title: Photoconverted brain endothelial cells, rep3

city: Stockholm

first: Michael

last: Vanlandewijck

address: Blickagången 6

institute: Karolinska Institute

data_processing:
Demultiplexing with bcl2fastq
Alignment against the zebrafish Danio_rerio.GRCz11.95 build using Bowtie2
Removal of adapter sequencing with TrimGalore
Removal of duplets using samtools
Generation of a count matrix with FeatureCounts from the SubRead package
Assembly: Danio.Rerio.GRCz11
Supplementary files format and content: Count files, with every column a cell and every row a gene.

source_name: Brain

growth_protocol: Standard

extract_protocol:
Photoconversion ofTg(fli1:Gal4)ubs3;(UAS:Kaede)rk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope (Carl Zeiss, objective lenses: Plan-Apochromat ×20/0.8 M27). Briefly, anesthetised embryos were mounted laterally in 1% low-melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser (five iterations of 50 s). After isolation from the agarose, embryos were washed in Ca2+/Mg2+-free HBSS (Hank’s Balanced Salt Solution, Gibco) and dissociated at 28.5 °C for 30 min in TrypLE select (Thermo Fischer Scientific, 12563011). Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS, filtered, and submitted to FACS (BD Biosciences FACSAria III).
Single-cell cDNA libraries were prepared according to the established protocol for Smart-Seq2. In brief, poly-adenylated mRNA was transcribed to cDNA using oligo(dT) primer and SuperScript II reverse transcriptase (ThermoFisher Scientific). Synthesis of second strand cDNA was achieved using a template switching oligo, and the double stranded cDNA was then amplified using polymerase chain reaction (PCR) for 23 – 26 cycles. After bead purification, overall cDNA quality was controlled (QC) by analyzing randomly selected single cell samples (wells) on a 2100 Bioanalyzer with a DNA High sensitivity chip (Agilent Biotechnologies). When the sample (plate) passed the QC, the cDNA was fragmented and tagged (tagmented) using Tn5 transposase, and each single cell sample (well) was uniquely indexed using Illumina Nextera XT index kits (set A-D). Thereafter, the indexed single-cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer (Illumina), using dual indexing and 50 base read-length.
ScRNA-Seq with Smart-seq2

treatment_protocol: Morpholino injection

tag: tissue

value: Brain

tag: age

value: 30 hpf

value: Endothelial cells

value: WT and gpr124 morpholino


title: SMCTRAP-Athero_121_Input

status: Public on Feb 08 2024

type: SRA

city: Kuopio

first: Aarthi

last: Ravindran

address: Neulaniementie 2, 70150 Kuopio

country: Finland

institute: University of Eastern Finland

library_source: transcriptomic

data_processing:
Sequencing reads were processed using the nf-core RNA-Seq pipeline (version 1.4.2) with the mm10 mouse genome.
Assembly: mm10
Supplementary files format and content: raw count matrix

molecule: total RNA

organism: Mus musculus

source_name: Thoracic aorta

growth_protocol: The mice were housed under standard conditions with a 12-hour light/dark cycle and were given access to a rodent chow diet (Teklad Global Rodent diet 2016 for maintenance and Teklad Global Rodent 2018s while breeding) and water ad libitum.

extract_protocol:
Mice were euthanized in CO2 chamber (Metos) and the tissues were dissected while the mice were kept on ice after perfusing with ice-cold 1X PBS (Gibco). Aorta was snap-frozen using liquid nitrogen for TRAP-Seq. The frozen aortic tissue was pulverized using a TissueLyser II bead mill (QIAGEN) and added with low salt lysis buffer for homogenization. 5% of lysate was used for the bulk RNA extraction and the remaining lysate was immunoprecipitated with anti-GFP clone 19F7 and clone 19C8 antibodies. The Biotinylated Protein L (0.5 mg; Pierce #29997) and Dynabeads MyOne Streptavidin T1 (10mg/ml; Invitrogen 65602) are mixed to form bead-protein complex and capture the GFP antibodies in the samples. RNA from the lysate was extracted using RNeasy Micro Plus kit (QIAGEN, 74034).
The SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TaKaRa, 634411, 634412) was used for library preparation, followed by single-end 76-bp sequencing on an Illumina NextSeq 500 instrument.

value: Thoracic aorta

tag: genotype

tag: animal group

value: TRAP-Atherosclerosis

tag: Sex

value: Female

tag: rna fraction

value: total RNA extraction from the 5% of total lysate (Input)


title: PB02004_tumor_roi008_PanCK_T

type: protein

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

description: protein detected by antibody

hyb_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

data_processing: Raw count data of antibody-captured protein copy numbers in each segment were normalized by scaling with geometric mean of the counts of the housekeeping proteins

label: fluorescent barcode

molecule: protein

organism: Homo sapiens

treatment_protocol: Pre-treatment tumor and liver biopsy tissues were obtained from patients with unresectable hepatocellular carcinoma trated with bavituximab and pembrolizumab.

tag: patient id

tag: tissue type

value: tumor

tag: region of interest (roi) number

tag: segment type

value: cancer cell enriched

tag: positive immuno-fluorescent morphology marker

value: PanCK

tag: radiographic objective response

value: partial response (PR)


title: OE ctrl, repB

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

description:
total RNA-seq
single-end

data_processing:
RNA-seq: Reads from the RNA-seq experiments were trimmed and filtered using the FASTX toolkit (v.0.10.1; http://hannonlab.cshl.edu/fastx_toolkit ). Mapping was performed using READemption (v.1.01) (Förstner et al., 2014) against the genome sequence for F. nucleatum subsp. nucleatum ATCC 23726 (NZ_CP028109.1) downloaded from the National Center for Biotechnology Information (NCBI). Differential gene expression analysis was carried using DEseq2 (v.1.18.01) (Love et al., 2014). All analysis for each was carried for biological triplicates and considered significant with a false-discovery rate ≤ 0.05.
dRNA-seq: Reads were processed and maps as described for the RNA-seq data excluding the DEseq analysis. For the prediction of transcriptional start sites (TSS) and small regulatory RNAs (sRNA), we used the modular, command-line tool ANNOgesic (Yu et al., 2018). All parameters were kept at the default setting, unless stated otherwise. Secondary TSSs were excluded if a primary TSS was within seven nucleotides distance. For annotation of 5’ untranslated regions (5’UTRs) the default settings for maximum length was corrected to 300 nt.
Term-seq: Reads were processed and maps as described for the RNA-seq data excluding the DEseq analysis.
Assembly: NZ_CP028109.1
Supplementary files format and content: wiggle files

organism: Fusobacterium nucleatum subsp. nucleatum ATCC 23726

source_name: bacterial culture

growth_protocol: All bacteria were grown in Columbia broth. Cells were grown to mid-exponential phase prior to harvest.

extract_protocol:
Total RNA-seq: Total RNA was extracted using the hot phenol protocol. Bacterial cultures were grown to the desired OD600, mixed with 0.2 volumes of STOP solution (95% ethanol, 5% phenol) and snap-frozen at –80°C if not directly processed. The bacterial solution was centrifuged for 20min, 4500rpm at 4°C and the supernatant was completely discarded. Cells were suspended in 600μl of 10mg/ml lysozyme in TE buffer (pH8.0) and incubated at 37°C for 10min. Next, 60μl of 10% w/v SDS was added and everything mixed by inversion. Samples were incubated in a water bath at 64°C, 1-2min before adding 66μl 3MNaOAc, pH5.2. Next, 750μl acid phenol (Roti-Aqua phenol) was added, followed by incubation for 5min. at 64°C. Samples were briefly placed on ice to cool before centrifugation for 15min, 13,000rpm at 4°C. The aqueous layer was transferred into a 2ml phase lock gel tube (Eppendorf), 750μl chloroform (Roth, #Y015.2) was added, and everything centrifuged for 12min, 13,000rpm at room temperature. For ethanol precipitation, the aqueous layer was transferred to a fresh tube, 2 volumes of 30:1 mix (EtOH:3MNaOAc, pH6.5) was added and incubated overnight at -20°C. Precipitated RNA was harvested by centrifugation, washed with cold 75% v/v ethanol and air-dried. Purified RNA was resuspended in 50µl RNase-free water and stored at -80°C.
RNA-seq: For preparation cDNA library of the immunoprecipitated RNA samples, NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) was used. Briefly, 3.5 μl of RNA was mixed with 1 μl of 3’ SR Adaptor (diluted 1:10 in nuclease-free water) and incubated in a preheated thermal cycler for 2 min at 70 °C. The samples were transferred to ice and added with the premixed 3’ ligation mix (5 μl 3’ Ligation Reaction Buffer, 1.5 μl 3’ Ligation Enzyme Mix). The ligation mixture was then incubated for 1 h at 25 °C. 0.25 μl of SR RT Primer and 2.5 μl nuclease-free water were added to the mixture and incubated at 75 °C for 5 min, 37 °C for 15 min and followed by 25 °C for 15 min. To ligate the 5’ SR adaptor, the 5’ ligation mixture (0.5 μl 1:10 diluted 5’ SR Adaptor, 0.5 μl 10x 5’ ligation reaction buffer, 1.25 μl 5’ ligation enzyme mix) was added to each sample and incubated for 1 h at 25 °C. For synthesis first strand of cDNA, reverse transcription mix (4 μl first strand synthesis reaction buffer, 0.5 μl murine RNase inhibitor, 0.5 μl M-MLV reverse transcriptase) was added to each reaction and incubated for 1 h at 50 °C followed by 15 min at 70 °C to inactivate the reverse transcription reaction. 5 μl of cDNA was then proceeded to PCR amplification with the PCR mix (12.5 μl LongAmp Taq 2x master mix, 0.625 μl SR primer, 6.25 μl nuclease-free water) and 0.625 μl index (X) primer. PCR program (30s at 94°C, 15 s at 94 °C, 30 s at 62 °C and 15 s at 70 °C for 19 cycles, 5 s at 70 °C) was carried out. PCR products were mixed with 25 μl of GLII buffer and loaded on 6 % polyAcrylamide gel containing 8 M urea. After staining the gel for 10 min in 1x TBE buffer with a 1:10,000 dilution of SYBR Gold Nucleic Acid Gel Stain (Invitrogen), the bands in the range of 130- 1000 bp were cut into small pieces and transfer to a 2 ml LoBind tube. 500 μl of DNA elution buffer was added and incubated at the room temperature for 2 h. After transferring the elute and the gel debris to centrifuge tube filters (Sigma) and centrifugation (5000 rpm, 1 min), the elute was recovered by adding 1 μl liner acrylamide (NEB) and precipitating in ethanol at -80°C for 1 h. After precipitation, the pellet was washed with 80% ethanol and resuspended in 12 μl nuclease free water (NEB). 1 μl of the prepared cDNA library was subjected to Bioanalyzer analysis.  Amplified cDNAs were pooled and sequenced on an illumine NextSeq 2000 platform by the CoreUnit Sysmed from the University of Wuerzburg.
dRNA-seq: Library preparation for dRNA-seq was accomplished by Vertis Biotechnology AG. In brief, total RNA was analyzed on a Shimadzu MultiNA microchip electrophoresis system. 23S/16S ratio for all samples was 1.3. RNA was fragmented via ultrasound (4 pulses a 30 sec, 4 °C) and subsequently treated with T4 Polynucleotide Kinase (NEB). Half of the samples were then treated with terminator exonuclease (TEX) for dRNA-seq. For the cDNA synthesis, the RNA fragments were poly(A)-tailed and 5’PPP structures were removed with RNA 5’ Polyphosphatase (Epicentre). The RNA sequencing adapter with the barcodes were ligated to the 5’-monophosphate of the fragments. First strand cDNA was synthesized with an oligo(dT)-adapter primer and M-MLV reverse transcriptase. Amplification of cDNA was done via PCR to an approximate amount of 10 20 ng/µl. cDNA was purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed with Shimadzu MultiNA microchip electrophoresis. Equimolar amounts of the samples were pooled for sequencing. cDNAs had a size between 200 and 550 bp. The library pool was fractionated via differential clean-up with the Agencourt AMPure kit. The cDNA pool was checked with capillary electrophoresis as stated above.
Term-seq: The term-seq libraries were generated by first ligating the 5’ TruSeq Illumina adapter to 3’ hydroxyl ends of rRNA-depleted RNA via a probe-based approach. This RNA was used as input for first-strand cDNA synthesis using M-MLV reverse transcriptase. The cDNA was fragmented via ultrasound followed by the ligation of the 3’ TruSeq Illumina adapter. cDNA was PCR amplified with a high-fidelity DNA polymerase and purified with Agencourt AMPure XP beads (Catalogue number: A63881; Beckman Coulter Genomics). The resulting libraries were analyzed via capillary electrophoresis.

