title: WholeBlood_CRC305DGENT1573034_Day3


title: WholeBlood_CRC305DGENT2413052_Day3

status: Public on Dec 31 2019

type: RNA

city: London

first: David

last: Lewis

address: Du Cane Road

department: ICRF

country: United Kingdom

institute: Imperial College London

description: Whole blood gene expression of participant on day

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented and hybridized to custom whole genome human 8 × 60K multipack microarrays (Agilent-048908) following the manufacturers instructions. 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) according the manufacturers protocol.

scan_protocol: Slides were scanned immediately after washing using a high resolution DNA Microarray Scanner (G2505B, Agilent Technologies) with 3 µm resoltion and 20 bit image depth

data_processing: The scanned microarray images were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Blood, PaxGene

label_protocol: Total RNA was amplified and labeled with the low input Quick-Amp Labelling Kit (Agilent Technologies) with cyanine 3-CTP followed by precipitation, purification, and quantification.

extract_protocol: mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer

treatment_protocol: Microarray experiments were performed as single-color hybridization. Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

tag: participant

tag: gender

value: female

tag: age

tag: race

value: white

tag: ethnicity

value: not american hispanic or latino

tag: protocol

tag: treatment

value: FLUADD

tag: day

tag: tissue

value: whole blood


title: WholeBlood_CRC305DGENT2433059_Day3


title: PC3_OVlnc_rep1

city: Shanghai

first: Xiaolei

last: Shi

address: 168 Changhai Road

department: Department of Urology

country: China

institute: Shanghai Changhai Hospital

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 9 out of 18 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: PC3 human prostate cancer cells, overexpression lnc, replicate 1

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: PC3 was cultured with F-12 medium (GIBCO) supplemented with 10% fetal bovine serum, incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to the manufacture’s protocol. Reverse transcription was performed using ReverTra Ace RT Kit (TOYOBO, Japan). RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: PC3 cells was transfected with lentiviruses of lncAPP-OV and lncAPP-shRNA.

tag: cell line

tag: genotype/variation

value: overexpression  of lncAPP

value: prostate

value: male


title: WholeBlood_CRC305DGENT0111015_Day1


title: PC3_KDnc_rep2

source_name: PC3 human prostate cancer cells, knockdown negative control, replicate 2

value: knnockdown of lncAPP


title: WholeBlood_CRC305DGENT1341027_Day0


title: WholeBlood_CRC305DGENT1233028_Day0


title: PC3_KDnc_rep3

source_name: PC3 human prostate cancer cells, knockdown negative control, replicate 3


title: PC3_KDnc_rep1

source_name: PC3 human prostate cancer cells, knockdown negative control, replicate 1


title: paps1-3 pollen - wild type C

type: SRA

city: Potsdam

first: Michael

last: Lenhard

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

description:
WT-C
178192_GCCAAT_L002

library_source: transcriptomic

data_processing:
TopHat2 (Kim et al., 2013; doi:10.1186/gb-2013-14-4-r36) mapping with reference annotation.
Read counts per transcript were extracted using HTSeq-count (Anders et al. 2014; doi:10.1093/bioinformatics/btu638).
Genome_build: TAIR10 (www.arabidopsis.org)
Supplementary_files_format_and_content: Raw read counts.

organism: Arabidopsis thaliana

source_name: wild type_pollen

growth_protocol: To characterize gene expression in paps1-3 mutant pollen, pollen was collected from PAPS1 pLat52::RFP / paps1-3  plants. Plant growth and pollen isolation were performed as previously described (Borges et al. 2012; doi:10.1186/1746-4811-8-44). Flow sorting of pollen according to RFP fluorescence was performed as previously described (Kappel et al. 2015; doi:10.1371/journal.pgen.1005474).

extract_protocol:
Total RNA was isolated using a Rneasy Mini kit (Qiagen) and RNA integrity and amount of ribosomal RNA was assessed using an Agilent 2100 Bioanalyser with RNA 6000 Nano Assay (Agilent Technologies).
Illumina-compatible sequencing libraries were generated using the Ovation RNA-seq system v2 (NuGen) and sequenced on an Illumina HiSeq2000 instrument at the IPK Gatersleben in paired-end mode with 101 bases for read 1 and 99 bases for read 2.

tag: accession

value: Col

value: wild type

value: pollen


title: WholeBlood_CRC305DGENT0051016_Day1


title: paps1-3 pollen - wild type B

description:
WT-B
178191_ACAGTG_L002


title: PC3_KDlnc_rep3

source_name: PC3 human prostate cancer cells, knockdown lnc, replicate 3


title: PC3_KDlnc_rep2

source_name: PC3 human prostate cancer cells, knockdown lnc, replicate 2


title: WholeBlood_CRC305DGENT1671048_Day7

value: PLACEBOD


title: WholeBlood_CRC305DGENT2441054_Day1


title: PC3_KDlnc_rep1

source_name: PC3 human prostate cancer cells, knockdown lnc, replicate 1


title: paps1-3 pollen - sample C

description:
MU-C
178195_GTTTCG_L002


title: WholeBlood_CRC305DGENT1531041_Day0


title: WholeBlood_CRC305DGENT1713056_Day3


title: WholeBlood_CRC305DGENT1531041_Day1


title: paps1-3 pollen - sample B

description:
MU-B
178194_AGTCAA_L002


title: Ishikawa_MPA resistant_rep1

city: Jinan

first: Jie

last: Jiang

address: Department of Obstetrics and Gynecology, Qi Lu Hospital, No.107 Wenhua Road, Jinan250012, Shandong, China

department: Department of Obstetrics and Gynecology

institute: Qi Lu Hospital, Shandong University

description: Gene expression of MPA resistant IshikawaPR replicate 1

hyb_protocol: Array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology).1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: Ishikawa,resistant,replicate 1

label_protocol: Sample labeling were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Cells were Cultured in PRMI-1640 medium(Hyclone Laboratories,Loga,UT,USA) supplemented with 10% fetal bovine serum(FBS;Gibco,Sydney,Australia) in a humidified atmosphere containing 5% CO2 at 37℃.

extract_protocol: RNA was extracted and RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: MPA(Sigma-Aldrich,St.Louis,MO,USA)was used to establish progetin-resistant cell line of Ishikawa cell. Cells were cultured in toutine medium supplemented with MPA started with a concentration at 1μM. When the density of survival cells was high at approximated 80-90% confluence, cells were cultured in 0.02%EDTA and 0.25% trpsin solution and passed. Routine medium containing MPA was replaced every 2-3 days. The concentration of MPA increased 2.5 μM every 4 weeks. When the concentration of MPA reached 10 μM and the proliferation of cells was the same as original Ishikawa cells, stable progestin-resistant Ishikawa cell  line had been establlished.

tag: cell type

value: IshikawaPR


title: WholeBlood_CRC305DGENT1331025_Day3


title: WholeBlood_CRC305DGENT0011001_Day21


title: Ishikawa_MPA sensitive_rep2

description: Gene expression of MPA sensitive Ishikawa replicate 2

source_name: Ishikawa,sensitive,replicate 2

value: Ishikawa


title: Ishikawa_MPA resistant_rep2

description: Gene expression of MPA resistant IshikawaPR replicate 2

source_name: Ishikawa,resistant,replicate 2


title: Ishikawa_MPA resistant_rep3

description: Gene expression of MPA resistant IshikawaPR replicate 3

source_name: Ishikawa,resistant,replicate 3


title: WholeBlood_CRC305DGENT0171010_Day1


title: paps1-3 pollen - wild type A

description:
WT-A
178190_TGACCA_L002


title: Ishikawa_MPA sensitive_rep1

description: Gene expression of MPA sensitive Ishikawa replicate 1

source_name: Ishikawa,sensitive,replicate 1


title: miRNA Control

city: Fulda

first: Daniela

last: Fussbroich

address: Leipziger Str. 123

institute: University of Applied Sciences Fulda

data_processing:
PhiX Sequencing Control v3 and the MiSeq™ Desktop Sequencer (all Illumina Inc., San Diego, USA) for Base Calling
Results were processed according to Bioo Scientific Small RNA analysis pipeline.
Cutadapt V1.14 was used to remove adapter sequences and random bases and to discard too short reads
bowtie 2 (V2.2.9; http://www.bowtie-bio.sourceforge.net) was used to align readouts to murine mature miRNAs from miRBase (mature.fs, v21, June 2014; http://www.mirbase.org)
miRUtils (v1.0.0; http://www.mirutils.sourceforge.net) was used to process the aligned files
Genome_build: Mus musculus GRCm38 (v21)
Supplementary_files_format_and_content: coverage files including total reads per mapped miRNA

organism: synthetic RNA

source_name: NEXTflex Small RNA-Seq Kit v3

growth_protocol: Mice were purchased at the age of 6-8 weeks.

extract_protocol:
Lungs were removed, stored immediately in RNA later, and RNA was harvested using miRNeasy Mini Kit.
RNA libraries were prepared with 1 ug of total RNA for sequencing using standard NEXTflex Small RNA-Seq Kit v3.

treatment_protocol: Mice were first sensitized for 10 consecutive days with 40 µg house dust mite extract to induce allergic asthma and thereafter supplemented with the LCPUFA combination for 24 days. Within the last 3 days, mice daily received repetitive doses of HDM (recall).

