title: pupa Verson's glands

city: Lexington

first: Jin mo

last: Koo

state: Kentucky

address: 100 South Limestone Street

institute: University of Kentucky

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were mapped to the genome (ZJU_Sfru_1.1) using CLC genomic benchwork (parameters- mismatch cost 2, insertion cost 3, deletion cost 3, length fraction 0.8, and similarity fraction 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: ZJU_Sfru_1.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Spodoptera frugiperda

source_name: Verson's glands from pupa

extract_protocol:
RNA was isolated using Trizol (Molecular Research Center Inc., Cincinnati, OH).
size fractionation

value: Verson's glands from pupa


title: prepupa Verson's glands

status: Public on Mar 01 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

source_name: Verson's glands from prepupa

tag: tissue

value: Verson's glands from prepupa


title: Caenorhabditis elegans-high glucose induce with naringin-rep3

city: Zhengzhou

first: Panpan

last: Wang

address: 郑州市高新区科学大道100号郑州大学

department: College of Public Health

country: China

institute: 郑州大学

data_processing:
The trimmed data was aligned to reference genome (WBcel235) by Hisat2 (2.1.0). The StringTie (1.3.3) software was applied to estimate transcription abundance and get the count data of genes and transcripts. Differentially expressed analysis was conducted by “Ballgown” (2.10.0) of the R package. The mRNAs which mean expression in all samples were greater than 1 were eligible for next analysis.  CircRNAs were identified and quantitated by the software of STAR (2.5.2b) and CIRCexplorer2 (2.3.2). Count data of circRNA were used to perform differentially expressed analysis using “edgeR” of R package.
Assembly: WBcel235
Supplementary files format and content: tab-delimited text files include count, FPKM values for each Sample.

organism: Caenorhabditis elegans

source_name: whole individual

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

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

treatment_protocol: Naringin was dissolved to 25μM, and the L4-larvae of C. elegans was exposed to 2% glucose, 2% glucose with DMSO and 2% glucose with naringin mixed with NGM and then added with OP50 at 20 °C.

tag: strain background

tag: genotype

value: wild type

tag: treatment

value: high glucose induce with naringin


title: last instar (L6) Verson's glands

source_name: Verson's glands from last instar (L6) larvae


title: Plasma_MCI_006

type: RNA

city: shanghai

first: wei

last: zhang

address: 600 South Wan Ping Road

department: Geriatric Psychiatry

institute: Shanghai Mental Health Center

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

data_processing: After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

organism: Homo sapiens

source_name: plasma

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: Blood samples of all participants were collected after fasting for 12 hours. Then plasma was separated by centrifugation at 3,000 rpm for 20 minutes at 4C.

tag: age

tag: gender

value: male


title: Kasumi-1_SMARCA5FKBP12_0hdTAG47_1 [PRO-seq]

city: Nashville

first: Scott

middle: W

last: Hiebert

state: TN

address: 512 B Preston Research Building

department: Biochemistry

institute: Vanderbilt University

description: biotinylated RNA

data_processing:
Library strategy: PRO-seq
Adaptors were trimmed and short/low quality sequence filtered by Trimmomatic-0.32: ILLUMINACLIP:adaptor.txt:2:30:7 TRAILING:15 MINLEN:15
Reverse complement sequence was generated using fastx_reverse_complement from the FASTX toolkit (v 0.0.13).
Reverse complement sequences were aligned to the human genome (hg19)+ S2 genome using bowtie2 (v2.2.2).
samtools -view generated .bam file with hg19 chromosomes.
Differential transcript analysis was carried out using the Nascent RNA Sequencing Analysis (NRSA) pipeline - pause_PROseq.pl with DESeq normalization.
Differential eRNA analysis was carried out using the Nascent RNA Sequencing Analysis (NRSA) pipeline - eRNA.pl
Bedgraph files were generated by Homer makeUCSCfile.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Homer-generated bedgraph files. neg.bedGraph: negative strand, plus.bedGraph: positive strand.
Supplementary_files_format_and_content: Differential gene transcription analysis generated by NRSA; tab-delimited text files. gb_change.txt: gene body changes, Enhancer_change: eRNA changes.

source_name: Kasumi-1 cells

growth_protocol: Kasumi-1 cells were grown in RPMI +20% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine.

extract_protocol:
Following nuclear run-on, total RNA was isolated by Trizol extraction and biotinylated RNA isolated by streptavidin bead binding.
Following hydrolysis of RNA, 3' adaptors were ligated to biotinylated RNA fragments. After 5'Cap removal and end repair, 5' adaptors were also ligated. Adaptor-ligated RNA fragments were reverse transcribed and cDNA libraries amplified using indexed primers.

treatment_protocol: Cells were treated with 500 nM dTAG-47 for the indicated timepoints.

tag: cell line

tag: genotype/variation

value: Untreated

tag: time point


title: DG_2

city: changsha

first: Hao

last: Wu

address: shaunghe Road 728

institute: Hunan Fisheries Science Institute

data_processing:
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000.
Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
The featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: ncbi_refseq_cyprinus_carpio_common_carp_genome_gcf_000951615_1
Supplementary_files_format_and_content: execl files include FPKM values for each sample

organism: Carassius gibelio

source_name: gills tissue

extract_protocol:
The total RNA was extracted using an RNA isolation kit (TaKaRa, Dalian, China) according to the manufacturer’s instructions. The RNA integrity was determined by 1.0% agarose gel electrophoresis, and Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA.Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: exposed to deltamethrin for 24h

value: gills tissue

value: juvenile fish


title: Caenorhabditis elegans-high glucose induce with naringin-rep2

address: 郑州市高新区科学大道100号郑州大学


title: Kasumi-1_parental_2 [PRO-seq]

description: biotinylated RNA

value: Parental


title: DG_3


title: DG_1


title: Caenorhabditis elegans-high glucose induce with DMSO-rep3

address: 郑州市高新区科学大道100号郑州大学

value: high glucose induce with DMSO


title: Kasumi-1_parental_1 [PRO-seq]

description: biotinylated RNA


title: Caenorhabditis elegans-high glucose induce with naringin-rep1

address: 郑州市高新区科学大道100号郑州大学


title: CG_3

value: Control


title: Normal Lung FFPE MeDIP-seq

city: St. Louis

first: Ting

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

description: TW ID: TW1044

library_source: genomic

data_processing:
Read lengths and sequencing information for each sample is as follows: GM12878 Traditional MRE-seq: 1x75bp single-end (NextSeq).  GM12878 Capture MRE-seq: 1x75bp single-end (NextSeq).  GM12878 (1 min Sonicated) Capture MRE-seq: 2x75 paired-end (processed as single-end) (NextSeq).  GM12878 (10 min Sonicated) Capture MRE-seq: 2x75 paired-end (processed as single-end) (NextSeq).  GM12878 MeDIP-seq: 2x101 paired-end (HiSeq).  Normal Lung FFPE Capture MRE-seq: 2x75 paired-end (NextSeq).  Normal Lung FFPE MeDIP-seq: 2x75 paired-end (NextSeq).
Traditional MRE-seq, Capture MRE-seq, and MeDIP-seq reads were filtered using cutadapt to remove adapter sequences, with a quality filter of q = 10 and removing reads less than 20 nucleotides long
Traditional MRE-seq, Capture MRE-seq, and MeDIP-seq reads were all aligned to the hg19 genome assembly using BWA mem
MRE files were processed using methylQA in "mre" mode with parameter -c 4 (unless sequenced with a predominantly non-MRE-library, in which case -c 1 was used (see explanation in manuscript)), MeDIP files were processed using methylQA in "medip" mode (and default -c)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated for each sample using methylQA. Values indicate the number of MeDIP-seq or MRE-seq reads in the genomic interval indicated.

molecule: genomic DNA

source_name: Normal lung FFPE tissue

growth_protocol: GM12878 cell line was cultured in RPMI 1640 containing 2mM L-glutamine and 15% FBS in a T25 flask at 37°C under 5% carbon dioxide.

extract_protocol:
DNA was extract from GM12878 cells using Quick DNA plus kit (Zymo, D4074), DNA was extracted from the normal lung FFPE tissue using Quick DNA FFPE Kit (Zymo, D3067) with the modification indicated in this study.
MeDIP-seq and Traditional MRE-seq are from the paper: "Tost J. (eds) DNA Methylation Protocols. Methods in Molecular Biology, vol 1708". Capture MRE-seq is modified based on Traditional MRE-seq.

treatment_protocol: no treatment

tag: cell type

value: Normal lung

tag: dna quality

value: FFPE

tag: data type

value: MeDIP-seq


title: P54d7_FcrL5pos_TETpos_IgDneg_MBC_2

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description: geneRpkm.detected.csv

data_processing:
Raw sequencing reads were mapped to the hg38 using STAR and the UCSC KnownGene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor and normalized to fragments per kilobase per million (FPKM).  Genes were filtered for detection based on being expressed at greater than or equal to 10 reads per million in all samples for at least one group.
Genome_build: hg38
Supplementary_files_format_and_content: Annotation file containing RPKM normalized read counts for all detected genes.

molecule: polyA RNA

source_name: FCRL5 positive HA+IgD neg B cell

extract_protocol:
Cells were FACS sorted from PBMCs according to the indicated sort markers into RLT+1%Bme using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
All purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). Final libraries were constructed using 400 pg of cDNA as input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

tag: donor id

tag: Sex

value: Male

tag: sorting markers

value: IgDneg  CD38 lo/med CD19+ CD3 neg CD4 neg

tag: h1 tetramer

value: positive

value: PBMC

tag: days post influenza pr8 infection


title: Caenorhabditis elegans-high glucose induce with DMSO-rep2

address: 郑州市高新区科学大道100号郑州大学

value: wild type


title: CG_1

tag: tissue


title: Caenorhabditis elegans-high glucose induce with DMSO-rep1

address: 郑州市高新区科学大道100号郑州大学

tag: strain background


title: Normal Lung FFPE Capture MRE-seq

description: TW ID: TW1010

value: Capture MRE-seq


title: Caenorhabditis elegans-high glucose induce-rep3

address: 郑州市高新区科学大道100号郑州大学

tag: genotype

value: high glucose induce


title: GM12878 MeDIP-seq

description: TW ID: TW246

source_name: GM12878 cell line

value: B lymphocyte

value: Good / Normal


title: GM12878 (10 min Sonicated) Capture MRE-seq

description: TW ID: TW789

value: 10 minutes sonicated


title: PRE_Case_25

type: genomic

city: Grand Rapids

first: Hyo Sik

last: Jang

state: Michigan

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: DNA methylome

hyb_protocol: An extension reaction was performed using fluorophore-labeled nucleotides per the manufacturer’s protocol.

scan_protocol: Array BeadChips were scanned on the Illumina iScan system to produce IDAT files.

