title: RNAs from non inoculated seed and collected at 6 days after sowing - pad3_water [pad3_water_6d_REP2]

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

description:
At_count.csv
Abra_count.csv

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
SOAPnuke: version：v1.5.2, parameters: -l 15 -q 0.5 -n 0.1, website: https://github.com/BGI-flexlab/SOAPnuke
Transcript mapping against Arabidopsis reference transcriptome Araport v11 using Salmon algorithm
Transcript mapping against Alternaria brassicicola (Abra43) reference transcritome (Belmas et al. 2018) PHFN00000000 (GeneBank number) using Salmon algorithm.
Assembly: Araport11_genes.201606.cdna.fasta downlaoded from arabidopsis.org. abra_mygenomebrowser_011021_mrna.fasta downloaded from GenBank number PHFN00000000 (https://www.ncbi.nlm.nih.gov/nuccore/PHFN00000000)
Supplementary files format and content: tab-delimited text files include count values for each sample

organism: Arabidopsis thaliana

growth_protocol: Seeds were sowed in petri dishes containing 0.8% agarose (SIGMA) and cultures were incubated in a controlled growth chamber for 3, 6 and 10 days under a 16 h photoperiod (170 µmol photons m2 s-1) at 22 °C (light period)/20 °C (dark period) and a constant 70% relative humidity (Ortega-Cuadros et al. 2022)

extract_protocol:
Seeds were collected at 3, 6 and 10 days after sowing. RNA extraction was performed using NucleoSpin® RNA Plus kit (Macherey-Nagel, Düren, Germany) according to the modifications of (Ortega-Cuadros et al. 2022). RNA quantification and quality was measured  with a NanoDrop ND-100 (NanoDrop Technologies, DE, USA) and a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) respectively (Ortega-Cuadros et al. 2022)
RNA samples were sent to Beijing Genomics Institute (BGI)  for cDNA library construction and paired-end sequencing (PE100, 40M) using the DNBseq™ technology

treatment_protocol: Seeds were inoculated with 10⁴ conidia/mL of Abra 43 and seeds imbibed in water, without Alternaria brassicicola  were used as control.

tag: genotype/treatment

value: pad3 non inoculated_6d

tag: developmental stage

value: Collected at 6 days after sowing

value: entire seed


title: Ciprofloxacin (12 ng/mL) 50 min post-treatment; BR 1

status: Public on Mar 26 2024

type: SRA

city: Trondheim

first: Amanda

middle: Holstad

last: Singleton

address: Erling Skjalgsons gate 1

department: Department of Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

library_source: transcriptomic

data_processing:
FASTQ files were generated using bcl2fastq2 Conversion Software v 2.20.0.422. Processing of the sequence data was done with the ProkSeq v 2.0 program using Docker, with the  E. coli K-12 substr. MG1655 reference genome ASM584v2 (RefSeq: GCF_000005845.2) and corresponding reference transcriptome. ProkSeq is a docker based, full RNA-Seq pipeline for prokaryotes, which includes quality assessment, alignment, gene counting, and analysis. The count tables countFile.csv, countFileNucleotideAvgCount.csv and countFile_TPM_CPM.tsv were exported from ProkSeq and used for further analysis.
The sample counts were were analyzed in R using the quasi-likelihood test in EdgeR v 3.36.0 from Bioconductor. Poorly expressed genes were filtered out, and library size was normalized using trimmed mean of M-value (TMM). Differentially expressed genes were defined with FDR < 0.05 and presented as LFC compared to the control.
Assembly: ASM584v2 (RefSeq: GCF_000005845.2)
Supplementary files format and content: The processed data file (countFile.csv) contains the count for each sample of each identified gene.

molecule: total RNA

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

growth_protocol: The E. coli pre-culture was diluted to OD600 = 0.0125. E. coli was grown in cation-adjusted Mueller-Hinton broth in 1 1L Applikon bioreactors as batch culitvation. Stirring was adjusted between 200 and 600 rpm to maintain a dissolved oxygen concentration above 40%. The aeration rate was kept at 500 mL min-1. pH 7 was maintained by automatic titration of 3 M HCl and 4 M NaOH.

extract_protocol:
Transcriptomics was sampled according to the protocol provided with RNeasy Mini kit (Qiagen). The sample volume was based on OD600 at each sampling timepoint to ensure 3.35 x 10^8 cells per sample. The sample was immediately added to 2 volumes of RNA protect and vortexed. After minimum 5 min, the samples were centrifuged (10 min, max rcf). The supernatant was discarded, and the pellet was frozen in N2 (l). RNA was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer's protocol 4 (Enzymatic lysis and Proteinase K digestion of bacteria) and protocol 7 (Purification of total RNA) with on-column Dnase (Qiagen) digestion. The RNA concentration in each sample was measured using NanoDrop-1000 spectrophotometer. Isolated RNA was sent to the Genomics Core Facility at NTNU for further processing and sequencing.
RNA sequencing libraries were prepared using the QIAseq FastSelect 5S/16S/23S kit (Qiagen) for rRNA removal and the QIAseq stranded RNA Lib kit (Qiagen) for library construction, according to the manufacturer's instructions.  Briefly, 500 ng total RNA was used as starting material. Removal of ribosomal RNA (rRNA) was conducted by a combined heat fragmentation (89°C for 7 min) and FastSelect hybridization protocol (75-4°C ramping process) where the FastSelect reagent inhibited reverse transcription of bacterial rRNA. Next, purification was conducted using QIAseq Beads followed by a first-strand synthesis using a RNase H- Reverse Transcriptase (RT) in combination with random primers, a second-strand synthesis, end-repair, A-addition, and adapter ligation. The second-strand synthesis was performed using 5’phosphorylated random primers which enable subsequent strand-specific ligation. DNA fragments were further enriched by CleanStart library amplification (15 cycles of PCR reaction). Finally, the libraries were purified using the QIAseq Beads, quantitated by qPCR using Collibri Library Quantification Kit (Thermo Fisher Scientific), and validated using Perkin Elmer DNA 1K/12K/Hi Sensitivity Assay LabChip on a Labchip GX instrument (Perkin Elmer, USA). The size range of the DNA fragments were measured to be in the range of 270 to 570 bp and peaked around 355 bp. Prior to sequencing, libraries were normalized and pooled to 2.3 pM and subjected to clustering on three NextSeq 500 HO flowcells (Illumina, USA).

treatment_protocol: At OD600 = 0.2, E. coli was treated with 12 ng/mL ciprofloxacin.

tag: strain

tag: genotype

value: WT

tag: treatment

value: Ciprofloxacin 12 ng/mL


title: PFA 33980 | 003 | Full ROI

city: Woodland

first: Sonny

middle: Ramirez

last: Elizaldi

state: CA

address: County Road 98 and, Hutchison Dr

department: Immunology

country: USA

institute: University of California Davis

description: FFPE Spatial Transcriptome sequencing

data_processing:
Raw sequencing data was processed using Nanostring's GeoMx DSP Control Center
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Library strategy: Spatial Transcriptomics

organism: Macaca mulatta

source_name: Brain - Hippocampus

extract_protocol:
5um sections were cut from Paraformaldehyde-Fixed Paraffin-Embedded slides.  Samples were incubated with either DNA-oligo barcoded RNA-ISH probes or antibodies which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Spatial transcriptome sequencing libraries were prepared with Nanostring reagents according to manufacturer's specifications

treatment_protocol: Rhesus macaques were intravenously inoculated with SIVCL757

tag: tissue

value: Brain - Hippocampus

value: N/A - healthy

tag: panel

value: (v1.0) Human NGS Immune Cell Profiling Protein Core, (v1.0) Human NGS Glial Cell Subtyping Protein, (v1.0) Human NGS Autophagy Protein, (v1.0) Human NGS Parkinson's Pathology Protein, (v1.0) Human NGS Alzheimer's Pathology Extended Protein, (v1.0) Human NGS Alzheimer's Pathology Protein, (v1.0) Human NGS Cell Death Protein, (v1.0) Human NGS Neural Cell Typing Protein, (v1.0) Human NGS PI3K/AKT Signaling Protein, (v1.0) Human NGS Pan-Tumor Protein Module, (v1.0) Human NGS MAPK Signaling Protein, (v1.0) Human NGS Immune Cell Typing Protein Module, (v1.0) Human NGS Immune Activation Status Protein Module, (v1.1) Human NGS IO Drug Target Protein Module, (v1.1) Human NGS Myeloid Module


title: 22Rv1-WT-3-RNA-seq

city: Tianjin

first: Yuyang

last: Qian

state: Tianjin

address: 94 Weijin Road

department: cell and genetic department

country: China

institute: Nankai university

description: 22Rv1 WT vs HKI RNA-seq

data_processing:
Clean reeas of RNA-seq were mapped to hg38 using STAR.RNA-seq datasets were performed using the TOPMed RNA-seq pipeline . Differentially expressed genes were identified using DESeq2 according to default parameters .Genes with an absolute log2 fold change > 1 and an adjusted P-value < 0.05 were considered as differentially expressed ones
Clean reads of ChIRP-seq were mapped to hg38 using STAR. Normalized bigwigs of even, odd, and merged files were generated using the ChIRP-seq processing scripts . Peaks of merged bigwig were called using MACS2, and called peaks were filtered to exclude blacklist regions from ENCODE. Peaks with correlation of even and odd > 0.8, FDR < 0.05, and read coverage > 2-fold of the input were kept as confident HOTAIR target regions.
Clean reads of ChIP-seq and Cut and tag were mapped to hg38 using STAR.Biological replicates that showed a good correlation (Pearson correlation coefficient > 0.8) were merged for downstream analysis, including peak calling and plots.  Peaks for histone modifications were called using MACS2 , peaks for transcription factors were called using SPP.Genomic annotation for called peaks was performed using Homer  with default parameters. Normalized coverage track (bigWig) files were generated using bamCoverage from deepTools.
Assembly: hg38
Supplementary files format and content: xlsx file  include genes counts values and bw files include ChIP, ChIRP, Cut and tag signal peaks for each Sample

organism: Homo sapiens

source_name: 22Rv1_Cell line

growth_protocol: 22Rv1 cell line was cultured in 1640 medium supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
RNA-seq:Total RNA was extracted using TRIzol according to the manufacturer’s instruction. Then, ribosomal RNA was deleted from 5 μg of total extracted RNA using the Ribo-Zero Gold Kit, using Illumina novaseq 6000. ChIRP-seq: Cells were fixed with glutaraldehyde  for 10 min and nucleus was isolated and sheared to 100-500 bp fragments by sonication, then hybridized with DNA probes. Libraries were prepared using the NEBNext DNA library kit according to the manufacturer's instructions (New England BioLabs), using Illumina novaseq 6000. ChIP-sq:Cells were fixed with formaldehyde  for 10 min and nucleus was isolated and sheared to 200-500 bp DNA fragments by sonication, then immunoprecipitated with the corresponding antibodies. Libraries were prepared using the NEBNext DNA library kit according to the manufacturer's instructions (New England BioLabs), using Illumina novaseq 6000. Cut and tag: The experiments were performed using Hyperactive Universal  CUT & Tag Assay Kit (Vazyme, TD901). Briefly, Cells were incubated with Concanavalin A- Coated beads and then incubated with antibody. DNA sequencing library was built by pA-Tn5 transpose, then sequenced by Illumina novaseq 6000.
RNA-seq, ChIRP-seq , ChIP-seq and Cut and tag  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HKI cell lines were acquired by Crispr/Cas9 mediated HOTAIR poly-A knock in .