value: NEXTflex Small RNA-Seq Kit v3


title: WholeBlood_CRC305DGENT0073006_Day21


title: WholeBlood_CRC305DGENT0021002_Day3


title: WholeBlood_CRC305DGENT0263008_Day1


title: WholeBlood_CRC305DGENT1313027_Day0


title: WholeBlood_CRC305DGENT0313004_Day3


title: Ishikawa_MPA sensitive_rep3

description: Gene expression of MPA sensitive Ishikawa replicate 3

source_name: Ishikawa,sensitive,replicate 3


title: paps1-3 pollen - sample A

description:
MU-A
178193_CAGATC_L002


title: WholeBlood_CRC305DGENT0181014_Day21


title: IPF11_in

city: Los angeles

first: Xue

last: Liu

state: CA

address: AHSP A9404, 127 S. San Vicente Blvd

department: Medicine

country: USA

institute: Cedars-Sinai Medical Center

data_processing:
Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20. Cell Ranger software v3.0.2 (10X Genomics) was used for barcodes identification, reads alignment and UMI quantification with default parameter. Briefly, raw reads were aligned to the human reference genome GRCh38, then expression counts for each gene in all samples were collapsed and normalized to unique molecular identifier (UMI). The results are a large digital expression matrix with gene identities as rows and cell barcodes as columns.
To obtain two-dimensional projections of the population’s dynamics, principal component analysis (PCA) was firstly run on the normalized gene-barcode matrix of the top 5,000 most variable genes to reduce the number of feature dimensions using Seurat package version 3.0 in R v3.3.1. The top 5,000 most variable genes were identified based on their mean and dispersion as described by Macoscko et al. After running PCA, t-distributed stochastic neighbor embedding (t-SNE) analysis was performed to further reduce these components to visualize cells in a two-dimensional space.
Based on their relative position in the t-SNE plot, an unsupervised graph-based clustering was performed to group cells for the clustering analysis and cluster-specific marker genes were also identified using Seurat software. A graphical user interface browser- Loupe v1.0.3 (10X Genomics), was deployed to present the heatmaps of identified marker genes and to interactively explore gene expression in the whole single cell population.
Supplementary_files_format_and_content: CSV files generated using Cell Ranger software v3.0.2

source_name: human lung of IPF patient

growth_protocol: Human lung fibroblasts were isolated from surgical lung biopsies or lung transplant explants obtained from patients with IPF. The diagnosis of IPF was arrived at by standard accepted American Thoracic Society recommendations (ATS/ERS, 2000). The tissues were minced, digested, and cultured in DMEM supplemented with 15% FBS and Antibiotic-An- timycotic (Thermo Fisher Scientific).

extract_protocol:
For RNA-seq, the invasive and noninvasive cells were harvested separately by trypsin digestion.
scRNA-seq libraries were prepared per the Single Cell 30Reagent Kit UserGuide v2 (10x Genomics Chromium Single cell 3' RNA v2). Cellular suspensions were loaded on a ChromiumController instrument (10x Genomics) to generate single-cell gel bead-in-emulsions (GEMs). GEM-reverse transcriptions (GEM-RTs) were performedin a Veriti 96-well thermal cycler (Thermo Fisher Scientific). After RT, GEMs were harvested and the cDNAs were amplified and cleaned up with theSPRIselect Reagent Kit (Beckman Coulter). Indexed sequencing librarieswere constructed using the Chromium Single-Cell 30Library Kit (10x Geno-mics) for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, liga-tion cleanup, sample index PCR, and PCR cleanup. The barcoded sequencinglibraries were quantified by quantitative PCR using the KAPA LibraryQuantification Kit (KAPA Biosystems).

treatment_protocol: Human lung fibroblasts (2.5 × 104 to 10.0 × 104 cells per well for 24-well plates and 1.0 × 106 cells per well for 6-well plates) in 10% FBS were loaded into the top chamber of a BioCoat Matrigel Invasion Chamber (BD Biosciences). PDGF-BB (10 ng/ml; Peprotech) was used as a chemoattractant in the bottom chamber. After 24 hours at 37°C with 5% CO2, invasive cells had passed through the matrigel layer and clung to the bottom of the insert membrane. Cells remaining on the upper chamber were defined as noninvasive fibroblasts.

tag: donor

value: human lung fibroblasts

tag: passages

tag: diagnosis

value: Idiopathic pulmonary fibrosis (IPF)

tag: invasive phenotype

value: invasive


title: IPF11_non

value: non-invasive


title: cc003_14_in

source_name: human lung of healthy donor

value: healthy control


title: IPF1_in


title: cc003_14_non


title: IPF_non


title: cc3_non


title: cc3_in


title: WholeBlood_CRC305DGENT2463060_Day1

source_name: Peripheral Blood, PaxGene

tag: participant

value: female

value: white

value: not american hispanic or latino

value: FLUADD

value: whole blood


title: WholeBlood_CRC305DGENT2381052_Day3

tag: gender

value: male


title: WholeBlood_CRC305DGENT2291044_Day0

tag: age


title: WholeBlood_CRC305DGENT1483036_Day21

tag: race


title: WholeBlood_CRC305DGENT1581031_Day0

tag: ethnicity


title: WholeBlood_CRC305DGENT1281024_Day21

tag: protocol


title: WholeBlood_CRC305DGENT1883049_Day0

tag: treatment


title: WholeBlood_CRC305DGENT2361060_Day3

tag: day


title: WholeBlood_CRC305DGENT1623033_Day1

tag: tissue


title: WholeBlood_CRC305DGENT0241003_Day7


title: WholeBlood_CRC305DGENT1671048_Day3


title: WholeBlood_CRC305DGENT0153020_Day7


title: WholeBlood_CRC305DGENT1843044_Day21


title: WholeBlood_CRC305DGENT0131009_Day0


title: WholeBlood_CRC305DGENT0291007_Day1


title: WholeBlood_CRC305DGENT1843044_Day1


title: WholeBlood_CRC305DGENT1603032_Day3


title: WholeBlood_CRC305DGENT1331025_Day21


title: WholeBlood_CRC305DGENT0373010_Day7


title: WholeBlood_CRC305DGENT1243023_Day1


title: WholeBlood_CRC305DGENT1531041_Day21


title: 6_EBOV_CD14+

first: Harry

last: Pickering

state: Greater London

address: LSHTM, Keppel Street

institute: London School of Hygiene and Tropical Medicine

data_processing:
trim low quality tails, polyA tails and adapters;bbmap; k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 int=f
align to human genome (hg38); STAR aligner; --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate
indexed BAM files; samtools
counted reads per sample; HTSeq-count
normalised counts by variance stabilising transformation; DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated ensembl transcript and read count per sample (.txt)

source_name: PBMC

growth_protocol: Human PBMC purified by gradient centrifugation, stimulated in vitro for 15h hours with 10 ug/ml EbovGP

extract_protocol:
RNA was extracted from cell pellets using Norgen RNA/DNA purification kits
Library preparation was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina

value: PBMC

tag: cell fraction

tag: stimulation condition

value: EbovGP


title: WholeBlood_CRC305DGENT2423054_Day0


title: 6_Med_CD14-

value: CD14 depleted

value: Unstimulated


title: 6_Med_CD14+


title: WholeBlood_CRC305DGENT1823053_Day0


title: 6_EBOV_CD14-


title: WholeBlood_CRC305DGENT1611036_Day7


title: 5_EBOV_CD14-


title: 5_EBOV_CD14+


title: 5_Med_CD14-


title: WholeBlood_CRC305DGENT2453055_Day21


title: WholeBlood_CRC305DGENT1581031_Day7


title: WholeBlood_CRC305DGENT1321028_Day1


title: 5_Med_CD14+


title: WholeBlood_CRC305DGENT1433024_Day21


title: 4_EBOV_CD14+


title: 4_Med_CD14+


title: 4_EBOV_CD14-


title: 3_EBOV_CD14-


title: 3_EBOV_CD14+


title: 3_Med_CD14-


title: 4_Med_CD14-


title: 3_Med_CD14+


title: 2_EBOV_CD14-


title: genomic DNA from normal colon sample 334

type: genomic

city: Seattle

first: Ting

last: Wang

state: WA

address: 1100 Fairview Ave. N.

department: Clinical Research

institute: Fred Hutchinson Cancer Research Center

description: normal colon sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 and EPIC Beadchip arrays using standard Illumina protocol

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

data_processing: Raw IDAT files of the two methylation arrays were read into R with the minfi package separately, the combineArrays function was utilized to combine the two arrays’ data together. Then the data was preprocessed with background and dye bias correction using the Noob method, following by the Functional normalization. CpG probes that were SNP-associated, cross-reactive, located on sex chromosomes and unreliably detected (>10% of samples with detection P-value > 0.01), with the exception of those epigenetic clock CpGs, were excluded from the analysis

