title: s_NC_IgG_4

city: New York

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
The output data (FASTQ files) are mapped to the target genome using the rnaStar aligner version 2.5.0a [Dobin2012]. We use the 2 pass mapping method outlined in [Engström2013] in which the reads are mapped twice. The first mapping pass uses a list of known annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done (on the second pass the RemoveNoncanoncial flag is used).
After mapping we post process the output SAM files using the PICARD tools version 1.124 to: add read groups, AddOrReplaceReadGroups which in additional sorts the file and coverts it to the compressed BAM format.
We then compute the expression count matrix from the mapped reads using HTSeq version 0.5.3 (www-huber.embl.de/users/anders/HTSeq) and gene annotation from Gencode version M8.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimted text file containing raw transcript counts

source_name: 4T1 control tumor treated with IgG control

growth_protocol: tumor cells (10^6 cells) were implanted into naïve syngeneic mice

extract_protocol:
Frozen tissue was homogenized in TRIzol Reagent (ThermoFisher catalog # 15596018) using the QIAGEN TissueLyser at 15Hz for 2-3 minutes with a Stainless Steel Bead (QIAGEN catalog # 69989). Phase separation was induced with chloroform. RNA was precipitated with isopropanol and linear acrylamide and washed with 75% ethanol. The samples were resuspended in RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR.
Samples were barcoded and run on a HiSeq 4000 in a PE50 run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 51 million paired reads was generated per sample and the percent of mRNA bases averaged 69%.

treatment_protocol: Three days after tumor injection, mice were treated 3 times with anti-CTLA-4 or IgG control for 3 times 3 days apart before tumor harvesting and processing for RNAseq analysis

value: BALB/cAnN

value: implanted tumor

tag: cell line

value: IgG


title: 1_Rtkn2_AT1_C

status: Public on Mar 08 2021

type: SRA

city: Memphis

first: Danielle

middle: R.

last: Little

state: Tennessee

address: 262 Danny Thomas Pl Rm D2031

department: Developmental Neurobiology

country: USA

institute: St. Jude Children's Research Hospital

library_source: genomic

data_processing:
Fastqc was run on the raw Fastq files to determine initial quality of reads.
Trimmomatic was performed to remove barcodes and poor quality bases.
Fastqc was run for quality control.
Bowtie alignment to the mm10 genomic with -m1 -k1 -v1 parameters and filtered for unmapped reads with sam file output
Convert sam to bam using samtools, then sort file
Picard mark duplicates
index bam file
Filter bam files: samtools  -b –f 3 –F 4 –F 256 –F 1024 –F 2048 –q 30
quality control run SPP
Call peaks using MACs2
Genome_build: mm10
Supplementary_files_format_and_content: peaks.broadPeak
Supplementary_files_format_and_content: bedgraph

molecule: genomic DNA

organism: Mus musculus

source_name: AT1 cells

extract_protocol:
Perfused lungs were collected from anesthetized mice as described above. Previously published protocols for cell dissociation and sorting cells were used with minor modifications11. Extra-pulmonary airways and connective tissues were removed from lungs, which were then minced with forceps and digested in Liebovitz media (Gibco, 21083-027) for scRNA-seq, ATAC-seq, or scATAC-seq with 2 mg/mL collagenase type I (Worthington, CLS-1, LS004197), 0.5 mg/mL DNase I (Worthington, D, LS002007), and 2 mg/mL elastase (Worthingon, ESL, LS002294) for 30 min at 37 °C. To stop the digestion, fetal bovine serum (FBS, Invitrogen, 10082-139) was added to a final concentration of 20%. Tissues were triturated until homogenous and filtered through a 70 µm cell strainer (Falcon, 352350) on ice in a 4 °C cold room and transferred to a 2 mL tube. The sample was then centrifuged at 1,537 rcf for 1 min; then 1 mL red blood cell lysis buffer (15 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 8.0) was added and incubated for 3 min before centrifugation again at 1,537 rcf. The red blood cell lysis buffer incubation was repeated to remove residual red blood cells. Liebovitz+10% FBS was used to wash and resuspend samples, which were then filtrated through a 35 mm cell strainer into a 5 mL glass tube and had SYTOX Blue (1:1000, Invitrogen, S34857) added. After refiltering, samples were for ATAC-seq were sorted for GFP positive cells from a RosaSun1GFP reporter activated by Wnt3aCre, Rtkn2CreER, or SftpcCreER on a BD FACSAria IIIu cell sorter with a 70 mm nozzle. Samples for scRNA-seq or scATAC-seq were stained with CD45-PE/Cy7 (BioLegend, 103114), ECAD-PE (BioLegend, 147304), and ICAM2-A647 (Invitrogen, A15452) antibodies (1:250 dilutions for all antibodies) for 30 min followed by a wash and being resuspended with Liebovitz meda+10% FBS and addition of SYTOX Blue. Samples were then filtered through a 35 mm cell strainer into a 5 mL glass tube again and sorted by a BD FACSAria Fusion sorter or a with a 70 mm nozzle.
The OMNI-ATAC protocol68 was followed with minor modifications. 60,000-100,000 sorted GFP cells were centrifuged at 384 rcf for 5 min at 4 °C. The cell pellet was then resuspended by pipetting three times in 50 µl of cold ATAC-RSB lysis buffer (0.1% NP-40, 0.1% Tween, 0.01% Digitonin, 10 mM Tris-HCl pH 8.1, 10 mM NaCl, 3 mM MgCl2) and incubated for 3 min. Then 1 mL of cold ATAC-RSB + Tween (10 mM Tris-HCl pH 8.1, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween) was added. The sample tube was then inverted three times and centrifuged at 384 rcf for 10 min at 4 °C. After discarding the supernatant, the pellet was resuspended in transposition mixture composed of 22.5 µl of Reaction Mix (PBS, 2.2% Digitonin, 2.2% Tween 20), 25 µl of transposase buffer (10 mM MgCl2, 20mM Tris- HCl, 20% Dimethyl Formamide), and 2.5 µl of Tn5 enzyme (NX#-TDE1, Tagment DNA Enzyme,15027865, Illumina) and incubated at 37 °C for 30 min in a thermocycler. Samples were then purified using the MinElute PCR Purification kit (Qiagen, 29004) and eluted with 10 µL of H2O. Amplification and barcoding of ATAC libraries was carried out using the Greenleaf primers for 12 cycles of PCR enrichment following the standard OMNI-ATAC amplification PCR program. A volume of 5 µL was taken after amplification to examine amplification efficiency prior to size selection. A double-sided size selection was then performed (.5 x -1.8 x volume) using the SPRIselect reagent (Beckman Coulter, B23318). Samples were then verified for library size and absence of primer dimers by gel electrophoresis and concentration was measured using the Qubit HS dsDNA assay (ThermoFisher Scientific, Q32851).

treatment_protocol: 2 doses of 3 mg of Tamoxifen 2 days apart, lungs were harvested 5 days after the 1st dose.

tag: cell type

value: AT1 cells

tag: age

tag: days post tamoxifen

tag: dose of tamoxifen

value: 6 mg

tag: genotype

value: Rosa Sun1GFP/+; Rtkn2 CreER/+


title: 1_NKX2-1_Rtkn2_AT1_M

value: Nkx2-1 CKO/CKO; Rosa Sun1GFP/+; Rtkn2 CreER/+


title: s_NC_IgG_3

state: NY

library_source: transcriptomic

molecule: total RNA

tag: strain

tag: tissue

tag: treatment


title: 2_Rtkn2_AT1_C


title: s_NC_aC_4

source_name: 4T1 control tumor treated with anti-CTLA-4


title: s_NC_aC_5


title: 20016 Day 4+dasatinib

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

description:
P16D4dasa
Drop-Seq
assembloid_counts.csv
assembloid_metadata.csv

data_processing:
Initial Drop-seq (Macosko et al., 2015) data processing was performed using Drop-seq_tools-2.3.0 following the protocol described by Nemesh (seqAlignmentCookbook_v2.28Sep2018.pdf, http://mccarrolllab.com/dropseq).
Reads were aligned to the hg38 (Human) reference genome concatenated with ERCC annotations using STAR-2.5.3a with the Gencode21 (Human) as reference transcriptome.
Uniquely mapped reads, with ≤ 1 insertion or deletion, were used in quantification. Finally, the DigitalExpression tool was used to obtain the digital gene expression (DGE) matrix for each sample.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: assembloid_metadata.csv: Cell metadata as comma-separated values.
Supplementary_files_format_and_content: assembloid_counts.csv: Raw counts matrix as comma-separated values.

molecule: polyA RNA

organism: Homo sapiens

source_name: Human Endometrium

growth_protocol:
Tissue dissociation protocol: Endometrial pipelle biopsies were dissociated as described previously (Barros, Brosens and Brighton (2016) Isolation and Primary Culture of Various Cell Types from Whole Human Endometrial Biopsies, Bio-Protocol: 6(22); DOI: 10.21769/BioProtoc.2028).
Cell culture (growth and 3D culture): Endometrial assembloids were generated by co-culturing endometrial stromal cells and epithelial gland organoids in a collagen hydrogel. Assembloid cultures were grown for four days in Expansion Medium (ExM)+E2 prior to the treatment protocol.

extract_protocol:
Cells in suspension were captured and lysed singly in nanoliter droplets, as described by Macosko et al. (Cell. 2015 May 21;161(5):1202-1214. doi: 10.1016/j.cell.2015.05.002. PMID: 26000488) using a Nadia instrument (Dolomite Bio).
Libraries were prepared as described by Macosko et al. (Cell. 2015 May 21;161(5):1202-1214. doi: 10.1016/j.cell.2015.05.002. PMID: 26000488).

treatment_protocol: Samples were either untreated, or decidualized for 4 days with cAMP+MPA+E2 with or without dasatinib.

tag: sample type

value: Endometrial Assembloid

value: Stromal and epithelial cells

tag: differentiation protocol

value: Four days cAMP + MPA + E2 + dasatinib

tag: patient id (anonymised lab code)


title: 20018 Day 4+dasatinib

description:
P18D4dasa
Drop-Seq
assembloid_counts.csv
assembloid_metadata.csv


title: 20016 Day 4

description:
P16D4
Drop-Seq
assembloid_counts.csv
assembloid_metadata.csv

value: Four days cAMP + MPA + E2


title: 20009 Day 4

description:
P09D4
Drop-Seq
assembloid_counts.csv
assembloid_metadata.csv


title: 20018 Day 4

description:
P18D4
Drop-Seq
assembloid_counts.csv
assembloid_metadata.csv


title: 20009 Day 4+dasatinib

description:
P09D4dasa
Drop-Seq
assembloid_counts.csv
assembloid_metadata.csv


title: s_NC_aC_2


title: s_NC_aC_3


title: s_NC_aC_1


title: 20018 Day 0

description:
P18D0
Drop-Seq
assembloid_counts.csv
assembloid_metadata.csv

value: Undifferentiated


title: IQ3neg_1910B

city: Singapore

first: Ying

last: Li

state: --- Select a state ---

address: 14 Medical Dr, Singapore

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Raw reads were aligned to mouse reference genome version GRCm38 gencode M23 (downloaded from https://www.gencodegenes.org/) using STAR aligner version 2.7.1a with default parameters (Dobin et al., Bioinformatics 2013)
Read counts per gene were generated using featureCounts function in the subread package version 2.0.0. (Liao et al., Nucleic Acids Res 2013)
Counts per million (cpm) values were calculated using cpm function of the edgeR R package (Robinson et al., Bioinformatics 2010)
Expression data is normalized based on total mappable counts  in CPM
Genome_build: mm10

source_name: Stomach

extract_protocol:
Isolated mouse stomach was chopped into 2 mm2 pieces and incubated with chelating buffer (5 mM EDTA and 0.52 mM DTT in PBS) for 2 h at 4oC on a shaking platform, then gastric units were released by vigorous shaking in cold dissociation buffer (54.8 mM D-sorbitol and 44 mM Sucrose in PBS). Isolated mouse gastric units were incubated in TrypLE Express (Thermo Fisher Scientific) with Y-27632 (Merck) for 12 minutes at 37oC with repetitive pipetting for digestion into single cells. The cells were passed through a 30 μm cell strainer (Miltenyi Biotech) and labeled with antibodies in HBSS with 2% FBS. Antibodies for the flow cytometry are as follows: anti-EpCAM APC/Cy7-conjugated (BioLegend). Dead cells were excluded by DAPI staining, and labeled cells were sorted by using FACSAria II (BD Bioscience). RNA in FACS-sorted Iqgap3high (IQ3pos) and Iqgap3low/neg (IQ3neg) cells of Iqgap3-2A-tdTomato mice was extracted using NucleoSpin RNA XS (MACHEREY-NAGEL) by following the manufacturer’s manual.
RNA were sent to Beijing Genomics Institute (BGI) for PCR amplification, transcriptome library preparation and sequencing.
SMART-SeqII

value: Stomach (corpus)

value: 6-8 weeks

tag: numbers

value: 4 mice

tag: facs antibody

value: EpCAM (BioLegend, 118217)

tag: cell population

value: Iqgap3low/neg epithelial cell


title: IQ3pos_1910A

value: Iqgap3high epithelial cell


title: s_NC_IgG_1

value: BALB/cAnN

value: implanted tumor


title: s_NC_IgG_5

value: IgG


title: IQ3pos_1909A

value: 3 mice


title: s_KD_IgG_5

source_name: 4T1 LDHA-KD tumor treated with IgG control


title: IQ3neg_1909B


title: The MRW treatment sample-MRW-3

city: Lanzhou

last: Qi

state: Anning District

address: Yingmen Village

country: China

institute: Gansu agricultural university

data_processing:
Sequence data were processed using the SMRTlink 7.0 software. Circular consensus sequence (CCS) was generated from subread BAM files, parameters: min_length 50, max_drop_fraction 0.8, no_polish TRUE, min_zscore -9999.0, min_passes 1, min_predicted_accuracy 0.8, max_length 15000. CCS.BAM files were output, which were then classified into full length and non-full length reads using lima, removing polyA using refine. Full-length fasta files produced were then fed into the cluster step, which does isoform-level clustering (n*log(n)), followed by final Arrow polishing, hq_quiver_min_accuracy 0.99, bin_by_primer false, bin_size_kb 1, qv_trim_5p 100, qv_trim_3p 30.
Genome_build: Ld3_vu
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Lilium davidii var. unicolor

source_name: Scales irrigated with MRW

growth_protocol: Middle scales without damage caused by disease or pets were selected. After soaking in 1000 mL distilled water (the control) and different concentrations of MRW solution for 3 h. Exfoliated scales (three biological replicates, 40 scales in each) were embedded concave upward ex vitro into wet substrate (perlite and vermiculite as the rate of 1:3). Then, it was cultivated with growth condition as 25 ℃:18 ℃ (day: night temperatures) in the dark for 10 days, later under a 14 h (day)/10 h (night), with irrigating each 3 days by different concentrations solution.

