title: LPS+sh-U90926-2

city: Nanjing

first: jian

last: chen

address: zhongshan road #321

department: Neurology

institute: Nanjing Drum Town hospital

description: gene expression in LPS-activated microglia with U90926 knockdown or not

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Gene Expression(8*60K)for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: microglia, LPS3h+sh-U90927

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

growth_protocol: DMEM supplemented with 10% FBS, 100 U/mL penicillin, and 100 mg/mL streptomycin

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Vector or sh-U90926 virus (MOI=50) was added to microglia cultured in 12 well, 48 hours later, microglia were treated with LPS (100ng/ml) for 3h

tag: cell type

value: primary microglia

tag: genotype/variation


title: CG0000-6730 [Blood]

status: Public on Oct 24 2020

type: genomic

city: New York

first: Alejandro

last: Martin Trujillo

address: Hess Center for Science and Medicine at Mount Sinai,1470 Madison Avenue, 8th Floor

country: USA

institute: Icahn school of medicine at mount sinai hospital

description: tissue

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Raw Beta values were background and color corrected and quantile normalized using lumi and methylumi R packages. Finally, resulting Beta values were corrected for Infinium probe design biases
Processed data file includes: Average Beta and detection Pvalue
The file SignalIntensitiesData.GeoSubmission.AMT.txt includes Unmethylated, methylated signal intensities and detection P value for all Blood samples. Raw data for Heart samples are provided in the idat files.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: tissue

value: Blood

tag: diagnosis

value: congenital heart defect


title: OLC46_TLOm1 125 nM azacitidine

type: SRA

first: Owen

middle: A

last: O"Connor

state: NY

address: 51 West 51st Street

department: enter for Lymphoid Malignancies

institute: Columbia University Medical Center

library_source: transcriptomic

data_processing:
Alignment with STARv2.5.3
Gene-level raw counts summarization with STARTv2.5.3 quant-mode
Variance stabilization (normalization) with DESeq2 (R bioconductor package)
Gene expression signature generation with limma (R bioconductor package)
Genome_build: GRCh37.p2
Supplementary_files_format_and_content: Tab delimited text output of raw counts from STAR alignment and gene count quantification

molecule: polyA RNA

source_name: TLOm1 Adult T-cell leukemia

growth_protocol: The cells grown in logarithomic phase during treatment

extract_protocol:
RNAs were extracted with using Qiagen Rneasy mini kit
Strand specific sequencing libraries were generated from rRNA depleted total RNAs using the TruSeq Stranded mRNA kit by Illumina

treatment_protocol: All the samples were treated with indicated concentration of drugs for 96 hours with drug addition every 24 hours.

tag: cell line

tag: treatment

value: 125 nM azacitidine


title: LPS+sh-U90926-3

type: RNA

country: China

molecule: total RNA

organism: Mus musculus

source_name: microglia, LPS3h+sh-U90928


title: CG0023-9220 [Blood]

description: tissue


title: LPS+Vector-3

source_name: microglia, LPS3h+Vector

value: LPS+Vector


title: LPS+sh-U90926-1

source_name: microglia, LPS3h+sh-U90926


title: OLC32_PF382 500 nM azacitidine

source_name: PF382 T-cell Acute Lymphoblastic Leukemia

value: 500 nM azacitidine


title: OLC31_PF82 250 nM azacitidine

value: 250 nM azacitidine


title: LPS+Vector-1


title: ∆AbcR1, OD 015, rep2

city: Bochum

first: Franz

last: Narberhaus

state: NRW

address: Universitätsstraße 150

department: Microbial Biology

country: Germany

institute: Ruhr University Bochum

description: Delta AbcR1 vs WT_15.csv

data_processing:
Adapter sequences were removed via cutadapt 1.18 with Python 3.7.9 (options: -j 4 -q 10)
Cleaned reads were mapped with bwa (0.7.17-r1188) mem on default settings.
Duplicate reads were removed with Samtools 1.10.
Differential gene expression was analyzed  with DESeq2. A maximal adjusted p value of 0.05 was used as threshold.
Genome_build: NCBI ID: 13606; 671 small RNA genes were added from Wilms et al. (2012, DOI: 10.4161/rna.17212), Lee et al. (2013, DOI: 10.1371/journal.pone.0070720) and from Möller et al. (2014, DOI: 10.1371/journal.pone.0110427)
Supplementary_files_format_and_content: Files include the binary logarithm of the fold change of each gene in the mutant and the corresponding p values.

organism: Agrobacterium fabrum str. C58

source_name: Agrobacterium fabrum C58 ∆AbcR1 at optical density (600 nm) 1.5; total RNA

growth_protocol: Cells were grown at 30 °C in YEB medium. Samples were taken at an optical density (600 nm) of 0.5 or 1.5.

extract_protocol:
RNA was extracted via hot-phenol method as described in Wilms et al. (2012, DOI: 10.4161/rna.17212). Samples were treated with RNase-free DNase.
RNA libraries were prepared by Novogene. 1 µg of RNA was used. Sequencing libraries were generated with NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to manufacturer's instructions. Index codes were added to attribute sequences to each sample. Fragmentation was done with divalent cations in NEBNext First Strand Synthesis Reaction Buffer (5x) at elevated temperature. First strand synthesis was carried out with random hexamer primers and M-MuLV reverse transcriptase. Second strand was synthesized with DNA polymerase I and RNase H. Blunt ends were created from overhangs via exonuclease/polymerase activites. DNA 3' ends were adenylated and NEBNext Adaptors with hairpin loop were ligated. Fragments were purified with the AMPure XP system (Backman Cooulter, USA). The cDNA was incubated at 37 °C for 15 min with 3 µl USER Enzyme (NEB, USA) and then at 95 °C for 5 min.The subsequent PCR was done with Phusion High-Fidelity DNA polymerase, Universail PCR primers and Index (X) Primer. The PCR products were purified via AMPure XP system and the quality was assured via Agilent Bioanalyzer 2100.
RNA-Seq (Illumina NovaSeq 6000 platform)

value: Grown to OD 1.5 in YEB medium at 30 °C

tag: genotype


title: ∆AbcR1, OD 015, rep1

description: Delta AbcR1 vs WT_15.csv


title: ∆AbcR1, OD 015, rep3

description: Delta AbcR1 vs WT_15.csv


title: OLC30_PF382 125 nM azacitidine


title: LPS+Vector-2


title: OLC47_TLOm1 250 nM azacitidine


title: ∆AbcR1, OD 0.5, rep3

description: Delta AbcR1 vs WT_05.csv

source_name: Agrobacterium fabrum C58 ∆AbcR1 at optical density (600 nm) 0.5; total RNA

value: Grown to OD 0.5 in YEB medium at 30 °C


title: CG0023-6053 [Blood]

description: tissue


title: OLC28_PF382 untreated

value: untreated


title: Cervix

city: Puebla

first: Patricia

last: Martinez-Morales

address: Centro de Investigación Biomédica de Oriente Instituto Mexicano del Seguro Social HGZ No. 5 Km 4.5 Carretera Federal Atlixco-Metepec 74360 Metepec, Puebla, México

country: Mexico

institute: CONACYT-IMSS

description: One replicate array

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

scan_protocol: Acquisition and quantification of array images was performed in GenePix 4100A with its accompanying software GenePix from Molecular Devices. All images were captured using 10 µm resolution. For each spot the Alexa555 and Alexa647 density mean value and background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics.

data_processing:
For each spot the Alexa555 and Alexa647 density mean value and background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics. Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean. zi = (Ri – mean(R)) / sd(R) Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes.
Data were then normalized and analyzed with genArise software (Institute of Cellular Physiology, UNAM). Genes with a Z score ≥ 2 or ≤ -2 were considered with altered expression (Table z score).

label: Alexa 555

source_name: Normal cervix

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Alexa555 or dUTP-Alexa647 employing the First-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

extract_protocol: Total RNA from normal cervix tissue and cervical cancer tissue was obtained with RNeasy Plus system (Qiagen, Hilden, Germany)

treatment_protocol: Biopsies were collected and maintained in RNA later solution (Qiagen, Hilden, Germany) at -80°C

value: Normal cervix tissue

label: Alexa 647

source_name: Cervical cancer

value: Cervical cancer tissue


title: ∆AbcR1, OD 0.5, rep2

description: Delta AbcR1 vs WT_05.csv


title: OLC44_TLOm1 untreated


title: OLC64_HH 250 nM azacitidine

source_name: HH Cutaneous T cell Lymphoma

value: HH


title: OLC63_HH 125 nM azacitidine


title: ∆AbcR1, OD 0.5, rep1

description: Delta AbcR1 vs WT_05.csv


title: GmNAC81 80 days 3

city: Viçosa

first: Otavio Jose

middle: Bernardes

last: Brustolini

state: MG

address: Av. PHRolfs, S/N

department: Bioquimica e Biologia Molecular

country: Brazil

institute: Universidade Federal de Viçosa

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Glycine max Wm82.a2.v1 whole genome using HISAT 2 v2.1.0 with default parameters
Reads were counted by Rsubread/featureCounts with parameters -p (isPairedEnd)

organism: Glycine max

source_name: GmNAC81-3 at R6 developmental stage

growth_protocol: Under normal growth condition

extract_protocol:
User Guide Trizol™Reagent Invitrogen
TruSeq® Stranded Sample Preparation utilizando o Low Sample (LS) Protocol da Illumina

value: GmNAC81 overexpression

value: leaf

tag: developmental stage


title: ∆vtlR/lsrB, OD 0.5, rep3

description: Delta vtlR lsrB vs WT_05.csv

source_name: Agrobacterium fabrum C58 ∆vtlR/lsrB at optical density (600 nm) 0.5; total RNA

value: <delta>vtlR/lsrB (<delta>atu2186)


title: GmNAC81 80 days 2


title: Wild Type 80 days 3

source_name: BR16 at R6 developmental stage

value: Wild Type


title: GmNAC81 20 days 3

source_name: GmNAC81-3 at V3 developmental stage


title: GmNAC81 80 days 1


title: GmNAC81 20 days 2


title: Wild Type 80 days 2


title: ∆vtlR/lsrB, OD 0.5, rep2

description: Delta vtlR lsrB vs WT_05.csv


title: OLC60_HH untreated

source_name: HH Cutaneous T-cell Lymphoma


title: Wild Type 80 days 1


title: ∆vtlR/lsrB, OD 0.5, rep1

description: Delta vtlR lsrB vs WT_05.csv


title: Wild Type 20 days 3

source_name: BR16 at V3 developmental stage


title: Wild Type 20 days 2


title: Wild Type 20 days 1


title: OLC62_HH 50 nM azacitidine

value: 50 nM azacitidine


title: 110-12_RNA_CKF4034_RNA_Rep3_Mo

city: Athens

first: Zachary

last: Lewis

state: GA

address: 1000 Cedar St. Biosciences Bldg

department: Microbiology

institute: University of Georgia

data_processing:
Trimmed with TrimGalore! Version version 4.0 parameters --length 20 --fastqc
alignment with bwa mem version 0.7.15/ parameters -M
conversion to bam and sorted and indexed with samtools version 1.9/
create tag directory with HOMER version 4.8/ parameters -keepOne
tdfs created with IGVtools
Genome_build: MG8 GenBank (GCA_000002495.2)
Supplementary_files_format_and_content: tdf files

organism: Pyricularia oryzae

source_name: rice blast fungus mycelium

growth_protocol: 5 days liquid culture growth for ChIP/RNA samples

extract_protocol:
Cells lysed using probe sonicator
Illumina TruSeq ChIP / Illumina TruSeq stranded RNA

tag: synonym

value: Magnaporthe oryzae

value: mycelium


title: 110-11_RNA_CKF4034_RNA_Rep2_Mo


title: GmNAC81 20 days 1


title: 110-10_RNA_CKF4034_RNA_Rep1_Mo


title: 110-9_RNA_CKF3472_RNA_Rep3_Mo


title: 110-8_RNA_CKF3472_RNA_Rep2_Mo


title: A549-ACE2 plus DMSO rep 3

city: New York City

first: Zharko

last: Daniloski

state: New York

address: 1 Washington square village, 2P

department: Biology

institute: New York University

description: note for each sample there are 4 raw files (1 per lane)

data_processing:
Reads were aligned to hg19 using STAR aligner via the RNA-Seq Alignment application (Basespace, Illumina). Alignments to the SARS-CoV-2 genome (GenBank: MN985325.1) were determined using bowtie (Robinson et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Raw guide counts per gene per sample

source_name: A549-ACE2 plus DMSO

growth_protocol: A549-ACE2 cells were grown in DMEM supplemented with 10% FBS

extract_protocol:
RNA was extracted using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.
RNA-seq libraries were built from 1ug of RNA per sample.

