 2

data_processing:
FASTQs were adaptor trimmed using Bbtools bbduk (v 38.87) using supplied adaptor reference file adaptors.fa with parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo
FASTQs were aligned to hg38 reference genome using hisat2 *v 2.1.0)
Sequence reads were assigned to genomic features using featureCounts (v 2.0.1) using ensemble_v105_hg38.gtf
Assembly: hg38
Supplementary files format and content: featureCounts output

extract_protocol:
Total RNA was extracted from cells using miRNeasy Mini Kit (Qiagen) following manufacturer's protocol includng the optional Dnase digest.
Universsal Plus mRNA-seq library preparation kit

value: breast cancer


title: Genomic_screen_MOLM13_start_rep2

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
20bp sgRNA sequence was extracted from each read.
Each 20bp sequence was aligned to the human TKOv3 CRISPR library with Bowtie.
Count table was generated through counting the frequency of each sgRNA.
Supplementary files format and content: tab-delimited counts file
Library strategy: CRISPR Screen

source_name: Huamn AML cell line

extract_protocol:
Cells were lysed with Tris/SDS buffer supplemented with protease inhibitor, and DNA was precipitated with 40% isopropanol
Region contatining sgRNA sequence was amplified with two sequenctial PCR and final product was gel purified--genomic library is recovered

value: AML

value: parental


title: MIA10

value: Blood serum


title: MDA-MB-231 10 uM cadmium replicate 1


title: Genomic_screen_MOLM13_end_099_rep2

value: 12 doublings


title: MIA7


title: MIA6


title: MIA9


title: MIA5


title: MDA-MB-231 control biological replicate 1


title: MIA4


title: PMAIonomycin_stimulated

city: Vancouver

first: Stuart

middle: E

last: Turvey

state: BC

address: 938 W 28th Ave

country: Canada

institute: BC Children's Hospital Research Institute

data_processing:
RNA was sequenced on the Illumina NextSeq 2000 with Paired-end (2 x 115bp)
R1 and R2 reads were filtered based on read length, quality, and highest single nucleotide frequency. R1 reads are annotated to identify cell labels, unique molecular identifiers, and filtered for >6 Poly(T) tail. Bowtie2 version 2.2.9 was used to map the R2 reads to the reference sequences
R1 and R2, with the same cell label, UMI sequence, and gene were collapsed into a single molecule
Putative cells were determined by considering all reads associated with Distribution-based error correction (DBEC)-adjusted molecules. The minimum second derivative along the cumulative reads curve is identified as the inflexion point, after which the cells are labelled as noise. Filtered putative reads that align to a sample tag sequence were used to identify sample labels for a cell
Labelled DBEC-adjusted molecule counts are present in a tab-delimited .txt format. Each file has a label for sample-specific cell labeling
Genome_build: Homo sapiens (UCSC hg19)
Supplementary_files_format_and_content: Raw counts are presented as tab delimited .txt files

source_name: PBMCs

growth_protocol: NFAT1 deficient patient PBMCs were isolated from whole blood and cultured in RPMI with 10% FBS overnight before stimulation

extract_protocol:
Cells from each donor were labelled with sample tags, washed with stain buffer and pooled together in cold sample buffer to obtain ~25,000 cells for each of the unstimulated and stimulated samples. Two nanowell cartridges were primed and loaded with the pooled samples for 15min at room temperature on the BD Rhapsody Express instrument. Cell capture beads were prepared and loaded onto the cartridge. The cartridge was washed, cells were lysed, and beads were retrieved with mRNA molecules attached to every bead.
The samples underwent reverse transcription and Exonuclease I treatment. cDNA was amplified using a custom immune panel via PCR. mRNA PCR products were separated from sample tag products with double-sided size selection using AMPure beads. Separated products were further amplified using PCR and then purified. PCR products were then PCR amplified using two index primers, one for unstimulated and one for stimulated. Libraries were diluted to 650pM and multiplexed for paired-end (2 x 115bp) sequencing on a NextSeq2000 Sequencing System (Illumina) at 200 cycles P3 for 1.1 billion reads.

treatment_protocol: Stimulated with PMA (50ngml) 1uM Ionomycin, or left untreated for 4 hours

tag: stimulation condition

value: Stimulated


title: MIA2


title: MIA1


title: MIA3


title: 231_10uMCd_2

description: 10 uM cadmium replicate 2

data_processing:
FASTQ files were run using ENCODE ATAC-seq pipeline 1.8.0
bam files generated for each replicate were merged using samtools merge
bigwig files were generated for merged bam files using deeptools Bamcoverage
Assembly: hg38
Supplementary files format and content: bigwig files contain coverage tracks using  CPM

extract_protocol: Active Motif: ATAC-Seq kit


title: MIA11


title: 231_10uMCd_1

description: 10 uM cadmium replicate 1


title: DPASEKO_48h_Rep1

city: Durham

first: Abani

last: Naik

state: North Carolina

address: 207 Research drive, Jones Bldg, Room 316

department: Immunology

institute: Duke University

data_processing:
Miseq software from Illumina was used to base calling and demultiplexing.
The sequences were then aligned to a reference library of TCRA gene segments from modified 129 mouse strain from IMGT using MixCR (Version 3.0.7).
The unique clones based on CDR2+FR3+CDR3 region from the recombined Tcra sequences were identified using parameter ‘-OassemblingFeatures=[CDR2+FR3+CDR3]’.
Clone sequences in human readable format were generated using mixcr -Xmx5G -Xms5G exportClones
Frequencies of unique rearrangements were calculated using vdjtools-1.2.1.Plots with TraV and TraJ segments were generated as .txt files using vdjtools-1.2.1.jar Convert -S mixcr
Assembly: Customized strain 129 V-alpha, V-delta, and J-alpha reference library.
Supplementary files format and content: CSV files with sequences, gene segment identities, and counts of unique Tcra clones. These .CSV files can be converted to heatmaps using gplots and RColorBRewer packages

organism: Mus musculus

source_name: pre-selection DP thymocytes

growth_protocol:
4-6 week old mice were injected i.p. with 1 mg Tamoxifen 48 hours prior to sacrifice. Thymocytes were harvested.
Total thymocytes were harvested from 4-6 week-old mice.

extract_protocol:
Trizol (Life Technologies) was used to extract total RNA from sorted pre-selection DP thymocytes.
Template-switch RACE was used to ligate adapaters to the 5' ends and amplify Tcra transcripts. Illumia adapters were added to the 5' template-switch oligo and the antisense Trac-specific primer.

treatment_protocol: Thymocytes were subjected to FACS. Sorting was performed on either the Astrios (Beckman Coulter), MoFlo XDP (Beckman Coulter), or FACSDiVa (Becton Dickinson). All samples are CD3e(-) DP thymocytes.

tag: strain

value: C57BL/6J with strain 129 TcrdCreER at Tcra-Tcrd loci. Also contains Rosa26ZsG/ZsG

value: Homozygous DPASEKO. TcrdCreER. Rosa26ZsG/+.

value: thumus

value: ZsGreen+ pre-selection DP thymocytes


title: DPASEKO_48h_Rep2


title: Unstimulated

value: Unstimulated


title: AIS34

value: adenocarcinoma in situ


title: WT_48h_Rep2

value: Homozygous WT. TcrdCreER. Rosa26ZsG/+.


title: 231_nocd_2

description: control biological replicate 2

value: breast

value: noen


title: AIS35


title: AIS36


title: AIS33


title: AIS32


title: Genomic_screen_MOLM13_end_DMSO_rep2


title: MDA-MB-231 control biological replicate 2


title: AIS31


title: WT_48h_Rep1


title: MIA8

value: minimally invasive adenocarcinoma


title: mRNA of IgAN3

city: Changsha

first: Hong

state: Hunan

address: Renmin Road 139#

department: Nephrology

institute: The Second Xiangya Hospital, Central South University

description:
GSE145652_mRNA_gene_expression.txt
IgAN_3 mRNA

data_processing:
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: FASTA file includes sequences for all MSTRG* gene IDs.
Supplementary_files_format_and_content: FPKM

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: IgAN

value: PBMCs


title: AIS30


title: AIS29


title: AIS28


title: AIS27


title: DPASEKO_24h_Rep1

growth_protocol:
4-6 week old mice were injected i.p. with 1 mg Tamoxifen 24 hours prior to sacrifice. Thymocytes were harvested.
Total thymocytes were harvested from 4-6 week-old mice.


title: AIS25


title: mRNA of IgAN1

description:
GSE145652_mRNA_gene_expression.txt
IgAN_1 mRNA


title: AIS26


title: 231_nocd_1

description: control biological replicate 1


title: mRNA of Control 3

description:
GSE145652_mRNA_gene_expression.txt
Crtl_3 mRNA

value: control


title: AIS24


title: AIS23


title: mRNA of IgAN2

description:
GSE145652_mRNA_gene_expression.txt
IgAN_2 mRNA


title: mRNA of Control 2

description:
GSE145652_mRNA_gene_expression.txt
Ctrl_2 mRNA


title: AIS22


title: WT_24h_Rep1


title: WT_24h_Rep2


title: DPASEKO_Steadystate_rep1

growth_protocol:
Thymocytes were harvested from 4-6 week-old mice.
Total thymocytes were harvested from 4-6 week-old mice.

value: pre-selection DP thymocytes


title: DPASEKO_steadystate_Rep2


title: AIS19

value: Blood serum


title: AIS20


title: AIS18


title: AIS17


title: DPASE KO_24h_Rep2


title: WT_Steadystate_Rep2


title: mRNA of Control 1

description:
GSE145652_mRNA_gene_expression.txt
Ctrl_1 mRNA


title: AIS16


title: WT_Steadystate_Rep1


title: AIS14


title: AIS15


title: SUP-M2 shGOLM1 replicate 2

city: shanghai

first: zhenguo

last: zi

state: shanghai

address: Building 5, 100 Banxia Road, Pudong New Area, Shanghai

institute: Shanghai Jiao Tong university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/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: mm10
Supplementary files format and content: tab-delimited text files include counts and FPKM values for each Sample