extract_protocol:
Scales of Lilium were separately sampled after treatment of MRW and distilled water for 10 days, frozen in liquid nitrogen and stored at -80°C until RNA preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After scales cutting, Lilium scales were irrigated each 3 days by100% MRW or distilled water

tag: time point

value: 10 days after cutting

value: scale

value: irrigated with methane-rich water (MRW)


title: The control sample-Con-2

source_name: Scales irrigated with distilled water

value: irrigated with distilled water


title: The control sample-Con-1


title: The control sample-Con-3


title: The MRW treatment sample-MRW-2


title: The MRW treatment sample-MRW-1


title: 20009 Day 0

description:
P09D0
Drop-Seq
assembloid_counts.csv
assembloid_metadata.csv

value: Endometrial Assembloid

value: Stromal and epithelial cells


title: CPB pupa

city: Kota Kinabalu

first: Chia

middle: Lock

last: Tan

state: Sabah

address: Zon Komersial 1, Taman Perindustrian Kota Kinabalu Selatan, Jalan Norowot, Kota Kinabalu, Sabah, Malaysia

country: Malaysia

institute: Lembaga Koko Malaysia

data_processing:
Filtering was proceeded to remove low quality reads and adapter sequence according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads of which average quality scores of each read is less than 20. Furthermore, bases of both ends less than Q20 of filtered reads were removed additionally. This process is to enhance the quality of reads due to mRNA degradation in both ends of it as time goes on (Martin and Wang, 2011). The whole filtering process was performed using the in-house scripts.
Transcriptome assembly was performed by Trinity. All options were set to default values
To overcome chimeric reads, grouping the assembled transcripts by TGICL (Pertea et al., 2003), a pipeline for transcriptome analysis in which the sequences are clustered based on pairwise sequence similarity, was progressed for removal of the overlapping and the chimera sequences. And, extraction of the representative sequence was carried out by CAP3 (Huang and Madan, 1999): a sequence assembly program. The criterion of sequence similarity for grouping was set to 0.94 value.
Protein coding sequence (CDS) was extracted from the reconstructed transcripts by TransDecoder
Blast and InterProScan were applied for homology search to make a prediction of the function of CDS in unigene.
NCBI Blast 2.2.29+ was applied for nucleotide sequence-based homology search. The function of CDS was predicted by Blastx to search all possible proteins matched with unigene sequence against the SwissProt db. The criterion regarding significance of the similarity was set to E-value < 1e-5.
InterProScan is another tool for homology search using protein sequence. The search was progressed by InterProScan v5 against ProDom, PfamA, Panther, SMART, SuperFamily and Gene3d databases based on E-value < 1e-5.
Gene expression level was measured with RSEM (Li and Dewey, 2011).
TCC package was applied for DEG analysis through the iterative DEGES/DEseq method. Normalization was progressed three times to search meaningful DEGs between comparable samples (Kadota et al., 2012). The DEGs were identified based on the qvalue threshold less than 0.05.
Genome_build: TBI.unigene.fa
Supplementary_files_format_and_content: text file with expected count, TPM, FPKM

organism: Conopomorpha cramerella

source_name: cocoa pod borer

extract_protocol:
Approximately thirty of each larvae, pupae and moth were collected and kept in RNA Later® and maintained in -70oC freezer. The samples were grind to fine powder in liquid nitrogen before RNA isolation. Total RNA from CPB larvae, pupae and moth were extracted using the GeneAll Hybrid-R™ kit (GeneAll Biotechnology, Seoul, Korea).
The libraries were prepared for 150bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina, CA, USA).

tag: development stage

value: pupa

value: wild type


title: s_KD_IgG_4

tag: cell line


title: CPB moth

value: moth


title: s_KD_IgG_3


title: CPB larva

value: larva


title: s_KD_IgG_2


title: s_KD_IgG_1


title: 20016 Day 0

description:
P16D0
Drop-Seq
assembloid_counts.csv
assembloid_metadata.csv

tag: cell type

value: Undifferentiated


title: s_KD_aC_5

source_name: 4T1 LDHA-KD tumor treated with anti-CTLA-4


title: iFTSEC283 p53R175H treated with vehicle control (Replicate 2)

city: Tampa

first: Alvaro

last: Monteiro

state: FL

address: 12902 Magnolia Dr

institute: H. Lee Moffitt Cancer Center

data_processing:
Sequencing reads were subjected to adaptor trimming, series of quality assessment before being aligned with Tophat v2.0.13 against human reference genome hs37d5.
Quantification of read counts aligned to the region associated with each gene was performed using HTSeq v0.6.1 based on GENCODE v19.
Read counts of all samples were normalized using the median-of-ratios method implemented in R/Bioconductor package DESeq2 v1.6.3.
Differential expression analysis between the two groups was performed by dispersion estimation and statistical model fitting procedures implemented in DESeq2.
Genome_build: hs37d5
Supplementary_files_format_and_content: Text file of normalized gene abundance

source_name: Fallopian tube secretory cells

growth_protocol: iFTSEC283 and iFTSEC283p53R175H cells (authenticated by STR analysis) were cultured in NOSE medium consisting of MCDB105 and Medium 199 (1:1) supplemented with 15% fetal bovine serum, 0.5 mg/ml hydrocortisone, 10 ng/ml epidermal growth factor, 5 mg/ml insulin, and 34 mg protein/ml bovine pituitary extract.

extract_protocol:
Cells were harvested from 100mm plate at 80% confluency and processed for total RNA extraction using the RNeasy Plus Mini Kit following the manufacturer’s protocol
Libraries were prepared using the Nugen Universal RNA Seq Kit (NuGEN Technologies, San Carlos, CA) followed by sequencing using Illumina NextSeq500 instrument

treatment_protocol: Cells were treated for 137 consecutive days with either 10μM NE or vehicle control (water), media was changed every two days and cells were split 1:5 or 1:6 every seven days

value: iFTSEC283 p53R175H

value: Fallopian tube secretory cells

value: Mock treated with water for 137 days

value: p53R175H overexpressing


title: iFTSEC283 p53R175H treated with 10μM NE (Replicate 1)

value: Treated with 10 μM NE for 137 days


title: iFTSEC283 p53R175H treated with 10μM NE (Replicate 2)


title: s_KD_aC_2

value: BALB/cAnN

value: implanted tumor


title: iFTSEC283 p53R175H treated with vehicle control (Replicate 1)


title: s_KD_aC_1


title: iFTSEC283 treated with vehicle control  (Replicate 3)

value: Wild type


title: iFTSEC283 p53R175H treated with vehicle control (Replicate 3)


title: Corpus HDT-48hr rep2

data_processing:
Raw reads were aligned to mouse reference genome version GRCm38 gencode M23 (downloaded from https://www.gencodegenes.org/) using STAR aligner version 2.7.1a with default parameters (Dobin et al., Bioinformatics 2013)
Read counts per gene were generated using featureCounts function in the subread package version 2.0.0. (Liao et al., Nucleic Acids Res 2013)
Counts per million (cpm) values were calculated using cpm function of the edgeR R package (Robinson et al., Bioinformatics 2010)
Expression data is normalized based on total mappable counts
Genome_build: mm10

extract_protocol:
RNA was extracted from HDT-treated or untreated mouse stomach corpus using the RNeasy Mini Kit (QIAGEN) with on-column genomic DNA digestion using the RNase-free DNase Set (QIAGEN).
RNA were sent to Beijing Genomics Institute (BGI) for transcriptome library preparation and sequencing.

treatment_protocol: To induce tissue damage in the mouse stomach, 6-8 weeks old mice were given a single intraperitoneally injection of HDT (5 mg per 20 g body weight).

value: HDT-48hr rep2

value: Stomach (corpus)

tag: age

value: 6-8 weeks

value: 1 mouse


title: iFTSEC283 treated with vehicle control  (Replicate 2)


title: s_KD_aC_4


title: canine primary osteosarcoma sample5

type: RNA

city: Toronto

first: Jinchang

last: Lu

state: Ontario

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre, University of Toronto

description: Gene profile in canine osteosarcoma tissue 5

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Canine (V2) Gene Expression Microarray (G2519F) 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 (G2505B-C) using one color scan setting for 1x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent).

organism: Canis lupus familiaris

source_name: canine primary osteosarcoma tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug 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).

growth_protocol: Canine OS specimens were obtained from University of Guelph veterinarian clinics.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit (Qiagen) with on-column DNase I treatment

value: canine primary osteosarcoma tissue

tag: breed

value: Rottweiler X (Canine Mixed Breed)

value: 9 yrs

tag: gender

value: FS

value: DLG2 deleted


title: canine primary osteosarcoma sample8

description: Gene profile in canine osteosarcoma tissue 8

value: Great Pyrenees

value: 7 yrs

tag: genotype


title: canine primary osteosarcoma sample4

description: Gene profile in canine osteosarcoma tissue 4

value: Mixed Breed (Labrador Retriever/X)

value: 10 yrs

value: DLG2 wild type


title: s_KD_aC_3

tag: strain

value: BALB/cAnN


title: canine primary osteosarcoma sample7

description: Gene profile in canine osteosarcoma tissue 7

tag: tissue

value: Bull Mastiff

value: 8 yrs

value: MC


title: Corpus HDT-48hr rep1

tag: treatment

value: HDT-48hr rep1

value: Stomach (corpus)

value: wild type


title: iFTSEC283 p53R175H treated with 10μM NE (Replicate 3)

value: iFTSEC283 p53R175H

value: Fallopian tube secretory cells

value: Treated with 10 μM NE for 137 days

value: p53R175H overexpressing


title: canine primary osteosarcoma sample6

description: Gene profile in canine osteosarcoma tissue 6

value: canine primary osteosarcoma tissue

value: Greyhound

value: 6 yrs

value: DLG2 deleted


title: canine primary osteosarcoma sample3

description: Gene profile in canine osteosarcoma tissue 3

value: Boxer

value: 12 yrs

value: FS


title: iFTSEC283 treated with 10μM NE (Replicate 3)

value: Wild type


title: canine primary osteosarcoma sample2

description: Gene profile in canine osteosarcoma tissue 2

value: Mixed Breed (German Shepherd/Collie/X)

value: 8 yrs


title: iFTSEC283 treated with 10μM NE (Replicate 2)


title: iFTSEC283 treated with 10μM NE (Replicate 1)


title: Corpus Vehicle-48hr rep2

value: Vehicle-48hr rep2

value: 6-8 weeks

value: 1 mouse


title: 30956RB_C5_lncRNA

city: Jinan

first: Rusong

last: Zhao

state: Shandong

address: 44 Wenhua xi Road

department: Center for Reproductive Medicine

institute: Shandong University

data_processing:
The rRNA-depleted RNA samples were further processed in accordance with the Illumina protocol (New England Biolabs, Massachusetts, USA).
After cDNA synthesis, the samples were sequenced with an Illumina HiSeq 2500 using the paired-end (PE) sequencing strategy.
The overall quality of the RNA‐seq data was evaluated by FastQC. Clean reads were aligned to the reference genome (Ensembl release 95, Homo sapiens) using TopHat2 (v2.0.14)  with the default parameters.
MeDIP‐seq reads were mapped to the human genome using BWA software
MACS2 was used to call peaks and DMRs were identified using the Cummerbund and ChIPpeakAnno packages in R.
Genome_build: Ensembl release 95, Homo sapiens
Supplementary_files_format_and_content: peak files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: ovarian

