title: Group 1 COVID-19 [PR1798_28_a]

value: mild→mild

value: F

value: Group 1 COVID-19


title: genomic_DNA_from_Surgical_resection_GBM-556

status: Public on Mar 31 2022

type: genomic

city: Lausanne

first: Pierre

last: Bady

address: Quartier UNIL-Sorge

department: Swiss Institute of Bioinformatics

country: Switzerland

institute: CHUV / BCF / SIB

description: grade IV glioma tumor sample from EORTC26981 study

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2 was used for primary data acqusition. Raw data was imported into R and further processed using R/Bioconductor package “minfi”. The raw pre-processing (Illumina method) was used for data normalization.
normalized (Illumina pre-processing) Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Surgical resection GBM-556

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using Qiagen AllPrep DNA/RNA Kit (Qiagen, 80204).

tag: patient

tag: batch

tag: gender

value: Male

tag: disease state

value: GBM

tag: age

tag: treatment

value: RT

value: FFPE


title: Group 2 COVID-19 [PR1798_01_a]

type: SRA

city: San Francisco

first: Tsukasa

last: Kadota

state: CA

address: 513 Parnassus Ave.

department: Medicine

country: USA

institute: UCSF

library_source: transcriptomic

data_processing:
Single-end sequenced reads were checked by FastQC. The QIAseq miRNA Library specific 3′ adapter sequence was trimmed from the 3’ ends of sequenced reads using cutadapt.
Reads with less than 16 bp insert sequences or with less than 10 bp Unique Molecular Index (UMI) were discarded.
Alignment of reads was performed using bowtie.
miRBase Release 22.1 was used for miRNAs.
The StrandNGS was applied to normalize the data using the transcript per million (TPM) method and to determine significant differentially expressed miRNAs between groups.
Genome_build: hg38
Supplementary_files_format_and_content: .xlsx file was generated by Qiagen online primary data analysing tool: (http://ngsdataanalysis.sabiosciences.com/QIAseqmiRNA).
Supplementary_files_format_and_content: TPM

molecule: total RNA

source_name: circulating miRNAs

extract_protocol:
Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was Total RNA was extracted from aliquots (200 μL) of the serum samples using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol.
The miRNA sequencing library was prepared using the QIAseq miRNA Library Kit (Qiagen, 331502)

tag: who category

value: mild→ severe

tag: Sex

value: M

tag: group

value: Group 2 COVID-19


title: Group 2 COVID-19 [PR1798_02_a]


title: 5hmC_Seal_E147

city: Chicago

first: Wei

last: Zhang

state: IL

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

library_source: genomic

data_processing:
Library strategy: 5hmC-Seal
raw sequencing reads were trimmed for adaptor sequences using Trimmomatic
Low quality bases were also trimmed , followed by alignment to the current human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode,Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length.
Alignments with Mapping Quality Score ≥ 10 were counted for gene bodies, according to the gene start and gene end annotations by the GENCODE Project(release 19), using featureCounts without strand information.
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: Plasma

extract_protocol:
CfDNA samples from T2D patients were prepared from peripheral blood with EDTA anticoagulation. Briefly, 5 mL of peripheral blood was collected from each subject, and plasma was separated within 4 h by centrifuging twice, one at 1 350× g for 12 min, and another at 13 500× g for 5 min. The processed plasma samples were stored at –80 °C immediately. CfDNA was extracted using the Circulating Nucleic Acid Kit (Qiagen, Germany) according to the manufacturer’s instructions. On average, 1-2 ng of cfDNA was obtained from each cfDNA sample. The quality of cfDNA was checked using the standard molecular biology approach
Each cfDNA sample was first repaired and ligated with adaptors. Next, the T4 bacteriophage enzyme β-glucosyltransferase (β-GT) was used to transfer an engineered glucose moiety containing an azide-group to 5hmC in duplex DNA. A biotin tag was then installed onto the azide group using Huisgen cycloaddition (click) chemistry, followed by capturing of 5hmC-containing DNA fragments using avidin beads. The 5hmC-Seal library for each cfDNA sample was then constructed through PCR amplification, followed by paired-end sequencing (PE38) at Shanghai Epican Genetech, Co. Ltd. (Shanghai, China), using the Illumina NextSeq500 platform according to Illumina’s protocol. We randomized cfDNA samples when constructing the 5hmC-Seal libraries and sequencing.

tag: population

value: Chinese

tag: diagnosis

tag: tissue

value: plasma

tag: molecule subtype

value: cfDNA


title: genomic_DNA_from_Surgical_resection_GBM-567

source_name: Surgical resection GBM-567


title: Group 1 COVID-19 [PR1798_27_a]


title: 5hmC_Seal_E130


title: genomic_DNA_from_Surgical_resection_GBM-548

source_name: Surgical resection GBM-548

value: Female


title: genomic_DNA_from_Surgical_resection_GBM-542

source_name: Surgical resection GBM-542


title: Group 1 COVID-19 [PR1798_26_a]


title: genomic_DNA_from_Surgical_resection_GBM-541

source_name: Surgical resection GBM-541

value: TMZ+RT


title: 5hmC_Seal_E117


title: 5hmC_Seal_E45


title: genomic_DNA_from_Surgical_resection_GBM-539

source_name: Surgical resection GBM-539


title: genomic_DNA_from_Surgical_resection_GBM-538

source_name: Surgical resection GBM-538


title: 5hmC_Seal_E114


title: Group 1 COVID-19 [PR1798_24_a]


title: Group 1 COVID-19 [PR1798_29_a]


title: 5hmC_Seal_E104


title: Group 1 COVID-19 [PR1798_23_a]


title: genomic_DNA_from_Surgical_resection_GBM-555

source_name: Surgical resection GBM-555


title: siPCSK9_2_S5

city: Paris

first: Raphael

last: Scharfmann

address: 123 boulevard Port Royal

department: Endocrinology, Métabolism et Diabetes

country: France

institute: Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104

data_processing:
Demultiplexing was performed with the AOZAN software (Ecole Normale Supérieure, Paris).
Alignment to GRCh38 was performed using STAR version 2.7.1a.
QC was performed with Picard and STAR.
Read count and TPM quantification were performed with RSEM.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files were generated with RSEM and contain counts and TPM values

molecule: polyA RNA

growth_protocol: EndoC-bH1 cells were cultured in low glucose DMEM medium (5.6 mmol/l, Thermo Fisher Scientific) supplemented with 2% BSA fraction V (Roche Diagnostics), 50 µM 2-beta-mercaptoethanol, 10 mM nicotinamide (Calbiochem), 5.5 μg/mL transferrin (Sigma-Aldrich), 6.7 ng/mL sodium selenite (Sigma-Aldrich), 100 units/mL penicillin, and 100 μg/mL streptomycin (Thermo Fisher Scientific).

extract_protocol:
RNA was extracted with RNeasy Micro Kit (Qiagen). RNA quality was evaluated with Agilent 2100 Bioanalyzer. Samples had RIN >8.5.
Sequencing libraries were constructed with TruSeq Stranded mRNA kit. Sequencing was performed on Illumina Nextseq 500 instrument in paired-end mode.

treatment_protocol: EndoC-bH1 cells were treated with either control siRNA or PCSK9 siRNA.

tag: cell line

tag: time


title: Group 1 COVID-19 [PR1798_22_a]


title: genomic_DNA_from_Surgical_resection_GBM-44

source_name: Surgical resection GBM-44


title: Group 1 COVID-19 [PR1798_20_a]


title: Group 1 COVID-19 [PR1798_21_a]


title: siPCSK9_1_S4


title: genomic_DNA_from_Surgical_resection_GBM-156

source_name: Surgical resection GBM-156


title: genomic_DNA_from_Surgical_resection_GBM-535

source_name: Surgical resection GBM-535


title: siPCSK9_3_S6


title: siControl_3_S3

value: siControl


title: Group 1 COVID-19 [PR1798_19_a]


title: genomic_DNA_from_Surgical_resection_GBM-530

source_name: Surgical resection GBM-530


title: Group 1 COVID-19 [PR1798_25_a]


title: siControl_2_S2


title: siControl_1_S1


title: Group 1 COVID-19 [PR1798_18_a]


title: Group 1 COVID-19 [PR1798_17_a]


title: genomic_DNA_from_Surgical_resection_GBM-523

source_name: Surgical resection GBM-523


title: genomic_DNA_from_Surgical_resection_GBM-517

source_name: Surgical resection GBM-517


title: genomic_DNA_from_Surgical_resection_GBM-512

source_name: Surgical resection GBM-512


title: Group 1 COVID-19 [PR1798_16_a]


title: genomic_DNA_from_Surgical_resection_GBM-510

source_name: Surgical resection GBM-510


title: Group 1 COVID-19 [PR1798_13_a]

source_name: circulating miRNAs


title: Group 1 COVID-19 [PR1798_14_a]


title: Normal sample of Monkey RM23 (RRBS)

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

data_processing:
FASTQC toolkit was performed for quality control of FASTQ files
TrimGalore was performed to trim adapters and low-quality reads
Diversity trimming and filtering were completed with NuGEN’s diversity trimming scripts
Processed fastq files were aligned to the reference genome (Mmul_10) with bismark bisulfite mapper.
The methylation information was extracted with bismark methylation extractor script.
Genome_build: Mmul_10
Supplementary_files_format_and_content: bedGraph file with the estimated methylation rate

organism: Macaca mulatta

source_name: COLON

extract_protocol:
Macro-dissection was performed to decrease the admixture of adjacent normal tissue and to enrich the percentage of tumor material for subsequent RNA extraction. De-paraffinization of FFPE tumor and adjacent normal specimens was performed using QIAGEN de-paraffinization solution (QIAGEN, Valencia, CA). DNA and RNA from 19 tumor and adjacent normal samples was extracted using the AllPrep DNA/RNA FFPE Kit (QIAGEN) following the manufacturer’s protocol. In the case of the unavailability of FFPE samples, genomic DNA and RNA were extracted from fresh frozen tumor (n=2) and normal (n=3) samples using the ZR-Duet DNA/RNA MiniPrep extraction kit (ZYMO RESEARCH, Irvine, CA). Quantification was performed with a NanoDrop One™ spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and Qubit™ Fluorometer 2.0 (Qubit, San Francisco, CA) using dsDNA and RNA assay kits. RNA integrity was analyzed using the Tape Station RNA assay kit (Agilent Technologies, Santa Clara, CA).
DNA libraries of RRBS were constructed from FFPE tissue samples of 14 tumors/adjacent normal tissue pairs using the Ovation RRBS Methyl-Seq System at The Epigenomics Profiling Core (EpiCore) of MDACC. In preparation, DNA was digested with a restriction enzyme and selected for size based on established protocols used in the EpiCore. Post-adapter ligation ensured enrichment for CpG islands, and DNA was bisulfite-treated, amplified with universal primers, and qualified libraries were then sequenced on Novaseq6000™ and MiSeq sequencers at the UTMDACC ATG

value: Normal

tag: msi status

value: MSI-H

tag: sample id

tag: mlh1 c.1029 (c>g) germline mutation status

value: Wild type


title: genomic_DNA_from_Surgical_resection_GBM-134

source_name: Surgical resection GBM-134

tag: patient

tag: batch


title: Tumor sample of Monkey RM23 (RRBS)

value: Tumor

tag: gender


title: Sample 7_Endothelial cells from wild type mice brain

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

data_processing:
Library strategy: TRAP
The sequence reads were aligned to the Ensembl mouse gene assembly (GRCm38) using Tophat2 software (version 2.1.1).
FPKM summary was performed using the Cufflinks tool (version 2.2.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files with RPKM values for each sample

organism: Mus musculus

extract_protocol:
GL261 tumors were dissected under a stereological microscope. GFP tagged polysomes was isolated using anti-GFP bound Dynabeads (Qiagen). After extensive washing, mRNA of endothelial cells from healthy brain tissue and GL261 tumor tissue were obtained by Trizol and further purified by RNeasyMicro kit (Qiagen).
Ribosome-RNA was removed from the sample using RiboGone kit (Clontech Laboratories). The RNA concentration and quality was measured by Agilent 2100 bioanalyzer. Samples with RIN value >7 were selected for further cDNA synthesis and purification. Three mouse samples from each group (healthy wild type mice, healthy Eltd1-/- mice, GL261 tumor wild type mice and GL261 tumor Eltd1-/- mice) were selected for library preparation using SMARTer® Stranded RNA-Seq Kit (Clontech Laboratories), and were submitted for sequencing on HiSeq2500.