tag: cell line


title: PFA 33980 | 009 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: Ciprofloxacin (12 ng/mL) 25 min post-treatment; BR 1


title: PFA 33980 | 002 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: RNAs from non inoculated seed and collected at 6 days after sowing - pad3_water [pad3_water_6d_REP1]

description:
At_count.csv
Abra_count.csv


title: 22Rv1-WT-1-RNA-seq

description: 22Rv1 WT vs HKI RNA-seq


title: Ciprofloxacin (12 ng/mL) 10 min post-treatment; BR 1


title: WT, 12 min, biol rep 1 (Sample 46)

city: Würzburg

first: Laura

last: Jenniches

address: Josef-Schneider-Straße 2/D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Adapters were removed with Cutadapt v4.1
Alignment: STAR 2.6.0a (Dobin et al., 2013)
Quantification: htseq-count 2.0.2
Assembly: FQ312003.1, HE654724.1, HE654725.1 and HE654726.1
Supplementary files format and content: counts
Library strategy: RIF-seq

organism: Salmonella enterica subsp. enterica serovar Typhimurium

growth_protocol: Overnight growth from single colonies at 37 °C in LB medium

extract_protocol:
Hot phenol extraction followed by DNase treatment.
RNA-seq libraries were prepared by Vertis AG (Freising-Weihenstephan, Germany). The ribodepleted RNA samples were fragmented using ultrasound (4 pulses of 30 s each at 4 C). Subsequently, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3' adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/ul using a high fidelity DNA polymerase. cDNA was purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics).

treatment_protocol: The cultures were treated with 500µl/ml of rifampicin (stock solution 50mg/ml resuspended in DMSO)

value: 12 min after rif. treatment


title: PFA 33980 | 001 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: PFA 35595 | 012 | Full ROI

description: FFPE Spatial Transcriptome sequencing

value: Chronic SIV CL757 infection


title: RNAs from non inoculated seed and collected at 3 days after sowing - pad3_water [pad3_water_3d_REP2]

description:
At_count.csv
Abra_count.csv

value: pad3 non inoculated_3d

value: Collected at 3 days after sowing


title: WT, 3 min, biol rep 1 (Sample 44)

value: 3 min after rif. treatment


title: RNAs from non inoculated seed and collected at 3 days after sowing - pad3_water [pad3_water_3d_REP1]

description:
At_count.csv
Abra_count.csv


title: PFA 35595 | 011 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: RNAs from non inoculated seed and collected at 6 days after sowing - pad3o_water [pad3_water_6d_REP3]

description:
At_count.csv
Abra_count.csv


title: ΔproQ, 0 min, biol rep 1 (Sample 48)

value: {delta}proQ

value: 0 min after rif. treatment


title: WT, 0 min, biol rep 1 (Sample 43)


title: Ciprofloxacin (12 ng/mL) 1 min pre-treatment; BR 1


title: RNAs from infected seed and collected at 6 days after sowing - pad3_inoc [pad3_inoc_6d_REP3]

description:
At_count.csv
Abra_count.csv

value: pad3 inoculated with Abra43_6d


title: ΔcspCE, 16 min, biol rep 3 (Sample 42)

value: {delta}cspCE

value: 16 min after rif. treatment


title: Hi-C_NeuN-_H4

city: Moscow

first: Ilya

middle: Andreevich

last: Pletenev

address: Bolshoy Boulevard 30, bld. 1

country: Russia

institute: Skoltech

library_source: genomic

data_processing:
Fastq files were preprocessed with trimmomatic (Bolger, A. M., Lohse, M., & Usadel, B., 2014)
Preprocessed files were provided as input for distiller pipeline (https://github.com/open2c/distiller-nf) with default parameters to obtain mcool files(https://github.com/open2c/distiller-nf, v.0.3.3)
Most of the Hi-C analysis was performed on Hi-C matrices merged by cell type. Merging was done at 1 kbp resolution using cooler.merge_coolers() function of a cooler library (Abdennur and Mirny 2020), v.0.8.11.
The resulting merged Hi-C maps were sampled to the equal number of contact pairs using cooltools.sample() function of a cooltools library (Open2C et al. 2022), v.0.5.1.
To avoid possible bias due to Hi-C ligation artifacts, the values at the main diagonal were removed prior to sampling using cooler and custom python code.
Resulting .cool files with Hi-C matrices were ICE normalized (Imakaev et al. 2012) using “cooler balance” command with default parameters.
Assembly: hg38
Supplementary files format and content: *.mcool – Hi-C matrix (see https://github.com/open2c/cooler)
Supplementary files format and content: PC1* - values of an eigenvector that defines compartments
Supplementary files format and content: fithic.h3k27me3.NeuN+.hi-c_merged.res-100kb.bedpe.gz – coordinates of neuronal H3K27me3-enriched polycomb contacts
Supplementary files format and content: Loops* - coordinates of chromatin loops
Supplementary files format and content: TAD_boundaries_* - coordinates of TAD boundaries

molecule: genomic DNA

source_name: Left posterior superior temporal gyrus (Wernicke's area - BA22p)

extract_protocol:
Post-mortem human brain samples were obtained via National BioService Russian Biospecimen CRO (St. Petersburg, Russia). Informed consent for using human tissues for research was obtained in writing form from all donors or their next of kin by the tissue provider bank. Sampled brain tissue of all subjects was defined as healthy by medical pathologists. All subjects had sudden death with no prolonged agony state and had no history of neurologic and psychiatric disorders or alcohol and drug abuse. Post-mortem brain frontal blocks 1-1,5 cm thick were stored at -80°C warped in a foil, in zip-lock packages. For sample dissection, The Atlas of the Human Brain (AHB) (Mai 2016) was used to locate the area of interest, a posterior part of the superior temporal gyrus of the left hemisphere (posterior Brodmann area 22 (BA22p), Wernicke's area). Frontal blocks with surfaces nearest to AHB level: 60 (MNI: -36.57; ICL: 34.82; MCP: 20.08) were placed into the cryostat Leica CM1950 chamber with -20°C before dissection for 15-20 min on custom-made aluminum support. A tissue piece of approximately 150 mg weight was cut out from a selected area using a metal scalpel. Dissected samples were then collected with tweezers, put into tubes, and placed in dry ice immediately. All materials used during dissection (scalpels, tweezers, tubes) were sterile and chilled using dry ice before use.
Preparation of bulk Hi-C libraries from 11 samples of human brain tissue was performed as previously described (Lieberman-Aiden et al. 2009; Ulianov et al. 2016) with optimal changes to brain tissue (Eremenko et al. 2021). Approximately 200,000-400,000 sorted nuclei for the sample were lysed in a solution of lysis buffer containing 150 mM Tris-HCI pH7.5-8, 150 mM NaCI, 0.5% (v/v) NP-40, 1% (v/v), Triton-X100, 1x Protease Inhibitor (CALBIOCHEM, #539137) on ice for 15 min, centrifuged at +4 °C 5000g for 7 min, the pellet was resuspended and washed in 1.12Х restriction enzyme DPN II buffer. After the final wash, the pellet suspension in 1.12Х DPN II buffer with added 0.3% SDS has incubated for 60 min 1400 rpm at +37°C. Further, the reaction was quenched with 1.8% Triton X-100 for 60 min at 1400 rpm at +37°C, and the 500U DPN II restriction enzyme was added, the suspension was left overnight at 1400 rpm at +37°C. After that, the additional amount of 200U DPN II restriction enzyme was added to the digested nuclei and incubated for the next 120 min at 1400 rpm at +37°C. After that, the restriction was unactivated at +65°C for 20 min. The digested DNA samples were washed and resuspended in 1.2XNEB2, and after that digested ends were marked with biotin during the incubation in the mix of 1М biotin-14dATP, 10x NEB2, 10mM dCTP, 10mM dGTP, 10mM dTTP, 5U/ul Klenow (NEB #M0210S) for 90 min 900 rpm at +37 °C. The resulting blunt ends were washed with 1X T4 DNA ligase buffer and chromatin fragments were proximally ligated with 50 U T4 DNA ligase (Fermentas) for 6 h 1400 rpm at +37 °C. Then the 0.5% SDS with 20 μg/ml proteinase K was added to samples for overnight incubation at +65 °C. The following step was DNA purification with phenol–chloroform extraction and precipitation with 2.5 volumes of 96% ethanol, 0.1 volumes of 3M sodium acetate, 20 μg/ml glycogen, and 9.4 μg/ml tRNA for 60 min at −80 °C. After the centrifugation step at 20000g for 20 min, +4°C the pellet was dissolved in 10 mM Tris-HCl pH 8.0 with the addition of RNase A and incubated for 45 min at +37°C. The next step was DNA sample purification on 2.5 volumes of magnetic AMPure XP beads with the following DNA elution in 10 mM Tris-HCl for 15 min at +55°C. Eluted DNA was fragmented by sonication with Power 15 regime, 4 repeats for 30 s with 3 min break. Sonicated DNA samples were then concentrated on Amicon columns 14000g/5 min with double 10 10 mM Tris-HCl pH 8.0 washing. The resulting biotin-marked fragments were isolated using Dynabeads MyOne Streptavidin C1 (Invitrogen #65001) and diluted in TWB buffer (1M Tris-HCl pH 8.0, 50 mM EDTA, 5M NaCl, 1% Tween). All subsequent steps were performed on that bead-bound DNA fraction including DNA ends repair with repair mix (10Х ligase NEB buffer, 10 mM dNTP mix, T4 DNA Pol, T4 PNK, 1 ul Klenow) for 30 min at room temperature, and PolyA tail adding reaction with a mix containing 10Х NEB2, 10 mМ dATP, Klenow (exo-) and incubation for 30 min at +37°C and then for 20 min at +65°C. Then beads were washed with 1X T4 ligase buffer for 3 min at room temperature 900 rpm, and the ligation reaction was performed with a ligation mix of 10X T4 ligase buffer, adapter, 5 U T4 ligase (Fermentas) for 2.5 h at room temperature. Finally, libraries were PCR amplified using Illumina  forward  and reverse primers and KAPA HiFi HotStart for 16 cycles to select the appropriate cycle for amplified DNA fragments collection (the 6, 9, 12, and 15 cycles were collected and checked for DNA quantity on chosen cycle). Last, up to the chosen number of cycles Hi-C libraries were PCR amplified, and resulting fragments were purified using 1.5 volumes AMPure XP magnetic beads.

tag: cell type

value: NeuN-


title: Ciprofloxacin (12 ng/mL) 1 min post-treatment; BR 1


title: RNAs from infected seed and collected at 6 days after sowing - pad3_inoc [pad3_inoc_6d_REP2]

description:
At_count.csv
Abra_count.csv

value: Collected at 6 days after sowing

value: entire seed


title: PFA 35595 | 009 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: RNAs from infected seed and collected at 6 days after sowing - pad3_inoc [pad3_inoc_6d_REP1]

description:
At_count.csv
Abra_count.csv


title: ΔcspCE, 8 min, biol rep 3 (Sample 41)

value: 8 min after rif. treatment


title: Hi-C_NeuN-_H3

value: Left posterior superior temporal gyrus (Wernicke's area - BA22p)


title: PFA 35595 | 008 | Full ROI

description: FFPE Spatial Transcriptome sequencing

value: Brain - Hippocampus


title: RNAs from non inoculated seed and collected at 3 days after sowing - pad3_water [pad3_water_3d_REP3]

description:
At_count.csv
Abra_count.csv


title: 22Rv1-WT-2-RNA-seq

description: 22Rv1 WT vs HKI RNA-seq


title: Hi-C_NeuN-_H2


title: RNAs from infected seed and collected at 3 days after sowing - pad3_inoc [pad3_inoc_3d_REP3]

description:
At_count.csv
Abra_count.csv

value: pad3 inoculated with Abra43_3d


title: Hi-C_NeuN-_H1


title: ΔcspCE, 2 min, biol rep 3 (Sample 39)

value: 2 min after rif. treatment


title: WT, 6 min, biol rep 1 (Sample 45)

value: WT

value: 6 min after rif. treatment


title: ΔcspCE, 4 min, biol rep 3 (Sample 40)