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen, CA, USA) and purified using an RNeasy Mini Kit (Qiagen, CA, USA);MeDIP was performed to analyze genome-wide methylation using the Zymo Research DNA Methylation IP Kit (Cat #D5101; Zymo Research, CA, USA).
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols

value: Granulosa cells

value: ovarian

tag: disease state

value: Polycystic ovary syndrome


title: H1-hESC-R2

city: Worcester

first: Job

last: Dekker

state: MA

address: 368 Plantation Street, AS5-1049

department: Program in Systems Biology

institute: University of Massachusetts Medical School

description:
H1 embryonic stem cells from Maehr lab
hESC_Atacseq.mRp.clN_peaks.narrowPeak
hESC_Atacseq.mRp.clN.bigWig

data_processing:
All datasets proseed uning nf-core  ATAC Seq pipeline  ( https://nf-co.re/atacseq )
BWA is used for mapping the fastq files to hg38 reference genome
MACS2 with default parameters is used to find the enriched peaks
BEDtools intersect is used to find the loop anchors that have MACS2 peaks.
Genome_build: hg38
Supplementary_files_format_and_content: bw files  for genome wide read coverage, bed files for peaks

growth_protocol: 4DN Protocols are  used to culture the cells. Protocols can be found here: https://data.4dnucleome.org/resources/experimental-resources/cell-lines

extract_protocol:
The  referenced protocols are used to generate these datasets. Cut&Tag: Kaya-Okur et al. 2020, Cut&Run:  Janssens et al. 2019, ATAC-Seq:Buenrostro JD et al. 2013.
Libraries were prepared for sequencing using standard Illumina protocols

tag: protocol

value: ATAC-Seq

tag: enzyme

tag: antibody


title: 30548RB_C4_lncRNA


title: H1-hESC-R1


title: 26146RB_C3_lncRNA


title: Corpus Vehicle-48hr rep1

value: Vehicle-48hr rep1

value: Stomach (corpus)

value: wild type

tag: numbers


title: genomic DNA from PBMC C4

type: genomic

city: Hsinchu

first: Tingwen

last: Chen

address: No. 75, Boat Street, East District

country: Taiwan

institute: National Yang Ming Chiao Tung University

description: normal PBMC sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: PBMC Normal90

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Kit according to standard instructions

value: normal


title: HFF1_Smc1_2_2020JUL28_PE40_chip

description:
Subclone c6 of HFF-hTERT
HFFc6_SMC1_CT.mRp.clN_peaks.narrowPeak
HFFc6_SMC1_CT.mRp.clN.bigWig

data_processing:
Library strategy: Cut&Tag
All datasets proseed uning nf-core  ATAC Seq pipeline  ( https://nf-co.re/atacseq )
BWA is used for mapping the fastq files to hg38 reference genome
MACS2 with default parameters is used to find the enriched peaks
BEDtools intersect is used to find the loop anchors that have MACS2 peaks.
Genome_build: hg38
Supplementary_files_format_and_content: bw files  for genome wide read coverage, bed files for peaks

value: Cut&Tag


title: 29620RB_C2_lncRNA


title: TKO-D7-1048011-7

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

description:
primary
CHX-Cre

data_processing:
Initial QC performed using FastQC v 0.11.2
mapping with Tophat
cufflinks v 2.0.1.3 was used to generate FPKM estimates
Genome_build: mm10
Supplementary_files_format_and_content: matrix of fpkm values per sample

source_name: retinal tissue

extract_protocol:
total RNA was extracted using Thermo Fisher TotalRNA kit
TruSeq RNA v2

tag: developmental stage

tag: group

value: tumor


title: HFF1_Smc1_1_2020JUL28_PE40_chip


title: 31612RB_C1_lncRNA


title: APP-Psen1/+;Cx3cr1-Cre::ERT2/+; Vhl Flox/– 12 month-age-old, treated with tamoxifen rep 3

city: Sevilla

first: María Isabel

middle: Álvarez

last: Vergara

state: Sevilla

address: C/Manuel Siurot, sn

country: Spain

institute: Instituto de Biomedicina de Sevilla

description: ARN from CD45/CD11b+ microglial cells from the brain cortex

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Raw data from the extraction software Expression Console was imported to the R statistical processing environment using the LIMMA/Bioconductor package. Quality of the data was assessed using Array Quality Metrics package. Data were normalized using Robust Multi-Array (RMA) method using LIMMA/Bioconductor package
probe group file: MTA-1_0 data
meta-probeset file: MTA-1_0.na34.mm10.transcript.csv

label: biotin

source_name: microglial cells from the brain cortex

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: microglial cells from brain cortex were isolated using specific markers (CD45/CD11b+) by flow cytometry. Whole transcript from each sample was extracted with Trizol.

value: microglial cells from the brain cortex

value: Treated with tamoxifen

value: 12 month


title: APP-Psen1/+;Cx3cr1-Cre::ERT2/+; Vhl Flox/– 12 month-age-old, non treated rep 3

value: Non treated


title: APP-Psen1/+;Cx3cr1-Cre::ERT2/+; Vhl Flox/– 12 month-age-old, treated with tamoxifen rep 1


title: APP-Psen1/+;Cx3cr1-Cre::ERT2/+; Vhl Flox/– 12 month-age-old, non treated rep 2


title: APP-Psen1/+;Cx3cr1-Cre::ERT2/+; Vhl Flox/– 12 month-age-old, non treated rep 1


title: genomic DNA from PBMC C6

description: normal PBMC sample

source_name: PBMC Normal109


title: genomic DNA from PBMC COPD16-2

description: PBMC sample from follow up COPD patients

source_name: PBMC COPD16-2

value: COPD


title: genomic DNA from PBMC COPD236-2

description: normal PBMC sample

source_name: PBMC COPD236-2


title: APP-Psen1/+;Cx3cr1-Cre::ERT2/+; Vhl Flox/– 12 month-age-old, treated with tamoxifen rep 2


title: genomic DNA from PBMC C5

description: normal PBMC sample

source_name: PBMC Normal98


title: TKO-D7-1048011-6

description:
primary
CHX-Cre


title: HFF1_CTCF_2_2020JUL28_PE40_chip

description:
Subclone c6 of HFF-hTERT
HFFc6_CTCF_CT.mRp.clN_peaks.narrowPeak
HFFc6_CTCF_CT.mRp.clN.bigWig

value: CTCF


title: genomic DNA from PBMC C1

description: normal PBMC sample

source_name: PBMC Normal50


title: genomic DNA from PBMC C2

description: normal PBMC sample

source_name: PBMC Normal69


title: TKO-D7-1048011-3

description:
primary
CHX-Cre


title: TKO-D7-1048011-5

description:
primary
CHX-Cre


title: U54-HelaS3-M-EGS-HindIII-20180730-R1-T1

description: In situ Hi-C with HindIII on HeLa-S3 (mitotic) with 1% Formaldehyde and 3mM EGS crosslinking

data_processing:
Distiller (https://github.com/mirnylab/distiller-nf) pipeline is used to process Hi-C and Micro-C datasets.
Sequencing reads were mapped to hg38 using bwa mem with flags-SP.
Mapped reads were parsed and classified using the pairtools package  (https://github.com/mirnylab/pairtools ) to get 4DN-compliant pairs files.
PCR and/optical duplicates removed by matching the positions of aligned reads with 2bp flexibility.
Pairs were filtered using mapping quality scores (MAPQ >  30)  on each side of aligned chimeric read, binned into multiple resolutions and low coverage bins are removed.
Multiresolution cooler files are created using cooler package (https://github.com/mirnylab/cooler.git)
Genome_build: hg38
Supplementary_files_format_and_content: HDF5, Multiresolution cooler files (https://github.com/open2c/cooltools)
Supplementary_files_format_and_content: Compartment Calls (https://github.com/open2c/cooltools)
Supplementary_files_format_and_content: Insulation Boundaries (https://github.com/open2c/cooltools)
Supplementary_files_format_and_content: Loop Calls (https://github.com/open2c/cooltools)

source_name: Hela S3

growth_protocol: 4DN Protocols are  used to culture the cells. Protocols can be found here: https://data.4dnucleome.org/resources/experimental-resources/cell-lines, https://data.4dnucleome.org/biosources/4DNSRGTEEYSL/?redirected_from=%2F4DNSRGTEEYSL. Hela S3 syncronization protocols are adopted from Abramo et al.2019. Nat Cell Biol.

extract_protocol:
Nuclei was extracted by lyse cells in lysis buffer containing NP40 and protease inhibitor.
DNA library was generated by biotin fill-in followed blunt end ligation. Then removal of biotin from un-ligated ends, sonication, end repair, biotin pull-down, Illumina adaptor ligation and paired end PCR.
Hi-C library generated Hi-C 2.0 protocol. Belaghzal et at.2017.

value: in situ Hi-C

value: HindIII

value: Hela S3


title: genomic DNA from PBMC COPD192

description: PBMC sample from COPD patients

source_name: PBMC COPD192


title: genomic DNA from PBMC C3

description: normal PBMC sample

source_name: PBMC Normal73


title: genomic DNA from PBMC COPD249

source_name: PBMC COPD249


title: 31680RB_P3_lncRNA

value: Granulosa cells

value: ovarian

value: Polycystic ovary syndrome


title: 30644RB_P5_lncRNA


title: TKO-D7-1048011-4

description:
primary
CHX-Cre


title: genomic DNA from PBMC COPD172-2

source_name: PBMC COPD172-2


title: TKO-D7-1048011-2

description:
primary
CHX-Cre


title: 30686RB_P4_lncRNA


title: HFF1_CTCF_1_2020JUL28_PE40_chip


title: U54-HelaS3-G1-DSG-HindIII-20180730-R1-T1

description: In situ Hi-C with HindIII on HeLa-S3 (G1 phase) with 1% Formaldehyde and 3mM DSG crosslinking


title: TKO-D7-1048010-4

description:
primary
CHX-Cre


title: 29615RB_P2_lncRNA


title: 31533RB_P1_lncRNA


title: genomic DNA from PBMC COPD168

description: PBMC sample from COPD patients

source_name: PBMC COPD168


title: genomic DNA from PBMC COPD172

description: PBMC sample from COPD patients

source_name: PBMC COPD172


title: tdTomato_negative_TAAR_enhancer2_tdTomato_Tg_RNAseq

city: Shanghai

first: Qian

address: 280 South Chongqing Road, Building No.5, Room 408

department: Department of Anatomy and Physiology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
RNA-seq Reads were trimmed by Trimmomatic (version 0.36) and then quantified TPM values using salmon 1.4.0 package
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing TPM values

source_name: main olfactory epithelim (MOE)

extract_protocol:
Total RNAs of FACS enriched cells were extracted by the FastPure cell/tissue total RNA isolation kit (Vazyme).
Libraries of FACS enriched cells were prepared by the VAHTS universal V6 RNA-seq library prep kit for Illumina (Vazyme).

value: adult

value: TAAR enhancer 2-tdTomato transgenic


title: genomic DNA from PBMC COPD236

description: PBMC sample from COPD patients

source_name: PBMC COPD236


title: O_F_83_CC_RNAseq

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences and mapped to the human reference transcriptome (Ensembl hg38) using Salmon with the following parameters: --libType A, --validateMappings --rangeFactorizationBins 4 -p 20
Genome_build: hg38
Supplementary_files_format_and_content: comma separated values, scores represent….
Supplementary_files_format_and_content: Scores represent Transcript Per Million and number of quasi-mapped reads

source_name: Vastus_ lateralis_muscle_biopsy

extract_protocol:
Skeletal muscle biopsies were pulverized on liquid nitrogen, and either digested and cloned using ribosome profiling methods (Ingolia et al., Nature Protocols, 2013) or prepared using standard RNAseq protocols.
Total RNASeq libraries were prepared by homogenizing pulverized tissue in a buffer containing proteinase K. Digestion was performed at 55°C for 10 minutes, before extraction using the Qiagen Fibrous Tissue kit. Total RNAs were then extracted using the Qiagen Fibrous Tissue kit. After quality checking on the Agilent Bioanalyzer, the rRNA was depleted using the RiboMinus kit according to the manufacturer’s protocols. cDNA was prepared using a NuGen Ovation RNA-Seq system V2 and fragmented by sonication using a Biorupter for library preparation. Libraries were prepared using the Illumina TruSeq ChIP library preparation kit. RNA-seq libraries were sequenced paired-end on an Illumina NextSeq, with a read depth between 600 million and 800 million reads.

treatment_protocol: Study participants were from the Baltimore Longitudinal Study of Aging (BLSA), a longitudinal study of aging supported by the National Institute on Aging. As previously reported, a 6-mm Bergström biopsy of 200 to 400 mg of vastus lateralis muscle was obtained from each of five healthy individuals after anaesthetization with 2% Lidocaine. Samples were snap-frozen in liquid nitrogen and stored frozen until further processing.

value: 83 years

tag: age group

value: old (O)

value: Female

tag: ethnicity

value: Caucasian

value: skeletal muscle

tag: health status

value: healthy


title: MAF_41_AA_RNAseq

tag: age

value: 41 years

value: middle-aged


title: genomic DNA from PBMC COPD164

description: PBMC sample from COPD patients

source_name: PBMC COPD164

value: COPD


title: genomic DNA from PBMC COPD138

description: PBMC sample from COPD patients

source_name: PBMC COPD138


title: TKO-D0-1084380-9

description:
primary
CHX-Cre

source_name: retinal tissue

value: pre-tumorigenic


title: O_M_85_CC_RNAseq

value: 85 years

value: Male


title: TKO-D7-1048010-3

description:
primary
CHX-Cre

value: tumor


title: iFTSEC283 treated with vehicle control  (Replicate 1)

source_name: Fallopian tube secretory cells

tag: cell line

tag: cell type

value: Fallopian tube secretory cells

value: Mock treated with water for 137 days

value: Wild type


title: genomic DNA from PBMC COPD154

description: PBMC sample from COPD patients

source_name: PBMC COPD154


title: 29620RB_C2_miRNA

source_name: ovarian

value: Granulosa cells

value: ovarian

value: Polycystic ovary syndrome


title: 30956RB_C5_miRNA


title: 31612RB_C1_miRNA


title: 26146RB_C3_miRNA


title: ribo_rapa_3h_wt

city: Yokohama

first: Shiho

last: Makino

address: 4259-S2-12 Nagatsuta-cho, Midori-ku

country: Japan

institute: Tokyo Institute of Technology

data_processing:
Library strategy: Ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA alignment with bowtie2 v2.1.0 (Sample 1~12), rRNA and other non-coding RNA alignment with STAR v2.7.0a (Sample 13~22)
Alignment with TopHat v2.0.9 (Sample 1~12) or STAR v2.7.0a (Sample 13~22)
Read quantitation using HTSeq v0.6.1 (Sample 1~12) or custom scripts (Sample 13~22)
Genome_build: sacCer3
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. read counts (Sample 1~12), 1. transcript name;2. CDS region (nt) used for read counting;3. read counts (Sample 13~22)