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA samples were extracted from the fresh frozen normal colon mucosa tissue samples using the DNeasy Blood and Tissue Kit (Qiagen). Genomic DNA quantification was performed using the Quant-iT PicoGreen DNA assay kit (Life Technologies). 500 ng of DNA from each sample was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research, Irvine, USA)

tag: source

value: GICaRes

tag: array platform_id

value: EPIC

tag: run date

value: M

tag: crc risk

value: Medium


title: genomic DNA from normal colon sample 333

description: normal colon sample

value: F

value: Low


title: 2_EBOV_CD14+

tag: cell type


title: 2_Med_CD14-


title: genomic DNA from normal colon sample 329

description: normal colon sample


title: 2_Med_CD14+


title: genomic DNA from normal colon sample 328

description: normal colon sample


title: genomic DNA from normal colon sample 332

description: normal colon sample


title: genomic DNA from normal colon sample 327

description: normal colon sample


title: ChIP_input

city: Irvine

first: Ali

last: Mortazavi

state: California

address: 2300 Biological Sciences III

department: Developmental & Cell Biology

institute: University of California Irvine

library_source: genomic

data_processing:
Adapter sequences and low quality base pairs from the paired-ends reads were trimmed using Trimmomatic v. 0.35 using the following parameters: “PE [read1.fastq] [read2.fastq] pe_read1.fastq.gz se_read1.fastq.gz pe_read2.fastq.gz se_read2.fastq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:8:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:17 MINLEN:30”.
The trimmed reads were mapped to the genome sequence from Hydra 2.0 Genome Project (https://research.nhgri.nih.gov/hydra/) using Bowtie v. 1.2 with the following parameters: “-X 2000 -v 3 -m 3 -k 1 –best”.
Duplicate reads were removed using "rmdup" of Samtools v. 1.7.
Genome_build: Hydra 2.0 Genome (https://research.nhgri.nih.gov/hydra/)
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage v. 3.1.0 from DeepTools package. Scores represent normalized (reads per million) ChIP-seq signal.

organism: Hydra vulgaris

growth_protocol: Hydra vulgaris polyps were fed freshly hatched Artemia salina nauplii twice per week.  Animals were starved for at least 1 day before any tissue manipulation.

extract_protocol: ChIP-seq libraries were prepared using the ChIPmentation protocol v. 1.14. Briefly, tissues were crosslinked in 1% formaldehyde. The crosslinked chromatin samples were sonicated using A Qsonica sonicator using the following settings: 50%, total 15 minutes, 30 seconds on and 30 seconds off. The chromatin samples were sonicated to an average size range of 200-700 bp. The following antibodies were used for immunoprecipitation: H3K4me3 Rabbit mAb (Cell Signaling Technology, Cat. No. 9751), H3K4me2 Rabbit pAb (Millipore-Sigma, Cat. No. 07030), and H3K27ac Rabbit pAb (Active Motif, Cat. No. 39133). Dynabeads M-280 sheep anti-rabbit IgG beads (Thermo Fisher Scientific, Cat. No. 11203D) were used for immunoprecipitation. The sequencing libraries were prepared according to protocol.  The library qualities were assessed on a Bioanalyzer and the libraries were sequenced as 43-bp paired-end reads on an Illumina NextSeq 500. Each experiment was performed with two biological replicates.

treatment_protocol: For each sample, 1-day starved asexual hydra polyps were selected. For regeneration, twenty animals per sample (with two biological replicates) were bisected at the region 1 (R1) and region 2 (R2) border (Fig 1B) and allowed to undergo head regeneration for a specific period of time (0, 2, 4, 6, 12, 24, or 48 hours). Then the R2 regions of the animals of a sample were isolated for crosslinking and immunoprecipitation. The following tissues were collected for the body map samples: ten whole animals and head (hypostome + tentacles) tissues from 20 animals.

value: whole animal

tag: chip antibody


title: WholeHydra_H3K4me3_rep2

value: H3K4me3 (Cell Signaling Technology, Cat. No. 9751)


title: genomic DNA from normal colon sample 325

description: normal colon sample


title: 1_EBOV_CD14+


title: genomic DNA from normal colon sample 323

description: normal colon sample


title: genomic DNA from normal colon sample 319

description: normal colon sample


title: genomic DNA from normal colon sample 322

description: normal colon sample


title: genomic DNA from normal colon sample 320

description: normal colon sample


title: genomic DNA from normal colon sample 331

description: normal colon sample


title: genomic DNA from normal colon sample 318

description: normal colon sample


title: genomic DNA from normal colon sample 312

description: normal colon sample


title: Head_H3K4me3_rep2

value: head


title: 1_Med_CD14-


title: genomic DNA from normal colon sample 317

description: normal colon sample


title: genomic DNA from normal colon sample 316

description: normal colon sample


title: genomic DNA from normal colon sample 314

description: normal colon sample


title: 1_Med_CD14+


title: Head_H3K4me3_rep1


title: genomic DNA from normal colon sample 326

description: normal colon sample


title: genomic DNA from normal colon sample 330

description: normal colon sample


title: genomic DNA from normal colon sample 313

description: normal colon sample


title: WholeHydra_H3K4me3_rep1


title: genomic DNA from normal colon sample 324

description: normal colon sample


title: Reg_H3K4me3_24hr_rep2

value: regenerating head


title: Hep-2C_U2: Uninfected

data_processing:
trim low quality tails, polyA tails and adapters (bbmap): k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 int=f
align to human genome (hg38)  (STAR aligner): --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate
indexed BAM files (samtools)
counted reads per sample (HTSeq-count)
normalised counts by variance stabilising transformation (DESeq2)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated ensembl transcript and read count per sample (.txt)

source_name: cultured Hep-2C cells

growth_protocol: Hep-2C cells incubated with inoculum for 3 hours, then grown with media (plus supplement) for 36 hours.

value: Uninfected

tag: time point

value: 36 hours


title: genomic DNA from normal colon sample 311

description: normal colon sample

tag: gender


title: genomic DNA from normal colon sample 321

description: normal colon sample

tag: age


title: Hep-2C_U1: Uninfected


title: Reg_H3K4me3_24hr_rep1


title: genomic DNA from normal colon sample 310

description: normal colon sample


title: 1_EBOV_CD14-


title: genomic DNA from normal colon sample 315

description: normal colon sample


title: Reg_H3K4me3_6hr_rep2


title: Hep-2C_B3: B/Tunis-864 infected

value: B/Tunis-864 infected (MOI 1)


title: Reg_H3K4me3_6hr_rep1


title: Reg_H3K4me3_4hr_rep2


title: Hep-2C_B1: B/Tunis-864 infected


title: genomic DNA from normal colon sample 307

description: normal colon sample


title: Hep-2C_U3: Uninfected


title: Hep-2C_A3: A/2497 infected

value: A/2497 infected (MOI 1)


title: Hep-2C_B2: B/Tunis-864 infected


title: Hep-2C_A1: A/2497 infected


title: Hep-2C_A2: A/2497 infected


title: Reg_H3K4me3_0hr_rep2


title: genomic DNA from normal colon sample 309

description: normal colon sample


title: Reg_H3K4me3_4hr_rep1


title: genomic DNA from normal colon sample 308

description: normal colon sample


title: Reg_H3K4me3_0hr_rep1


title: WholeHydra_H3K4me2_rep2

value: H3K4me2 (Millipore-Sigma, Cat. No. 07030)


title: genomic DNA from normal colon sample 305

description: normal colon sample


title: WholeHydra_H3K4me2_rep1


title: Head_H3K4me2_rep2


title: genomic DNA from normal colon sample 304

description: normal colon sample


title: Reg_H3K4me2_6hr_rep2


title: Head_H3K4me2_rep1


title: Reg_H3K4me2_24hr_rep2


title: Reg_H3K4me2_6hr_rep1


title: genomic DNA from normal colon sample 302

description: normal colon sample


title: Reg_H3K4me2_4hr_rep2


title: Reg_H3K4me2_24hr_rep1


title: genomic DNA from normal colon sample 303

description: normal colon sample


title: Reg_H3K4me2_0hr_rep2


title: Reg_H3K4me2_4hr_rep1


title: Reg_H3K4me2_0hr_rep1


title: genomic DNA from normal colon sample 301

description: normal colon sample


title: WholeHydra_H3K27ac_rep2

value: H3K27ac (Active Motif, Cat. No. 39133)


title: Head_H3K27ac_rep2


title: genomic DNA from normal colon sample 296

description: normal colon sample


title: genomic DNA from normal colon sample 306

description: normal colon sample


title: genomic DNA from normal colon sample 298

description: normal colon sample


title: Reg_H3K27ac_24hr_rep2


title: WholeHydra_H3K27ac_rep1


title: genomic DNA from normal colon sample 293

description: normal colon sample


title: Reg_H3K27ac_24hr_rep1


title: genomic DNA from normal colon sample 300

description: normal colon sample


title: Reg_H3K27ac_6hr_rep2


title: Reg_H3K27ac_6hr_rep1


title: genomic DNA from normal colon sample 295

description: normal colon sample


title: Head_H3K27ac_rep1


title: genomic DNA from normal colon sample 297

description: normal colon sample


title: genomic DNA from normal colon sample 284

description: normal colon sample


title: genomic DNA from normal colon sample 292

description: normal colon sample


title: genomic DNA from normal colon sample 291

description: normal colon sample


title: genomic DNA from normal colon sample 289

description: normal colon sample


title: genomic DNA from normal colon sample 282

description: normal colon sample


title: genomic DNA from normal colon sample 299

description: normal colon sample


title: genomic DNA from normal colon sample 287

description: normal colon sample


title: Reg_H3K27ac_0hr_rep2


title: Reg_H3K27ac_4hr_rep1


title: genomic DNA from normal colon sample 290

description: normal colon sample


title: genomic DNA from normal colon sample 283

description: normal colon sample


title: genomic DNA from normal colon sample 294

description: normal colon sample


title: Tentacles_ATAC_rep2

data_processing:
Adapter sequences and low quality base pairs from the paired-ends reads were trimmed using Trimmomatic v. 0.35 using the following parameters: “PE [read1.fastq] [read2.fastq] pe_read1.fastq.gz se_read1.fastq.gz pe_read2.fastq.gz se_read2.fastq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:8:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:17 MINLEN:30”.
The trimmed reads were first mapped to Hydra mitochondrial DNA sequences to filter the mitochondrial reads. The unmapped reads were mapped to the genome sequence from Hydra 2.0 Genome Project (https://research.nhgri.nih.gov/hydra/) using Bowtie v1.2 with the following parameters: -X 2000 -v 3 -m 3 -k 1 –best.
Peaks were called using Homer v. 4.9 using the following parameters: "-size 500 -minDist 50 -fdr 0.01 -style factor". Overlapping peaks between the two replicates of each sample were kept for downstream analysis. The peaks from all samples were merged using Bedtools v. 2.23.0. The read coverage of peaks for each sample was obtained using “coverageBed” function of Bedtools. The read counts for each sample were normalized for efficiency (number of reads within peaks divided by total number of mapped reads) and reads per million.
Genome_build: Hydra 2.0 Genome (https://research.nhgri.nih.gov/hydra/)
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage v. 3.1.0 from DeepTools package. Scores represent normalized ATAC-seq signal.