treatment_protocol: A549-ACE2 cells were treated with DMSO or Amlodipine at 10 uM and infected with SARS-CoV-2 at MOI of 0.1

value: human alveolar basal epithelial carcinoma cells

value: DMSO only


title: A549-ACE2 plus DMSO rep 1


title: A549-ACE2 plus DMSO and SARS-CoV-2 rep 3

source_name: A549-ACE2 plus DMSO and SARS-CoV-2

value: DMSO and SARS-CoV-2


title: A549-ACE2 plus DMSO rep 2


title: 110-7_RNA_CKF3472_RNA_Rep1_Mo


title: 110-6_RNA_CKF3790AB_RNA_Rep3_Mo


title: A549-ACE2 plus Amlodipine only rep 3

source_name: A549-ACE2 plus Amlodipine only

value: Amlodipine only


title: E1: solitary_eimyoma_from_patient E

city: Chendu

first: Luqi

last: Xue

state: Sichuan

address: Renming road 3rd 20

institute: West China Second University Hospital

hyb_protocol: 1.Prepare the hybridization mix in a PCR tube as follows:Labeled sample 12.5ul, 2×Hybridization buffer 90ul, Nuclease-free Buffer 77.5ul. 2.Incubate at 95°C for 2 min. During the incubation the target preparation should be protected from light. 3.Leave on ice for at least 2 min. and up to 15min. Briefly spin the reaction after ice incubation. 4.Take cover slide out of the package. 5.Carefully laid the miRCURYTM Array on top of the assembly of cover slide and spacer, where the printed side of array should be facing toward the cover slide, to form a hybridization assembly. The printed side of array is on the side of the label. 6.Insert the hybridization assembly into a (3.1 x 9cm) heat-shrank hybridization (hyb.) bag. Sample loading side of the hybridization assembly should face the opening side of film bag. Lower the assembly to the end of the bag (Assembly viewed from the other side). 7.Clip the bag with a clipper “securely” from the opening end. Immerse the assembly to the rim of the slide in 95℃ hot water swiftly (approximately 2~5 sec). Do not dip the assembly too far into the water to avoid water leaking into the assembly. The hyb. bag will shrink and tightly wrap around the assembly. 8.Remove the assembly from water and wipe off the water from the assembly. Trim off the excess film from the top of the assembly. Keep the assembly in a 50℃ oven for at least 10 minutes. 9.Load the180ul target hybridization mix into the assembly through the sample loading opening. Fill up the hybridization space with 1X Hybridization buffer till the liquid level reaches to approximately 5 mm (0.5cm) away from the top rim. 10.Cut the second Hyb. Bag to approximately one-half of its original length. 11.Keep the assembly vertical and slip on the shortened hyb. bag from step 11 all the way until the assembly reaches the end of the hyb. bag. 12.Use a pair of forceps to hold onto the top of the assembly. Immerse the entire assembly into 95℃ hot water with the assembly in upright position. 13.Place the hybridization assembly into a 56℃ oven and set it on a rotator. Remember to rotate the assembly at 2 rotations per minute (RPM) for overnight. 14.After hybridization, disassembled the hybridization assembly, and wash the slides at 56℃ for 2min. using Wash buffer A. 15.Wash briefly at room temperature in Wash buffer B. 16.Wash for 2min. at room temperature in Wash buffer B. 17.Wash for 2min. at room temperature in Wash buffer C. 18.Wash briefly in water. 19.Dry the slides by centrifugation for 5 min. at 200* g(1000rpm). Scan slides immediately after drying.

scan_protocol: 1.Scanning is performed with the Axon GenePix 4000B microarray scanner. 2.GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing:
1.The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged.
2.We use Median Normalization Method to obtain “Normalized Data”, Normalized Data= (Foreground-Background)_x001F_/_x001F_median, the median is 50 percent quantile of microRNA intensity which is larger than 30 in all samples after background correction.
3.After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test.
4.Unsupervised hierarchical clustering and Correlation analysis was performed on miRNA data.

label: Hy3 fluorescent label

source_name: multiple leimyoma from patient E

label_protocol:
1.Place all kit components on ice and thaw for 15- 20 min. Mix thoroughly by vortexing followed by brief centrifugation.
2.Combine reagents(Total RNA,CIP buffer,CIP enzyme) . Mix on ice:Reagent should be combined in an RNase-free microcentrifuge tube and should be mixed by pipetting up and down to ensure that all reagents are mixed thoroughly. In order to minimize variation between slides, master mixes is prepared for CIP reaction.
3.Incubate 30 min.at 37℃, using a PCR cycler with heated lid.
4.Stop the enzyme reaction and denaturate the RNA by incubation at 95℃ followed by snap cooling on ice.
5.Leave on ice for at least 2 min. and up to 15min. Briefly spin the reaction after incubation on ice.
6.Combine reagents(CIP reaction from step5, Labeling buffer, Fluorescent label, DMSO,Labeling enzyme). Mix on ice.
7.Mix the reagents by gentle vortexing or by pipetting up and down to ensure that all reagents are mixed thoroughly.
8.Incubate at 16°C for 1hour, using a PCR cycler with heated lid. Protect the reaction from light.
9.Incubate for 15 min. at 65°C. After stopping the labeling procedure, briefly spin the reaction and leave it at 4°C. The labeled sample is now ready for hybridization on the array. Hybridization on the array. Hybridization should preferably occur within 1-2h.

extract_protocol: The frozen 12 tissues were cryopulverised to fine powder with the BioPulverizer (BioSpe, America). The powdered tissue was homogenised with TRIzol Reagent (Invitrogen) using the Mini-beater-16 (BioSpec), and total RNA was purified using the RNeasy Mini Kit (Qiagen). The quality of the total RNA was verified by spectrophotometry using NanoDropND-1000 (ND-1000, Nanodrop Technologies). The integrity of RNA was evaluated by denaturing agarose gel electrophoresis.

tag: gender

value: female

value: mutiple leimyoma diagnosed according to surgical findings

tag: age

value: 30 years

tag: diameter of leimyoma

tag: number of leimyoma


title: F1: solitary_eimyoma_from_patient F

source_name: multiple leimyoma from patient F

value: 49 years


title: F2: normal_myometrium_from_patient F

source_name: adjacent normal myometrium of mutiple leimyoma F

value: adjacent normal myometrium of multiple leimyoma


title: A549-ACE2 plus DMSO and SARS-CoV-2 rep 2


title: E2: normal_myometrium_from_patient E

source_name: adjacent normal myometrium of mutiple leimyoma E


title: A549-ACE2 plus Amlodipine only rep 2


title: D2: normal_myometrium_from_patient D

source_name: adjacent normal myometrium of mutiple leimyoma D

value: 44 years


title: Tissue_Healthy control1_rep1

city: Guangzhou

first: Yudong

last: Liu

state: Guangdong

address: No. 56, Lingyuan west road

department: Department of Implantology

institute: Sun Yat-sen University

description:
LncRNA and mRNA expression in healthy periodontal tissue
HP003R

hyb_protocol: 0.6 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 40 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in a rotating Agilent Hybridization Oven. The hybridized arrays were washed in Gene Expression Wash Buffer 1 (part number 5188-5325, Agilent, CA, USA) and Gene Expression Wash Buffer 2 (part number 5188-5326, Agilent, CA, USA).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (part number G2565BA, Agilent, CA, USA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 6 out of 18 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: Healthy periodontal tissue

label_protocol: The extracted RNA was amplified and transcribed into cyanine-3 (Cy3) labeled cRNAs using a Quick Amp Labeling Kit, One-Color (part number 5190-0442, Agilent, CA, USA) according to the manufacturer's instructions. Then the labeled cRNAs were purified using an RNeasy Mini Kit (Qiagen, CA, USA). The yield and specific activity of cRNAs were determined by NanoDrop ND-1000.

extract_protocol: Tissue samples of peri-implantitis group, periodontitis group, and healthy control had been homogenized using Mini-Bead-Beater-16 (BioSpec, U.S.) and total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, U.S.) according to the manufacturer’s protocol. The amount and quality of RNA was measured by NanoDrop ND 1000. The RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Samples that meet the standard were selected for further experiments.

treatment_protocol: Tissue samples were gently collected during surgical treatments, i.e., open surgical treatments of peri-implantitis and periodontitis, wisdom teeth removal and surgical crown lengthening. Then the samples were put into RNAlater (Ambion, Life Technologies, Darmstadt, Germany) immediately and stored at 4°C overnight. Then the samples were frozen at -80°C for long-term storage.