data_processing:
IDATs were processed with the R Bioconductor (release 3.8) package sesame (version 1.0.0) using the default openSesame pipeline. Probe masking was performed using the standard mask list in sesame, including probes that overlap with SNPs and repeat elements. De-identified files were generated by removing data from the SNP probes using the deidentify function in sesame.
Processed data were generated as tab-delimited text file containing β values defined as Sm /(Sm+Su) for each locus, where Sm and Su represent signal intensities for methylated and unmethylated allele.

label: Cy3 and Cy5

source_name: Tumor needle biospy

label_protocol: DNA was bisulfite-converted using the Zymo EZ DNA Methylation Kit (Zymo Research), cleaned using the Zymo-Spin binding columns, and processed through the EPIC array protocol. For FFPE samples, BS converted eluate from the spin columns was used as input for the Infinium HD FFPE DNA Restore kit and processed through the separate restoration workflow. BS converted DNA was denatured, amplified, and hybridized to the EPIC bead chip.

extract_protocol: DNA was extracted from frozen tissues and FFPE solid tissues using a modification of the AllPrep DNA/RNA kit (Qiagen) and the AllPrep DNA/RNA FFPE kit (Qiagen), respectively. DNA was quantified by Qubit fluorimetry (Life Technologies). Only Patients yielding a minimum of 250ng of tumor DNA were included in this study.

tag: treatment timepoint

value: Pre-treatment


title: Multidrug-resistant cell line, K562R, rep3

city: Guiyang

first: Yunsheng

last: Ran

state: Guizhou

address: No. 9 Beijing Road, Guiyang City, Guizhou Province

department: Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D

institute: Guizhou Medical University

description:
A2495
chronic myeloid leukemia

hyb_protocol: Use the Hybridization program to heat the hybridization solution. At the same time, 80 μl of pre-hybridization solution was injected into the chip, and the hybridization oven was pre-hybridized at 45°C for 10 min. Aspirate the pre-hybridization solution from the chip and inject 80 μl of the hybridization solution. Put in hybridization oven, 45℃, 60rpm hybridization for 16 hours (do not exceed 18 hours).

scan_protocol: Automated dyeing was performed with a GeneChip Fluidics Station 450 instrument. Scan with GeneChip Scanner 3000 after dyeing to obtain data.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: multidrug-resistant cell line K562R

label_protocol: After total RNA samples were analyzed by Agilent 2100, cDNA was prepared using GeneChip WT PLUS Kit.

growth_protocol: Parent CML cell lines K562 and multidrug-resistant cell line K562R cells were maintained in RPMI 1640 medium with 10% FBS.

extract_protocol:
Collect cells in each group, transfer them to 1.5mL EP tubes, centrifuge (1000rpm, 5min), wash once with PBS or normal saline, centrifuge (1000rpm, 5min), add 1000μl Trizol, shake and mix well.
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: phenotype

value: TKI-resistant


title: PRE_Case_31

description: DNA methylome


title: CG_2

tag: treatment

value: gills tissue

tag: age

value: juvenile fish


title: Multidrug-resistant cell line, K562R, rep2

description:
A2494
chronic myeloid leukemia

tag: cell line


title: PRE_Case_24

description: DNA methylome


title: PRE_Case_28

description: DNA methylome


title: Caenorhabditis elegans-high glucose induce-rep1

address: 郑州市高新区科学大道100号郑州大学


title: Caenorhabditis elegans-high glucose induce-rep2

address: 郑州市高新区科学大道100号郑州大学


title: GM12878 (1 min Sonicated) Capture MRE-seq

description: TW ID: TW788

value: 1 minute sonicated


title: Caenorhabditis elegans-control-rep3

address: 郑州市高新区科学大道100号郑州大学

value: untreated


title: GM12878 Capture MRE-seq

description: TW ID: TW775


title: Caenorhabditis elegans-control-rep2

address: 郑州市高新区科学大道100号郑州大学


title: PRE_Case_21

description: DNA methylome


title: PRE_Case_27

description: DNA methylome


title: GM12878 Traditional MRE-seq

description: TW ID: TW774

value: Traditional MRE-seq


title: PRE_Case_16

description: DNA methylome


title: Caenorhabditis elegans-control-rep1

address: 郑州市高新区科学大道100号郑州大学


title: PRE_Case_20

description: DNA methylome


title: CML parent cell line, K562, rep3

description:
A2492
chronic myeloid leukemia

source_name: CML parent cell line K562 without drug treatment

value: TKI-sensitive


title: CML parent cell line, K562, rep2

description:
A2491
chronic myeloid leukemia


title: CML parent cell line, K562, rep1

description:
A2490
chronic myeloid leukemia


title: Pistil 2N, replicate 2, snRNAseq

status: Public on Feb 28 2023

city: Singapore

last: Yu

address: 16 Science Drive 4

country: Singapore

institute: National University of Singapore

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: IRGSP1.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Oryza sativa Japonica Group

source_name: pistil

growth_protocol: Rice (Oryza sativa ssp. Japonica cultivar Nipponbare) plants were grown in the potting soil mixed with sand in climate chambers with a relative humidity of 70%, under the following circadian rhythm: 10 h light at 30℃ and 14 h dark at 25℃.

extract_protocol:
Dissected pistils were frozen in liquid nitrogen and ground to powder. The powder was suspended by nucleus isolation buffer. Then, the crude nuclei were enriched from the slurry by applying 10 μm mini cell strainer, and were subsequently purified by PI-labeled FANS. The purified nuclei adjusted by the nucleus count were subjected to GEM partitioning
Library was performed according to the manufacter’s instructions. For 2N nuclei: Chromium Next GEM single cell 3’ v3.1 protocol, Rev_D, 10x Genomics. For 1N nuclei: Chromium Next GEM Single Cell 3' LT v3.1, protocol, 10x Genomics).

value: pistil

tag: developmental stage

value: heading stage


title: Pistil 1N, replicate 1, snRNAseq

description: 10x Genomics


title: SH-EP

city: Leipzig

first: Jörg

last: Fallmann

address: Härtelstraße 16ß18

country: Germany

institute: Leipzig University

data_processing:
Fastq raw data cleaning with cutadapt-3.4 (cutadapt -e 0.2 -m 1 -g AAGCAGTGGTATCAACGCAGAGTAC -o FileName_5pTrimmed.fastq.gz FileName.fastq.gz then cutadapt -e 0.2 -m 1 -a GTACTCTGCGTTGATACCACTGCTT -o TrimmedFileName.fastq.gz FileName_5pTrimmed.fastq.gz)
circRNA identification with CIRI-long-v1.0.3 (CIRI-long call -i TrimmedFileName.fastq.gz -o step1 -r genome.fa -p SampleName -a genome.gtf -t 10 then CIRI-long collapse -i SampleFile.lst -o step2 -p SampleName -r genome.fa -a genome.gtf -t 10)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files reporting  circRNA candidates, header included

source_name: neuroblastoma cell line

growth_protocol: Standard cell culture of wild-type cell lines.

extract_protocol:
Cells were harvested and RNA was isolated with Trizol.
Depletion of ribosomal RNA. Exonuclease digest and negative selection of poly(A) transcripts to enrich for circular RNAs. cDNA library preparation (SMARTer) and PCR amplification, according to Fuchs et al. PMID 36070299
Oxford Nanopore long-read RNA sequencing (SQK-LSK109 kit with native barcoding kit EXP-NBD104, BC01-04)

treatment_protocol: No special treatment of the cells was applied.

tag: cancer type

value: neuroblastoma


title: LS


title: Multidrug-resistant cell line, K562R, rep1

description:
A2493
chronic myeloid leukemia


title: SK-N-FI


title: Pistil 2N, replicate 1, snRNAseq

description: 10x Genomics

value: wild type


title: SH-SY5Y


title: Lan-5


title: male Lxn-/- rep3

first: Ying

last: Liang

state: KY

address: 760 press avenue

data_processing:
Individually indexed libraries were proportionally pooled and sequenced using NextSeq 550 sequencer (Illumina, San Diego, CA) under the sequencing setting of single read 1x85 bp.
Sequencing reads were trimmed and filtered using Trim Galore to remove adapters and low-quality reads
Reads from mouse samples were mapped to Ensembl GRCm38 transcripts annotation using RSEM
Assembly: GRCm38
Supplementary files format and content: Processed data files are in txt format and contain the following contents: Ensembl gene ID, Ensembl transcript(s) ID, length, effective length, expected count, TPM, FPKM

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
LSK cells were flow cytometrically sorted from bone marrow cells by using cell surface marker Lineage-, Sca1+, and cKit +. Total RNA was isolated by using NEBNext Ultra RNA Library Prep Kit.
NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs) was used for library preparation under PCR cycle number of 9.

value: Bone marrow

tag: cell type

value: LSK cells

value: latexin knockout


title: male Lxn-/- rep2


title: PRE_Case_18

description: DNA methylome


title: IMR-5


title: POST_Case_21

description: DNA methylome

value: Post-treatment


title: male WT rep3

value: WT


title: POST_Case_24

description: DNA methylome


title: male WT rep1


title: male Lxn-/- rep1


title: female  Lxn-/- rep4


title: POST_Case_14

description: DNA methylome


title: male WT rep2


title: female  Lxn-/- rep1


title: PRE_Case_19

description: DNA methylome

value: Pre-treatment


title: PRE_Case_23

description: DNA methylome


title: PRE_Case_7

description: DNA methylome


title: female WT rep2


title: female  Lxn-/- rep2


title: PRE_Case_12

description: DNA methylome


title: Producer3_5

city: Heidelberg

first: Geetha

last: Venkatesh

address: Im Neuenheimer Feld 580

institute: DKFZ

data_processing:
Basecalling with: bcl2fastq 2.20.0.422
Preprocessing, read trimming: Trimmomatic 0.38
Preprocessing, quality filtering: Trimmomatic 0.38
BS-mapping: BSMAP 2.9
Computation of methylation ratios: methratio.py (part of bsmap package)
Assembly: GCA_020271785.1
Supplementary files format and content: bedGraph-format containing the genomic methylation ratios and coverage values of the respective sample

organism: Penaeus vannamei

source_name: Abdominal musculature

extract_protocol:
Genomic DNA was extracted from abdominal muscle using a Tissue Ruptor (Qiagen), followed by proteinase K digestion and isopropanol precipitation
Accel-NGS Methyl-Seq DNA

value: Abdominal musculature

tag: location


title: Producer3_4


title: Producer3_3


title: female WT rep4


title: Producer2_3


title: PRE_Case_14

description: DNA methylome


title: Producer3_2


title: POST_Case_4

description: DNA methylome


title: female WT rep1


title: POST_Case_7

description: DNA methylome


title: Producer3_1


title: Producer2_4


title: Producer2_5


title: EV2_FBS_Normo

city: Genova

first: simona

last: coco

address: L.go R. Benzi, 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

description: miRNA profiling

hyb_protocol: After adding Hyb Spike-In, each sample was hybridized at 55°C for 20 hours on G4872A-070156 Human miRNA Microarray, Release 21.0, 8 x 60K (Agilent Technologies). The supplement of a commercial synthetic DNA poly-A oligonucleotide 3’ labeled pCp-Cy3, was added to the final hybridization mix. The 30-mer synthetic oligonucleotide (HPLC purified) was synthesized by TIB Molbiol s.r.l. (Genova, Italy) at 50 amol/μL.