tag: strain

value: Brain

tag: cell type

value: endothelial

tag: age

value: adult


title: genomic_DNA_from_Surgical_resection_GBM-528

source_name: Surgical resection GBM-528

value: Male

tag: disease state

value: GBM

tag: treatment

value: FFPE


title: genomic_DNA_from_Surgical_resection_GBM-495

source_name: Surgical resection GBM-495

value: RT


title: Tumor sample of Monkey RM33 (RRBS)


title: genomic_DNA_from_Surgical_resection_GBM-478

source_name: Surgical resection GBM-478


title: genomic_DNA_from_Surgical_resection_GBM-469

source_name: Surgical resection GBM-469


title: Healthy donor [PR1798_41_a]

tag: who category

value: uninfected

tag: Sex

value: F

tag: group

value: Healthy donor


title: genomic_DNA_from_Surgical_resection_GBM-492

source_name: Surgical resection GBM-492


title: Group 1 COVID-19 [PR1798_12_a]

value: mild→mild

value: M

value: Group 1 COVID-19


title: genomic_DNA_from_Surgical_resection_GBM-506

source_name: Surgical resection GBM-506

value: TMZ+RT


title: Group 1 COVID-19 [PR1798_10_a]


title: Group 1 COVID-19 [PR1798_09_a]


title: Group 1 COVID-19 [PR1798_08_a]


title: Group 1 COVID-19 [PR1798_15_a]


title: Healthy donor [PR1798_40_a]


title: Healthy donor [PR1798_39_a]


title: Healthy donor [PR1798_38_a]


title: genomic_DNA_from_Surgical_resection_GBM-479

source_name: Surgical resection GBM-479


title: genomic_DNA_from_Surgical_resection_GBM-464

source_name: Surgical resection GBM-464

value: Female


title: Healthy donor [PR1798_37_a]


title: Healthy donor [PR1798_36_a]


title: genomic_DNA_from_Surgical_resection_GBM-487

source_name: Surgical resection GBM-487


title: genomic_DNA_from_Surgical_resection_GBM-450

source_name: Surgical resection GBM-450


title: Group 1 COVID-19 [PR1798_11_a]


title: Normal sample of Monkey RM33 (RRBS)

tag: tissue

value: Normal

value: MSI-H

value: Wild type


title: genomic_DNA_from_Surgical_resection_GBM-466

source_name: Surgical resection GBM-466


title: genomic_DNA_from_Surgical_resection_GBM-457

source_name: Surgical resection GBM-457


title: Healthy donor [PR1798_35_a]


title: S77A_TCDD

city: GALVESTON

first: Kamil

last: Khanipov

address: 301 University Blvd

institute: University of Texas Medical Branch

data_processing:
The sequenced reads were trimmed and filtered based on adapter content and quality by a modified-Mott trimming algorithm (CLC Genomics Workbench 21, Qiagen). Filtered sequencing reads were locally aligned against the Homo sapiens (hg38) reference genome with annotated genes and transcripts (83). The resulting gene counts were normalized, and differential expression analysis on the complete list of genes and transcripts was used to evaluate the level and significance of mRNA expression changes (84). All genes with a fold change ≥1.5 were included in the pathway analysis using Ingenuity Pathway Analysis to highlight molecular function, biological process, and cellular component.
Genome_build: hg38
Supplementary_files_format_and_content: Differential gene expression as processed by CLC Genomics Workbench

source_name: Hepa-BpRc1 cell line

growth_protocol: Karpas 299 cells were propagated in RPMI-1640 medium (Corning, 15-041-CV) complete with 10% FBS (Atlanta Biologicals, S11550) and 2 mM GlutaMAX (Gibco, 35050-061) at 37 °C, 5% CO2. Hepa-1c1c7 cells were cultured in MEM Alpha (1X) + 2 mM GlutaMAX (Gibco, 32561-037) with 10% FBS at 37 °C, 5% CO2. Stable BpRc1 cells, an Arnt-null variant of Hepa-1c1c7 cells, were cultured in DMEM (Corning, 15-018-CV) with 10% FBS, 2 mM GlutaMAX, and 2 mg/mL puromycin (Invivogen, ant-pr) at 37 °C, 5% CO2. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) (Cerilliant, ED-901-C), a high affinity AhR ligand, was used to activate the AhR pathway in samples that include TCDD in the label. TCDD was added to a final concentration of 10 nM and incubated for 2 hours, followed by total RNA collection.

extract_protocol:
Total RNA was extracted using QIAshredder (Qiagen, 79656) and RNeasy Kits (Qiagen, 74104)
TruSeq

treatment_protocol: 1 × 107 Karpas 299 or Peer cells were transfected with 4 uM of target siRNA duplexes using a Bio-Rad Gene Pulser Xcell electroporator set on infinite resistance, 300 V for Karpas 299 cells or 250 V for Peer cells, and 950 microfarads. Cells were suspended in RPMI-1640 medium containing 20% FBS and 2 mM GlutaMAX. Sixteen hours post-transfection, dead cells were removed by centrifugation at 400 × g for 20 min with Ficoll-Paque PLUS (GE Healthcare, 17-1440-02). The live cell layer was then transferred to RPMI-1640 medium complete with 10% FBS and 2 mM GlutaMAX at 0.5 × 106 cells/mL for 24 hours. The siRNA (MilliporeSigma) target sequences are as follows: siA-1 5’-UGC CAG GUC GGA UGA UGA GCA-3′, siA-3 5’-CGG UUU GCC AGG GAA AAU C-3’, siA-1/3 5’-GAC UCG UAC UUC CCA GUU U-3’ and 5’-CUU UGC UCC UGA GAC UGG A-3’, and AhR (MilliporeSigma, SASI_Hs01_00140202). The target sequence for siControl is a scrambled siA-1/3 sequence (31).

value: Hepatoma, liver epithelial

value: lentivirus transduced for stable expression of ARNT isoform 1 S77A mutant + TCDD


title: Healthy donor [PR1798_33_a]


title: genomic_DNA_from_Surgical_resection_GBM-474

source_name: Surgical resection GBM-474

value: Male


title: 1c1c7_TCDD

source_name: Hepa-1c1c7 cell line

value: TCDD


title: Healthy donor [PR1798_34_a]

source_name: circulating miRNAs


title: genomic_DNA_from_Surgical_resection_GBM-442

source_name: Surgical resection GBM-442

value: GBM

value: FFPE


title: genomic_DNA_from_Surgical_resection_GBM-440

source_name: Surgical resection GBM-440

value: RT


title: genomic_DNA_from_Surgical_resection_GBM-448

source_name: Surgical resection GBM-448


title: Healthy donor [PR1798_32_a]

value: uninfected


title: C28M

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

country: South Korea

institute: Chungbuk National University

description: flounder under 28℃

data_processing:
mRNA-Seq reads were mapped to reference flounder genome NCBI 8255) using Tuxedo protocol.
Using TopHat2 software and Cufflinks package, FPKM (fragments per kilobase of transcript per million mapped reads) values of each gene were calculated and used for subsequent data analysis.
DEGs (differentially expressed genes) were performed using GeneSpring v.7.3
Genome_build: flounder genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Paralichthys olivaceus

source_name: Muscle

growth_protocol: At nine months (bodyweight 308 ± 1.23 g), 120 individuals were originally maintained in a large tank containing 3 t of natural seawater.

extract_protocol:
Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructinos.
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: For temperature treatments (eight treatment groups), 15 fishes per treatment were transferred to a 1-t tank and acclimated to 12℃. Water temperature stimulation was performed under acute and chronic conditions. . In the acute water temperature stimulation, fishes in the seawater (12℃) were sequentially transferred to seawater at 18℃, 23℃, and 28℃ at 3 h intervals. For chronic water temperature stimulation, fishes in seawater (12℃) were exposed to a temperature gradually elevated by 3℃/h to reach 18℃, 23℃, and 28℃ and maintained at that temperature for at least 20 h.

value: tissue

value: 9 months


title: genomic_DNA_from_Surgical_resection_GBM-430

source_name: Surgical resection GBM-430


title: genomic_DNA_from_Surgical_resection_GBM-329

source_name: Surgical resection GBM-329


title: WT_iso1_TCDD

value: lentivirus transduced for stable expression of ARNT isoform 1 + TCDD


title: genomic_DNA_from_Surgical_resection_GBM-326

source_name: Surgical resection GBM-326


title: 1c1c7_DMSO

value: DMSO


title: hpGUS[G:U]-13

city: Acton

first: Ian

middle: K

last: Greaves

state: act

address: clunies ross street

country: Australia

institute: csiro

data_processing:
Adapters were removed using cutadapt
Bowtie V1.0 was used to align reads to genome
reads were normalized to reads per million
Custom pearl scripts were used to extract reads mapped to hairpin constructs and gene targets (EIN2, PDS, GUS transgene)
Genome_build: TAIR 10
Supplementary_files_format_and_content: Single excel file with read counts to hairpin transgenes and target genes

organism: Arabidopsis thaliana

source_name: 3 week old whole plant

growth_protocol: Plant seeds were sown either directly into soil, or placed first on MS plate for germination followed by transferring seedlings to soil. Plants were grown in a growth room (16 hours light/8 hours dark) at 22-24 °C.