value: 4 min after rif. treatment


title: PFA 35595 | 007 | Full ROI

description: FFPE Spatial Transcriptome sequencing

value: Chronic SIV CL757 infection

value: (v1.0) Human NGS Immune Cell Profiling Protein Core, (v1.0) Human NGS Glial Cell Subtyping Protein, (v1.0) Human NGS Autophagy Protein, (v1.0) Human NGS Parkinson's Pathology Protein, (v1.0) Human NGS Alzheimer's Pathology Extended Protein, (v1.0) Human NGS Alzheimer's Pathology Protein, (v1.0) Human NGS Cell Death Protein, (v1.0) Human NGS Neural Cell Typing Protein, (v1.0) Human NGS PI3K/AKT Signaling Protein, (v1.0) Human NGS Pan-Tumor Protein Module, (v1.0) Human NGS MAPK Signaling Protein, (v1.0) Human NGS Immune Cell Typing Protein Module, (v1.0) Human NGS Immune Activation Status Protein Module, (v1.1) Human NGS IO Drug Target Protein Module, (v1.1) Human NGS Myeloid Module


title: Hi-C_NeuN+_H4

value: NeuN+


title: RNAs from infected seed and collected at 3 days after sowing - pad3_inoc [pad3_inoc_3d_REP2]

description:
At_count.csv
Abra_count.csv

value: Collected at 3 days after sowing


title: ΔcspCE, 0 min, biol rep 3 (Sample 38)

value: {delta}cspCE

value: 0 min after rif. treatment


title: RNAs from infected seed and collected at 3 days after sowing - pad3_inoc [pad3_inoc_3d_REP1]

description:
At_count.csv
Abra_count.csv


title: PFA 35595 | 005 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: WT, 16 min, biol rep 3 (Sample 37)

value: 16 min after rif. treatment


title: PFA 35595 | 006 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: Hi-C_NeuN+_H3


title: PFA 35595 | 010 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: RNAs from non inoculated seed and collected at 6 days after sowing - qko_water [qko_water_6d_REP3]

description:
At_count.csv
Abra_count.csv

value: qko non inoculated_6d

value: Collected at 6 days after sowing


title: Hi-C_NeuN+_H2


title: PFA 35595 | 004 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: WT, 8 min, biol rep 3 (Sample 36)

value: 8 min after rif. treatment


title: RNAs from non inoculated seed and collected at 6 days after sowing - qko_water [qko_water_6d_REP2]

description:
At_count.csv
Abra_count.csv

value: entire seed


title: Untreated control 50 min post-treatment; BR 1

value: Untreated control


title: PFA 35595 | 003 | Full ROI

description: FFPE Spatial Transcriptome sequencing

value: Brain - Hippocampus


title: WT, 4 min, biol rep 3 (Sample 35)


title: RNAs from non inoculated seed and collected at 6 days after sowing - qko_water [qko_water_6d_REP1]

description:
At_count.csv
Abra_count.csv


title: E14 paused 3

city: Munich

first: Francisca

last: Rojas Ringeling

address: Feodor-Lynen-Straße 25, 81377

department: Biochemistry

institute: Ludwig Maximilian University of Munich

library_source: other

data_processing:
Alignment of reads to the genome with the mapper.pl script from MirDeep2 version 2.0.1.2 (options -j -l 17)
Quantification of miRNas with the miRDeep2.pl script, providing the aligned collapsed reads sequences, the mature miRNAs sequence from the organism, the precursor sequences from the organism, as well as precursor sequences from Rattus norvegicus and Homo sapiens.
Assembly: GRCm38
Supplementary files format and content: Tabular separated file, one column for miRNA identifier, one column for counts

molecule: other

organism: Mus musculus

source_name: ESC

extract_protocol:
Small RNA was extracted using miRNeasy kit (Qiagen, 217004).In brief, the cell pellet was homogenized in Qiazol and incubated on a benchtop for 5 min. Chloroform was added to the homogenate and was shaken vigorously for 15 sec and incubated at room temperature for 3 min. The homogenate was centrifuged at 12000 g for 15 mins at 4C.. To the aqueous layer, 70% ethanol was added and shaken vigorously. The sample was then pipetted into RNeasy Mini spin column and centrifuged at room temperature. The flow-through contains the miRNA and other small RNA. To the flow-through, 100% ethanol was added and shaken vigorously. The sample was pipetted into a RNeasy MinElute spin column (Qiagen Cat No: 74204). The column was washed with buffers RWT, RPE and 80% ethanol. Small RNAs were extracted in 14ul of RNase free water.
10 ng RNA was used as input. Small RNA libraries were prepared using the SMARTer smRNA-seq Kit for Illumina (Takara, 635031) with 12 amplification cycles followed by bead size selection (ratio 0.95x-0.7x), followed by an additional clean-up step with the bead to sample ratio of 0.95x. Library QC was done using Qubit and BioAnalyzer and the final libraries were quantified using KAPA Library Quantification Kit (Roche, 07960140001 ). Libraries were diluted to 2 nM final concentration for pooling. Pooled libraries were sequenced on a HiSeq4000 flowcell with single-end 75 bp reads to get ~15M reads per sample.

value: ESC

value: mTOR inhibited pause


title: WT, 2 min, biol rep 3 (Sample 34)

value: WT

value: 2 min after rif. treatment


title: RNAs from non inoculated seed and collected at 3 days after sowing - qko_water [qko_water_3d_REP3]

description:
At_count.csv
Abra_count.csv

value: qko non inoculated_3d


title: E14 WT rep 3

value: wt


title: PFA 35595 | 002 | Full ROI

description: FFPE Spatial Transcriptome sequencing

value: Chronic SIV CL757 infection

value: (v1.0) Human NGS Immune Cell Profiling Protein Core, (v1.0) Human NGS Glial Cell Subtyping Protein, (v1.0) Human NGS Autophagy Protein, (v1.0) Human NGS Parkinson's Pathology Protein, (v1.0) Human NGS Alzheimer's Pathology Extended Protein, (v1.0) Human NGS Alzheimer's Pathology Protein, (v1.0) Human NGS Cell Death Protein, (v1.0) Human NGS Neural Cell Typing Protein, (v1.0) Human NGS PI3K/AKT Signaling Protein, (v1.0) Human NGS Pan-Tumor Protein Module, (v1.0) Human NGS MAPK Signaling Protein, (v1.0) Human NGS Immune Cell Typing Protein Module, (v1.0) Human NGS Immune Activation Status Protein Module, (v1.1) Human NGS IO Drug Target Protein Module, (v1.1) Human NGS Myeloid Module


title: PFA 35595 | 001 | Full ROI

description: FFPE Spatial Transcriptome sequencing


title: WT, 0 min, biol rep 3 (Sample 33)


title: RNAs from non inoculated seed and collected at 3 days after sowing - qko_water [qko_water_3d_REP2]

description:
At_count.csv
Abra_count.csv

value: Collected at 3 days after sowing


title: E14 paused 2


title: ΔcspCE, 16 min, biol rep 2 (Sample 32)

value: {delta}cspCE


title: ΔcspCE, 8 min, biol rep 2 (Sample 31)


title: E14 WT rep 2


title: RNAs from non inoculated seed and collected at 3 days after sowing - qko_water [qko_water_3d_REP1]

description:
At_count.csv
Abra_count.csv


title: RNAs from infected seed and collected at 6 days after sowing - qko_inoc [qko_inoc_6d_REP3]

description:
At_count.csv
Abra_count.csv

value: qko inoculated with Abra43_6d


title: E14 WT rep 1


title: ΔcspCE, 2 min, biol rep 2 (Sample 29)


title: E14 paused 1


title: RNAs from infected seed and collected at 6 days after sowing - qko_inoc [qko_inoc_6d_REP1]

description:
At_count.csv
Abra_count.csv


title: ΔcspCE, 0 min, biol rep 2 (Sample 28)

value: 0 min after rif. treatment


title: TS paused 3

source_name: TSC

value: TSC


title: Hi-C_NeuN+_H1

value: Left posterior superior temporal gyrus (Wernicke's area - BA22p)

value: NeuN+


title: WT, 16 min, biol rep 2 (Sample 27)

value: 16 min after rif. treatment


title: RNAs from infected seed and collected at 3 days after sowing - qko_inoc [qko_inoc_3d_REP2]

description:
At_count.csv
Abra_count.csv

value: qko inoculated with Abra43_3d

value: entire seed


title: TS WT rep 3


title: RNAs from infected seed and collected at 6 days after sowing - qko_inoc [qko_inoc_6d_REP2]

description:
At_count.csv
Abra_count.csv

value: Collected at 6 days after sowing


title: RNAs from infected seed and collected at 3 days after sowing - qko_inoc [qko_inoc_3d_REP1]

description:
At_count.csv
Abra_count.csv


title: TS paused 2

value: mTOR inhibited pause


title: WT, 8 min, biol rep 2 (Sample 26)

value: WT

value: 8 min after rif. treatment


title: TS WT rep 2


title: RNAs from infected seed and collected at 3 days after sowing - qko_inoc [qko_inoc_3d_REP3]

description:
At_count.csv
Abra_count.csv


title: WT, 4 min, biol rep 2 (Sample 25)

value: 4 min after rif. treatment


title: RNAs from non inoculated seed and collected at 10 days after sowing - cyp_water [cyp_water_10d_REP3]

description:
At_count.csv
Abra_count.csv

value: cyp non inoculated_10d

value: Collected at 10 days after sowing


title: WT, 2 min, biol rep 2 (Sample 24)

value: 2 min after rif. treatment


title: TS paused 1


title: RNAs from non inoculated seed and collected at 10 days after sowing - cyp_water [cyp_water_10d_REP2]

description:
At_count.csv
Abra_count.csv


title: WT, 0 min, biol rep 2 (Sample 23)


title: ΔcspCE, 16 min, biol rep 1 (Sample 22)

value: {delta}cspCE


title: TS WT rep 1


title: RNAs from non inoculated seed and collected at 10 days after sowing - cyp_water [cyp_water_10d_REP1]

description:
At_count.csv
Abra_count.csv


title: RNAs from non inoculated seed and collected at 6 days after sowing - cyp_water [cyp_water_6d_REP3]

description:
At_count.csv
Abra_count.csv

value: cyp non inoculated_6d


title: ΔcspCE, 8 min, biol rep 1 (Sample 21)


title: RNAs from non inoculated seed and collected at 6 days after sowing - cyp_water [cyp_water_6d_REP2]

description:
At_count.csv
Abra_count.csv


title: ΔcspCE, 4 min, biol rep 2 (Sample 30)


title: ΔcspCE, 4 min, biol rep 1 (Sample 20)


title: RNAs from non inoculated seed and collected at 6 days after sowing - cyp_water [cyp_water_6d_REP1]

description:
At_count.csv
Abra_count.csv


title: D1_S25_L004

city: Denver

first: Nathan

last: Jackson

state: CO

address: 1400 Jackson St.

department: Center for Genes, Environment, and Health

institute: National Jewish Health

data_processing:
Raw sequencing reads were trimmed using skewer (v0.2.2) with the following parameters: end-quality=15, mean-quality=25, min=30.
Read alignment to the human reference genome GRCh38 was performed using HISAT2 (v2.1.0) with default parameters.
Gene quantification was performed using htseq-count (v0.9.1) and GRCh38 Ensemble v84 gene transcript model with the following parameters: stranded=reverse, a=20, mode=intersection-nonempty.
Assembly: hg38
Supplementary files format and content: count.matrix.hgnc.ENS84.txt contains raw gene counts based on the data processing above.

source_name: skin

growth_protocol: Normal human embryonic keratinocytes (NHEK) were cultured in EpiLife medium containing 1.3 mM CaCl2 for 3 days.

extract_protocol:
RNA extractions performed using the Qiagen RNeasy Kit.
Whole transcriptome libraries were constructed using the KAPA mRNA HyperPrep library kit (Roche Sequencing and Life Science, Kapa Biosystems, Wilmington, MA) from 250ng of total input RNA with the Beckman Coulter Biomek FXP automation system (Beckman Coulter, Fullerton, CA) according to the manufacturers protocol. Barcoded libraries were pooled and sequenced using 150bp paired-end reads on the Illumina NovaSeq 6000 system (Illumina, San Diego, CA).