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

value: Anaplastic Large Cell Lymphoma Cell

value: GOLM1 knockout


title: SUP-M2 shGOLM1 replicate 1


title: SUP-M2 shscramble replicate 2


title: AIS13


title: AIS21


title: AIS10


title: WT_unstim_3

data_processing:
De-multiplexed read sequences were aligned to a reference sequence using RNA-Seq Alignment app (v1.1.1) on Illumina Basespace, using Spliced Transcripts Alignment to a Reference (STAR) aligner and Cufflinks 2 for assembly and estimation of gene expression.
Expression data was normalized to reads between samples using the edgeR package in R (R Foundation, Vienna, Austria).
Normalized counts were filtered to remove low counts using the filterByExpr function in edgeR. Principal component analysis (PCA) was done on log2(normalized counts+0.25) in R using the PCA function.
Differential expression between unstimulated and stimulated samples for all three STAT6-transduced Jurkat T cells was accomplished using Limma. Differentially expressed genes were defined as those with fold change (FC) greater than 1.25 and adjusted p-value less than 0.05.
Pathway analysis was done by first performing Gene Set Enrichment Analysis (GSEA) with 1000 permutations using the Molecular Signatures Database Hallmark module. Signal-to-noise ratio was used for gene ranking and the obtained NESs and P-values were further adjusted using the Benjamini-Hochberg method. Pathways with an adjusted P-value < 0.05 were considered significant. Leading edge genes from significant pathways between STAT6 WT and STAT6 c.1256A>G Jurkat were identified (no significantly upregulated pathways were identified between STAT6 Wild Type and STAT6 c.1144G>C). Expression levels of these genes were then determined in each of the three groups (Wild Type, c.1144G>C, c.1256A>G) under both stimulated and unstimulated conditions. Sample level enrichment analyses (SLEA) scores were computed as previously described(Kulpa et al., 2019). Briefly, z-scores were computed for gene sets of interest for each sample. The mean expression levels of significant genes were compared to the expression of 1000 random gene sets of the same size. The difference between observed and expected mean expression was then calculated and represented on heatmaps.
Assembly: Homo sapiens (UCSC hg19)
Supplementary files format and content: Processed counts are presented as .txt files

source_name: Jurkat

extract_protocol:
RNA was extracted in triplicate using a RNeasy Mini Plus Kit (Qiagen) according to manufacturer’s recommendations.
RNA was prepared following the standard protocol for the NEBNext Ultra II Stranded mRNA (New England Biolabs) and sequenced on the Illumina NextSeq 500 with Paired End 42 bp × 42 bp reads.

treatment_protocol: Human Jurkat T cells stably transduced with WT-STAT6 or STAT6 variants (p.E382Q or p.D419G), were either left untreated or treated with IL-4 (100ng/mL) for 4 hours. After this RNA was extracted.

value: Jurkat

value: WT

value: Untreated


title: WT_unstim_2


title: AIS11


title: AIS9


title: AIS12


title: HLT.batch2

city: Xiamen

first: Fan

last: Gao

state: Fujian

address: 668 Jimei Road

institute: Huaqiao University

data_processing:
Raw reads in which >10% of bases were N or > 50% of bases had low (<= 5) quality scores, as well as reads containing sequence adapters or long homopolymeric tracks, were removed. After removing low quality reads, the reads were then aligned to the GRCh37/hg19 version of the human genome using Bowtie2 (v2.2.9) with default settings.
The  sRNA-seq data from the three K562 bio-replicates were combined and used to generate RPKM for each sncRNA. The  sRNA-seq data from each HEK293 sample was used to generate RPKM for each sncRNA
Assembly: GRCh37/hg19
Supplementary files format and content: The processed files contain read counts (columns 5) and RPKM values (columns 6) for each unique small RNA with unique 5’ and 3’ coordinates.

source_name: HEK293 cells, biol rep2, sRNA-seq

growth_protocol: K562 and HEK293FT cells were maintained in respectively RPMI 1640 (ThermoFisher Scientific, US) and DMEM (Sigma) supplemented with 10% fetal bovine serum (ThermoFisher Scientific, US) and 1% pen/strep (ThermoFisher Scientific, US) at 37 °C in 5% CO2.

extract_protocol:
Total RNA was isolated from 1-2 million cells with E.Z.N.A. Total RNA Kit I (Omega) and precipitated by isopropyl alcohol.
Small RNA-seq libraries for small RNA-seq were constructed using NEB Next Multiplex Small RNA Library Prep Set for Illumina (NEB) following manufacturer's protocols. After library construction, PCR products corresponding to small RNAs in the range of 20-40 nt were purified by PAGE and used for small RNA-seq.

treatment_protocol: The genomic regions containing each of the 34 sncRNA plus upstream and downstream 200 bp were separately amplified using PCR from K562 genomic DNA and cloned into the lentiviral vector. Plasmids corresponding to over-expression vector containing each sncRNAs were prepared separately, mixed equally and the 2.5 μg of the plasmids pool was used to transiently transfect 1 million HEK293 cells using Epfect Transfection Reagent (Syngentech, China). After 8 h, the transfection medium was replaced with the fresh culture medium with or without Dox and cells were cultured for additional 24h. In parallel, cells transfected with an “empty” vector, without the sncRNA-containing regions, were used a “blank” control and were grown without Dox (Macklin Inc, 24390-14-5). Each transfection experiment was done in parallel on 2 independent batches of cells. Transfected cells were then selected using the MoFlo Astrios EQ flow cell sorter (Beckman Coulter) using GFP expression.

value: HEK293 cells

value: Transfected with control vectors and induced without Dox for 24h


title: WT_unstim_1


title: AIS8

value: adenocarcinoma in situ


title: HWT.batch2

value: Transfected with sRNAs overexpression vectors and induced without Dox for 24h


title: HDT.batch2

value: Transfected with sRNAs overexpression vectors and induced with Dox for 24h


title: 1256_unstim_3


title: AIS7


title: AIS6


title: AIS5


title: 1256_unstim_2


title: 1256_unstim_1


title: HWT.batch1

source_name: HEK293 cells, biol rep1, sRNA-seq


title: HLT.batch1


title: WT TE2 [20220125_209813940423_01_10]

city: Norfolk

first: Petra

last: Popovics

state: Virginia

address: 651 Colley Avenue Room 422

institute: Eastern Virginia Medical School

description: Total RNA was diluted equally and was analyzed with the Ncounter system according to the manufacturer`s instructions.

hyb_protocol: RNA expression was analyzed with the nCounter mouse fibrosis panel (NS_Mm_Fibrosis_V2.0).

data_processing: Analysis of differentially expressed genes, cell-type enrichment and gene set analysis was performed using the nCounter Advanced Analysis Software. The data was normalized via the Nanostring Advanced Analysis tool. It uses the geNorm algorithm for mRNA, choosing only the most stable housekeeping genes.

source_name: ventral prostate

extract_protocol: Ventral lobe RNA was stabilized in RNAlater (Thermo Fisher Scientific) and total RNA was isolated from ventral lobes using the Qiagen RNeasy Micro kit with on-column DNAse digestion (Germantown, MD, USA). RNA quantity and quality was measured with a NanoDrop.

treatment_protocol: Two month-old mice were implanted with 25 mg T and 2.5 mg E2 obtained from Sigma Chemical Co. or underwent sham surgery.

tag: agent

tag: age

value: 2 month


title: 1144_unstim_3


title: AIS4

source_name: Extracellular vesicles


title: HDT.batch1


title: 1144_unstim_2


title: SUP-M2 shscramble replicate 1


title: wild type sham control [20220125_209813940423_01_08]

value: sham


title: WT TE2 [20220125_209813940423_01_09]


title: AIS2


title: K562 sRNA L2

description: Merged.RPKM.txt

source_name: K562 cells, biol rep2, sRNA-seq

value: chronic myelogenous leukemia cell line


title: K562 sRNA L3

description: Merged.RPKM.txt

source_name: K562 cells, biol rep3, sRNA-seq


title: AIS1


title: WT_3

value: IL4 treated


title: WT_2


title: Benign53

value: Benign


title: RT4 cell line H3K27ac input

city: İZMİR

first: Serap

last: Erkek Özhan

state: BALÇOVA

address: İzmir Biyotıp ve Genom Merkezi (IBG), Dokuz Eylül Üniversitesi Sağlık Yerleşkesi, Mithatpaşa Caddesi No:58/5

country: Turkey

institute: Izmir Biomedicine and Genome Center

data_processing:
Read alignment was done using Burrows Wheeler Aligner (BWA) version 0.7.17-r1188
Peak calling was performed using Macs2 with the broad option for H3K27ac ChIP-Seq data while FRA1 and FLI1 transcription factor "united" peak finding was performed using HOMER algorithm, by using two biological replicates with the code getDifferentialPeaksReplicates.pl with specifying the style as factor (-style factor) and using (-F 2), (-L 2) options.
Assembly: hg38
Supplementary files format and content: broadpeak and bed files

growth_protocol: T24, J82, RT4 and HT1376 cell lines were grown in Dubacco’s Modified Eagle Medium (Gibco), and  RT112 and 5637 were grown in Roswell Park Memorial Institute (RPMI) 1640 Medium supplemented with 10% FBS and 1% Penicillin.

extract_protocol:
Chromatin extraction and chromatin immunoprecipitation was performed following Schubeler Lab Protocol (Weber et al. 2007).
ChIP-seq libraries were prepared using Illumina Kits at EMBL's GeneCore Facility & TruSeq DNA Sample prep Kit at Macrogen

treatment_protocol: No specific treatments were applied.

value: Bladder cancer cell


title: WT TE2 [20220125_209813940423_01_02]


title: wild type sham control [20220125_209813940423_01_07]


title: wild type sham control [20220125_209813940423_01_01]


title: WT_1


title: 1256_IL4_3


title: Benign51

value: Blood serum


title: RT112 cell line H3K27ac input


title: 1256_IL4_2


title: AIS3


title: RT112 cell line H3K27ac ChIP

value: H3K27ac (ActiveMotif 39133)


title: 1144_unstim_1


title: Benign50


title: control brain_rep3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Both Bx alleles are wildtype