treatment_protocol: No specific treatment was applied.

tag: growth phase

value: Mid-exponential

value: WT carrying control plasmid


title: SMCTRAP-Athero_115_IP

value: Male

value: smooth muscle cell specific ribosome-associated RNA (IP)


title: SMCTRAP-Athero_68_Input


title: PB02004_tumor_roi008_Rest_F

description: protein detected by antibody

scan_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

value: fibrous tissue enriched


title: SMCTRAP-Athero_115_Input


title: Water_rep7

city: Ann Arbor

first: Laura

middle: A

last: Kresty

state: MI

address: 1500 E Medical Center Dr

department: Surgery

institute: University of Michigan

library_source: genomic

data_processing:
Sequence data was processed in QIIME using published protocols.
Operational taxonomic units (OTU) were identified using Greengenes and aligned with PyNAST to construct phylogenetic trees using Fast Tree 2.0.
Assembly: Greengenes 13_8
Supplementary files format and content: csv file includes raw count of OTUs in each sample

molecule: genomic DNA

organism: rat gut metagenome

source_name: Sprague-Dawley

extract_protocol:
Total genomic DNA was isolated from fecal pellets using the PowerLyzer® PowerSoil® DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, CA) according to manufacturer’s instructions with one modification. Fecal samples were transferred to glass bead tubes with 750 µL bead solution, incubated 65°C for 10 min and transferred to 95°C 10 min. DNA samples were eluted with 100 µL of Solution C6 and stored at -80°C until sequencing.
PCR amplicon libraries targeting the 16S rRNA encoding genes present in metagenomic DNA were produced using a barcoded primer set adapted for the Illumina MiSeq.
16s rRNA Sequencing

tag: strain

value: Sprague-Dawley

value: M

tag: treatment

value: Water


title: PB02004_liver_roi009_ImmuneCell

description: protein detected by antibody

label_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

value: liver

value: immune cell enriched


title: OE ctrl, repA

description:
total RNA-seq
single-end


title: Water_rep6


title: SMCTRAP-Athero_123_IP

value: Thoracic aorta

value: TRAP-Atherosclerosis


title: SMCTRAP-Athero_123_Input

value: Female

value: total RNA extraction from the 5% of total lysate (Input)


title: Term-seq WT, repC

description:
term-seq
single-end

value: WT


title: SMCTRAP-Athero_112_IP


title: Water_rep5


title: Term-seq WT, repB

description:
term-seq
single-end


title: Term-seq WT, repA

description:
term-seq
single-end


title: PB02004_liver_roi009_Fibrosis

description: protein detected by antibody

extract_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

value: SMA


title: Water_rep4


title: SMCTRAP-Athero_112_Input


title: Water_rep3


title: SMCTRAP-Athero_10_IP


title: PB02004_liver_roi009_nonTumorLiver

description: protein detected by antibody

value: non-tumor liver

value: partial response (PR)


title: PB02004_liver_roi009_BileDuct

description: protein detected by antibody

value: bile duct

value: PanCK


title: dRNA-seq WT, repC

description:
dRNA-seq
single-end

value: Mid-exponential


title: Water_rep2


title: dRNA-seq WT, repC tex

description:
dRNA-seq
single-end

value: TEX-treated


title: SMCTRAP-Athero_109_IP

value: Male

value: smooth muscle cell specific ribosome-associated RNA (IP)


title: PB01004_tumor_roi008_ImmuneCell

description: protein detected by antibody

value: tumor


title: dRNA-seq WT, repB tex

description:
dRNA-seq
single-end


title: PB02004_tumor_roi003_CancerCell

description: protein detected by antibody

value: cancer cell enriched


title: SMCTRAP-Athero_109_Input


title: CPAC_rep6

value: Sprague-Dawley

value: M

value: CPAC


title: dRNA-seq WT, repB

description:
dRNA-seq
single-end


title: Water_rep1

value: Water


title: SMCTRAP_98_Input

value: Thoracic aorta

value: EGFP (+)

value: TRAP-Control

value: Female

value: total RNA extraction from the 5% of total lysate (Input)


title: dRNA-seq WT, repA tex

description:
dRNA-seq
single-end

value: WT


title: SMCTRAP_98_IP


title: dRNA-seq WT, repA

description:
dRNA-seq
single-end


title: PB02001_tumor_roi001_ImmuneCell

description: protein detected by antibody

value: immune cell enriched

value: stable disease (SD)


title: PB01004_tumor_roi007_CancerCell

description: protein detected by antibody

value: partial response (PR)


title: SMCTRAP-Athero_10_Input

value: TRAP-Atherosclerosis

value: Male


title: SMCTRAP_89_Input


title: SMCTRAP_89_IP

value: smooth muscle cell specific ribosome-associated RNA (IP)


title: PB02001_tumor_roi001_Rest_F

description: protein detected by antibody

value: tumor

value: fibrous tissue enriched


title: PC1, 210506, PcN (Input)

city: Bethesda

first: Ousmane

middle: Hamadoun

last: Cisse

state: MD

address: 10 Center Dr,

institute: National Institutes of Health

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Hiseq X  output.
To remove rat DNA, ChIP-seq reads were aligned to the rat genome ( GCF_000001895.5)  using Bowtie2 version 2.2.5. Only unmapped  reads were retained.
ChIP-seq reads were aligned to the Pneumocystis carinii genome using bwa mem version 0.7.17-r1188
Peaks were called uing MACS v3.0.0a5 with the significance cut-off q-value <=0.05 (narrowPeak files)
bigWig files were generated using the bamCoverage from deepTools package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate (bins per millions; bin size; 50 bp)
Assembly: GCF_001477545.1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Pneumocystis carinii

source_name: lungs

extract_protocol:
Cells were fixed with formaldehyde for 10 minutes using the active motif Low cell ChIP-seq (cat # 53084). After quenching and cell lysis, chromatin was sonicated using a Q800R3 Sonicator (Qsonica) with recirculating chiller.
ChIP-seq libraries were prepared using the active motif Low cell ChIP-seq (cat # 53084) that include the Next Gen DNA library kit and Next Gen Indexing kit. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using SPRIselect  beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: lungs

tag: cell line

value: infected rat 1

tag: cell type

value: infection level 5+

value: collect date:01/18/00

tag: chip antibody

value: pre immune serum


title: CPAC_rep2

value: Sprague-Dawley

value: M

value: CPAC


title: PB02001_tumor_roi001_PanCK_T

description: protein detected by antibody

value: cancer cell enriched

value: PanCK


title: PC1, 210506, PcC

tag: tissue

value: CENP-C (Genescript # 1525058 )


title: SMCTRAP_84_IP

value: Thoracic aorta

tag: genotype

value: EGFP (+)

value: TRAP-Control


title: PB02001_tumor_roi002_ImmuneCell

description: protein detected by antibody

value: immune cell enriched

value: stable disease (SD)


title: PB02001_tumor_roi002_CancerCell

description: protein detected by antibody

value: tumor


title: SMCTRAP_84_Input

tag: animal group

value: Male

value: total RNA extraction from the 5% of total lysate (Input)


title: PC1, 210506, PcH

value: lungs

value: infected rat 1

value: infection level 5+

value: H3 (Abcam # ab1791)


title: CPAC_rep5

value: Sprague-Dawley

tag: Sex

value: M


title: EGDA_CPAC_rep5

value: Reflux+CPAC


title: EGDA_CPAC_rep4


title: CPAC_rep4

value: CPAC


title: PC1, 210506, PcA

value: collect date:01/18/00

value: CENP-A (Genescript #1598083)


title: PB02001_liver_roi003_nonTumorLiver

description: protein detected by antibody

value: liver

value: non-tumor liver


title: PB02001_liver_roi003_ImmuneCell

description: protein detected by antibody

value: immune cell enriched


title: PC2, 210927, Pc_H3K4me2

value: infected rat 2

value: collect date:11/07/00

value: H3K4me2 (Abcam # ab8580)


title: SMCTRAP_80_IP

value: Thoracic aorta

value: EGFP (+)

value: TRAP-Control

value: Female

tag: rna fraction

value: smooth muscle cell specific ribosome-associated RNA (IP)


title: CPAC_rep3

value: Sprague-Dawley


title: SMCTRAP_80_Input

value: total RNA extraction from the 5% of total lysate (Input)


title: EGDA_CPAC_rep3

value: M

value: Reflux+CPAC


title: PC2, 210927, Pc_H3K9me3

value: lungs

value: infection level 5+

value: H3K9me3 (Abcam # ab8898)


title: SMCTRAP_76_IP


title: SMCTRAP_76_Input


title: OE FoxJ, repB

description:
total RNA-seq
single-end

value: Mid-exponential

value: WT carrying plasmid for FoxJ overexpression


title: EGDA_CPAC_rep1


title: CPAC_rep1

value: CPAC


title: PC2, 210927, Pc_Input

value: infected rat 2

value: collect date:11/07/00

value: no antibody (Input)


title: PB02005_liver_roi005_nonTumorLiver

description: protein detected by antibody

tag: patient id

value: liver

value: non-tumor liver

value: stable disease (SD)


title: EGDA_rep7

value: Reflux


title: PC2, 210927, Pc_H4


title: EGDA_rep6

value: Sprague-Dawley


title: PB02005_liver_roi005_ImmuneCell

description: protein detected by antibody

tag: tissue type

value: immune cell enriched


title: SMCTRAP_73_IP

value: Thoracic aorta

value: EGFP (+)

value: TRAP-Control

value: Male

value: smooth muscle cell specific ribosome-associated RNA (IP)