growth_protocol: Hydra vulgaris polyps were fed freshly hatched Artemia salina nauplii twice per week.  Animals were starved for at least 1 day before any tissue manipulation and nuclei isolation.

extract_protocol:
Nuclei from tissues were isolated using the following protocol. Briefly, Hydra tissues were washed in ice-cold PBS once. The tissues were homogenized in 1 mL of dissociation medium (3.6 mM KCl, 6 mM CaCl2, 1.2 mM MgSO4, 6 mM sodium citrate, 6 mM sodium pyruvate, 6 mM glucose, 12.5 mM TES, stored in 4°C) in a tissue homogenizer. The solution of homogenized tissue was transferred to an eppendorf tube and centrifuged at 500g for 5 min. The supernatant was removed. The cells were resuspended in 50 μL of cold cell lysis buffer (10 mM Tris-HCl, pH
7.4, 10 mM NaCl, 3 mM MgCl2, stored in 4°C) + 0.2% IGEPAL. The sample was immediately spun down at 90g for 8 min. The supernatant was transferred to a fresh eppendorf tube and spun down at 500g for 12 min. The supernatant was removed and the nuclei pellet resuspended in 50 μL ice-cold PBS to remove mitochondrial DNA. The sample was spun down at 500g for 12 min to collect the nuclei for tagmentation.
The chromatin in the nuclei pellet was tagmented using 1 μL of Tn5 enzyme and sequencing libraries prepared according to the protocol in Buenrostro et al. 2013 with the following modification: DNA fragments in the final sequencing library were size selected for 100-500 bp on a 2% agarose gel. The library qualities were assessed using a Bioanalyzer and the libraries were sequenced as 43-bp paired-end reads on an Illumina NextSeq 500. Each sample was performed with two biological replicates.

treatment_protocol: For chromatin profiling experiments using ATAC-seq, the Hydra polyps were first incubated in a cocktail of four antibiotics for one week with feeding, followed by one week of recovery in sterile medium. This was done to remove commensal bacteria from the Hydra polyps before Tn5 tagmentation during ATAC-seq and avoid contamination from tagmented bacterial DNA. For each sample, 1-day starved asexual hydra polyps were selected. For regeneration, twenty animals per sample (with two biological replicates) were bisected at the region 1 (R1) and region 2 (R2) border below the hypostome and allowed to undergo head regeneration for a specific period of time (0, 2, 4, 6, 12, 24, or 48 hours). Then the R2 regions of the animals of a sample were isolated for nuclei isolation and tagmentation (ATAC-seq). The following tissues were collected for the body map samples: foot, budding zone, body column, hypostome, and tentacles from 20 animals.

value: tentacles


title: genomic DNA from normal colon sample 281

description: normal colon sample

value: GICaRes


title: Kiaa1429Zp3cKO-4 Oocyte

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

data_processing:
Sequence are mapped to mm10 refernece using STAR
HTSeq is used to calculate the reads count of each exon
Genome_build: mm10
Supplementary_files_format_and_content: plain txt file, each contains two column. First column means the gene ID, the second column means the read count

organism: Mus musculus

source_name: Kiaa1429Zp3cKO-4 Oocyte

growth_protocol: Mice were housed under SPF environmental conditions with free access to water and food, 20–22°C ,50–70% humidity, and a 12/12-hour light and dark cycle in the Animal Core Facility of Nanjing Medical University. Animal care and experimental procedures were conducted according to the guidelines of the Animal Research Committee of Nanjing Medical University.

extract_protocol:
The collected GV oocyte were washed twice with 1xPBS and then immediately placed in lysis buffer( Combine 0.2% (vol/vol) Triton X-100 and 2 U µl–1 RNase inhibitor).The lysis solution also contains free dNTPs and tailed oligo-dT oligonucleotides (30-nt poly-dT stretch and a 25-nt universal 5′ anchor sequence) that are prepared of the Reverse Trianscription reaction on polyadenylated RNA sequences.
After the first reaction of reverse transcription, we used template-switching oligos to obtain the yield of full-length cDNA. Then, we performed RT-PCR to  maximize cDNA (After 90 min at 42 °C (the optimal conditions for Superscript II, according to the manufacturer), we raised the temperature to 50 °C for 2 min to promote the unfolding of any RNA secondary structures. We then lowered it to 42 °C again for 2 min and repeated this cycle a total of ten).After the first-strand reaction,We used tagmentation to quickly and efficiently construct sequencing libraries from the amplified cDNA. The fragments in the tagmented DNA library have an average size that ranges from 200 to 300 bp and then purified for Illimina. The  quantity of the libraries was assessed and defined by qPCR, respectively. All samples showed a concentration of higher than 3nM and were sequenced using HiSeq XTen (Illumina) with paired-end 150-bp sequencing.

treatment_protocol: 3-week-old female mice were intraperitoneally injected with 5 IU pregnant mare serum gonadotropin (PMSG, Ningbo Sansheng Pharmaceutical Corporation, Zhejiang, China) to stimulate antral follicle development. After 48 hours, Fully grown GV oocytes (At least 70 μm diameter) were isolated by gently puncturing antral follicles with a sterile insulin syringe needle under the visual field of a dissecting microscope and released in M2 medium (Sigma, M7167) supplemented with 2.5mM Milrinone (Sigma, M4659).

tag: strain

value: GV oocyte

tag: genotype


title: Reg_H3K27ac_0hr_rep1


title: Tentacles_ATAC_rep1


title: genomic DNA from normal colon sample 288

description: normal colon sample

value: EPIC


title: Kiaa1429Zp3cKO-3 Oocyte

source_name: Kiaa1429Zp3cKO-3 Oocyte


title: Reg_H3K27ac_4hr_rep2


title: genomic DNA from normal colon sample 285

description: normal colon sample

value: M


title: Kiaa1429Zp3cKO-2 Oocyte

source_name: Kiaa1429Zp3cKO-2 Oocyte


title: Hypostome_ATAC_rep1

value: hypostome


title: genomic DNA from normal colon sample 276

description: normal colon sample

value: F

value: Medium


title: genomic DNA from normal colon sample 286

description: normal colon sample


title: Hypostome_ATAC_rep2


title: Kiaa1429Zp3cKO-1 Oocyte

source_name: Kiaa1429Zp3cKO-1 Oocyte


title: Foot_ATAC_rep2

value: foot


title: genomic DNA from normal colon sample 275

description: normal colon sample


title: Control-4 Oocyte

source_name: Control-4 Oocyte


title: genomic DNA from normal colon sample 279

description: normal colon sample


title: BuddingZone_ATAC_rep1

value: budding zone


title: genomic DNA from normal colon sample 273

description: normal colon sample


title: genomic DNA from normal colon sample 274

description: normal colon sample


title: Control-2 Oocyte

source_name: Control-2 Oocyte


title: genomic DNA from normal colon sample 280

description: normal colon sample


title: Foot_ATAC_rep1


title: BodyColumn_ATAC_rep2

value: body column


title: Control-3 Oocyte

source_name: Control-3 Oocyte


title: BodyColumn_ATAC_rep1


title: genomic DNA from normal colon sample 271

description: normal colon sample


title: genomic DNA from normal colon sample 278

description: normal colon sample


title: p300_ICBP112A485_2_ChIPSeq

city: Boston

first: Beth

last: Zucconi

state: Massachusetts

address: 77 Avenue Louis Pasteur, NRB 164

institute: Brigham & Women's Hospital

data_processing:
ChiLin pipeline.
QC with FastQC.
Align with Bowtie.
Peak calling by MACS2.
Pearson correlation with wigCorrelate; %overlap between replicates determined.
Peaks annotated with HOMER after removal of blacklisted regions.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

source_name: Androgen dependent prostate cancer cell line

extract_protocol:
Chromatin shearing followed by p300 immunoprecipitation.
Swift Biosciences Accel-NGS 2S

treatment_protocol: LNCaP cells were divided into 4 different drug treatment groups (including control) and were treated with I-CBP112 and/or A-485 for 24 h.