extract_protocol:
Total RNA was extracted using Trizol
Standard illumina library sRNA-seq library preparation by service provider

tag: ecotype

value: Columbia

tag: genotype

value: hpGUS[G:U] transgene

value: 3 week old whole plant

tag: target gene

value: GUS


title: hpGUS[1:4]-a

description: 1mismatch every 4 bases of the sense strand

value: hpGUS[1:4] transgene


title: genomic_DNA_from_Surgical_resection_GBM-454

source_name: Surgical resection GBM-454

value: TMZ+RT


title: C23M

description: flounder under 23℃


title: genomic_DNA_from_Surgical_resection_GBM-318

source_name: Surgical resection GBM-318

value: Female


title: genomic_DNA_from_Surgical_resection_GBM-321

source_name: Surgical resection GBM-321

value: Male


title: genomic_DNA_from_Surgical_resection_GBM-316

source_name: Surgical resection GBM-316


title: hpGUS[WT]-3

value: hpGUS[WT] transgene


title: hpEIN2[G:U]-13

value: hpEIN2[G:U] transgene


title: hpGUS[G:U]-12


title: C18L

description: flounder under 18℃

source_name: Liver


title: C12L

description: flounder under 12℃


title: C18M

description: flounder under 18℃


title: hpEIN2[WT]-17

value: hpEIN2[WT] transgene


title: hpEIN2[G:U]-12


title: hpGUS[1:4]-b


title: C28G

description: flounder under 28℃

source_name: Gill


title: genomic_DNA_from_Surgical_resection_GBM-274

source_name: Surgical resection GBM-274

value: GBM

value: FFPE


title: genomic_DNA_from_Surgical_resection_GBM-304

source_name: Surgical resection GBM-304

value: RT


title: genomic_DNA_from_Surgical_resection_GBM-267

source_name: Surgical resection GBM-267


title: hpEIN2[WT]-15


title: C23G

description: flounder under 23℃

value: tissue

value: 9 months


title: C23L

description: flounder under 23℃


title: C12M

description: flounder under 12℃


title: C28L

description: flounder under 28℃


title: C18G

description: flounder under 18℃


title: genomic_DNA_from_Surgical_resection_GBM-288

source_name: Surgical resection GBM-288


title: M1

city: Shanghai

first: LI

last: TAO

state: Shanghai

address: Yangpu district Songhu Road

country: China

institute: Fudan University

data_processing:
The library products were sequenced using an Illumina NovaSeq platform.
The clean reads were aligned to the genome of C. albicans SC5314 using HiSat v2.0.5 with default parameters.
Relative gene expression levels were calculated using the FPKM (Fragments Per kb per Million reads) method. Differentially expressed genes were analyzed with the DESeq2 R package.
Genome_build: Candida albicans SC5314 genome (ASM18296v1)
Supplementary_files_format_and_content: text files containing FPKM values for each Sample

organism: Candida albicans

source_name: Candida albicans

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WT

value: mutanocyclin


title: M2


title: Ear KO, 3hr, PBS

type: RNA

city: Setagaya-ku

first: Kosuke

last: Tanegashima

state: Tokyo

address: 2-1-6 Kamikitazawa

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

description: Gene expression after 3hr in PBS-injeced ear skin

hyb_protocol: 0.60 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression Microarray 8x60K Ver.2.0 for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44K array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Ear KO, 3hr, PBS

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Mouse ears were dissoluved in TRIZOL, and total RNA were extracted with standerd protcol. RNA was further purified with Rnasy kit.

treatment_protocol: 10microL of PBS with or without 10^7 CFUs of S. aureus were injected intradermally into the pinnae of each ear using a 30G insulin syringe at ZT4. After 3 hours post injection, mice were sacrificed by cervical dislocation. Their ears were dissected and then treated with RNA later to stabilize their RNA.

value: PBS

value: ear

value: male


title: genomic_DNA_from_Surgical_resection_GBM-262

source_name: Surgical resection GBM-262


title: A28M

description: flounder under 28℃

source_name: Muscle


title: Ear WT, 3hr, S.aureus

description: Gene expression after 3hr in S.aureus-injeced ear skin

source_name: Ear WT, 3hr, S.aureus

value: S. aureus infection


title: C12G

description: flounder under 12℃


title: Ear KO, 3hr, S.aureus

source_name: Ear KO, 3hr, S.aureus


title: genomic_DNA_from_Surgical_resection_GBM-265

source_name: Surgical resection GBM-265


title: D2

value: DMSO


title: genomic_DNA_from_Surgical_resection_GBM-261

source_name: Surgical resection GBM-261


title: A23M

description: flounder under 23℃


title: D1


title: A18M

description: flounder under 18℃


title: A12M

description: flounder under 12℃


title: genomic_DNA_from_Surgical_resection_GBM-260

source_name: Surgical resection GBM-260

value: TMZ+RT


title: genomic_DNA_from_Surgical_resection_GBM-253

source_name: Surgical resection GBM-253

value: Male


title: Ear WT, 3hr, PBS

source_name: Ear WT, 3hr, PBS


title: genomic_DNA_from_Surgical_resection_GBM-250

source_name: Surgical resection GBM-250


title: A28L

description: flounder under 28℃

source_name: Liver


title: genomic_DNA_from_Surgical_resection_GBM-248

source_name: Surgical resection GBM-248


title: A23L

description: flounder under 23℃


title: A18L

description: flounder under 18℃


title: genomic_DNA_from_Surgical_resection_GBM-233

source_name: Surgical resection GBM-233


title: A12L

description: flounder under 12℃


title: genomic_DNA_from_Surgical_resection_GBM-229

source_name: Surgical resection GBM-229


title: BH0188-5 (KO)

city: Taipei

first: Chun-Hao

middle: James

last: Hung

state: TAIWAN

address: 128 Academia Road, Section 2, Nankang, Taipei, Taiwan

country: Taiwan

institute: Institute of Molecular Biology, Academia Sinica

description: Gene expression data from embryos fetal liver

hyb_protocol: biotinylated cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Array following the standard protocols

scan_protocol: Genome-scale gene expression profiling using the Mouse Genome Array 430A 2.0 (Affymetrix, Inc.).

data_processing: Standard MAS5.0 method was applied to normalize the gene expression data. Gene expression values were log-transformed for later comparative analysis. Statistical analysis was carried out using R 3.0.2 language (R Development Core Team, 2013, http://www.R-project.org)

label: biotin

source_name: Fetal livers

label_protocol: standard protocols

growth_protocol: Primary fetal liver cells without culture

extract_protocol: E14.5 mouse fetal livers from WT and Eklf-/- mouse fetuses were homogenized by repeated pipetting in phosphate-buffered saline (PBS) (10 mM phosphate, 0.15 M NaCl [pH 7.4]). Total RNAs were then isolated with Trizol reagent (Invitrogen).

treatment_protocol: EKLF knock-out gene to compare with WT cells

value: liver

value: EKLF KO


title: A28G

description: flounder under 28℃

source_name: Gill


title: A23G

description: flounder under 23℃


title: genomic_DNA_from_Surgical_resection_GBM-225

source_name: Surgical resection GBM-225

value: Female


title: BH0188-4 (KO)


title: genomic_DNA_from_Surgical_resection_GBM-218

source_name: Surgical resection GBM-218

value: GBM


title: genomic_DNA_from_Surgical_resection_GBM-212

source_name: Surgical resection GBM-212

value: FFPE


title: Liver, WT

city: Suita

first: Takahiro

last: Kodama

state: Osaka

address: 2-2 Yamadaoka

department: Department of Gastroenterology and Hepatology

institute: Osaka university, Graduate School of Medicine

data_processing:
Instrument model: DNBSEQ-G400RS
Sequencing was performed on a DNBSEQ-G400RS platform in 2 x 100 bp paired-end mode.
The FASTQ files for each replicate were processed by the BD Rhapsody WTA bioinformatics workflow (BD Biosciences) on the Seven Bridges Genomics (SBG) cloud platform using default parameters and output as "RSEC-adjusted molecules".
Cell labeling information is captured by the bases in the three sections (CLS1, CLS2, and CLS3) according to each R1 read.
Two common sequences (L1, L2) separate the three CLSs, and the presence of L1 and L2 relates to how the capture oligonucleotide probes are constructed on the beads. By design, each CLS has one of 96 default sequences, which have a Hamming distance of at least 4 bases and an edit distance of at least 2 bases. A cell label is defined by a unique combination of the default sequences of the three CLSs. Therefore, the maximum number of cell labels is 96^3 (884,736). Cell labels are represented by indices from 1 to 96^3.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes BD Rhapsody sequences of cell label sections.
Supplementary_files_format_and_content: The csv files represent RSEC-adjusted molecules.

extract_protocol:
mRNA was extracted from fresh tissues with BD Rhapsody Cartridge Reagent Kit
Rhapsody libraries were converted to libraries for DNBSEQ using MGIEasy Universal Library Conversion Kit (App-A)
scRNA-Seq

value: Liver

value: Wild type


title: BH0188-2 (KO)


title: BH0188-3 (KO)


title: BH0153-4 (WT)


title: A18G

description: flounder under 18℃

value: tissue

value: 9 months


title: BH0153-1 (WT)

value: WT


title: BH0153-2 (WT)


title: A12G

description: flounder under 12℃


title: genomic_DNA_from_Surgical_resection_GBM-210

source_name: Surgical resection GBM-210

value: RT


title: Liver, DKO

value: Alb-CreERT2(+) Pten fl/fl Traf3 fl/fl


title: E8L5-3

city: Köln

first: Maria

last: Albani

address: Carl-von-Linné-Weg 10

department: Botanical institute

country: Germany

institute: University of Cologne

data_processing:
Reads derived from the Illumina library were aligned to the reference genome (A. alpina_V5) using STAR
Raw read counts per gene were quantified with HTSeq v0.5.4p1
Differential expression between samples was determined using DESeq
The differentially expressed genes with more than 2-fold change and an adjusted p-value below 0.05 were obtained using DESeq2 and selected for further analysis.
Genome_build: Arabis alpina V5 genome
Supplementary_files_format_and_content: excel files include average count and log2foldchange for each Sample and csv files including all the raws counts used for Deseq

organism: Arabis alpina

source_name: eop089 5 weeks old leaf grown in long days replicate 3

growth_protocol: Plants are grown for at long day

extract_protocol:
RNA was isolated using RNeasy Plant RNA isolation kit (Qiagen) according to manufacturer's instructions
polyA enrichment was conducted with 1 µg total RNA using NEBNext Poly(A) mRNA Magnetics Isolation Module (New England Biolabs), followed by library preparation with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). Quality and quantity were assessed at all steps via capillary electrophoresis (TapeStation, Agilent Technologies) and fluorometry (Qubit, Thermo Fisher Scientific). Sequencing was performed on HiSeq2500 (Illumina) with 1 x 100 bp single reads.