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Images were quantified using Agilent Feature Extraction Software. Raw data was normalized using  Agilent GeneSpring GX Software : 75th Percentile Shift Normalization

organism: Drosophila melanogaster

source_name: larval brains

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

extract_protocol: RNA extracted from w1118 and Bx7 larval brains using the Trizol method as per the manufacturer′s instructions (TRI Reagent, Sigma-Aldrich)

tag: larval stage

value: third instar

tag: gender

value: female


title: Benign49


title: 1256_IL4_1

value: Jurkat


title: Bx mutant brain_rep3

description: Both Bx alleles are mutant and lack a 2 kb fragment from its genomic region


title: Bx mutant brain_rep1


title: J82 cell line H3K27ac input

value: Untreated


title: Benign48


title: 1144_IL4_3


title: K562 sRNA L1

description: Merged.RPKM.txt

source_name: K562 cells, biol rep1, sRNA-seq


title: Benign52


title: Bx mutant brain_rep2


title: J82 cell line H3K27ac ChIP


title: RT4 cell line H3K27ac ChIP


title: Benign47


title: 1144_IL4_1


title: 5637 cell line H3K27ac ChIP


title: control brain_rep2

description: Both Bx alleles are wildtype


title: Benign46


title: Benign45


title: Genomic_screen_MOLM13_start_rep1

value: AML

value: parental


title: HT1376 cell line H3K27ac input


title: Genomic_screen_MOLM13_end_DMSO_rep1

value: DMSO

value: 12 doublings


title: M_Input

first: Jiahui

last: Du

address: Zhizaoju Road 639

institute: Shanghai Jiao Tong University

data_processing:
Clean reads were aligned to the GRCm39 mouse genome using Bowtie 2 (v2.3.5.1)
Multiple aligned reads were filtered out using Picard
Then the unique mapped reads without duplicated reads were called for peaks using MACS3
The peaks were annotated using ChIPseeker
motif analyses were carried out using the MEME (v4.1.2)
Assembly: Mus_musculus.GRCm39.
Supplementary files format and content: Excel files include peak annotation

source_name: bone marrow-derived monocytes (BMDMs)

growth_protocol: Bone marrow cells were harvested from murine tibias and femurs of C57BL/6 mice and cultured in α-minimum essential medium containing 10% FBS and 1% penicillin-streptomycin overnight.

extract_protocol:
BMDMs were harvested and  fixed with 1% formaldehyde for 10 minutes.The Simple ChIP Plus Enzymatic Chromatin IP Kit (Magnetic Beads; Cell Signaling Technology 9005) were used following the manufacturer’s instructions.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit.

treatment_protocol: For osteoclast induction, BMDMs were cultured into complete media with 50 ng/ml recombinant soluble murine M-CSF (PeproTech, 315-02),100 ng/ml recombinant soluble murine RANKL.

value: bone marrow-derived monocytes (BMDMs)

value: M-CSF and RANKL


title: control brain_rep1

description: Both Bx alleles are wildtype


title: Benign44


title: Lung, bleo injured 2 months, scRNAseq

first: zixin

last: liu

address: 320 Yueyang road, Life Science Research Building A2112

institute: Center for Excellence in Molecular Cell Science

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Each scRNA-seq data set was processed by CellRanger (v6.1.1) pipeline to perform the alignment against the modified mouse reference genome mm10, filter the alignment and count barcodes and UMIs
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole lung

extract_protocol:
The lung epithelial cells isolation procedure included two rounds of digestion by two different enzyme cocktail (enzyme mixture 1: collagenase type I (500 U ml-1, Gibco, 17100–017), elastase (4 U ml-1, Worthington Biochemical Corporation, LS002279), and dispase (5 U ml-1, BD Biosciences, 354235) in DMEM/F12 (Gibco, 10565018); enzyme mixture 2: 0.1% Trypsin-EDTA (Gibco, 25200072) and DNase I (0.33 U ml-1; Worthington Biochemical Corporation LS002139) in DMEM/F12 (Gibco, 10565018)). In brief, the mice was euthanized by CO2 inhalation and then 10 ml of cold PBS was perfused through the right ventricle. After injecting 1.5 ml of enzyme mixture 1 through trachea, the lung lobes was collected and cut in to pieces, and additional 2.5 ml of enzyme mixture 1 was added before incubating the sample at 37 °C for 20 minutes on orbital shaker (~100 r.p.m). The digestion was ended by adding equal volume of cold DMEM/F12 with 10% of FBS (Gibco, 10099141) to the digestion medium, and the tissue was disturbed by pipetting before centrifuged at 1000g and 4 °C for 5 minutes. The supernatant was discarded and the pellet was resuspended with 2 ml of enzyme mixture 2 for incubating at 37 °C for 20 minutes. The digestion was stopped by adding equal volume of DMEM/F12 containing of 10% FBS and then filtered with 100 μm strainer and centrifuged at 1000g and 4 °C for 5 minutes. The pellet was resuspended by 2-3 ml of red blood cell lysis buffer (eBioscience, 00-4333-57) and incubated at room temperature for 3 minutes and then was stopped by adding 3 ml of cold PBS. The sample was filtered through 40 μm stainer and then centrifuged and resuspended in PBS. For MACS and FACS combined isolation, the cells was incubated with Epcam-APC (1:100, eBioscience, 17-5791-82) at 4 °C for 30 minutes and ended by adding cold PBS and centrifuged at 1000g and 4 °C for 5 minutes. For each adult lung, the pellet was resuspended in 80 μl of PBS and followed by 320 μl of anti-APC MicroBeads (Miltenyi Biotec, 130-090-855), then mixed the cells and beads well by pipetting and incubated at 4 °C for 15 minutes. After washing the sample with PBS and centrifuging at 1000g and 4 °C for 5 minutes, the pellet was resuspended in 500 ul of PBS and performed MACS positive isolation by autoMACS Pro Separator (Miltenyi Biotec). The positive selected cells were stained with DAPI and then performed FACS isolation by gating DAPI– Epcam+ tdTomato+ cells.
The cell suspense was loaded in 10x Chromium controller to generate GEMs, which were further processed into single cell 5ʹ gene expression libraries using Chromium Single Cell 5ʹ Library Kit (v2 Chemistry).

value: whole lung

value: lung epithelial cells

value: p63-CreER R26-tdT

value: bleo injured 2 months


title: Lung, bleo injured 14 days, scRNAseq

description: 10x Genomics

value: bleo injured 14 days


title: Genomic_screen_MOLM13_end_099_rep1


title: Lung, bleo injured 5 months, scRNAseq

description: 10x Genomics

value: bleo injured 5 months


title: HT1376 cell line H3K27ac ChIP

value: Bladder cancer cell

value: H3K27ac (ActiveMotif 39133)


title: T24 cell line H3K27ac input


title: MR

value: anti-BRD9 antibody (Bethyl Laboratories, A700-153)


title: Benign42

data_processing:
Raw reads were filtered using FastQC and Trimmomatic. Then, aligned to the GRCh38 human genome assembly using STAR.
Gene expression levels were calculated in size factor. Annotations of exlRNA in the human genome were retrieved from the Ensembl (V96).
Feature selection was performed by R package boruta to find all relevant variables for machine learning.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized values for each sample

extract_protocol:
EVs were purified from 0.5-1 mL serum using the exoRNeasy Midi kit (Qiagen; Cat#77144) according to the manufacturer’s instructions. For RNA extraction, EVs were lysed on column with 1 mL Trizol reagent (Invitrogen; Cat#15596026) and the RNA pellet was dissolved in 11 μL of deionized water treated with DEPC (diethylpyrocarbonate).
EV long RNA libraries were constructed using poly(A) independent extracellular RNA sequencing . Briefly, 1 ng RNA was reverse transcribed with random primer by SMART technology. cDNA was purified twice using Ampure XP beads (Beckman Coulter, Cat# A63881) and amplified with indexed primers. 200–500 base-paired PCR products were size-selected using Ampure XP beads.

value: Blood serum

value: Benign


title: 5637 cell line H3K27ac input

value: Untreated


title: T24 cell line H3K27ac ChIP


title: Benign43


title: T24 cell line FLI1 Input


title: Benign41


title: T24 cell line FLI1 ChIP

value: FLI1 (Abcam ab15289)


title: R12

data_processing:
Raw reads were trimmed using Cutadapt.
Trimmed reads were aligned with the GRCm39 genome using HISAT2
Read count extraction and normalization were performed using htseq-count.
Assembly: Mus_musculus.GRCm39.
Supplementary files format and content: Excel files include read count and fpkm values for each sample

extract_protocol:
BMDMs was collected for RNA isolation using TRIzol.
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit

treatment_protocol: For osteoclast induction, BMDMs were cultured into complete media with 50 ng/ml recombinant soluble murine M-CSF (PeproTech, 315-02),100 ng/ml recombinant soluble murine RANKL. Then the cells were treated with either vehicle or dBRD9, JQ1, DEX, iBRD9.

value: M-CSF, RANKL,JQ1


title: R11


title: R10


title: T24 cell line FRA1 Input


title: Post-FACS 4-M [HBx-LPMC-4-M_S19]

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

description:
Colon FACS
rnaseq_post_facs_normalized_counts.tsv
rnaseq_post_facs_Macrophages_HBx_positive-vs-Macrophages_negative.diffexp.tsv
rnaseq_post_facs_Macrophages_HBx_positive-vs-Macrophages_negative.merged_go.tsv

data_processing:
FASTQ reads were quality-checked and adaptor-trimmed with Trimmomatic and then mapped to the human hg38 reference genomes with STAR for RNA-Seq or Bowtie2 for ChIP-Seq.
Only for RNA-Seq: Concomitantly, human unmapped reads were subjected to metatranscriptomics profiling by Kraken2 and mapped to the HBV reference genome (NC_003977.2) with Bowtie2.
Only for RNA-Seq: Differential gene expression and microbiota abundance were performed with DESeq2.
Only for RNA-Seq: Human functional enrichment analysis was performed with geneSCF.
Only for ChIP-Seq: ChIP peak calling and gene-centric annotation were performed with MACS3 and ChIPseeker, respectively.
Only for ChIP-Seq: Motif discovery was performed with MEME.
Only for ChIP-Seq: Chromatin state correlation and Hidden Markov modeling were performed with bamCoverage and ChromHMM, respectively.
Assembly: hg38
Supplementary files format and content: *.diffexp.tsv: DESeq2 Differential gene expression table
Supplementary files format and content: *merged_go.tsv: geneSCF result table
Supplementary files format and content: *_normalized_counts.tsv: DESeq2 Normalized count table
Supplementary files format and content: *bed: MACS3 narrow peaks

source_name: Colon

growth_protocol: Caco-2 cell lines were seeded in 96-well cell culture plates (1×10^3 cells/well) in 10%FBS DMEM medium supplemented with antibiotics.  Mucosal biopsies collected from healthy donors were washed twice in RPMI medium (Lonza, Cat. #: 12-167Q) supplemented with Fetal Bovine Serum (Euroclone, Cat. # ECS0186L), UltraGlutamine™ I (Lonza, Cat. #: BE17-605E/U1, final concentration: 2 mM), HEPES Buffer (Euroclone, Cat. #: ECM0180D, final concentration: 10 mM), and with an antibiotics mixture of Penicillin-Streptomycin-Amphotericin B (Lonza, Cat. #: 17-745E, final concentration: 100 mU/mL;100 mg/mL;0.25 mg/mL), Gentamicin Sulfate (Lonza, Cat. #: 17-518Z, final concentration: 0.5 mg/mL), and Puromycin (Invivogen, Cat. #: ant-pr-1, final concentration: 0.1 mg/mL).