tag: cell line

value: LNCaP-FGC

value: ICBP112 and A485

value: p300 (Developmental Studies Hybridoma Bank, University of Iowa, ENCITp300-1)


title: p300_A485_2_ChIPSeq

value: Androgen dependent prostate cancer cell line

tag: treatment


title: Reg_ATAC_48hr_rep1

value: regenerating head


title: p300_ICBP112_2_ChIPSeq


title: genomic DNA from normal colon sample 268

description: normal colon sample


title: Reg_ATAC_48hr_rep2


title: Reg_ATAC_24hr_rep2


title: Reg_ATAC_24hr_rep1


title: genomic DNA from normal colon sample 272

description: normal colon sample

value: Low


title: genomic DNA from normal colon sample 277

description: normal colon sample


title: p300_DMSO_2_ChIPSeq

value: DMSO


title: Reg_ATAC_12hr_rep2


title: genomic DNA from normal colon sample 269

description: normal colon sample

value: ColoCare

value: High


title: Reg_ATAC_12hr_rep1


title: BuddingZone_ATAC_rep2


title: genomic DNA from normal colon sample 266

description: normal colon sample

value: GICaRes

value: EPIC


title: Reg_ATAC_6hr_rep2


title: p300_ICBP112A485_1_ChIPSeq


title: genomic DNA from normal colon sample 267

description: normal colon sample


title: p300_ICBP112_1_ChIPSeq


title: Reg_ATAC_4hr_rep2


title: Reg_ATAC_6hr_rep1


title: p300_A485_1_ChIPSeq


title: Reg_ATAC_4hr_rep1


title: p300_DMSO_1_ChIPSeq


title: Control-1 Oocyte

source_name: Control-1 Oocyte

value: GV oocyte


title: Reg_ATAC_2hr_rep1


title: Reg_ATAC_2hr_rep2


title: Reg_ATAC_0hr_rep2


title: Reg_ATAC_0hr_rep1


title: genomic DNA from normal colon sample 270

description: normal colon sample

value: M


title: genomic DNA from normal colon sample 261

description: normal colon sample

value: Medium


title: genomic DNA from normal colon sample 259

description: normal colon sample

value: F


title: genomic DNA from normal colon sample 260

description: normal colon sample


title: genomic DNA from normal colon sample 258

description: normal colon sample


title: aorta_hight fat diet+exercise_12 week_rep1

city: changsha

first: fan

last: zheng

state: Hunan

address: Xiangya Road 87#

institute: Xiangya hospital

description: Gene expression after high fat diet and exercise 60min for 12 weeks in mice aorta

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse lncRNA (4*180K,Design ID:049801)for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

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

source_name: aorta, high fat diet+exercise, 12week

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

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

treatment_protocol: 24 h after the end of exercise intervention, all mice were fasted overnight and euthanized by chloral hydrate (10%, 0.4 mL/100 g body weight). The aorta of each mouse was withdrawn and stored in liquid nitrogen until further analysis.

tag: group

value: high fat diet+exercise

value: aorta

value: male


title: genomic DNA from normal colon sample 255

description: normal colon sample


title: genomic DNA from normal colon sample 254

description: normal colon sample


title: aorta_hight fat diet+exercise_12 week_rep3

tag: tissue


title: genomic DNA from normal colon sample 264

description: normal colon sample


title: genomic DNA from normal colon sample 253

description: normal colon sample


title: genomic DNA from normal colon sample 257

description: normal colon sample


title: aorta_normal diet_12 week_rep3

description: Gene expression after normal diet for 12 weeks in mice aorta

source_name: aorta, normal diet, 12week

value: normal diet


title: genomic DNA from normal colon sample 265

description: normal colon sample


title: genomic DNA from normal colon sample 251

description: normal colon sample


title: genomic DNA from normal colon sample 262

description: normal colon sample


title: genomic DNA from normal colon sample 263

description: normal colon sample


title: aorta_high fat diet_12 week_rep3

description: Gene expression after high fat diet for 12 weeks in mice aorta

source_name: aorta, high fat diet, 12week

value: high fat diet


title: aorta_high fat diet_12 week_rep2


title: genomic DNA from normal colon sample 250

description: normal colon sample


title: genomic DNA from normal colon sample 256

description: normal colon sample


title: aorta_hight fat diet+exercise_12 week_rep2


title: genomic DNA from normal colon sample 243

description: normal colon sample


title: aorta_high fat diet_12 week_rep1


title: genomic DNA from normal colon sample 244

description: normal colon sample


title: aorta_normal diet_12 week_rep2


title: genomic DNA from normal colon sample 249

description: normal colon sample


title: genomic DNA from normal colon sample 252

description: normal colon sample


title: genomic DNA from normal colon sample 242

description: normal colon sample


title: genomic DNA from normal colon sample 248

description: normal colon sample


title: genomic DNA from normal colon sample 241

description: normal colon sample


title: genomic DNA from normal colon sample 247

description: normal colon sample


title: genomic DNA from normal colon sample 246

description: normal colon sample


title: aorta_normal diet_12 week_rep1


title: genomic DNA from normal colon sample 240

description: normal colon sample


title: genomic DNA from normal colon sample 238

description: normal colon sample


title: Anti-CD137_7dpi_BCR

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 (v3.0.2)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v3.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
single-cell V(D)J , Cell Ranger Single Cell Software Suite (v3.0.2)
alignment, Cell Ranger Single Cell Software Suite (v3.0.2)
Genome_build: vdj_GRCm38_alts_ensembl
Supplementary_files_format_and_content: csv files with contig and clonotypes information.

molecule: polyA RNA

source_name: Isolated single cells from spleens of wild type mice that were infected with chikungunya virus at day 0 and administered agonistic anti-CD137 antibody

extract_protocol:
At 4 weeks of age, male mice were anesthetized with ketamine hydrochloride (80 mg/kg) and xylazine (15 mg/kg) and inoculated s.c. in the left rear footpad with 103 focus-forming units (FFU) of CHIKV in 10 μl of PBS. At 2 days post-infection, infected mice were administered either agonistic anti-CD137 monoclonal antibody (mAb) or isotype mAb. At the termination of experiments, mice were euthanized and perfused via intracardiac injection with PBS. Spleens were minced and incubated for 30 min at 37C in 2 ml digestion buffer (1 mg/ml collagenase (Sigma) and 100 μg/mL DNase I (Sigma) in Dulbecco’s Modified Eagle’s medium (DMEM) containing 2% FBS in a 24-well plate. Cell suspensions were passed through a 100 μm cell strainer. After rinsing with 10% FBS, 5 mM EDTA in DMEM, erythrocytes were lysed with 1 mL of ACK Lysing Buffer (Gibco) per spleen for 2 min. Cells were washed with DMEM and centrifuged, followed by rinsing with washing buffer (2% FBS, 5 mM EDTA in PBS).
Isolated single nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing, and libraries were prepared using Chromium Single Cell 5′ Reagent Kits in a BSL-3 level laboratory according to manufacturer’s protocol (10x Genomics). For B Cell repertoire libraries, amplified cDNA underwent two rounds of Target Enrichment using nested primer pairs specific for mouse B cell Ig constant regions. The generated scRNAseq libraries were sequenced a NovaSeq S4 flow cell.

tag: mouse genotype

value: wt

value: splenocytes


title: Isotype_7dpi_BCR

source_name: Isolated single cells from spleens of wild type mice that were infected with chikungunya virus at day 0 and administered isotype monoclonal antibody


title: genomic DNA from normal colon sample 245

description: normal colon sample


title: Naïve_BCR

source_name: Isolated single cells from spleens of wild type mice


title: Anti-CD137_7dpi

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v3.0.2)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v3.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
single-cell 5′ gene counting , Cell Ranger Single Cell Software Suite (v3.0.2)
alignment, Cell Ranger Single Cell Software Suite (v3.0.2)
Genome_build: mm10
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.


title: Isotype_7dpi


title: genomic DNA from normal colon sample 236

description: normal colon sample


title: genomic DNA from normal colon sample 233

description: normal colon sample


title: genomic DNA from normal colon sample 239

description: normal colon sample


title: genomic DNA from normal colon sample 224

description: normal colon sample


title: genomic DNA from normal colon sample 234

description: normal colon sample

value: Low


title: genomic DNA from normal colon sample 228

description: normal colon sample


title: Anti-CD137_3dpi


title: Isotype_3dpi


title: genomic DNA from normal colon sample 231

description: normal colon sample


title: genomic DNA from normal colon sample 229

description: normal colon sample


title: genomic DNA from normal colon sample 230

description: normal colon sample


title: genomic DNA from normal colon sample 237

description: normal colon sample


title: Naïve


title: Trem2_KO_5XFAD3

source_name: Isolated single nuclei from brain of Trem2 KO 5XFAD mice

extract_protocol:
Mice were aged to 7 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1000 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer.
Isolated single nuclei were subjected to droplet-based 5’ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5’ Reagent Kits as per manufacturer’s instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer.