treatment_protocol: Differentiated NHEKs were treated with 200 ng/ml of IL-36-gamma (R&D systems) for 2 days.

value: skin

value: Epidermis


title: D2_S26_L004


title: D12_IL36R_S30_L004


title: D3_S27_L004


title: D11_IL36R_S29_L004


title: ΔcspCE, 2 min, biol rep 1 (Sample 19)


title: STEMI-Patients without Cardiogenic shock 6

type: RNA

city: Barcelona

first: Lina

last: Badimon

state: BARCELONA

address: Carrer de Sant Antoni Maria Claret, 167

department: ICCC-Cardiovascular Program

country: Spain

institute: Research Institut- HSCSP

description: Circulating miRNA data in Non-cardiogenic shock state

hyb_protocol: Hybridization was performed on Affymetrix miRNA 4.0 arrays and cartridges were incubated at 48°C with 60 rpm rotation for 48 h using Affymetrix Hybridization Oven 600. After, each array was washed and stained using the FS450_002 fluidics script in Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by using the GeneChip scanner 3000 7G System

data_processing: The data were explored using the Transcriptome Analysis Console software (TAC 4.0) for data summarization and normalization by RMA+DABG procedure (implemented in TAC 4.0 software).

label: Biotin

source_name: Plasma

label_protocol: We used Affymetrix FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, Rev3) to label 8 ul of total RNA isolated with miRNeasy Serum/Plasma Advanced Kit (Qiagen Inc) from each sample, according to manufacturers instructions. RNA quantitation was not considered due to low levels of total RNA isolated from plasma.

growth_protocol: STEMI-patients plasma (200uL) was used for isolation of circulating miRNAs

extract_protocol: To isolate plasma miRNAs, we used plasma from STEMI-patients and miRNeasy Serum/Plasma Advanced Kit (Qiagen Inc), according to manufacturer’s instructions.

treatment_protocol: No treatment

tag: follow-up period

value: STEMI-patients with or without Cardiogenic shock within 30-days follow-up period after hospitalization

tag: stemi-condition

value: Non-Cardiogenic shock (Non-CS)

tag: Sex

value: Female

tag: age


title: STEMI-Patients without Cardiogenic shock 9


title: RNAs from non inoculated seed and collected at 3 days after sowing - cyp_water [cyp_water_3d_REP2]

description:
At_count.csv
Abra_count.csv

value: cyp non inoculated_3d

value: Collected at 3 days after sowing


title: ΔcspCE, 0 min, biol rep 1 (Sample 18)

value: 0 min after rif. treatment


title: STEMI-Patients without Cardiogenic shock 8

value: Male


title: D10_IL36R_S28_L004


title: STEMI-Patients without Cardiogenic shock 5


title: WT, 16 min, biol rep 1 (Sample 17)

value: WT

value: 16 min after rif. treatment


title: RNAs from non inoculated seed and collected at 3 days after sowing - cyp_water [cyp_water_3d_REP1]

description:
At_count.csv
Abra_count.csv

value: entire seed


title: STEMI-Patients without Cardiogenic shock 10


title: RNAs from infected seed and collected at 10 days after sowing - cyp_inoc [cyp_inoc_10d_REP3]

description:
At_count.csv
Abra_count.csv

value: cyp inoculated with Abra43_10d


title: WT, 8 min, biol rep 1 (Sample 16)

value: 8 min after rif. treatment


title: ∆BOV_1602_SDS replicate 3 [1602_453_S36]

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
CLC Genomic Workbench 21.0.4
Paired-end sequences were mapped to NC_009504 and NC_009505 using CLC Genomic Workbench (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
RPKM, TPM, CPM, and total counts of each replicate was calculated using the gene expression tool in CLC Genomic Workbench
Assembly: NC_009504 and NC_009505
Supplementary files format and content: excel file, contains RPKM, TPM, CPM, and total counts of each replicate

organism: Brucella ovis

source_name: B. ovis cells

growth_protocol: B. ovis strains were grown on TSAB for 2 days. Cells were collected in Brucella broth and OD600 was adjusted to 0.3 x 10-3. 200 uL of cells were plated onto TSAB and spread evenly with sterile cotton swabs. WT and ∆BOV_1602 grown on TSAB were incubated for 3 days.

extract_protocol:
Cells were collected from plates and resuspended in 1 mL TRIzol. Samples were stored at -80˚C until RNA extraction.  To extract the RNA, samples were thawed and incubated at 65˚C for 10 minutes. 200 µl of chloroform was added to each sample and mixed by vortexing for 15 seconds. Samples were then incubated at room temperature for 5 minutes. Samples were spun at 17,000 x g for 15 minutes at 4˚C and the aqueous layer was collected. Sample was mixed with 500 µl isopropanol and stored at -20˚C for 2h. After thawing, samples were spun down at 13, 300 x g for 30 minutes at 4˚C. Supernatants were discarded and 1 ml of ice cold 70% ethanol was added. Samples were spun down at 13,300 x g at 4˚C for 5 minutes. Supernatants were discarded and pellets were let completely dry. 100 µl RNAse-free H2O was added to each sample and incubated at 60˚C for 10 minutes. RNA samples were cleaned up using RNeasy Mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina Stranded RNA library preparation with RiboZero Plus rRNA depletion.

treatment_protocol: B. ovis strains were grown on TSAB for 2 days. Cells were collected in Brucella broth and OD600 was adjusted to 0.3 x 10-3. 200 uL of cells were plated onto TSAB + 0.004% SDS and spread evenly with sterile cotton swabs. ∆BOV_1602 grown on TSAB + 0.004% SDS were incubated for 3 days. WT grown on TSAB + 0.004% SDS were incubated for 4 days.

value: B. ovis cells

value: BOV_1602 deletion mutant


title: ∆BOV_1602_SDS replicate 2 [1602_452_S35]


title: STEMI-Patients without Cardiogenic shock 2


title: STEMI-Patients without Cardiogenic shock 3


title: WT, 4 min, biol rep 1 (Sample 15)

value: 4 min after rif. treatment


title: STEMI-Patients without Cardiogenic shock 7


title: ∆BOV_1602_SDS replicate 1 [1602_451_S34]


title: RNAs from infected seed and collected at 10 days after sowing - cyp_inoc [cyp_inoc_10d_REP2]

description:
At_count.csv
Abra_count.csv

value: Collected at 10 days after sowing


title: RNAs from non inoculated seed and collected at 3 days after sowing - cyp_water [cyp_water_3d_REP3]

description:
At_count.csv
Abra_count.csv


title: RNAs from infected seed and collected at 10 days after sowing - cyp_inoc [cyp_inoc_10d_REP1]

description:
At_count.csv
Abra_count.csv


title: WT, 2 min, biol rep 1 (Sample 14)

value: 2 min after rif. treatment


title: WT_SDS replicate 3 [WT_450_S33]


title: RNAs from infected seed and collected at 6 days after sowing - cyp_inoc [cyp_inoc_6d_REP3]

description:
At_count.csv
Abra_count.csv

value: cyp inoculated with Abra43_6d

value: Collected at 6 days after sowing


title: WT, 0 min, biol rep 1 (Sample 13)


title: RNAs from infected seed and collected at 6 days after sowing - cyp_inoc [cyp_inoc_6d_REP2]

description:
At_count.csv
Abra_count.csv


title: WT_SDS replicate 1 [WT_448_S31]


title: WT_SDS replicate 2 [WT_449_S32]


title: ∆BOV_1602 replicate 3 [1602_444_S27]


title: Muscle, SAX4

city: Durham

first: Paul

last: Rosenberg

state: North Carolina

address: Research Drive

department: Medicine

institute: DUMC

data_processing:
CLC Genomics Workbench
Assembly: mm10
Supplementary files format and content: raw counts
Supplementary files format and content: RPKM for each sample

source_name: Muscle

extract_protocol:
RNA easy kit
SMARTER RNA prep kit

value: Muscle

value: Sax


title: STEMI-Patients without Cardiogenic shock 1

value: STEMI-patients with or without Cardiogenic shock within 30-days follow-up period after hospitalization

value: Non-Cardiogenic shock (Non-CS)

value: Female


title: RNAs from infected seed and collected at 6 days after sowing - cyp_inoc [cyp_inoc_6d_REP1]

description:
At_count.csv
Abra_count.csv


title: Muscle, SAX3


title: Muscle, SAX2


title: STEMI-Patients without Cardiogenic shock 4

value: Male


title: STEMI-Patients with Cardiogenic shock 8

description: Circulating miRNA data in Cardiogenic shock state

value: Cardiogenic shock (CS)


title: STEMI-Patients with Cardiogenic shock 9


title: ∆BOV_1602 replicate 2 [1602_443_S26]


title: STEMI-Patients with Cardiogenic shock 10


title: RNAs from infected seed and collected at 3 days after sowing - cyp_inoc [cyp_inoc_3d_REP3]

description:
At_count.csv
Abra_count.csv

value: cyp inoculated with Abra43_3d

value: Collected at 3 days after sowing

value: entire seed


title: Muscle, SAX1


title: ∆BOV_1602 replicate 1 [1602_442_S25]

value: B. ovis cells


title: STEMI-Patients with Cardiogenic shock 6


title: RNAs from infected seed and collected at 3 days after sowing - cyp_inoc [cyp_inoc_3d_REP2]

description:
At_count.csv
Abra_count.csv


title: Muscle, WT4

value: WT


title: WT replicate 3 [WT_441_S24]


title: RNAs from infected seed and collected at 3 days after sowing - cyp_inoc [cyp_inoc_3d_REP1]

description:
At_count.csv
Abra_count.csv


title: STEMI-Patients with Cardiogenic shock 7


title: STEMI-Patients with Cardiogenic shock 4


title: Muscle, WT3


title: Muscle, WT2


title: WT replicate 2 [WT_440_S23]


title: WT replicate 1 [WT_439_S22]


title: STEMI-Patients with Cardiogenic shock 5


title: Control RNA14-TAP_2h

city: Umea

first: ALEXANDER

last: VERGARA

address: Historiegrand 9, 1002

department: Physics

country: Sweden

institute: Umea University

description: Control for Rna14-TAP_U1_2h

data_processing:
Reads were mapped using Bowtie2 to the sacCer3 reference genome. After mapping of reads, we called narrow peaks at an average fragment size of 300 bp and an FDR value < 0.05
ChIP-seq using an untagged wild type strain was used as control for peak calling and enrichment analyses
Assembly: sacCer3
Supplementary files format and content: bigwig files (narrow peaks)

organism: Saccharomyces cerevisiae

growth_protocol: For experiments using cells at different growth phases, single colonies of Saccharomyces cerevisiae BY4742 cells were inoculated into 10 ml of YPD medium (1% yeast extract, 2% bacto-peptone and 2% glucose), precultivated in YPD at 30 ◦C, diluted in fresh YPD to an OD600nm of 0.1 to 0.15 and cultivated for 2 h at 30 ºC after which the first samples (labelled 0 h in the figures) were harvested. Subsequent samples were harvested at 2 h, 4 h and 6 h after the 0 h point

extract_protocol:
Cell lysis and separation of chromatin fractions were performed using the standard protocol Svejstrup et al., (2003), except that we used ammonium sulfate to 0.5 M final concentration instead of 1 M to release chromatin-associated proteins, as we have described previously
DNA fragments were then cleaned using the ChIP DNA clean & concentratorTM kit (ZYMO RESEARCH). Aliquots of 1 to 2 ng of DNA from each sample were tested for proper shearing using a fragment analyzer (Agilent 2100 Bioanalyzer G2938C), and then sent for library preparation using the SMARTer ThruPLEX kit and subsequent pair-ended sequencing using Illumina NovaSeq S4-200 cycle flow cells in individual lanes.