title: PB02005_liver_roi005_BileDuct

description: protein detected by antibody

tag: region of interest (roi) number

value: bile duct

value: PanCK


title: PC2, 210927, Pc_H3

value: lungs

value: infection level 5+

value: H3 (Abcam # ab1791)


title: EGDA_rep5

value: M


title: PB01004_tumor_roi006_CancerCell

description: protein detected by antibody

value: tumor

tag: segment type

value: cancer cell enriched

value: partial response (PR)


title: EGDA_rep4

value: Reflux


title: PC2, 210927, Pc_C

value: infected rat 2

value: collect date:11/07/00

value: CENP-C (Genescript # 1525058 )


title: SMCTRAP_73_Input

value: Thoracic aorta

value: EGFP (+)

value: total RNA extraction from the 5% of total lysate (Input)


title: PB02005_tumor_roi004_CancerCell

description: protein detected by antibody

tag: positive immuno-fluorescent morphology marker

value: stable disease (SD)


title: EGDA_CPAC_rep2

value: Sprague-Dawley

value: Reflux+CPAC


title: PC2, 210927, Pc_A

value: lungs

value: CENP-A (Genescript #1598083)


title: PB01004_liver_roi009_Fibrosis

description: protein detected by antibody

value: liver

value: fibrous tissue enriched

value: SMA

tag: radiographic objective response


title: PB01004_liver_roi009_nonTumorLiver

description: protein detected by antibody

value: non-tumor liver


title: SMCTRAP_45_IP

value: TRAP-Control

value: Female

value: smooth muscle cell specific ribosome-associated RNA (IP)


title: PC2, 210927, Pc_H3K9me2

value: infected rat 2

value: infection level 5+

value: collect date:11/07/00

value: H3K9me2 (Abcam # ab1220)


title: EGDA_rep2

value: M

value: Reflux


title: SMCTRAP_75_IP

value: Thoracic aorta

value: EGFP (+)


title: PB02005_liver_roi005_Fibrosis

description: protein detected by antibody

value: stable disease (SD)


title: SMCTRAP_45_Input

value: total RNA extraction from the 5% of total lysate (Input)


title: PC, 220606, Pc_C_d14

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Hiseq X  output.
To remove rat DNA, ChIP-seq reads were aligned to the rat genome ( GCF_000001895.5)  using Bowtie2 version 2.2.5. Only unmapped  reads were retained.
ChIP-seq reads were aligned to the Pneumocystis carinii genome using bwa mem version 0.7.17-r1188
Peaks were called uing MACS v3.0.0a5 with the significance cut-off q-value <=0.05 (narrowPeak files)
bigWig files were generated using the bamCoverage from deepTools package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate (bins per millions; bin size; 50 bp)
Assembly: GCF_001477545.1
Supplementary files format and content: bigWig, narrowPeak

source_name: coculture day 14

value: coculture day 14

value: Pneumocystis + epithelial cell lines

value: culture date:3/31/22

value: CENP-C (Genescript # 1525058 )


title: EGDA_rep3

value: Sprague-Dawley


title: PB01004_liver_roi009_BileDuct

description: protein detected by antibody

value: liver

value: bile duct

value: PanCK

value: partial response (PR)


title: SMCTRAP_41_IP

value: TRAP-Control

value: Female

value: smooth muscle cell specific ribosome-associated RNA (IP)


title: EGDA_rep1

value: M

value: Reflux


title: SMCTRAP_41_Input

value: Thoracic aorta

value: EGFP (+)


title: PC, 220606, Pc_A_d14

value: CENP-A (Genescript #1598083)


title: HOS cells shSET1

status: Public on Feb 07 2024

city: Yamaguchi

first: Naoki

last: Kohyanagi

address: 1677-1, Yoshida

country: Japan

institute: The univercity of Yamaguchi

data_processing:
The obtained next-generation sequencing data were subjected to reads cleaning with TrimGalore (version 0.6.6)
Trimmed sequence reads were mapped to the reference genome (hg38) with HISAT2 (version 2.2.1)
Read count extraction and normalization with the TPM method using StringTie (version 2.1.5)
Assembly: hg38
Supplementary files format and content: Comma-separated csv file including raw counts for each sample

source_name: Bone

growth_protocol: HOS osteosarcoma cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and 1×antibiotic/antimycotic (AA) solution (Life Technologies).

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen). 0.5 μg of RNA was reverse transcribed using QuantiTect Reverse Transcription Kit (QIAGEN).
RNA libraries were prepared according to the manual using the MGIEasy RNA Directional Library Prep Set (MGI Tech Co Ltd)

treatment_protocol: SET knockdown was induced by treatment 500 ng/ml doxycycline for 2 days.

value: Bone

value: HOS

value: Osteosarcoma

value: SET knockdown


title: HOS cells shNT2

value: WT


title: PB01004_tumor_roi008_CancerCell

description: protein detected by antibody

value: tumor

value: cancer cell enriched

value: Rest


title: SiFBXO22-2 3

city: Wuhan

first: Yunshang

last: Chen

address: No. 1277 Jiefang Avenue

country: China

institute: Wuhan Union Hospital

data_processing:
The RNA integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies).
Paired-end libraries sequencing20 with MGISEQ2000 were prepared with the mRNA-seq sample prep kit (Illumina) according to the manufacturer’s specifications.
Illumina data analysis pipeline was then used for sequence analysis. All samples were allocated to lanes and processed in blinded fashion to keep bias to a minimum
Assembly: hg38
Supplementary files format and content: Analysis description: Calculate the expression read count using the Stringtie-1.3.3b software. Then, the gene and transcript FPKM were calculated. In this process we simply filtered the expression:1）Remove genes or transcripts with length less than 100 bp. ;2）If the FPKM of a gene or transcript is less than 0.0001, it is considered to be expressed as 0. Remove genes with a table of 0 in all samples.

source_name: Lung

growth_protocol: All the cells were cultured in DMEM/F12 medium containing 10% FBS and 100 μg/mL penicillin and streptomycin in 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: A549 cells transfected with Scrambled or SiRNAs targeting REV1 for 48 hours.

value: Lung

value: Human lung adenocarcinoma cells

value: SiFBXO22-2 tranfected


title: HOS cells shNT1


title: SiFBXO22-2 2


title: SiFBXO22-2 1


title: PB01004_liver_roi009_ImmuneCell

description: protein detected by antibody

value: liver

value: immune cell enriched

value: partial response (PR)


title: SiFBXO22-1 2

value: SiFBXO22-1 tranfected


title: SiFBXO22-1 3


title: Scramble 3

value: Scramble

value: Scramble tranfected


title: Scramble 2


title: SiFBXO22-1 1


title: Old mouse endothelial-enriched RNAs from LCA_3

city: Atlanta

first: Sandeep

last: Kumar

state: GA

address: 1760 Haygood Dr.

department: Biomedical Engineering

institute: Emory University

data_processing:
Reads were aligned to mm9, counted, filtered, and normalized using Partek Flow software following the standard procedures.
Alignment was performed with the STAR aligner using Partek Flow Software and the mapped reads were counted
Genes with low counts across libraries were filtered and features  with count-per-million > 0.5 in at least 2 samples were retained.
mRNAs and LNCRNAs were identified and quantitated using standard mouse genome builty
The normalized counts were compared with the RCA vs LCA groups in the Young vs. the Old mice sets
Genome_build: mm9

source_name: endothelial-enriched RNA carotid artery lumen

extract_protocol:
The lysates were flash frozen using liquid nitrogen, and RNA was harvested using Qiazol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All mice were fed standard chow diet.  Partial carotid ligation surgery was performed on the LCA and RNA was left untouched.  2-days post ligation mice were sacrificed and endothelial enriched RNAs were flushed out.

value: endothelial cells carotid artery

tag: age


title: SMCTRAP_75_Input

value: Thoracic aorta

value: EGFP (+)

value: TRAP-Control

value: Female

value: total RNA extraction from the 5% of total lysate (Input)


title: PC, 220606, Input

value: coculture day 14

value: Pneumocystis + epithelial cell lines

value: culture date:3/31/22

value: pre immune serum


title: Old mouse endothelial-enriched RNAs from RCA_3

tag: strain

value: endothelial-enriched RNA carotid artery lumen


title: Old mouse endothelial-enriched RNAs from LCA_2

tag: treatment


title: Old mouse endothelial-enriched RNAs from RCA_2


title: Young mouse endothelial-enriched RNAs from LCA_3


title: Old mouse endothelial-enriched RNAs from RCA_1


title: Scramble 1

value: Lung

tag: cell line

value: Human lung adenocarcinoma cells


title: Young mouse endothelial-enriched RNAs from LCA_2


title: Young mouse endothelial-enriched RNAs from LCA_1


title: HOS cells shSET2

value: Bone

value: HOS

tag: cell type

value: Osteosarcoma

value: SET knockdown


title: Control167

type: genomic

city: London

first: Laurence

middle: Bruce

last: Lovat

address: 43-45 Foley Street

department: Division of Surgery & Interventional Science

country: United Kingdom

institute: University College London

description: Saliva Sample from Control

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

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

data_processing:
raw .idat files were read via the minfi package in the R programming environment, data was normalised using Functional Normalisation in R
Average Beta value and detection P-values

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Saliva samples were collected using the Oragene DNA OG/600 saliva collection kit (DNAGenotek, Ottawa, Canada). All participants were required to fast for a minimum of one hour prior to sample collection.