value: The 5th and 6th leaf

value: eop089 mutant

value: 5 weeks

tag: accession

value: Pajares


title: genomic_DNA_from_Surgical_resection_GBM-189

source_name: Surgical resection GBM-189

value: Male


title: genomic_DNA_from_Surgical_resection_GBM-230

source_name: Surgical resection GBM-230

value: TMZ+RT


title: genomic_DNA_from_Surgical_resection_GBM-178

source_name: Surgical resection GBM-178


title: genomic_DNA_from_Surgical_resection_GBM-187

source_name: Surgical resection GBM-187


title: E8L5-1

source_name: eop089 5 weeks old leaf grown in long days replicate 1


title: genomic_DNA_from_Surgical_resection_GBM-185

source_name: Surgical resection GBM-185


title: E8A5-3

source_name: eop089 5 weeks old apex grown in long days replicate 3

value: dissected shoot apices


title: E8A5-2

source_name: eop089 5 weeks old apex grown in long days replicate 2


title: genomic_DNA_from_Surgical_resection_GBM-167

source_name: Surgical resection GBM-167

value: Female


title: E8A5-1

source_name: eop089 5 weeks old apex grown in long days replicate 1


title: E8L5-2

source_name: eop089 5 weeks old leaf grown in long days replicate 2


title: genomic_DNA_from_Surgical_resection_GBM-161

source_name: Surgical resection GBM-161

value: GBM


title: NS_C3_14

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from neurosphere U87MG cells treated with PEF after 24h

hyb_protocol: 5.5ug of sscDNA were fragmentated and 5.2 uf were hybridized for 16 hr at 45°C on GeneChip Human Clariom S Array (GPL23159 Platform). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA

label_protocol: Biotinylated cRNA were prepared according to the standardThermoFisher protocol starting  from 100ng of Total RNA using the ThermoFisher WTA Kit

growth_protocol: U87MG cells were cultured in DMEM with 10% FBS (ML) or DMEM-F12 with B27 20ng/mL FGF2 and EGF

extract_protocol: RNA was extracted using Trizol

treatment_protocol: 5  Electrical pulses with an inter-pools interval of 1 Hz

value: Pulsed Electric Field (PEF)

tag: sample

value: Neurosphere


title: NS_C3_16


title: NS_C3_13


title: NS_C3_15


title: BH0153-3 (WT)

source_name: Fetal livers

value: liver


title: E8A3-3

source_name: eop089 3 weeks old apex grown in long days replicate 3

value: 3 weeks


title: NS_Sham_11

description: Gene expression data from neurosphere U87MG cells untreated

value: Sham


title: genomic_DNA_from_Surgical_resection_GBM-158

source_name: Surgical resection GBM-158

tag: patient

value: FFPE


title: NS_Sham_12


title: E8A3-2

source_name: eop089 3 weeks old apex grown in long days replicate 2


title: genomic_DNA_from_Surgical_resection_GBM-157

source_name: Surgical resection GBM-157

tag: batch


title: NS_Sham_9


title: genomic_DNA_from_Surgical_resection_GBM-145

source_name: Surgical resection GBM-145

tag: gender


title: ML_C3_9

description: Gene expression data from monolayer U87MG cells treated with PEF after 24h

value: Monolayer


title: genomic_DNA_from_Surgical_resection_GBM-144

source_name: Surgical resection GBM-144


title: E8A3-1

source_name: eop089 3 weeks old apex grown in long days replicate 1


title: ML_C3_8


title: E5L5-3

source_name: eop055 5 weeks old leaf grown in long days replicate 3

value: eop055 mutant


title: ML_C3_7


title: NS_Sham_10


title: E5L5-2

source_name: eop055 5 weeks old leaf grown in long days replicate 2

value: The 5th and 6th leaf


title: genomic_DNA_from_Surgical_resection_GBM-135

source_name: Surgical resection GBM-135

value: RT


title: E5L5-1

source_name: eop055 5 weeks old leaf grown in long days replicate 1

value: 5 weeks


title: ML_C3_6


title: genomic_DNA_from_Surgical_resection_GBM-133

source_name: Surgical resection GBM-133


title: PL5-3

source_name: pep1-1 5 weeks old leaf grown in long days replicate 3

value: pep1-1 mutant

value: Pajares


title: genomic_DNA_from_Surgical_resection_GBM-155

source_name: Surgical resection GBM-155

value: Male

value: TMZ+RT


title: genomic_DNA_from_Surgical_resection_GBM-131

source_name: Surgical resection GBM-131

value: Female


title: genomic_DNA_from_Surgical_resection_GBM-124

source_name: Surgical resection GBM-124

value: GBM


title: PL5-1

source_name: pep1-1 5 weeks old leaf grown in long days replicate 1


title: ML_Sham_3

description: Gene expression data from monolayer U87MG cells untreated


title: E5A3-3

source_name: eop055 3 weeks old apex grown in long days replicate 3

value: dissected shoot apices


title: genomic_DNA_from_Surgical_resection_GBM-129

source_name: Surgical resection GBM-129


title: genomic_DNA_from_Surgical_resection_GBM-119

source_name: Surgical resection GBM-119


title: E5A3-1

source_name: eop055 3 weeks old apex grown in long days replicate 1


title: PA3-3

source_name: pep1-1 3 weeks old apex grown in long days replicate 3


title: genomic_DNA_from_Surgical_resection_GBM-111

source_name: Surgical resection GBM-111


title: FTVSV6hIP

city: Beijing

first: Lili

last: Cao

address: datun Road

institute: Chinese Academy of Sciences

data_processing:
After clustering, the libraries were sequenced on Illumina Hiseq X Ten platform using (2 3 150bp) paired-end module.
The raw images were transformed into raw reads by base calling using CASAVA (https://support. illumina.com.cn/sequencing/sequencing_software/casava.html).
Then, raw reads in a fastq format were first processed using inhouse perl scripts.
Clean reads were obtained by removing reads with adapters, reads in which unknown bases were more than 5% and low-quality reads (the percentage of low quality bases was over 50% in a read, we defined the low quality base to be the base whose sequencing quality was no more than 10).
At the same time, Q20, Q30, GC content of the clean data were calculated (Vazyme Biotech, Nanjing, China).
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: THP-1 cells

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS, 100 U/mL Penicillin-Streptomycin.

extract_protocol:
Total RNA was isolated using the RNA simple Total RNA kit (TIANGEN)
The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina (Vazyme Biotech, Nanjing, China) following the manufacturer’s recommendations.

treatment_protocol: without or with 0.1 MOI VSV infection for 6 hours or 24 hours

tag: antibody

value: SAFA antibody

tag: agent

value: VSV

tag: time point

value: 6 hours


title: genomic_DNA_from_Surgical_resection_GBM-117

source_name: Surgical resection GBM-117

tag: disease state

tag: age


title: FTVSV24hIP

value: 24 hours


title: PL5-2

source_name: pep1-1 5 weeks old leaf grown in long days replicate 2


title: FTVSV24hinput


title: genomic_DNA_from_Surgical_resection_GBM-109

source_name: Surgical resection GBM-109

tag: treatment

value: FFPE


title: FTVSV6hinput


title: PA3-2

source_name: pep1-1 3 weeks old apex grown in long days replicate 2

value: 3 weeks


title: PA3-1

source_name: pep1-1 3 weeks old apex grown in long days replicate 1


title: ML_Sham_4

value: Sham

value: Monolayer


title: E5A3-2

source_name: eop055 3 weeks old apex grown in long days replicate 2

value: eop055 mutant


title: genomic_DNA_from_Surgical_resection_GBM-105

source_name: Surgical resection GBM-105

value: RT


title: ML_Sham_1


title: ML_Sham_2


title: Podocyte_UM51_24h_ANGII_2

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description: replicate 2

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol for Affymetrix Clariom S Assay Gene Expression Array

data_processing: The data were normalised using RMA normalisation from R/Bioconductor

source_name: UdRPC-derived podocyte treated with ANGII

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: UdRPCs were cultured in Proliferation Medium (PM) composed of 50% DMEM high Glucose and 50% Keratinocyte medium supplemented with 5% FCS, 0.5% NEAA, 0.25% Gtx and 0.5% Penicillin and Streptomycin at 37°C (Gibco, Carlsbad, United States) under hypoxic conditions. For differentiation, the cells were seeded at low and high density in 6- or 12-well plates coated with 0,2% type 1 Collagen (Gibco) and grown in PM for 24 hours. After this the medium was changed to advanced RPMI (Gibco) supplemented with 0.5% FCS, 1% Penicillin and Streptomycin and 30 µM retinoic acid. Typical podocyte morphology was observed after 7 days.

extract_protocol: The RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and the manufactural protocol. The quality of the RNA was checked with a NanodropTM spectrophotometer (Thermo Scientific).

treatment_protocol: ANG II (Sigma Aldrich, St. Louis, Missouri, United States) was diluted in the culture medium to a final concentration of 100 µM. Cells were incubated for 6h and 24h with ANGII and the conditioned medium was kept for secretome analyses.

tag: cell type


title: Ftconinput

value: Mock


title: Podocyte_UM51_24h_ANGII_1

description: replicate 1

value: UdRPC-derived podocyte treated with ANGII


title: Podocyte_UM48_24h_ANGII_2

description: replicate 2


title: Podocyte_UM51_6h_ANGII_2

description: replicate 2


title: Podocyte_UM48_24h_ANGII_1

description: replicate 1


title: E5A5-3

source_name: eop055 5 weeks old apex grown in long days replicate 3

value: 5 weeks

value: Pajares


title: Podocyte_UM48_6h_ANGII_2

description: replicate 2


title: FTconIP


title: E5A5-2

source_name: eop055 5 weeks old apex grown in long days replicate 2


title: THP1-+WT-VSV

treatment_protocol: without or with 0.1 MOI VSV infection for 24 hours

tag: cell line

value: THP-1 cells

value: SAFA-/- +WT VSV infection for 24 hours


title: THP1-+WT-Mock

value: SAFA-/- +WT Mock


title: THP1-+RGG-VSV

value: SAFA-/- +RGG VSV infection for 24 hours


title: PA5-3

source_name: pep1-1 5 weeks old apex grown in long days replicate 3

tag: tissue

value: dissected shoot apices

value: pep1-1 mutant


title: Podocyte_UM48_2

description: replicate 2

source_name: UdRPC-derived podocyte

value: UdRPC-derived podocyte


title: Podocyte_UM51_2

description: replicate 2


title: genomic_DNA_from_Surgical_resection_GBM-90

city: Lausanne

first: Pierre

last: Bady

address: Quartier UNIL-Sorge

institute: CHUV / BCF / SIB

data_processing:
BeadStudio software v3.2 was used for primary data acqusition. Raw data was imported into R and further processed using R/Bioconductor package “minfi”. The raw pre-processing (Illumina method) was used for data normalization.
normalized (Illumina pre-processing) Average Beta

source_name: Surgical resection GBM-90

extract_protocol: Genomic DNA was isolated using Qiagen AllPrep DNA/RNA Kit (Qiagen, 80204).