value: Wt

tag: chip antibody

value: IgG

tag: time (hrs)


title: STEMI-Patients with Cardiogenic shock 2


title: Input for CenH3 ChIP-seq in episuppressor 3-75 biol Rep2

status: Public on Mar 25 2024

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

data_processing:
For ChIPseq: Adapter trimming with cutadapt, mapping with Bowtie2 and bigwigs generated with Deeptools.
For ONT: Base calling was performed with dorado, reads were aligned with minimap2 and consensus methylation calls were produced with modkit. Methylaiton ratios were extracted with bedtools and converted to bigwigs with UCSC tools.
Assembly: ColCEN v1.2
Supplementary files format and content: For ChIPseq: Bigwig files representating log fold change of count per million IP/Input for each biological replicate or normalized coverage for Inputs.
Supplementary files format and content: For ONT: Bigwigs files of scaled methylation ratio [0-1] at each cytosine, with ratios on the negative strand being multiplied by -1. One file for each sequence context: CG (.cpg), CHG (.chg) and CHH (.chh).

source_name: seedlings

growth_protocol: Plants were grown on MS media for ChIPseq and on soil for ONT sequencing.

extract_protocol:
ChIP was performed as previously described (Inagaki et al., 2017). Genomic DNA was extracted with Qiagen Dneasy Plant for ONT.
ChIP-seq libraries were made with NEBNext Ultra II DNA Library Prep Kit. ONT libraries were made with ONT SQK-NBD114.24 Ligation sequencing
ChIP-seq and direct methylation sequencing (WGS)

treatment_protocol: Crosslinking with 1% FA followed by quencing with 0.125M Glycine

value: seedlings

tag: background

value: episuppressor 3-75

value: crosslinking


title: STEMI-Patients with Cardiogenic shock 3


title: Input for CenH3 ChIP-seq in ddm1;rdr1;rdr2;rdr6 ATHILA-hp5 biol Rep2

value: ddm1;rdr1;rdr2;rdr6 ATHILA-hp5


title: CenH3 ChIP-seq in episuppressor 3-75 biol Rep2

value: anti-CenH3 (Talbert et al. 2002)


title: Muscle, WT1

value: Muscle


title: CenH3 ChIP-seq in episuppressor 3-75 biol Rep1


title: Input for CenH3 ChIP-seq in ddm1;rdr1;rdr2;rdr6 ATHILA-hp5biol Rep1


title: CenH3 ChIP-seq in ddm1;rdr1;rdr2;rdr6 ATHILA-hp5 biol Rep2


title: CenH3 ChIP-seq in ddm1;rdr1;rdr2;rdr6 ATHILA-hp5 biol Rep1


title: CenH3 ChIP-seq in ddm1;rdr1;rdr2;rdr6 biol Rep2


title: Input for CenH3 ChIP-seq in ddm1;rdr1;rdr2;rdr6 biol Rep1


title: CenH3 ChIP-seq in ddm1;rdr1;rdr2;rdr6 biol Rep1


title: Input for CenH3 ChIP-seq in ddm1;rdr1;rdr2 biol Rep2


title: Input for CenH3 ChIP-seq in ddm1;rdr1;rdr2 biol Rep1


title: STEMI-Patients with Cardiogenic shock 1

value: STEMI-patients with or without Cardiogenic shock within 30-days follow-up period after hospitalization


title: CenH3 ChIP-seq in rdr1;rdr2;rdr6 biol Rep2


title: CenH3 ChIP-seq in ddm1;rdr1;rdr2 biol Rep1


title: Input for CenH3 ChIP-seq in rdr1;rdr2;rdr6 biol Rep2


title: Rna14-TAP_2h

description: Rna14-TAP TAP-Ab 2h


title: CenH3 ChIP-seq in ddm1;rdr1;rdr2 biol Rep2


title: CenH3 ChIP-seq in rdr1;rdr2;rdr6 biol Rep1


title: Input for CenH3 ChIP-seq in rdr1;rdr2;rdr6 biol Rep1


title: Input for CenH3 ChIP-seq in episuppressor 3-75 biol Rep1


title: Input for CenH3 ChIP-seq in WT biol Rep1

value: wild-type


title: CenH3 ChIP-seq in WT biol Rep1


title: Input for H3K9me2 ChIP-seq in ddm1;rdr1;rdr2;rdr6 ATHILA-hp5 biol Rep2


title: CenH3 ChIP-seq in WT biol Rep2


title: H3K9me2 ChIP-seq in ddm1;rdr1;rdr2;rdr6 ATHILA-hp5 biol Rep2

value: anti-H3K9me2 (abcam ab1220)


title: H3K9me2 ChIP-seq in ddm1;rdr1;rdr2;rdr6 biol Rep2


title: Input for H3K9me2 ChIP-seq in ddm1;rdr1;rdr2;rdr6 biol Rep2


title: Input for CenH3 ChIP-seq in ddm1;rdr1;rdr2;rdr6 biol Rep2


title: H3K9me2 ChIP-seq in ddm1;rdr1;rdr2;rdr6 biol Rep1


title: H3K9me2 ChIP-seq in ddm1;rdr1;rdr2;rdr6 ATHILA-hp5 biol Rep1


title: Input for H3K9me2 ChIP-seq in ddm1;rdr1;rdr2;rdr6 ATHILA-hp5biol Rep1


title: Input for H3K9me2 ChIP-seq in ddm1;rdr1;rdr2 biol Rep2


title: H3K9me2 ChIP-seq in ddm1;rdr1;rdr2 biol Rep1


title: H3K9me2 ChIP-seq in ddm1;rdr1;rdr2 biol Rep2


title: Input for H3K9me2 ChIP-seq in rdr1;rdr2;rdr6 biol Rep1


title: Input for H3K9me2 ChIP-seq in ddm1;rdr1;rdr2 biol Rep1


title: Input for H3K9me2 ChIP-seq in ddm1;rdr1;rdr2;rdr6 biol Rep1


title: Brg1cko-2_S24

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Tophat with default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
Assembly: mm10
Supplementary files format and content: format:xls ; Contain the estimated expression values produced by Cufflinks.

source_name: oligodendrocyte

extract_protocol:
RNA from control and Brg1 mutant oligodendrocytes were extracted using TRIZOL (Life Technologies) followed by purification using an RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit.

tag: sample group

value: Mutant

value: p5  pups

value: Brg1 fl/fl; Oli1 cre


title: Brg1cko-1_S23


title: CTRL-2_S22

value: Control

value: Brg1 fl/+


title: CTRL-1_S21


title: H3K9me2 ChIP-seq in rdr1;rdr2;rdr6 biol Rep2


title: DIPG_CSFE17_2D

type: genomic

city: Rome

first: Evelina

last: Miele

address: Viale Baldelli 38

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE17_2D
cell line

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

scan_protocol: Arrays were imaged using iScan Platform using standard recommended Illumina setting

data_processing: GenomeStudio software v2.0

label: Cy3 and Cy5

source_name: cell serum-free early 2D

label_protocol: Standard Illumina Protocol

growth_protocol: Cell lines are cultured in 2D or 3D cultures and in serum- or free serum- media.

extract_protocol: Genomic DNA was extracted with phenol- chloroform and precipitated with isopropanol.

value: diffuse intrinsic pontine glioma cells


title: DIPG_CSFE10_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE10_2D
cell line


title: Input for CenH3 ChIP-seq in WT biol Rep2


title: DIPG_CSFE5a_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE5a_2D
cell line


title: DIPG_CSFE3_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE3_2D
cell line


title: DIPG_CSFL2_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFL2_2D
cell line

source_name: cell serum-free late 2D


title: DIPG_CSFE5b_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE5b_2D
cell line


title: DIPG_CSFE15_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE15_2D
cell line


title: DIPG_CSFE1_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE1_2D
cell line


title: DIPG_CSFE11_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE11_2D
cell line


title: DIPG_CSFE12_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE12_2D
cell line


title: Input for H3K9me2 ChIP-seq in rdr1;rdr2;rdr6 biol Rep2


title: DIPG_CSFL13_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFL13_2D
cell line


title: DIPG_CSFL7_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFL7_2D
cell line


title: DIPG_CSFE8a_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE8a_2D
cell line


title: DIPG_CSFL4_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFL4_2D
cell line


title: DIPG_CSFE6a_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE6a_2D
cell line


title: DIPG_CSFL9b_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFL9b_2D
cell line


title: H3K9me2 ChIP-seq in rdr1;rdr2;rdr6 biol Rep1


title: DIPG_CSFE6b_3D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE6b_3D
cell line

source_name: cell serum-free early 3D


title: DIPG_CSFL13_3D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFL13_3D
cell line

source_name: cell serum-free late 3D


title: DIPG_CSFL13b_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFL13b_2D
cell line


title: DIPG_CSFE6a_3D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE6a_3D
cell line


title: DIPG_CSFL13c_3D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFL13c_3D
cell line


title: DIPG_CSFL7_3D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFL7_3D
cell line


title: DIPG_T1

description:
DNA from tumor tissue
diffuse_intrinsic_pontine_glioma_1
formalin-fixed

source_name: tumor

value: diffuse intrinsic pontine glioma


title: DIPG_T18

description:
DNA from tumor tissue
diffuse_intrinsic_pontine_glioma_18
frozen tissue


title: DIPG_CSFE1_3D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE1_3D
cell line


title: DIPG_T19

description:
DNA from tumor tissue
diffuse_intrinsic_pontine_glioma_19
formalin-fixed


title: DIPG_T21

description:
DNA from tumor tissue
diffuse_intrinsic_pontine_glioma_21
formalin-fixed


title: DIPG_T22

description:
DNA from tumor tissue
diffuse_intrinsic_pontine_glioma_22
formalin-fixed


title: DIPG_T20

description:
DNA from tumor tissue
diffuse_intrinsic_pontine_glioma_20
formalin-fixed


title: DIPG_T2

description:
DNA from tumor tissue
diffuse_intrinsic_pontine_glioma_2
frozen tissue


title: DIPG_T24

description:
DNA from tumor tissue
diffuse_intrinsic_pontine_glioma_24
formalin-fixed


title: DIPG_T3a

description:
DNA from tumor tissue
diffuse_intrinsic_pontine_glioma_3a
formalin-fixed


title: DIPG_T3b

description:
DNA from tumor tissue
diffuse_intrinsic_pontine_glioma_3b
formalin-fixed


title: DIPG_T4

description:
DNA from tumor tissue
diffuse_intrinsic_pontine_glioma_4
frozen tissue


title: DIPG_CSFE16_2D

description:
DNA from tumor cell lines
diffuse_intrinsic_pontine_glioma_cells_CSFE16_2D
cell line


title: DIPG_T5

description:
DNA from tumor tissue
diffuse_intrinsic_pontine_glioma_5
formalin-fixed


title: EPN_CSFE1_2D

description:
DNA from tumor cell lines
ependimoma_cells_CSFE1_2D
cell line

value: ependimoma cells


title: EPN_CSFE2_2D

description:
DNA from tumor cell lines
ependimoma_cells_CSFE2_2D
cell line


title: EPN_T3

description:
DNA from tumor tissue
ependimoma_3
formalin-fixed

value: ependimoma


title: EPN_T4

description:
DNA from tumor tissue
ependimoma_4
formalin-fixed


title: EPN_T2

description:
DNA from tumor tissue
ependimoma_2
formalin-fixed


title: EPN_T5

description:
DNA from tumor tissue
ependimoma_5
formalin-fixed


title: EPN_T7

description:
DNA from tumor tissue
ependimoma_7
formalin-fixed


title: EPN_T8

description:
DNA from tumor tissue
ependimoma_8
formalin-fixed


title: EPN_T9

description:
DNA from tumor tissue
ependimoma_9
formalin-fixed


title: HGG_CSFE2_3D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFE2_3D
cell line

value: high grade glioma cells


title: HGG_CSFE3_3D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFE3_3D
cell line


title: HGG_CSFL8a_3D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFL8a_3D
cell line


title: HGG_CSFE1a_2D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFE1a_2D
cell line


title: HGG_CSFL8b_3D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFL8b_3D
cell line