tag: subject status

value: healthy individual

value: male

value: Healthy periodontal tissue

tag: tooth site

tag: probe depth


title: A549-ACE2 plus DMSO and SARS-CoV-2 rep 1


title: Tissue_Healthy control4_rep1

description:
LncRNA and mRNA expression in healthy periodontal tissue
HP011R


title: Tissue_Periodontitis_Patient6_rep1

description:
LncRNA and mRNA expression in inflamed periodontal tissue
P027R

source_name: Inflamed periodontal tissue

value: periodontitis patient

value: Inflamed periodontal tissue


title: Tissue_Periodontitis_Patient5_rep1

description:
LncRNA and mRNA expression in inflamed periodontal tissue
P022R


title: 110-5_RNA_CKF3790AB_RNA_Rep2_Mo

value: Magnaporthe oryzae


title: 110-4_RNA_CKF3790AB_RNA_Rep1_Mo

value: mycelium


title: A549-ACE2 plus Amlodipine only rep 1

value: human alveolar basal epithelial carcinoma cells


title: A549-ACE2 plus Amlodipine and SARS-CoV-2 rep 3

value: Amlodipine and infected with SARS-CoV-2


title: Tissue_Healthy control3_rep1

description:
LncRNA and mRNA expression in healthy periodontal tissue
HP006R


title: Tissue_Healthy control6_rep1

description:
LncRNA and mRNA expression in healthy periodontal tissue
HP024R


title: D1: solitary_eimyoma_from_patient D

source_name: multiple leimyoma from patient D

value: more than 50


title: C2: normal_myometrium_from_patient C

source_name: adjacent normal myometrium of solitary leimyoma C

value: 43 years


title: A549-ACE2 plus Amlodipine and SARS-CoV-2 rep 1


title: 110-3_RNA_CKF558_RNA_Rep3_Mo


title: Tissue_Healthy control5_rep1

description:
LncRNA and mRNA expression in healthy periodontal tissue
HP013R

value: female


title: 110-1_RNA_CKF558_RNA_Rep1_Mo


title: 110-2_RNA_CKF558_RNA_Rep2_Mo


title: Tissue_Periodontitis_Patient2_rep1

description:
LncRNA and mRNA expression in inflamed periodontal tissue
P006R


title: 110-27_ChIP_mogti1_K36me3_rep2_Mo_5days

library_source: genomic

tag: chip antibody


title: Tissue_Periodontitis_Patient3_rep1

description:
LncRNA and mRNA expression in inflamed periodontal tissue
P011R


title: B1: solitary_eimyoma_from_patient B

source_name: solitary leimyoma from patient B

value: solitary leimyoma diagnosed according to surgical findings


title: ECCITE-seq GDO Rep2_Lane2: A549-ACE2

data_processing:
library strategy: ECCITE-seq (Expanded CRISPR-compatible Cellular Indexing of Transcriptomes and Epitopes by sequencing)
ECCITE-seq RNA reads were mapped to the human genome (hg38, ensembl v97). Transcripts were quanitfied using CellRanger v3.0.1
HTO and GDO counts were quantified using CITE-seq-count v1.4.2. (https://github.com/Hoohm/CITE-seq-Count)
Cells were demultiplexed based on their HTO counts into their experimental conditions after normalization (centered log ratio transformation, margin = 2) using the HTOdemux or MULTISeqDemux function in Seurat.
gRNA identitied were assigned using MULTISeqDemux unless otherwise specified in the methods section of the manuscript.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data provided in standard CellRanger output format for cDNA, GDO, and HTO. Each sample has 3 tab separated files separate into features, barcodes and a sparse matrix file.

source_name: ECCITE-seq GDO: A549-ACE2

growth_protocol: Human alveolar basal epithelial carcinoma cells (A549, ATCC CCL-185) were maintained at 37C and 5% CO2 in D10 media, which consists of DMEM (Caisson Labs) with 10% Serum Plus II Medium Supplement (Sigma-Aldrich)

extract_protocol: ECCITE-seq (10x genomics 5prime V1): We divided the ECCITE-seq pool into several sub-pools and performed cell-hashing. Cell hashing was performed as described in a previously published protocol (Mimitou et al., 2019). For the ECCITE-seq experiment, we ran four lanes of a 10x Genomics 5’ kit (Chromium Single Cell Immune Profiling Solution v1.0, #1000014, #1000020, #1000151) targeting recovery of 12,000 cells per lane (superloading) in experiment 1 and 20,000 cells in experiment 2. Gene expression (mRNA), hashtags (Hashtag-derived oligos, HTOs) and guide RNA (Guide-derived oligos, GDOs) libraries were constructed by following 10x Genomics and ECCITE-seq protocols.

treatment_protocol: Lentivirus was produced via transfection of the minipool with appropriate packaging plasmids (psPAX2: Addgene 12260; pMD2.G: Addgene 12259) using polyethylenimine (PEI) reagent in HEK293FT. The target A549ACE2 cells were transduced in presence of polybrene (10 μg/mL, Santa Cruz) (ECCITE-Seq replicate 1) or without (ECCITE-seq replicate 2) at very low MOI to ensure entry of a single virus per cell. The survival was below 5% after 2 days of selection with 2 μg/mL puromycin (Thermo) for both ECCITE-seq experiments. On day 10 post-transduction, the cells were collected and processed for ECCITE-seq.

tag: cell type

value: human alveolar basal epithelial carcinoma cell line

value: trangenic ACE2 overexpression


title: B2: normal_myometrium_from_patient B

source_name: adjacent normal myometrium of solitary leimyoma B

value: 49 years


title: C1: solitary_eimyoma_from_patient C

source_name: solitary leimyoma from patient C


title: ECCITE-seq GDO Rep2_Lane1: A549-ACE2

tag: genotype/variation


title: 110-26_ChIP_mogti1_K27me3_rep2_Mo_5days

source_name: rice blast fungus mycelium

tag: tissue

value: #81 get info


title: Tissue_Periodontitis_Patient1_rep1

description:
LncRNA and mRNA expression in inflamed periodontal tissue
P001R


title: ECCITE-seq HTO Rep2_Lane2: A549-ACE2

source_name: ECCITE-seq HTO: A549-ACE2


title: A2: normal_myometrium_from_patient A

source_name: adjacent normal myometrium of solitary leimyoma A

value: 33 years


title: 110-25_ChIP_mogti1_K9me3_rep2_Mo_5days

value: #84 get info


title: ECCITE-seq HTO Rep2_Lane1: A549-ACE2


title: J-Lat_8.4_EGCG-treated

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description: EGCG

hyb_protocol: genomic DNA was bisulfite-converted using an EZ DNA methylation Kit (ZYMO research). DNA methylation level was measured using the Illumina Infinium HD Methylation Assay. Bisulfite converted DNA was hybridized with the Illumina HumanMethylation850 BeadChip 850K array (8 samples/chip), as described previously. (Dedeurwaerder et al, Epigenomics 2011).

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

data_processing: Raw data (uncorrected probe intensity values) from the Infinium Methylation arrays were processed according to the recommended steps of Dedeurwaerder et al : Probes of low quality (detection p-value < 0.05) and cross-reactive probes based on the extended annotation of Mc Cartney et al. were removed. Additionally, probes targeting X and Y-chromosomes were removed from the analysis. Beta-values were computed using the following formula: Beta-value = M/[U+M] where M and U are the raw “methylated” and “unmethylated” signals, respectively. Beta-values were corrected for type I and type II bias using the peak-based correction (dedeurwaerder et al).

source_name: J-Lat treated with EGCG drug

label_protocol: Standard Illumina Protocol

growth_protocol: The CD4+ T-lymphoid J-Lat 8.4 cell line was obtained from the AIDS Research and Reference Reagent Program (National Institute of Allergy and Infectious Diseases [NIAID], National Institute of Health [NIH]). Cell lines and primary cell models were grown in RPMI 1640 medium (Gibco-BRL) supplemented with 10 % foetal bovine serum, 50 U/ml of penicillin and 50 µg/mL of streptomycin. All cells were cultivated at 37°C in a humidified 95 % air / 5 % CO2 atmosphere.

extract_protocol: Genomic DNA was extracted using the DNeasy Blood and Tissue kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Cells were either treated or not for 24h with 70µg/mL of EGCG (E4143, Sigma Aldrich) or mock-transduced, transduced with a control non-targeting shRNA (SHC016, Sigma Aldrich) or a UHRF1-targeting shRNA (Sigma Aldrich).

value: CD4+ T-lymphoid J-Lat 8.4

tag: experiment

value: treated

tag: condition

value: EGCG


title: ECCITE-seq cDNA Rep2_Lane2: A549-ACE2

source_name: ECCITE-seq cDNA: A549-ACE2

tag: cell line


title: J-Lat_8.4_shUHRF1-transduced

source_name: J-Lat transduced with a shRNA targeting UHRF1 gene

value: transduced


title: Tissue_Peri-implantitis_Patient6_rep1

description:
LncRNA and mRNA expression in inflamed peri-implant tissue
I025R

source_name: Inflamed peri-implant tissue

value: peri-implantitis patient

value: male

value: Inflamed peri-implant tissue


title: w_477

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
Peired-end reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to the reference sequence (mm10 from UCSC)
Mouse reference was used for gene annotation and counting (gencode vM17). Uniquely mapped reads were quantified using HTSeq python suite using protein coding genes by exon.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Input tables are included as tab separated files.

source_name: Brain

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. All RNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer (Agilent).
Samples were randomized for library preparation and sequencing. 2ug of total RNA were enriched for mRNA with poly-A selection beads. Libraries and sequencing were performed at the BGI Americas Corporation (Cambridge, MA).

value: whole cortex

tag: genotype

value: Mef2c wild type

value: M

tag: rin

tag: protocol

value: Protocol 1


title: Tissue_Peri-implantitis_Patient3_rep1

description:
LncRNA and mRNA expression in inflamed peri-implant tissue
I011R

tag: gender

value: female


title: 110-22_ChIP_dkmt6+kmt6?_K27me3_rep1_Mo_5days

tag: synonym

value: Magnaporthe oryzae

value: mycelium


title: Tissue_Peri-implantitis_Patient5_rep1

description:
LncRNA and mRNA expression in inflamed peri-implant tissue
I022R

tag: age


title: J-Lat_8.4_mock-transduced

source_name: J-Lat transduced with mock control

value: Mock


title: A549-ACE2 plus Amlodipine and SARS-CoV-2 rep 2

value: human alveolar basal epithelial carcinoma cells

tag: treatment

value: Amlodipine and infected with SARS-CoV-2


title: 110-24_ChIP_mogti1_K4me2_rep2_Mo_5days


title: w_498


title: J-Lat_8.4_mock-treated

source_name: J-Lat treated with mock control

value: CD4+ T-lymphoid J-Lat 8.4


title: A1: solitary_eimyoma_from_patient A

source_name: solitary leimyoma from patient A

value: solitary leimyoma diagnosed according to surgical findings

value: 33 years

tag: diameter of leimyoma

tag: number of leimyoma


title: h_501

value: Mef2c heterozygous

value: F


title: ECCITE-seq GDO Rep1_Lane2: A549-ACE2

value: human alveolar basal epithelial carcinoma cell line

value: trangenic ACE2 overexpression


title: w_502

value: whole cortex


title: Tissue_Peri-implantitis_Patient4_rep1

description:
LncRNA and mRNA expression in inflamed peri-implant tissue
I021R

tag: subject status

value: peri-implantitis patient

value: male

value: Inflamed peri-implant tissue

tag: tooth site

tag: probe depth


title: 110-20_ChIP_dkmt6+kmt6?_K27me3_rep2_Mo_5days

tag: chip antibody

value: #81 get info


title: 110-23_ChIP_mogti1_input_rep2_Mo_5days

value: Magnaporthe oryzae

tag: tissue

value: input


title: ECCITE-seq HTO Rep1_Lane2: A549-ACE2

tag: cell type

tag: genotype/variation


title: J-Lat_8.4_non-targeting_shRNA-transduced

description: shNT

source_name: J-Lat transduced with a non-targeting control shRNA

tag: cell line

tag: experiment

value: transduced

tag: condition

value: shNT


title: ECCITE-seq cDNA Rep2_Lane1: A549-ACE2


title: ste12-induced-LNM-rep3

city: Taipei

first: Yen-Ping

last: Hsueh

state: -- Select --

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
Adapter trimming and quality filtering of pair-end raw reads with Fastp version 0.20.0 (fastp  -l 100 -f 0 -F 0 -t 10 -T 10 -i R1.fastq.gz -I R2.fastq.gz)
Mapping and quantification of reads against a reference transcriptome of A. oligospora TWF154 was done with Salmon v1.0.0 (salmon quant -i Ao_TWF154_Salmon_Index -l A --numBootstraps 200 -1 R1_filtered.fastq.gz -2 R2_filtered.fastq.gz
Transcript abundance estimates from Salmon were converted to a Sleuth-compatible format using the Wasabi package version 0.2
Likelihood ratio and Wald tests were performed to establish overall and differential expression for each transcript using the Sleuth program
Supplementary_files_format_and_content: Spreedsheet table with all the betas, normalized TPMs, and statistics from LTR tests merged toegher.