value: Female

value: GBM

value: TMZ+RT

value: FFPE


title: PA5-2

source_name: pep1-1 5 weeks old apex grown in long days replicate 2


title: THP1-+RGG-Mock

value: SAFA-/- +RGG Mock


title: genomic_DNA_from_Surgical_resection_GBM-104

source_name: Surgical resection GBM-104

value: Male


title: E5A5-1

source_name: eop055 5 weeks old apex grown in long days replicate 1

value: eop055 mutant


title: THP1-KO-VSV

source_name: THP-1 cells

value: SAFA-/- VSV infection for 24 hours


title: genomic_DNA_from_Surgical_resection_GBM-86

source_name: Surgical resection GBM-86


title: THP1-KO-Mock

value: SAFA-/- Mock


title: Podocyte_UM48_6h_ANGII_1

description: replicate 1

value: UdRPC-derived podocyte treated with ANGII


title: Podocyte_UM51_6h_ANGII_1

description: replicate 1


title: genomic_DNA_from_Surgical_resection_GBM-93

source_name: Surgical resection GBM-93


title: Normal sample of Monkey RM25 (RNAseq)

data_processing:
FASTQC toolkit was performed for quality control of FASTQ files
The fastp tool was performed to trim adapters and low-quality reads
Cleaned reads of total RNA sequencing were aligned to the reference genome using the STAR RNA sequencing aligner.
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: COLON

extract_protocol:
Macro-dissection was performed to decrease the admixture of adjacent normal tissue and to enrich the percentage of tumor material for subsequent RNA extraction. De-paraffinization of FFPE tumor and adjacent normal specimens was performed using QIAGEN de-paraffinization solution (QIAGEN, Valencia, CA). DNA and RNA from 19 tumor and adjacent normal samples was extracted using the AllPrep DNA/RNA FFPE Kit (QIAGEN) following the manufacturer’s protocol. In the case of the unavailability of FFPE samples, genomic DNA and RNA were extracted from fresh frozen tumor (n=2) and normal (n=3) samples using the ZR-Duet DNA/RNA MiniPrep extraction kit (ZYMO RESEARCH, Irvine, CA). Quantification was performed with a NanoDrop One™ spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and Qubit™ Fluorometer 2.0 (Qubit, San Francisco, CA) using dsDNA and RNA assay kits. RNA integrity was analyzed using the Tape Station RNA assay kit (Agilent Technologies, Santa Clara, CA).
Truseq stranded total RNA library preparation kit (Illumina®, San Diego, CA) was used to prepare libraries of 21 tumors and 20 matched normal RNA samples

value: Normal

tag: msi status

value: MSI-H

tag: sample id

tag: mlh1 c.1029 (c>g) germline mutation status

value: Wild type


title: genomic_DNA_from_Surgical_resection_GBM-92

source_name: Surgical resection GBM-92

value: RT


title: Tumor sample of Monkey RM25 (RNAseq)

value: Tumor


title: PA5-1

source_name: pep1-1 5 weeks old apex grown in long days replicate 1

value: dissected shoot apices

tag: genotype

value: pep1-1 mutant

value: 5 weeks

tag: accession

value: Pajares


title: Normal sample of Monkey RM38 (RNAseq)

value: Heterozygous


title: UdRPC_UM48

description: replicate 1

source_name: Urine-derived renal progenitor cell (UdRPC)


title: genomic_DNA_from_Surgical_resection_GBM-85

source_name: Surgical resection GBM-85

tag: patient

value: GBM

value: FFPE


title: Podocyte_UM51_1

description: replicate 1

value: UdRPC-derived podocyte


title: Tumor sample of Monkey RM31 (RNAseq)

value: Female


title: genomic_DNA_from_Surgical_resection_GBM-75

source_name: Surgical resection GBM-75

tag: batch

value: Male


title: THP1-WT-Mock

value: THP-1 cells

value: WT-Mock


title: genomic_DNA_from_Surgical_resection_GBM-43

source_name: Surgical resection GBM-43

tag: gender


title: genomic_DNA_from_Surgical_resection_GBM-39

source_name: Surgical resection GBM-39

value: TMZ+RT


title: genomic_DNA_from_Surgical_resection_GBM-52

source_name: Surgical resection GBM-52


title: genomic_DNA_from_Surgical_resection_GBM-82

source_name: Surgical resection GBM-82


title: genomic_DNA_from_Surgical_resection_GBM-62

source_name: Surgical resection GBM-62


title: Podocyte_UM48_1

description: replicate 1

source_name: UdRPC-derived podocyte


title: UdRPC_UM51

description: replicate 1

value: Urine-derived renal progenitor cell (UdRPC)


title: genomic_DNA_from_Surgical_resection_GBM-80

source_name: Surgical resection GBM-80


title: Tumor sample of Monkey RM38 (RNAseq)

value: MSI-H


title: Normal sample of Monkey RM31 (RNAseq)

value: Normal


title: UdRPC_UF45

description: replicate 1


title: Normal sample of Monkey RM37 (RNAseq)

value: Wild type


title: HCT 116_siBRG1_1

city: Kyoto

first: Takaaki

last: Yoshikawa

address: 54 Shogoin-Kawahara-cho

department: Gastroenterology and Hepatology

institute: Kyoto University Graduate School of Medicine

description: gene expression of BRG1-suppressed HCT 116 cells

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)
RMA Analysis(background correction, summarization, normalization) performed using Affymetrix Power Tools (APT) Software.

source_name: HCT 116 siBRG1

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: HCT 116

tag: knockdown


title: Normal sample of Monkey RM30 (RNAseq)


title: THP1-WT-VSV

source_name: THP-1 cells

tag: agent

value: WT-VSV infection for 24 hours


title: genomic_DNA_from_Surgical_resection_GBM-36

source_name: Surgical resection GBM-36

value: RT


title: genomic_DNA_from_Surgical_resection_GBM-32

source_name: Surgical resection GBM-32


title: genomic_DNA_from_Surgical_resection_GBM-27

source_name: Surgical resection GBM-27


title: Podocyte_UF45

description: replicate 1


title: HCT 116_siControl_3

description: gene expression of control HCT 116 cells

source_name: HCT 118 siControl

value: siControl


title: genomic_DNA_from_Surgical_resection_GBM-26

source_name: Surgical resection GBM-26


title: Normal sample of Monkey RM27 (RNAseq)

source_name: COLON


title: Tumor sample of Monkey RM37 (RNAseq)

value: Tumor


title: Tumor sample of Monkey RM30 (RNAseq)


title: Normal sample of Monkey RM40 (RNAseq)


title: Tumor sample of Monkey RM27 (RNAseq)


title: genomic_DNA_from_Surgical_resection_GBM-30

source_name: Surgical resection GBM-30

value: GBM


title: Normal sample of Monkey RM23 (RNAseq)


title: 2W - rep 2.2

city: London

first: Ana

last: O'Loghlen

address: 4 Newark St

country: United Kingdom

institute: Queen Mary University of London

description: Genomic DNA from MCF7 cells infected with a genome-wide CRISPR/Cas9 library

data_processing:
Cutadapt used to trim adapters
Bowtie used to align the trimmed sequences to human hg19
Fasta files aligned to the human genome hg 19 using BLAT (settings blat -stepSize=5 -repMatch=2253 -minScore=20 -minIdentity=100)
Sequences that aligned to multiple places in the genome were identified and summarized
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Genome_build: hg19
Supplementary_files_format_and_content: Enrichment

source_name: MCF7 cells treated with Palbo for 2 weeks

growth_protocol: Cells were grown in supplemented high glucose DMEM

extract_protocol:
At the end of the experiment, genomic DNA was extracted at days 0 and day 14 after infection using the QIAmp Blood and Cell Culture DNA midi kit (Qiagen).
Amplyfication using GeCKOv2 plasmid specific primers

treatment_protocol: Cells werere treated with or without Palboclib for 14 days

value: MCF7 breast cancer cell line

value: Palbociblib


title: DLD1_siBRG1_3

description: gene expression of BRG1-suppressed DLD1 cells

source_name: DLD1 siBRG1


title: HCT 116_siBRG1_2

source_name: HCT 116 siBRG2


title: genomic_DNA_from_Surgical_resection_GBM-23

source_name: Surgical resection GBM-23

value: FFPE


title: Tumor sample of Monkey RM40 (RNAseq)

value: Female


title: 2W - rep 1.2


title: HCT 116_siControl_2

source_name: HCT 117 siControl


title: DLD1_siBRG1_2


title: Tumor sample of Monkey RM23 (RNAseq)


title: HCT 116_siControl_1

source_name: HCT 116 siControl


title: DLD1_siControl_3

description: gene expression of control DLD1 cells

source_name: DLD1 siControl


title: HCT 116_siBRG1_3

source_name: HCT 116 siBRG3


title: 2W - rep 1.1


title: DLD1_siControl_2

description: gene expression of control DLD1 cells


title: genomic_DNA_from_Surgical_resection_GBM-17

source_name: Surgical resection GBM-17

value: Male


title: genomic_DNA_from_Surgical_resection_GBM-19

source_name: Surgical resection GBM-19


title: DLD1_siControl_1

description: gene expression of control DLD1 cells


title: CTL - rep 2.2

source_name: MCF7 treated with DMSO

value: DMSO


title: DLD1_siBRG1_1


title: genomic_DNA_from_Surgical_resection_GBM-15

source_name: Surgical resection GBM-15


title: genomic_DNA_from_Surgical_resection_GBM-16

source_name: Surgical resection GBM-16

value: TMZ+RT


title: genomic_DNA_from_Surgical_resection_GBM-7

source_name: Surgical resection GBM-7


title: Tumor sample of Monkey RM33 (RNAseq)


title: Normal sample of Monkey RM33 (RNAseq)


title: Normal sample of Monkey RM26 (RNAseq)

value: MSS


title: genomic_DNA_from_Surgical_resection_GBM-4

source_name: Surgical resection GBM-4


title: CTL - rep 2.1


title: CTL - rep 1.2


title: genomic_DNA_from_Surgical_resection_GBM-2

source_name: Surgical resection GBM-2


title: CTL - rep 1.1


title: Tumor sample of Monkey RM26 (RNAseq)

source_name: COLON


title: Streptococcus mutans CHX treated sample: replicate R3

status: Public on Mar 30 2022

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

institute: Quantitative Biology Center (QBiC)

description:
Sample CHX R3
QPDAM098AM_SM-10-3

data_processing:
The Nextflow-based nf-core pipeline nf-core/rnaseq (version 1.4.2; https://github.com/nf-core/rnaseq) was used for the RNAseq Bioinfomatics analysis.
As part of this workflow, FastQC (version v0.11.8) was used to determine quality of the FASTQ files (Andrews, 2010). Subsequently, adapter trimming was conducted with Trim Galore (version 0.6.4) (Krueger & Andrews, 2012). STAR aligner (version 2.6.1, (Dobin et al., 2012)) was used to map the reads that passed the quality control against the latest assembly (RefSeq assembly accession GCF_000347875.1) of the strain ATCC 25175, downloaded from NCBI. Note that the gtf file for the S. mutans genome had to be modified to be used for the nf-core/rnaseq workflow, by removing empty fields for the tag “transcript_id” in the 9th column of that gtf file. The RNA-seq data quality control was performed with RSeQC (version 3.0.1) (Wang et al., 2012) and read counting of the features (e.g. genes) with featureCounts (version 1.6.4) (Liao et al., 2014). An aggregation of the quality control for the RNAseq analysis was performed with MultiQC (version 1.7; http://multiqc.info/) (Ewels et al., 2016).
The analysis of the differential gene expression was performed in the R language (version 3.5.1) using DESeq2 (version 1.22) through the nextflow based workflow qbic-pipelines/rnadeseq (https://github.com/qbic-pipelines/rnadeseq, version 1.3.2). Genes were considered differentially expressed genes (DEGs) when the Benjamini-Hochberg multiple testing adjusted p-value (Benjamini & Hochberg, 1995) was smaller than 0.05 (padj < 0.05).
Genes were further filtered for biological relevance if the log2 Fold Change (FC) in expression between the two considered groups was above the threshold of 1.0 and less than -1.0.
Biocyc database was used for pathway analysis (Karp et al., 2019). All DEGs were included, and enrichment was calculated using Fisher's exact test (p ≤ 0.05).
Genome_build: RefSeq assembly accession GCF_000347875.1 (ATCC25175_V1); strain ATCC 25175.
Supplementary_files_format_and_content: merged_gene_counts_Smutans.txt: Raw counts as standard output from the featureCounts step of the nf-core pipeline nf-core/rnaseq (version 1.4.2; https://github.com/nf-core/rnaseq) workflow, showing raw read count values for each gene as row in each sample as separate column.