value: Trem2-/- 5XFAD

value: nuclei of brain

value: 7 months


title: genomic DNA from normal colon sample 220

description: normal colon sample

value: GICaRes


title: genomic DNA from normal colon sample 227

description: normal colon sample

value: ColoCare

value: EPIC

value: High


title: genomic DNA from normal colon sample 232

description: normal colon sample


title: genomic DNA from normal colon sample 215

description: normal colon sample

value: M

value: Medium


title: genomic DNA from normal colon sample 226

description: normal colon sample


title: genomic DNA from normal colon sample 223

description: normal colon sample


title: genomic DNA from normal colon sample 225

description: normal colon sample


title: genomic DNA from normal colon sample 221

description: normal colon sample

value: F


title: genomic DNA from normal colon sample 235

description: normal colon sample


title: genomic DNA from normal colon sample 214

description: normal colon sample


title: genomic DNA from normal colon sample 222

description: normal colon sample


title: genomic DNA from normal colon sample 217

description: normal colon sample


title: WT_5XFAD2

source_name: Isolated single nuclei from brain of 5XFAD mice


title: Trem2_KO_5XFAD2


title: genomic DNA from normal colon sample 218

description: normal colon sample


title: Trem2_KO3

source_name: Isolated single nuclei from brain of Trem2 KO mice


title: Trem2_KO2


title: genomic DNA from normal colon sample 216

description: normal colon sample


title: genomic DNA from normal colon sample 219

description: normal colon sample


title: Trem2_KO_5XFAD1


title: WT_5XFAD3


title: Trem2_KO1


title: genomic DNA from normal colon sample 211

description: normal colon sample


title: Mitotic pT431 CTCF ChIP-seq replicate 2

city: Bloomington

first: Gabriel

middle: E

last: Zentner

state: IN

address: 915 E 3rd St

department: Biology

institute: Indiana University

data_processing:
Paired FASTQ files were aligned with Bowtie2
Alignment SAM files were used to create tag directories with HOMER
Peaks were called using HOMER findPeaks
HOMER makeUCSCfile was used to generate bigWig files for signal visualization
Genome_build: hg38
Supplementary_files_format_and_content: bw: reads/10 million-normalized signal tracks (HOMER default); txt: CTCF peaks from asynchronous pan-CTCF ChIP-seq replicate 1

source_name: Mitotic pT431 CTCF ChIP-seq

growth_protocol: MDA-MB-435 cells were grown in DMEM + 50 U/mL penicillin, 50 μg/mL streptomycin, and 10% FBS.

extract_protocol:
ChIP_protocol.pdf
Libraries were constructed with the NEBNext Ultra II DNA Library Prep Kit for Illumina at the Indiana University Center for Genomics and Bioinformatics

treatment_protocol: To enrich mitotic cells, cells were first treated with 2 mM thymidine for 24 h to arrest cells in S phase. Cells were washed and cultured without thymidine for 3 h. Cells were then incubated with 100 ng/mL nocodazole for 16 h to arrest cells in prometaphase. Mitotic cells were collected by shake-off.

value: MDA-MB-435 melanoma cells

tag: cell cycle stage

value: Mitosis (nocodazole-arrested)

value: rabbit anti-pT431 CTCF (custom)


title: WT_5XFAD1


title: genomic DNA from normal colon sample 212

description: normal colon sample

tag: source


title: Mitotic pT431 CTCF ChIP-seq replicate 1


title: WT2

source_name: Isolated single nuclei from brain of wild type mice


title: genomic DNA from normal colon sample 213

description: normal colon sample

tag: array platform_id


title: Asynchronous pan-CTCF ChIP-seq replicate 2

source_name: Asynchronous pan-CTCF ChIP-seq

value: Mixed (asynchronous)

value: rabbit anti-CTCF (Millipore 07-729)


title: Asynchronous pan-CTCF ChIP-seq replicate 1


title: WT1

value: wt


title: ♂DBA/2J x ♀C57/BL6J blastocyst cells rep2

data_processing:
Sequencing data were mapped mm10 reference genome using GMAP and STAR seperately
transcriptome of each pacbio sample were assembled by cufflinks
TPM of transcript were calculated using salmon
Genome_build: mm10
Supplementary_files_format_and_content: gtf file for pacbio sequencing data; plain txt file for illumina RNA-seq data, each file contain 2 column, the first column represents the transcript id and tpm
Supplementary_files_format_and_content: We do not have quantitative processed data for Pacbio data. The TPM results are calculated using gff generated from Pacbio data as references.

source_name: ♂DBA/2J x ♀C57/BL6J blastocyst cells

growth_protocol: Mice were maintained in an Assessment and Accreditation of Laboratory Animal Care credited specific pathogen free facility under a 12 h light, 12 h dark cycle.

extract_protocol:
Sperm were collected from the epididymis of DBA/2N males. MII oocytes were derived from 3 to 5 week-old C57BL/6J females induced to superovulate by injection of 7.5IU pregnant mare serum gonadotropin (PMSG, San Sheng), followed by injection of 7.5IU human chorionic gonadotropin (hCG, San Sheng) 48h later. Embryos were collected from the oviduct of the superovulated females after mating them with DBA/2N males. Oocytes and embryos were isolated in M2 medium (Sigma) at 20h post-hCG, then while oocytes were lyse directly, the embryos were not lyse until they develop to defined stages: zygotes (24-26h post hCG), two-cell stage (46-48h post-hCG), four-cell stage (54-58h post-hCG), eight-cell stage (68-70h post-hCG), blastocyst stage (94-96h post-hCG), with culturing in KSOM media (Merck Millipore) at 37℃ with 5% CO2.
Embryos were lysed in 50 μl of guanidine isothiocyanate solution (Invitrogen, 15577-018) at 42°C for 15 min. Nuclease-free water was added to 200 μl, and 3 volumes of absolute ethanol, 1/10 volume of 3 M acetate sodium (Invitrogen, AM9740) and 2 μl of glycogen (Roche, 10901393001) were added and mixed uniformly. After treatment at -80 °C for 2 h, total RNA was pelleted by centrifugation at 12,000g for 40 min. Total RNA pellets were dissolved in lysis solution and used as template for the first cDNA synthesis, cDNA was amplified by Smart-seq2 protocol1.
2 μg of each amplified cDNA is was transformed into SMRTbell templates using the PacBio SMRTbell Express Template Prep Kit. The libraries were sequenced using the PacBio Sequel System in Berry Genomics Company (Beijing, China).The sequencing libraries were constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech, TD502-01) according to the manufacturer’s instruction. All libraries were sequenced on Illumina NovaSeq 6000 platform with a 150-bp paired-end module in Berry Genomics Company (Beijing, China).

value: DBA/2J x C57/BL6J

value: blastocyst cells


title: genomic DNA from normal colon sample 209

description: normal colon sample

tag: run date


title: ♂DBA/2J x ♀C57/BL6J blastocyst cells rep1


title: WT3

value: nuclei of brain


title: genomic DNA from normal colon sample 210

description: normal colon sample

tag: crc risk


title: ♂DBA/2J x ♀C57/BL6J 8cell cells rep2

source_name: ♂DBA/2J x ♀C57/BL6J 8cell cells

tag: cell type

value: 8cell cells


title: genomic DNA from normal colon sample 208

description: normal colon sample

value: GICaRes

value: Low


title: ♂DBA/2J x ♀C57/BL6J 4cell cells rep1

source_name: ♂DBA/2J x ♀C57/BL6J 4cell cells

value: 4cell cells


title: genomic DNA from normal colon sample 204

description: normal colon sample

value: ColoCare

value: EPIC

value: High


title: ♂DBA/2J x ♀C57/BL6J 2cell cells rep1

source_name: ♂DBA/2J x ♀C57/BL6J 2cell cells

value: 2cell cells


title: ♂DBA/2J x ♀C57/BL6J 1cell cells rep2

source_name: ♂DBA/2J x ♀C57/BL6J 1cell cells

value: 1cell cells


title: ♂DBA/2J x ♀C57/BL6J 1cell cells rep1


title: C57/BL6J oocyte cells rep2

source_name: C57/BL6J oocyte cells

value: oocyte cells


title: ♂DBA/2J x ♀C57/BL6J 8cell cells rep1


title: genomic DNA from normal colon sample 206

description: normal colon sample

value: F

value: Medium


title: genomic DNA from normal colon sample 199

description: normal colon sample

value: M


title: ♂DBA/2J x ♀C57/BL6J 2cell cells rep2


title: C57/BL6J oocyte cells rep1


title: genomic DNA from normal colon sample 203

description: normal colon sample


title: genomic DNA from normal colon sample 205

description: normal colon sample


title: genomic DNA from normal colon sample 198

description: normal colon sample


title: DBA/2J sperm cells rep1

source_name: DBA/2J sperm cells

value: sperm cells


title: DBA/2J sperm cells rep2


title: ♂DBA/2J x ♀C57/BL6J 4cell cells rep2

value: DBA/2J x C57/BL6J


title: genomic DNA from normal colon sample 195

description: normal colon sample


title: genomic DNA from normal colon sample 200

description: normal colon sample


title: genomic DNA from normal colon sample 201

description: normal colon sample


title: genomic DNA from normal colon sample 191

description: normal colon sample


title: genomic DNA from normal colon sample 190

description: normal colon sample


title: genomic DNA from normal colon sample 196

description: normal colon sample


title: genomic DNA from normal colon sample 197

description: normal colon sample


title: genomic DNA from normal colon sample 189

description: normal colon sample


title: genomic DNA from normal colon sample 207

description: normal colon sample


title: genomic DNA from normal colon sample 185

description: normal colon sample


title: genomic DNA from normal colon sample 192

description: normal colon sample


title: genomic DNA from normal colon sample 182

description: normal colon sample


title: genomic DNA from normal colon sample 183

description: normal colon sample


title: genomic DNA from normal colon sample 193

description: normal colon sample


title: genomic DNA from normal colon sample 186

description: normal colon sample


title: genomic DNA from normal colon sample 184

description: normal colon sample


title: genomic DNA from normal colon sample 188

description: normal colon sample


title: genomic DNA from normal colon sample 181

description: normal colon sample


title: Esrrb_KO_serum_rep3

first: Ed

last: Curry

address: Hammersmith Hospital, Du Cane Road

description: 4C-seq at Klf4 locus

data_processing:
Library strategy: 4C-seq
Adapter removal with cutadapt.
Alignment to mm9 reference genome with Bowtie2 with the option ‘very-sensitive’ in single-end mode.
Low-quality reads (MAPQ < 10) were discarded.
FourCSeq package was used to map reads from the forward and reverse PCR primer to valid restriction sites.
Reads were normalized compared with DESeq2 discarding reads that mapped in trans.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files contain RPKM counts in bins of 5 kb surrounding the viewpoint.