scan_protocol: Microarrays were scanned (3 microns, 20 bit) on an Agilent microarray scanner (part number G2505C) and data extracted using Agilent feature extraction v.12.0.0.7. QC metrics from feature extraction were used to evaluate the success of the labeling and hybridization.

data_processing: Pre-processing, filtering and differential expression analysis were carried out using the Limma package, available within Bioconductor. Background correction and between array normalization were carried out using the normexp method, with an offset = 20, and the quantile method, respectively. Replicated probes were then averaged.

label: Cyanine 3-pCp

source_name: EV from primary Bone Marrow Stromal Cells

label_protocol: EV-RNA samples were processed using the Agilent miRNA complete labeling and hybridization kit (part number 5190-0456) and Agilent miRNA spike-in kit (part number 5190-1934). The Agilent miRNA microarray was performed using 50 ng of purified EV- RNA.

growth_protocol: Cells were cultured in Alpha-MEM-GlutaMAX, supplemented with 100 U/ml penicillin-100 mg/ml streptomycin mixture and (i) 10% FBS, 1 ng/ml Fibroblast Growth Factor-2 for standard culture conditions, (FBS-samples) or (ii) Xeno-free Purstem supplement (XFS-samples).

extract_protocol: Extracellular Vesicles (EVs) were suspended in 1 ml of Qiazol reagent (Qiagen); EV-RNA was extracted with the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions and stored at -80 °C. MiRNA content was evaluated by the Qubit® 2.0 Fluorometer using the Qubit® microRNA Assay Kit (Thermo Fisher Scientific) and small RNA quality and size were assessed by Agilent 2100 Bioanalyzer using the Small RNA chip (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: hBMSCs were cultured until 60% confluence. Then, the medium was discarded and, after three PBS 1X washes, replaced with α-MEM-GlutaMax medium with only 100 U/ml of Penicillin-100 mg/ml Streptomycin (basal medium). Cells were maintained under normoxic (20% O2 and 5% CO2 at 37 °C) or hypoxic (1% O2 and 5% CO2 at 37 °C in a hypoxic incubator) conditions, for 72 h. Conditioned media (CM) were collected and centrifuged at 300 g for 10 min at 4 °C to eliminate dead cells and debris, and at 2,000 g for 20 min at 4 °C to get rid of apoptotic bodies. Clarified CM was then ultracentrifuged at 10,000 g for 40 min at 4 °C, and finally at 100,000 g for 2 h at 4 °C, to pellet small-size EVs (sEVs).


title: PRE_Case_3

description: DNA methylome


title: Producer2_1


title: PRE_Case_4

description: DNA methylome


title: EV2_FBS_Hypo

description: miRNA profiling


title: Producer2_2


title: POST_Case_3

description: DNA methylome


title: Producer1_3


title: Producer1_2


title: EV1_FBS_Hypo

description: miRNA profiling


title: Producer1_1


title: Bt_HD73_pCER_plus_HCT_biol rep 3

city: JOUY-EN-JOSAS

first: Alicia

last: Nevers

address: Domaine de Vilvert

department: Micalis

country: France

institute: Institut national de la recherche agronomique (Inrae)

data_processing:
Demultiplexing using bcl2fastq2-2.18.12
Adaptors trimming with Cutadapt 3.2
Read alignment to references genome with Bowtie2 in Galaxy. Write unaligned reads (in fastq format) to separate file(s): False; Write aligned reads (in fastq format) to separate file(s): False; Do you want to set paired-end options?: no  Will you select a reference genome from your history or use a built-in index?: indexed; Select reference genome: internal genomes uploaded from NCBI; Set read groups information?: do_not_set; Select analysis mode: simple; Do you want to use presets?: Very fast end-to-end (--very-fast); Save the bowtie2 mapping statistics to the history: True
Read counting with MulticovBed in Galaxy. Calculation based on strandedness?: Only overlaps occurring on the **same** strand.; minimum overlap required as a fraction of A: 1e-09; Require that the fraction of overlap be reciprocal for A and B: False; Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage: False; Minimum mapping quality (MAPQ) allowed:0; Include duplicate reads: True; Include failed-QC reads: False; Only count proper pairs: False
CP001179 (pCER270); CP001177 (Chromosome) and CP001178-CP001181 (plasmids) for AH187 = Bc_F4810-72; CP004069 (Chromosome) and CP004069-CP004076 (plasmids) excluding  CP004072 (pAW63) for B_th_HD73; in-house unpublished genome for B_we_KBABA6
Supplementary files format and content: raw count txt files
Supplementary files format and content: BweKBAB6_pXO16tcR_corrV170303.txt is a file with FASTA sequences corresponding to each transcriptional feature

organism: Bacillus thuringiensis

source_name: liquid bacterial culture

growth_protocol: For RNA preparation, LB cultures were collected two hours (early stationary phase) after the beginning of stationary phase, whereas in HCT medium the cultures were collected four hours after the onset of the stationary phase (commitment to sporulation). The onset of the stationary phase is determined as the end of the exponential growth and corresponds to an inflection of the growth curve.

extract_protocol:
RNA extraction was performed using Trizol and 1-bromo-3-chloropropane
After ribosomal RNA depletion, NextSeq 500/550 High Output Kit v2 was used to construct library
Single-read 75 sequencing run

tag: strain

value: liquid bacterial culture

tag: time

value: Commitment to sporulation

value: pAW63{delta}; pCER270+

tag: medium

value: HCT (sporulation medium)


title: EV1_FBS_Normo

description: miRNA profiling


title: Producer1_4


title: Bt_HD73_pCER_minus_HCT_biol rep 2

value: pAW63{delta}; pCER270-


title: Bt_HD73_pCER_plus_HCT_biol rep 2


title: PRE_Case_1

description: DNA methylome


title: Bt_HD73_pCER_plus_LB_biol rep 1

value: Early stationary phase

value: LB


title: Bt_HD73_pCER_plus_HCT_biol rep 1


title: POST_Case_2

description: DNA methylome


title: Bt_HD73_pCER_minus_LB_biol rep 3


title: EV1_XFS_Hypo

description: miRNA profiling


title: Bt_HD73_pCER_plus_LB_biol rep 2


title: EV1_XFS_Normo

description: miRNA profiling


title: Panc1 resistant to gemcitabine cells

city: Amsterdam

first: Elisa

last: Giovannetti

address: de boelelaan

country: Netherlands

institute: Amsterdam UMC

data_processing:
FASTQ files were checked for quality reads and adapters were removed with Trimmomatic. Successfully quality passed reads were mapped to the human reference genome (Hg19) with STAR mapping tool and gene counts were extracted with HTSeq.
Normalization and differential analysis were performed with Bbtest (Pham T.V. et al.)
Assembly: Hg19
Supplementary files format and content: raw data in txt
Supplementary files format and content: normalized data in xlsx

source_name: pancreatic ductal adenocarcinoma

growth_protocol: Cells were grown in RPMI supplemented with 10% (v/v) heat-inactivated FBS and 1% (v/v) penicilin-streptomycin. Gemcitabine reistant cells were cultured without any drug treatment and periodically tested for gemcitabine resistance, to ensure their stable resistance.

extract_protocol:
Remove medium, wash the cells twice with PBS and detach by adding trypsin-EDTA and incubating at 37 °C for 3 min. Add culture medium and harvest 106 cells.  Spin down samples at 300 x g for 3 min, remove supernatant and extract total mRNA using commercially available silica membrane spin columns, by following the manufacturer`s protocol.  Determine the concentration and purity of total RNA by using a UV-Vis spectrophotometer. The samples were stored at - 80 °C.  Total RNA integrity was assessed by electrophoresis of 200 ng of sample on 1% agarose gel stained with ethidium bromide.
Use 2 µg of total mRNA per each sample. Follow mRNA library preparation protocol according to manufacturer's instructions. Determine quality and concentration of each library by using a bioanalyzer system. Pool the libraries in a single sample up to a final concentration of 10 nmol/L and measure it with the bioanalyzer.
Use high-throughput sequencing system with Single Read 100 bp mode.

value: pancreatic ductal adenocarcinoma

value: Panc 1

value: immortalized cell line

value: Resistant to Gem


title: Bt_HD73_pCER_minus_LB_biol rep 1


title: EV2_XFS_Normo

description: miRNA profiling

value: Bone marrow


title: Bt_HD73_pCER_minus_HCT_biol rep 3


title: Bt_HD73_pCER_minus_HCT_biol rep 1


title: EV2_XFS_Hypo

description: miRNA profiling


title: Panc1 WT cells


title: EPIC_LUSC6

city: New York

first: Yingqian

middle: Ada

last: Zhan

state: New York

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

institute: MSKCC

data_processing:
The Bismark pipeline was adopted to map bisulfite-treated EPIC sequencing reads and determine cytosine methylation states.
Trim Galore v0.6.4 was used to remove raw reads with low-quality (less than 20) and adapter sequences.
The trimmed sequence reads were C(G) to T(A) converted and mapped to similarly converted reference human genome (hg19) using default Bowtie 2 settings within Bismark.
Duplicated reads were discarded. The remaining alignments were then used for cytosine methylation calling by Bismark methylation extractor.
bigWig files were generated using bedGraphToBigWig from kentUtils.
Assembly: hg19
Supplementary files format and content: bigWig for cytosine read coverage
Supplementary files format and content: bigWig for cytosine methylation rate
Library strategy: EPIC (TruSeq methyl-capture)

source_name: Lung

extract_protocol:
FFPE sections were deparaffinized in mineral oil. Briefly, 800µL mineral oil (Fisher Scientific, #AC415080010) and 180µL Buffer PKD were mixed with the sections, Proteinase K was added for tissue digestion, and the sample was incubated at 56 °C for 15 min. Phase separation was encouraged with centrifugation, and the aqueous phase was chilled 3 min to precipitate RNA. After centrifugation for 15 min at 20,000 g, RNA-containing supernatant was removed for extraction, while DNA remained in the pellet. Nucleic acids were subsequently extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN, #80204) according to the manufacturer’s instructions. RNA was eluted in nuclease-free water and DNA in 0.5X Buffer ATE.
After PicoGreen quantification (ThermoFisher, #P11496) and quality control by Agilent BioAnalyzer, 170–750 ng of genomic DNA was sheared using a LE220-plus Focused-ultrasonicator (Covaris, #500569). Samples were cleaned using Sample Purification Beads from the TruSeq Methyl Capture EPIC LT Library Prep Kit (Illumina, #FC-151-1002) according to the manufacturer’s instructions with modifications. Briefly, samples were incubated for 5 min after addition of SPB, 50 µL RSB was added for resuspension, and resuspended samples were incubated for 2 min. Sequencing libraries were prepared using the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) without PCR amplification. Post-ligation cleanup proceeded according to Illumina’s instructions with 110 µL Sample Purification Mix. After purification, 3–4 samples were pooled equimolar and methylome regions were captured using EPIC oligos. Capture pools were bisulfite converted and amplified with 11–12 cycles of PCR. Pools were sequenced on a NovaSeq 6000 or HiSeq 4000 in a 150/150 bp or 100 bp/100 bp paired end run, using the NovaSeq 6000 S4 Reagent Kit (300 Cycles) or HiSeq 3000/4000 SBS Kit (Illumina). The average number of read pairs per sample was 51 million.