tag: disease subtype

value: Non-Dysplastic Barrett's Esophageus


title: Young mouse endothelial-enriched RNAs from RCA_1

tag: tissue

value: endothelial cells carotid artery


title: Control165

description: Saliva Sample from Control

value: Male


title: Control164

description: Saliva Sample from Control


title: Control162

description: Saliva Sample from Control


title: Control161

description: Saliva Sample from Control


title: Control159

description: Saliva Sample from Control


title: Control157

description: Saliva Sample from Control


title: Control156

description: Saliva Sample from Control


title: Control163

description: Saliva Sample from Control


title: Control160

description: Saliva Sample from Control


title: Control158

description: Saliva Sample from Control


title: Control154

description: Saliva Sample from Control


title: Old mouse endothelial-enriched RNAs from LCA_1


title: Control153

description: Saliva Sample from Control


title: Young mouse endothelial-enriched RNAs from RCA_3


title: Control155

description: Saliva Sample from Control


title: Control152

description: Saliva Sample from Control


title: Control145

description: Saliva Sample from Control


title: Control149

description: Saliva Sample from Control


title: Control150

description: Saliva Sample from Control


title: Control151

description: Saliva Sample from Control


title: Young mouse endothelial-enriched RNAs from RCA_2


title: Control148

description: Saliva Sample from Control


title: Control147

description: Saliva Sample from Control


title: Control141

description: Saliva Sample from Control


title: Control166

description: Saliva Sample from Control


title: Control143

description: Saliva Sample from Control


title: Control139

description: Saliva Sample from Control


title: Control144

description: Saliva Sample from Control


title: Control140

description: Saliva Sample from Control


title: Control146

description: Saliva Sample from Control


title: Control138

description: Saliva Sample from Control


title: Control142

description: Saliva Sample from Control


title: Control131

description: Saliva Sample from Control


title: Control134

description: Saliva Sample from Control


title: Control133

description: Saliva Sample from Control


title: Control129

description: Saliva Sample from Control


title: Control135

description: Saliva Sample from Control


title: Control130

description: Saliva Sample from Control


title: Control125

description: Saliva Sample from Control


title: Control126

description: Saliva Sample from Control


title: Control124

description: Saliva Sample from Control


title: Control127

description: Saliva Sample from Control


title: Control123

description: Saliva Sample from Control


title: Control119

description: Saliva Sample from Control


title: Control121

description: Saliva Sample from Control


title: Control118

description: Saliva Sample from Control


title: Control117

description: Saliva Sample from Control


title: Control122

description: Saliva Sample from Control


title: Control120

description: Saliva Sample from Control


title: Control116

description: Saliva Sample from Control


title: Control115

description: Saliva Sample from Control

value: No Positive Diagnosis


title: Control113

description: Saliva Sample from Control


title: Control112

description: Saliva Sample from Control

value: Female


title: Control114

description: Saliva Sample from Control


title: Control137

description: Saliva Sample from Control


title: Control110

description: Saliva Sample from Control


title: Control109

description: Saliva Sample from Control


title: Control132

description: Saliva Sample from Control


title: Control108

description: Saliva Sample from Control


title: Control107

description: Saliva Sample from Control


title: Control104

description: Saliva Sample from Control


title: Control102

description: Saliva Sample from Control


title: Control103

description: Saliva Sample from Control


title: Control106

description: Saliva Sample from Control


title: Control101

description: Saliva Sample from Control


title: Control100

description: Saliva Sample from Control


title: Control99

description: Saliva Sample from Control


title: Control98

description: Saliva Sample from Control


title: Control97

description: Saliva Sample from Control


title: Control96

description: Saliva Sample from Control


title: Control94

description: Saliva Sample from Control


title: Control92

description: Saliva Sample from Control


title: Control95

description: Saliva Sample from Control


title: Control91

description: Saliva Sample from Control


title: Control90

description: Saliva Sample from Control


title: Control136

description: Saliva Sample from Control


title: Control111

description: Saliva Sample from Control


title: Control89

description: Saliva Sample from Control


title: Control88

description: Saliva Sample from Control


title: Control86

description: Saliva Sample from Control


title: Control85

description: Saliva Sample from Control


title: Control87

description: Saliva Sample from Control


title: Control81

description: Saliva Sample from Control


title: Control78

description: Saliva Sample from Control


title: Control84

description: Saliva Sample from Control


title: Control82

description: Saliva Sample from Control


title: Control93

description: Saliva Sample from Control


title: Control105

description: Saliva Sample from Control


title: Control75

description: Saliva Sample from Control


title: Control77

description: Saliva Sample from Control


title: Control74

description: Saliva Sample from Control

value: Healthy Voluteer


title: Control79

description: Saliva Sample from Control


title: Control72

description: Saliva Sample from Control


title: Control70

description: Saliva Sample from Control


title: Control65

description: Saliva Sample from Control


title: Control61

description: Saliva Sample from Control


title: Control62

description: Saliva Sample from Control


title: Control60

description: Saliva Sample from Control


title: Control68

description: Saliva Sample from Control


title: Control69

description: Saliva Sample from Control


title: Control66

description: Saliva Sample from Control


title: Control83

description: Saliva Sample from Control


title: Control67

description: Saliva Sample from Control


title: Control63

description: Saliva Sample from Control


title: Control59

description: Saliva Sample from Control


title: Control80

description: Saliva Sample from Control


title: Control58

description: Saliva Sample from Control


title: Control76

description: Saliva Sample from Control


title: Control55

description: Saliva Sample from Control


title: Control71

description: Saliva Sample from Control


title: Control50

description: Saliva Sample from Control


title: Control49

description: Saliva Sample from Control


title: Control128

description: Saliva Sample from Control


title: Control57

description: Saliva Sample from Control


title: Control48

description: Saliva Sample from Control


title: Control46

description: Saliva Sample from Control


title: Control44

description: Saliva Sample from Control


title: Control43

description: Saliva Sample from Control


title: Control42

description: Saliva Sample from Control


title: Control53

description: Saliva Sample from Control


title: Control56

description: Saliva Sample from Control


title: Control52

description: Saliva Sample from Control


title: Control45

description: Saliva Sample from Control


title: Control54

description: Saliva Sample from Control


title: Control51

description: Saliva Sample from Control


title: Control64

description: Saliva Sample from Control


title: Control73

description: Saliva Sample from Control


title: Control35

description: Saliva Sample from Control


title: Control41

description: Saliva Sample from Control


title: Control30

description: Saliva Sample from Control


title: Control29

description: Saliva Sample from Control


title: Control24

description: Saliva Sample from Control


title: Control33

description: Saliva Sample from Control


title: Control32

description: Saliva Sample from Control


title: Control38

description: Saliva Sample from Control


title: Control31

description: Saliva Sample from Control


title: Control21

description: Saliva Sample from Control


title: Control34

description: Saliva Sample from Control


title: Control40

description: Saliva Sample from Control


title: Control47

description: Saliva Sample from Control


title: Control39

description: Saliva Sample from Control


title: Control18

description: Saliva Sample from Control


title: Control28

description: Saliva Sample from Control


title: Control17

description: Saliva Sample from Control


title: Control12

description: Saliva Sample from Control


title: Control25

description: Saliva Sample from Control


title: Control26

description: Saliva Sample from Control


title: Control22

description: Saliva Sample from Control


title: Control16

description: Saliva Sample from Control


title: Control23

description: Saliva Sample from Control


title: Control15

description: Saliva Sample from Control


title: Control14

description: Saliva Sample from Control


title: Control13

description: Saliva Sample from Control


title: Control 3 Replicate

description: Saliva Sample from Control

source_name: Control 3 Replicate


title: Control 4 Replicate

description: Saliva Sample from Control

source_name: Control 4 Replicate


title: Control 3

description: Saliva Sample from Control

source_name: Control 3


title: Control11

description: Saliva Sample from Control


title: Control10

description: Saliva Sample from Control


title: Control9

description: Saliva Sample from Control


title: Control 1

description: Saliva Sample from Control

source_name: Control 1


title: Control7

description: Saliva Sample from Control


title: Control8

description: Saliva Sample from Control


title: Cancer 97

description: Saliva Sample from Cancer

source_name: Cancer 97

value: High Grade Dysplasia


title: Control5

description: Saliva Sample from Control


title: Cancer 95

description: Saliva Sample from Cancer

source_name: Cancer 95


title: Control 4

description: Saliva Sample from Control

source_name: Control 4


title: Control6

description: Saliva Sample from Control


title: Control 2 Replicate

description: Saliva Sample from Control

source_name: Control 2 Replicate


title: Control 2

description: Saliva Sample from Control

source_name: Control 2


title: Cancer 98

description: Saliva Sample from Cancer

source_name: Cancer 98


title: Control 1 Replicate

description: Saliva Sample from Control

source_name: Control 1 Replicate


title: Cancer 94

description: Saliva Sample from Cancer

source_name: Cancer 94


title: Cancer 96

description: Saliva Sample from Cancer

source_name: Cancer 96


title: Cancer 93

description: Saliva Sample from Cancer

source_name: Cancer 93


title: Cancer 82

description: Saliva Sample from Cancer

source_name: Cancer 82

value: Intramucosal


title: Cancer 88

description: Saliva Sample from Cancer

source_name: Cancer 88


title: Cancer 89

description: Saliva Sample from Cancer

source_name: Cancer 89


title: Cancer 90

description: Saliva Sample from Cancer

source_name: Cancer 90


title: Cancer 87

description: Saliva Sample from Cancer

source_name: Cancer 87


title: Cancer 80

description: Saliva Sample from Cancer

source_name: Cancer 80


title: Cancer 84

description: Saliva Sample from Cancer

source_name: Cancer 84


title: Cancer 85

description: Saliva Sample from Cancer

source_name: Cancer 85


title: Cancer 91

description: Saliva Sample from Cancer

source_name: Cancer 91


title: Cancer 83

description: Saliva Sample from Cancer

source_name: Cancer 83


title: Cancer 79

description: Saliva Sample from Cancer

source_name: Cancer 79


title: Cancer 86

description: Saliva Sample from Cancer

source_name: Cancer 86


title: Cancer 78

description: Saliva Sample from Cancer

source_name: Cancer 78


title: Cancer 75

description: Saliva Sample from Cancer

source_name: Cancer 75


title: Cancer 77

description: Saliva Sample from Cancer

source_name: Cancer 77


title: Cancer 74

description: Saliva Sample from Cancer

source_name: Cancer 74


title: Cancer 73

description: Saliva Sample from Cancer

source_name: Cancer 73


title: Cancer 71

description: Saliva Sample from Cancer

source_name: Cancer 71


title: Cancer 92

description: Saliva Sample from Cancer