extract_protocol:
RNA was extracted from human and mouse colon tissues using the PureZOL RNA isolation reagent (Bio-Rad, Hercules, CA; cat. no: 7326890) according to the manufacturer’s instructions.  Chromatin immunoprecipitation was performed at the Galseq Srl NGS facility in Milan.
Library preparation and RNA-Seq were performed at the Galseq Srl NGS facility in Milan.

treatment_protocol: Each biopsy was washed, plated, and transduced with lentiviral particles carrying either the HBx-IRES-GFP or the GFP encoding sequences as control. Transduced biopsies were maintained at 37°C for 48 hours and then washed twice in phosphate-buffered saline (PBS) 1x. Biopsies consequently underwent digestion using collagenase type 2 (Worthington Biochemical Corporation, Cat. #: LS004176, final concentration: 7.5 mg/mL), followed by gentle compression through 70 μm and 100 μm cell strainer (Falcon, Cat. #: 352350, 352360) to extrude cell clumps. The obtained cellular pool was collected after centrifuge and frozen for the RNA-Seq analysis.

value: Colon

value: Macrophages

value: FACS


title: Benign40


title: Post-FACS 3-M [AP01-HBx-LPMC-3-M]


title: R9

value: bone marrow-derived monocytes (BMDMs)

value: M-CSF, RANKL,dBRD9


title: Benign39


title: Post-FACS 2-M [AP01-HBx-LPMC-2-M]


title: Benign38


title: R8


title: Post-FACS 4-F [HBx-LPMC-4-F_S20]

description:
Colon FACS
rnaseq_post_facs_normalized_counts.tsv

value: Fibrobalsts


title: Microglia RNA-seq rep2

city: Heidelberg

first: Carl

last: Herrmann

address: INF 267

department: Medical Faculty

country: Germany

institute: University Heidelberg

data_processing:
Processing was performed using nf-core pipeline (v1.3)
Reads were aligned to the hg38 genome by HISAT2
TPM were measured using stringTie (v2.1.5)
Gene counts were obtained through featureCounts
Assembly: hg38

molecule: nuclear RNA

source_name: Microglia

extract_protocol:
RNA was isolated from 2.5x10^6 untreated microglia cells with NucleoSpin RNA Mini kit
RNA libraries were constructed according to standard Illumina protocols

value: uninfected


title: 1144_IL4_2

value: Jurkat

value: IL4 treated


title: Benign37


title: R24

value: M-CSF, RANKL,DEX, iBRD9


title: R7


title: Post-FACS 3-F [AP01-HBx-LPMC-3-F]


title: Post-FACS 2-F [AP01-HBx-LPMC-2-F]


title: Microglia RNA-seq rep1


title: Post-FACS 4-EP [HBx-LPMC-4-EP_S18]

description:
Colon FACS
rnaseq_post_facs_normalized_counts.tsv
rnaseq_post_facs_Epithelium_HBx_positive-vs-Epithelium_negative.diffexp.tsv
rnaseq_post_facs_Epithelium_HBx_positive-vs-Epithelium_negative.merged_go.tsv

value: Epithelium


title: Benign36


title: Microglia Input rep1D

description: Sequenced on Nov 2019 (SE)

data_processing:
Trimming performed with trimGalore v0.4
Read alignment with bowtie2 v2.3 (--very-sensitive -q -p 10 -X 2000) to hg38
Peaks were called using MACS2 v2.1 (-q 0.05 —nomodel) using broad cut-off=0.1
BigWigs were produced using deeptools v3.0 function bamCoverage (--normalizeUsing RPKM --ignoreDuplicates -bs 40)
Assembly: hg38
Supplementary files format and content: peak files and bigwig files with coverage (for the runs with only one replicate or where replicates were sequenced on different dates, the remaining processed data were merged and included on Supplementary Files)

extract_protocol:
10x10^6 million microglia cells were fixed with 1% formaldehyde/PBS  followed by quenching with 0.125 M glycine. After washing with  cold PBS, pellet was resuspended in swelling buffer, cytosol was removed and nuclei sonicated. Lysates were cleared and 2-8 microgram of chromatin were incubated with corresponding amounts of antibody overnight at 4°C. The next day, chromatin was captured with Protein A/G beads, washed and eluted with TE buffer, 1% SDS, 100 mM NaCl. 0.5 mg/ml Proteinase K were added, and samples were incubated for 2 h at 55°C and overnight at 65°C. The next day, RNA was digested. Supernatant was removed from the magnetic beads and DNA was purified with AMpure beads XP clean up according to manufacturer’s instructions.
ChIP libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®  (NEB) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (NEB) according to manufacturer’s instructions.

value: untreated


title: Microglia H3K27ac rep2

description: Sequenced on Nov 2019 (SE)

value: H3K27ac (ab4729, Abcam)


title: Benign34

value: Blood serum

value: Benign


title: Post-FACS 3-EP [HBx-LPMC-3-EP_S24]


title: R23


title: R3

value: M-CSF, RANKL


title: Microglia Input rep1C

description: Sequenced on Jan 2020


title: T24 cell line FRA1 ChIP

value: Bladder cancer cell

value: Untreated

value: FRA1 (Cell Signaling 5281)


title: Post-FACS 2-EP [AP01-HBx-LPMC-2-EP]

value: Colon

value: FACS


title: Benign33


title: R2

value: bone marrow-derived monocytes (BMDMs)


title: Microglia H3K9me2 rep1

description: Sequenced on Jan 2020

value: H3K9me2 (ab1220, Abcam)


title: Microglia RNA-seq rep3

value: uninfected


title: Benign32


title: Post-FACS 4-EN [HBx-LPMC-4-EN_S14]

description:
Colon FACS
rnaseq_post_facs_normalized_counts.tsv
rnaseq_post_facs_Endothelium_HBx_positive-vs-Endothelium_negative.diffexp.tsv
rnaseq_post_facs_Endothelium_HBx_positive-vs-Endothelium_negative.merged_go.tsv

value: Endothelium


title: Microglia H3K27ac rep1

description: Sequenced on Jan 2020


title: Benign31


title: R1


title: Microglia Input rep1B

description: Sequenced on Oct 2020


title: Post-FACS 3-EN [HBx-LPMC-3-EN_S15]


title: Benign35


title: MRI4

treatment_protocol: For osteoclast induction, BMDMs were cultured into complete media with 50 ng/ml recombinant soluble murine M-CSF (PeproTech, 315-02),100 ng/ml recombinant soluble murine RANKL. For the BRD9 inhibitor experiments, the cells were treated with either vehicle or iBRD9 inhibitor

value: M-CSF,RANKL and iBRD9


title: Benign30


title: Microglia H3K27me3 rep2

description: Sequenced on Oct 2020

value: H3K27me3 (C36B11, Cell Signaling)


title: R22

value: M-CSF, RANKL,DEX, iBRD9


title: Post-FACS 2-EN [AP01-HBx-LPMC-2-EN]


title: Microglia H3K27me3 rep1

description: Sequenced on Oct 2020

value: untreated


title: MRI2


title: Post-FACS 4-D [HBx-LPMC-4-D_S17]

description:
Colon FACS
rnaseq_post_facs_normalized_counts.tsv
rnaseq_post_facs_Dendritic_cells_HBx_positive-vs-Dendritic_cells_negative.diffexp.tsv
rnaseq_post_facs_Dendritic_cells_HBx_positive-vs-Dendritic_cells_negative.merged_go.tsv

value: Dendritic cells


title: Benign28

value: Blood serum


title: MRI1


title: Benign27

value: Benign


title: Microglia H3K36me3 rep2

description: Sequenced on Oct 2020

value: H3K36me3 (ab9050, Abcam)


title: Post-FACS 3-D [HBx-LPMC-3-D_S13]


title: MR4

value: M-CSF and RANKL


title: Microglia H3K36me3 rep1

description: Sequenced on Oct 2020


title: Post-FACS 2-D [AP01-HBx-LPMC-2-D]


title: MR3


title: Microglia Input rep1A

description: Sequenced on Feb 2021


title: Benign26


title: Post-FACS 4-T8 [HBx-LPMC-4-T8_S22]

description:
Colon FACS
rnaseq_post_facs_normalized_counts.tsv
rnaseq_post_facs_CD8_T_cells_HBx_positive-vs-CD8_T_cells_negative.diffexp.tsv
rnaseq_post_facs_CD8_T_cells_HBx_positive-vs-CD8_T_cells_negative.merged_go.tsv

value: CD8 T cells


title: MR2


title: Post-FACS 3-T8 [AP01-HBx-LPMC-3-T8]


title: Benign25


title: Benign24


title: MRI3


title: Microglia H3K4me1 rep2

description: Sequenced on Feb 2021

value: H3K4me1 (ab8895, Abcam)


title: MR1


title: Post-FACS 2-T8 [AP01-HBx-LPMC-2-T8]

value: Colon


title: Benign23


title: Microglia H3K4me1 rep1

description: Sequenced on Feb 2021


title: Benign29


title: Post-FACS 4-T4 [HBx-LPMC-4-T4_S21]

value: CD4 T cells

value: FACS


title: Benign22


title: Microglia H3K9me3 rep2

description: Sequenced on Feb 2021

value: H3K9me3 (ab8898, Abcam)


title: MI4

value: bone marrow-derived monocytes (BMDMs)

value: M-CSF and iBRD9


title: Post-FACS 3-T4 [AP01-HBx-LPMC-3-T4]


title: MI3


title: Benign21


title: Post-FACS 2-T4 [AP01-HBx-LPMC-2-T4]


title: N2-Patient-PMAIono

description:
rawcounts.txt
processedcounts.txt

data_processing:
RNA was sequenced on the Illumina NextSeq 500 with Paired End 42bp x 42bp reads
Read sequences were aligned to the Homo sapiens reference sequence (UCSC hg19) using STAR aligner (version STAR_2.5.0b)
Assembly of transcripts and measurement of abundance was done using Cufflinks (Version 2.2.1)
TMM analysis using EdgeR was used for raw count normalization
filterByExpr (EdgeR) and removeBatchEffect (limma) were used for obtaining procesed counts
Genome_build: Homo sapiens (UCSC hg19)
Supplementary_files_format_and_content: Raw counts and processed counts are presented as tab delimited .txt files

source_name: Chondrocytes from osteochondroma

growth_protocol: Patient-derived cells were isolated from an osteochondroma. Cells were then infected with either NFATC2-WT (Rescued) or Empty Vector (EV) (labeled "patient") lentiviral particles and subsequently propagated in complete DMEM.