title: HGG_CSFE4b_2D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFE4b_2D
cell line


title: DIPG_T23

description:
DNA from tumor tissue
diffuse_intrinsic_pontine_glioma_23
formalin-fixed


title: HGG_CSFE5b_3D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFE5b_3D
cell line


title: HGG_CSFE5a_3D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFE5a_3D
cell line


title: HGG_CSFE7_2D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFE7_2D
cell line


title: HGG_CSFL6_3D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFL6_3D
cell line


title: HGG_CSFL9_2D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFL9_2D
cell line


title: HGG_KNS42_10_2D

description:
DNA from tumor cell lines
high_grade_glioma_cells_KNS42_10_2D
cell line

source_name: commercial cell line 2D


title: HGG_CSFE6_3D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFE6_3D
cell line


title: HGG_CSFL8c_2D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFL8c_2D
cell line


title: EPN_T6

description:
DNA from tumor tissue
ependimoma_6
formalin-fixed


title: EPN_T1

description:
DNA from tumor tissue
ependimoma_1
formalin-fixed


title: HGG_T1

description:
DNA from tumor tissue
high_grade_glioma_1
frozen tissue

value: high grade glioma


title: HGG_T15

description:
DNA from tumor tissue
high_grade_glioma_15
formalin-fixed


title: HGG_T14

description:
DNA from tumor tissue
high_grade_glioma_14
formalin-fixed


title: HGG_T11

description:
DNA from tumor tissue
high_grade_glioma_11
formalin-fixed


title: HGG_T13

description:
DNA from tumor tissue
high_grade_glioma_13
formalin-fixed


title: HGG_T12

description:
DNA from tumor tissue
high_grade_glioma_12
formalin-fixed


title: HGG_CSFE4a_2D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFE4a_2D
cell line


title: HGG_T18

description:
DNA from tumor tissue
high_grade_glioma_18
formalin-fixed


title: HGG_T16

description:
DNA from tumor tissue
high_grade_glioma_16
formalin-fixed


title: HGG_CSFL2_3D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFL2_3D
cell line


title: HGG_T17

description:
DNA from tumor tissue
high_grade_glioma_17
formalin-fixed


title: HGG_CSFE1b_3D

description:
DNA from tumor cell lines
high_grade_glioma_cells_CSFE1b_3D
cell line


title: HGG_T19

description:
DNA from tumor tissue
high_grade_glioma_19
formalin-fixed


title: HGG_T21

description:
DNA from tumor tissue
high_grade_glioma_21
formalin-fixed


title: HGG_T20

description:
DNA from tumor tissue
high_grade_glioma_20
formalin-fixed


title: HGG_T25

description:
DNA from tumor tissue
high_grade_glioma_25
formalin-fixed


title: HGG_T23

description:
DNA from tumor tissue
high_grade_glioma_23
formalin-fixed


title: HGG_T24

description:
DNA from tumor tissue
high_grade_glioma_24
formalin-fixed


title: HGG_T4

description:
DNA from tumor tissue
high_grade_glioma_4
frozen tissue


title: HGG_T3

description:
DNA from tumor tissue
high_grade_glioma_3
formalin-fixed


title: HGG_T5

description:
DNA from tumor tissue
high_grade_glioma_5
frozen tissue


title: HGG_T6

description:
DNA from tumor tissue
high_grade_glioma_6
frozen tissue


title: HGG_T8

description:
DNA from tumor tissue
high_grade_glioma_8
frozen tissue


title: LGG_CSE4_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSE4_2D
cell line

source_name: cell serum early 2D

value: low grade glioma cells


title: LGG_CSFL12_3D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSFL12_3D
cell line


title: LGG_CSFE14_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSFE14_2D
cell line


title: LGG_CSL13_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSL13_2D
cell line

source_name: cell serum late 2D


title: LGG_CSL10b_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSL10b_2D
cell line


title: LGG_CSL2_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSL2_2D
cell line


title: HGG_T2

description:
DNA from tumor tissue
high_grade_glioma_2
formalin-fixed


title: LGG_CSL10a_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSL10a_2D
cell line


title: LGG_CSL5_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSL5_2D
cell line


title: LGG_CSL6_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSL6_2D
cell line


title: LGG_CSL7_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSL7_2D
cell line


title: LGG_CSL8_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSL8_2D
cell line


title: LGG_CSL4_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSL4_2D
cell line


title: LGG_CSL9_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSL9_2D
cell line


title: HGG_T22

description:
DNA from tumor tissue
high_grade_glioma_22
formalin-fixed


title: LGG_CSL11b_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSL11b_2D
cell line


title: LGG_CSL11a_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSL11a_2D
cell line


title: LGG_CSE3_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSE3_2D
cell line


title: LGG_CSE1a_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSE1a_2D
cell line


title: HGG_T7

description:
DNA from tumor tissue
high_grade_glioma_7
frozen tissue


title: LGG_CSFE13_3D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSFE13_3D
cell line


title: LGG_CSL3_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSL3_2D
cell line


title: LGG_T12

description:
DNA from tumor tissue
low_grade_glioma_12
frozen tissue

value: low grade glioma


title: LGG_CSFL9_3D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSFL9_3D
cell line


title: LGG_T14

description:
DNA from tumor tissue
low_grade_glioma_14
frozen tissue


title: LGG_CSE11_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSE11_2D
cell line


title: LGG_T13

description:
DNA from tumor tissue
low_grade_glioma_13
formalin-fixed


title: LGG_T5

description:
DNA from tumor tissue
low_grade_glioma_5
formalin-fixed


title: LGG_T2

description:
DNA from tumor tissue
low_grade_glioma_2
formalin-fixed


title: LGG_CSL12_2D

description:
DNA from tumor cell lines
low_grade_glioma_cells_CSL12_2D
cell line


title: LGG_T11

description:
DNA from tumor tissue
low_grade_glioma_11
frozen tissue


title: LGG_T7

description:
DNA from tumor tissue
low_grade_glioma_7
formalin-fixed


title: LGG_T9

description:
DNA from tumor tissue
low_grade_glioma_9
formalin-fixed


title: LGG_T1

description:
DNA from tumor tissue
low_grade_glioma_1
formalin-fixed


title: LGG_T3

description:
DNA from tumor tissue
low_grade_glioma_3
frozen tissue


title: LGG_T15b

description:
DNA from tumor tissue
low_grade_glioma_15b
formalin-fixed


title: LGG_T15a

description:
DNA from tumor tissue
low_grade_glioma_15a
formalin-fixed


title: LGG_T6

description:
DNA from tumor tissue
low_grade_glioma_6
formalin-fixed


title: LGG_T17

description:
DNA from tumor tissue
low_grade_glioma_17
formalin-fixed


title: LGG_T16

description:
DNA from tumor tissue
low_grade_glioma_16
formalin-fixed


title: LGG_T19

description:
DNA from tumor tissue
low_grade_glioma_19
formalin-fixed


title: LGG_T20a

description:
DNA from tumor tissue
low_grade_glioma_20a
formalin-fixed


title: LGG_T21

description:
DNA from tumor tissue
low_grade_glioma_21
formalin-fixed


title: LGG_T18

description:
DNA from tumor tissue
low_grade_glioma_18
formalin-fixed


title: LGG_T20b

description:
DNA from tumor tissue
low_grade_glioma_20b
formalin-fixed


title: LGG_T4

description:
DNA from tumor tissue
low_grade_glioma_4
formalin-fixed


title: LGG_T24

description:
DNA from tumor tissue
low_grade_glioma_24
formalin-fixed


title: LGG_T25

description:
DNA from tumor tissue
low_grade_glioma_25
formalin-fixed


title: LGG_T28

description:
DNA from tumor tissue
low_grade_glioma_28
formalin-fixed


title: LGG_T26

description:
DNA from tumor tissue
low_grade_glioma_26
formalin-fixed


title: LGG_T27

description:
DNA from tumor tissue
low_grade_glioma_27
frozen tissue


title: LGG_T29

description:
DNA from tumor tissue
low_grade_glioma_29
formalin-fixed


title: LGG_T30

description:
DNA from tumor tissue
low_grade_glioma_30
formalin-fixed


title: LGG_T8

description:
DNA from tumor tissue
low_grade_glioma_8
formalin-fixed


title: LGG_T31

description:
DNA from tumor tissue
low_grade_glioma_31
formalin-fixed


title: LGG_T33

description:
DNA from tumor tissue
low_grade_glioma_33
formalin-fixed


title: LGG_T32

description:
DNA from tumor tissue
low_grade_glioma_32
formalin-fixed


title: LGG_T35

description:
DNA from tumor tissue
low_grade_glioma_35
formalin-fixed


title: LGG_T36

description:
DNA from tumor tissue
low_grade_glioma_36
formalin-fixed


title: LGG_T34

description:
DNA from tumor tissue
low_grade_glioma_34
frozen tissue


title: LGG_T37

description:
DNA from tumor tissue
low_grade_glioma_37
formalin-fixed


title: LGG_T39

description:
DNA from tumor tissue
low_grade_glioma_39
formalin-fixed


title: LGG_T43

description:
DNA from tumor tissue
low_grade_glioma_43
frozen tissue


title: LGG_T42

description:
DNA from tumor tissue
low_grade_glioma_42
frozen tissue


title: LGG_T38

description:
DNA from tumor tissue
low_grade_glioma_38
frozen tissue


title: LGG_T45

description:
DNA from tumor tissue
low_grade_glioma_45
formalin-fixed


title: MB_CSFE4_2D

description:
DNA from tumor cell lines
medulloblastoma_cells_CSFE4_2D
cell line

value: medulloblastoma cells


title: MB_CSE2_2D

description:
DNA from tumor cell lines
medulloblastoma_cells_CSE2_2D
cell line


title: MB_CSFL3b_3D

description:
DNA from tumor cell lines
medulloblastoma_cells_CSFL3b_3D
cell line


title: MB_CSL2_2D

description:
DNA from tumor cell lines
medulloblastoma_cells_CSL2_2D
cell line


title: LGG_T22

description:
DNA from tumor tissue
low_grade_glioma_22
frozen tissue


title: MB_CSFL3a_3D

description:
DNA from tumor cell lines
medulloblastoma_cells_CSFL3a_3D
cell line


title: MB_DAOY_ST65_2D

description:
DNA from tumor cell lines
medulloblastoma_cells_DDAOY_ST65_2D
cell line


title: LGG_T23

description:
DNA from tumor tissue
low_grade_glioma_23
frozen tissue


title: MB_CHLA_CSFL62

description:
DNA from tumor cell lines
medulloblastoma_cells_CHLA_CSFL62
cell line

source_name: commercial cell line - serum-free late 2D


title: MB_CSFL1a_3D

description:
DNA from tumor cell lines
medulloblastoma_cells_CSFL1a_3D
cell line


title: MB_D283_ST63_2D-3D

description:
DNA from tumor cell lines
medulloblastoma_cells_D283_ST63_2D-3D
cell line

source_name: commercial cell line 2D-3D


title: MB_CSFL1b_3D

description:
DNA from tumor cell lines
medulloblastoma_cells_CSFL1b_3D
cell line


title: MB_G3_O66

description:
DNA from tumor tissue
medulloblastoma_66
cell line

source_name: organoid

value: medulloblastoma


title: MB_G3_O67

description:
DNA from tumor tissue
medulloblastoma_67
cell line


title: MB_CSFE5_2D

description:
DNA from tumor cell lines
medulloblastoma_cells_CSFE5_2D
cell line


title: MB_D341_ST64_3D

description:
DNA from tumor cell lines
medulloblastoma_cells_D341_ST64_3D
cell line