source_name: Cancer 92


title: Cancer 69

description: Saliva Sample from Cancer

source_name: Cancer 69


title: Cancer 68

description: Saliva Sample from Cancer

source_name: Cancer 68


title: Cancer 81

description: Saliva Sample from Cancer

source_name: Cancer 81


title: Cancer 66

description: Saliva Sample from Cancer

source_name: Cancer 66


title: Cancer 67

description: Saliva Sample from Cancer

source_name: Cancer 67


title: Cancer 65

description: Saliva Sample from Cancer

source_name: Cancer 65


title: Cancer 64

description: Saliva Sample from Cancer

source_name: Cancer 64


title: Cancer 76

description: Saliva Sample from Cancer

source_name: Cancer 76


title: Cancer 58

description: Saliva Sample from Cancer

source_name: Cancer 58

value: Invasive Esophageal Carcinoma


title: Cancer 59

description: Saliva Sample from Cancer

source_name: Cancer 59


title: Cancer 60

description: Saliva Sample from Cancer

source_name: Cancer 60


title: Cancer 57

description: Saliva Sample from Cancer

source_name: Cancer 57


title: Cancer 62

description: Saliva Sample from Cancer

source_name: Cancer 62


title: Cancer 61

description: Saliva Sample from Cancer

source_name: Cancer 61


title: Cancer 56

description: Saliva Sample from Cancer

source_name: Cancer 56


title: Cancer 53

description: Saliva Sample from Cancer

source_name: Cancer 53


title: Cancer 72

description: Saliva Sample from Cancer

source_name: Cancer 72


title: Cancer 50

description: Saliva Sample from Cancer

source_name: Cancer 50


title: Cancer 55

description: Saliva Sample from Cancer

source_name: Cancer 55


title: Cancer 54

description: Saliva Sample from Cancer

source_name: Cancer 54


title: Cancer 51

description: Saliva Sample from Cancer

source_name: Cancer 51


title: Cancer 52

description: Saliva Sample from Cancer

source_name: Cancer 52


title: Cancer 49

description: Saliva Sample from Cancer

source_name: Cancer 49


title: Cancer 48

description: Saliva Sample from Cancer

source_name: Cancer 48


title: Cancer 47

description: Saliva Sample from Cancer

source_name: Cancer 47


title: Cancer 63

description: Saliva Sample from Cancer

source_name: Cancer 63


title: Cancer 46

description: Saliva Sample from Cancer

source_name: Cancer 46


title: Cancer 45

description: Saliva Sample from Cancer

source_name: Cancer 45


title: Cancer 42

description: Saliva Sample from Cancer

source_name: Cancer 42


title: Cancer 44

description: Saliva Sample from Cancer

source_name: Cancer 44


title: Cancer 41

description: Saliva Sample from Cancer

source_name: Cancer 41


title: Cancer 37

description: Saliva Sample from Cancer

source_name: Cancer 37


title: Cancer 43

description: Saliva Sample from Cancer

source_name: Cancer 43


title: Cancer 35

description: Saliva Sample from Cancer

source_name: Cancer 35


title: Cancer 36

description: Saliva Sample from Cancer

source_name: Cancer 36


title: Cancer 34

description: Saliva Sample from Cancer

source_name: Cancer 34


title: Cancer 70

description: Saliva Sample from Cancer

source_name: Cancer 70


title: Cancer 32

description: Saliva Sample from Cancer

source_name: Cancer 32


title: Cancer 38

description: Saliva Sample from Cancer

source_name: Cancer 38


title: Control36

description: Saliva Sample from Control


title: Cancer 31

description: Saliva Sample from Cancer

source_name: Cancer 31


title: Cancer 30

description: Saliva Sample from Cancer

source_name: Cancer 30


title: Cancer 28

description: Saliva Sample from Cancer

source_name: Cancer 28


title: Cancer 26

description: Saliva Sample from Cancer

source_name: Cancer 26


title: Cancer 27

description: Saliva Sample from Cancer

source_name: Cancer 27


title: Cancer 29

description: Saliva Sample from Cancer

source_name: Cancer 29


title: Cancer 24

description: Saliva Sample from Cancer

source_name: Cancer 24


title: Cancer 23

description: Saliva Sample from Cancer

source_name: Cancer 23


title: Cancer 22

description: Saliva Sample from Cancer

source_name: Cancer 22


title: Cancer 40

description: Saliva Sample from Cancer

source_name: Cancer 40


title: Cancer 19

description: Saliva Sample from Cancer

source_name: Cancer 19


title: Cancer 20

description: Saliva Sample from Cancer

source_name: Cancer 20


title: Cancer 21

description: Saliva Sample from Cancer

source_name: Cancer 21


title: Cancer 39

description: Saliva Sample from Cancer

source_name: Cancer 39


title: Cancer 14

description: Saliva Sample from Cancer

source_name: Cancer 14


title: Cancer 18

description: Saliva Sample from Cancer

source_name: Cancer 18


title: Cancer 33

description: Saliva Sample from Cancer

source_name: Cancer 33


title: Cancer 16

description: Saliva Sample from Cancer

source_name: Cancer 16


title: Cancer 17

description: Saliva Sample from Cancer

source_name: Cancer 17


title: Cancer 12

description: Saliva Sample from Cancer

source_name: Cancer 12


title: Cancer 11

description: Saliva Sample from Cancer

source_name: Cancer 11


title: Cancer 15

description: Saliva Sample from Cancer

source_name: Cancer 15


title: Cancer 8

description: Saliva Sample from Cancer

source_name: Cancer 8


title: Cancer 7

description: Saliva Sample from Cancer

source_name: Cancer 7


title: Cancer 9

description: Saliva Sample from Cancer

source_name: Cancer 9


title: Cancer 25

description: Saliva Sample from Cancer

source_name: Cancer 25


title: Cancer 6

description: Saliva Sample from Cancer

source_name: Cancer 6


title: Cancer 6 Replicate

description: Saliva Sample from Cancer

source_name: Cancer 6 Replicate


title: Cancer 5

description: Saliva Sample from Cancer

source_name: Cancer 5


title: Cancer 5 Replicate

description: Saliva Sample from Cancer

source_name: Cancer 5 Replicate


title: Cancer 4

description: Saliva Sample from Cancer

source_name: Cancer 4


title: Cancer 4 Replicate

description: Saliva Sample from Cancer

source_name: Cancer 4 Replicate


title: Cancer 3 Replicate

description: Saliva Sample from Cancer

source_name: Cancer 3 Replicate


title: Cancer 3

description: Saliva Sample from Cancer

source_name: Cancer 3


title: Cancer 2

description: Saliva Sample from Cancer

source_name: Cancer 2


title: Cancer 13

description: Saliva Sample from Cancer

source_name: Cancer 13


title: Cancer 1  Replicate

description: Saliva Sample from Cancer

source_name: Cancer 1  Replicate


title: Cancer 1

description: Saliva Sample from Cancer

source_name: Cancer 1


title: Control37

description: Saliva Sample from Control


title: Control19

description: Saliva Sample from Control


title: SpermB_Goat

city: Beijing

first: Siqian

address: 2rd, Yuanmingyuan West Road

department: College of Animal Science and Technology

institute: China Agricultural University

data_processing:
FastQC v 0.11.2 and Trim Galore v 0.4.0 was used to assess the quality of the sequence data and filter low-quality reads (q < 30), respectively. The cleaned data were then mapped to the sscrofa11.1 genomes using bowtie2 under the Bismark software (0.14.5) with default parameters
Duplicated reads were removed using deduplicate_bismark
symmetric-cpgs was employed to obtain methyl CpG site information using methpipe software
Assembly: ARS-UCD1.2, Oar_rambouillet_v1.0, ARS1
Supplementary files format and content: CpG report files

organism: Capra hircus

source_name: sperm

extract_protocol:
DNA was extracted according to the TIANamp Genomic DNA Kit protocol
DNA libraries were prepared for sequencing using standard Illumina protocols

value: sperm

tag: developmental stage

value: adult


title: SpermC_Goat


title: Cancer 10

description: Saliva Sample from Cancer

source_name: Cancer 10


title: E15.5 brain, male, KO1

city: Setagaya

first: Shiori

last: Kinoshita

state: Tokyo

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

data_processing:
All 150 bp paired-end reads were trimmed to a length of 75 bp using FASTX-toolkit (v0.0.14) to 103 ensure the same analytical conditions as the 75 bp paired-end reads.
Reads with adapter sequences were trimmed by cutadapt (v.2.6).
Reads were aligned to the mouse genome (mm10) using HISAT2 (v.2.1.0).
Transcripts were assembled and quantified using Stringtie (v.2.0.6).
Gene counts matrix were generated by the Python script “prepDE.py” to extract read count information from StringTie output.
Assembly: mm10
Supplementary files format and content: Gene counts matrix from Stringtie in comma-separated file format.

source_name: brain

extract_protocol:
Total RNA was extracted from E15.5 brain in WT and Nsd2 KO mice using AllPrep DNA/RNA Mini Kit (QIAGEN).
Ribosomal RNA was depleted using NEBNext rRNA Depletion Kit or Kit v2 (Human/Mouse/Rat) (New England Biolabs) and cDNA libraries were generated using NEBNext Ultra Ⅱ Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocol.

value: brain

tag: genotype

value: Nsd2 knockout

value: male


title: E15.5 brain, male, KO2

tag: Sex


title: SpermA_Goat


title: E15.5 brain, male, WT3

value: WT


title: MuscleC_Goat

source_name: muscle

value: muscle


title: E15.5 brain, male, WT2


title: MuscleB_Goat


title: E15.5 brain, male, WT1


title: MuscleA_Goat


title: Input

data_processing:
Reads with adapter sequences were trimmed by cutadapt (v.2.6).
ChIP-seq reads were aligned to the mouse genome (mm10) using BWA-MEM (v.0.7.17).
PCR duplicates were removed by Picard (v.2.17.11) and bam files of each biological replicates were merged using SAMtools (v1.6).
Bigwig tracks were generated using bamCoverage in deepTools (v.3.3.0) with options “--normalizeUsing CPM.”
To calculate normalized H3K36me2 ChIP signal, read counts were divided by input read counts using bamCompare in deepTools (v.3.3.0) with options “--normalizeUsing CPM, -- operation ratio, --binSize 10000”.
Assembly: mm10
Supplementary files format and content: bigWig files

extract_protocol:
ChIP experiments were carried out using ChIP Reagents (Nippon Gene). ChIP was performed in E15.5 WT and Nsd2 KO brain. Fresh brain tissue was minced and fixed with 1% paraformaldehyde in D-PBS (-) for 10 min at room temperature and quenched with 2 M glycine for 5 min. Tissue was resuspended in NP-40 buffer containing proteinase inhibitor cocktail (Nacalai Tesque) and homogenated by BioMAsher (Nippi). Homogenized tissue was incubated for 10 min on ice and centrifuged to collect nuclear pellets. Nuclear pellet was resuspended in SDS Lysis buffer and lysate was sonicated to fragment chromatin for 15 min (Duty:5, PIP:105, cycles/burst:200) in Covaris S220 (Covaris). The fragmented chromatin was centrifuged to remove debris and immunoprecipitated with Dynabeads Protein A (Thermo Fisher) conjugated anti-H3K36me2 (ab9049, Abcam) in ChIP dilution buffer with protease inhibitor cocktail for 4 hr at 4℃ rotating. The beads were washed with 1 x RIPA buffer - 150 mM, 1 x RIPA buffer - 500 mM, LiCl buffer (250 mM LiCl, 10 mM Tris-HCl(pH8.0), 0.5% NP- 40, 0.5% Sodium deoxycholate, 1 mM EDTA) and TE buffer (pH 8.0). The beads were incubated in ChIP direct elution buffer with Proteinase K at 65 ℃ overnight. ChIP DNA was purified using AMPure XP beads (Beckman Coluter) following the manufacturer’s protocol.
ChIP-seq libraries were generated using NEBNext Ultra Ⅱ DNA Library prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocol.

tag: chip antibody


title: Cancer 2 Replicate

description: Saliva Sample from Cancer

source_name: Cancer 2 Replicate


title: KO2_H3K36me2

value: H3K36me2(ab9049, Abcam)


title: BrainB_Goat


title: WT1_H3K36me2


title: KO1_H3K36me2


title: BrainA_Goat


title: DMSO_4_S4

city: Boston

first: VICTOR

last: BARRERA BURGOS

state: Massachusetts

address: Landmark 401 Park Drive 3 East

department: Biostatistics

institute: Harvard School of Public Health

description:
raw_counts.csv
tpm_counts.csv

data_processing:
Sequenced reads were assessed for low-quality sequence, then mapped against the WBcel235 transcriptome where reads were quantified at the transcript level using Salmon
Transcript-level abundance estimates  from Salmon were collapsed to gene-leve estimates and  converted to raw count values using the R Bioconductor package tximport
Differentially expressed genes were identified using the R Bioconductor package DESeq2
Assembly: Wormbase assembly  WBcel235, Annotation Version WS272
Supplementary files format and content: comma separated file of raw count matrix where columns correspond to samples and rows correspond to genes;
Supplementary files format and content: comma separated file of transcript per million counts where columns correspond to samples and rows correspond to genes