organism: Streptococcus mutans DSM 20523

source_name: bacterial cell culture

growth_protocol: Gram-positive Streptococcus mutans (DSM 20523; ATCC 25175) was obtained from the German Collection of Microorganisms and Cell Cultures GmbH (DSMZ; Braunschweig, Germany) and was used as reference strains in this study. S. mutans was grown in Brain-Heart-Infusion (BHI; Sigma-Aldrich, St. Louis, MO, USA) broth and on BHI agar plates. Planktonic cultures (5 mL) were grown aerobically overnight at 37 °C. Afterwards, suspensions were harvested by centrifugation (ROTINA 420 R, Hettich Lab Technology, Tuttlingen, Germany) and resuspended in BHI yielding an optical density (OD) of 2.0, as measured by means of a spectrophotometer at 600 nm (Ultrospec 3300 pro; Amersham Biosciences, Amersham, United Kingdom).

extract_protocol:
RNA extraction and sequencing were performed by the NGS Competence Center Tübingen (NCCT), the sequencing partner of the Quantitative Biology Center (QBiC), Tübingen, Germany. RNA of all samples was isolated with the Quick-RNATM Fungal/Bacterial Miniprep Kit (Zymo Research, Freiburg, Germany). RNA extraction was followed by DNase I treatment in solution using the DNase I recombinant Kit (Roche, Basel, CH) and purification and concentration of RNA using the RNA Clean & Concentrator-5 Kit (Zymo Research, Freiburg, Germany).
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit with 100 ng total RNA as input. Sequencing was performed on the Illumina NextSeq 500using a High Output Kit (version 2.5; 75 cycles) with 1% PhiX spike-in (Illumina, San Diego, CA, USA).

treatment_protocol: Samples were either incubated with 200 μL distilled water or 200 µL CHX for 5 min.

value: Chlorhexidine


title: Streptococcus mutans control sample: replicate R5

description:
Sample UC R5
QPDAM080AJ_SM-00-5

value: Control


title: Streptococcus mutans CHX treated sample: replicate R5

description:
Sample CHX R5
QPDAM100A3_SM-10-5


title: Streptococcus mutans CHX treated sample: replicate R1

description:
Sample CHX R1
QPDAM096A6_SM-10-1


title: Streptococcus mutans CHX treated sample: replicate R4

description:
Sample CHX R4
QPDAM099AU_SM-10-4


title: Streptococcus mutans control sample: replicate R3

description:
Sample UC R3
QPDAM078A8_SM-00-3


title: Streptococcus mutans control sample: replicate R1

description:
Sample UC R1
QPDAM076AQ_SM-00-1


title: Streptococcus mutans control sample: replicate R2

description:
Sample UC R2
QPDAM077A0_SM-00-2


title: Streptococcus mutans CHX treated sample: replicate R2

description:
Sample CHX R2
QPDAM097AE_SM-10-2


title: Streptococcus mutans control sample: replicate R4

description:
Sample UC R4
QPDAM079AG_SM-00-4


title: Japanese flounder_2d_VH_8

city: Matsuyama

first: Kei

last: Nakayama

address: 2-5 Bunkyo-cho

department: Center for Marine Environmental Studies

institute: Ehime University

description:
Gene expression in flounder infected with VHSV and/or exposed to heavy oil
Agilent-022357

hyb_protocol: The Agilent 8x15 k custom oligo DNA microarray was hybridized with the fragmented labelled cRNA for 15 h at 65 °C as described in the Agilent Low RNA Fluorescent Linear Amp Kit protocol.

scan_protocol: The hybridized microarray slides were scanned by Agilent DNA Microarray Scanner. Scan area: 61x21.6 mm; Scan resolution: 5 µm; 5 µm Scanning mode: Single Pass; Dye channel: Green; Green PMT: XDR Hi 100%, XDR Lo 10%.

data_processing: Initial quality control of data from each slide was performed using Spike-In Control RNA. The intensities of spots were digitalized using Feature Extraction ver 9.5.3.1 (Agilent Technologies). We then obtained more reliable data sets, through systematic removal of the data flagged as one of the following descriptions: not positive and significant, not above background, saturated, not uniform, a population outlier, or manually marked. The digitalized fluorescent intensities were logarithmically transformed and normalized per chip by 75th percentile using GeneSpring GX 10.0 (Agilent Technologies).

source_name: kidney, 2d, heavy oil, VHSV

label_protocol: Two-hundred nanograms of the total RNA added One-Color Spike-Mix (Agilent Technologies) were used to synthesize Cy3-labeled cRNA using Low RNA Fluorescent Linear Amp Kit (Agilent Technologies).

extract_protocol: Total RNA in the kidney from each fish was extracted using TRIzol reagent. To remove contaminated genomic DNA, the crude RNA was further purified using an RNeasy column.

treatment_protocol: Fish were infected with VHSV, followed by heavy oil exposure.

value: kidney


title: D4_P38α_ff_1

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

data_processing:
BGI Zebracall software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR package of R.
Assembly: mm10

source_name: Whole uteri

growth_protocol: Mice were housed in the animal care facility of Xiamen University according to the guidelines for the care and use of laboratory animals. All experimental procedures were approved by the Animal Welfare Committee of Research Organization (X200811), Xiamen University.

extract_protocol:
Total RNA was extracted from D4 uteri using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: time

value: pregnant day 4

value: P38{alpha} ff


title: D4_P38α_dd_1

value: P38{alpha} dd


title: D4_P38α_ff_2


title: Japanese flounder_2d_VH_5


title: Japanese flounder_2d_HO_7

source_name: kidney, 2d, heavy oil, MEM


title: Japanese flounder_2d_CO_8

source_name: kidney, 2d, chemical-free, MEM


title: Japanese flounder_2d_CO_5


title: Japanese flounder_2d_VI_6

source_name: kidney, 2d, chemical-free, VHSV


title: Ko_4

city: Zaragoza

first: Jesus

last: Osada

state: Spain

address: C/ Miguel Servet 177

department: Biochemistry and Molecular Biology

country: Spain

institute: Universidad de Zaragoza

description: 16 hours fasting

data_processing:
After reads filtering, we map clean reads to reference genome (mm10) using HISAT2
After genome mapping, we use StringTie to reconstruct transcripts, and with genome annotation information we identify novel transcripts by using Cuffcompare(a tool of Cufflinks) and predict the coding ability of those new transcripts using CPC. In total, we identify 5,419 novel transcripts.
GATK was used to call  SNP  and  INDEL  variant for each sample. Final results are stored in VCF format.
rMATS then detected differentially splicing gene (DSG) between samples. DSGs are regulated by alternative splicing (AS), five types of AS events were screened, including Skipped Exon (SE), Alternative 5' Splicing Site (A5SS), Alternative 3' Splicing Site (A3SS), Mutually exclusive exons (MXE) and Retained Intron (RI).
After novel transcript detection, novel coding transcripts were merged with reference transcripts to get complete reference, then clean reads were mapped to it using Bowtie2, followed by calculating gene expression level for each sample with RSEM
Genome_build: mm10
Supplementary_files_format_and_content: bam files

source_name: Liver

extract_protocol:
Total RNA was extracted using Quick-RNA MiniPrep kit (Cat.No:R1055, ZYMO Research, Irvine, CA, USA).
The first step involves purifying the poly-A containing mRNA molecules using poly-T oligoattached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

treatment_protocol: PBS wash of liver sections

value: liver

value: Txndc5 Knockout

tag: diet

value: Mice over 4 weeks chow purified diet


title: Ko_2

description: 16 hours fasting


title: Japanese flounder_2d_VH_2


title: Japanese flounder_2d_HO_6


title: Japanese flounder_2d_HO_2


title: Japanese flounder_2d_CO_4


title: Uninjected stage 10.5 replicate 2

city: Irvine

first: Kitt

middle: D.

last: Paraiso

address: 4410 Nat Sci II, University of California, Irvine

department: Department of Developmental and Cell Biology

institute: University of California, Irvine

data_processing:
RNA-seq gene expression calling: Reads were aligned using RSEM v.1.2.12 (Li and Dewey 2011) and Bowtie v2.2.7 (Langmead and Salzberg 2012) to the Xenopus tropicalis genome version 9.0 (Mitros et al., 2019; Karimi et al., 2018). Transcripts per million were extracted from RSEM results output.
Genome_build: Xenopus tropicalis v9.0
Supplementary_files_format_and_content: tcf7l1-MO-expression-tpm.txt.gz: Gene expression of RNA-seq datasets in transcripts per million.

organism: Xenopus tropicalis

source_name: Whole embryos

growth_protocol: Xenopus tropicalis females were injected with 10 units of Chorulon (Merck and Co.) 1-3 nights before embryo collection and 100 units of Chorulon on the day of embryo collection. Eggs were collected in a dish coated with 0.1% BSA in 1/9x MMR. The eggs are in vitro fertilized with sperm suspension in 0.1% BSA in 1/9x MMR. The embryos are dejellied with 3% cysteine in 1/9x MMR, pH 7.8, 10 minutes after fertilization and are then ready for manipulation. Embryos were staged using the Nieukwoop-Faber developmental table.

extract_protocol: Embryos were injected with Total RNA was isolated at indicated stages using a Nucleo-spin RNA kit (Machery-Nagel). RNA-seq libraries were generated using Smart-seq2 cDNA synthesis followed by tagmentation (Picelli et al., 2014).

tag: tissue type

value: whole embryos at N&F stage 10.5

value: Nigerian strain


title: Japanese flounder_2d_VI_7


title: Wt_2

description: 16 hours fasting

value: wild-type


title: Wt_1

description: 16 hours fasting


title: Uninjected stage 10.5 replicate 1


title: Uninjected stage 10 replicate 2

value: whole embryos at N&F stage 10


title: Wt_5

description: 16 hours fasting


title: Uninjected stage 9.5 replicate 2

value: whole embryos at N&F stage 9.5


title: D4_P38α_dd_2


title: Japanese flounder_2d_VI_5


title: Ko_3

description: 16 hours fasting


title: Uninjected stage 9.5 replicate 1


title: Tcf7l1 MO stage 10 replicate 1


title: Uninjected stage 10 replicate 1


title: Tcf7l1 MO stage 10.5 replicate 2


title: Tcf7l1 MO stage 10.5 replicate 1


title: Tcf7l1 MO stage 10 replicate 2


title: Tcf7l1 MO stage 9.5 replicate 2


title: Tcf7l1 MO stage 9.5 replicate 1


title: 8W-post-TAC1

city: Guangzhou

first: Xiang

last: Li

state: Guangdong

address: 11 fengxin road, guangzhou science city

institute: Guangdong Laboratory Animals Monitoring Institute

hyb_protocol: 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 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed and fixed.