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown in YPD (2% peptone, 1% yeast extract, and 2% glucose) medium. For autophagy induction, yeast cells were grown in YPD medium with 0.2 µM rapamycin.

extract_protocol:
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling) or TruSeq (illumina) (for mRNA-seq)
Rnase I footprinting, ribosome pelleting, RNA extraction

tag: growth protocol

value: YPD +rapamycin for 3 h

tag: genotype

value: WT

tag: molecule subtype

value: total RNA


title: ribo_rapa_2h_wt

value: YPD +rapamycin for 2 h


title: genomic DNA from PBMC COPD129

description: PBMC sample from COPD patients

source_name: PBMC COPD129


title: 30548RB_C4_miRNA

tag: tissue


title: GFP_positive_TAAR_enhancer1_GFP_Tg_RNAseq

tag: strain

value: adult

value: TAAR enhancer 1-GFP transgenic


title: TKO-D0-1084379-6

description:
primary
CHX-Cre


title: genomic DNA from PBMC COPD87

description: PBMC sample from COPD patients

source_name: PBMC COPD87

tag: disease state

value: COPD


title: MAF_43_CC_RNAseq

value: 43 years

value: middle-aged

tag: gender

value: Female

value: Caucasian

value: skeletal muscle

value: healthy


title: GFP_negative_TAAR_enhancer1_GFP_Tg_RNAseq


title: TKO-D0-1084380-5

description:
primary
CHX-Cre

value: pre-tumorigenic


title: TKO-D0-1084380-3

description:
primary
CHX-Cre


title: MAM_46_CC_RNAseq

value: 46 years

value: Male


title: TKO-D0-1084380-1

description:
primary
CHX-Cre


title: RDM15_FLAG_ChIP_rep2 (additional sequencing of GSM4668648)

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

data_processing:
The paired-end reads were mapped to the TAIR10 genome of Arabidopsis thaliana (TAIR10) with bowtie2 (Langmead and Salzberg 2012) with parameter "--very-sensitive --no-unal --no-mixed --no-discordant -k 5" . To remove potential PCR duplicates, markdup from SAMtools  (Li et al. 2009) was used. After mapping, only uniquely mapped reads were retained.
Genome_build: TAIR10
Supplementary_files_format_and_content: The bedGraph files were generated using genomeCoverageBed from bedtools with parameters "-bg -pc".

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Plants were grown in air-conditioned rooms at 22 °C with 16 h-8 h light-dark cycle.

extract_protocol:
Genomic DNA was extracted from two-week-old seedlings using the Plant DNeasy mini kit (Qiagen).
Preparation of DNA libraries for ChIP-Seq using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®.

tag: chip antibody

value: FLAG


title: genomic DNA from PBMC COPD40

description: PBMC sample from COPD patients

source_name: PBMC COPD40


title: 29615RB_P2_miRNA

value: Granulosa cells

value: ovarian

value: Polycystic ovary syndrome


title: tdTomato_positive_TAAR_enhancer2_tdTomato_Tg_RNAseq

value: TAAR enhancer 2-tdTomato transgenic


title: genomic DNA from PBMC COPD16

description: PBMC sample from COPD patients

source_name: PBMC COPD16


title: RDM15_FLAG_ChIP_rep1 (additional sequencing of GSM4668646)


title: TKO-D0-1084380-2

description:
primary
CHX-Cre


title: 30644RB_P5_miRNA


title: 30686RB_P4_miRNA


title: 31533RB_P1_miRNA


title: Col0_H3K4me1_Input_rep2

data_processing:
Bisulfite-Seq: the raw data were trimmed using Trimmomatic (Bolger, Lohse, and Usadel 2014) with parameters "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:50". Only clean paired-end reads were mapped to TAIR10 genome using tool BSMAP (Xi and Li 2009) with parameters "-m 0 -w 2" (other parameters were used the default value).  To remove potential PCR duplicates, the "rmdup" command of SAMtools (Li et al. 2009) was used. methratio.py script from BSMAP was used to extract methylation ratios from mapping results.
Small RNA Sequencing: the adapter was removed using "fastx_clipper" command from FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). After adapter sequences were trimmed, clean reads with size ranging from 18 to 31-nt were mapped to the Arabidopsis genome (TAIR10) using Bowtie (Langmead et al. 2009) with parameters "-v 0 -k 10". Reads that have overlap with annotated tRNAs, rRNAs, snRNAs, or snoRNAs were excluded.
ChIP-Seq: The paired-end reads were mapped to the TAIR10 genome of Arabidopsis thaliana (TAIR10) with bowtie2 (Langmead and Salzberg 2012) with parameter "--very-sensitive --no-unal --no-mixed --no-discordant -k 5" . To remove potential PCR duplicates, markdup from SAMtools  (Li et al. 2009) was used. After mapping, only uniquely mapped reads were retained.
Genome_build: TAIR10
Supplementary_files_format_and_content: Small RNA Sequencing: The bedGraph files for 24nt siRNAs were generated using genomeCoverageBed from bedtools with parameters  "-bga -split".
Supplementary_files_format_and_content: For ChIP-Seq: The bedGraph files were generated using genomeCoverageBed from bedtools with parameters "-bg -pc".

extract_protocol:
Preparation of DNA libraries for ChIP-Seq using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®.
Genomic DNA was extracted from two-week-old seedlings using the Plant DNeasy mini kit (Qiagen).Total RNA extracted from two-week-old Col-0, rdm15-2 and rdm15-3 seedlings using the TRIzol (invitrogen) method.

tag: ecotype

value: wildtype


title: 31680RB_P3_miRNA


title: TKO-D0-1048083-7

description:
primary
CHX-Cre

tag: developmental stage


title: ribo_rapa_1h_wt

value: YPD +rapamycin for 1 h

value: WT

value: total RNA


title: ribo_growing_wt_rep2

value: YPD


title: TKO-D0-1048083-1

description:
primary
CHX-Cre

tag: group


title: rna_rapa_3h_wt

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA alignment with bowtie2 v2.1.0 (Sample 1~12), rRNA and other non-coding RNA alignment with STAR v2.7.0a (Sample 13~22)
Alignment with TopHat v2.0.9 (Sample 1~12) or STAR v2.7.0a (Sample 13~22)
Read quantitation using HTSeq v0.6.1 (Sample 1~12) or custom scripts (Sample 13~22)
Genome_build: sacCer3
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. read counts (Sample 1~12), 1. transcript name;2. CDS region (nt) used for read counting;3. read counts (Sample 13~22)

extract_protocol:
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling) or TruSeq (illumina) (for mRNA-seq)
Truseq standard total RNA library prep

value: YPD +rapamycin for 3 h


title: TKO-D0-1048037-7

description:
primary
CHX-Cre


title: RDM15_FLAG_ChIP_rep2

tag: antibody


title: 30548RB_C4_mRNA


title: RDM15_FLAG_Input_rep2


title: ribo_growing_wt_rep1


title: 30956RB_C5_mRNA


title: Col0_H3K4me1_Input_rep1


title: TKO-D0-1048037-2

description:
primary
CHX-Cre


title: DKO-D7-1047920-3

description:
primary
CHX-Cre


title: Col0_H3K4me1_ChIP_rep2


title: rna_rapa_1h_wt


title: rna_rapa_2h_wt

value: YPD +rapamycin for 2 h


title: RDM15_FLAG_ChIP_rep1


title: 26146RB_C3_mRNA


title: rna_growing_wt_rep2


title: DKO-D7-1047920-2

description:
primary
CHX-Cre


title: Col0_H3K4me1_ChIP_rep1


title: RDM15_FLAG_Input_rep1


title: DKO-D7-1047920-1

description:
primary
CHX-Cre


title: 29620RB_C2_mRNA


title: rna_growing_wt_rep1


title: DKO-D7-1047918-2

description:
primary
CHX-Cre


title: rdm15-3_sRNA_rep2

extract_protocol:
Preparation of Small RNA libraries for small RNA Sequencing using NEBNext® Small RNA Library Prep Set for Illumina® (Multiplex Compatible);
Genomic DNA was extracted from two-week-old seedlings using the Plant DNeasy mini kit (Qiagen).Total RNA extracted from two-week-old Col-0, rdm15-2 and rdm15-3 seedlings using the TRIzol (invitrogen) method.


title: 31612RB_C1_mRNA


title: DKO-D7-1047918-1

description:
primary
CHX-Cre


title: rna_rapa_rny1atg2_vacuole_rep2

source_name: X2180-1a; rny1Δ::natNT2, atg2Δ::kanMX6

value: vacuolar RNA


title: 30644RB_P5_mRNA


title: rna_rapa_rny1atg2_vacuole_rep1


title: rdm15-3_sRNA_rep1


title: rdm15-2_sRNA_rep1


title: 30686RB_P4_mRNA


title: DKO-D7-1047823-5

description:
primary
CHX-Cre


title: DKO-D7-1047823-4

description:
primary
CHX-Cre


title: Col0_sRNA_rep2


title: rdm15-2_sRNA_rep2


title: rna_rapa_rny1atg2_total_rep1


title: rna_rapa_rny1atg2_total_rep2


title: 29615RB_P2_mRNA


title: rna_rapa_rny1_vacuole_rep2

source_name: X2180-1a; rny1Δ::natNT2


title: Col0_sRNA_rep1


title: DKO-D0-1047823-8

description:
primary
CHX-Cre


title: DKO-D0-1047823-7

description:
primary
CHX-Cre


title: rna_rapa_rny1_vacuole_rep1


title: DKO-D0-1047823-5

description:
primary
CHX-Cre


title: 31533RB_P1_mRNA


title: rdm15-3_BS_rep2

description: treated with bisulfite

extract_protocol:
Preparation of DNA libraries for Bisulfite-Seq using NEBNext Ultra II DNA Library Prep Kit for Illumina® and Epitect Plus DNA Bisulfite Kit (Qiagen).
Genomic DNA was extracted from two-week-old seedlings using the Plant DNeasy mini kit (Qiagen).Total RNA extracted from two-week-old Col-0, rdm15-2 and rdm15-3 seedlings using the TRIzol (invitrogen) method.


title: 30956RB_C5_MeDIP


title: rna_rapa_rny1_total_rep2


title: 30548RB_C4_MeDIP


title: 31680RB_P3_mRNA


title: DKO-D0-1047823-4

description:
primary
CHX-Cre


title: rdm15-2_BS_rep2

description: treated with bisulfite


title: rdm15-3_BS_rep1

description: treated with bisulfite


title: DKO-D0-1047823-2

description:
primary
CHX-Cre


title: rna_rapa_rny1_total_rep1


title: DKO-D0-1047823-1

description:
primary
CHX-Cre


title: 26146RB_C3_MeDIP


title: rdm15-2_BS_rep1

description: treated with bisulfite


title: DKO-D0-1032037-3

description:
primary
CHX-Cre


title: rna_growing_rny1atg2_total


title: Col0_BS_rep2

description: treated with bisulfite


title: rna_growing_rny1atg2_vacuole


title: 31612RB_C1_MeDIP


title: Col0_BS_rep1

description: treated with bisulfite


title: 30644RB_P5_MeDIP


title: rna_growing_rny1_vacuole


title: ZsGreen-positive_TAAR6-Cre&ZsGreen_RNAseq-1

data_processing:
RNA-seq Reads were trimmed by Trimmomatic (version 0.36) and then aligned to the mouse reference genome (GRCm38/mm10, downloaded from UCSC, http://genome.ucsc.edu/) using Hisat2 (version 2.1.0).
TPM values were calculated using Cufflinks (version 2.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing raw counts and normalized counts obtained from DESeq2 package

extract_protocol:
Total RNAs of FACS enriched cells were extracted with a RNeasy Mini kit (Qiagen) with DNase treatment.
Libraries of FACS enriched cells were prepared with the Smart-seq2 procedure, similar to our previous work (Tan, L., Li, Q. & Xie, X.S. Olfactory sensory neurons transiently express multiple olfactory receptors during development. Mol Syst Biol 11, 844, 2015).


title: rna_growing_rny1_total


title: DKO-D0-1032037-1-2

description:
primary
CHX-Cre


title: CHX-D7-1048043-5-6

description:
primary
CHX-Cre

value: normal

value: wt


title: 30686RB_P4_MeDIP


title: 31680RB_P3_MeDIP


title: CHX-D7-1048043-1-3-4

description:
primary
CHX-Cre


title: GFP-positive_TAAR5-Cre&L10-GFP_RNAseq-7


title: GFP-positive_TAAR5-Cre&L10-GFP_RNAseq-6


title: CHX-D7-1047745-8

description:
primary
CHX-Cre

value: deltaRb


title: 29615RB_P2_MeDIP


title: GFP-positive_TAAR5-Cre&L10-GFP_RNAseq-5


title: 29620RB_C2_MeDIP


title: 31533RB_P1_MeDIP


title: CHX-D7-1047745-6

description:
primary
CHX-Cre


title: GFP-positive_TAAR5-Cre&L10-GFP_RNAseq-3


title: CHX-D7-1047745-7

description:
primary
CHX-Cre


title: GFP-positive_TAAR5-Cre&L10-GFP_RNAseq-4


title: GFP-positive_TAAR5-Cre&L10-GFP_RNAseq-1


title: SD2056

city: New York

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
fastq format were aligned to Human Genome HG19 using the RNA-seq STAR aligner (Dobin et al., 2013)
Mapped reads for each sample were counted for each gene in annotation files in GTF format (gencode.v19.annotation.gtf available for download from GENECODE website (http://www.gencodegenes.org/releases/19.html) using the FeatureCounts read summarization program (Liao et al., 2014) as reported in Chiappinelli et al., Cell 2015.
Genome_build: hg19
Supplementary_files_format_and_content: Individual count files were merged to the Matrix by an in-house R script.