source_name: Esrrb -/- embryonic stem cells

growth_protocol: Mouse ESCs were routinely cultured on 0.1% gelatin coated plates and maintained in GMEM media supplemented with 10% FBS (serum) or 2i, MEM non-essential amino acids, beta-mercaptoethanol, L-glutamine, sodium pyruvate, sodium bicarbonate, penicillin/streptomycin, LIF prepared in-house and the appropriate drug selection. Mouse ESRRB KO ESCs (Martello G et al. 2012) and control populations have been previously described.

extract_protocol:
10 million cells were crosslinked for 13 min with 2% paraformaldehyde in ESC culture medium, quenched with glycine and lysed in 15 ml lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 0.2% NP-40, 1× protease inhibitors) for 30 min at 4 °C. Nuclei were then incubated with 0.25% SDS for 30 min in NEB buffer3 followed by Triton X-100 treatment for 30 min, both at 37 °C. Nuclei were then digested with 700 U DpnII enzyme (NEB) overnight at 37 °C. Enzyme was inactivated at 65 °C for 15 min followed by ‘in nuclei’ ligation at 16 °C with 2,000 U T4 ligase (NEB) (nagano, 2015). Samples were then treated with protease K and RNaseA and DNA was purified by phenol–chloroform (Sigma: 77618). DNA was further digested with 50 U BfaI, and purified with QIAquick PCR purification columns followed by a second ligation at 16 °C.
1,000 ng of 4C-seq library was amplified with bait-specific inverse primers as described previously (Atlasi, 2019) and using the Expand Long template PCR system (Roche 11759060001) for 28 PCR cycles. PCR products were then purified and 50 ng DNA was used for library preparation using KAPA Hyperprep kit (Roche 07962363001) and 5 PCR cycles. Libraries were sequenced on the Illumina NextSeq 500.

value: Embryonic stem cells

tag: esrrb status

value: Knock-out

tag: culture media

value: Serum


title: genomic DNA from normal colon sample 187

description: normal colon sample

value: GICaRes

tag: gender


title: Esrrb_KO_serum_rep2

description: 4C-seq at Klf4 locus


title: genomic DNA from normal colon sample 180

description: normal colon sample

tag: age


title: Esrrb_KO_serum_rep1

description: 4C-seq at Klf4 locus


title: Esrrb_wt_2i_rep3

description: 4C-seq at Klf4 locus

source_name: Esrrb fl/fl embryonic stem cells

value: Wild-type


title: genomic DNA from normal colon sample 176

description: normal colon sample


title: genomic DNA from normal colon sample 178

description: normal colon sample


title: genomic DNA from normal colon sample 179

description: normal colon sample


title: genomic DNA from normal colon sample 172

description: normal colon sample


title: Esrrb_wt_2i_rep2

description: 4C-seq at Klf4 locus


title: genomic DNA from normal colon sample 174

description: normal colon sample


title: genomic DNA from normal colon sample 177

description: normal colon sample

value: Low


title: genomic DNA from normal colon sample 194

description: normal colon sample


title: genomic DNA from normal colon sample 171

description: normal colon sample

value: ColoCare


title: genomic DNA from normal colon sample 202

description: normal colon sample

value: EPIC


title: Esrrb_wt_2i_rep1

description: 4C-seq at Klf4 locus


title: Esrrb_wt_serum_rep3

description: 4C-seq at Klf4 locus


title: genomic DNA from normal colon sample 169

description: normal colon sample


title: Esrrb_wt_serum_rep2

description: 4C-seq at Klf4 locus


title: genomic DNA from normal colon sample 167

description: normal colon sample

value: High


title: genomic DNA from normal colon sample 164

description: normal colon sample


title: genomic DNA from normal colon sample 173

description: normal colon sample


title: genomic DNA from normal colon sample 168

description: normal colon sample


title: Esrrb_wt_serum_rep1

description: 4C-seq at Klf4 locus


title: genomic DNA from normal colon sample 163

description: normal colon sample


title: genomic DNA from normal colon sample 161

description: normal colon sample


title: genomic DNA from normal colon sample 166

description: normal colon sample


title: genomic DNA from normal colon sample 170

description: normal colon sample


title: genomic DNA from normal colon sample 165

description: normal colon sample


title: genomic DNA from normal colon sample 175

description: normal colon sample


title: genomic DNA from normal colon sample 158

description: normal colon sample


title: genomic DNA from normal colon sample 160

description: normal colon sample


title: genomic DNA from normal colon sample 162

description: normal colon sample


title: genomic DNA from normal colon sample 159

description: normal colon sample


title: genomic DNA from normal colon sample 157

description: normal colon sample


title: genomic DNA from normal colon sample 156

description: normal colon sample


title: genomic DNA from normal colon sample 151

description: normal colon sample


title: KO-oil-str-1

city: Seoul

first: Hyunjung

middle: Jade

last: Lim

address: 120 Neungdong-ro

department: Veterinary Medicine

country: South Korea

institute: Konkuk University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: uterine stromal cell

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: uterine stromal cells from oil-injected OVX mice

tag: strain


title: genomic DNA from normal colon sample 155

description: normal colon sample


title: genomic DNA from normal colon sample 154

description: normal colon sample


title: genomic DNA from normal colon sample 147

description: normal colon sample


title: genomic DNA from normal colon sample 152

description: normal colon sample


title: CON-oil-str-1

tag: genotype


title: genomic DNA from normal colon sample 148

description: normal colon sample


title: KO-E2-str-1

value: uterine stromal cells from E2-injected OVX mice


title: genomic DNA from normal colon sample 136

description: normal colon sample


title: genomic DNA from normal colon sample 153

description: normal colon sample


title: KO-E2-str-2


title: CON-oil-str-2


title: genomic DNA from normal colon sample 143

description: normal colon sample


title: CON-E2-str-2


title: genomic DNA from normal colon sample 149

description: normal colon sample


title: genomic DNA from normal colon sample 138

description: normal colon sample


title: CON-E2-str-1


title: KO-oil-str-2


title: 2.0M_NaCl 3

city: Cuernavaca

first: Maria

middle: del Rayo

last: Sanchez-Carbente

state: Morelos

address: Universidad 1001. Col Chamilpa

department: Center for Research on Biotechnology

country: Mexico

institute: Autonomous University of the State of Morelos

data_processing:
Sequence reads were filtered/trimmed by quality using FASTQC/Trimmomatic (cutoff: Q20) and de novo assembly was performed with Trinity
Mapping of reads to the assembled transcriptome was done by SMALT. Raw counts were quantified using Samtools
Expression levels were reported in transcripts per million (TPM) obtained by the RSEM program using mappings obtained by Bowtie2 software
Supplementary_files_format_and_content: tab-delimited text files include raw count and transcript abundance values expressed in TPM for each Sample.

organism: Aspergillus sydowii

source_name: Mycelium

growth_protocol: The fungus was cultivated on a semi-solid fermentation of autoclaved (121°C for 15 min) wheat straw. Three plugs of fresh mycelium grown on PDA without NaCl were inoculated onto 3.0 g of wheat straw soaked with thirty milliliters of Voegel’s medium (without NaCl [No NaCl], and with 0.5 M NaCl or 2.0 M NaCl) in 25.0 cm Petri dishes and cultured for 7 days at 28 °C without agitation.

extract_protocol:
The mycelium was collected by adding 15 ml of diethyl-pyrocarbonate (DEPC)-treated water to recover the biomass from the Petri dishes and vortexed in sterile conical tubes. Samples were ground with liquid nitrogen and RNA purification was performed by the Tri-Reagent method.
Libraries were constructed with the TruSeq Stranded mRNA HT kit (Illumina)

tag: culture time

value: 7 days

tag: agent


title: genomic DNA from normal colon sample 150

description: normal colon sample


title: 2.0M_NaCl 2


title: genomic DNA from normal colon sample 134

description: normal colon sample

value: F


title: genomic DNA from normal colon sample 145

description: normal colon sample


title: genomic DNA from normal colon sample 142

description: normal colon sample


title: genomic DNA from normal colon sample 144

description: normal colon sample


title: bPAC - High (JPF70)

city: San Francisco

first: Joao Pedro

last: Fons

address: 1700 4th Street, Room BH409C

department: Biochemistry and Biopysics

institute: UCSF

data_processing:
bases called by Illumina software
aligning and gene count using Integrated QuantSeq data analysis pipeline on Bluebee platform
Genome_build: canFam3.1
Supplementary_files_format_and_content: txt; counts per gene

organism: Canis lupus familiaris

source_name: bPAC - High

growth_protocol: Cells were grown in 6 well plates, with DMEM supplemented with 0.5% FCS and 1X GlutaMAX and no phenol red

extract_protocol:
RNA was extracted using Lexogen's SPLIT RNA Extraction Kit
Lexogen's QUANTSEQ 3' FWD

treatment_protocol: Cell were illuminated for 2h with no, low or high dose of light, 16h after plating

value: MDCKI + bPAC

tag: treatment

value: High dose of light


title: bPAC - High (JPF72)


title: genomic DNA from normal colon sample 141

description: normal colon sample

value: M

value: Medium


title: bPAC - Low (JPF64)