organism: Orbilia oligospora

source_name: TWF154 reference strain

growth_protocol: Fungal mycelium were plated on low nutritent medium (LNM) agar plates for 5 days at 25 °C

extract_protocol:
Total RNA was extracted from lyophilized samples via a Trizol-chloroform based protocol
Library preparation for total RNA samples (Genomic Core Facility, Institute of Molecular Biology, Academia Sinica) were carried out using the Illumina TruSeq stranded mRNA library preparation kit.

treatment_protocol: Approximately 2000 C. elegans N2 strain at L4 larval stage were placed on each fungal plate. The nematodes were washed away after 4 hours of treatment with deionized water. The fungal mycelium was immediately collected with a  cell scraper, frozen in liquid nitrogen, and lyophilized.

tag: strain

tag: genotype

value: ku70::hph ste12::nat1

value: Treated


title: w_473

value: Mef2c wild type

tag: gender

tag: rin

tag: protocol

value: Protocol 1


title: ECCITE-seq HTO Rep1_Lane1: A549-ACE2


title: Tissue_Peri-implantitis_Patient1_rep1

description:
LncRNA and mRNA expression in inflamed peri-implant tissue
I003R

tag: age


title: Tissue_Peri-implantitis_Patient2_rep1

description:
LncRNA and mRNA expression in inflamed peri-implant tissue
I009R

value: female


title: ste12-control-LNM-rep1

tag: treatment

value: Untreated


title: ste12-control-LNM-rep3


title: h_499

value: Mef2c heterozygous

value: M


title: ste12-induced-LNM-rep1


title: ECCITE-seq GDO Rep1_Lane1: A549-ACE2

value: human alveolar basal epithelial carcinoma cell line

value: trangenic ACE2 overexpression


title: ku70-induced-LNM-rep2


title: 110-16_ChIP_WT_K9me3_rep2_Mo_5days

tag: synonym

value: mycelium

value: #84 get info


title: 110-19_ChIP_dkmt6+kmt6?_input_rep2_Mo_5days


title: CRISPR screen SARS-CoV-2 MOI 0.3

description: guide RNA was recovered from genomic DNA by PCR.

data_processing:
Sequencing reads were demultiplexed upon sequencing based on Illumina i7 barcodes present in PCR2 reverse primers using Illumina BaseSpace.
Adaptor trimming was performed by treating the hU6 promoter sequence as a 5’ adapter, using cutadapt v1.13 [-e 0.2 -O 5 -m 20 -g TCTTGTGGAAAGGACGAAACACCG].
Processed guide RNA sequences were aligned to the GeCKOv2 reference allowing for up to 1 mismatch using bowtie v1.1.2  [-a --best --strata -v 1 –norc] with alignment rates of 81% to 86%.
Genome_build: The reference sequence for each guide is available here: https://www.addgene.org/pooled-library/zhang-human-gecko-v2/
Supplementary_files_format_and_content: Raw guide counts per gene per sample.

growth_protocol: A549-ACE2 cells were grown in DMEM supplemented with 10% FBS.

extract_protocol:
Genomic DNA (gDNA) was extracted using a previously described protocol (Chen et al., 2015). For the first PCR reaction, we used all gDNA available for each sample.
We performed 2 PCR reactions. PCR1 was performed using Taq-B polymerase (Enzymatics) and used multiple reactions where each reaction contained up to 10 µg gDNA per 100 mL PCR reaction. PCR1 products for each sample were pooled and used for amplification with barcoded PCR2 primers. For each sample, we performed 12 PCR2 reactions (using 5 µL of the pooled PCR1 product per PCR2 reaction) with Q5 polymerase (NEB). PCR2 products were pooled and then normalized within each biological sample before combining uniquely-barcoded separate biological samples. The pooled product was then gel-purified from a 2% E-gel EX (Life Technologies) using the QiaQuick gel extraction kit (Qiagen). The purified, pooled library was then quantified with Tapestation 4200 (Agilent Technologies). PCR products were run on a 2% agarose gel and the correct size band was extracted. Sequencing was performed on the NextSeq 550 instrument using the HighOutput Mode v2 with 75 bp paired-end reads (Illumina). All PCR1 and PCR2 primer sequences, including full barcodes, are listed on the GeCKO website (http://genome-engineering.org/gecko ).

treatment_protocol: A549-ACE2 cells were infected with SARS-CoV-2 at MOI of 0.01 or 0.3.

value: Adenocarcinomic human alveolar basal epithelial cells

value: SARS-CoV-2 infection at MOI 0.3

tag: time point

value: 6 days post-infection


title: ste12-control-LNM-rep2


title: 110-18_ChIP_WT_K36me3_rep2_Mo_5days

value: Magnaporthe oryzae


title: ste12-induced-LNM-rep2


title: 110-17_ChIP_WT_K27me3_rep2_Mo_5days

value: #81 get info


title: h_471

value: whole cortex


title: 107-93_ChIP_3790AB_mogti1_K36me3_rep1_Mo_5days


title: 110-13_ChIP_WT_input_rep2_Mo_5days

value: input


title: ku70-induced-LNM-rep1

value: Treated


title: h_472

value: F

value: Protocol 1


title: 110-15_ChIP_WT_K4me2_rep3_Mo_5days


title: CRISPR screen SARS-CoV-2 MOI 0.01

value: SARS-CoV-2 infection at MOI 0.01


title: Human Liver Biopsy  PT-20

city: Tübingen

first: MENGJIE

last: QIU

address: Otfried-Müller-Str. 37

institute: M3 Forschungszentrum für Malignom, Metabolom und Mikrobiom

description: Human Liver Biopsy

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000.
De-multiplexing and barcode processing were performed using the Cell Ranger Software Suite (Version 4.0.0). Specifically, the reads were aligned to the human GRCh38 using STAR1.Finally, a gene-barcode matrix containing the cell barcodes and gene expression counts for each individual sample was generated by counting the single-cell 3’ UMIs.
The gene barcode matrix was then imported to Seurat v3 in R (v4.0.2). Quality control was implemented by removing cells with more than 10% mitochondrial genes, fewer than 200 genes per cell or more than 6000 genes per cell. Then, the data was normalized, scaled and integrated within Seurat v3 to remove batch effects across samples. In this project, only CD3+ cells were retained for the downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample; A gene expression matrix, a document of barcodes and a document of all features are included for each sample.
Supplementary_files_format_and_content: A comma-delimited text file including the integrated and processed gene expression matrix for CD3+ cells in 10 samples
Supplementary_files_format_and_content: A comma-delimited text file including the metadata of the integrated matrix processed by Seurat

source_name: Liver

growth_protocol: Tissues were immediately digested and single cells harvested and stored.

extract_protocol:
Collected  liver tissue samples were placed in complete media (RPMI+10% FBS) on ice and  immediately further processed. Single cell suspensions were generated by  mincing freshly obtained liver tissue specimen into 1 mm cubic pieces,  followed by enzymatic digestion using the Miltenyi tumor dissociation  kit. Digestion was carried for 20 minutes at 37°C with constant shaking and stopped by adding RPMI +20%FBS. The digested tissues were then passed through a 70 um cell strainer and centrifuged at 350 g for 10 minutes. RBC lysis was carried out with ACK lysis buffer (Thermo Fischer Scientific Cat no. A1049201) and cells were washed with complete media and once more strained through a 45 µm mesh.
Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128)

treatment_protocol: Naïve human liver biopsy samples without any additional treatment

tag: pathology

value: Healthy Human Liver

value: Liver Biopsy

value: Undergoing Bariatric surgery

tag: sample type

value: CD45+ Single cells from Liver


title: ku70-control-LNM-rep3

value: Untreated


title: GeCKOv2 plasmid library

description: guide RNA was recovered from plasmid by PCR.

source_name: plasmid

value: GeCKOv2 plasmid library


title: 110-14_ChIP_WT_K4me2_rep2_Mo_5days

tag: tissue

value: mycelium

tag: chip antibody


title: CRISPR screen pre-infection

tag: cell type

value: Adenocarcinomic human alveolar basal epithelial cells

value: Pre-infection


title: 107-91_ChIP_3790AB_mogti1_K9me3_rep1_Mo_5days

value: Magnaporthe oryzae


title: ECCITE-seq cDNA Rep1_Lane2: A549-ACE2

tag: cell line

value: human alveolar basal epithelial carcinoma cell line

tag: genotype/variation

value: trangenic ACE2 overexpression


title: ECCITE-seq cDNA Rep1_Lane1: A549-ACE2


title: ku70-control-LNM-rep2


title: ku70-control-LNM-rep1


title: Human Liver Biopsy  PT-19

description: Human Liver Biopsy

value: NASH


title: 107-90_ChIP_3790AB_mogti1_K4me2_rep1_Mo_5days


title: Human Liver Biopsy  PT-21

description: Human Liver Biopsy


title: FS_Beta3

city: Boston

first: Nabil

last: Rabhi

state: Massachusetts

address: Silvio Conte Building, 72 E. Concord St

department: Biochemistry

institute: Boston University

data_processing:
The Cell Ranger Single-Cell Software Suite (v.3.1.0) was used to perform sample demultiplexing, barcode processing, single-cell 3′ counting, and counts alignment to mm10 mouse reference genome
Cellranger mkfastq was used to demultiplexes raw base call files
Cellranger count was used to takes FASTQ files from cellranger mkfastq and performs alignment, filtering, barcode counting, and UMI counting.
Genome_build: mm10
Supplementary_files_format_and_content: matrix file, barcodes file and features file for each sample

source_name: inguinal adipose tissue stromal vascular fraction

extract_protocol:
inguinal white adipose tissues (WAT) from control and CL- and cold-treated mice were collected after CL treatment and processed for SVC isolation using mouse adipose tissue dissociation kit (Miltenyi biotec) according to manufactures.
10x Chromium 3'v3 libraries

treatment_protocol: One replicate was  intraperitoneally treated in vivo with CL 316,243 (1 mg/kg) for 3 days and the second one was exposed to cold (4C) for 3 days

value: inguinal adipose

tag: tissue fraction

value: stromal vascular

tag: single cell protocol

value: 10X genomic


title: FS_4C

tag: strain

value: 4 C


title: Human Liver Biopsy  PT-17

description: Human Liver Biopsy

value: Healthy Human Liver


title: Tissue_Healthy control2_rep1

description:
LncRNA and mRNA expression in healthy periodontal tissue
HP004R

source_name: Healthy periodontal tissue

tag: subject status

value: healthy individual

tag: gender

value: male

value: Healthy periodontal tissue

tag: tooth site

tag: probe depth


title: 107-92_ChIP_3790AB_mogti1_K27me3_rep1_Mo_5days

source_name: rice blast fungus mycelium

value: H3K27me3 (Cell Signaling 9733, Lot 8)


title: FS_Veh

tag: treatment

value: Saline


title: 107-89_ChIP_3790AB_mogti1_Input_rep1_Mo_5days

tag: synonym

value: mycelium

value: input


title: OCI-LY10 combo 24h

city: Badalona

first: Gael

last: Roue

address: Ctra de Can Ruti, Camí de les Escoles s/n

department: Lymphoma Translational lab

country: Spain

institute: Josep Carreras Leukaemia Research Institute

description: OCI-LY10 combo

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the Gene Titan instrument.