source_name: Melanoma tumor

growth_protocol: human melanoma tumor biopsies

extract_protocol:
Total RNA was purified from tissue samples using AllPrep DNA/RNA Mini Kit (cat. no. 80204) from QIAGEN according to the manufacturer's instructions.
After RiboGreen quantification and quality control by BioAnalyzer, 2µg of total RNA were processed for TruSeq mRNA-Seq to generate 2x50bp paired-end reads with HiSeq 2500 in high output mode at the New York Genome Center

value: Melanoma tumor

tag: treatment

value: pre ipilimumab

tag: biosite

value: cutaneous

value: F


title: CHX-D7-1047745-5

description:
primary
CHX-Cre


title: NR8727

tag: age

value: M


title: CHX-D7-1047745-3

description:
primary
CHX-Cre


title: GFP-positive_TAAR5-Cre&L10-GFP_RNAseq-2

source_name: main olfactory epithelim (MOE)


title: CHX-D7-1047745-1

description:
primary
CHX-Cre


title: CHX-D0-1047739-3

description:
primary
CHX-Cre


title: ZsGreen-negative_TAAR6-Cre&ZsGreen_RNAseq-10


title: SD1494.1


title: NR5784


title: GFP-negative_TAAR5-Cre&L10-GFP_RNAseq-9


title: CHX-D0-1047739-2

description:
primary
CHX-Cre


title: anti-OSM 1

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from whole lung homogenate of C57/BL6 mice treated with anti-OSM antibody and E. coli.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene10stmmentrezgcdf R package (version 16.0.0).

source_name: whole lung homogenate

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Male and female C57BL/6J mice were obtained from Jackson Laboratories at 6-7 weeks of age. Prior to infection, they were housed at the Boston University animal facility and provided with an ad libitum supply of standard chow. Mice were infected at 10-12 weeks of age. All animal protocols were approved by the BU Institutional Animal Care and Use Committee (IACUC).

extract_protocol: Frozen left lobes in RLT buffer were homogenized using a Bullet Blender (Next Advance, Troy, NY) per the manufacturer’s instruction. Cellular debris was removed by centrifugation (max speed 3 minutes). RNA was isolated using the RNeasy micro kit (Qiagen), following the manufacturer’s instructions. RNA was eluted in 50µl RNase-free water.

treatment_protocol: After anesthetization with ketamine and xylazine, the left lung lobes of C57Bl/6J mice were intratracheally infected with 1E6 CFU E. coli plus either 10 ng IgG control antibody or neutralizing anti-OSM antibody. After 6 hours of infection, whole left lung lobes were harvested, frozen at -80˚C and stored for future RNA isolation.

value: whole lung

value: anti-OSM antibody and E. coli

value: 10-12 weeks


title: TAAR_enhancer2_KO_homo_3

description: TAAR_enhancer2_KO_raw_counts_all.csv, TAAR_enhancer2_KO_normalized_counts_all.csv

data_processing:
RNA-seq Reads were trimmed by Trimmomatic (version 0.36) and then aligned to the mouse reference genome (GRCm38/mm10, downloaded from UCSC, http://genome.ucsc.edu/) using Hisat2 (version 2.1.0).
Next, raw counts of genes were quantified using featureCounts from Subread package (version 1.6.2). Normalized counts were obtained by normalizing raw counts with size factors using the "median ratio method" in DESeq2 1.20.0 package.
Subsequent differentiated expressed gene analysis was performed using DESeq2 with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing raw counts and normalized counts obtained from DESeq2 package

extract_protocol:
Total RNAs of the whole MOE tissues were extracted with a RNeasy Mini kit (Qiagen) with DNase treatment.
Libraries of the whole MOE tissues were prepared with an NEBNext Ultra Directional RNA kit (NEB) with polyA bead selection.

value: homozygous


title: TAAR5-Cre&ZsGreen_ATACseq-2

data_processing:
Reads were mapped to the mouse reference genome (mm10) using Bowtie 2 (version 2.2.9) with the following parameters: --local –X 2000.
Significant ATAC-seq peaks were identified using MACS2 (version 2.1.1.20160309) with the “--nomodel --shift -100 --extsize 200 --keep-dup all” parameters and the default threshold of q value (adjusted p value) at 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

source_name: TAAR OSNs sorted from Taar5-ires-Cre; lox-ZsGreen mice

extract_protocol:
Follow the protocol in Buenrostro, J.D., Wu, B., Chang, H.Y. & Greenleaf, W.J. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol 109, 21 29 21-29 (2015)
Follow the protocol in Buenrostro, J.D., Wu, B., Chang, H.Y. & Greenleaf, W.J. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol 109, 21 29 21-29 (2015)

value: Taar5-ires-Cre; lox-ZsGreen


title: Control IgG 3

description: Gene expression data from whole lung homogenate of C57/BL6 mice treated with control IgG and E. coli.

value: control IgG and E. coli


title: Control IgG 1


title: GFP-negative_TAAR5-Cre&L10-GFP_RNAseq-8


title: SD2051

first: Bic

last: MSKCC

value: acral


title: Control IgG 2


title: OMPiGFP_ATACseq-3

source_name: GFP-positive OSNs sorted from Omp-ires-GFP mice

value: Omp-ires-GFP


title: CHX-D0-1047739-1

description:
primary
CHX-Cre


title: TAAR_enhancer2_KO_homo_2


title: TAAR5-Cre&ZsGreen_ATACseq-3


title: GFP-negative_TAAR5-Cre&L10-GFP_RNAseq-7


title: anti-OSM 3


title: CHX-D0-1032030-4-5

description:
primary
CHX-Cre


title: SD7357.1

value: post ipilimumab

value: unknown


title: TAAR_enhancer2_KO_homo_1


title: CHX-D0-1032030-3

description:
primary
CHX-Cre

value: normal

value: wt


title: GFP-negative_TAAR5-Cre&L10-GFP_RNAseq-6


title: SD6494.2

value: Melanoma tumor


title: TAAR_enhancer2_KO_het_3

value: heterozygous


title: GFP-negative_TAAR5-Cre&L10-GFP_RNAseq-5


title: NR3549

value: pre ipilimumab

value: cutaneous


title: GFP-negative_TAAR5-Cre&L10-GFP_RNAseq-4


title: TAAR_enhancer2_KO_het_2


title: CHX-D0-1032030-1

description:
primary
CHX-Cre


title: GFP-negative_TAAR5-Cre&L10-GFP_RNAseq-3


title: NR1867

value: M


title: TAAR_enhancer2_KO_het_1


title: SD6336.1


title: TAAR_enhancer2_KO_WT_3

value: wild type


title: GFP-negative_TAAR5-Cre&L10-GFP_RNAseq-2


title: GFP-negative_TAAR5-Cre&L10-GFP_RNAseq-1


title: SD5038


title: TAAR_enhancer2_KO_WT_2


title: NR9705

value: F


title: SD0346


title: CHX-D0-1032030-2

description:
primary
CHX-Cre


title: TAAR_enhancer2_KO_WT_1


title: NR9521


title: TAAR6-Cre&ZsGreen_ATACseq-3

source_name: TAAR OSNs sorted from Taar6-ires-Cre; lox-ZsGreen mice

value: Taar6-ires-Cre; lox-ZsGreen


title: SD6336.2


title: TAAR-enhancer1-KO-homo-3

description: TAAR_enhancer1_KO_raw_counts_all.csv, TAAR_enhancer1_KO_normalized_counts_all.csv

data_processing:
RNA-seq Reads were trimmed by Trimmomatic (version 0.36) and then aligned to the mouse reference genome (GRCm38/mm10, downloaded from UCSC, http://genome.ucsc.edu/) using Hisat2 (version 2.1.0).
Next, raw counts of genes were quantified using HTSeq (version 0.6.1p1). Normalized counts were obtained by normalizing raw counts with size factors using the "median ratio method" in DESeq2 1.20.0 package.
Subsequent differentiated expressed gene analysis was performed using DESeq2 with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing raw counts and normalized counts obtained from DESeq2 package

value: homozygous


title: TAAR-enhancer1-KO-homo-2


title: canine primary osteosarcoma sample9

description: canine primary osteosarcoma matched sample9

hyb_protocol: After sample denaturation and pre-annealing with 5µl of Canine Hybloc™ DNA, hybridization was performed at 65°C with shaking for 24 hours. After hybridization, slides were washed sequential

scan_protocol: Agilent G2565C DNA Scanner

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and LOWESS normalization.

source_name: canine primary osteosarcoma tissue

label_protocol: 750ng of test DNA and control DNA were double-digested and labeled by random priming (Agilent) for 2 hours using Cy5-dUTP for the test DNA and Cy3-dUTP (Agilent) for the control DNA. Labeled DNAs were incubated at 65°C for 10 minutes and then purified.

extract_protocol: Genomic DNA were extracted using phenol chloroform and treated with RNaseA (Invitrogen) for 1 hour at 37°C

value: canine primary osteosarcoma tissue

tag: breed

value: Great Pyrenees

value: 5 yrs

value: MC

source_name: normal bone tissue

value: normal bone tissue


title: TAAR6-Cre&ZsGreen_ATACseq-2


title: TAAR6-Cre&ZsGreen_ATACseq-1


title: NR4949

value: post ipilimumab

value: unknown


title: TAAR-enhancer1-KO-homo-1


title: NR4810


title: TAAR5-Cre&L10-GFP_ATACseq-1

source_name: TAAR OSNs sorted from Taar5-ires-Cre; lox-L10-GFP mice

value: Taar5-ires-Cre; lox-L10-GFP


title: TAAR-enhancer1-KO-het-3


title: OMPiGFP_ATACseq-2

value: Omp-ires-GFP


title: canine primary osteosarcoma sample8

description: canine primary osteosarcoma matched sample8

value: 7 yrs

value: FS


title: canine primary osteosarcoma sample7

description: canine primary osteosarcoma matched sample7

value: Bull Mastiff

value: 8 yrs


title: canine primary osteosarcoma sample6

description: canine primary osteosarcoma matched sample6

value: Greyhound

value: 6 yrs


title: NR4631

value: Melanoma tumor

value: cutaneous

value: M


title: TAAR-enhancer1-KO-het-2

value: heterozygous


title: OMPiGFP_ATACseq-1

value: Adult


title: NR9449

value: F


title: CR7623


title: TAAR-enhancer1-KO-het-1


title: ASO2

first: donghong

last: Cai

address: Yueyang Street

institute: PICB, CAS

description: ribo- strand specific RNA-seq (PE)

data_processing:
Reads were mapped to human reference genome by STAR (020201)
Then the mapping files were quantified counts by HTSeq package in python for the following analysis
DEseq package in R program was used to identify the differentially expressed genes (DEG) with the following defined cutoff padj <0.1 and log2FC > 0.8 or < -0.8
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

growth_protocol: IMR90 were maintained in MEM supplemented with 10% FBS and 1% penicillin/Streptomycin.

extract_protocol:
Total RNA isolated from cultured cells or under different treatment was extracted by Trizol (Invitrogen) according to the manufacturer’s manual.
The ribo- strand specific RNA-seq libraries were constructed by using NEBNext® rRNA Depletion Kit and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®. Briefly, total RNA were removed the ribosomal RNA from cytoplasmic and mitochondrial fraction. The ribo- RNA were reverse transcribed into cDNA and follow with second strand systhesis wiht dUTP. Then dsDNAs were ligated to adapters by end prepair with dT. PCR with specific index for sequencing.