scan_protocol: After fixing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering.

label_protocol: Total RNA from were digested with Rnase R to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA labeling 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

extract_protocol: The purity and concentration of total RNA samples were determined with NanoDrop ND-1000.

tag: group

value: heart


title: 2W - rep 2.1

source_name: MCF7 cells treated with Palbo for 2 weeks

tag: cell line

value: MCF7 breast cancer cell line

tag: treatment

value: Palbociblib


title: 4W-post-TAC1

tag: tissue


title: Sham2

value: Sham


title: 4W-post-TAC2


title: 462_OR773_0

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

institute: UNC Eshelman School of Pharmacy

description: mouse liver RNA

hyb_protocol: Fifteen micrograms of labeled cRNA was fragmented and prepared for hybridization on HT MG430 PM peg arrays.

scan_protocol: The Gene Titan robotic instrumentation (Affymetrix) was used to perform the hybridization, washing and scanning of the peg arrays.

data_processing: Probes containing SNPs in the genome of 45 CC strains were masked using the “kill-list” option in the APT module “apt-probeset-summarize”. Affymetrix CEL files were normalized using the Robust Multi-array Average (RMA) method with log2 transformation implemented in Affymetrix Power Tools (APT, v 1.17.0). A second pre-filtering step was then performed to eliminate lowly expressed probe sets defined as the maximum of log2 transformed expression level across samples less than an empirically chosen cutoff. Principal component analysis (PCA) and hierarchical clustering was used to evaluate the overall performance of the arrays. Seven (7) animals were identified as outliers (strains CC004, CC010, CC023, CC027, CC028, CC042, CC053, one animal each strain) and were removed from subsequent analysis.

source_name: mouse, liver

label_protocol: Double-stranded cDNA was synthesized from 50-150 ng (dependent on RNA yield) of total RNA, then transcribed to biotin-labeled cRNA using the 3’ Express IVT kit (Affymetrix).

growth_protocol: Eight (8) male mice from each of 45 CC lines  were purchased from the University of North Carolina, Chapel Hill.  Animals were acclimated for approximately 7 days prior to dosing. At the initiation of treatment, mice were approximately 8-10 weeks of age.

extract_protocol: Total cellular RNA was isolated using Trizol reagent (Invitrogen) and further purified using the QIAcube automated system (Qiagen). Following purification, the quantity of RNA was determined spectrophotometrically and the integrity of the RNA was evaluated with the Agilent 2100 Bioanalyzer.

treatment_protocol: Within each CC line, 4 animals were treated with a single dose of vehicle (0.5% w/v methylcellulose in purified water) and 4 were treated with TAK-875 (600 mg/kg). Test and control articles were administered by oral gavage in a dosing volume of 10 ml/kg. Animals were assigned to treatment groups using a randomization method based on bodyweight. Vehicle- and TAK-875-treated animals within each line were treated in pairs, and pairs within each line were randomized over the course of the study to minimize batch (treatment group) effects.

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 456_IL16188_600

description: mouse liver RNA


title: 457_IL16188_600

description: mouse liver RNA


title: 461_OR773_0

description: mouse liver RNA


title: 8W-post-TAC2


title: 467_OR773_600

description: mouse liver RNA


title: 2W-post-TAC2


title: 465_OR773_600

description: mouse liver RNA


title: 466_OR773_600

description: mouse liver RNA


title: Sham1


title: 453_IL16188_0

description: mouse liver RNA


title: 2W-post-TAC1


title: 463_OR773_0

description: mouse liver RNA


title: 455_IL16188_600

description: mouse liver RNA


title: 454_IL16188_0

description: mouse liver RNA


title: 458_IL16188_600

description: mouse liver RNA


title: 451_IL16188_0

description: mouse liver RNA


title: 448_OR3564_600

description: mouse liver RNA


title: 452_IL16188_0

description: mouse liver RNA


title: 446_OR3564_600

description: mouse liver RNA


title: 444_OR3564_0

description: mouse liver RNA


title: 447_OR3564_600

description: mouse liver RNA


title: 442_OR3564_0

description: mouse liver RNA


title: 443_OR3564_0

description: mouse liver RNA


title: 428_AU18042_600

description: mouse liver RNA


title: 426_AU18042_600

description: mouse liver RNA


title: 424_AU18042_0

description: mouse liver RNA


title: 441_OR3564_0

description: mouse liver RNA


title: 437_OR4410_600

description: mouse liver RNA


title: 427_AU18042_600

description: mouse liver RNA


title: 416_AU18018_600

description: mouse liver RNA


title: 445_OR3564_600

description: mouse liver RNA


title: 412_AU18018_0

description: mouse liver RNA


title: 432_OR4410_0

description: mouse liver RNA


title: 417_AU18018_600

description: mouse liver RNA


title: 423_AU18042_0

description: mouse liver RNA


title: 422_AU18042_0

description: mouse liver RNA


title: 433_OR4410_0

description: mouse liver RNA


title: 415_AU18018_600

description: mouse liver RNA


title: 438_OR4410_600

description: mouse liver RNA


title: 418_AU18018_600

description: mouse liver RNA


title: 436_OR4410_600

description: mouse liver RNA


title: 414_AU18018_0

description: mouse liver RNA


title: 434_OR4410_0

description: mouse liver RNA


title: 407_IL16072_600

description: mouse liver RNA


title: 406_IL16072_600

description: mouse liver RNA


title: 413_AU18018_0

description: mouse liver RNA


title: 411_AU18018_0

description: mouse liver RNA


title: EL4 T-bet cells stimulated

first: Arnulf

last: Hertweck

address: Gower Street

department: UCL Cancer Institute

institute: University College London

data_processing:
Pooled libraries were sequenced on HiSeq 3000 (Illumina) using 75 bp paired-end reads
Raw reads were ﬁltered for base quality using FastQC with default parameters and adapters sequences were removed with Trim Galore!
Reads passing quality filtering criteria were aligned to GRCm38 using BWA-MEM with default settings
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: EL4 cell line

growth_protocol: EL4 cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 4 mM L-alanyl-L-glutamine, 25 mM D-glucose, 1 mM sodium pyruvate, 10 mM HEPES, 100 U/ml penicillin and 100 µg/ml streptomycin

extract_protocol:
50,000 cells were washed in 50 μl cold PBS (500g, 5 min, 4°C) and re-suspended in 50 μl cold lysis buffer I (10 mM Tris-Cl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.5% IGEPAL CA-630) and spun (500g, 10 min, 4°C). The supernatant was removed, and lysed cells re-suspended in 50 μl transposase reaction mix, containing 10 mM Tris pH8.0, 5 mM MgCl2, 10% dimethylformamide and 2.5 μl Tn5 transposon + transposase reagent (TDE1 Illumina). Reactions were incubated at 37°C for 45 min, with shaking at 500 rpm. Following transposition, 150 μl reverse-crosslinking buffer (50 mM Tris-Cl, 1 mM EDTA, 1% SDS, 0.2 M NaCl) was added to reactions, and incubated at 65°C overnight at 1000 rpm before DNA purification, using the MinElute PCR purification kit (Qiagen).
Transposed DNA was amplified by PCR for 5 cycles, using KAPA HiFi HotStart ReadyMix, 1.25 μM Ad1 primer and 1.25 μM Ad2.x indexed primers, as described (Buenrostro et al., 2013). 5 μl of each reaction was taken for qPCR as described, using KAPA HiFi HotStart ReadyMix and 50X KAPA Low ROX for signal normalisation, to determine the additional number of PCR cycles for library amplification. PCR reactions were purified using MinElute gel extraction kit (Qiagen) according to the manufacturer’s instruction, and fragments between 100-1000 bp in size were selected for sequencing. DNA Fragmentation of the library was measured using the Bioanalyzer High Sensitivity DNA assay (Agilent), and library concentration quantified by qPCR analysis, using Illumina Library Quantification kit (KAPA). DNA from multiple libraries was pooled at equimolar concentrations to a final concentration of 4 nM.

treatment_protocol: EL4 cells were stimulated with 50 ng/ml PMA and 1 μg/ml ionomycin at 37°C for 4 hrs, or left unstimulated

value: PMA  + inomomycin

tag: ectopically expressed protein

value: FLAG-T-bet


title: EL4 T-bet cells unstimulated

value: unstimulated


title: EL4 GFP cells unstimulated


title: EL4 GFP cells stimulated


title: 405_IL16072_600

description: mouse liver RNA


title: 404_IL16072_0

description: mouse liver RNA


title: 402_IL16072_0

description: mouse liver RNA


title: 401_IL16072_0

description: mouse liver RNA


title: 397_IL16034_600

description: mouse liver RNA


title: 395_IL16034_600

description: mouse liver RNA


title: 396_IL16034_600

description: mouse liver RNA


title: 403_IL16072_0

description: mouse liver RNA


title: 398_IL16034_600

description: mouse liver RNA


title: 394_IL16034_0

description: mouse liver RNA


title: 387_IL16012_600

description: mouse liver RNA


title: 392_IL16034_0

description: mouse liver RNA


title: 408_IL16072_600

description: mouse liver RNA


title: 393_IL16034_0

description: mouse liver RNA


title: U87, TMZ-sensitive cell line-3

city: Shenzhen

first: Zhou

last: Jian

address: Shenzhen

institute: Shenzhen University

description: LncRNA and mRNA expression profiles from TMZ-sensitive cell line

hyb_protocol: The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols.