data_processing:
Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software (AGCC) (Affymetrix).
Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm implemented in the Expression Console Software v1.1 (Affymetrix).

label: biotin

source_name: OCI-LY10 combo 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA

growth_protocol: ABC-DLBCL cells at exponential phase were set at 1x10e6 cells/ml for the experiment

extract_protocol: Total RNA was extracted using the Trizol reagent

treatment_protocol: ABC-DLBCL cells were treated with 50µM IRAKI for 6h +/- CPI203 500nM for 18h

value: Combo

tag: time


title: Tissue_Periodontitis_Patient4_rep1

description:
LncRNA and mRNA expression in inflamed periodontal tissue
P012R

source_name: Inflamed periodontal tissue

value: periodontitis patient

value: female

tag: age

value: Inflamed periodontal tissue


title: Human Liver Biopsy  PT-16

description: Human Liver Biopsy

tag: pathology

value: Liver Biopsy

value: Undergoing Bariatric surgery

tag: sample type

value: CD45+ Single cells from Liver


title: RIPseq-Input-Mouse-Testis-rep5

city: Worcester

first: Tianxiong

last: Yu

state: MA

address: 364 Plantation St

institute: Umass Med

data_processing:
ChIP-seq data were mapped to the rhesus reference genome rheMac8 using Bowtie2 (version 1.1.0) with the parameter --very-sensitive. We then calculated read density normalized by sequencing depth (bigWig) across the rhesus genome.
Gene annotations and rRNA sequences are fetched from Ensembl (Release 82). All RIP-seq data were first mapped to ribosomal RNAs (rRNAs) using Bowtie2 (version 2.2.5) with default parameters to remove rRNAs (Langmead and Salzberg, 2012). Unmapped reads were then mapped to the mm10 genome from the UCSC genome browser using STAR (version 020201) allowing up to 2 mismatch and up to 100 mapping locations (Dobin et al., 2013). We then calculated read density normalized by sequencing depth (bigWig) across the mouse genome.
Genome_build: mm10, rheMac8
Supplementary_files_format_and_content: bigWig

source_name: Testis

extract_protocol:
One four-month-old mouse testis (C57BL/6J) was lysed in 1ml lysis buffer (pH 7.5 HEPES 50mM; KCl150mM; MgCl2 3.2mM; NP40 0.5%; PMSF 1mM; 1X Proteinase Inhibitor (Roche); and 0.4 U/ul RNAseOUT (Invitrogen)) in Dounce homogenizer.  The lysate was sonicated in Bioruptor (Diagenode; medium strength, 15 sec on/1 min off for 10 mins).  The lysate was cleared by centrifugation for 15min at 15000rpm 4°C.  One hundred microliter lysate was saved for input RNA extraction.  Rabbit anti-THOC2 or mouse anti-THOC1 antibody was conjugated to the Dynabeads (Invitrogen) protein A and protein G respectively in citric phosphate (CP) buffer (7.10 g Na2HPO4, 11.5g Citric acid in 1L water, pH 5.6) for 2 hours at room temperature with rotation.  The antibody-conjugated beads were washed three times with CP buffer with 0.1% Tween 20 and incubated with mouse testis lysate overnight at 4oC with rotation.  The beads were washed in cold lysis buffer three times.  The immunoprecipitated RNA and input RNA were extracted by RNeasy Mini kit (Qiagen).
The extracted RNA was used to generated RNA-seq library as described previously (Zhang, Z., Theurkauf, W.E., Weng, Z., and Zamore, P.D. (2012). Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence 3, 9.).

tag: tissue

value: Testis

tag: antibody

value: Input

tag: Stage

value: adult, four month


title: OCI-LY3 combo 24h

description: OCI-LY3 combo

source_name: OCI-LY3 combo 24h

tag: cell line


title: OCI-LY10 Control 24h

description: OCI-LY10 Control

source_name: OCI-LY10 Control 24h

value: Control


title: OCI-HBL1 500nM CPI203 24h

description: HBL-1 CPI203

source_name: OCI-HBL1 500nM CPI203 24h


title: OCI-HBL1 Control 24h

description: HBL-1 Control

source_name: OCI-HBL1 Control 24h


title: OCI-HBL1 combo 24h

description: HBL-1 combo

source_name: OCI-HBL1 combo 24h


title: RIPseq-Input-Mouse-Testis-rep3


title: OCI-HBL1 50µM IRAKi 6h

description: HBL-1 IRAKi

source_name: OCI-HBL1 50µM IRAKi 6h

value: IRAKi


title: OCI-LY10 500nM CPI203 24h

description: OCI-LY10 CPI203

source_name: OCI-LY10 500nM CPI203 24h


title: OCI-LY3 50µM IRAKi 6h

description: OCI-LY3 IRAKi

source_name: OCI-LY3 50µM IRAKi 6h


title: 107-88_ChIP_3721_dkmt6+kmt6_K27me3_rep2_Mo_5days

value: Magnaporthe oryzae

tag: chip antibody


title: 107-87_ChIP_3721_dkmt6+kmt6_Input_rep2_Mo_5days


title: RIPseq-Input-Mouse-Testis-rep2


title: 107-86_ChIP_3472_dkmt6_K27me3_rep2_Mo_5days

value: H3K27me3 (Cell Signaling 9733, Lot 8)


title: OCI-LY10 50µM IRAKi 6h

description: OCI-LY10 IRAKi

source_name: OCI-LY10 50µM IRAKi 6h


title: Human Liver Biopsy  PT-11

description: Human Liver Biopsy

source_name: Liver

value: Boderline NASH


title: 107-85_ChIP_3472_dkmt6_Input_rep2_Mo_5days

value: mycelium


title: RIPseq-Input-Mouse-Testis-rep1


title: Human Liver Biopsy  PT-12

description: Human Liver Biopsy

value: Healthy Human Liver


title: OCI-LY3 500nM CPI203 24h

description: OCI-LY3 CPI203

source_name: OCI-LY3 500nM CPI203 24h


title: Human Liver Biopsy  PT-8

description: Human Liver Biopsy

value: NASH


title: OCI-LY3 Control 24h

description: OCI-LY3 Control

source_name: OCI-LY3 Control 24h


title: RIPseq-Input-Mouse-Testis-rep4


title: RIPseq-HPR1-Mouse-Testis-rep3


title: control

city: seoul

first: heejae

last: han

address: dogokdong 146-92

country: South Korea

institute: yonsei gangnam severance

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

source_name: Lung

growth_protocol: Female BALB/c mice, between 5 and 6 weeks old (Orient, Daejeon, Korea), were maintained at conventional animal facilities under pathogen-free conditions, and 5 mice were assigned in each group.

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

treatment_protocol: To establish the PM10-induced murine model (PM10 model), PM10 (ERMCZ-120® certified reference material; Sigma-Aldrich, St Louis, MO, USA; 100 μg [PM100] or 200 μg [PM200]) suspended in 20 μL normal saline was intranasally administered four times over 2 weeks. To establish the OVA-induced asthma murine model (OVA model), mice were sensitized with 20 μg OVA (Sigma-Aldrich, St Louis, MO, USA) suspended in 1% aluminum hydroxide (Resorptar, Indergen, New York, NY, USA) by intraperitoneal injection on days 1 and 14. On days 21, 22, and 23, the OVA-sensitized mice were challenged intranasally with 30 µL of OVA (1 mg/mL) in saline solution. An OVA/PM10-treated model was established by the above two treatments simultaneously.

value: BALB/c

value: lung

tag: agent

value: control

tag: Sex

value: Female


title: PM10

tag: strain


title: Human Liver Biopsy  PT-5

description: Human Liver Biopsy

value: Liver Biopsy

value: Undergoing Bariatric surgery


title: Human Liver Biopsy  PT-9

description: Human Liver Biopsy

value: CD45+ Single cells from Liver


title: 107-83_ChIP_558_WT_K27me3_rep2_Mo_5days

source_name: rice blast fungus mycelium


title: Patient_8-2

city: Chicago

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior

institute: Northwestern University

description:
main.h5ad
supplement.h5ad
Sample_19

data_processing:
Reads were demultiplexed using with cellranger mkfastq command (v3.1.0). Reads were aligned to a custom built genome (human GRCh38.93 and SARS-CoV-2 NC_045512.2) and counted by gene by cell with cellranger count command (v3.1.0), producing raw and filtered gene expression matrices.
Doublets were identified and removed with scrublet v0.2.1. Ambient RNA was corrected with FastCAR (https://github.com/LungCellAtlas/FastCAR).
Samples were processed with scanpy v1.5.1, low-quality cells were removed and samples were integrated with BBKNN v1.3.12
Sample 16 contained cells from patients A and B. To assign cells to correct patients, we used souporcell v2.0 with the list of common variants for GRCh38 genome, provided on the souporcell page (https://github.com/wheaton5/souporcell) on samples 14, 15 and 16 with the number of clusters k=2. We used Pearson correlation between genotypic clusters in samples 14 & 16 and 15 & 16 to determine which genotypic clusters come from the same patients. Genotypic doublets and unassigned cells were discarded.
Genome_build: custom (human GRCh38.93 and SARS-CoV-2 NC_045512.2)
Supplementary_files_format_and_content: gene expression count matrices; anndata objects; cell metadata

source_name: Sorted macrophages and T cells

extract_protocol: Libraries were prepared with 10x Genomics 5' gene expression (GEX) reagents according to the manufacturer protocol (CG000086_RevM).

tag: individual

tag: disease state

value: COVID-19 Positive

tag: day after intubation

tag: cell type

value: Sorted macrophages and T cells


title: Patient_8-1

description:
main.h5ad
supplement.h5ad
Sample_18


title: 105-65_ChIP_CKF3721_dkmt6;kmt6+_K27me3_Rep1_Mo_5days

tag: synonym


title: RIPseq-HPR1-Mouse-Testis-rep2

value: Testis

value: adult, four month


title: day3.pab.3

city: Shanghai

first: Xiaoning

last: Ding

state: Shanghai

address: 1678 Dongfang Rd.