source_name: commercial cell line 3D


title: MB_G3_O69

description:
DNA from tumor tissue
medulloblastoma_69
cell line


title: LGG_T40

description:
DNA from tumor tissue
low_grade_glioma_40
frozen tissue


title: LGG_T41

description:
DNA from tumor tissue
low_grade_glioma_41
formalin-fixed


title: MB_G3_O70

description:
DNA from tumor tissue
medulloblastoma_70
cell line


title: MB_G3_O71

description:
DNA from tumor tissue
medulloblastoma_71
cell line


title: MB_G3_O72

description:
DNA from tumor tissue
medulloblastoma_72
cell line


title: MB_G3_O74

description:
DNA from tumor tissue
medulloblastoma_74
cell line


title: MB_G3_O73

description:
DNA from tumor tissue
medulloblastoma_73
cell line


title: MB_G3_T1

description:
DNA from tumor tissue
medulloblastoma_1
frozen tissue


title: MB_G3_T10

description:
DNA from tumor tissue
medulloblastoma_10
formalin-fixed


title: MB_G3_T12

description:
DNA from tumor tissue
medulloblastoma_12
formalin-fixed


title: MB_G3_T16

description:
DNA from tumor tissue
medulloblastoma_16
frozen tissue


title: MB_G3_T32

description:
DNA from tumor tissue
medulloblastoma_32
formalin-fixed


title: MB_G3_T20

description:
DNA from tumor tissue
medulloblastoma_20
frozen tissue


title: MB_G3_T33

description:
DNA from tumor tissue
medulloblastoma_33
formalin-fixed


title: MB_G3_T28

description:
DNA from tumor tissue
medulloblastoma_28
formalin-fixed


title: MB_G3_T39

description:
DNA from tumor tissue
medulloblastoma_39
formalin-fixed


title: MB_G3_T40

description:
DNA from tumor tissue
medulloblastoma_40
formalin-fixed


title: MB_G3_T24

description:
DNA from tumor tissue
medulloblastoma_24
formalin-fixed


title: MB_G3_T41

description:
DNA from tumor tissue
medulloblastoma_41
formalin-fixed


title: MB_G4_T13

description:
DNA from tumor tissue
medulloblastoma_13
formalin-fixed


title: MB_G3_T42

description:
DNA from tumor tissue
medulloblastoma_42
formalin-fixed


title: MB_G3_O68

description:
DNA from tumor tissue
medulloblastoma_68
cell line


title: MB_G4_T14

description:
DNA from tumor tissue
medulloblastoma_14
formalin-fixed


title: MB_G4_T17

description:
DNA from tumor tissue
medulloblastoma_17
frozen tissue


title: MB_G4_T21

description:
DNA from tumor tissue
medulloblastoma_21
frozen tissue


title: MB_G4_T15

description:
DNA from tumor tissue
medulloblastoma_15
formalin-fixed


title: MB_G4_T19

description:
DNA from tumor tissue
medulloblastoma_19
frozen tissue


title: MB_G4_T26

description:
DNA from tumor tissue
medulloblastoma_26
formalin-fixed


title: MB_G4_T29

description:
DNA from tumor tissue
medulloblastoma_29
formalin-fixed


title: MB_G4_T18

description:
DNA from tumor tissue
medulloblastoma_18
frozen tissue


title: MB_G4_T25

description:
DNA from tumor tissue
medulloblastoma_25
formalin-fixed


title: MB_G4_T31

description:
DNA from tumor tissue
medulloblastoma_31
frozen tissue


title: MB_G4_T34

description:
DNA from tumor tissue
medulloblastoma_34
formalin-fixed


title: MB_G4_T30

description:
DNA from tumor tissue
medulloblastoma_30
formalin-fixed


title: MB_G4_T43

description:
DNA from tumor tissue
medulloblastoma_43
frozen tissue


title: MB_G4_T37

description:
DNA from tumor tissue
medulloblastoma_37
formalin-fixed


title: MB_G4_T38

description:
DNA from tumor tissue
medulloblastoma_38
formalin-fixed


title: MB_G4_T7

description:
DNA from tumor tissue
medulloblastoma_7
formalin-fixed


title: MB_G4_T44

description:
DNA from tumor tissue
medulloblastoma_44
formalin-fixed


title: MB_SHHa_T2

description:
DNA from tumor tissue
medulloblastoma_2
frozen tissue


title: MB_G4_T9

description:
DNA from tumor tissue
medulloblastoma_9
formalin-fixed


title: MB_G4_T45

description:
DNA from tumor tissue
medulloblastoma_45
formalin-fixed


title: MB_G4_T5

description:
DNA from tumor tissue
medulloblastoma_5
formalin-fixed


title: MB_SHHa_T27

description:
DNA from tumor tissue
medulloblastoma_27
formalin-fixed


title: MB_SHHa_T4

description:
DNA from tumor tissue
medulloblastoma_4
formalin-fixed


title: MB_SHHa_T54

description:
DNA from tumor tissue
medulloblastoma_54
frozen tissue


title: MB_SHHa_T55

description:
DNA from tumor tissue
medulloblastoma_55
frozen tissue


title: MB_SHHa_T59

description:
DNA from tumor tissue
medulloblastoma_59
formalin-fixed


title: MB_SHHb_T23

description:
DNA from tumor tissue
medulloblastoma_23
formalin-fixed


title: MB_SHHa_T56

description:
DNA from tumor tissue
medulloblastoma_56
formalin-fixed


title: MB_SHHb_T3

description:
DNA from tumor tissue
medulloblastoma_3
frozen tissue


title: MB_SHHb_T36

description:
DNA from tumor tissue
medulloblastoma_36
frozen tissue


title: MB_SHHb_T51

description:
DNA from tumor tissue
medulloblastoma_51
frozen tissue


title: MB_SHHb_T61

description:
DNA from tumor tissue
medulloblastoma_61
formalin-fixed


title: MB_SHHb_T52

description:
DNA from tumor tissue
medulloblastoma_52
frozen tissue


title: MB_SHHb_T60

description:
DNA from tumor tissue
medulloblastoma_60
formalin-fixed


title: MB_SHHb_T35

description:
DNA from tumor tissue
medulloblastoma_35
formalin-fixed


title: MB_WNT_T11

description:
DNA from tumor tissue
medulloblastoma_11
formalin-fixed


title: MB_WNT_T46

description:
DNA from tumor tissue
medulloblastoma_46
formalin-fixed


title: MB_WNT_T47

description:
DNA from tumor tissue
medulloblastoma_47
formalin-fixed


title: MB_WNT_T49

description:
DNA from tumor tissue
medulloblastoma_49
formalin-fixed


title: MB_WNT_T50

description:
DNA from tumor tissue
medulloblastoma_50
formalin-fixed


title: MB_WNT_T58

description:
DNA from tumor tissue
medulloblastoma_58
frozen tissue


title: MB_WNT_T8

description:
DNA from tumor tissue
medulloblastoma_8
formalin-fixed


title: MNG_T2

description:
DNA from tumor tissue
meningioma_2
formalin-fixed

value: meningioma


title: MB_SHHa_T53

description:
DNA from tumor tissue
medulloblastoma_53
frozen tissue


title: MB_WNT_T57

description:
DNA from tumor tissue
medulloblastoma_57
frozen tissue


title: MB_SHHa_T22

description:
DNA from tumor tissue
medulloblastoma_22
formalin-fixed


title: MNG_T3

description:
DNA from tumor tissue
meningioma_3
formalin-fixed


title: MNG_T4

description:
DNA from tumor tissue
meningioma_4
formalin-fixed


title: MNG_T1

description:
DNA from tumor tissue
meningioma_1
formalin-fixed


title: Adjacent non-tumor tissue, rep35 [A3946367BY]

city: Zhengzhou

first: shuaifeng

last: wang

state: Henan

address: No.1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
*library strategy: Full length 16s rDNA
The raw data obtained from sequencer were filtered by qcat and NanoFILT tools to obtain high-quality target sequences for subsequent analysis.
Assembly: SILVA
Supplementary files format and content: tab-delimited text files include OUT for each Samples
Supplementary files format and content: tab-delimited text files include tax
Supplementary files format and content: tab-delimited text files include grouping information

organism: metagenomes

source_name: lung

growth_protocol: All of the samples were selected from patients, who have signed informed consent forms.

extract_protocol:
The Zymo Research BIOMICS DNA Microprep Kit (Cat # D4301) was used for microbial gDNA purification. The integrity of gDNA was detected by 0.8% agarose gel electrophoresis, followed by nucleic acid concentration detection using Tecan F200 (PicoGreen dye method).
Use specific primers with a Barcode full-length of 16S to amplify the designated region of the sample, The primer information is as follows:(8F: 5’AGAGTTTGATCATGGCTCAG3’; 1492R: 5’CGGTTACCTTGTTACGACTT3’). Each sample undergoes 3 replicates, and each PCR reaction terminates at the linear amplification stage. After PCR, the PCR products of the same sample were mixed and subjected to electrophoresis detection. The PCR products were cut and recovered using a gel recovery kit, and the target DNA fragments were washed and recovered using TE buffer. The PCR recovered products were detected and quantified using Qubit 2.0 (Thermo Fisher, Inc., USA), and after passing the quality control, the Nanopore R9.4.1 library kit was used for machine library construction.

treatment_protocol: The tissues obtained after surgery were quickly rinsed with sterile physiological saline, then immediately frozen in 2ml eppendof tube with liquid nitrogen, and then transferred to a -80 degree freezer for storage.

value: lung

tag: tissue type

value: Adjacent non-tumor tissue

tag: Stage

tag: nicotine exposure


title: Adjacent non-tumor tissue, rep36 [A3739430AP]


title: Tumor tissue, rep36 [A3739430ZL]

value: Tumor tissue

value: IB

value: no


title: Adjacent non-tumor tissue, rep34 [A4297218BY]


title: Adjacent non-tumor tissue, rep37 [A3641760AP]


title: Tumor tissue, rep35 [A3946367ZL]

value: II


title: Tumor tissue, rep34 [A4297218ZL]

value: yes


title: Tumor tissue, rep37 [A3641760ZL]

value: IA


title: Adjacent non-tumor tissue, rep33 [A4737600BY]


title: Tumor tissue, rep33 [A4737600ZL]


title: MB_WNT_T48

description:
DNA from tumor tissue
medulloblastoma_48
formalin-fixed


title: Adjacent non-tumor tissue, rep31 [A4748312BY]


title: Tumor tissue, rep32 [A4739028ZL]


title: Adjacent non-tumor tissue, rep32 [A4739028BY]


title: Tumor tissue, rep31 [A4748312ZL]


title: Adjacent non-tumor tissue, rep29 [A4760756BY]


title: Adjacent non-tumor tissue, rep30 [A4760000BY]


title: Adjacent non-tumor tissue, rep28 [A4761420BY]


title: MB_WNT_T6

description:
DNA from tumor tissue
medulloblastoma_6
formalin-fixed


title: Tumor tissue, rep30 [A4760000ZL]


title: Tumor tissue, rep29 [A4760756ZL]


title: Adjacent non-tumor tissue, rep27 [A4762457BY]


title: Tumor tissue, rep28 [A4761420ZL]


title: Tumor tissue, rep27 [A4762457ZL]


title: Adjacent non-tumor tissue, rep26 [A4765344BY]


title: Adjacent non-tumor tissue, rep24 [A4766212AP]


title: Adjacent non-tumor tissue, rep25 [A4765635BY]


title: Tumor tissue, rep26 [A4765344ZL]


title: Tumor tissue, rep24 [A4766212ZL]


title: Tumor tissue, rep25 [A4765635ZL]


title: Adjacent non-tumor tissue, rep22 [A4771829BY]


title: Adjacent non-tumor tissue, rep23 [A4766237BY]


title: Adjacent non-tumor tissue, rep20 [A4773198BY]


title: Tumor tissue, rep21 [A4771977ZL]


title: Tumor tissue, rep22 [A4771829ZL]


title: Adjacent non-tumor tissue, rep19 [A4773654AP]


title: Adjacent non-tumor tissue, rep21 [A4771977BY]


title: Tumor tissue, rep23 [A4766237ZL]


title: Adjacent non-tumor tissue, rep18 [A4773790BY]


title: Tumor tissue, rep20 [A4773198ZL]