value: Lung

tag: disease state

value: Lung squamous carcinoma

value: Control


title: EPIC_LUSC8


title: EPIC_LUSC5


title: EPIC_LUSC4


title: Bt_HD73_pCER_minus_LB_biol rep 2


title: EPIC_LUSC2


title: EPIC_LUSC1


title: EPIC_LUAD8

value: Lung adenocarcinoma


title: EPIC_LUAD9


title: EPIC_LUAD16


title: female WT rep3

value: LSK cells

value: WT


title: EPIC_LUAD5


title: EPIC_LUAD7


title: EPIC_LUSC9


title: EPIC_LUSC3


title: EPIC_TLUSC11

value: Transforming


title: EPIC_LUAD1


title: EPIC_LUAD2


title: EPIC_TLUSC10


title: female  Lxn-/- rep3

value: latexin knockout


title: EPIC_TLUAD10


title: EPIC_TLUAD11


title: EPIC_LUAD3


title: EPIC_TLUSC7


title: EPIC_TLUSC9


title: EPIC_LUAD6


title: POST_Case_1

description: DNA methylome

value: Post-treatment


title: EPIC_TLUSC4


title: EPIC_TLUSC5


title: EPIC_TLUAD5


title: EPIC_LUAD4


title: EPIC_TLUAD9


title: EPIC_TLUAD4


title: EPIC_TLUAD1


title: EPIC_TLUAD2


title: EPIC_TLUAD3


title: Malta_4

organism: Procambarus virginalis

value: Abdominal musculature

value: Malta


title: EPIC_TLUSC3


title: Ukraine_1

value: Ukraine


title: EPIC_TLUSC1


title: Malta_2


title: Madagascar4_1_Rano


title: Madagascar2_4_Anji


title: Madagascar2_5_Anji


title: Madagascar3_1_Iho


title: Madagascar2_2_Anji


title: Madagascar2_3_Anji


title: Germany3_4_Sing


title: Germany3_3_Sing


title: Germany3_2_Sing


title: Germany2_4_Reil


title: Germany2_5_Reil


title: Germany3_1_Sing


title: Madagascar2_1_Anji


title: Germany2_2_Reil


title: Malta_3


title: Singapore_T3_1

extract_protocol:
Genomic DNA was extracted from abdominal muscle using a Tissue Ruptor (Qiagen), followed by proteinase K digestion and isopropanol precipitation
SureSelectXT Methyl-Seq Target Enrichment System

tag: time point

value: 13 months


title: Singapore_T3_3

tag: tissue


title: Malta_1


title: Germany2_1_Reil


title: Germany2_3_Reil


title: Singapore_T2_4

value: 4 months


title: Singapore_T2_2


title: Singapore_T1_2

value: 1 month


title: Singapore_T2_1


title: Singapore_T1_4


title: Singapore_T3_2


title: Singapore_T0_3

value: 0 month


title: Singapore_T1_1


title: Producer1_5


title: Singapore_T0_2


title: Germany1_1_Mur


title: Singapore_T0_1


title: Singapore_T2_3


title: Clone22, MUT

city: Rennes

first: Laura

last: Mary

address: Rue Henri Le Guilloux

department: Pôle de Biologie

institute: CHU de Rennes

data_processing:
The HISAT2 algorithm (Kim et al., 2015) was used to map the reads on the reference genome.
Sequencing data filtering was performed using SOAPnuke algorithm (Chen et al., 2018).
Bowtie2 (Langmead and Salzberg, 2012) and RSEM (Li and Dewey, 2011) protocol was then used to align the reads to the reference genes and quantify gene expression.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM, TPM and read count values for each Sample

growth_protocol: HEK293T cells and clone 22 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA extraction was performed using the NucleoSpin RNA kit (Macherey-Nagel).
Transcriptome library was performed with the DNB preparation kit (BGI).

value: Human embryonic renal cells

value: PBX1 knockdown

value: Arg107Gln PBX1-coding plasmid transfection


title: Clone22, WT

value: WT PBX1-coding plasmid transfection


title: Singapore_T0_4


title: Hek, WT


title: TWCM-388-NR-post

city: Saint Louis

first: Kory

last: Lavine

state: Missouri

address: 660 S. Euclid Ave

department: Internal Medicine - Cardiology

institute: Washington University School of Medicine

data_processing:
Cell Ranger V3, aligned to GRCh38 transcriptome, or custom pre-mrna reference
QC and Filtering: Seurat V3/V4
Unsupervised Clustering: Seurat V3/V4
Assembly: GRCh38 V3.0.0
Supplementary files format and content: .rds objects

source_name: heart

extract_protocol:
Cardiac tissues from LVAD cores at the time of LVAD implant (U/RR-pre) and adjacent to core samples at the time of explant (U/RR-post) from paired patient were flash frozen using liquid nitrogen. Identical regions from the apex of LV from explanted donors were used. Single nuclei suspensions were generated as previously described. In brief: flash frozen sections were minced with a razor blade, transferred to a Dounce Homogenizer containing 1 mL of lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40 in nuclease-free water) on ice. Samples were homogenized using five strokes, an additional 1 mL of lysis buffer added, and incubated on ice for 15 mins. Samples were then filtered with a 40μm filter and filter was rinsed with 1mL of lysis buffer. The mixture was then centrifuged at 500g for 5 min 4 °C, resuspended in 1mL nuclei wash buffer (2% BSA and 0.2 U μl−1 RNase inhibitor (Thermo Fisher, cat. no. AM2694) in 1× PBS) and, filtered using a 20m pluristrainer (Pluriselect, cat. No. SKU43-50020-03). Filtered solution as centrifuged using the above criteria and resuspended in 300 μL Nuclei Wash Buffer and transferred into a 5mL tube for flow cytometry. Subsequently, 1 μl DRAQ5 (5 mM solution; Thermo Fisher, cat. no. 62251) was added, sample gently vortexed, and allowed to incubate for 5 min prior to sorting. DRAQ5+ nuclei were sorted into 300 μL Nuclei Wash Buffer using a BD FACS Melody (BD Biosciences) with a 100 µM nozzle. Sorted nuclei were then centrifuged using the above conditions and resuspended in Nuclei Wash Buffer for a final target concentration of 1,000 nuclei/μL – nuclei were counted on a hemocytometer. Based on the nuclei concentration, 10,000 target nuclei were loaded onto a Chip G for GEM generation using the Chromium Single Cell 5ʹ Reagent v1.1 kit from 10X Genomics. Reverse transcription, barcoding, complementary DNA amplification and purification for library preparation were performed as per the Chromium 5ʹ v1.1 protocol at the McDonnel Genome Institute. Sequencing was performed on a NovaSeq 6000 platform (Illumina) at a target read depth of 100,000 at the McDonnel Genome Institute.
Chromium Single Cell 5ʹ Reagent v1.1 kit from 10X Genomics

value: heart

tag: condition

value: non-responder post


title: TWCM-388-NR-pre

value: non-responder pre


title: TWCM-376-NR-pre


title: TWCM-376-NR-post


title: EPIC_LUSC11

value: Lung

value: Lung squamous carcinoma

tag: genotype

value: Control


title: TWCM-463-R-pre

value: responder pre


title: TWCM-378-NR-pre


title: TWCM-463-R-post

value: responder post


title: TWCM-296-R-post


title: TWCM-378-NR-post


title: TWCM-296-R-pre


title: Sup Test group replicate 1

city: Fuzhou

first: Hongbin

last: Luo

address: No.20,Chazhong road,Taijiang district

institute: Fujian medical university

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10x Blocking Agent and 1 μL of 25x Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2x Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-circRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 6 samples were retained for further “m6A quantity” analyses. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities.

source_name: Osteoarthritis Synovial Tissues

label_protocol: The “IP” RNAs and “Sup” RNAs digested with RNase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. The enriched “IP” RNAs and “Sup” RNAs were then added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labeling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit. The concentration and specific activity (pmol dye/μg cRNA) were measured with NanoDrop ND-1000.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Tissues were collected fromtotal knee replacement surgury and promptly cooled at -80℃ refrigerator.

value: synovial tissue

tag: modification

value: supernatant unmodified circRNAs


title: Sup Test group replicate 3


title: Sup Control group replicate 3

source_name: Rheumatoid Arthritis Synovial Tissues


title: Sup Control group replicate 2


title: Hek, MUT

value: WT


title: IP Test group replicate 1

value: IP enriched m6A methylated circRNAs


title: Sup Test group replicate 2


title: IP Control group replicate 1


title: IP Control group replicate 2


title: Sup Control group replicate 1


title: IP Test group replicate 2


title: IP Test group replicate 3


title: IP Control group replicate 3


title: TWCM-397-NR-pre


title: TWCM-190-R-post


title: TWCM-397-NR-post


title: TWCM-363-NR-pre


title: TWCM-190-R-pre


title: TWCM-239-R-post


title: TWCM-410-NR-pre


title: TWCM-359-NR-pre


title: TWCM-410-NR-post


title: TWCM-229-R-pre


title: TWCM-359-NR-post


title: TWCM-370-NR-pre


title: TWCM-239-R-pre


title: TWCM-370-NR-post


title: TWCM-363-NR-post


title: TWCM-371-NR-post


title: TWCM-371-NR-pre


title: TWCM-373-NR-Post


title: TWCM-LV-LV

description: TWCM-LV-LV

value: Donor


title: TWCM-373-NR-Pre


title: TWCM-RV-RV

description: TWCM-RV-RV


title: Single cell LXR treatment, T0901317, 30nM, Rep 2

city: Cambridge

first: Gokul

last: Ramaswami

state: MA

address: One Kendall Square, 1400 West, 3rd Floor

institute: CAMP4 Therapeutics

data_processing:
Fastq files for each scRNA-seq sample were processed by CellRanger (10X Genomics) to generate count matrices of genes per cell. Count matrices were processed for downstream analyses using Seurat version 3.2.
Assembly: hg38
Supplementary files format and content: Tab-separated barcodes files, features files, and matrix files

source_name: iPSC-derived microglia

growth_protocol: iPSC-derived microglia were obtained from FujiFilm Cellular Dynamics Incorporated (clone01279.107, lot 105093). Cells were thawed at 37 C. Each vial was rinsed with 1 mL of culture medium and spun at 1,000 x g for 10 minutes. Cells were transferred to 8 mL of culture medium and plated at a density of 5 x 10^4 cells/cm^2 in a 6-well format. Cells were grown between 0 and 4 days in culture.