department: Shanghai Children's Medical Center

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Alignment was performed using STAR (version 2.5.2b) to mouse genome (Gencode, GRCm38) and mouse transcripts gtf file (Gencode vM10). The following STAR parameter was used: "STAR --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesCommand gunzip -c --outSAMunmapped Within KeepPairs"
Read counts for individual samples were compiled by genes.
Genome_build: mm10
Supplementary_files_format_and_content: text file with raw read count of each gene

source_name: Heart

extract_protocol:
The hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The neonatal mice were anaesthetized by hypothermia. It led to asystole and reversible apnea and prevented excessive blood loss. Next, they were transferred to ice bed and fixed in the supine position under a stereomicroscope. Following a transverse skin incision，horizontal thoracotomy was performed by dissecting intercostal muscles and cutting the sternum. The incision site was at the second intercostal space for mice and the third intercostal space for rats. After opening the pericardium, we carefully separated the pulmonary artery from the aorta under microscope. A 11-0 nylon thread was positioned under pulmonary artery and a 31G needle was placed upon the pulmonary artery. The pulmonary artery and needle were then tied together by the thread. After the needle was quickly removed，a fixed constricted opening equal to the diameter of the needle was created in the lumen of pulmonary artery. The sternum and thoracic wall were sutured with a 10-0nylon thread. Afterwards, neonates were removed from ice bed and placed under a heat plate to warm up for several minutes until natural movements and a red/pink complexion were achieved. Neonates were then returned to their mother. The sham group underwent the same procedure except the banding step

value: heart

value: postnatal day 3

tag: treatment

value: pulmonary artery banding surgery on P0


title: day3.pab.2

tag: age


title: 107-82_ChIP_558_WT_Input_rep2_Mo_5days

value: Magnaporthe oryzae

value: mycelium

value: input


title: RIPseq-HPR1-Mouse-Testis-rep1

source_name: Testis


title: day3.pab.1


title: RIPseq-THOC2-Mouse-Testis-rep3


title: Patient_7

description:
main.h5ad
supplement.h5ad
Sample_17


title: Patient_A+B

description:
main.h5ad
supplement.h5ad
Sample_16


title: RIPseq-rabbitIgG-Mouse-Testis-rep1

value: rabbit IgG


title: RIPseq-THOC2-Mouse-Testis-rep2


title: 107-84_ChIP_558_WT_K36me3_rep2_Mo_5days


title: 105-63_ChIP_CKF3472_dkmt6_K27me3_Rep1_Mo_5days

value: H3K27me3 (Cell Signaling 9733, Lot 8)


title: RIPseq-THOC2-Mouse-Testis-rep1


title: Patient_A

description:
main.h5ad
supplement.h5ad
Sample_14


title: 105-62_ChIP_CKF3472_dkmt6_input_Rep1_Mo_5days


title: RIPseq-HPR1-Mouse-Testis-rep5


title: 105-61_ChIP_CKF558_WT_K36me3_Rep1_Mo_5days


title: RIPseq-HPR1-Mouse-Testis-rep4


title: day7.pab.1

value: postnatal day 7


title: Patient_9-2

description:
main.h5ad
supplement.h5ad
Sample_13


title: day7.pab.2


title: day7.sham.3

value: sham surgery on P0


title: 105-60_ChIP_CKF558_WT_K27me3_Rep1_Mo_5days


title: Patient_9-1

description:
main.h5ad
supplement.h5ad
Sample_12


title: RIPseq-mouseIgG-Mouse-Testis-rep3

value: mouse IgG


title: day3.sham.3


title: 105-58_ChIP_CKF558_WT_K4me2_Rep1_Mo_5days


title: Patient_C-2

description:
supplement.h5ad
Sample_11

value: COVID-19 Negative


title: RIPseq-mouseIgG-Mouse-Testis-rep2


title: day3.sham.2


title: 105-64_ChIP_CKF3721_dkmt6;kmt6+_input_Rep1_Mo_5days


title: Mouse_M3_NucSeq

status: Public on Oct 23 2020

city: Bethesda

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

data_processing:
Data was processed through cellranger suite v3.1.0.
Fastq files were generated from raw BCL files using "cellranger mkfastq" with default settings.
Expression matrix were generated using "cellranger count" with default settings.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: filtered output in HSF format containing gene expression matrix in single-cell resolution.

source_name: Retina

extract_protocol:
Isolation of nuclei was performed using a detergent based lysis
Nuclei suspension was passed through 10x Genomics' protocol for "Chromium Single Cell 3' v2" following manufacturers instructions.

value: 3 month

tag: genotype

value: WT

tag: preparation

value: nuclei suspension


title: Patient_C-1

description:
supplement.h5ad
Sample_10

value: Sorted macrophages and T cells


title: day7.sham.2

tag: tissue


title: day3.sham.1


title: Patient_B

description:
main.h5ad
supplement.h5ad
Sample_15

value: COVID-19 Positive


title: 105-57_ChIP_CKF558_WT_input_Rep1_Mo_5days

data_processing:
Trimmed with TrimGalore! Version version 4.0 parameters --length 20 --fastqc
alignment with bwa mem version 0.7.15/ parameters -M
conversion to bam and sorted and indexed with samtools version 1.9/
create tag directory with HOMER version 4.8/ parameters -keepOne
tdfs created with IGVtools
Genome_build: MG8 GenBank (GCA_000002495.2)
Supplementary_files_format_and_content: tdf files

extract_protocol:
Cells lysed using probe sonicator
Illumina TruSeq ChIP / Illumina TruSeq stranded RNA


title: day7.sham.1

value: heart


title: 110-21_ChIP_dkmt6+kmt6?_input_rep1_Mo_5days


title: Ly5.1 WT rep3

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description: week 6 of mixed chimeras of Ltbr-/- and Ly5.1 BM LSKs, transplanted into lethally irradiated Ly5.1/Ly5.2 mice

data_processing:
Primary data analysis was performed with the Illumina RTA v2.4.11 .
The  sequence assembly and alignment was performed using the SeqMan NGen software v.16 and analyzed using ArrayStar software v.16 (DNASTAR, USA).
The level of gene expression was assessed using regularized logarithm (rlog) values from Bioconductor (DESeq2).
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Tab-delimited text file includes raw DESeq2 values.

source_name: LT/ST-HSCs

extract_protocol:
Total RNA was extracted from FACS-purified LT/ST-HSCs using the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Libraries were generated from 20ng total RNA using the TruSeq Stranded mRNA Library Prep Kit High Throughput (Illumina, San Diego, CA, USA).

treatment_protocol: Ltbr-/- and Ly5.1 LT/ST-HSCs isolated from week 6 chimeric mice.

tag: donor strain

value: bone marrow

tag: donor age

value: 7-13 weeks


title: Ly5.1 WT rep2


title: 105-59_ChIP_CKF558_WT_K9me3_Rep1_Mo_5days

value: Magnaporthe oryzae


title: Ly5.1 WT rep1


title: Ltbr KO  rep3

value: Ltbr KO

value: 10-13 weeks


title: EP_DMC1_ChIPSeq Rep 2

city: Bar Harbor

first: Natalie

middle: R

last: Powers

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description:
Sample 4
DMC1 ChIP-seq, B6.Prdm9EP/EP Rep2
EPHom_DMC1_ChIP_merge_mm10_RPM.bedgraph
EPHom_DMC1_merge_DMC1Peaks.bed
EPHom_DMC1_merge_DMC1peaks_Hotspots.bed
EPHom_DMC1_merge_DMC1peaks_DefaultSites.bed
Fastq file containing selected reads from single-stranded fragments: EPHom_DMC1_ChIP_Rep2_single-stranded.fastq.gz (SRR12060571)

data_processing:
(Samples 1 and 2) Single-end ChIP-Seq reads were trimmed with Trimmomatic and aligned to the mm10 genome assembly using BWA v0.7.9a
(Samples 1 and 2) ChIP-Seq reads were filtered to remove duplicates and to keep only uniquely mapped reads
(Samples 1 and 2) ChIP-Seq peaks were called using MACS v1.4
(Samples 3 and 4) Paired-end ChIP-Seq reads were trimmed with Trimmomatic and aligned to the mm10 genome assembly using BWA v0.5.10-tpx
(Samples 3 and 4) Bam files were parsed for detection of single-ended reads indicative of single-stranded fragments, using the micro-homologous region
(Samples 3 and 4) Fastq files containing only the selected reads were generated
(Samples 3 and 4) Fastq files containing only the selected reads were aligned to the mm10 genome using BWA v0.7.9a
(Samples 3 and 4) ChIP-seq peaks were called using MACS v2.1.0.20151222
Genome_build: mm10

source_name: spermatocytes

extract_protocol:
Testes were decapsulated, fixed with 1% formaldehyde, and homogenized to isolate germ cells. Cells were lysed, and chromatin was fragmented by sonication. Cross-links were reversed and chromatin eluted by incubation at 65 degrees Celsius. After high-speed spin soluble chromatin was removed and used for ChIP with anti-DMC1 antibody.
For library preparation, DNA was first end-repaired by incubation with 1 × T4 DNA Ligase Reaction Buffer with 0.25 mM dNTP, 3 units of T4 DNA polymerase (NEB, M0203S), 1 unit of Klenow Enzyme (NEB, M0210S) and 10 units of T4 PNK (NEB, B0202S) at 20°C for 30 min, followed by addition of 3′-A overhangs using Klenow Fragment 3′-5′ exo- (NEB, M0212S). After denaturation of DNA at 95°C for 3 min, adapters from the TruSeq Nano DNA LD Library Prep Kit (set A, Illumina, FC-121-4001) were ligated with a Quick Ligation kit (NEB, M2200S). The libraries then were amplified using PCR Enhancer mix and primer cocktail (Illumina, FC-121-4001) for 12 cycles. For each step, DNA was purified by MinElute Reaction Cleanup Kit.