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole organism

extract_protocol:
Samples of 1,000 col-121 worms each following 24-hour exposure to either DMSO alone (0.1%) or DEET dissolved in DMSO (0.1M) were collected in 500 ml of Trizol (Invitrogen) and prepared using the Direct-zol RNA miniprep kit (Zymo Research) by following the manufacturer’s instructions. Four independent biological repeats per condition were used for Illumina NextSeq High 2x38 using Kapa mRNA HyperPrep kit (Roche).
RNA libraries for RNA-seq were prepared using Kapa mRNA HyperPrep kit (Roche).

value: Whole organism

tag: pair (batch)

value: DMSO


title: WT2_H3K36me2


title: E15.5 brain, male, KO3


title: DMSO_3_S3

description:
raw_counts.csv
tpm_counts.csv

treatment_protocol: 24-hour exposure to either DMSO alone (0.1%) or DEET dissolved in DMSO (0.1M)


title: DMSO_2_S2

description:
raw_counts.csv
tpm_counts.csv


title: YUMM3_3-CTRL_GFP_3

city: Lausanne

first: Giovanna

last: Ambrosini

address: Station 19

country: Switzerland

institute: EPFL

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
sequencing libraries were demultiplexed into individual FASTQ files
sequencing reads were quantified using Cell Ranger v5 and 10X Genomics pre-built mouse reference genome, which was modified to include the GFP sequence
Low quality cells were flagged and excluded using the scuttle Bioconductor package (v1.0.0) with default parameters based on percentage of mitochondrial reads, library size, and number of genes detected per cell
Potential doublets were also excluded using the scDblFinder package from Bioconductor (v1.3.25)
Cells that passed the quality control were imported into the Seurat R package (v4.0.2) for further analysis
Data normalization and feature selection was performend using the SCTransform functionality with default settings from Seurat.
Dimensionality reduction and data integration were performed using Pearson residuals obtained from SCTransform
Unsupervised clustering of integrated data was done using FindNeighbors and FindClusters functionalities with default settings
Literature-derived marker genes and cell type-specific signatures obtained from PanglaoDB database were used to annotate major cell types
We used the presto R package (https://github.com/immunogenomics/presto) that provides a fast implementation of Wilcoxon rank sum test and auROC analysis to further derive cluster- and cell type-specific marker genes, as well as to perform differential expression analysis between ꞵA and Ctrl samples.
We used predictive power defined as abs(AUC-0.5)*2, along with log fold change for gene ranking. We defined the predictive power multiplied by logFC as the ranking statistic to perform pre-ranked GSEA of Hallmark pathways from MSigDB, using the fGSEA package (v1.15.2) from Bioconductor
Assembly: 10X Genomics pre-built mouse reference genome
Supplementary files format and content: filtered_feature_bc_matrix.h5 (count matrix in H5 format)

source_name: tumor

growth_protocol: YUMM3.3 mouse melanoma cells were maintained in DMEM/F12 (Gibco) medium supplemented with 10% fetal bovine serum, 50 µg/mL gentamicin (Gibco, Thermo Fisher Scientific, Waltham, MA, USA), and 1% GlutaMAX (Gibco).

extract_protocol:
YUMM3.3-Ctrl.GFP and -ꞵA.GFP tumors were dissected, minced using rounded scissors, and digested in Dnase-I (0.02mg/mL, Sigma) and collagenase (1mg/mL, Sigma) in RPMI using a gentleMACS Octo Dissociator (Miltenyi). In total, we collected six Ctrl and six ꞵA tumors. Two tumors of each genotype were pooled for each biological replicate based on tumor volumes to have comparable starting amounts for each replicate. To minimize the time that cells spent on the ice, samples were randomized, and live single-cell sorted on two machines (Becton Dickinson FACSAria II and ACSAria Fusion) into GFPhi tumor cells and GFPint stromal populations. For dead staining, Propidium Iodide Solution (421301, Biolegend) was added to the cells immediately before sorting. Immediately after sorting, cells were counted, centrifuged at 300g for 5 min at RT, and resuspended at a density of 1000 cells/μl in DMEM supplemented with 10% filtered FBS. GFPhi fractions were added back to GFPint cells to account for 10% of the final volume
Cell concentrations and quality were assessed using trypan blue staining. Samples contained less than 5% dead cells and 3-5% doublets. Single-cell RNA sequences were prepared using 10x Genomics Chromium v3.1 kit according to the manufactur's instruction

treatment_protocol: 2.5x105 YUMM3.3 cells were injected subcutaneously into the right flank of 10 week old female C57BL/6 mice (Charles River laboratories) and grown for 13 days

value: 10 weeks

value: tumor

value: dissociated YUMM3.3 GFP mouse melanoma tumors enriched for non-Tumor cells (lymphocytes, endothelial, fibroblasts and others)

tag: condition

value: Ctrl


title: DMSO_1_S1

description:
raw_counts.csv
tpm_counts.csv


title: YUMM3_3-CTRL_GFP_2

description: 10x genomics

value: C57BL/6 mice (Charles River laboratories)


title: YUMM3_3-CTRL_GFP_1

description: 10x genomics


title: DEET_4_S8

description:
raw_counts.csv
tpm_counts.csv

value: DEET


title: YUMM3_3-ActA_GFP_3

description: 10x genomics

value: ActA


title: YUMM3_3-ActA_GFP_1

description: 10x genomics


title: YUMM3_3-ActA_GFP_2

description: 10x genomics


title: DEET_2_S6

description:
raw_counts.csv
tpm_counts.csv


title: Testis, Tas1r3 KO 2

city: Seoul

first: Hobin

last: Seong

state: KOREA, REPUBLIC OF

address: Gwanak-ro 1, Seoul National University

country: South Korea

institute: Seoul National University

data_processing:
Partek® Flow® v7.0
Raw sequence reads were trimmed and filtered by removing adaptor sequences and low-quality sequence reads.
Trimmed high-quality sequence reads were mapped and aligned using STAR method.
Aligned reads in gene transcripts were quantified to RefSeq transcripts using the Partek E/M method and normalized as FPKM using the mixed-model approach in Partek® Flow® v7.0
Assembly: mm39
Supplementary files format and content: Excel worksheet files include FPKM values, gene location, transcript id and gene symbol for each Sample

source_name: Testis

extract_protocol:
RNA was harvested using RNAqueous 4PCR Kits (Ambion). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ion Total RNA-Seq Kit v2 following manufacturer's protocols.

value: Testis

value: Male

value: Tas1r3 KO

value: Normal diet (18 weeks)


title: BrainC_Goat

value: brain

value: adult


title: Control27

description: Saliva Sample from Control

value: Healthy Voluteer


title: Control20

description: Saliva Sample from Control


title: Testis, WT 2

value: WT


title: Testis, WT 1


title: DEET_1_S5

description:
raw_counts.csv
tpm_counts.csv

value: Whole organism


title: Control102

city: Singapore

first: Qiaoyang

last: Sun

address: 20 College Rd

department: Neurology

country: Singapore

institute: National Neuroscience Institute

data_processing:
The sequencing quality of the fastq files of MeDIP-seq was assessed before mapping to the hg19 using BWA. PCR duplicates were removed if both ends were at the same positions. Total number of mapped reads, mapping quality and fragment size were evaluated. For samples passing quality cut-offs, we proceeded to identification of differential methylation using both QSEA package in the R BioConductor and MACS2 and obtained the union of the two results as tentative candidates for downstream analysis. For each identified candidate, methylation level was quantified using featureCounts and normalized to Reads Per Million mapped reads (RPM). These normalized RPM counts cross different samples were further employed to extract the DMRs between two groups, e.g. pre-AML/MDS cases and controls or pre-AML and pre-MDS.
Assembly: hg19
Supplementary files format and content: log2 normalized counts (10 bg)

source_name: Peripheral blood

growth_protocol: whole blood

extract_protocol:
Total genomic DNA was extracted from 0.5 ml of whole blood using Qiagen DNeasy Blood & Tissue Kits.
The total genomic DNA was ultrasonic fragmented to 150-300 bp using Covaris M220 machine, following by end-repair and A-tailing using Kapa HyperPrep Kit (Kapa Biosystems). The A-tailed DNA were then ligated with the NEBNext adaptor, purified with AMPure XP beads (Beckman Coulter) and then digested with USER enzyme (New England BioLabs) to release the dU loop structure of the adapter. The products were further purified using Qiagen MinElute PCR Purification Kit. Subsequently, MeDIP immunoprecipitation using MagMeDIP kit (Diagenode) was performed following previously described protocols. An average of 100ng of fragmented DNA were used for the MeDIP immunoprecipitation

treatment_protocol: whole blood

value: Peripheral blood

value: Blood

value: Healthy Control

value: 5-methylcytosine (5-mC) Antibody


title: Control085


title: Control154


title: Control119


title: Control068


title: Testis, Tas1r3 KO 1


title: Control136


title: Control153


title: Control017


title: Control034


title: Control135


title: DEET_3_S7

description:
raw_counts.csv
tpm_counts.csv


title: SpermC_Sheep

organism: Ovis aries

value: sperm


title: SpermB_Sheep


title: Control118


title: Control101


title: SpermA_Sheep


title: Control051


title: Control084


title: MuscleB_Sheep

value: muscle


title: MuscleC_Sheep


title: MuscleA_Sheep


title: Control067


title: Control033


title: Control016


title: BrainC_Sheep


title: BrainB_Sheep


title: Control152


title: Control134


title: Control117


title: tank18, ant-mix

city: Duluth

first: Phillip

last: Ankley

state: MN

address: 6201 Congdon Blvd

institute: U.S. EPA

data_processing:
Trimmomatic (trimmed to a minimum Phred score of 20 and a minimum length of 35 bases with remainign default)
Abundance of transcripts was estimated using Salmon (version 1.10.2) with the reference RBT transcriptome USDA_OmykA_1.1 (GenBank Acc. no. GCA_013265735.3)
Transcripts were mapped  to genes using GenomicFeatures (version 1.52.1) (Lawrence et al., 2013) and corresponding gtf file (Oncorhynchus_mykiss.USDA_OmykA_1.1.110.gtf).
Assembly: GCA_013265735.3
Supplementary files format and content: csv file of the respective mapped ensembl raw gene abundance in each sample

organism: Oncorhynchus mykiss

source_name: Brain

extract_protocol:
RNeasy Plus Universal Mini Kit with QIAzol Lysis Reagent
mRNA Stranded Illumina Nextera

value: Brain

value: ant-mix


title: Control100


title: tank15, ant-mix


title: tank16, control

value: control


title: tank14, ant-mix


title: tank17, control


title: Control049


title: Control083


title: BrainA_Sheep


title: tank13, ery

value: ery


title: Control066


title: Control032


title: tank12, control


title: tank11, ery


title: Control015


title: Control193


title: Control133


title: Control116


title: Control099


title: tank8, control


title: Control151


title: tank9, ant-mix


title: Control082


title: tank7, ery


title: Control050


title: tank6, ant-mix


title: tank5, ery


title: Control065


title: Control048


title: Control014


title: tank10l, ery


title: tank2, ant-mix


title: tank1, control


title: tank3, ery


title: Control031


title: S3 er-EGFP-PARP1cd

city: Bergen

first: Mathias

last: Ziegler

address: Jonas Lies vei 91

country: Norway

institute: University of Bergen

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Hisat2 v2.0.5
Supplementary files format and content: Tab-delimeted xls file includes read count of genes of every sample
Supplementary files format and content: Tab-delimeted xls file includes FPKM of genes of every sample

source_name: Uterus; Cervix

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

extract_protocol:
Extraction was done by Novogene's transcriptome sequencing facility
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.
For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.
The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: Cells were harvested at around 80% confluency by trypsination and shock-frozen in liquid nitrogen.