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 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 two groups were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable LncRNAs and mRNAs expression pattern among samples.

source_name: glioblastoma multiforme (GBM)

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling.

growth_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% under optimum conditions.

extract_protocol: Total RNA was extracted using Trizol Reagent (Thermo Fisher Scientific) following the manufacture’s instructions. RNA Quantification and Quality Assurance by NanoDrop ND-1000. RNA Integrity and gDNA contamination test by Denaturing Agarose Gel Electrophoresis.

treatment_protocol: The resistant cell line was obtained by progressive adaptation of the parental sensitive cells (U87) to increasing concentrations of TMZ.

tag: disease state

value: glioblastoma multiforme (GBM)

value: brain

tag: phenotype

value: TMZ-sensitive


title: 388_IL16012_600

description: mouse liver RNA


title: U87, TMZ-resistant cell line-3

description: LncRNA and mRNA expression profiles from TMZ-resistant cell line

value: TMZ-resistant


title: 386_IL16012_600

description: mouse liver RNA


title: 381_IL16012_0

description: mouse liver RNA


title: 385_IL16012_600

description: mouse liver RNA


title: U87, TMZ-resistant cell line-2


title: U87, TMZ-sensitive cell line-2


title: 383_IL16012_0

description: mouse liver RNA


title: 384_IL16012_0

description: mouse liver RNA


title: U87, TMZ-resistant cell line-1


title: 391_IL16034_0

description: mouse liver RNA


title: 378_IL16785_600

description: mouse liver RNA


title: 382_IL16012_0

description: mouse liver RNA


title: 375_IL16785_600

description: mouse liver RNA


title: 374_IL16785_0

description: mouse liver RNA


title: 376_IL16785_600

description: mouse liver RNA


title: U87, TMZ-sensitive cell line-1


title: 373_IL16785_0

description: mouse liver RNA


title: 377_IL16785_600

description: mouse liver RNA


title: HeLa-2 RNA-seq

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Basecalling was performed using RTA version 2.4.11
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 1.8.4) allowing 1 mismatch.
Trimming of adapters and low-quality bases was performed using CutAdapt (v.1.16).
Mapping to the hybrid genome containing hg38 and HPV16 or HPV18 was performed using STAR 2.5.2b
The following parameters were used: "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 clip3pAdapterSeq - --readFilesCommand zcat --runThreadN 32 --outSAMtype BAM Unsorted --chimSegmentMin 20"
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing output of STAR Chimeric.out.junction

source_name: HeLa cell

growth_protocol: All cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Thermo Fisher Scientific, Waltham, MA) with 10% fetal bovine serum (FBS, GE Healthcare, Logan, UT) at 37°C under a 5% CO2 atmosphere.

extract_protocol:
The total RNA was isolated using TriPure Reagent (Millipore-Sigma, Part No. 11667165001)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HeLa

tag: gender

value: female

tag: cancer type

value: Cervical


title: HeLa-1 RNA-seq


title: 364_OR15119_0

description: mouse liver RNA


title: 367_OR15119_600

description: mouse liver RNA


title: 358_AU8052_600

description: mouse liver RNA


title: 366_OR15119_600

description: mouse liver RNA


title: 362_OR15119_0

description: mouse liver RNA


title: 357_AU8052_600

description: mouse liver RNA


title: 356_AU8052_600

description: mouse liver RNA


title: 372_IL16785_0

description: mouse liver RNA


title: 363_OR15119_0

description: mouse liver RNA


title: 351_AU8052_0

description: mouse liver RNA


title: 371_IL16785_0

description: mouse liver RNA


title: 355_AU8052_600

description: mouse liver RNA


title: 534, POST, PG

city: Ribeirão Preto

first: Guilherme

middle: Da Silva

last: Rodrigues

address: Avenida Bandeirantes, 3900

country: Brazil

institute: Universidade de São Paulo

description: SAMPLE 99

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation Beadchip EPIC using standard Illumina protocol

data_processing:
Champ package for Rstudio was used to process data.
Matrix_Processed.txt value definition:  BMIQ normalized (provide the normalization method) Average Beta corrected by cell lineages

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from the collected whole blood, the technique adopted was automated by magnetic spheres, using the Maxwell MDx equipment.

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: li

value: PG

tag: time

value: POST

value: peripheral blood

tag: cell type

value: leukocytes


title: 553, POST, PG

description: SAMPLE 98

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: disease state

tag: tissue


title: 506, POST, PG

description: SAMPLE 100

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb

tag: ni


title: 348_AU8046_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 347_AU8046_600

description: mouse liver RNA


title: 346_AU8046_600

description: mouse liver RNA


title: 352_AU8052_0

description: mouse liver RNA


title: 368_OR15119_600

description: mouse liver RNA


title: 345_AU8046_600

description: mouse liver RNA


title: 344_AU8046_0

description: mouse liver RNA


title: 519, POST, PG

description: SAMPLE 97

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: li

tag: disease state

tag: time

tag: tissue

tag: cell type


title: 343_AU8046_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: HeLa-3 RNA-seq

tag: cell line

tag: gender

tag: cancer type


title: 353_AU8052_0

description: mouse liver RNA


title: 354_AU8052_0

description: mouse liver RNA


title: 342_AU8046_0

description: mouse liver RNA


title: 510, POST, PG

description: SAMPLE 93

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb

tag: ni


title: 513, POST, PG

description: SAMPLE 95

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: li

tag: disease state

tag: time

tag: tissue

tag: cell type


title: 539, POST, PG

description: SAMPLE 94

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as


title: 206, POST, PG

description: SAMPLE 89

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cd

tag: pb

tag: ni

tag: li

tag: disease state


title: 512, POST, PG

description: SAMPLE 96

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: time

tag: tissue

tag: cell type


title: 536, POST, PG

description: SAMPLE 90

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb


title: 545, POST, PG

description: SAMPLE 91

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: ni

tag: li

tag: disease state


title: 516, POST, PG

description: SAMPLE 92

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: insulin ui/ml

tag: al

tag: time

tag: tissue

tag: cell type


title: 210, POST, PG

description: SAMPLE 88

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb


title: IELp Ctrl_rep_2 [ATAC-seq]

city: Bethesda

first: Jia

last: Nie

address: Building 37, Room 3016

data_processing:
Basecalling was performed using RTA 2.4.11 for IELp Ctrl/KO_rep_1, using RTA 3.9.2 for IELp Ctrl/KO_rep_2
Barcode was demultiplexed with mkfastq in Cellranger 1.2.0
Alignment, tagging and gene counting were done with Cellranger 1.2.0
Genome_build: mm10
Supplementary_files_format_and_content: h5, tsv.gz,

source_name: Thymus

extract_protocol:
Chrominum Single Cell ATAC reagent Kits v1.1 per the manufacturer instructions (10X genomics)
IELp Ctrl/KO_rep_1: 2 10x Genomics Single Cell Chromium ATAC libraries were sequenced on one NextSeq 2000 P3 run and combined with a previous NextSeq 2000 P2 run. The sequencing run was setup as a 2x51 cycles symmetric run. R1: 51bp, Index1: 8bp, Index2: 16bp, R2: 51bp. IELp Ctrl/KO_rep_2: 2 10x Genomics Single Cell Chromium ATAC libraries were sequenced on one NextSeq 2000 run. The sequencing run was setup as a 50 cycles + 50 cycles symmetric run. R1: 50bp, Index1: 8bp, Index2: 16bp, R2: 50bp.

tag: strain

tag: population

tag: genotype

value: Cd4 Cre- lrffl/fl


title: 335_AU8034_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 337_AU8034_600

description: mouse liver RNA


title: IELp Ctrl_rep_1 [ATAC-seq]


title: Mimic2

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

institute: Goethe University Frankfurt

data_processing:
data were processed using the blue-bee pipeline (https://lexogen.bluebee.com/quantseq/)
trimming: bbduk v35.92
alignment: STAR Aligner with modifi_x001E_ed ENCODE settings
gene read counting: HTSeq-count with kit-specic options (FWD)
differential analysis: DESeq2 Pipeline
Genome_build: human genome (GRCh38)
Supplementary_files_format_and_content: text file containing the normalized read counts for miR-200c-3p mimic- and control-transfected macrophages.

source_name: peripheral blood

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated using Pancoll gradients and seeded onto high-adherence culture dishes in RPMI 1640 medium supplemented with 100 U/mL penicillin and 100 µg/mL streptomycin. Non-adherent cells were washed away after 1 h and the remaining cells were maintained in  RPMI 1640 medium supplemented with 100 U/mL penicillin, 100 µg/mL streptomycin and 5% AB-positive human serum for 7 days to allow for differentiation to macrophages.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
cDNA libraries were generated with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD with UDI for Illumina (Lexogen).

treatment_protocol: Macrophages were transfected with MISSION® hsa-miR-200c-3p mimic or MISSION® miR negative control 2 (Sigma) using HiPerfect (Qiagen) and harvested 72 h after transfection.

tag: cell type

value: primary human macrophages

tag: treatment

value: miR-200c-3p mimic transfection


title: Ctr4

value: control transfection


title: Mimic4


title: 334_AU8034_0

description: mouse liver RNA


title: Mimic3


title: 336_AU8034_600

description: mouse liver RNA


title: 278, POST, PG

description: SAMPLE 87

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state

tag: time

tag: tissue


title: Ctr3

tag: cell type

tag: treatment


title: 332_AU8034_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 341_AU8046_0

description: mouse liver RNA


title: 331_AU8034_0

description: mouse liver RNA


title: 333_AU8034_0

description: mouse liver RNA


title: Ctr2


title: 338_AU8034_600

description: mouse liver RNA


title: 328_AU8033_600

description: mouse liver RNA


title: 182, POST, PG

description: SAMPLE 86

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb


title: Ctr1

tag: cell type

tag: treatment


title: Mimic1


title: 327_AU8033_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 233, POST, PG

description: SAMPLE 85

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state

tag: time

tag: tissue


title: Control without treatment

city: Hong Kong

first: Wing Tung

last: Lee

address: Room Y934, 9/F, Lee Shau Kee Building, The Hong Kong Polytechnic University, Hung Hom, Kowloon

department: Department of Health Technology and Informatics

country: Hong Kong

institute: The Hong Kong Polytechnic University (PolyU)

data_processing:
Raw reads from RNA-seq were checked by FastQC v0.11.9 and trimmed by trim_galore v0.6.7.
The filtered clean reads were mapped to reference genome by HISAT2 (version 2.2.1). StringTie and ASprofile were used for transcript assembly and quantification respectively.
Cufflinks software was then used to quantify transcripts and gene expression levels using mapped reads’ positional information on the gene.
Gene expression level was calculated in the form of fragments per kilobase million (FPKM) and calcalated by GenomicFeatures (Rpackage). Genes with undetected expression level in all the samples were excluded in the following analysis.
Genome_build: Mycobacterium bovis BCG strain Russia 368, complete genome
Supplementary_files_format_and_content: text file includes FPKM values for each Sample

organism: Mycobacterium tuberculosis variant bovis BCG

source_name: Control without treatment

extract_protocol:
RNeasy Plus Mini Kit (cat. no. 74134) was used to prepare the RNA sample
TruSeq Stranded Total RNA with Ribo-Zero Plus

tag: treatment

value: Control without


title: ST-193 (hydrochloride) treatment

source_name: ST-193 (hydrochloride) treatment

value: ST-193 (hydrochloride)


title: Shikonin treatment

source_name: Shikonin treatment

value: Shikonin


title: 287, POST, PG

description: SAMPLE 83

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

tag: cell type


title: ST-193 treatment

source_name: ST-193 treatment


title: Trifluoperazine (dihydrochloride) treatment

value: Trifluoperazine (dihydrochloride)


title: Bicyclol treatment

source_name: Bicyclol treatment

value: Bicyclol


title: 249, POST, PG

description: SAMPLE 81

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state

tag: time


title: 325_AU8033_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 326_AU8033_600

description: mouse liver RNA


title: Bay 41-4109 (racemate) treatment

source_name: Bay 41-4109 (racemate) treatment

tag: treatment

value: Bay 41-4109 (racemate)


title: 227, POST, PG

description: SAMPLE 80

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

tag: tissue

tag: cell type