value: spermatocytes

value: Adult


title: Ltbr KO  rep1

value: 13 weeks


title: EP_DMC1_ChIPSeq Rep 1

description:
Sample 3
DMC1 ChIP-seq, B6.Prdm9EP/EP Rep1
EPHom_DMC1_ChIP_merge_mm10_RPM.bedgraph
EPHom_DMC1_merge_DMC1Peaks.bed
EPHom_DMC1_merge_DMC1peaks_Hotspots.bed
EPHom_DMC1_merge_DMC1peaks_DefaultSites.bed
Fastq file containing selected reads from single-stranded fragments: EPHom_DMC1_ChIP_Rep1_single-stranded.fastq.gz (SRR12060569)


title: Py_PCE_B_plus_TEX

city: Würzburg

first: Thorsten

last: Bischler

address: Josef-Schneider-Straße 2 / D15

department: Core Unit SysMed

institute: University of Wuerzburg

data_processing:
Demultiplexing
Fastq quality trimming using FastX version 0.0.13 and a cut-off value of 20
Fastq to fasta conversion using FastX
poly(A) trimming  (READemption 0.3.5, Förstner et al., 2014)
Size filtering: discarding reads shorter than 12 nt (READemption 0.3.5, Förstner et al., 2014)
Read mapping using segemehl version 0.2.0 (Hoffmann et al., 2009) with an accuracy cut-off of 95% (READemption 0.3.5, Förstner et al., 2014)
Coverage calculation and normalization (READemption 0.3.5, Förstner et al., 2014)
Genome_build: CP007201.1
Supplementary_files_format_and_content: wiggle

organism: Sulfurospirillum multivorans

growth_protocol: S. multivorans (DSMZ 12446T) was cultivated under anaerobic conditions at 28°C in a defined mineral medium (Scholz-Muramatsu et al., 1995) without vitamin B12 (cyanocobalamin) and yeast extract. Pyruvate (40 mM) was used as electron donor and fumarate (40 mM) or PCE as electron acceptor. PCE was added to the medium (10 mM nominal concentration) from a hexadecane stock solution (0.5 M). Pre-cultures were grown in rubber-stoppered 200 ml glass serum bottles and the main cultures in rubber-stoppered 2 l glass bottles. The ratio of aqueous to gas phase was always 1:1. In order to generate S. multivorans cells with down-regulated pceA gene expression (John et al., 2009), the organism was cultivated for 60 transfers on pyruvate (40 mM) and fumarate (40 mM). The resulting culture was used as inoculum for all pre-cultures. The bacterial growth was photometrically monitored by measuring the optical density at 578 nm.

extract_protocol:
Frozen cell pellets were thawed on ice and resuspended in 600 µl lysis solution containing 0.5 mg/ml lysozyme in TE buffer, pH 8.0, and 60 µl 10% SDS. The cells were lysed by incubating the samples for 1-2 min at 64 °C. After the incubation, 1 M NaOAc, pH 5.2 (66 µl) was added and the sample was mixed by inversion. Total RNA was extracted using the hot-phenol method by adding 750 µl phenol. The solution was mixed by inversion and incubated for 6 min at 64 °C. Afterwards, the samples were mixed 6-10 times by inversion and cooled on ice. After centrifugation for 15 min at 14000 x g at 4 °C the aqueous layer was transferred and the chloroform extraction was performed in a 2 ml Phase Lock Gel tube (Eppendorf, Hamburg, Germany). 750 µl chloroform was added and mixed by inversion. After centrifugation for 12 min at 14000 x g at 15 °C, the aqueous layer was used for the ethanol precipitation. To the RNA containing sample, 0.1 volume 3 M NaOAc, pH 5.2 and two volumes of 96% ethanol (-20 °C) were added. The sample incubated for 2 h at -20 °C. Ethanol was discarded after centrifugation for 20 min at 14000 x g and 4 °C. The RNA was washed once with 200 µl -20 °C 70% ethanol. Ethanol was removed and the RNA was subjected to library preparation.
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). In brief, the RNA samples were poly(A)-tailed using poly(A) polymerase. Terminator exonuclease treatment (+TEX) and mock treatment without the enzyme (-TEX) were carried out after poly(A)-tailing. In this way, corresponding cDNA pairs were generated. Then, the 5'PPP structures were removed using tobacco acid pyrophosphatase (TAP). Afterwards, an RNA adapter was ligated to the 5’-monophosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and were analyzed by capillary electrophoresis. A library-specific barcode for multiplex sequencing was included as part of a 3'-sequencing adapter.

treatment_protocol: RNA was isolated from S. multivorans cells, harvested after four transfers on 40 mM pyruvate and 10 mM nominal PCE containing medium at an OD578 ≈ 0.26 and after 64 transfers on pyruvate and fumarate (40 mM each) at an OD578 ≈ 0.43. The cell suspension (PCE-cultivated cells: 30 ml, fumarate-cultivated cells: 18 ml)  was mixed by inversion with  1/6 amount of 95% v/v ethanol / 5% v/v Roti-Aqua-phenol followed by 10 min centrifugation at 1700 x g at 4 °C. The cells were snap-frozen in liquid nitrogen and stored at -80 °C.

value: DSMZ 12446T

tag: electron acceptor

value: tetrachloroethene (PCE)

value: Terminator exonuclease treatment (+TEX)


title: Py_PCE_B_minus_TEX

value: mock treatment without the enzyme (-TEX)


title: Py_PCE_A_plus_TEX


title: RIPseq-mouseIgG-Mouse-Testis-rep1

value: Testis

tag: antibody

value: mouse IgG

tag: Stage

value: adult, four month


title: Py_Fu_B_minus_TEX

value: Fumarate


title: Py_Fu_B_plus_TEX


title: Ltbr KO  rep2

value: 10 weeks


title: Py_PCE_A_minus_TEX


title: Py_Fu_A_plus_TEX


title: Py_Fu_A_minus_TEX


title: UVM11 rep3

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

description:
hda17 mutant strain UVM11
SMDSU1mlphKs.b3

data_processing:
base calling by CASAVA
read alignment by RNA-STAR (STAR_2.4.0j)
expression estimates by cuffdiff (v2.2.1)
Genome_build: Chlamydomonas reinhardtii v5.5 (phytozome.net)
Supplementary_files_format_and_content: A tab-delimited text file which includes FPKM values for each sample.

organism: Chlamydomonas reinhardtii

source_name: liquid-grown cultures of algae

growth_protocol: mid-log growth, photo-heterotrophic

extract_protocol:
TRIzol extraction / EtOH precipitation
TruSeq Stranded Total RNA LT

treatment_protocol: no treatment

value: srta mutant


title: UVM11 rep2

description:
hda17 mutant strain UVM11
SMDSU1mlphKs.b2


title: UVM11 rep4

description:
hda17 mutant strain UVM11
SMDSU1mlphKs.b4


title: UVM11-C9 rep2

description: SRTA complemented strain UVM11-C9

value: SRTA complemented


title: UVM11-C1 rep2

description: SRTA complemented strain UVM11-C1


title: UVM11-C9 rep1

description: SRTA complemented strain UVM11-C9


title: UVM11 rep5

description: srta mutant strain UVM11


title: UVM11-C1 rep3

description: SRTA complemented strain UVM11-C1


title: UVM11 rep6

description: srta mutant strain UVM11


title: UVM11-C9 rep3

description: SRTA complemented strain UVM11-C9


title: UVM11-C1 rep1

description: SRTA complemented strain UVM11-C1


title: UVM4 rep4

description:
hda17 mutant strain UVM4
SMDSU4mlphKs.b4


title: UVM4 rep2

description:
hda17 mutant strain UVM4
SMDSU4mlphKs.b2


title: UVM11 rep1

description:
hda17 mutant strain UVM11
SMDSU1mlphKs.b1


title: UVM4 rep3

description:
hda17 mutant strain UVM4
SMDSU4mlphKs.b3


title: Elow47 rep4

description:
WT parental strain of UVM4 and UVM11
SMDSELmlphKs.b4

value: SRTA WT


title: Elow47 rep3

description:
WT parental strain of UVM4 and UVM11
SMDSELmlphKs.b3


title: UVM4 rep1

description:
hda17 mutant strain UVM4
SMDSU4mlphKs.b1


title: Elow47 rep2

description:
WT parental strain of UVM4 and UVM11
SMDSELmlphKs.b2


title: UVM11 rep7

description: srta mutant strain UVM11


title: PlCS.13: WT_Muscle_Smoke_Rep_13

city: Gainesville

first: VIJAYENDRAN

last: CHANDRAN

state: FL

address: Assistant Professor, Department of Pediatrics,  University of Florida, School of Medicine, 1600 SW Archer Road, Box 100296

institute: University of Florida

data_processing:
Bluebee’s genomics analysis platform
Sequencing targeted mean 7 million 65-nt single-stranded reads per sample, which were mapped to the mouse transcriptome and quantified as transcripts per million mapped reads using the STAR aligner. All sequencing data were uploaded to Illumina’s BaseSpace in real-time for downstream analysis of quality control. Raw Illumina (fastq.gz) sequencing files were downloaded from BaseSpace, and uploaded to Bluebee’s genomics analysis platform (https://www.bluebee.com) to align reads against the mouse genome.
After combining treatment replicate files, a DESeq2 application within Bluebee (Lexogen Quantseq DE 1.2) was used to identify significant treatment-related effects on transcript abundance (relative to controls) based on a false discovery rate (FDR) p-adjusted value <0.1.
Genome_build: mm9
Supplementary_files_format_and_content: csv file contains raw gene counts for every gene and every sample

source_name: Muscle

extract_protocol:
Plantaris muscles were removed, flash frozen, and RNA was harvested using the RNeasy Tissue Mini Kit (Qiagen), according to manufacturer’s instructions. RNA was reverse transcribed to complementary DNA (Lexogen QuantSeq 3′ FWD), and sequenced on a HiSeq 4000 instrument (Illumina).
RNA libraries were prepared for sequencing using  manufacturer’s instructions  (Lexogen QuantSeq 3′ FWD)

value: Plantaris muscle

value: wild type

value: Exposed to tobacco smoke for 16 weeks


title: PlCS.12: WT_Muscle_Smoke_Rep_12


title: PlCS.8: WT_Muscle_Smoke_Rep_8


title: Elow47 rep1

description:
WT parental strain of UVM4 and UVM11
SMDSELmlphKs.b1


title: PlCS.10: WT_Muscle_Smoke_Rep_10


title: PlCS.6: WT_Muscle_Smoke_Rep_6


title: PlAir.7: WT_Muscle_Air_Rep_7

value: Exposed to normal air


title: PlCS.3: WT_Muscle_Smoke_Rep_3


title: PlAir.9: WT_Muscle_Air_Rep_9


title: PlAir.6: WT_Muscle_Air_Rep_6


title: PlCS.2: WT_Muscle_Smoke_Rep_2


title: PlAir.5: WT_Muscle_Air_Rep_5


title: PlAir.11: WT_Muscle_Air_Rep_11


title: PlAir.4: WT_Muscle_Air_Rep_4


title: PlAir.10: WT_Muscle_Air_Rep_10


title: PlCS.7: WT_Muscle_Smoke_Rep_7


title: PlAir.8: WT_Muscle_Air_Rep_8


title: PlCS.11: WT_Muscle_Smoke_Rep_11


title: PlCS.9: WT_Muscle_Smoke_Rep_9


title: PlAir.3: WT_Muscle_Air_Rep_3


title: THP1-1

city: Guangzhou

first: Ran

last: Wei

address: Dongfengdong Road 651, Guangzhou

institute: Sun Yat-sen University Cancer Center

hyb_protocol: The pre-hybridization of HOA v7 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The Matrix value is normalized intensities. The pairwised comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

source_name: cell line

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

growth_protocol: MHCC-97H and HepG2 cells were maintained in DMEM (Hyclone) with 10% fetal bovine serum (FBS, Gibco), and THP-1 cells were cultured in RPMI 1640 medium (Hyclone) with 10% FBS.