title: Tumor tissue, rep18 [A4773790ZL]


title: Tumor tissue, rep17 [A4774138ZL]


title: Adjacent non-tumor tissue, rep16 [A4774588BY]


title: Tumor tissue, rep16 [A4774588ZL]


title: Adjacent non-tumor tissue, rep15 [A4776030AP]


title: Adjacent non-tumor tissue, rep14 [A4778880BY]


title: Tumor tissue, rep15 [A4776030ZL]


title: Adjacent non-tumor tissue, rep17 [A4774138BY]


title: Adjacent non-tumor tissue, rep12 [A4779400AP]


title: Tumor tissue, rep13 [A4779313ZL]


title: Tumor tissue, rep12 [A4779400ZL]


title: Adjacent non-tumor tissue, rep11 [A4781506AP]


title: Adjacent non-tumor tissue, rep13 [A4779313BY]


title: Adjacent non-tumor tissue, rep10 [A4784026AP]


title: Tumor tissue, rep11 [A4781506ZL]


title: Tumor tissue, rep9 [A4788657ZL]


title: Adjacent non-tumor tissue, rep9 [A4788657AP]


title: Tumor tissue, rep19 [A4773654ZL]


title: Adjacent non-tumor tissue, rep8 [A4788819AP]


title: Adjacent non-tumor tissue, rep6 [A4794481AP]


title: Tumor tissue, rep6 [A4794481ZL]


title: Tumor tissue, rep8 [A4788819ZL]


title: Tumor tissue, rep5 [A4796392ZL]


title: Tumor tissue, rep7 [A4790046ZL]


title: Adjacent non-tumor tissue, rep7 [A4790046AP]


title: Adjacent non-tumor tissue, rep5 [A4796392AP]


title: Tumor tissue, rep4 [A4799446ZL]


title: Adjacent non-tumor tissue, rep3 [A4800817AP]


title: Adjacent non-tumor tissue, rep4 [A4799446AP]


title: Adjacent non-tumor tissue, rep1 [LNH_BY]


title: Tumor tissue, rep14 [A4778880ZL]


title: Tumor tissue, rep2 [A4811437ZL]


title: Tumor tissue, rep1 [LNH_ZL]


title: Tumor tissue, rep3 [A4800817ZL]


title: yeast strain WLH, centrifuged, rep1

first: Qianxi

last: He

address: Yaguan road 135

institute: Tianjin University

data_processing:
Pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to indexreference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
Assembly: YarliW29
Supplementary files format and content: txt.tab-Expression values of all genes
Supplementary files format and content: txt.tab-Significantly differentially expressed genes with fold changes

organism: Yarrowia lipolytica

growth_protocol: Strains WLH (control) and F19 were cultivated in SD-leu medium with 2.4 mM furfural at 30℃ for 48 hours.

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 1 μg total RNA was used for following library preparation.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions

treatment_protocol: Cultures were centrifuged at 4℃ and percipitants were washed by PBS and frozen by liquid nitrogen.

value: yeast cell

tag: strain

value: WLH


title: yeast strain F19, centrifuged, rep1


title: Tumor tissue, rep10 [A4784026ZL]


title: yeast strain WLH, centrifuged, rep2


title: Mock LA ND3

first: Sònia

last: Guedan

address: Carrer Roselló 153

institute: Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS)

hyb_protocol: According to manufacturer's protocol (Nanostring)

scan_protocol: nCounter® Sprint Profiler

data_processing: Data analysis was conducted using the Rosalind Platform

source_name: Normal Donor T cells

growth_protocol: T cells were cultured in RPMI-1640 supplemented with 10% of FBS, 100 mg/mL of P/S, 10 mM Glutamax and 10 mM Hepes. (NEAA). SKOV3 (ovarian cystadenocarcinoma) were cultured in DMEM (Dubbeco’s Modified Eagle’s Medium high glucose, GlutaMAX™ pyruvate). All cells were regularly validated to be Mycoplasma free and authenticated in 2019 by IDEXX Bioanalytics using the Human 9-Marker STR Profile.

extract_protocol: RNA was extracted using the RNeasy Mini kit (Qiagen) following manufacturer's protocol.

treatment_protocol: CAR-T cells were cocultured with SKOV3 tumour cells (effector/target ratio of 1:3) for 48h.

tag: individual

value: Normal donor 3

tag: knock out

value: Mock

tag: car

tag: affinity

value: Low


title: PD-1 KO HA ND2

label_protocol: According to manufacturer's protocol (Nanostring)

value: Normal donor 2

value: High


title: PD-1 KO LA ND3


title: PD-1 KO HA ND3


title: PD-1 KO LA ND1

value: Normal donor 1


title: PD-1 KO LA ND2


title: Adjacent non-tumor tissue, rep2 [A4811437AP]

tag: tissue


title: IGR37, DHRS3 6 hr OA, Rep 1 [D_OA]

city: New York

first: Eleanor

last: Johns

address: 417 E 68th Street

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
FASTQ reads were trimmed with Trimmomatic v 0.39.1
Reads were mapped and quantified with Salmon v1.10.2 using selective alignment with the GRCh38 ference genome2
Downstream analysis was done in R studio using DESeq2 v1.36 with default parameters
Assembly: GRCh38
Supplementary files format and content: csv file contains log2FC with padj <0.05 as generated by DESeq2
Supplementary files format and content: File contains normalized counts generated by DESeq2

growth_protocol: For RNA-seq of IGR37 DHRS3 OE cells, 3 replicates of 1 million cells each were seeded in 10 cm dishes. Cells were allowed to grow for 2 days and then collected for RNA-seq and snap frozen.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Rneasy Plus Mini Kit (Qiagen, Hilden, Germany). Total RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA)
Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. rRNA depletion sequencing library was prepared by using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Hilden, Germany). RNA sequencing library preparation used NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer(ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.

treatment_protocol: Cells were either grown in normal media or treated with Oleic Acid for 6 hours prior to harvesting

tag: cell line

tag: cell type

value: Melanoma Cell Line

tag: genotype

value: DHRS3-V5 OE

tag: treatment

value: 6 hour 200 uM Oleic Acid


title: IGR37, DHRS3 6 hr OA, Rep 2 [D_OA.1]


title: Mock LA ND1


title: Mock LA ND2


title: IGR37, Control 6 hr OA, Rep 2 [EV_OA.1]

value: WT


title: Mock HA ND3


title: IGR37, DHRS3, Rep 2 [D.1]

value: Normal Media


title: yeast strain F19, centrifuged, rep2


title: Mock HA ND2


title: IGR37, Control 6 hr OA, Rep 3 [EV_OA.2]


title: IGR37, Control, Rep 2 [EV.1]


title: IGR37, DHRS3, 6 hr OA, Rep 3 [D_OA.2]


title: Mock HA ND1


title: IGR37, Control, Rep 1 [EV]

description: EV


title: IGR37, Control, Rep 3 [EV.2]


title: A2780_Combination_dark

city: Wenzhou

first: Kejie

last: Chen

state: Zhejiang

address: Chashan

institute: Wenzhou Medical University

description: with TMPyP4 and H2O2 in dark conditions

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …

source_name: OVARY

growth_protocol: Cells were incubated at 37 ℃ in 5% CO2 and maintained in DMEM medium with 10% FBS and 100 U/mL penicillin and streptomycin.

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: The control group was cultured in nomral medium. A2780 cultured in common medium for 46 hours and then treated with H2O2 (200 µM) for 2 hours and incubated for another 24 hours is the H2O2 group. A2780 treated with TMPyP4 (5 µM) for 72 hours is the TMPyP4_dark group. A2780 treated with TMPyP4 (5 µM) for 72 hours, and exposed to a 600 nm white light for 3 minutes at 48 hours is the TMPyP4_light group. A2780 treated with TMPyP4 (5 µM) for 46 hours and then treated with H2O2 (200 µM) for 2 hours and then incubated with TMPyP4 for another 24 hours is the combination_dark group. A2780 treated with TMPyP4 (5 µM) for 46 hours and then treated with H2O2 (200 µM) for 2 hours, followed by a exposure to 600 nm white light for 3 minutes, and then incubated with TMPyP4 for another 24 hours is the combination_light group.

value: OVARY

value: Human ovarian cancer cells A2780

value: Epithelial cell

value: A2780 treated with TMPyP4 (5 uM) for 46 hours and then treated with H2O2 (200 uM) for 2 hours and then incubated with TMPyP4 for another 24 hours


title: A2780_Combination_light

description: with TMPyP4 and H2O2 in light conditions

value: A2780 treated with TMPyP4 (5 uM) for 46 hours and then treated with H2O2 (200 uM) for 2 hours, followed by a exposure to 600 nm white light for 3 minutes, and then incubated with TMPyP4 for another 24 hours


title: A2780_TMPyP4_dark

description: with TMPyP4 in dark conditions

value: A2780 treated with TMPyP4 (5 uM) for 72 hours


title: A2780_TMPyP4_light

description: with TMPyP4 in light conditions

value: A2780 treated with TMPyP4 (5 uM) for 72 hours, and exposed to a 600 nm white light for 3 minutes at 48 hours


title: IGR37, DHRS3, Rep 1 [D]

description: D


title: IGR37, DHRS3, Rep 3 [D.2]


title: PD-1 KO HA ND1


title: A2780_H2O2

description: with H2O2

value: A2780 cultured in common medium for 46 hours and then treated with H2O2 (200 uM) for 2 hours and incubated for another 24 hours


title: A2780_Control

description: without any drugs

value: A2780 cultured in common medium


title: IGR37, Control 6 hr OA, Rep 1 [EV_OA]


title: ChIPseq_H3K27ac_OCILY1_FOXO1_FKBP_6B

city: Nashville

first: Scott

last: Hiebert

state: Tennessee

address: 2220 Pierce Ave, Hiebert Lab PRB 512

institute: Vanderbilt University

data_processing:
Adaptor trimming: Adaptors were trimmed using Trimmomatic with flollowing settings ILLUMINACLIP:adaptorfile:2:30:7, LEADING:15, TRAILING:15, MINLEN:15
File conversion and read filtering: SAM fies were converted to BAM files using samtools view with the options -S -b. Low quality reads were removed using samtools view with the following options -F 4 and -q 10. Filtered BAM files were sorted and indexed using samtools sort and samtools index respectively.
Spike-in quantication and removal: Spike-in reads were quantified using samtools idxstats to quantify reads aligned to each chromosome. Reads aligned to dm3 chromosomes were summed in R to calculate the total number of spike-in reads. A bam file containing only hg19 reads was created using samtools view with the following options -bh and the names of the hg19 chromosomes. These files were resorted and indexed as described in the previous step.
Differential analysis: Peaks were called using MACS2, reads were quantified with DiffBind, and differential analysis was performed with DEseq2.
Assembly: hg19/dm3 (ChiP) hg19/Ecoli (C&R)
Supplementary files format and content: Counts tables. Tab delimted file containing peak location, raw counts for each replicate, normalized counts for each replicate, and DEseq2 output for indicated comparison.

source_name: DLBCL Cell Line

growth_protocol: NU-DUL-1 and SU-DHL-4 cells were cultured in RPMI 1640 + 10% Fetalplex +1% L-Glutamine + 1% PenStrep. OCI-LY1 cells were cultured in IDMDM + 10% FetalPlex +1% L-Glutamine + 1% PenStrep. Cells were subcultured the day before the experiment, incubated at 37C with 5% CO2, and harvested while in log phase growth.

extract_protocol:
ChIP-seq experiments were performed as previously described (Zhang et al., Molecular Cell, 2022). CUT&RUN experients were performed using the EpiCypher CUTANA CUT&RUN Kit according to the manufacturer's reccommendations.
Libraries were constucted using the NEBNext Ultra II DNA Library Prep kit according to the manufacturer's protocol.

treatment_protocol: dTAG-47 was added to culture medium to a final concentration of 500 nm at the indicated timepoints.

value: GC-DLBCL

value: 6h dTAG-47

tag: chip antibody