extract_protocol:
GEM encapsulation and single cell indexing reactions were performed using the 10X Genomics Chromium Controller (cat#:1000202, version 3.1 chemistry).
Single-cell 3’ RNA-seq libraries were prepared according to the manufacturer’s instructions (10X Genomics, cat#: 1000121),

treatment_protocol: At day 3, cells were treated with either DMSO or different doses (30 nM or 100 nM) of T0901317 (MedChem Express #HY-10626) and GW3569 (30 nM or 300 nM) (MedChem Express #HY-10627A) and incubated for 24 hours.

value: iPSC-derived microglia

tag: replicate

value: Day 4


title: Single cell LXR treatment, T0901317, 30nM, Rep 1

tag: treatment


title: Single cell LXR treatment, T0901317, 100nM, Rep 1


title: Single cell LXR treatment, T0901317, 100nM, Rep 2


title: Single cell LXR treatment, GW3965, 300nM, Rep 2


title: Single cell LXR treatment, DMSO, Rep 2

value: DMSO


title: Single cell LXR treatment, GW3965, 30nM, Rep 2


title: Single cell LXR treatment, GW3965, 30nM, Rep 1


title: Single cell LXR treatment, DMSO, Rep 1


title: Single cell time course, Day 4, Rep 3


title: NM1 WT bone marrow 03

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Subsequent analysis, including quality trimming, was executed using the BioSAILs workflow execution system. Trimmomatic (version 0.36) was used for quality trimming of the raw reads to get rid of low-quality bases, systematic base-calling errors and sequencing adapter contamination(Bolger et al., 2014). The quality of the sequenced reads pre/post quality trimming was assessed by FastQC and only the reads that passed quality trimming in pairs were selected for downstream analysis (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The quality-trimmed RNA-Seq reads were aligned to the Mus musculus GRCm38 (mm10) genome using HISAT2 (version 2.0.4)(Kim et al., 2015). The conversion and sorting of SAM alignment files for each sequenced sample to BAM format were done by using SAMtools (version 0.1.19)(Li et al., 2009). The BAM alignment files were processed using HTseq-count, using the reference annotation file to produce raw counts for each sample.
Assembly: GRCm38

source_name: Bone marrow tissue

growth_protocol: Wild type and NM1 KO C57/Bl6 mice (8 months old; 25-35 g in weight) were used for the analysis(Venit et al., 2013). The mice were housed in a pathogen-free sterile ventilation system supplied with sterile woodchip and ad libitum feed and water supply. Mice were kept in a room maintained at a temperature of 21-24 °C on a schedule of 12 h light/dark cycle. All animal experiments were performed after approval by the NYUAD-IACUC (Protocol 20-0004).

extract_protocol:
Bone marrow was isolated according to the previously published protocol (Amend et al., 2016). In short, femurs and tibiae were taken from euthanized mice and cleaned from surrounding muscles, connective tissues and epiphysis parts of each long bone. All bones from single mice were placed in the 0.5ml tube with the hole on the bottom nested in the 1.5ml collection tube. Bones were spin down at 14000 x g in a microcentrifuge for 15 seconds to pellet the bone marrow at the bottom of the bigger tube. For each bone marrow sample, femurs and tibiae from single NM1 WT or KO mice were used. RNA was isolated by RNAzol according to manufacturer’s protocol and final RNA concentration measured by Qubit RNA BR Assay Kit.
Three replicates were prepared for each genotype. 500ng of total RNA was used for the RNA-Seq library preparation by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) and sequenced with the NextSeq 500/550 sequencing platform (performed at the NYUAD Sequencing Center).

value: Bone marrow tissue


title: NM1 WT bone marrow 02


title: Single cell time course, Day 4, Rep 2


title: Single cell time course, Day 3, Rep 3

value: Day 3


title: Single cell time course, Day 4, Rep 1


title: Single cell time course, Day 3, Rep 2


title: Single cell LXR treatment, GW3965, 300nM, Rep 1


title: Single cell time course, Day 2, Rep 1

value: Day 2


title: Single cell time course, Day 2, Rep 3


title: Single cell time course, Day 3, Rep 1


title: Single cell time course, Day 1, Rep 3

value: Day 1


title: Single cell time course, Day 1, Rep 2


title: Single cell time course, Day 2, Rep 2


title: NM1 KO bone marrow 01

value: KO


title: NM1 KO bone marrow 02


title: CandR_H3K9me3_p5424_wt

city: Marseille

first: Nori

last: SADOUNI

address: 169 Avenue Luminy

institute: TAGC INSERM U1090

data_processing:
FastQ files were trimmed using sickle with -q 20 option and mapped to the mm9 reference genome using bowtie2 with default parameters
Sam files were converted using samtools to BAM files.
Bigwig files were generated using deeptools bamCoverage using bins of 20 and normalized using RPKM
Assembly: mm9
Supplementary files format and content: bw
Library strategy: Cut and Run

growth_protocol: Mouse P5424 T cells were cultured in RPMI medium supplemented with heat-inactivated 10% FBS (PAA) at 37 °C, 5% CO2.

extract_protocol:
CUT&RUN and CUT&Tag was performed using a magnetic bead-based digitonin-permabilization and an enzyme-tethering protocol respectively.
Library preparation was carried out as per manufacturer’s instructions (NEBNext Ultra II DNA library prep Kit for Illumina) using 5ng material with average sizes about 150-350 bp, including adapters. Sequencing was carried out on an Illumina NextSeq 500. The quality of libraries was checked with the Bioanalyser DNA High sensitivity.

value: T cell

tag: cells used

tag: antibody


title: Single cell time course, Day 1, Rep 1


title: Single cell time course, Day 0, Rep 2

value: Day 0


title: Single cell time course, Day 0, Rep 1


title: Bulk LXR treatment, T0901317, 100nM, Rep1

data_processing:
Reads were aligned to the hg38 genome with STAR and we used RSEM to quantify the expression of Gencode version 24 genes in transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: iPSC-derived microglia were obtained from FujiFilm Cellular Dynamics Incorporated (clone01279.107, lot 105093). Cells were thawed at 37 C. Each vial was rinsed with 1 mL of culture medium and spun at 1,000 x g for 10 minutes. Cells were transferred to 8 mL of culture medium and plated at a density of 5 x 10^4 cells/cm^2 in a 48-well format. Cells were grown between 0 and 4 days in culture.

extract_protocol:
Medium was removed and cells were lysed directly on plate in RNA lysis buffer and processed using the MagMAX mirVana Total RNA Isolation Kit (Applied Biosystems, cat#: A27828) according to the manufacturer’s instructions. cDNA was generated from total RNA using SuperScript IV Reverse Transcriptase (Invitrogen, cat#:18090050).
Bulk RNA-seq library preparation was performed with 500ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, cat#:E7490) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, cat#:E7420).


title: Bulk LXR treatment, T0901317, 100nM, Rep2


title: Bulk LXR treatment, T0901317, 100nM, Rep4


title: CUTTAG_H3K27me3_p5424_wt

data_processing:
FastQ files were trimmed using sickle with -q 20 option and mapped to the mm9 reference genome using bowtie2 with default parameters
Sam files were converted using samtools to BAM files.
Bigwig files were generated using deeptools bamCoverage using bins of 20 and normalized using RPKM
Assembly: mm9
Supplementary files format and content: bw
Library strategy: Cut and Tag

tag: cell line


title: NM1 WT bone marrow 01


title: Bulk LXR treatment, T0901317, 30nM, Rep4


title: Single cell time course, Day 0, Rep 3


title: Bulk LXR treatment, T0901317, 100nM, Rep3


title: Bulk LXR treatment, T0901317, 30nM, Rep3


title: TWCM-229-R-post

value: heart


title: NM1 KO bone marrow 03


title: Bulk LXR treatment, T0901317, 30nM, Rep1


title: Bulk LXR treatment, GW3965, 300nM, Rep4


title: Bulk LXR treatment, GW3965, 300nM, Rep3


title: Bulk LXR treatment, GW3965, 300nM, Rep2


title: Bulk LXR treatment, GW3965, 300nM, Rep1


title: Bulk LXR treatment, T0901317, 30nM, Rep2


title: Bulk LXR treatment, GW3965, 30nM, Rep4


title: Bulk LXR treatment, GW3965, 30nM, Rep2


title: Bulk LXR treatment, GW3965, 30nM, Rep3


title: Bulk LXR treatment, GW3965, 30nM, Rep1


title: Bulk LXR treatment, DMSO, Rep4


title: T-ALL, MYC off 24 hours, rep 2

city: Stanford

first: Benjamin

middle: AH

last: Smith

state: CA

address: 290 Jane Stanford Way

institute: Stanford University

data_processing:
Adapters were trimmed with cutadapt (v1.16) in Python (v3.6.1).
The human MYC (hMYC) gene was appended to the mm10 reference genome.
Reads were then mapped to the mm10 reference genome with STAR (v2.5.4b) using the GENCODE vM16 comprehensive annotations.
Reads were then counted with featureCounts from Rsubread (v1.28.1).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes gene identity, gene length from featureCounts, counts, RPK, FPKM, TPM, and percentile of FPKM value.

source_name: T-ALL

growth_protocol: Murine T-ALL cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37 degrees C.

extract_protocol:
RNA was isolated using an RNeasy kit (Qiagen).
cDNA was generated from fragmentation of polyA-enriched RNA. Libraries were prepared by adapter ligation, PCR amplification, and circularization.

treatment_protocol: Cells were treated with doxycycline for the indicated amount of time prior to RNA collection and sequencing.