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: THP-1 cells were polarized into macrophages using PMA (Sigma, 100ng/ml) treatment for 24 hours. As for THP-1 derived TAM, THP-1 cells (2×106 cells) treated with PMA were placed on the lower chamber of a 6-well transwell plate. Meanwhile, HepG2 or MHCC-97H cells were placed on the 0.4μm porous membrane of upper chamber. After 24 hours, we co-cultured HepG2 or MHCC-97H cells with THP-1 derived macrophages. Then 48 hours later, macrophages were collected for RNA extraction. Next, we analyzed the differentially expressed genes in THP-1 cells-derived TAMs using whole genome expression profile analysis compared with THP-1 derived macrophages.

value: human leukemia monocytic cell line

value: periphery blood

value: untreated

tag: cell line


title: THP1-2


title: PlCS.5: WT_Muscle_Smoke_Rep_5

tag: strain


title: THP1-MHCC97H 48h

value: co-cultured with MHCC-97H for 48h


title: PlAir.2: WT_Muscle_Air_Rep_2


title: Znion-1

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

data_processing:
base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Acinetobacter baylyi ADP1

source_name: Acinetobacter baylyi ADP1 bacteria

growth_protocol: liquid LB culture at 30 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted from the mutants using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Acinetobacter baylyi ADP1 was cultured in 10 mL PBS (plus 40 mg/L COD) containing 0, 1 mg/L AgNPs or Ag ions, 1 mg/L CuO NPs or Cu ions, 10 mg/L ZnO NPs or Zn ions for 2 h, in triplicate, at 30 °C, without shaking

value: liquid LB culture


title: U87 cells with shNA

city: Shenzhen

first: Yue

last: Xiao

address: xueyuan road

institute: Shenzhen University

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: glioma cell line U87

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: U87 cells were infected with nfected with lentiviruses encoding USP39-targeting or negative control shRNA (shUSP39 or shNA) ,  cells with stable knockdown USP39 or negative control were screened by GFP and puromycin.

value: human glioma cell line

tag: genotype/variation

value: negative control shRNA


title: U87 NC


title: Znion-3


title: U87 cells with shUSP39

value: USP39-targeting shRNA


title: THP1-G2 48h

value: co-cultured with HepG2 for 48h


title: PlCS.4: WT_Muscle_Smoke_Rep_4


title: CuONP-2


title: Cuion-1


title: ZnONP-3


title: Cuion-3


title: ZnONP-2


title: OVA+PM10

value: BALB/c

value: lung

tag: agent

tag: Sex

value: Female


title: CuONP-3


title: PlAir.1: WT_Muscle_Air_Rep_1


title: Cuion-2


title: Metformin

city: Southampton

first: Jeremy

middle: Paul

last: Blaydes

state: Hampshire

address: Southampton General Hospital, Tremona Road

department: Faculty of Medicine

country: United Kingdom

institute: University of Southampton

description: 2 mM Metformin

data_processing:
basecalling - bcl2fastq
filtering, alignment - STAR aligner (v2.5.0a)
digital gene expression - Drop_Seq_tools_v1.0
Genome_build: hg19
Supplementary_files_format_and_content: Digital gene expression matrix format. (A row for each gene, and a column for each cell barcode and a UMI count matrix)

growth_protocol: MDA-MB-231 cells were adapted to culture in 2D in DMEM (high glucose) containing either 0 mM or 2 mM metformin, for 30 days. 0 mM = Wildtype, 2 mM = Metformin

extract_protocol:
Trypsin/ EDTA disaggregated mammospheres
PCR on bead then Nextera XT

treatment_protocol: Adapted cell cultures were plated on low attachment plates in mammosphere culture media. Resultant mammospheres were cultured for 10 days

tag: cell type

value: mammosphere

value: 2 mM Metformin


title: ZnONP-1


title: Agion-2


title: Agion-3


title: Agion-1


title: AgNP-2


title: Maize_Drought

city: Tuxtepec

first: Blanca

middle: Estela

last: Barrera-Figueroa

state: Oaxaca

address: Av. Circuito Central 200

department: Instituto de Biotecnología

institute: Universidad del Papaloapan

description: Plants were water-deprived by interrupting water supply until half their initial weight (water deficit). Then, water was added in small amounts daily to maintain a regular water deficit condition for 6 days.

data_processing:
Base calling was performed with the Illumina in-house software (Bustard)
Quality control, adapter trimming, removal of sequences smaller than 18nt and longer than 35nt, mapping to the B73 RefGen-v5, and normalization of counts, were carried out using CLC Genomics Workbench 12.
Filtered sequences were compared to conserved and known miRNA sequences from maize and other plants registered in the MiRBASE, with CLC Genomics Workbench 12.
Genome_build: B73 RefGen_v5
Supplementary_files_format_and_content: Text (txt) files with raw counts for every sequence in the corresponding library and matrix (xlsx) file with normalized counts for plant miRNAs.

organism: Zea mays subsp. mays

source_name: Shoot

growth_protocol: Maize seeds (Zea mays ssp. mays) of tropical homozygous line CML496, and teosinte (Zea mays ssp. parviglumis) were germinated directly in pots with Sunshine Mix 3, three seeds per pot. Maize and teosinte plantlets were maintained in a growth room at 23°C and 16h/8h light/dark cycle.

extract_protocol:
The shoots were removed, frozen in liquid nitrogen and processed with TRIzol to extract total RNA. The small RNA fraction of 20-30 nt was size-purified from total RNA on denaturing polyacrylamide gels.
Small RNA fractions purified from 12µg of total RNA were ligated to a preadenylated adapter in the 3'end. Next,  the 5' RNA Illumina adapter was ligated to the 5'end of small RNAs. The products with adapters in both ends were used in cDNA synthesis reactions followed by a 15 cycle PCR with primers compatible with Illumina. The products were purified, quantified, and sequenced on the Illumina HiSEQ2500.

tag: subspecies

value: mays

tag: developmental stage

value: 28 days after sowing

value: Drought for 6 days

tag: rna fraction

value: Small RNAs


title: Maize_Submergence

description: Plants were treated in empty 32 cm depth submergence tanks that were added with filtered tap water to increase the water column by 6 cm every 2 h for 10h, until the maximum capacity was reached and plants were fully submerged. The plants were maintained in this treatment for 48h.

tag: treatment

value: Submergence for 48 h


title: Wildtype

description: 0 mM Metformin

value: 0 mM Metformin


title: AgNP-1


title: Control-3


title: Maize_Control

description: Untreated

value: Untreated


title: Control-2

value: liquid LB culture


title: Control-1


title: AgNP-3


title: MCT11

city: Los Angeles

first: weibo

last: yu

address: Los Angeles

institute: UCLA

hyb_protocol: The Affymetrix WT PLUS Reagent Kit was used to prepare the RNA for hybridization to the HTA.

scan_protocol: Global gene expression profiles of the cells were generated using the Affymetrix GeneChip Human Transcriptome Array (HTA) 2.0 system.

data_processing: Data analysis was performed using the Affymetrix Expression Console software and Transcriptome Analysis Console software. Ingenuity Pathway Analysis (IPA) was followed to compare the changes in gene expression in different signaling pathways.

source_name: uroepithelium

label_protocol: Gene expression profiles of the cells were tested using the Affymetrix GeneChip Human Transcriptome Array 2.0 system. Nucleic acid was labeled with biotin.

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) streptomycin/penicillin (S/P).

extract_protocol: Total RNA was extracted from treated and untreated cells using a TRIzol reagent (Thermo Fisher Scientific). The RNA samples were then applied to a RNeasy Mini spin column for purification (RNeasy Miniprep Kit, Qiagen).

treatment_protocol: Cultured HUC-BC, HUC-PC and MCT-11 cells in 50% confluency were treated with 200 µM 4-ABP. Cells were exposed for 48 hours prior to harvesting for mechanotype analysis.

value: uroepithelial cell line

value: control


title: 4ABP treated PC

value: HUC-PC

value: 4ABP treated


title: BC

value: HUC-BC


title: PC


title: RCM-1_MTA 18 h_ rep1

city: Kagoshima

first: Shigehisa

last: Okamoto

address: 1-21-24 Korimoto

department: Food Science and Biotechnology

country: Japan

institute: Kagoshima University

description: Gene expression data from RCM-1 human colorectal cancer cells treated with methylthioacetic acid for 18 h.

hyb_protocol: Following fragmentation, 12.5 µg of cRNA were hybridized for 16 h on Human Genome U133 Plus 2.0 Array. Arrays were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix Expression Console to summarize the probe set intensity data of all genes on each array and then normalize the average intensity of the experimental array to that of the baseline array.

source_name: Colorectal cancer cells, methylthioacetic acid, 18 h

label_protocol: Biotinylated cRNA were prepared from total RNA with 3’ IVT Express kit.

growth_protocol: RCM-1 human colorectal cancer cells were cultured at 37°C in 5% CO2 atmosphere, in a medium made up of equal volumes of RPMI 1640 and Ham’s F12 containing 10% FBS and 10 μg/mL gentamicin.

extract_protocol: Extraction of total RNA was performed using the SV Total RNA Isolation System according to the manufacturer’s instructions (Promega).

treatment_protocol: RCM-1 human colorectal cancer cells were treated with either 1 mM methylthioacetic acid or vehicle (0.1% acetonitrile) for 0, 6, 12, and 18 h. Then, the medium was replaced with the vehicle medium and further cultured for up to 24 h after chemical application. The chemical-treated RCM-1 cells were directly subjected to RNA extraction.

value: rectum

value: colorectal cancer cell

tag: grade

value: well-differentiated

value: methylthioacetic acid

tag: time


title: 4ABP treated MCT11

tag: tissue


title: CuONP-1


title: GTT89_Spleen_Tregs

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description:
Splenic Treg Neuropilin-high cells: GTT89 mother (Rank Foxn1 KO) duplicate
GTT89_Spl_Treg_2_S51703

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 and 3.3.52 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.3 and 2.7.7.
BCL to BAM file conversion and demultiplexing with Illumina2bam 1.17 (http://wtsi-npg.github.io/illumina2bam/) and custom programmes based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.1a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.11 package DESeq2 1.28.1, running under R 4.0.2.
Genome_build: UCSC mm10 based on GRCm38
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: spleen

extract_protocol:
For the generation of full-length cDNA, the Smart-seq2 protocol (Picelli, S. et al, Nat Protoc. 2014 Jan;9(1):171-81. doi:10.1038/nprot.2014.006) was used.
The subsequent library preparation from the amplified cDNA was performed using the Nextera XT DNA library prep kit (Illumina).
For sequencing, libraries were pooled, diluted and sequenced on Illumina HiSeq 3000/4000 using 50 bp single-read chemistry.

value: spleen

value: regulatory T-cell

tag: gender

value: female

tag: genotype

value: Tnfrsf11a (Rank) Foxn1 knock-out

tag: pregnancy status

value: pregnant


title: GTT92_Spleen_Tregs

description:
Splenic Treg Neuropilin-high cells: GTT92 mother (Rank Foxn1 KO) duplicate
GTT92_Spl_Treg_2_S51707


title: GTT91_Spleen_Tregs

description:
Splenic Treg Neuropilin-high cells: GTT91 mother (Rank wt) duplicate
GTT91_Spl_Treg_2_S51708

value: Tnfrsf11a (Rank) Foxn1 wild-type