extract_protocol:
RNA was extracted with a RNeasy Mini Plus Kit (Qiagen)
RNA samples were prepared following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England BioLabs)

treatment_protocol: Stimulated with 20ng/mL IL-1b, PMA (50ngml) 1uM Ionomycin, or left untreated for 4 hours

tag: replicate number

value: PMAIonomycin


title: Benign20


title: Post-FACS 4-B [HBx-LPMC-4-B_S23]

value: B cells


title: Post-FACS 3-B [HBx-LPMC-3-B_S16]


title: M4

value: M-CSF


title: N2-Patient-IL1B

description:
rawcounts.txt
processedcounts.txt


title: Benign19


title: N2-Patient-unstim

description:
rawcounts.txt
processedcounts.txt

value: Unstim


title: N1-Rescue-PMAIono

description:
rawcounts.txt
processedcounts.txt


title: Benign17


title: Post-FACS 2-B [AP01-HBx-LPMC-2-B]


title: Ex-vivo HBx 3C [HBX_3C]

description:
Ex-vivo colon biopsy HBx lentiviral expression
rnaseq_ex_vivo_biopsies_normalized_counts.tsv
rnaseq_ex_vivo_biopsies_HBx-vs-GFP.diffexp.tsv
rnaseq_ex_vivo_biopsies_HBx-vs-GFP.merged_go.tsv

molecule: polyA RNA

source_name: Ex-vivo colon biopsy

value: Ex-vivo colon biopsy

value: HBx lentiviral expression


title: Benign16

value: Blood serum

value: Benign


title: Benign18


title: M2


title: Ex-vivo HBx 3B [HBX_3B]


title: Benign15


title: Microglia H3K9me3 rep1

description: Sequenced on Feb 2021

value: untreated


title: M1


title: Ex-vivo HBx 3A [HBX_3A]


title: N1-Rescue-unstim

description:
rawcounts.txt
processedcounts.txt


title: Ri-1

data_processing:
Library sequencing quality was assessed using Cutadapt (1.9.1).
Trimmed libraries were aligned to the GRCm39 mouse genome using Bowtie 2 (version 2.2.6)
PCR duplicates were removed and the number of mapped reads downsampled to a standard of ~20M using Picard (version 1.126)
ATAC-Seq peaks were called subsequently using MACS3
Assembly: Mus_musculus.GRCm39.
Supplementary files format and content: tab-delimited text files include DAR peak Annotation betweem two sample

extract_protocol:
BMDMs were harvested and then lysed for 10 minutes at 4 ℃ on the rotation mixer.
Then, 5000 cells from each group were used for preparation of ATAC-seq libraries according to the protocol described by Kaestner Lab (https://www.med.upenn.edu/kaestnerlab/protocols.html).

value: M-CSF,RANKL and iBRD9


title: Ex-vivo HBx 2C [HBX_2C]


title: Benign14


title: MI1


title: RO-1

value: M-CSF and RANKL


title: MI2


title: Benign13


title: N1-Patient-IL1B

description:
rawcounts.txt
processedcounts.txt


title: N1-Patient-PMAIono

description:
rawcounts.txt
processedcounts.txt


title: N1-Patient-unstim

description:
rawcounts.txt
processedcounts.txt


title: M3


title: K36M_DMOG_d4_WGBS_rep1

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

data_processing:
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the mm9 reference genome with bsmap using the following parameter: -v 0.01 -s 16 -w 100 -S 1 -R -u -q 20. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).  Methylation rates were called using mcall using default parameter and subsequently filtered for coverage (min 10 reads)
Assembly: mm9
Supplementary files format and content: Bigwig file of 10X filtered methylation rates

source_name: reprogramming intermediate

extract_protocol:
DNA for WGBS was extracted using a Qiagen Blood & Tissue DNeasy kit according to the manufacturer's recommendations.
WGBS libraries were produced with the TrueMethyl oxBS-Seq Module (Tecan) and Accel-NGS Methyl-Seq DNA Library Kit (Swift) according to the manufacturer’s instructions with the omission of the oxBS steps in the TrueMethyl protocol. Briefly, 300ng of gDNA was sheared to average fragment size of 200 bp using a Covaris S2 sonicator for 1 minute 30 seconds with the following settings: duty cycle 10%, intensity 5, cycles per burst 200. Resulting sheared gDNA was concentrated using Agencourt AMPure XP beads (Beckman Coulter) and then subjected to bisulfite conversion and desulfunation as outlined in the TrueMethyl oxBS-Seq Module. This bisulfite converted gDNA was then used as input for the Accel-NGS Methyl-Seq DNA Library Kit and yielded sequencable libraries.

value: reprogramming intermediate

value: DMOG


title: K36M_DMOG_d4_WGBS_rep2


title: Ex-vivo HBx 2B [HBX_2B]


title: Ex-vivo HBx 2A [HBX_2A]


title: N1-Rescue-IL1B

description:
rawcounts.txt
processedcounts.txt


title: N3-Rescue-PMAIono

description:
rawcounts.txt
processedcounts.txt


title: Benign11


title: K36M_d4_WGBS_rep2


title: Ex-vivo HBx 1C [HBX_1C]


title: N3-Rescue-IL1B

description:
rawcounts.txt
processedcounts.txt


title: Benign10


title: K36M_d4_WGBS_rep1


title: N3-Rescue-unstim

description:
rawcounts.txt
processedcounts.txt


title: Benign9


title: WT_d4_WGBS_rep2

value: WT


title: Benign8


title: Ex-vivo HBx 1A [HBX_1A]


title: N3-Patient-IL1B

description:
rawcounts.txt
processedcounts.txt


title: WT_d4_WGBS_rep1


title: Benign7


title: Ex-vivo GFP 3B [GFP_3B]

description:
Ex-vivo colon biopsy GFP lentiviral expression
rnaseq_ex_vivo_biopsies_normalized_counts.tsv
rnaseq_ex_vivo_biopsies_HBx-vs-GFP.diffexp.tsv
rnaseq_ex_vivo_biopsies_HBx-vs-GFP.merged_go.tsv

value: GFP lentiviral expression


title: Benign12


title: Benign6


title: Ex-vivo GFP 3A [GFP_3A]


title: N2-Rescue-PMAIono

description:
rawcounts.txt
processedcounts.txt


title: N3-Patient-unstim

description:
rawcounts.txt
processedcounts.txt


title: Benign5


title: K36M iPSC

data_processing:
Demultiplexed reads were trimmed using cutadapt and the Nugene diversity adapter trimming python script trimRRBSdiversityAdaptCustomers.py. Reads were then aligned to the mouse mm9 genome using BSMAP with the parameters: -v 0.1 -s 12 -q 20 -w 100 -S 1 -u -R -D C-CGG. Duplicate reads were removed using the Nugen deduplication script nudup.py. Methylation ratios were called using the MOABS mcall module.  Genome_build: mm9 (MGSCv37)
Assembly: mm9
Supplementary files format and content: tab deliminted file containing the following information: #chrom start end ratio totalC methC strand next Plus totalC methC Minus totalC methC localSeq

source_name: iPSC

growth_protocol: MEFs were cultured in DMEM 10%FBS, reprogramming was performed in AGi medium, iPSCs were passaged in S/L.

extract_protocol:
DNA for RRBS was extracted using a Qiagen Blood & Tissue DNeasy kit according to the manufacturer's recommendations.
Genomic DNA was quantified using a Qubit 3.0 Fluorometer. RRBS was performed on 100 ng of each sample using the NuGen Ovation RRBS Methyl-Seq System following the manufacturer’s recommendations. Bisulfite conversion of DNA was conducted using the Qiagen EpiTect Fast Bisulfite Conversion kit. Libraries were purified with Agencourt RNAclean XP beads and quality-assessed using an Agilent 4150 Tape-Station D1000 ScreenTape. Libraries were then sequenced on the Illumina NovaSeq6000, generating 100-bp single-end reads.

value: iPSC


title: Benign4


title: WT d8 rep 2


title: N2-Rescue-IL1B

description:
rawcounts.txt
processedcounts.txt


title: WT iPSC


title: Ex-vivo GFP 2C [GFP_2C]


title: Ex-vivo GFP 2B [GFP_2B]


title: K36M d8 rep 2


title: N3-Patient-PMAIono

description:
rawcounts.txt
processedcounts.txt


title: N2-Rescue-unstim

description:
rawcounts.txt
processedcounts.txt


title: TRE-sRNA-K562 cells,-Dox, biol rep2,0d

data_processing:
Raw read pairs in which at least one read contained >10% of N bases and/or > 50% of bases with low (<= 5) quality scores were removed. The quality filtered paired-end sequences were further filtered for the presence of expected sequence AGCAGAGCTCGTTTAGTGAACCGTCAGATCGCCTGGAGATTTCGTTAATTAAACCG at the beginning of read 1 and ATGTGCGCTCTGCCCACTGACGGGCACCGGAGCCAAGCTAGCTTTTGGTAGATCAGTTATAAAA at the beginning of read 2, then both of the expected sequences tags were removed and the read pairs were aligned to the human reference genome (GRCh37/hg19) using Bowtie 2.
Aligned reads were assigned to each of the 404 sncRNA overexpressing regions and used to generate counts for each such region in each library.
In each sample, the read count for each of the 404 DNA regions used to overexpress the sncRNAs  was first normalized to the sequencing depth of the corresponding NGS library to generate the normalized read count (NRC) for that region.
Assembly: GRCh37/hg19
Supplementary files format and content: The processed file contains raw and normalized read counts for each of the 404 DNA regions used to overexpress the sncRNAs for each sample.

source_name: cell line

growth_protocol: TRE-sRNA-K562 cells were maintained in RPMI 1640 (ThermoFisher Scientific, US) supplemented with 10% fetal bovine serum (ThermoFisher Scientific, US) and 1% pen/strep (ThermoFisher Scientific, US) at 37 °C in 5% CO2.

extract_protocol:
Genomic DNA was isolated from 2 million cells using TIANamp Genomic DNA Kit (Tiangen).
Two rounds of PCR were performed to prepare the sequencing library. For each sample, the sncRNA overexpressing regions were amplified in 5 parallel PCR reactions as follows. For the first round of PCR, Each reaction contained 1 μg genomic DNA, 1× Taq buffer, 10 mM of each dNTP (Takara), 0.5 μM of each P5-Lenti-forward primer (CTACACGACGCTCTTCCGATCTAGCAGAGCTCGTTTAGTGAACCG) and P7Lenti-reverse primer (GTTCAGACGTGTGCTCTTCCGATCTATGTGCGCTCTGCCCACTGA) and 2.5 U Taq DNA polymerase (Tiangen) in a total volume of 50 μl. Then, 2 μl of the 1st round PCR product were used for the 2nd round amplification with 1× Taq buffer, 10 mM of each dNTP, 0.5 μM of each Illumina-P5 primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and Illumina-P7 primer (CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) and 1 U of Taq DNA polymerase in 20 μl.Each PCR reaction was purified with 0.8 volumes of VAHTS DNA Clean Beads and the 5 PCR reactions for the same sample were pooled and subjected to NGS sequencing.