value: T-ALL

value: doxycycline

value: 24 hours


title: T-ALL, MYC off 24 hours, rep 3


title: Bulk LXR treatment, DMSO, Rep2


title: T-ALL, MYC off 8 hours, rep 3

value: 8 hours


title: Bulk time course, Day 4, Rep 1


title: Bulk time course, Day 4, Rep 2


title: T-ALL, MYC off 8 hours, rep 2


title: T-ALL, MYC off 24 hours, rep 1


title: T-ALL, MYC off 8 hours, rep 1


title: Bulk time course, Day 3, Rep 3


title: T-ALL, MYC off 4 hours, rep 3

value: 4 hours


title: T-ALL, MYC off 4 hours, rep 2


title: Bulk time course, Day 3, Rep 1


title: T-ALL, MYC off 2 hours, rep 3

value: 2 hours


title: T-ALL, MYC off 2 hours, rep 2


title: T-ALL, MYC off 4 hours, rep 1


title: T-ALL, MYC off 2 hours, rep 1


title: Bulk time course, Day 3, Rep 2

value: iPSC-derived microglia


title: Bulk time course, Day 2, Rep 3


title: T-ALL, MYC on 0 hours, rep 3

value: mock

value: 0 hours


title: Bulk time course, Day 2, Rep 1


title: T-ALL, MYC on 0 hours, rep 2


title: Bulk time course, Day 1, Rep 3


title: T-ALL, MYC on 0 hours, rep 1


title: Bulk time course, Day 2, Rep 2


title: Bulk LXR treatment, DMSO, Rep3

value: DMSO

value: Day 4


title: Bulk LXR treatment, DMSO, Rep1


title: Bulk time course, Day 4, Rep 3


title: Singapore_T1_3

value: Abdominal musculature

value: 1 month


title: Bulk time course, Day 0, Rep 3


title: Bulk time course, Day 1, Rep 2

value: Day 1


title: USA_5 [RRBS]

data_processing:
Basecalling with: bcl2fastq 2.20.0.422
Preprocessing, read trimming: Trimmomatic 0.38
Preprocessing, quality filtering: Trimmomatic 0.38
BS-mapping: BSMAP 2.9
Computation of methylation ratios: methratio.py (part of bsmap package)
Assembly: galGal5
Supplementary files format and content: bedGraph-format containing the genomic methylation ratios and coverage values of the respective sample

organism: Gallus gallus

source_name: Breast tissue

extract_protocol:
DNA from chicken breast was isolated using Purelink Genomic DNA Isolation MiniKit (Invitrogen)
Zymo-Seq RRBS

value: Breast tissue

value: USA


title: Bulk time course, Day 1, Rep 1


title: USA_6 [RRBS]


title: USA_4 [RRBS]


title: USA_1 [RRBS]


title: USA_3 [RRBS]


title: EPIC_LUAD14

value: Lung

value: Lung adenocarcinoma

value: Control


title: Bulk time course, Day 0, Rep 1

value: Day 0


title: Thailand_6 [RRBS]

value: Thailand


title: EPIC_LUAD12


title: USA_2 [RRBS]


title: Thailand_5 [RRBS]


title: Thailand_4 [RRBS]


title: Thailand_3 [RRBS]


title: Thailand_2 [RRBS]


title: Thailand_1 [RRBS]


title: Iran_6 [RRBS]

value: Iran


title: Iran_4 [RRBS]


title: Iran_1 [RRBS]


title: Germany_6 [RRBS]

value: Germany


title: Iran_2 [RRBS]


title: Germany_5 [RRBS]


title: Bulk time course, Day 0, Rep 2

value: iPSC-derived microglia


title: Iran_3 [RRBS]


title: P1662_IMR575_Tet1

data_processing:
Reads were aligned to GRCh38 using the GENCODE (v30) annotation and the STAR aligner (v2.7.1a) with the following non-standard parameters --sjdbOverhang 300 --twopassMode Basic --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000 --outSAMattributes NH NM MD AS XS nM HI.
Feature counting  was done using featureCounts (v1.5.1) with the following non-standard parameters when counting at the gene level -t exon -g gene_id -C -M --fraction -p -O -Q 4 -J
Assembly: GRCh38 using the GENCODE (v30)
Supplementary files format and content: Table reporting unque mapping read counts

source_name: Neuroblastoma cell line

growth_protocol: SK-N-SH neuroblastoma cells stably transfected with a tetracycline-inducible MYCN expression system were generated with the tetracycline repressor (TR) system (pcDNA™6TR, Invitrogen). Single clones were maintained by adding 500 µg/ml G418-BC (Merck) and 5µg/ml Blasticidin (ThermoFisher Scientific) as selection antibiotic to the culturing medium.

extract_protocol:
Cells were harvested and RNA was isolated with Trizol.
Depletion of ribosomal RNA was performed by enzymatic digestion. The ribodepletion was validated by qRT-PCR and a depletion of 95-99% was regularly reached. The ribodepleted RNA was used for generation of total RNA sequencing libraries with the TrueSeq Stranded mRNA kit (Illumina San Diego, USA) according to the manufacturer. The final libraries were stored at -20°C until sequencing. Libraries were sequenced on a HiSeq4000 (Illumina, San Diego, USA) with a paired-end read length of 2 × 150 nucleotides. On average 100 Mio read pairs were generated per sample.

treatment_protocol: Induction of MYCN expression by addition of tetracyclin to the growth medium for 5d. Induction of MYCN was confirmed by qRT-PCR and Western Blot.

tag: cancer type

value: Neuroblastoma

tag: knockdown

value: Induction


title: EPIC_LUAD13


title: Germany_3 [RRBS]

tag: location


title: P1662_IMR575_EtOH3


title: Germany_2 [RRBS]


title: P1662_IMR575_Tet2


title: Germany_1 [RRBS]


title: P1662_IMR575_EtOH2


title: Finland_6 [RRBS]

value: Finland


title: Finland_5 [RRBS]


title: Finland_4 [RRBS]


title: P1662_IMR575_EtOH1


title: Iran_5 [RRBS]


title: Finland_2 [RRBS]


title: Australia_6 [RRBS]

value: Australia


title: Australia_5 [RRBS]


title: PLC-8024 cells, siIGF2BP1, 3

city: Guangzhou

first: Binkui

last: Li

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

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: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA of cell was extracted by using Trizol. 1.0 ug of total RNA was used for the construction of sequencing libraries.
Library preparation were performed by Epibiotek (Guangzhou, China). Briefly, total RNA were treated to remove ribosomal RNA by using GeneRead™ rRNA Depletion Kit（Qiagen, Hilden, Germany, Cat No. 180211）. Ribosome depleted RNA was fragmented and then used for constructing strand-specific RNA libraries by using VAHTS Stranded RNA-seq Library Prep Kit for Illumina (Vazyme, Nanjing, China, Cat. No NR602) accoding to manufacturer instructions.

tag: cell type

value: hepatocellular carcinoma cell line

value: IGF2BP1 knockdown


title: Australia_4 [RRBS]


title: PLC-8024 cells, siIGF2BP1, 2


title: P1662_IMR575_Tet3


title: PLC-8024 cells, siIGF2BP1, 1


title: Australia_3 [RRBS]


title: PLC-8024 cells, siPRMT3, 3

value: PRMT3 knockdown


title: Australia_1 [RRBS]

value: Breast tissue


title: PLC-8024 cells, siPRMT3, 2


title: Australia_2 [RRBS]


title: PLC-8024 cells, siControl, 3

value: WT


title: PLC-8024 cells, siPRMT3, 1


title: Finland_3 [RRBS]


title: PLC-8024 cells, siControl, 1


title: T-ALL, MYC off, rep 3

extract_protocol:
RNA was isolated using an RNeasy kit (Qiagen) and assessed for degradation using a 2100 Bioanalyzer (Agilent).
cDNA was generated using the SMART-Seq v4 kit (Takara) with oligo(dT) priming, and libraries were prepared with the Nextera XT Library Prep Kit (Illumina).

treatment_protocol: Cells were treated with the indicated dose of doxycycline for the indicated amount of time prior to RNA collection and sequencing.

value: T-ALL

value: doxycycline, 500 pg/mL

tag: time

value: 48 hours


title: Germany_4 [RRBS]


title: PLC-8024 cells, siControl, 2


title: Bt_HD73_pCER_plus_LB_biol rep 3

tag: strain

value: liquid bacterial culture

value: Early stationary phase

value: pAW63{delta}; pCER270+

tag: medium

value: LB


title: T-ALL, MYC off, rep 1


title: T-ALL, MYC intermediate, rep 3

value: doxycycline, 20 pg/mL


title: Finland_1 [RRBS]


title: T-ALL, MYC intermediate, rep 2


title: T-ALL, MYC intermediate, rep 1


title: Subject 207, prior to motion sickness stimulus

city: Dayton

first: Michael

last: Markey

state: OH

address: 3640 Colonel Glenn Hwy.

department: Biochemistry and Molecular Biology

institute: Wright State Unviersity

hyb_protocol: Labeled samples were hybridized on GeneChipTM miR4.0 Arrays  ,  washed per manufacturer’s instructions with a GeneChip Hybrization, Wash, and Stain Kit on a GeneChip® Fluidics Station.

scan_protocol: Genechips were scanned on a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA, USA).

data_processing: Data summarization was performed by RMA+DABG for the human content of the arrays.  Annotation was performed using the most recent version for these arrays (miR-4.0-st-v1.annotations.20160922.csv). Gene expression was filtered by fold-change of at least 1.2, gene-level p-value of less than 0.05, and DABG<0.05.

source_name: serum

label_protocol: A FlashTagTM Biotin HSR RNA Labeling Kit (Thermo Fisher Scientific, Waltham, MA, USA) was used according to the manufacturer’s protocol for miRNA labeling.

extract_protocol: 10 mL of blood were collected in red-capped tubes (no anticoagulant, Becton Dickinson, Franklin Lakes, NJ) by a phlebotomist and allowed to clot at room temperature for 30 minutes post draw. Tubes were then centrifuged 20 minutes at 2,000 x g at 4C to precipitate cellular material. Supernatant was removed and transferred to cryotubes for RNA isolation. Total circulating RNA (primarily miRNA and other small RNA) from 200 µL of serum was isolated and purified with miRNeasy Serum/Plasma Kit (QIAGEN, Frederick, MD, USA). RNA quantity was measured using an Agilent Small RNA Kit on an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).

treatment_protocol: No treatment prior to extraction. See PMID 35594783 for motion sickness stimulus details.

tag: phenotype

value: Not Susceptible


title: T-ALL, MYC on, rep 3

tag: tissue

value: mock


title: T-ALL, MYC on, rep 1


title: T-ALL, MYC on, rep 2


title: Subject 203, prior to motion sickness stimulus


title: Subject 210, prior to motion sickness stimulus


title: Subject 205, prior to motion sickness stimulus

value: Susceptible


title: MethylC-Seq_LEAF_nrpd-kd

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using cutadapt.
The reads were aligned to IRGSP genome using Bismark and methylation extraction was done using Bismark protocol.
The methylation was calculated using the Bismark tool and cytosine coverage report was used to create the bedgraph files for methylation density genomewide.
Genome_build: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary_files_format_and_content: bigwig files showing the methylation status across the genome.

organism: Oryza sativa

source_name: vegetative leaf

growth_protocol: The plants were grown in green house with natural day-night cycles with temperature maintained around 28 degrees celsius.

extract_protocol:
Total DNA was extracted from the tissues using CTAB method.
Libraries were prepared exactly as per the NEBNext® Enzymatic Methyl-seq Kit (Catalog no-E7120) manufaturer protocol. Adapters used: Read 1-AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and Read2- AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: WT and pol IV knockdown lines were handled in the same manner.

value: vegetative leaf

tag: subspecies

value: Indica

tag: cultivar

value: Pusa Basmati 1 (PB1)

value: nrpd-kd


title: Subject 216, prior to motion sickness stimulus


title: T-ALL, MYC off, rep 2


title: Subject 201, prior to motion sickness stimulus


title: Subject 202, prior to motion sickness stimulus


title: Subject 213, prior to motion sickness stimulus


title: Subject 215, prior to motion sickness stimulus


title: Subject 206, prior to motion sickness stimulus


title: MethylC-Seq_LEAF_WT

tag: genotype

value: wt


title: ChIP_PolII_nrpd1-kd_Rep2

data_processing:
The reads obtained were trimmed using cutadapt and aligned to IRGSP rice genome with parameters -q -v 1 -m 100 -y -a --best –strata
The alignment files are converted to coverage files using bam coverage tool of Deeptools with the 100bp bin size.
Genome_build: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary_files_format_and_content: The coverage files of the ChIP seq alignments were provided in bigwig format.