value: Uterus; Cervix

value: HeLa S3

value: ER EGFP PARP1cd overexpression


title: parental HeLa cell


title: S3 cyto-EGFP-PARP1cd

value: cytosolic EGFP PARP1cd overexpression


title: S3 pex-EGFP-PARP1cd

value: peroxisomal EGFP PARP1cd overexpression


title: Control132


title: S3 mito-EGFP-PARP1cd

value: mitochondrial EGFP PARP1cd overexpression


title: Control150


title: Control081


title: 293 NMNAT3-knockout

source_name: Kidney; Embryo

value: Kidney; Embryo

value: NMNAT3 knockout


title: Control064

value: Peripheral blood

value: Blood


title: 293 SLC25A51-knockout

value: SLC25A51 knockout


title: Control030

value: Healthy Control

value: 5-methylcytosine (5-mC) Antibody


title: Control013


title: 293 pex-EGFP-PARP1cd

description: HEKpPARP


title: Control047


title: 293 er-EGFP-PARP1cd

description: HEKerPARP


title: Control166


title: Control167


title: Control115


title: Control131


title: Control098


title: Control114


title: 293 mito-EGFP-PARP1cd

description: HEKmPARP


title: parental 293 cell

value: WT


title: Control097


title: 293 SLC25A51-FLAG

value: SLC25A51 overexpression


title: Control063


title: Control012


title: Control029


title: Control165


title: SCC25-cell-rep3

first: Gang

state: Hubei

address: Guangba Rd.

institute: Wuhan University

data_processing:
Trimming and quality control of raw fastq files were performed with Fastp. Clean data were aligned to miRNA transcriptome using STAR with parameters: --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterMismatchNmax 1 --alignIntronMax 1 --alignSJDBoverhangMin 1000 --alignEndsType EndToEnd --sjdbGTFfile microRNA.subset.of.GENCODE.V24.gtf
Assembly: GENCODE.V24
Supplementary files format and content: comma-delimited csv files contains raw counts for each sample

source_name: cell line

growth_protocol: The human oral adenosquamous cell carcinoma cell line CAL27 and human oral squamous cell carcinoma cell line SCC25 were propagated under controlled conditions. They were cultured in Dulbecco's Modified Eagle Medium (DMEM) with high glucose concentration, supplemented with 10% fetal bovine serum (FBS). To maintain optimal growth conditions, both cell lines were incubated in a humidified environment at 37°C with an atmosphere containing 5% CO2. This setup ensures the maintenance of physiological pH levels and appropriate gas exchange, crucial for cell viability and proliferation.

extract_protocol:
Total RNA were extracted by TRIZOL according to manufacturer's instruction.
miRNA libraries for miRNA-seq were prepared with QIAseq miRNA Library Kit according to manufacturer's instruction

value: cell line

value: oral squamous cell carcinoma cell line


title: SCC25-sEV-rep2


title: SCC25-cell-rep1


title: Control148


title: SCC25-sEV-rep3


title: CAL27-sEV-rep2


title: Control130


title: CAL27-sEV-rep1


title: CAL27-sEV-rep3


title: SCC25-sEV-rep1


title: 293 cyto-EGFP-PARP1cd

description: HEKcPARP


title: Control149


title: Control113


title: CAL27-cell-rep2


title: Control096


title: CAL27-cell-rep1


title: Control046


title: Control062


title: tank4, control

value: Brain

value: control


title: Control080


title: CLL-13 patient, 6 months of ibrutinib (6m)

city: Barcelona

first: Daniel

last: Medina

address: Centre Cellex, 115-117 Natzaret

department: Experimental Hematology

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

data_processing:
RNA-seq reads were mapped against human reference genome (GRCh38) using STAR software version 2.7.8a with ENCODE parameters
Annotated genes were quantified with RSEM version 1.3.02 with default parameters, using the annotation version GENCODE v38
Differential expression analysis was performed using limma v3.54.2 R package
Counts were normalized with TMM25 and transformed with the ‘voom’ function into logCPM.
To account for repeated measures on the same individual before and after treatment, the limma duplicateCorrelation function was used. Each linear model was fitted with the voom-transformed counts and contrasts were extracted.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample.

source_name: Peripheral blood mononuclear cells

extract_protocol:
AllPrep DNA/RNA Mini kit (QIAGEN)
One paired-end library was prepared using the SMARTseq2 protocol

treatment_protocol: T cell enrichment with EasySep™ Human T Cell Isolation Kit (Stem cell)

value: Peripheral blood mononuclear cells

tag: patient diagnosis

value: CLL

tag: subject

value: Ibrutinib


title: CLL-13 patient, Before treatment (BT)

value: Baseline


title: Control045


title: Control079


title: SCC25-cell-rep2


title: CLL-01 patient, 6 months of ibrutinib (6m)


title: CLL-01 patient, Before treatment (BT)


title: Control028


title: Control011


title: CAL27-cell-rep3


title: Control147


title: Control129


title: Control112


title: CLL-02 patient, Before treatment (BT)


title: Control078


title: Control164


title: CLL-12 patient, Before treatment (BT)


title: CLL-03 patient, 6 months of ibrutinib (6m)


title: CLL-12 patient, 6 months of ibrutinib (6m)


title: CLL-02 patient, 6 months of ibrutinib (6m)


title: Control095


title: CLL-03 patient, Before treatment (BT)


title: Control061


title: CLL-05 patient, Before treatment (BT)


title: CLL-05 patient, 6 months of ibrutinib (6m)


title: Control044


title: Control027


title: CLL-10 patient, 6 months of ibrutinib (6m)


title: CLL-10 patient, Before treatment (BT)


title: Control010


title: CLL-04 patient, 6 months of ibrutinib (6m)


title: Control163


title: Control128


title: CLL-11 patient, 6 months of ibrutinib (6m)


title: CLL-04 patient, Before treatment (BT)


title: Control146


title: Control111


title: CLL-09 patient, 6 months of ibrutinib (6m)


title: Control077


title: CLL-07 patient, 6 months of ibrutinib (6m)


title: CLL-11 patient, Before treatment (BT)


title: Control060


title: HCT8 OV3

city: Guangzhou

first: Li

last: Xiong

state: Guangdong

address: 58 Zhongshan Road 2

department: Department of Endocrinology

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

growth_protocol: All of the cells were cultured at 37°C in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Thermo Fisher Scientific, St Peters, MO, USA) supplemented with 10% fetal bovine serum (FBS; Gibco, Thermo Fisher Scientific, St Peters, MO, USA) in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT8 cells transfected with control plasmid or GPT1 overexpression plasmid

value: colorectal cancer

value: GPT1 overexpression

value: HCT8 cells transfected with GPT1 overexpression plasmid


title: Control043

value: Peripheral blood

value: Blood


title: CLL-07 patient, Before treatment (BT)


title: Control162

value: Healthy Control


title: HCT8 OV2


title: CLL-09 patient, Before treatment (BT)


title: Control094

value: 5-methylcytosine (5-mC) Antibody


title: Control127


title: Control110


title: HCT8 OV1


title: Control145


title: Control026


title: Control093


title: Control009


title: HCT8 CON3

value: WT

value: HCT8 cells transfected with control plasmid


title: Control076


title: HCT8 CON2


title: Control059


title: HCT8 CON1


title: Control025


title: Bone marrow plasma cells, MM at diagnosis, patient 18

type: RNA

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on Clariom™ D Assay, human, according to the standard protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Normalized expression values were obtained using Robust Multi Array Average (RMA) procedure. A custom annotation pipeline was applied that combined GENCODE v25 (Ensembl v87) annotations with the CDF (Chip Definition File) version 24 for gene annotations freely available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/24.0.0/gencodeg.asp, in order to withdraw probes that map to regions where ambiguous detection due to transcript overlap might occur, as described in Todoerti K et al,  Methods Mol Biol. 2021;2348:45-53.

label: biotin

source_name: Highly purified PCs from MM patient

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100-250 nanograms of total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

extract_protocol: Extraction of total RNA was performed with RNAeasy kit according to the manufacturer's instructions (Qiagen).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

value: Bone marrow

value: plasma cells

tag: disease state

value: MM at diagnosis

tag: 1q21 status

value: POS


title: Control161


title: K562 Cells, 2000 nM Folic Acid, AICAR, 72hr, 3

first: Naama

last: Kanarek

address: 61 Binney St Rm 1126, Enders Building

department: Pathology

institute: Boston Children's Hospital

data_processing:
quality control was performed via fastQC
Reads were mapped to the mouse or human transcriptome using STAR aligner
Transcript quantification was performed using RSEM
Transcript abundance was imported into R using tximport
differential gene expression analysis was performed using DeSeq2
Assembly: hg38 and mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: K562 and MEL were maintained in RPMI + 10% fetal bovine serum (FBS) with antibiotics in humidified incubator at 37C and 5% CO2. Two dyas prior to experiment start, K562 and MEL cells were switched to folate free RPMI + 10% dialyzed FBS + 2,000 nM folic acid with antibiotics.

extract_protocol:
Rnazol RT (Sigma) was used to harvest RNA from cell samples.
Azenta Life Sciences prepared libraries

treatment_protocol: At t=0, cells were plated at 100,000 cells / mL in folate free RPMI + 10% dialyzed FBS + 2,000 nM or 100 nM folic acid. Treatment was performed with or without SHIN1 (1.25 uM) or AICAR (500 nM).