treatment_protocol: One million of the TRE-sRNA-K562 cells (>2000 cells for each sncRNA overexpressing region) were cultured in 10 ml medium with or without 1 μg/ml Dox in a T25 flask with 3 independent biological replicates performed for each +Dox or −Dox treatment. The medium with or without Dox was changed every two days. After 16 and 32 days, aliquots of 2 million cells were used for genomic DNA isolation while the rest of the cells were allowed to continue in culture until day 60. Cells immediately prior to the culture were also used for DNA isolation and this sample is referred to as “day 0”.

value: cell line

value: TRE-sRNA-K562 cells

value: Transfected with sRNAs overexpression lentivirus vector

value: Induction without Dox for 0d


title: Benign2


title: Ex-vivo GFP 2A [GFP_2A]


title: Ex-vivo HBx 1B [HBX_1B]


title: Ex-vivo GFP 3C [GFP_3C]


title: K36M d8 rep 1


title: Ex-vivo GFP 1C [GFP_1C]


title: Benign1


title: WT d8 rep 1


title: TRE-sRNA-K562 cells,-Dox, biol rep1,0d


title: Ex-vivo GFP 1B [GFP_1B]


title: K36M d4 rep 2


title: Ex-vivo GFP 1A [GFP_1A]


title: K36M d4 rep 1


title: Caco-2 HBx 3 [H3]

description:
Caco-2 HBx lentiviral expression
rnaseq_caco2_normalized_counts.tsv
rnaseq_caco2_HBx-vs-GFP.diffexp.tsv
rnaseq_caco2_HBx-vs-GFP.merged_go.tsv

value: Epithelium; Colon cell line


title: TRE-sRNA-K562 cells,-Dox, biol rep3,32d

value: Induction without Dox for 32d


title: TRE-sRNA-K562 cells,-Dox, biol rep3,60d

value: Induction without Dox for 60d


title: WT d4 rep 2


title: HC5

city: Hongkong

first: Zhongyi

state: Hongkong

address: L7-55 Paediatrics, Lab Block, Faculty of Medicine, 21 Sassoon Road, Pokfulam, HK

institute: The University of Hong Kong

data_processing:
De-multiplexed read sequences were aligned to a reference sequence and transcript expression were estimated using the DRAGEN RNA pipeline on Illumina Basespace.
Expression data was normalized to reads between samples using the edgeR package in R (R Foundation, Vienna, Austria).
Normalized counts were filtered to remove low counts using the filterByExpr function in edgeR(Chen et al., 2016). Principal component analysis (PCA) was done on log2(normalized counts+0.25) in R using the PCA function. Differential expression was conducted using Limma(Ritchie et al., 2015), on patient pre-treatment sample against 5 healthy controls.
Differentially expressed genes (adjusted p-value <0.05) were visualized using pheatmap in R. Cell type abundance was estimated using the LM22 signature matrix file in Cibersort(Newman et al., 2015). Cell types were reduced to nine immunologically relevant cell types: Neutrophils, Eosinophils, Mast cells, Dendritic cells, Monocytes, NK cells, CD4 T cells, CD8 T cells, Memory B cells, and Naïve B cells.
Assembly: Homo sapiens (UCSC hg19)
Supplementary files format and content: Processed counts are presented as .txt files

organism: Homo

source_name: Whole Blood

extract_protocol:
RNA was extracted with TRIzoL (Ambion #15596026, Carlsbad, USA).
Library preparation and Illumina sequencing (pair-end sequencing of 151bp) were done at the Genomics Core of the Centre for PanorOmic Sciences in LKS Faculty of Medicine of The University of Hong Kong. cDNA libraries were prepared by KAPA mRNA HyperPrep Kit KR1352-v3.16 (Roche #08098123702, Basel, Switzerland).
One microgram of total RNA was used as starting material. Manufacturer’s protocol was followed. In brief, Poly-A containing mRNA was collected by using poly-T oligo-attached magnetic beads. The purified mRNA was fragmented to 200 – 300 bp by incubating at 94oC for 6 min in the presence of magnesium ions. The fragmented mRNA was then applied as template to synthesize the first-strand cDNA by using random hexamer-primer and reverse transcriptase. In the second strand cDNA synthesis, the mRNA template was removed and a replacement strand was generated to form the blunt-end double-stranded (ds) cDNA. The ds-cDNA underwent 3’ adenylation and ligation with xGen® Dual Index UMI Adapters (Integrated DNA Technologies, Iowa, USA). The adaptor-ligated libraries were enriched by 10 cycles of polymerase chain reaction (PCR). The libraries were denatured and diluted to optimal concentration. Illumina NovaSeq 6000 was used for pair-end 151bp sequencing.

treatment_protocol: Human peripheral blood was collected in EDTA tubes. Erythrocytes were removed with RBC Lysis Solution (Qiagen #158904, Maryland, USA) and the resultant white cell pellet was washed once with PBS.

value: Whole Blood

tag: disease

value: healthy control


title: TRE-sRNA-K562 cells,-Dox, biol rep2,60d


title: HC3


title: Caco-2 HBx 2 [H2]

value: HBx lentiviral expression


title: HC4


title: HC2


title: TRE-sRNA-K562 cells,-Dox, biol rep2,32d


title: K36M d0

source_name: MEF

value: MEF


title: Benign3

first: Wei

address: 320 Yueyang Road

institute: Chinese Academy of Sciences

value: Blood serum

value: Benign


title: HC1


title: Caco-2 GFP 3 [G3]

description:
Caco-2 GFP lentiviral expression
rnaseq_caco2_normalized_counts.tsv
rnaseq_caco2_HBx-vs-GFP.diffexp.tsv
rnaseq_caco2_HBx-vs-GFP.merged_go.tsv


title: TRE-sRNA-K562 cells,-Dox, biol rep2,16d

value: Induction without Dox for 16d


title: Patient_Jun

value: severe early onset allergic disease

value: postdupilumab


title: Caco-2 GFP 2 [G2]

value: GFP lentiviral expression


title: sorted astrocytes 86E01 d70 rep3

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Reads were mapped using STAR 2.7.3a (Dobin et al., 2013) to the Drosophila genome assembly dm6.
Improperly paired reads were removed from bam files using samtools.
Reads per gene annotated in the FlyBase release 2019_05 were computed using an in-house R script based on the GenomicRanges (Lawrence et al., 2013) function summarizeOverlaps, which counts the number of reads overlapping the exons of each gene in the default "union" mode.
Genome_build: dm6
Supplementary_files_format_and_content: read_counts.txt provides the raw read counts for each gene produced using the specified data processing steps.

source_name: astrocytes

growth_protocol: Stocks were maintained and experiments conducted at 25˚C and 50% humidity on a 12-hour light/dark cycle using standard Bloomington Drosophila medium (Nutri-Fly).

extract_protocol:
RNA was purified with TRIzol.
Purified RNA in Smart-seq3 buffer (5% PEG8000, 0.1% Triton X-100, 0.5 U/μL RNase inhibitor, 0.5 μM Smart-seq3 oligo-dT primer, and 0.5 mM dNTP) was incubated at 70°C for 2 min to denature the RNA. Next, reverse transcription mix (25 mM Tris-HCl pH 8.3RT, 30 mM NaCl, 1 mM GTP, 2.5 mM MgCl2, 8 mM DTT, 0.5 U/μL RNase inhibitor, 2 μM TSO and 2 U/μL of maxima H-minus reverse transcriptase enzyme) was added to each sample. Reverse transcription and template switching were carried out at 42 °C for 90 min followed by 10 cycles of 50 °C for 2 min and 42 °C for 2 min. The reaction was terminated by incubating at 85 °C for 5 min. PCR pre-amplification was performed by directly adding KAPA HiFi HotStart ReadyMix and 0.5 μM forward primer and 0.1 μM reverse primer to a 50 μL reaction volume. The PCR was performed with the following cycle: 3 min at 98 °C for initial denaturation, 5–9 cycles (depending on the starting amount of RNA) of 20 s at 98 °C, 30 s at 65 °C, and 4 min at 72 °C. Final elongation was performed for 5 min at 72 °C. After PCR the cDNA was purified twice with 0.6x SPRIselect beads (Beckman Coulter, CA). Next, 600 pg of preamplified cDNA were tagmented with Tn5 transposase (Lucigen) pre-loaded with suitable adapters.  Libraries were further amplified for 14 cycles using custom Nextera-compatible primers with different indexes with KAPA HiFi HotStart ReadyMix. Libraries were loaded at 2.4 pM and sequenced on an Illumina Nextseq 500. The read configuration was 38 (read1), 8 (index1), 8 (index2), 38 (read2).

treatment_protocol: For sorted cells: Brains from young (5 days old) and old (70 days old) females were dissected, collected into a tube with cold Schneider’s medium (SM) containing 1% BSA and washed twice. Next, we added 200 μL of dissociating solution, which included 2 mg/mL collagenase I (Sigma-Aldrich, SCR103) and 20 μg/mL DNase I (Worthington, Cat#LS002006) in SM containing 1% BSA with 45 μM actinomycin D to block new transcription during enzyme digestion. Brains were dissociated at 25°C using a shaker at 500 rpm for 1 hour and vigorous pipetting every 20 min. Dissociated tissue was filtered through 100 μm cell strainers and sorted at cell sorting facility of the University of Pennsylvania. Dead cells were excluded by staining with 4,6-diamidino-2-phenylindole (DAPI). GFP+ cells gates were set according to the fluorescence profile of GFP- brain tissue. Desired glia populations were directly sorted into TRIzol for RNA extraction.