source_name: pre-emerged panicle

extract_protocol:
Sheared chromatin from the equally developed pre emerged panicle of WT and kd plants were incubated with appropriate antibodies bound to Protein G Dynabeads (Thermo Fisher, catalog number 10003D).  Washes, elution, de-crosslinking and DNA purification was done as described. The purified DNA was taken for library preparation.
The ChIP library was constructed using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (Catalog no-E7103L) as per manufacturer's instructions. The adapter sequence used is AGATCGGAAGAGCACACGTCTGAACTCCAGTCA. The sequencing was done in single end mode in a Illumina HiSeq2500 platform.

value: pre-emerged panicle

tag: chip antibody

value: PolII


title: 697-2_CTRL

first: Lawrence

middle: S.

last: Prince

state: California

address: 453 QUARRY RD

department: Pediatrics - Neonatology

data_processing:
Quality control of the raw fastq files was performed using the software tool FastQC v0.10.1 (Andrews, 2017).
Sequencing reads were aligned to the mouse genome (mm10) using the STAR v2.4.5a aligner (Dobin et al., 2013).
Read quantification was performed with htseq-count.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary E15 fetal lung mesenchymal cells

extract_protocol:
RNA was isolated using TRIzol (Ambion; LifeTechnologies) reagent and quantified with a Nanodrop 1000 (Thermo Fisher).
RNA quality was determined using an Agilent 4200 Development TapeStation (Aglient Technologies).
Samples with high RIN scores (>7) were selected for preparation of libraries with TruSeq RNA Library Prep Kit (Illumina) using 10 ng of RNA.
Libraries were sequenced with 50 bp single end reads to a depth of 30 million reads per sample.


title: ChIP_PolII_WT_Rep2


title: ChIP_H3K9me2_nrpd1-kd_Rep4


title: ChIP_H3K9me2_nrpd1-kd_Rep3


title: 697-1_CTRL-3

value: primary E15 fetal lung mesenchymal cells


title: Subject 211, prior to motion sickness stimulus


title: 697-3_CTRL-3


title: Subject 209, prior to motion sickness stimulus


title: Subject 208, prior to motion sickness stimulus


title: Subject 214, prior to motion sickness stimulus


title: 685-5_CTRL-3


title: 468-4_CTRL


title: 685-1_CTRL


title: 685-2_CTRL-3


title: 468-3_CTRL-2


title: Eggs, fertilized with UV irradiated sperm, rep7

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

data_processing:
Quality control, FastQC, v0.11.9
Filtering, Flexbar, 3.5.0
Alignment, STAR, 2.7.5c
Reads counting, Htseq-count, 1.99.2
Reads normalization, DESeq2 3.16
Assembly: OmykA_1.1
Supplementary files format and content: Processed data files include raw read counts for all samples in tabular format, text files (.txt)

organism: Oncorhynchus mykiss

source_name: rainbow trout from Rutki strain

extract_protocol:
Eggs preserved in RNA-later solution were incubated overnight in a refrigerator (4 °C) and finally stored at −80 °C until RNA purification. Two to three eggs, depending on their size, were used for RNA isolation for the transcriptomic study. RNA was isolated as previously described (Ocalewicz et al. 2019) using modified TRIzol procedure established at the Igor Babiak laboratory, University of Nordland, Norway. The quality of the obtained RNA was established using TapeStation4150 (Agilent Technologies) and RNA ScreenTape Assay allowing RIN (RNA Integrity Number) evaluation.
Good quality isolates (RIN>8) were quantified using Qubit™ RNA Assay Kits (Thermo Scientific) and 250 ng of a total RNA was used for library preparation with Illumina Stranded mRNA Prep kit (Illumina) and standard protocol. The final libraries were controlled for quality using D1000 Agilent ScreenTapes and TapeStation4150 system, and quantified using Qubit™ dsDNA BR Assay Kit (Thermo Scientyfic). Equimolar pool of libraries was finally commercially sequenced on NovaSeq6000 System (Illumina) in a paired-end read of 2x150 bp to obtain a high sequencing depth (i.e. minimum of 75M PE reads per sample).

value: oocytes/eggs

value: gametes

value: eggs

value: XX, Doubled Haploids

tag: treatment

value: fertilzed with UV irradiated sperm (G)


title: Eggs, fertilized with UV irradiated sperm, rep6


title: Eggs, fertilized with UV irradiated sperm, rep5


title: Subject 204, prior to motion sickness stimulus


title: DNA1149_T_RNA

city: Washington

first: Miriam

last: Bornhorst

state: DC

address: 111 Michigan Ave

institute: Children's National Hospital

data_processing:
RNA-seq Fastq files were aligned to GRCh38 reference genome using STAR, and gene expression data from the aligned file was calculed using RSEM.
Assembly: hg38
Supplementary files format and content: RSEM counts and isoforms file as txt files.

source_name: brain

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Kit following manufacturer’s guidelines
mRNA was selected from total RNA using poly-T oligo-attached magnetic beads

value: brain

tag: disease state

value: pediatric brain tumor


title: Eggs, fertilized with UV irradiated sperm, rep1


title: Eggs, fertilized with UV irradiated sperm, rep2


title: 697-5_CTRL


title: G_4

city: Dallas

first: Karthigayini

last: Sivaprakasam

state: Texas

address: Forest Road

institute: University of Texas Southwestern Medical Center

description: SMARTer Stranded total RNA v2-pico input w/rRNA Zap

data_processing:
PicardTools were used for basecalling
Files were aligned to human genome using HiSat2-2.1.0 and the duplicates were marked with picard tools
Raw counts were called with HTSEQ
Genome_build: GRCh38
Supplementary_files_format_and_content: HTSEQ file in text format

source_name: Fresh frozen laser captured Purkinje cells

extract_protocol:
A JoVE visual experiment video and protocol are available by the lead author that describes in detail how the purkinje cells were removed from post-mortem human brain. PMID: 30735198
Total RNA was extracted from approximately ~2000 Purkinje cells per patient using a Qiagen Rneasy Micro kit (Cat# 74004) with repeated loading of the spin column in step 3. Samples were eluted in 14uL of water with RNase inhibitors. RNA quality was checked using an Agilent bioanalyzer pico chip.
Library was constructed following manufacturers protocols of the SMARTer Stranded RNA-seq kit v2 Pico input (Cat# 634413), including indexing primers for 96 samples. 5ng inputs of total RNA were fragmented for 4 mins. Next, first strand synthesis and addition of illumina adapters, followed by AMpure bead cleanup. Samples underwent rRNA depletion with ZapR and R-probes. Library was amplified with 13 cycles and cleaned a second time with AMpure beads. Library cDNA was eluted in 15uL of Tris buffer.

tag: diagnosis

value: Essential Tremor

tag: gender

value: Female

tag: age

value: Purkinje Cells


title: Eggs, fertilized with UV irradiated sperm, rep4

tag: cell line


title: Eggs, fertilized with UV irradiated sperm, rep3


title: 685-7_CTRL-3


title: G_3

value: Male


title: Eggs, normal, rep7

value: fertilzed with non-irradiated sperm (F)


title: G_2


title: Eggs, normal, rep6


title: Eggs, normal, rep5


title: Eggs, normal, rep4


title: G_1


title: 697-4_CTRL


title: KO ILC3s

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
`
To generate single cell feature counts, the clean data of each sample were mapped to mouse reference genome (mm10) by the command “cell ranger count” within cell ranger toolkit (version 6.0.1) provided by 10X genomics.
For each sample, cells as outliers in feature count matrix were removed from further analysis.
Assembly: mm10

source_name: small intestinal LPL

extract_protocol:
ILC3 (CD45mid CD3- CD90.2high) cells were sorted from small intestine LPLs using flow cytometry.
Single-cell RNA libraries were generated using 10X Genomics chromium according to the manufacturer’s instructions.

value: type 3 innate lymphoid cells

value: small intestinal LPL


title: WT ILC3s

value: WT


title: Eggs, normal, rep3


title: F_6


title: Eggs, normal, rep2


title: F_5


title: Eggs, normal, rep1


title: Mouse GBM, UMBO, 2

city: PARIS

first: Isaias

last: Hernandez-Verdin

state: Ile-de-France

address: GH PITIE SALPETRIERE ICM IHU A, 47 Boulevard DE L'HOPITAL

department: Genetics and Development of Nervous System Tumors

institute: Institut du cerveau

data_processing:
Sequence reads were mapped to GrCM38/mm10 using STAR v2.7.2a (default parameters) software to the reference genome
Read count extraction and normalization were performed using DESeq2
Assembly: mm10 version GRCm38
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: Brain

growth_protocol: GL261 cells were cultured in Dulbecco's modified essential medium (DMEM) supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin. Cells were passaged twice weekly according to their confluence. GL261 was transduced with a luciferase/mKate2 vector and were inoculated into the right caudate nucleus-putamen (AP +1 mm, DV -0.25 mm, ML -0.15 mm) of 7-8 weeks old C57BL/6 females using a stereotactic injection frame. The growth of GL261-luciferase cells was confirmed by two IVIS imaging one week apart of intracranial cell injection. We observed that mice with bioluminescence values lower than 5.00+E05 photon/second would not develop GBM tumors during the characterization of tumor growth in our mouse models. Therefore, we have included mice with bioluminescence values over 5.00+E05 photon/second.

extract_protocol:
mRNA was extracted using Maxwell RSC simply RNA automated RNA purification kit (Promega, AS1340). RNA quality was analyzed using high-sensitivity RNA chips
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Mice were divided into two groups (UMBO group and vehicle group). The vehicle group was treated with inVivoPure pH 6.5 Dilution Buffer. (BXCELL, IP0065). Two treatment sessions (days 21 and 24) were applied in this experiment. Mice were sacrificed 24 hours after the last treatment by cervical dislocation, and the right hemisphere was stored in 5 mL RNALater.