value: Erythroid Leukemia Cells

value: 2000 nM folic acid + AICAR (500 nM)


title: Bone marrow plasma cells, MM at diagnosis, patient 17

value: NEG


title: Bone marrow plasma cells, MM at diagnosis, patient 16


title: Bone marrow plasma cells, MM at diagnosis, patient 15


title: K562 Cells, 2000 nM Folic Acid, AICAR, 72hr, 2


title: Control126


title: Bone marrow plasma cells, MM at diagnosis, patient 14


title: Control109


title: K562 Cells, 2000 nM Folic Acid, AICAR, 72hr, 1


title: Control092


title: Bone marrow plasma cells, MM at diagnosis, patient 13


title: K562 Cells, 2000 nM Folic Acid, SHIN1, 72hr, 2

value: 2000 nM folic acid + SHIN1 (1.25uM)


title: Control042


title: Control024


title: Control075


title: K562 Cells, 2000 nM Folic Acid, SHIN1, 72hr, 3


title: Control008


title: Control041


title: K562 Cells, 2000 nM Folic Acid, SHIN1, 72hr, 1


title: Control058


title: Control007


title: Control144


title: Bone marrow plasma cells, SMM at diagnosis, patient 11

value: SMM at diagnosis


title: Control143


title: Control160


title: K562 Cells, 100 nM Folic Acid, Vehicle, 72hr, 3

value: 100 nM folic acid + Vehicle


title: Control125


title: K562 Cells, 100 nM Folic Acid, Vehicle, 72hr, 2


title: Bone marrow plasma cells, MM at diagnosis, patient 12


title: Bone marrow plasma cells, MM at diagnosis, patient 11


title: Bone marrow plasma cells, SMM at diagnosis, patient 10


title: Bone marrow plasma cells, MM at diagnosis, patient 10


title: Control108


title: Control074


title: K562 Cells, 100 nM Folic Acid, Vehicle, 72hr, 1


title: Control091


title: Bone marrow plasma cells, SMM at diagnosis, patient 8


title: Control057


title: Control006


title: Control040


title: K562 Cells, 2000 nM Folic Acid, Vehicle, 72hr, 3

value: 2000 nM folic acid + Vehicle


title: K562 Cells, 2000 nM Folic Acid, Vehicle, 72hr, 2


title: Control159

value: Peripheral blood


title: K562 Cells, 2000 nM Folic Acid, Vehicle, 72hr, 1


title: PLC/PRF5 cells, EGR1 overexpression, biol rep 3

city: chongqing

first: Pan

last: Mingang

address: No. 1, Medical College Road, Yuzhong District, Chongqing

institute: ChongQing Medical University

data_processing:
Quantitative analysis of gene expression using StringTie software. StringTie adopts splicing and quantitative synchronization, and its quantitative results are more accurate compared to other methods. FPKM, as an indicator of transcript or gene expression level, refers to the expected number of transcript sequence fragments per thousand base pairs sequenced per million base pairs. The FPKM method can eliminate the influence of differences in gene length and sequencing quantity on calculating gene expression, and the calculated gene expression quantity can be directly used to compare gene expression differences between different products.
Assembly: hg38
Supplementary files format and content: All_gene_fpkm.list.txt: Tab-delimited text file includes gene expression profile based on FPKM method.

growth_protocol: MHCC97H and PLC/PRF5 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. Trizol was mixed with chloroform/isoamyl alcohol (24:1). The mix was shaked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand reaction system by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments with adapters were amplified by PCR, and the products were purified by Ampure XP Beads. The library was assessed quality and quantity using the Agilent 2100 bioanalyzer. Then, undergo DSN treatment. The DSN treated library was assessed quality to ensure the high quality of the sequencing data by two methods: checked the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantified the library using real-time quantitative PCR (qPCR). The qualified library was amplified on cBot to generate the cluster on the flowcell. And the amplified flowcell was sequenced on the Illumina Novaseq 6000 platform (Tsingke-Beijing, China).

value: Hepatocellular carcinoma cells

value: EGR1 overexpression


title: Control124

value: Blood

value: Healthy Control

value: 5-methylcytosine (5-mC) Antibody


title: Control090


title: Control107


title: Control023


title: Bone marrow plasma cells, MM at diagnosis, patient 9

value: Bone marrow


title: Control073


title: Control056


title: PLC/PRF5 cells, EGR1 overexpression, biol rep 2


title: Control039


title: Bone marrow plasma cells, SMM at diagnosis, patient 7

value: plasma cells


title: Control142


title: Bone marrow plasma cells, MM at diagnosis, patient 8

value: MM at diagnosis


title: Bone marrow plasma cells, SMM at diagnosis, patient 9


title: Bone marrow plasma cells, MM at diagnosis, patient 6


title: Bone marrow plasma cells, SMM at diagnosis, patient 6


title: Control005


title: Control123


title: PLC/PRF5 cells, control, biol rep 3

value: WT


title: Control141


title: Control158


title: Control089


title: Bone marrow plasma cells, MM at diagnosis, patient 7

value: POS


title: MHCC97H cells, EGR1 knockout, biol rep 3

value: EGR1 knockout


title: PLC/PRF5 cells, control, biol rep 2


title: Control106


title: Control072


title: Bone marrow plasma cells, SMM at diagnosis, patient 5

value: NEG


title: PLC/PRF5 cells, EGR1 overexpression, biol rep 1


title: Control038


title: Control022


title: Control055


title: MHCC97H cells, EGR1 knockout, biol rep 2


title: Bone marrow plasma cells, SMM at diagnosis, patient 4


title: Control021


title: Bone marrow plasma cells, SMM at diagnosis, patient 3


title: Control004


title: MHCC97H cells, EGR1 knockout, biol rep 1


title: PLC/PRF5 cells, control, biol rep 1


title: Control140


title: Control157


title: MHCC97H cells, Parental, biol rep 2


title: Control105


title: MHCC97H cells, Parental, biol rep 3


title: Control122


title: Bone marrow plasma cells, MM at diagnosis, patient 3


title: Control054


title: Control088


title: L7182

city: Leiden

first: Debora

last: Meijer

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Raw RNA-seq data was processed by the RNA-seq BioWDL pipeline using default settings, developed by the SASC (https://biowdl.github.io/, LUMC, Leiden, the Netherlands)
Reads were aligned against hg38 with STAR and expression quantification was performed using HTseq-count
Assembly: hg38
Supplementary files format and content: Tab-delimited tsv file with raw counts for each sample

extract_protocol:
RNA was isolated from tissue sections (thickness = 20 µm) in TRIzol (15596018, Ambion) according to manufacturer’s instructions. RNA purification was performed using RNaesy mini kit (74104, Qaigen) and included DNAse treatment according to manufacturer’s instructions
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the samples.

tag: disease

value: Osteosarcoma

value: tumor

tag: patient id

tag: progression status

value: primary


title: MexEF oprN efflux pump mutant

city: Princeton

first: Connor

last: Chain

address: Lewis Thomas Lab

institute: Princeton University

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.1.5)
Assembly: Read mapping was performed with HISAT21. Read quantification was performed using Subread’s feature Counts2 functionality.
Supplementary files format and content: HISAT2 output is included as Counts.xlsx

organism: Pseudomonas aeruginosa

source_name: bacteria

growth_protocol: Overnight cultures of wildtype PA14 or mutant strains grown 16h in LB broth

extract_protocol:
Cultures were pelleted at 4°C, resuspended in Trizol (Ambion 10296010), and incubated at 65°C before addition of chloroform. The aqueous layer was collected and RNA was isolated using a mirVana RNA extraction kit (ThermoFisher AM1560). DNAse treatment was performed on RNA using recombinant DNase I (Sigma-Aldrich 04716728001).
RNA samples were sent to Seq Center (Pittsburg, PA) for sequencing using the Illumina Stranded RNA library preparation with RiboZero Plus rRNA depletion.
Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

value: bacteria

tag: cell line

value: mexS mutant


title: Control020

value: Peripheral blood

tag: cell type


title: MexCD OprJ efflux pump mutant

value: nfxb mutant


title: Control003

value: Blood


title: Bone marrow plasma cells, MM at diagnosis, patient 2


title: Control037

value: Healthy Control


title: Bone marrow plasma cells, MM at diagnosis, patient 5


title: MHCC97H cells, Parental, biol rep 1

value: Hepatocellular carcinoma cells


title: wiltype

value: wildtype


title: L7179


title: L7181


title: Control156

value: 5-methylcytosine (5-mC) Antibody


title: Control071


title: L7178


title: Control138


title: Bone marrow plasma cells, SMM at diagnosis, patient 2

value: Bone marrow

value: plasma cells

value: SMM at diagnosis


title: G8.N.day3.5_S24

city: Sydney, Chippendale

first: Matthias

last: Windhagauer

state: NSW

address: 745 Harris St

country: Australia

institute: University of Technology Sydney

description: 1x75 bp format

data_processing:
Trimgalore! was used to to trim Fastq files using default parameters.
FastQC was used to for quality control of fastq files pre- and post trimming. Reports were compiled by MultiQC v1.11.
Subsequently the reads were pseudo-aligned to the Phaeodactylum-tricornutum.ASM15095v2 transcriptome using kallisto v0.44.0 to give gene-level counts. Counts were combined for multiple transcripts.
Genes were filtered as follows: at least 10 counts in at least 3 out of 4 replicates.
Assembly: ASM15095v2
Supplementary files format and content: All presented counts are voom-transformed.

organism: Phaeodactylum tricornutum CCAP 1055/1

source_name: PHB pathway harbouring cell line G8

extract_protocol:
A volume relative to 10^8 cells was added to 0.9% NaCl solution (-4°C) and centrifuged for 3 min. Total RNA extraction was done using Trizol aget following the protocol of the RNAeasy mini purification kit (Quiagen).
Samples were converted into libraries using the Illumina stranded mRNA library kit.

tag: time

value: Day 3 post induction

value: diatom

value: PHB pathway expression

tag: treatment

value: N-limitation + P-limitation


title: Control104

tag: tissue


title: L7177

value: Osteosarcoma

value: tumor

value: primary


title: Bone marrow plasma cells, MM at diagnosis, patient 4

value: MM at diagnosis

value: POS


title: Bone marrow plasma cells, SMM at diagnosis, patient 1


title: Control087

value: Peripheral blood

value: Blood

tag: genotype


title: Control053

value: Healthy Control


title: L7039

value: metastasis


title: G8.N.day3.1_S22

description: 1x75 bp format


title: Control019

value: 5-methylcytosine (5-mC) Antibody


title: G8.N.day3.4_S6

description: 1x75 bp format


title: Control155


title: L6621


title: Control121


title: Bone marrow plasma cells, MM at diagnosis, patient 1

value: Bone marrow


title: G8.N.day3.3_S23

description: 1x75 bp format


title: Control002


title: Control036


title: L6647


title: Control103


title: Control137


title: G8.N.day1.5_S15

description: 1x75 bp format

value: Day 1 post induction


title: Control070


title: G8.N.day1.4_S14

description: 1x75 bp format


title: G8.N.day1.3_S13

description: 1x75 bp format


title: G8.N.day1.1_S12

description: 1x75 bp format


title: L6581


title: Control018


title: Control086


title: MDS36


title: Control069


title: G8.day3.4_S5

description: 1x75 bp format

value: P-limitation (standard condition)


title: L6052


title: MDS33


title: Control035


title: Control052


title: L5757


title: L5450


title: L5465


title: MDS24


title: Control001


title: G8.day3.2_S8

description: 1x75 bp format

value: Day 3 post induction


title: G8.day3.1_S20

description: 1x75 bp format

value: diatom


title: G8.day3.9_S21

description: 1x75 bp format

value: PHB pathway expression


title: MDS18


title: G8.day1.9_S11

description: 1x75 bp format


title: Control120


title: MDS12


title: MDS30


title: MDS27


title: MDS09


title: L5164


title: MDS21


title: L5071


title: MDS15


title: L5062


title: G8.day1.4_S10

description: 1x75 bp format


title: G8.day1.1_S4

description: 1x75 bp format


title: MDS38


title: L4281


title: G8.day1.2_S7

description: 1x75 bp format


title: MDS06


title: L3499


title: MDS03


title: L3676

value: recurrence


title: MDS32


title: MDS35


title: MDS17


title: L3309

value: Osteosarcoma


title: MDS29