treatment_protocol: ASO knock down NFKBMARL-1

tag: cell type

value: Lung Fibroblast

tag: source

value: ATCC (CCL-186)

tag: cell line

value: ASO


title: TAAR_cluster_KO_RNA_seq_homo-4

tag: genotype

value: homozygous


title: CR9699.1

tag: tissue

value: post ipilimumab


title: TAAR-enhancer1-KO-WT-3

tag: strain

value: wild type


title: TAAR-enhancer1-KO-WT-2


title: TAAR_cluster_KO_RNA_seq_homo-3


title: canine primary osteosarcoma sample5

description: canine primary osteosarcoma matched sample5

value: canine primary osteosarcoma tissue

value: Rottweiler X (Canine Mixed Breed)

value: 9 yrs

value: FS

value: normal bone tissue


title: canine primary osteosarcoma sample4

description: canine primary osteosarcoma matched sample4

value: Mixed Breed (Labrador Retriever/X)

value: 10 yrs


title: ASO1

description: ribo- strand specific RNA-seq (PE)


title: O_F_83_CC_Riboseq

description: Ribosome-protected RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were clipped for adaptor sequence '5′-CTGTAGGCACCATCAAT-3′, trimmed for quality to 50 bp, quality checks were performed with FastQC.
Reads were mapped to databases containing human rRNAs (48 sequences), snoRNAs (562 sequences), snRNAs (36 sequences), and tRNAs (23 sequences) with Bowtie2 in Galaxy using default settings.
Unaligned reads were mapped to the human reference transcriptome (Ensembl hg38) using Salmon with the following parameters: --libType A, --validateMappings --rangeFactorizationBins 4 -p 20
Genome_build: hg38
Supplementary_files_format_and_content: comma separated values, scores represent….
Supplementary_files_format_and_content: Scores represent Transcript Per Million and number of quasi-mapped reads

source_name: Vastus_ lateralis_muscle_biopsy

extract_protocol:
Skeletal muscle biopsies were pulverized on liquid nitrogen, and either digested and cloned using ribosome profiling methods (Ingolia et al., Nature Protocols, 2013) or prepared using standard RNAseq protocols.
The ribosome profiling RNASeq library protocols were based on Ingolia, et al., 2018,  with some modifications. First, pulverized muscle powder was fully homogenized by trituration in a polysome buffer containing 1 M Tris-Cl, pH 7.5; 5 M NaCl; 1 M MgCl2; 1 M dithiothreitol; and 100 mg/ml cycloheximide (Sigma-Aldrich). The lysate was then cleared by centrifugation at 20,000 x g for 10 minutes at 4°C, then treated with 1% NP-40 (Sigma-Aldrich) and Turbo DNase (ThermoFisher) at 25 U/ml for 10 minutes on ice, and cleared again by centrifugation at 20,000 x g for 10 minutes at 4°C. The RNA concentration was then measured using Qubit High Sensitivity RNA kit according to the manufacturer’s protocol, and RNase I (ThermoFisher) was added to a concentration of 1 µg RNA:10 units RNase I. Digestion was performed at room temperature with agitation for 45 minutes. The digestion was stopped with 200 U of RNase inhibitor (SuperaseIn, ThermoFisher) and the digested sample was layered over 1 ml of 1 M sucrose cushion containing RNase inhibitor in a 13-mm x 51-mm ultracentrifugation tube (Beckman-Coulter), and ribosomes were then pelleted by ultracentrifugation in a TLA 100.3 rotor for 2 hours at 70,000 rpm at 4°C. The resulting pellet was resuspended in Qiazol (Qiagen), purified, and separated on a 15% TBE-urea gel. Footprint size selection, dephosphorylation, and linker ligation were performed according to the Ingolia procedure with the following modifications: footprint sizes were selected between 28-34 nucleotides, the Universal miRNA Cloning Linker (NEB) was used, and T4 RNA Ligase 2, truncated K227Q (NEB) was used. For rRNA depletion, the RiboZero kit (Illumina) was used after linker ligation, using the manufacturer’s protocol, with 8 µl of rRNA removal solution, 18 µl of RNase-free water, and 4 µl RiboZero buffer, for a total volume per sample of 40 µl. The reaction was then purified using the RNA clean and concentrator-5 (Zymo), eluting into 10 µl water. Reverse transcription, circularization, and PCR amplification were performed according to Ingolia et al., except that CircLigase 2 was substituted and ATP omitted from the circularization reaction. Ribosome profiling libraries were sequenced using an Illumina HiSeq 2500, single-end, 75-bp reads, with a maximum depth per sample of between 150 million and 250 million reads.
Ribo-Seq

value: 83 years

tag: age group

value: old (O)

value: Female

tag: ethnicity

value: Caucasian

value: skeletal muscle

tag: health status

value: healthy


title: TAAR_cluster_KO_RNA_seq_homo-2


title: canine primary osteosarcoma sample2

description: canine primary osteosarcoma matched sample2

value: Mixed Breed (German Shepherd/Collie/X)

value: 8 yrs

tag: gender

value: MC


title: NC2

description: ribo- strand specific RNA-seq (PE)

value: Lung Fibroblast

value: ATCC (CCL-186)

value: NC


title: canine primary osteosarcoma sample3

description: canine primary osteosarcoma matched sample3

value: canine primary osteosarcoma tissue

value: Boxer

value: 12 yrs


title: NC1

description: ribo- strand specific RNA-seq (PE)


title: TAAR_cluster_KO_RNA_seq_het-4

value: heterozygous


title: TAAR-enhancer1-KO-WT-1

value: wild type


title: TAAR_cluster_KO_RNA_seq_het-3


title: TAAR_cluster_KO_RNA_seq_homo-1

value: homozygous


title: CR1509

value: Melanoma tumor

value: post ipilimumab

value: cutaneous

value: F


title: Input ChIRP

description: ChIRP-seq

data_processing:
Library strategy: ChIRP-seq
Reads were mapped to human reference genome by STAR (020201)
For the mapped bam files, Homer (v4.11.1) were used to identify peaks.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

extract_protocol:
ChIRP-seq experiments were performed according to Chu et al. (Chu et al., 2011) with modification as follows. 107 cells were washed once by PBS and resuspended in 10ml PBS. Cells were harvested by trypsin digestion and crosslinked with 2mM DSG (Thermo Fisher) in PBS at RT for 30 min with gentle end to end rotation. Formaldehyde was added to a final concentration of 3.7% to crosslink for 10 min further, then quenched with 250mM glycine at RT for 10 min. The cells were then washed twice by ice cold PBS, pelleted and snap frozen by liquid nitrogen and stored at -80℃. Cell pellets were resuspended with nuclear lysis buffer and incubated on ice for 10min. Chromatin was sonicated into 200-500bp, centrifuged at high speed for 10min and the supernatant was moved to a new tube, with 10ul reserved as DNA Input. For hybridization, samples were incubated with 100 pmol probes per 1ml lysate, supplemented with 250ul of 5x hybridization buffer. The hybridization was conducted at 39 oC rotating for 3h. Prewashed 50 uL streptavidin M280 beads were then added and the incubation continued for an additional 3h. The beads were washed 5 times total with 0.1 X SSC wash buffer (0.1 X SSC, 1% SDS) at 42 oC for 5min. For the Rnase treatment control, after 3 times of washing, the beads were treated once with 10 ug/ml Rnase A at 37 oC in Rnase digestion buffer, before washing two more times. Beads were resuspended with 1ml 0.1X SSC wash buffer. 900ul of the sample was separated for DNA elution, 100ul for RNA elution. Following ChIP de-crosslink method and PK, Rnase A and Rnase H were added in the second step. DNA was purified using the MinElute PCR Purification Kit (QIAGEN), followed by constructing the sequence library by NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®.
The ChIRP-seq libraries were constructed by NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®. Briefly, the fragment DNA are ligated to adapters by TA ligation. Then PCR for 10 cycles with specific index for sequencing.

treatment_protocol: IMR90 under TNF and Bleomycin treatment


title: MA_F_43_CC_Riboseq

description: Ribosome-protected RNA

value: 43 years

value: middle-aged (MA)

value: Female

value: Caucasian

value: skeletal muscle

value: healthy


title: TAAR_cluster_KO_RNA_seq_het-2


title: O_M_85_CC_Riboseq

description: Ribosome-protected RNA

value: 85 years

value: old (O)

value: Male


title: MA_F_41_AA_Riboseq

description: Ribosome-protected RNA

value: 41 years


title: anti-OSM 2

value: whole lung

value: anti-OSM antibody and E. coli

value: 10-12 weeks


title: Bleomycin2 ChIRP

description: ChIRP-seq

value: Lung Fibroblast

value: ATCC (CCL-186)


title: DMSO2 ChIRP

description: ChIRP-seq


title: MA_M_46_CC_Riboseq

description: Ribosome-protected RNA

value: 46 years


title: Bleomycin1 ChIRP

description: ChIRP-seq


title: TAAR_enhancer1and2_dKO_homo-3

description: TAAR_enhancer1and2_dKO_raw_counts_all.csv, TAAR_enhancer1and2_dKO_normalized_counts_all.csv

value: homozygous


title: TAAR_enhancer1and2_dKO_homo-4


title: TAAR_enhancer1and2_dKO_homo-2


title: TAAR_enhancer1and2_dKO_homo-1


title: TAAR_enhancer1and2_dKO_het-3

value: heterozygous


title: DMSO1 ChIRP

description: ChIRP-seq


title: TAAR_cluster_KO_RNA_seq_WT-3

value: wild type


title: TAAR_cluster_KO_RNA_seq_WT-2


title: TAAR_enhancer1and2_dKO_het-1


title: TAAR_enhancer1and2_dKO_het-2


title: TAAR_cluster_KO_RNA_seq_WT-1


title: canine primary osteosarcoma sample1

description: canine primary osteosarcoma matched sample1

value: canine primary osteosarcoma tissue

value: Rottweiler

value: 7 yrs

value: MC

value: normal bone tissue


title: TNF2 ChIRP

description: ChIRP-seq


title: CT2 ChIRP

description: ChIRP-seq


title: TNF1 ChIRP

description: ChIRP-seq


title: TAAR_enhancer1and2_dKO_WT-3


title: E9.5 and E10.5 Baf155 KO yolk sac

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v2.0.1)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v2.0.1)
barcode processing, Cell Ranger Single Cell Software Suite (v2.0.1)
single-cell 5′ gene counting , Cell Ranger Single Cell Software Suite (v2.0.1)
alignment, Cell Ranger Single Cell Software Suite (v2.0.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: Isolated single nuclei from yolk sac of E9.5 and E10.5 Baf155 CKO mice

extract_protocol:
Yolk sacs were dissected from equal numbers of mouse E9.5 and E10.5 embryos per genotype, mixed together and dissociated with 0.25% collagenase at 37°C for 30 min. The cells were stored at −80°C in fetal bovine serum with 10% DMSO. When the 10x Genomics instrument was ready, the cells were thawed and washed, and stained with antibody against Ter119 (Ly76) (1:200, 12-5921-82, eBioscience). Dead cells and Ter119+ cells were excluded by sorting to enrich live non-erythroid cells.
Single cell suspension at 300 cells/mL in PBS were subjected to Chromium 10X Genomics library construction.The generated scRNAseq libraries were sequenced using a HiSeq2500 sequencer.

value: Baf155 CKO

value: nuclei of yolk sac


title: TAAR_enhancer1and2_dKO_WT-1

last: Li


title: E9.5 and E10.5  WT yolk sac

source_name: Isolated single nuclei from yolk sac of E9.5 and E10.5 wild type mice

value: wt


title: TAAR_cluster_KO_RNA_seq_het-1


title: HG, 6h, PU6 (SS2_16_390_P10)

status: Public on Mar 07 2021

city: Stockholm

first: Olov

last: Andersson

state: Solna

address: Tomtebodavägen 16

department: CMB

country: Sweden

institute: Karolinska Institute

data_processing:
The samples were analyzed by first demultiplexing the fastq files using deindexer (https://github.com/ws6/deindexer) using the nextera index adapters and the 384 well layout.
Individual fastq files were then mapped to the relevant genome assembly using the STAR aligner (Dobin et al. Bioinformatics 2013) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads that are saved in the BAM file.
The expression values were computed as reads per kilobase of gene model and million mappable reads (RPKMs) to normalize for varying sequencing depths across sequenced cells and the gene lengths. The expression values were computed per gene as described in Ramsköld et al. (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. 2013 PLoS ONE). The count matrix shows the individual counts aligning to each gene per cell.
Genome_build: mm9
Supplementary_files_format_and_content: csv file containing gene count for every gene and every cell (counts_raw.csv) or for genes and beta-cells after QC (counts.csv)
csv file containing gene count for every gene and every cell (fpkm_raw.csv) or for genes and beta-cells after QC (fpkm.csv)

source_name: HG, 6h, PU6

growth_protocol: Dissociated islets were cultured in RPMI 1640 medium containing 10% fetal bovine serum (FBS), 15 mM glucose, 2 mM glutamine, and 1% penicillin- streptomycin

extract_protocol:
One cell per well were plated in 384-well plate containing lysis buffer, oligo-dT primer and dNTP
library preparation was performed according to Picelli et al. (2014, Nature Protocol)

treatment_protocol: The cells were incubated with the compounds at different concentrations and durations in 1% DMSO. At the end of the treatment, cells were dissociated using accutase and FACS was performed

value: pancreatic endocrine cells

value: HG


title: HG, 6h, PU6 (SS2_16_390_P11)


title: CBL0137 treatment, biological replicate 3

city: Sydney

first: Chi Nam Ignatius

last: Pang

state: NSW

address: School of Biotechnology and Biomolecular Sciences, UNSW Australia

department: The NSW Systems Biology Initiative

country: Australia

institute: The University of New South Wales

description: Gene expression data from DIPG cancer cells, treated with CBL0137

hyb_protocol: As per Affymetrix protocol

scan_protocol: As per Affymetrix protocol

data_processing: The probes from the hugene20st microarray were assigned to Ensembl Genes using custom  chip definition file (CDF) hugene20sthsensgcdf (version 24.0.0) from (http://mbni.org/customcdf/24.0.0/ensg.download/hugene20sthsensgcdf_24.0.0.tar.gz). Data was analysed using Bioconductor/R, the RMA algorithm was used for array normalization, and batch effects were removed using remove unwanted variation (ruv) library and the RUVIII function with one unwanted factor (k=1).

source_name: DIPG neurospheres, treated with CBL0139

label_protocol: As per Affymetrix protocol

growth_protocol: HSJD-DIPG007 cells were cultured in DMEM/F12 and Neurobasal media (1:1) supplemented with HEPES, non-essential amino acids, antibiotic/antimycotic, pyruvate, glutamax, heparin, B27, human EGF, human FGF, PDGF-AA and PDGF-BB for 72 hours to form neurospheres.

extract_protocol: RNA was extracted using the RNeasy extraction kit (Qiagen; Cat No./ID: 74106) according to the manufacturer’s instruction.

treatment_protocol: 72 hours after incubation, cells were treated for 24 hours with DMSO or 1?M CBL0137.