value: Brain

tag: cell line_infection

value: UMBO


title: F_4

tag: cell type


title: F_2


title: Mouse GBM, UMBO, 1


title: E_6


title: F_1


title: Mouse GBM, VehiculeControl, 2

value: Vehicule


title: Sheep 3 + 4, scRNAseq

city: Auckland

first: Andrew

last: Jiang

address: 3 Symonds Street

country: New Zealand

institute: The University of Auckland

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Sequencing ready libraries were sequenced on HiSeq Xten platform to generate on average 417,947,486 (range: 377,815,731 – 527,195,602) 150 bp paired end reads. Alignment of reads was performed using the CellRanger v6.0.1 pipeline with STAR v 2.7.2a to the sheep Oar_rambouillet_v1.0 reference genome and annotation (Ensembl release 107).
Assembly: Oar_Rambouilletv1.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Ovis aries

source_name: Striatum

extract_protocol:
cells: Dissociation of neural tissue for scRNA-seq was performed using a modified protocol from 10X Genomics (10X Demonstrated Protocol, CG00055). In brief, 2 mL of 2 mg/mL Papain (Sigma) was added to 30 mg of tissue and incubated at 37 ºC for 20 minutes. The papain solution was then removed without disrupting the tissue, leaving enough solution to cover the tissue. The tissue was dissociated using a Pasteur pipette with 2 mL of Neurobasal media (ThermoFisher Scientific), leaving cell debris to settle on the bottom. The supernatant containing the cells were transferred to a new 15 mL centrifuge tube and centrifuged at 200 xg for 2 minutes. The supernatant was removed, and the cell pellet resuspended in 1 mL Neurobasal media. 5 µL of resuspended cells was stained with 5 µL trypan blue to assess the cellular membrane intactness and number of cells was assessed using the Countess II FL Automated Cell Counter (ThermoFisher Scientific). The cell suspension was diluted by an appropriate volume of Neurobasal media to a final titer of 1000 cells/µL. Cell suspensions from the tissues isolated from animals 1+2 and animals 2+3 were pooled resulting in a total of two cell suspensions.
Nuclei: Nuclei were extracted from frozen ovine brain tissue utilising an adapted protocol from Krishnaswami et al., 2016. Briefly, approximately 50-100 mg of brain tissue was transferred to a dounce homogenizer containing 1mL homogenization buffer, HB (250mM sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris buffer pH 8.0, 1µM DTT, 1X protease inhibitor, 0.4 U/µL RNaseIn (ThermoFisher Scientific), 0.2 U/µL Superasein (ThermoFisher Scientific), 0.1 % Triton X-100). Tissue was homogenised using 5 strokes with the loose dounce pestle A, followed by 10-15 strokes of tight dounce pestle B. The homogenate was filtered through a 40 µm strainer into 5 mL Eppendorf tubes and centrifuged at 1000 xg (4 oC) for 8 minutes. The supernatant was removed and the pellet was resuspended in 250 µL of HB. A 50% - 29% iodixanol gradient (OptiPrep™ Density Gradient Medium, Sigma) was prepared to allow removal of the myelin layer. 250 µL of 50 % iodixanol was added to the nuclei-HB mixture and slowly layered on top of 500 µL of 29 % iodixanol in a new Eppendorf tube. The resultant gradient was centrifuged at 13,000 xg (4 C) for 40 minutes. The supernatant and myelin was removed and the purified nuclei pellet was resuspended in 1 mL PBS, 1 % BSA, 0.2 U/µl RNAse inhibitor. 5 µL of resuspended nuclei was stained with 5 µL trypan blue and the quality and number of nuclei was assessed using the Countess II FL Automated Cell Counter (ThermoFisher Scientific). Nuclei suspensions from animals 1+2 and animals 3+4 were pooled resulting in a total of two nuclei suspensions.
Single cell and single nuclei RNA libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics) as per manufacturer’s instructions.

value: Striatum

value: 5 year old


title: Sheep 1 + 2, snRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Sequencing ready libraries were sequenced on HiSeq Xten platform to generate on average 417,947,486 (range: 377,815,731 – 527,195,602) 150 bp paired end reads. Alignment of reads was performed using the CellRanger v6.0.1 pipeline with STAR v 2.7.2a to the sheep Oar_rambouillet_v1.0 reference genome and annotation (Ensembl release 107).
Assembly: Oar_Rambouilletv1.0
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: snRNA-seq

molecule: nuclear RNA


title: Mouse GBM, VehiculeControl, 1


title: E_5


title: E_2


title: F_3


title: Sheep 3 + 4, snRNAseq

description: 10x Genomics


title: E_3


title: D_4


title: E_4


title: Bc_F4810_pCER_plus_HCT_biol rep 3

city: JOUY-EN-JOSAS

first: Alicia

last: Nevers

address: Domaine de Vilvert

institute: Institut national de la recherche agronomique (Inrae)

data_processing:
Demultiplexing using bcl2fastq2-2.18.12
Adaptors trimming with Cutadapt 3.2
Read alignment to references genome with Bowtie2 in Galaxy. Write unaligned reads (in fastq format) to separate file(s): False; Write aligned reads (in fastq format) to separate file(s): False; Do you want to set paired-end options?: no  Will you select a reference genome from your history or use a built-in index?: indexed; Select reference genome: internal genomes uploaded from NCBI; Set read groups information?: do_not_set; Select analysis mode: simple; Do you want to use presets?: Very fast end-to-end (--very-fast); Save the bowtie2 mapping statistics to the history: True
Read counting with MulticovBed in Galaxy. Calculation based on strandedness?: Only overlaps occurring on the **same** strand.; minimum overlap required as a fraction of A: 1e-09; Require that the fraction of overlap be reciprocal for A and B: False; Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage: False; Minimum mapping quality (MAPQ) allowed:0; Include duplicate reads: True; Include failed-QC reads: False; Only count proper pairs: False
CP001179 (pCER270); CP001177 (Chromosome) and CP001178-CP001181 (plasmids) for AH187 = Bc_F4810-72; CP004069 (Chromosome) and CP004069-CP004076 (plasmids) excluding  CP004072 (pAW63) for B_th_HD73; in-house unpublished genome for B_we_KBABA6
Supplementary files format and content: raw count txt files
Supplementary files format and content: BweKBAB6_pXO16tcR_corrV170303.txt is a file with FASTA sequences corresponding to each transcriptional feature

organism: Bacillus cereus

source_name: liquid bacterial culture

extract_protocol:
RNA extraction was performed using Trizol and 1-bromo-3-chloropropane
After ribosomal RNA depletion, NextSeq 500/550 High Output Kit v2 was used to construct library
Single-read 75 sequencing run

value: liquid bacterial culture

tag: time

value: Commitment to sporulation

value: HCT (sporulation medium)


title: Mouse GBM, VehiculeControl, 3

tag: strain


title: E_1


title: D_3


title: D_2


title: HF54_uninfected

city: San Antonio

first: Mahesh

last: Mohan

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

description: lncRNA and mRNA expression in colon epithelium, uninfected

hyb_protocol: ~1 μg of each labeled cRNA was fragmented by adding 5 μl 10x  Blocking Agent and 1μl  25x  Fragmentation Buffer in a 25 μl volume, then heated  to 60 °C for 30 min. Finally 25μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50μl of the hybridization solution was dispensed into the gasket slide and assembled with the Human LncRNA Microarray v4.0 slide. The labeled cRNAs were hybridized onto the slides by incubation at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent DNA Microarray Scanner (part number G2505C). Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired Human LncRNA Microarray images.

data_processing: Quantile normalization and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering between two compared groups. The threshold is Fold Change (FC) ³ 2.0 and P-value £ 0.05. False discovery rates (FDR) were adjusted from all the p-values by Benjamini-Hochberg method for multiple testing correction. Finally, Hierarchical Clustering was performed using R to show the distinguishable LncRNAs and mRNAs expression pattern among samples.

organism: Macaca mulatta

source_name: Colon epithelium_uninfected

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified using RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured using NanoDrop ND-1000.

extract_protocol: RNA was prepared using the miRneasy mini kit (catalog # 217004) (Qiagen, Germantown, MD, USA) following the manufacturer's recommendations.

value: Colon epithelium


title: HT73_uninfected


title: HE68_uninfected


title: Bc_F4810_pCER_plus_HCT_biol rep 2

tag: medium


title: Bc_F4810_pCER_plus_HCT_biol rep 1


title: D_1

value: Essential Tremor


title: JR17_VEH-SIV

description: lncRNA and mRNA expression in colon epithelium at 6MPI, VEH, SIV infected

source_name: Colon epithelium_VEH-SIV_6MPI

value: Female


title: Bc_F4810_pCER_minus_HCT_biol rep 3


title: KD98_VEH-SIV


title: D_6

value: Purkinje Cells


title: JC81_VEH-SIV

value: Male


title: C_6


title: Sheep 1 + 2, scRNAseq

description: 10x Genomics


title: Bc_F4810_pCER_minus_HCT_biol rep 2


title: C_5


title: IH96_VEH-SIV


title: Bc_F4810_pCER_minus_HCT_biol rep 1


title: HH07_uninfected


title: HR42_uninfected


title: C_4

value: Control


title: C_3


title: Bc_F4810_pCER_plus_LB_biol rep 3

value: Early stationary phase

value: LB


title: C_2


title: Bc_F4810_pCER_plus_LB_biol rep 2


title: JT80_THC-SIV

description: lncRNA and mRNA expression in colon epithelium at 6MPI, THC treated,SIV infected

source_name: Colon epithelium_THC-SIV_6MPI


title: C_1


title: HD08_uninfected


title: Bc_F4810_pCER_plus_LB_biol rep 1


title: IN24_VEH-SIV


title: IH69_THC-SIV


title: Bc_F4810_pCER_minus_LB_biol rep 3


title: B_6


title: WT_LPS2

city: JINJU

first: GU SEOB

last: ROH

address: 15, 816 Beon-gil, Jinju-daero

country: South Korea

institute: Gyeongsang National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Lung tissues

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

tag: strain background

value: LPS intratracheal instillation

value: lung


title: WT_LPS3

tag: tissue


title: Bw_KBAB6_pCER_plus_HCT_biol rep 2

organism: Bacillus mycoides


title: B_5


title: Bc_F4810_pCER_minus_LB_biol rep 1


title: WT_LPS1


title: GV60_THC-SIV


title: Bw_KBAB6_pCER_plus_HCT_biol rep 1


title: Bc_F4810_pCER_minus_LB_biol rep 2


title: B_4


title: JB82_THC-SIV


title: HI09_THC-SIV


title: Producer4_6

city: Heidelberg

first: Geetha

last: Venkatesh

address: Im Neuenheimer Feld 580

institute: DKFZ

data_processing:
Basecalling with: bcl2fastq 2.20.0.422
Preprocessing, read trimming: Trimmomatic 0.38
Preprocessing, quality filtering: Trimmomatic 0.38
BS-mapping: BSMAP 2.9
Computation of methylation ratios: methratio.py (part of bsmap package)
Assembly: GCA_020271785.1
Supplementary files format and content: bedGraph-format containing the genomic methylation ratios and coverage values of the respective sample

source_name: Abdominal musculature

extract_protocol:
Genomic DNA was extracted from abdominal muscle using a Tissue Ruptor (Qiagen), followed by proteinase K digestion and isopropanol precipitation
Accel-NGS Methyl-Seq DNA

value: Abdominal musculature

tag: location


title: WT_saline3

value: Saline intratracheal instillation

value: wild type


title: B_3


title: Bw_KBAB6_pCER_minus_HCT_biol rep 3


title: IA83_THC-SIV


title: WT_saline2


title: Producer4_5


title: Bw_KBAB6_pCER_minus_HCT_biol rep 2


title: Bw_KBAB6_pCER_plus_HCT_biol rep 3


title: WT_saline1


title: Bw_KBAB6_pCER_minus_HCT_biol rep 1


title: Producer4_4


title: A_6


title: Bw_KBAB6_pCER_plus_LB_biol rep 3


title: B_1