tag: driver line

tag: sorting

value: sorted cells


title: WT d0

tag: genotype

value: WT


title: sorted astrocytes 86E01 d70 rep2


title: Patient_Mar

tag: tissue


title: Caco-2 GFP 1 [G1]

tag: cell line


title: TRE-sRNA-K562 cells,-Dox, biol rep1,60d

value: cell line

value: TRE-sRNA-K562 cells

value: Transfected with sRNAs overexpression lentivirus vector

tag: treatment


title: TRE-sRNA-K562 cells,-Dox, biol rep1,32d

value: Induction without Dox for 32d


title: Patient_Dec


title: Caco-2 input-1 [Caco2-DAF-input-1]

description: Caco-2 ChIP input

value: Epithelium; Colon cell line

value: ChIP input


title: TRE-sRNA-K562 cells,-Dox, biol rep3,16d


title: Patient_Nov

value: Whole Blood


title: WT d4 rep 1

value: reprogramming intermediate


title: Caco-2 HBx 1 [H1]

value: HBx lentiviral expression


title: TRE-sRNA-K562 cells,-Dox, biol rep1,16d


title: sorted astrocytes 86E01 d70 rep1


title: Caco-2 HBx ChIP 3 [Caco2-DAF-ChIP-3]

description:
Caco-2 HBx ChIP
hbx_targets.go.tsv

value: HBx ChIP

tag: antibody

value: Abcam anti-V5 tag antibody ab15828.


title: sorted astrocytes 86E01 d5 rep3


title: Caco-2 HBx ChIP 2 [Caco2-DAF-ChIP-2]

description:
Caco-2 HBx ChIP
hbx_targets.go.tsv

tag: cell type


title: sorted astrocytes 86E01 d5 rep2


title: TRE-sRNA-K562 cells,+Dox, biol rep3,32d

value: Induction with Dox for 32d


title: Caco-2 HBx ChIP 1 [Caco2-DAF-ChIP-1]

description:
Caco-2 HBx ChIP
hbx_targets.go.tsv


title: sorted astrocytes 86E01 d5 rep1


title: TRE-sRNA-K562 cells,+Dox, biol rep3,60d

value: Induction with Dox for 60d


title: lung_control_7d

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

institute: Ruhr University Bochum

data_processing:
All RNAseq analysis steps were performed using CLC Genomics workbench v22.0.2 (Qiagen, Hilden, Germany). Raw fastq reads were checked for quality and trimmed accordingly.
Due to insufficient RNA depletion during library preparation for some samples, trimmed reads were mapped to 28S ribosomal RNA (LOC121137942) to delplete any contaminating rRNAs.  Remaining unmapped reads were then mapped to the golden hamster scaffold BCM_Maur_2.0.
Assembly: BCM_Maur_2.0
Supplementary files format and content: csv files with read counts and RPKM values

organism: Mesocricetus auratus

source_name: left lung lobe

growth_protocol: Male 5-7 weeks old Syrian gold hamsters (Mesocricetus auratus, raised by Janvier Labs, France) were kept in groups of three to four individuals. Animals were offered water and rodent pellets ad-libitum, fresh hay was offered daily. They were checked for clinical scores, body weight and body temperature on a daily basis. All animals were tested negative for SARS CoV-2 genome in oral and anal swabs and antibodies prior to the experiment.

extract_protocol:
RNA was extracted from homogenized samples using Direct-zol RNA Miniprep Kit (Zymo research, Freiburg, Germany) following manufacturer’s instructions. Extracted RNAs from 3 animals per group were pooled prior to library construction.
Polyadenylated RNAs were isolated with the NEBNext Poly(A) mRNA module (New England Biolabs) and a modified protocol of the NNSR priming method was used to produce cDNA libraries. Sequencing was performed on an Illumina NextSeq550 instrument with a 86 base, single-end setting, using a custom sequencing program.

treatment_protocol: 21 hamsters were infected orotracheally as described earlier (Blaurock et al., 2022) with 10^5 TCID50 of the ancestral SARS-CoV-2 (isolate 2019_nCoV Muc-IMB-1) per animal. Tissues from infected animals killed at day 1-7 and day 14 as well as mock-infected hamsters killed at day 7 were included in the study (n=3 per day). The left lung lobe was carefully removed, immersion-fixed in 10% neutral-buffered formalin, paraffin-embedded, and 2–3-μm sections were stained with hematoxylin and eosin (HE) for light microscopical examination. In parallel RNA extraction and Illumina RNAseq was performed.

value: left lung lobe

tag: virus strain

value: 2019_nCoV Muc-IMB-1

value: tissue homogenizate

tag: time

value: 7 d

tag: Sex

value: male


title: lung_SARS-CoV2pos_14dpi

value: 14 dpi


title: sorted ensheathing glia 56F03 d70 rep3

source_name: ensheathing glia

value: sorted cells


title: miRNA of IgAN3

last: Liu

data_processing:
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

source_name: PBMCs

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 1 µg of total RNA were used to prepare 6 small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

tag: disease state

value: IgAN

value: PBMCs


title: lung_SARS-CoV2pos_6dpi

value: 6 dpi


title: lung_SARS-CoV2pos_5dpi

value: 5 dpi


title: TRE-sRNA-K562 cells,+Dox, biol rep2,60d

value: cell line

value: TRE-sRNA-K562 cells

value: Transfected with sRNAs overexpression lentivirus vector


title: miRNA of IgAN2


title: sorted ensheathing glia 56F03 d70 rep1

tag: age


title: TRE-sRNA-K562 cells,+Dox, biol rep2,16d

value: Induction with Dox for 16d


title: miRNA of IgAN1


title: Patient_first

value: Whole Blood

value: severe early onset allergic disease

tag: agent


title: sorted ensheathing glia 56F03 d5 rep3


title: lung_SARS-CoV2pos_3dpi

value: left lung lobe

value: 3 dpi


title: TRE-sRNA-K562 cells,+Dox, biol rep1,60d

value: Induction with Dox for 60d


title: miRNA of Control 2

value: control


title: lung_SARS-CoV2pos_2dpi

value: 2019_nCoV Muc-IMB-1

value: tissue homogenizate

value: 2 dpi

value: male


title: lung_SARS-CoV2pos_1dpi

value: 1 dpi


title: TRE-sRNA-K562 cells,+Dox, biol rep1,32d

value: Induction with Dox for 32d


title: sorted ensheathing glia 56F03 d5 rep2

value: sorted cells


title: TRE-sRNA-K562 cells,+Dox, biol rep3,16d

value: cell line


title: miRNA of Control 1

value: PBMCs


title: miRNA of Control 3


title: sorted ensheathing glia 10E12 d70 rep3


title: sorted ensheathing glia 56F03 d5 rep1


title: RNA_Mycelia_H153G_Ag3uM

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

country: Japan

institute: RIKEN

description: RNA-Seq

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: C. orbiculare 104-T 43 (PRJNA171217)
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

organism: Colletotrichum orbiculare

source_name: mycelia

growth_protocol: For mycelia, a single colony of each strain was transferred onto 3.9% (w/v) potato dextrose agar (PDA)  and incubated for 3 d. The outer edges of colonies were transferred to 90-mm plastic dishes filled with 20 ml of 2.4% (w/v) potato dextrose broth (PDB) using plastic straws and incubated for 4 d. For conidia, The outer edges of colonies of each strain were transferred into six 300-ml flasks filled with 100 ml of PDA. Two milliliters of sterilized water was added to each flask, and the flasks were shaken well to ensure that the mycelial cells adhered to the entire surface of the PDA evenly and incubated for 6 d in the dark.

extract_protocol:
Cells were filtered, scraped, and soaked in liquid nitrogen with 600 µl of lysis buffer or 400 µl of Trizol reagent. The frozen cells and lysis buffer grains were milled by a Multi-beads Shocker at 2,800 rpm for 15 sec for 1 cycle.
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification. For RNA-Seq, Poly(A) selection and cDNA synthesis were performed using Illumina Stranded mRNA Prep, Ligation (Illumina) and subsequent steps were performed by TruSeq Stranded Total RNA Library Prep Gold (Illumina).

treatment_protocol: For mycelia, aglafoline (0.3 or 3 µM) or DMSO was added to dishes and incubated for 6 h. For conidia, conidia generated on the surface of PDA were suspended in 20 ml of sterilized water and collected by filteration and centrifugation. Twenty milliliters of resuspended conidia at 0.5 OD600 was dispensed in 50 ml ProteoSave SS tubes and then treated with aglafoline (0.3 or 3 µM) or DMSO for 6 h in the dark with shaking at 140 rpm.

value: Aglafoline 3 uM

value: mycelia


title: TRE-sRNA-K562 cells,+Dox, biol rep1,16d

value: TRE-sRNA-K562 cells

value: Transfected with sRNAs overexpression lentivirus vector

value: Induction with Dox for 16d


title: sorted ensheathing glia 56F03 d70 rep2


title: TRE-sRNA-K562 cells,+Dox, biol rep2,32d


title: RNA_Mycelia_H153G_DMSO2

description: RNA-Seq

value: DMSO


title: RNA_Mycelia_H153G_Ag0.3uM

description: RNA-Seq

value: Aglafoline 0.3 uM


title: sorted ensheathing glia 10E12 d70 rep2


title: RNA_Mycelia_H153G_DMSO1

description: RNA-Seq


title: sorted ensheathing glia 10E12 d5 rep3


title: sorted ensheathing glia 10E12 d70 rep1


title: siRNA-RP0581-1 subject 97286

city: Oxford

first: Enrique

middle: M

last: Toledo

address: Innovation Building, Old Road Campus, Roosevelt Drive

department: R&D

country: United Kingdom

institute: Novo Nordisk

data_processing:
Sequence reads were again aligned using STAR against the Ensembl mm10 transcriptome annotation
Count data from STAR output
Assembly: mm10
Supplementary files format and content: Count data from STAR output

source_name: DIO-NASH Liver

extract_protocol:
Approximately 10 mg of each liver tissue sample was homogenised in 0.55 mL phenol/guanidine-based QIAzol Lysis Reagent (Qiagen, 79306) using a Tissuelyser II (Qiagen). Liver tissue stored in RNAlater was used for primary analysis. The homogenate was extracted with 1-bromo-3-chloropropane (Sigma-Aldrich, B62404). RNA was extracted from 0.2 mL of the aqueous phase using the MagMax Technology (ThermoFisher Scientific) according to the manufacturer’s protocol. RNA was quantified using spectrometry at 260 and 280 nm. 10 ng - 1 µg purified RNA from each sample was used to generate a cDNA library using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. The cDNA library was then sequenced on a NextSeq 500 using NextSeq 500/550 High Output Kit V2 (Illumina).  Sequence reads were again aligned using STAR against the Ensembl mm10 transcriptome annotation.
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

value: DIO-NASH Liver

tag: strain

value: DIO-NASH

tag: sirna

value: siRNA

tag: subject

tag: file id

value: Male

value: 5 weeks

tag: diet

value: GAN diet (D09100310, Research Diets, USA)