title: HG, 6h, PU6 (SS2_16_390_P6)


title: HG, 6h, PU6 (SS2_16_390_P12)


title: CBL0137 treatment, biological replicate 2

source_name: DIPG neurospheres, treated with CBL0138


title: Control (DMSO), biological replicate 1

description: Gene expression data from DIPG cancer cells, control without treatment

source_name: DIPG neurosphere, control without treatment

value: control


title: TAAR_enhancer1and2_dKO_WT-2


title: HG, 6h, PU6 (SS2_16_390_P4)


title: CBL0137 treatment, biological replicate 1

source_name: DIPG neurospheres, treated with CBL0137


title: HG, 6h, PU6 (SS2_16_390_P8)


title: Harm+HG, 6h, PU6 (SS2_16_390_I15)

source_name: Harm+HG, 6h, PU6

value: Harm+HG


title: Harm+HG, 6h, PU6 (SS2_16_390_I13)


title: Harm+HG, 6h, PU6 (SS2_16_390_I16)


title: Harm+HG, 6h, PU6 (SS2_16_390_I14)


title: HG, 6h, PU6 (SS2_16_390_P3)


title: CT1 ChIRP

description: ChIRP-seq

value: Lung Fibroblast

value: ATCC (CCL-186)


title: HG, 6h, PU6 (SS2_16_390_P5)


title: HG, 6h, PU6 (SS2_16_390_O12)


title: HG, 6h, PU6 (SS2_16_390_P2)


title: HG, 6h, PU6 (SS2_16_390_O11)


title: HG, 6h, PU6 (SS2_16_390_O10)


title: HG, 6h, PU6 (SS2_16_390_P7)


title: HG, 6h, PU6 (SS2_16_390_P1)


title: Harm+HG, 6h, PU6 (SS2_16_390_I17)


title: Control (DMSO), biological replicate 2


title: HG, 6h, PU6 (SS2_16_390_O8)


title: HG, 6h, PU6 (SS2_16_390_O9)


title: Control (DMSO), biological replicate 3


title: HG, 6h, PU6 (SS2_16_390_P9)


title: HG, 6h, PU6 (SS2_16_390_O6)


title: HG, 6h, PU6 (SS2_16_390_O1)


title: HG, 6h, PU6 (SS2_16_390_O2)


title: HG, 6h, PU6 (SS2_16_390_N12)


title: HG, 6h, PU6 (SS2_16_390_N8)


title: HG, 6h, PU6 (SS2_16_390_N9)


title: HG, 6h, PU6 (SS2_16_390_O3)


title: HG, 6h, PU6 (SS2_16_390_N10)


title: HG, 6h, PU6 (SS2_16_390_N7)


title: HG, 6h, PU6 (SS2_16_390_M9)


title: HG, 6h, PU6 (SS2_16_390_N2)


title: HG, 6h, PU6 (SS2_16_390_N3)


title: HG, 6h, PU6 (SS2_16_390_M12)


title: HG, 6h, PU6 (SS2_16_390_N4)


title: HG, 6h, PU6 (SS2_16_390_M7)


title: HG, 6h, PU6 (SS2_16_390_N1)


title: HG, 6h, PU6 (SS2_16_390_N5)


title: HG, 6h, PU6 (SS2_16_390_M11)


title: HG, 6h, PU6 (SS2_16_390_M5)


title: HG, 6h, PU6 (SS2_16_390_M6)


title: HG, 6h, PU6 (SS2_16_390_O4)


title: HG, 6h, PU6 (SS2_16_390_N6)


title: HG, 6h, PU6 (SS2_16_390_O7)


title: HG, 6h, PU6 (SS2_16_390_M3)


title: HG, 6h, PU6 (SS2_16_390_N11)


title: HG, 6h, PU6 (SS2_16_390_M4)


title: HG, 6h, PU6 (SS2_16_390_O5)


title: HG, 6h, PU6 (SS2_16_390_M2)


title: HG, 6h, PU6 (SS2_16_390_M1)


title: HG, 6h, PU6 (SS2_16_390_L11)


title: HG, 6h, PU6 (SS2_16_390_L10)


title: HG, 6h, PU6 (SS2_16_390_M10)


title: HG, 6h, PU6 (SS2_16_390_L12)


title: HG, 6h, PU6 (SS2_16_390_L8)


title: HG, 6h, PU6 (SS2_16_390_M8)


title: HG, 6h, PU6 (SS2_16_390_L6)


title: HG, 6h, PU6 (SS2_16_390_L7)


title: HG, 6h, PU6 (SS2_16_390_L4)


title: HG, 6h, PU6 (SS2_16_390_L2)


title: HG, 6h, PU6 (SS2_16_390_L3)


title: HG, 6h, PU6 (SS2_16_390_K12)


title: HG, 6h, PU6 (SS2_16_390_K11)


title: HG, 6h, PU6 (SS2_16_390_L5)


title: HG, 6h, PU6 (SS2_16_390_K10)


title: HG, 6h, PU6 (SS2_16_390_K8)


title: HG, 6h, PU6 (SS2_16_390_K6)


title: HG, 6h, PU6 (SS2_16_390_K4)


title: HG, 6h, PU6 (SS2_16_390_K5)


title: HG, 6h, PU6 (SS2_16_390_K2)


title: HG, 6h, PU6 (SS2_16_390_K7)


title: HG, 6h, PU6 (SS2_16_390_K1)


title: HG, 6h, PU6 (SS2_16_390_K3)


title: HG, 6h, PU6 (SS2_16_390_J12)


title: HG, 6h, PU6 (SS2_16_390_J11)


title: HG, 6h, PU6 (SS2_16_390_L9)


title: HG, 6h, PU6 (SS2_16_390_J10)


title: HG, 6h, PU6 (SS2_16_390_J9)


title: HG, 6h, PU6 (SS2_16_390_J8)


title: HG, 6h, PU6 (SS2_16_390_J7)


title: HG, 6h, PU6 (SS2_16_390_J6)


title: HG, 6h, PU6 (SS2_16_390_L1)


title: HG, 6h, PU6 (SS2_16_390_J4)


title: HG, 6h, PU6 (SS2_16_390_K9)


title: HG, 6h, PU6 (SS2_16_390_J3)


title: HG, 6h, PU6 (SS2_16_390_J1)


title: HG, 6h, PU6 (SS2_16_390_J2)


title: HG, 6h, PU6 (SS2_16_390_I8)


title: HG, 6h, PU6 (SS2_16_390_I9)


title: HG, 6h, PU6 (SS2_16_390_I11)


title: HG, 6h, PU6 (SS2_16_390_I10)


title: HG, 6h, PU6 (SS2_16_390_I7)


title: HG, 6h, PU6 (SS2_16_390_I6)


title: HG, 6h, PU6 (SS2_16_390_I5)


title: HG, 6h, PU6 (SS2_16_390_I2)


title: HG, 6h, PU6 (SS2_16_390_I1)


title: HG, 6h, PU6 (SS2_16_390_I4)


title: Harm, 6h, PU6 (SS2_16_390_H24)

source_name: Harm, 6h, PU6

value: Harm


title: Harm, 6h, PU6 (SS2_16_390_H23)


title: Harm, 6h, PU6 (SS2_16_390_H21)


title: Harm, 6h, PU6 (SS2_16_390_H22)


title: HG, 6h, PU6 (SS2_16_390_J5)


title: Harm, 6h, PU6 (SS2_16_390_H20)


title: Harm, 6h, PU6 (SS2_16_390_H19)


title: Harm, 6h, PU6 (SS2_16_390_H18)


title: Harm, 6h, PU6 (SS2_16_390_H16)


title: HG, 6h, PU6 (SS2_16_390_I12)


title: Harm, 6h, PU6 (SS2_16_390_H14)


title: Harm, 6h, PU6 (SS2_16_390_H13)


title: Harm, 6h, PU6 (SS2_16_390_G24)


title: Harm, 6h, PU6 (SS2_16_390_H15)


title: Harm, 6h, PU6 (SS2_16_390_G23)


title: Harm, 6h, PU6 (SS2_16_390_G20)


title: Harm, 6h, PU6 (SS2_16_390_G22)


title: Harm, 6h, PU6 (SS2_16_390_G18)


title: Harm, 6h, PU6 (SS2_16_390_G17)


title: Harm, 6h, PU6 (SS2_16_390_G19)


title: Harm, 6h, PU6 (SS2_16_390_G21)


title: Harm, 6h, PU6 (SS2_16_390_G15)


title: Harm, 6h, PU6 (SS2_16_390_G13)


title: Harm, 6h, PU6 (SS2_16_390_G14)


title: HG, 6h, PU6 (SS2_16_390_I3)


title: Harm, 6h, PU6 (SS2_16_390_F21)


title: Harm, 6h, PU6 (SS2_16_390_F23)


title: Harm, 6h, PU6 (SS2_16_390_F20)


title: Harm, 6h, PU6 (SS2_16_390_F18)


title: Harm, 6h, PU6 (SS2_16_390_F17)


title: Harm, 6h, PU6 (SS2_16_390_F19)


title: Harm, 6h, PU6 (SS2_16_390_F22)


title: Harm, 6h, PU6 (SS2_16_390_H17)


title: Harm, 6h, PU6 (SS2_16_390_F16)


title: Harm, 6h, PU6 (SS2_16_390_F14)


title: Harm, 6h, PU6 (SS2_16_390_F13)


title: Harm, 6h, PU6 (SS2_16_390_F15)


title: Harm, 6h, PU6 (SS2_16_390_E22)


title: Harm, 6h, PU6 (SS2_16_390_E24)


title: Harm, 6h, PU6 (SS2_16_390_E23)


title: Harm, 6h, PU6 (SS2_16_390_E20)


title: Harm, 6h, PU6 (SS2_16_390_E21)


title: Harm, 6h, PU6 (SS2_16_390_E17)


title: Harm, 6h, PU6 (SS2_16_390_E18)


title: Harm, 6h, PU6 (SS2_16_390_E19)


title: Harm, 6h, PU6 (SS2_16_390_E13)


title: Harm, 6h, PU6 (SS2_16_390_E15)


title: Harm, 6h, PU6 (SS2_16_390_E16)


title: Harm, 6h, PU6 (SS2_16_390_F24)


title: Harm, 6h, PU6 (SS2_16_390_D21)


title: Harm, 6h, PU6 (SS2_16_390_E14)


title: Harm, 6h, PU6 (SS2_16_390_D24)


title: Harm, 6h, PU6 (SS2_16_390_D22)


title: Harm, 6h, PU6 (SS2_16_390_D20)


title: Harm, 6h, PU6 (SS2_16_390_D19)


title: Harm, 6h, PU6 (SS2_16_390_D17)


title: Harm, 6h, PU6 (SS2_16_390_D15)


title: Harm, 6h, PU6 (SS2_16_390_D16)


title: Harm, 6h, PU6 (SS2_16_390_D18)


title: Harm, 6h, PU6 (SS2_16_390_D14)


title: Harm, 6h, PU6 (SS2_16_390_C24)


title: Harm, 6h, PU6 (SS2_16_390_D13)


title: Harm, 6h, PU6 (SS2_16_390_C21)


title: Harm, 6h, PU6 (SS2_16_390_C23)


title: Harm, 6h, PU6 (SS2_16_390_C18)


title: Harm, 6h, PU6 (SS2_16_390_C17)


title: Harm, 6h, PU6 (SS2_16_390_C16)


title: Harm, 6h, PU6 (SS2_16_390_D23)


title: Harm, 6h, PU6 (SS2_16_390_C20)


title: Harm, 6h, PU6 (SS2_16_390_C19)


title: Harm, 6h, PU6 (SS2_16_390_C13)


title: Harm, 6h, PU6 (SS2_16_390_B24)


title: Harm, 6h, PU6 (SS2_16_390_B23)


title: Harm, 6h, PU6 (SS2_16_390_C15)


title: Harm, 6h, PU6 (SS2_16_390_C14)


title: Harm, 6h, PU6 (SS2_16_390_B22)


title: Harm, 6h, PU6 (SS2_16_390_B19)


title: Harm, 6h, PU6 (SS2_16_390_B21)


title: Harm, 6h, PU6 (SS2_16_390_B20)


title: Harm, 6h, PU6 (SS2_16_390_B17)


title: Harm, 6h, PU6 (SS2_16_390_B18)


title: Harm, 6h, PU6 (SS2_16_390_B16)


title: Harm, 6h, PU6 (SS2_16_390_B15)


title: Harm, 6h, PU6 (SS2_16_390_B13)


title: Harm, 6h, PU6 (SS2_16_390_B14)


title: Harm, 6h, PU6 (SS2_16_390_A24)


title: Harm, 6h, PU6 (SS2_16_390_A22)


title: Harm, 6h, PU6 (SS2_16_390_A20)


title: Harm, 6h, PU6 (SS2_16_390_A23)


title: Harm, 6h, PU6 (SS2_16_390_C22)


title: Harm, 6h, PU6 (SS2_16_390_A21)


title: Harm, 6h, PU6 (SS2_16_390_A19)


title: Harm, 6h, PU6 (SS2_16_390_A18)


title: Harm, 6h, PU6 (SS2_16_390_A14)


title: Harm, 6h, PU6 (SS2_16_390_A16)


title: Harm, 6h, PU6 (SS2_16_390_A13)


title: Harm, 6h, PU6 (SS2_16_390_A17)


title: DMSO, 6h, PU6 (SS2_16_390_H12)

source_name: DMSO, 6h, PU6

value: DMSO


title: DMSO, 6h, PU6 (SS2_16_390_H9)


title: DMSO, 6h, PU6 (SS2_16_390_H8)


title: DMSO, 6h, PU6 (SS2_16_390_H11)


title: DMSO, 6h, PU6 (SS2_16_390_H10)


title: DMSO, 6h, PU6 (SS2_16_390_G10)


title: DMSO, 6h, PU6 (SS2_16_390_G11)


title: DMSO, 6h, PU6 (SS2_16_390_H5)


title: DMSO, 6h, PU6 (SS2_16_390_G9)


title: DMSO, 6h, PU6 (SS2_16_390_H4)


title: DMSO, 6h, PU6 (SS2_16_390_H1)


title: DMSO, 6h, PU6 (SS2_16_390_G8)


title: DMSO, 6h, PU6 (SS2_16_390_G12)