title: siRNA-RP0581-1 subject 97323


title: siRNA-RP0581-1 subject 97304


title: siRNA-RP0581-1 subject 97298


title: RNA_Mycelia_WT_Ag3uM

description: RNA-Seq

tag: genotype


title: sorted ensheathing glia 10E12 d5 rep2

tag: driver line

tag: sorting


title: siRNA-RP0581-1 subject 97277

tag: tissue

tag: treatment


title: siRNA-RP0581-1 subject 97276


title: sorted ensheathing glia 10E12 d5 rep1


title: siRNA-RP0581-1 subject 97303


title: RNA_Mycelia_WT_Ag0.3uM

description: RNA-Seq


title: whole brain 86E01 d70 rep2

source_name: whole brain

value: whole brain


title: whole brain 86E01 d70 rep3


title: RNA_Conidia_H153G_Ag3uM

description: RNA-Seq

source_name: conidia

value: conidia


title: RNA_Mycelia_WT_DMSO1

description: RNA-Seq


title: siRNA-RP0581-1 subject 97265


title: whole brain 86E01 d70 rep1


title: siRNA-RP0581-1 subject 97297


title: whole brain 86E01 d5 rep3


title: DIO-NASH Vehicle subject 97267

value: Vehicle


title: whole brain 86E01 d5 rep2


title: RNA_Conidia_H153G_Ag0.3uM

description: RNA-Seq


title: RNA_Conidia_H153G_DMSO2

description: RNA-Seq


title: whole brain 86E01 d5 rep1


title: whole brain 56F03 d70 rep3


title: DIO-NASH Vehicle subject 97271


title: DIO-NASH Vehicle subject 97282


title: DIO-NASH Vehicle subject 97249


title: whole brain 56F03 d70 rep2


title: whole brain 56F03 d70 rep1


title: RNA_Conidia_WT_Ag0.3uM

description: RNA-Seq


title: RNA_Mycelia_WT_DMSO2

description: RNA-Seq


title: DIO-NASH Vehicle subject 97317


title: DIO-NASH Vehicle subject 97293


title: Ribo_Mycelia_H153G_Ag3uM

data_processing:
library strategy: Ribosome profiling
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: C. orbiculare 104-T 43 (PRJNA171217)
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

source_name: eIF4A-H153G_Aglafoline 3 µM

extract_protocol:
Cells were filtered, scraped, and soaked in liquid nitrogen with 600 µl of lysis buffer. The frozen cells and lysis buffer grains were milled by a Multi-beads Shocker at 2,800 rpm for 15 se for 1 cycle.
RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification.

value: Aglafoline 3 µM


title: whole brain 56F03 d5 rep1


title: Ribo_Mycelia_H153G_Ag0.3uM

source_name: eIF4A-H153G_Aglafoline 0.3 µM

value: Aglafoline 0.3 µM


title: Ribo_Mycelia_H153G_DMSO2


title: whole brain 56F03 d5 rep2


title: whole brain 10E12 d70 rep3


title: whole brain 10E12 d70 rep2


title: RNA_Conidia_WT_Ag3uM

description: RNA-Seq

value: Aglafoline 3 uM


title: RNA_Conidia_H153G_DMSO1

description: RNA-Seq


title: Ribo_Mycelia_WT_Ag3uM

source_name: eIF4A-WT_Aglafoline 3 µM


title: Ribo_Mycelia_WT_Ag0.3uM

source_name: eIF4A-WT_Aglafoline 0.3 µM


title: Ribo_Mycelia_H153G_DMSO1


title: DIO-NASH Vehicle subject 97291


title: whole brain 10E12 d70 rep1


title: sFlt1 c57Bl6/ICR crossbred male age 3 months rep2

city: Jerusalem

first: Tamar

last: Licht

address: Hadassah ein karem

department: Medical Neurobiology

country: Israel

institute: Hebrew University

description: columns S, Y in processed data

data_processing:
Multiplex samples Pool (1.65 pM including PhiX 1%) was loaded in NextSeq 500/550 High Output v2 kit (75 cycles) cartridge (catalog #FC-404-1005; Illumina, San Diego, CA) and loaded on NextSeq 500 System machine (Illumina), with 75 cycles and single-Read sequencing conditions.
Raw reads were quality-trimmed with cutadapt, v3.5, then poly-G and adapter sequences were removed from the 3' end
Processed reads were aligned to the mouse GRCm39 genome with Tophat, v2.2.1, allowing for 5 mismatches, using gene annotations from Ensembl release 106.
Raw counts per gene per sample were obtained with htseq-count, v2.0.1, then normalization was done with the DESeq2 package, v1.26.0.
second normalization of olfactory receptors signal, aiming to compensate for the probably smaller population of OSNs in the sFlt1 mice, following the method described in (PMID 23962816, 28438259) are found in processed data.
Assembly: GRCm39 ,Ensembl release 106
Supplementary files format and content: Excel table. First sheet is a full list of sequenced genes, raw and normalized reads. Second sheet are the olfactory receptors. Third sheet in annotation of genes representing different cells in the olfactory epithelium. Fourth sheet are olfactory receptor genes after double normalization to genes representing all receptor cells (as in PMID 23962816, 28438259).

source_name: olfactory epithelium

growth_protocol: mice housed in normal SPF conditions with food and water ad lib. Age 3m at sacrifice.

extract_protocol:
Nasal conchae were dissected and RNA was harvested using Quick RNA MicroPrep kit (Zymo). 200ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using ScreenTape Library Prep Kit (Agilent) following manufacturer's protocols.

treatment_protocol: transgenic mice are a cross of camk2a-tTa line and tet-sFlt1 line (as in PMID: 25689256). Tetracycline was replaced by fresh water at embryonic day 13.5. Olfactory bulb size at 2months was estimated by MRI.

value: olfactory epithelium

value: sFlt1 induction at e13.5

tag: olfactory bulb_size

value: 29% of normal


title: DIO-NASH Vehicle subject 97324


title: DIO-NASH Vehicle subject 97264


title: RNA_Conidia_WT_DMSO1

description: RNA-Seq

value: DMSO


title: DIO-NASH Vehicle subject 97253


title: sFlt1 c57Bl6/ICR crossbred male age 3 months rep3

description: columns T, Z in processed data

value: 14% of normal


title: sFlt1 c57Bl6/ICR crossbred male age 3 months rep1

description: columns R, X in processed data

value: 28% of normal


title: whole brain 10E12 d5 rep2


title: Ribo_Mycelia_WT_DMSO1


title: Ribo_Mycelia_WT_DMSO2


title: control c57Bl6/ICR crossbred male age 3 months rep3

description: columns Q, W in processed data

value: WT

value: no treatment

value: normal


title: whole brain 10E12 d5 rep3


title: Ribo_Conidia_H153G_Ag3uM


title: whole brain 56F03 d5 rep3


title: whole brain 10E12 d5 rep1


title: Ribo_Conidia_H153G_Ag0.3uM


title: control c57Bl6/ICR crossbred male age 3 months rep2

description: columns P, V in processed data


title: Ribo_Conidia_H153G_DMSO2


title: control c57Bl6/ICR crossbred male age 3 months rep1

description: columns O, U in processed data


title: GMEC3

city: Nanning

first: Sheng

last: Ye

address: No. 100 of Daxue East Road

institute: Guangxi University

data_processing:
Illumina seqencing reads were cleaned for quality control and tested the results using FastQC(version0.10.1).
Ribosome RNA were removed again from clean reads
High-quality reads were mapped to the refer genome to obtain BAM files
the read count for each gene in each sample was counted by HTSeq, and the fragments per kilobase of million mapped reads (FPKM) was then calculated
Differential expression analysis was performed using DESeq2 (v1.16.1) with read count
Genome_build: CaprahircusARS1; GCF_001704415.1
Supplementary_files_format_and_content: xls files include FPKM values for each Sample .

organism: Capra hircus

source_name: goat mammary epithelial cells (GMECs)

extract_protocol:
Extract total RNA from each sample,then use Ribo-Zero™ Gold Kits (Human/Mouse/Rat)  to delete rRNA
RNA fragmentation and short RNA strands were carried out by NEBNext First Strand Synthesis Reaction Buffer under elevated temperature. Subsequently， First cDNA strand was synthesized using random hexamer primers and RNA fragments as template. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were  purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair、 add poly(A)and adapter were implemented. Libraries were sequenced on Illumina HiSeq 2500

treatment_protocol: GEFs were seeded at a density of 5×10^5 cells per 60 mm dish and cultured in the incubator at 37.5°C in a humidified atmosphere of 5% CO2 with fibroblast culture medium; GMECs  were cultured in the incubator at 37.5°C in a humidified atmosphere of 5% CO2 with GMEC culture medium.

tag: cell type

value: Naturally derived mammary epithelial cells


title: GMEC2


title: B16F10 tumors, Transected 20

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd.

department: Department of Biomedical Informatics

institute: University of Pittsburgh

data_processing:
Alignment using HISAT2 2.1.0 build of Ensembl GRCm38 of primary assembly with default paired-end unstranded parameters and converting to sorted bam files using Samtools version 1.10
Counts were generated using HT-Seq 0.11.2 using Ensembl GRCm38 as GTF file and using position sorted order, reverse strandedness, gene_id GFF attribute, union mode, and exon feature type as parameters
edgeR in Rstudio using R version 4.0 including CPM values for each sample
Genome_build: GRCm38
Supplementary_files_format_and_content: Bunimovich_rawcounts.csv

source_name: B16F10 tumors, Transected

growth_protocol: B16F10 tumors were established in C57Bl/6 mice and grew for 17 days

extract_protocol:
Melanoma tumors were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used for the construction of sequencing libraries.
Illumina TruSeq stranded mRNA, cat #: 200205
NextSeq high output 150 cycle kit, paired end (2x75); 400 ng total RNA used per sample.

treatment_protocol: Two months before B16F10 injection, one group of mice were denervated: dorsal thoracic sensory neurons on the left side were removed and proximal nerve stubs were tied off with sutures

value: B16F10 melanoma tumor

value: Transected (denervated)


title: Ribo_Conidia_H153G_DMSO1


title: GMEC1


title: Ribo_Conidia_WT_Ag3uM


title: GEF2

source_name: goat ear fibroblasts (GEF)

value: Ear fibroblasts


title: B16F10 tumors, Transected 15


title: B16F10 tumors, Transected 19


title: Ribo_Conidia_WT_Ag0.3uM


title: B16F10 tumor, Control 11

source_name: B16F10 tumor, Control

value: Control (innervated)


title: B16F10 tumor, Control 13


title: Ribo_Conidia_WT_DMSO1


title: Ribo_Conidia_WT_DMSO2


title: GEF1


title: B16F10 tumor, Control 12