title: DMSO, 6h, PU6 (SS2_16_390_H3)


title: DMSO, 6h, PU6 (SS2_16_390_G7)


title: Harm, 6h, PU6 (SS2_16_390_A15)


title: DMSO, 6h, PU6 (SS2_16_390_G3)


title: DMSO, 6h, PU6 (SS2_16_390_G2)


title: DMSO, 6h, PU6 (SS2_16_390_G4)


title: DMSO, 6h, PU6 (SS2_16_390_G5)


title: DMSO, 6h, PU6 (SS2_16_390_G6)


title: DMSO, 6h, PU6 (SS2_16_390_G1)


title: DMSO, 6h, PU6 (SS2_16_390_H6)


title: DMSO, 6h, PU6 (SS2_16_390_H7)


title: DMSO, 6h, PU6 (SS2_16_390_F12)


title: DMSO, 6h, PU6 (SS2_16_390_F10)


title: DMSO, 6h, PU6 (SS2_16_390_H2)


title: DMSO, 6h, PU6 (SS2_16_390_F11)


title: DMSO, 6h, PU6 (SS2_16_390_F9)


title: DMSO, 6h, PU6 (SS2_16_390_F7)


title: DMSO, 6h, PU6 (SS2_16_390_F5)


title: DMSO, 6h, PU6 (SS2_16_390_F6)


title: DMSO, 6h, PU6 (SS2_16_390_F8)


title: DMSO, 6h, PU6 (SS2_16_390_F3)


title: DMSO, 6h, PU6 (SS2_16_390_F1)


title: DMSO, 6h, PU6 (SS2_16_390_E8)


title: DMSO, 6h, PU6 (SS2_16_390_E12)


title: DMSO, 6h, PU6 (SS2_16_390_E7)


title: DMSO, 6h, PU6 (SS2_16_390_E9)


title: DMSO, 6h, PU6 (SS2_16_390_E11)


title: DMSO, 6h, PU6 (SS2_16_390_F2)


title: DMSO, 6h, PU6 (SS2_16_390_E5)


title: DMSO, 6h, PU6 (SS2_16_390_E6)


title: DMSO, 6h, PU6 (SS2_16_390_E4)


title: DMSO, 6h, PU6 (SS2_16_390_E2)


title: DMSO, 6h, PU6 (SS2_16_390_E3)


title: DMSO, 6h, PU6 (SS2_16_390_D11)


title: DMSO, 6h, PU6 (SS2_16_390_D12)


title: DMSO, 6h, PU6 (SS2_16_390_D10)


title: DMSO, 6h, PU6 (SS2_16_390_D9)


title: DMSO, 6h, PU6 (SS2_16_390_E1)


title: DMSO, 6h, PU6 (SS2_16_390_D8)


title: DMSO, 6h, PU6 (SS2_16_390_D7)


title: DMSO, 6h, PU6 (SS2_16_390_D3)


title: DMSO, 6h, PU6 (SS2_16_390_C12)


title: DMSO, 6h, PU6 (SS2_16_390_D6)


title: DMSO, 6h, PU6 (SS2_16_390_D5)


title: DMSO, 6h, PU6 (SS2_16_390_D4)


title: DMSO, 6h, PU6 (SS2_16_390_D2)


title: DMSO, 6h, PU6 (SS2_16_390_F4)


title: DMSO, 6h, PU6 (SS2_16_390_D1)


title: DMSO, 6h, PU6 (SS2_16_390_E10)


title: DMSO, 6h, PU6 (SS2_16_390_C10)


title: DMSO, 6h, PU6 (SS2_16_390_C6)


title: DMSO, 6h, PU6 (SS2_16_390_C9)


title: DMSO, 6h, PU6 (SS2_16_390_C8)


title: DMSO, 6h, PU6 (SS2_16_390_C7)


title: DMSO, 6h, PU6 (SS2_16_390_C3)


title: DMSO, 6h, PU6 (SS2_16_390_C5)


title: DMSO, 6h, PU6 (SS2_16_390_C4)


title: DMSO, 6h, PU6 (SS2_16_390_C2)


title: DMSO, 6h, PU6 (SS2_16_390_C1)


title: DMSO, 6h, PU6 (SS2_16_390_B11)


title: DMSO, 6h, PU6 (SS2_16_390_B10)


title: DMSO, 6h, PU6 (SS2_16_390_B9)


title: DMSO, 6h, PU6 (SS2_16_390_B6)


title: DMSO, 6h, PU6 (SS2_16_390_B8)


title: DMSO, 6h, PU6 (SS2_16_390_B5)


title: DMSO, 6h, PU6 (SS2_16_390_B7)


title: DMSO, 6h, PU6 (SS2_16_390_B4)


title: DMSO, 6h, PU6 (SS2_16_390_B3)


title: Harm, 6h, PU6 (SS2_16_390_G16)


title: DMSO, 6h, PU6 (SS2_16_390_B1)


title: DMSO, 6h, PU6 (SS2_16_390_B2)


title: DMSO, 6h, PU6 (SS2_16_390_A10)


title: DMSO, 6h, PU6 (SS2_16_390_A11)


title: DMSO, 6h, PU6 (SS2_16_390_A9)


title: DMSO, 6h, PU6 (SS2_16_390_A8)


title: DMSO, 6h, PU6 (SS2_16_390_A12)


title: DMSO, 6h, PU6 (SS2_16_390_A7)


title: DMSO, 6h, PU6 (SS2_16_390_C11)


title: DMSO, 6h, PU6 (SS2_16_390_A6)


title: DMSO, 6h, PU6 (SS2_16_390_B12)


title: DMSO, 6h, PU6 (SS2_16_390_A5)


title: Harm+HG, 48h, PU5 (SS2_16_265_P23)

source_name: Harm+HG, 48h, PU5

value: 48h (2days)


title: DMSO, 6h, PU6 (SS2_16_390_A3)


title: Harm+HG, 48h, PU5 (SS2_16_265_P24)


title: DMSO, 6h, PU6 (SS2_16_390_A2)


title: Harm+HG, 48h, PU5 (SS2_16_265_O22)


title: Harm+HG, 48h, PU5 (SS2_16_265_O21)


title: Harm+HG, 48h, PU5 (SS2_16_265_O23)


title: Harm+HG, 48h, PU5 (SS2_16_265_P19)


title: Harm+HG, 48h, PU5 (SS2_16_265_P21)


title: Harm+HG, 48h, PU5 (SS2_16_265_O19)


title: Harm+HG, 48h, PU5 (SS2_16_265_P22)


title: Harm+HG, 48h, PU5 (SS2_16_265_P20)


title: Harm+HG, 48h, PU5 (SS2_16_265_O18)


title: DMSO, 6h, PU6 (SS2_16_390_A1)


title: Harm+HG, 48h, PU5 (SS2_16_265_P14)


title: Harm+HG, 48h, PU5 (SS2_16_265_P16)


title: Harm+HG, 48h, PU5 (SS2_16_265_O20)


title: Harm+HG, 48h, PU5 (SS2_16_265_P13)


title: Harm+HG, 48h, PU5 (SS2_16_265_O17)


title: Harm+HG, 48h, PU5 (SS2_16_265_O15)


title: Harm+HG, 48h, PU5 (SS2_16_265_O14)


title: Harm+HG, 48h, PU5 (SS2_16_265_P18)


title: Harm+HG, 48h, PU5 (SS2_16_265_N24)


title: Harm+HG, 48h, PU5 (SS2_16_265_P17)


title: Harm+HG, 48h, PU5 (SS2_16_265_P15)


title: DMSO, 6h, PU6 (SS2_16_390_A4)


title: Harm+HG, 48h, PU5 (SS2_16_265_N23)


title: Harm+HG, 48h, PU5 (SS2_16_265_O24)


title: Harm+HG, 48h, PU5 (SS2_16_265_O16)


title: Harm+HG, 48h, PU5 (SS2_16_265_N20)


title: Harm+HG, 48h, PU5 (SS2_16_265_N16)


title: Harm+HG, 48h, PU5 (SS2_16_265_N17)


title: Harm+HG, 48h, PU5 (SS2_16_265_O13)


title: Harm+HG, 48h, PU5 (SS2_16_265_N14)


title: Harm+HG, 48h, PU5 (SS2_16_265_N18)


title: Harm+HG, 48h, PU5 (SS2_16_265_M20)


title: Harm+HG, 48h, PU5 (SS2_16_265_M17)


title: Harm+HG, 48h, PU5 (SS2_16_265_N21)


title: Harm+HG, 48h, PU5 (SS2_16_265_N19)


title: Harm+HG, 48h, PU5 (SS2_16_265_N13)


title: Harm+HG, 48h, PU5 (SS2_16_265_M23)


title: Harm+HG, 48h, PU5 (SS2_16_265_M19)


title: Harm+HG, 48h, PU5 (SS2_16_265_M15)


title: Harm+HG, 48h, PU5 (SS2_16_265_M22)


title: Harm+HG, 48h, PU5 (SS2_16_265_L24)


title: Harm+HG, 48h, PU5 (SS2_16_265_M21)


title: Harm+HG, 48h, PU5 (SS2_16_265_M14)


title: Harm+HG, 48h, PU5 (SS2_16_265_M18)


title: Harm+HG, 48h, PU5 (SS2_16_265_M13)


title: Harm+HG, 48h, PU5 (SS2_16_265_L21)


title: Harm+HG, 48h, PU5 (SS2_16_265_L20)


title: Harm+HG, 48h, PU5 (SS2_16_265_M16)


title: Harm+HG, 48h, PU5 (SS2_16_265_L23)


title: Harm+HG, 48h, PU5 (SS2_16_265_N22)


title: Harm+HG, 48h, PU5 (SS2_16_265_L22)


title: Harm+HG, 48h, PU5 (SS2_16_265_N15)


title: Harm+HG, 48h, PU5 (SS2_16_265_L18)


title: Harm+HG, 48h, PU5 (SS2_16_265_M24)


title: Harm+HG, 48h, PU5 (SS2_16_265_L19)


title: Harm+HG, 48h, PU5 (SS2_16_265_L16)


title: Harm+HG, 48h, PU5 (SS2_16_265_L17)


title: Harm+HG, 48h, PU5 (SS2_16_265_L14)


title: Harm+HG, 48h, PU5 (SS2_16_265_K22)


title: Harm+HG, 48h, PU5 (SS2_16_265_K20)


title: Harm+HG, 48h, PU5 (SS2_16_265_L15)


title: Harm+HG, 48h, PU5 (SS2_16_265_K23)


title: Harm+HG, 48h, PU5 (SS2_16_265_K24)


title: Harm+HG, 48h, PU5 (SS2_16_265_K18)


title: Harm+HG, 48h, PU5 (SS2_16_265_K14)


title: Harm+HG, 48h, PU5 (SS2_16_265_K17)


title: Harm+HG, 48h, PU5 (SS2_16_265_K16)


title: Harm+HG, 48h, PU5 (SS2_16_265_K15)


title: Harm+HG, 48h, PU5 (SS2_16_265_K13)


title: Harm+HG, 48h, PU5 (SS2_16_265_J24)


title: Harm+HG, 48h, PU5 (SS2_16_265_J21)


title: Harm+HG, 48h, PU5 (SS2_16_265_J23)


title: Harm+HG, 48h, PU5 (SS2_16_265_J22)


title: Harm+HG, 48h, PU5 (SS2_16_265_J20)


title: Harm+HG, 48h, PU5 (SS2_16_265_J18)


title: Harm+HG, 48h, PU5 (SS2_16_265_J17)


title: Harm+HG, 48h, PU5 (SS2_16_265_J16)


title: Harm+HG, 48h, PU5 (SS2_16_265_J15)


title: Harm+HG, 48h, PU5 (SS2_16_265_L13)


title: Harm+HG, 48h, PU5 (SS2_16_265_K21)


title: Harm+HG, 48h, PU5 (SS2_16_265_K19)


title: Harm+HG, 48h, PU5 (SS2_16_265_J14)


title: Harm+HG, 48h, PU5 (SS2_16_265_J13)


title: Harm+HG, 48h, PU5 (SS2_16_265_I22)


title: Harm+HG, 48h, PU5 (SS2_16_265_I24)


title: Harm+HG, 48h, PU5 (SS2_16_265_I19)


title: Harm+HG, 48h, PU5 (SS2_16_265_I16)


title: Harm+HG, 48h, PU5 (SS2_16_265_I21)


title: Harm+HG, 48h, PU5 (SS2_16_265_I13)


title: Harm+HG, 48h, PU5 (SS2_16_265_I17)


title: Harm+HG, 48h, PU5 (SS2_16_265_J19)


title: Harm+HG, 48h, PU5 (SS2_16_265_I14)


title: Harm+HG, 48h, PU5 (SS2_16_265_I18)


title: HG, 48h, PU5 (SS2_16_265_P10)

source_name: HG, 48h, PU5


title: HG, 48h, PU5 (SS2_16_265_P12)


title: HG, 48h, PU5 (SS2_16_265_P9)


title: HG, 48h, PU5 (SS2_16_265_P8)


title: HG, 48h, PU5 (SS2_16_265_P4)


title: Harm+HG, 48h, PU5 (SS2_16_265_I23)


title: HG, 48h, PU5 (SS2_16_265_P6)


title: HG, 48h, PU5 (SS2_16_265_P3)


title: HG, 48h, PU5 (SS2_16_265_P11)


title: HG, 48h, PU5 (SS2_16_265_P2)


title: HG, 48h, PU5 (SS2_16_265_P1)


title: Harm+HG, 48h, PU5 (SS2_16_265_I15)


title: HG, 48h, PU5 (SS2_16_265_O8)


title: Harm+HG, 48h, PU5 (SS2_16_265_I20)