source_name: bPAC - Low

value: Low dose of light


title: genomic DNA from normal colon sample 137

description: normal colon sample


title: genomic DNA from normal colon sample 139

description: normal colon sample


title: genomic DNA from normal colon sample 133

description: normal colon sample


title: 0.5M_NaCl 2


title: bPAC - High (JPF69)


title: genomic DNA from normal colon sample 135

description: normal colon sample


title: genomic DNA from normal colon sample 132

description: normal colon sample


title: No_NaCl 3


title: 0.5M_NaCl 1


title: No_NaCl 1


title: No_NaCl 2


title: genomic DNA from normal colon sample 131

description: normal colon sample


title: genomic DNA from normal colon sample 146

description: normal colon sample


title: Parent - Low (JPF58)

source_name: Parent - Low

value: MDCKI


title: Parent - Low (JPF60)


title: Parent - High (JPF65)

source_name: Parent - High


title: genomic DNA from normal colon sample 140

description: normal colon sample


title: Parent - Low (JPF57)


title: bPAC - Control (JPF55)

source_name: bPAC - Control

value: Control


title: bPAC - Control (JPF53)


title: bPAC - Control (JPF54)


title: genomic DNA from normal colon sample 130

description: normal colon sample

value: GICaRes


title: bPAC - Low (JPF63)


title: Parent - Control (JPF51)

source_name: Parent - Control


title: Parent - Control (JPF52)


title: Ex6DEL_GN 2

city: Ottawa

first: David

last: Picketts

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

description: Tn5 fragmented genomic DNA

data_processing:
Trimming with atactk (v0.1.5)
Alignment to mm10 with Bowtie2 (v2.3.4)
Duplicates were removed, Picard tools (v2.17.0)
Peak calling with macs2
RPKM normalization (deepTools2)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files contain merged normalized (RPKM) replicate data

source_name: Cerebellar Granule Neuron

growth_protocol: GNPs were isolated from P4-P6 murine cerebella and plated in serum-free NeurobasalA media (Lee et al., 2009)

extract_protocol:
DNA tagmentation according to Buenrostro et al., 2013 with slight modification to tagmentation step.
Libraries were prepared and amplified according to Buenrostro et al., 2013 using Nextera Tn5 Transposase Kit (Illumina, cat # FC-121-1030).

treatment_protocol: GNPs collected either 2h after plating or allowed to differentiate into GNs in vitro for 72h

tag: tissue

value: Cerebellar Granule Neuron

value: FVB/N

value: loss of Snf2l activity (Ex6DEL)

tag: differentiation

value: differentiated


title: Ex6DEL_GNP 1

description: Tn5 fragmented genomic DNA

source_name: Cerebellar Granule Neuron Progenitor

value: Cerebellar Granule Neuron Progenitor

value: undifferentiated


title: Parent - Control (JPF50)


title: Ex6DEL_GN 1

description: Tn5 fragmented genomic DNA


title: ♂DBA/2J x ♀C57/BL6J blastocyst cells pacbio

source_name: ♂DBA/2J x ♀C57/BL6J blastocyst cells

value: DBA/2J x C57/BL6J

value: blastocyst cells


title: 0.5M_NaCl 3

value: 7 days


title: ♂DBA/2J x ♀C57/BL6J 2cell cells pacbio

source_name: ♂DBA/2J x ♀C57/BL6J 2cell cells

value: 2cell cells


title: WT_GN 2

description: Tn5 fragmented genomic DNA

value: wild type


title: C57/BL6J oocyte cells pacbio

value: oocyte cells


title: ♂DBA/2J x ♀C57/BL6J 1cell cells pacbio

source_name: ♂DBA/2J x ♀C57/BL6J 1cell cells

value: 1cell cells


title: WT_GNP 2

description: Tn5 fragmented genomic DNA


title: WT_GNP 1

description: Tn5 fragmented genomic DNA


title: WT_GN 1

description: Tn5 fragmented genomic DNA


title: DBA/2J  sperm cells pacbio

source_name: DBA/2J  sperm cells

value: sperm cells


title: B6J_H3K4me3_ChIP

city: New Haven

first: Akiko

last: Iwasaki

state: CT

address: 300 Cedar Street

institute: Yale University School of Medicine

data_processing:
RNA-seq of cellular genes:
Btrim to trim adapters and low-quality read
Tophat2 to map reads
DEseq2 to analyze differential gene expression
RNA-seq of ERV or VL30:
Btrim to trim adapters and low-quality read
BWA-mem to map reads
SAMtools processing of unmapped reads
BEDTools to read mapping counts to ERV
DEseq2 to analyze differential gene expression
RNA-seq RepEnrich:
Btrim to trim adapters and low-quality read
Bowtie to map reads
SAMtools processing of uniquely mapped reads
RepEnrich analysis of non-uniquely mapped reads
DEseq2 to analyze differential gene expression
ChIP-seq:
Bowtie2
Picard to remove duplicates
deepTools to count reads and generate bigWig files
Genome_build: mm10
Genome_build: ChIP-seq: Unique ERV and VL30 loci
Supplementary_files_format_and_content: RNA-seq of cellular genes: Excel spreadsheet of Deseq output
Supplementary_files_format_and_content: RNA-seq of ERV or VL30: Excel spreadsheet of Deseq output
Supplementary_files_format_and_content: RNA-seq RepEnrich: Excel spreadsheet of Deseq output
Supplementary_files_format_and_content: ChIP-seq: bigWig files of normalized reads mapped to unique ERV and VL30 loci

source_name: bone marrow-derived macrophage

extract_protocol:
Lysates were clarified from sonicated nuclei from paraformaldehyde-fixed cells and histone-DNA complexes were isolated with antibody.
NEBNext® Ultra II DNA Library Prep Kit for Illumina (E7645) was used with 100ng of total DNA for the construction of sequencing libraries

value: bone marrow-derived macrophage

tag: chip antibody

tag: chip antibody info.


title: Ex6DEL_GNP 2

description: Tn5 fragmented genomic DNA


title: B6J_H3K27Ac_ChIP

extract_protocol:
Lysates were clarified from sonicated nuclei from paraformaldehyde-fixed cells and histone-DNA complexes were isolated with antibody.
NEBNext® Ultra II DNA Library Prep Kit for Illumina (E7645) was used with 5ng of total DNA for the construction of sequencing libraries


title: ♂DBA/2J x ♀C57/BL6J 8cell cells pacbio

source_name: ♂DBA/2J x ♀C57/BL6J 8cell cells

value: 8cell cells


title: B6J_H3K9me3_ChIP


title: aptamer-2

city: Coimbatore

first: Nikhil

last: Maroli

state: TAMIL NADU

address: Bharathiar University

department: Physics

country: India

institute: DRDO BU CLS

description: single stranded DNA aptamers

data_processing:
ssDNA sequence retrieval from sequence scanner software v2.0
ssDNA linear chain generation using Discover studio 2016 version
MD simulation of the linear ssDNA using Gromacs 2018 version and generation of 3D structure
molecular modeling of ssDNA aptamer using MD simulations
Supplementary_files_format_and_content: PDB files contains the three-dimensional structure of the aptamer

organism: Salmonella enterica subsp. enterica serovar Paratyphi A

source_name: Aptamer library

extract_protocol: ssDNA aptamers specific towards S. Paratyphi A was selected by whole cell SELEX strategy from random aptamer library. Generated aptamers were cloned into pGEMT easy vector by TA cloning strategy and positive cloned were sequenced and characterized for its activity.

tag: library

value: Aptamer library


title: aptamer-3

description: single stranded DNA aptamers


title: aptamer-1

description: single stranded DNA aptamers


title: ♂DBA/2J x ♀C57/BL6J 4cell cells pacbio

source_name: ♂DBA/2J x ♀C57/BL6J 4cell cells

value: 4cell cells


title: B6N_input_ChIP


title: A549+Src shRNA

city: Xi'an

first: Yang

last: Zhao

state: Shaanxi

address: No.157, fifth west road

department: Oncology

institute: Second affiliated hospital of Xi'an Jiaotong University

description: LncRNA expression profiling of A549 +c-Src shRNA.

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent 2565CA), gridded, and analyzed using Agilent Feature Extraction software version 10.10.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Quantile normalized

source_name: A549 cell-epithelial

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: The A549 cell lines were purchased from ATCC (Rockville, MD, USA) and cultured in DMEM (Gibco, USA) supplemented with 10% fetal bovine serum (Gibco, USA).

extract_protocol: Total RNA of cells was extracted by TRIzol® (Invitrogen, USA) according to the manufacturer’s instructions.

treatment_protocol: No treatment.

tag: cell line

value: Lung adenocarcinoma cell line

tag: shRNA

value: c-Src

tag: phenotype

value: Epithelial-like


title: B6N_H3K4me3_ChIP

tag: cell type


title: B6N_H3K27Ac_ChIP


title: A549+Casp8 shRNA

description: LncRNA expression profiling of A549 +Caspase-8 shRNA.


title: B6N_H3K9me3_ChIP


title: A549+Control

description: LncRNA expression profiling of A549 +Control shRNA.

source_name: A549 cell-mesenchymal

value: Control

value: Mesenchymal-like


title: NctA-S_0.5mg/mL_Itra_Input_Rep2

city: Manchester

first: Michael

middle: J

last: Bromley

state: Greater Manchester

address: 46 Grafton Street

department: Division of Infection, Immunity, and Respiratory mediciney

institute: The University of Manchester

data_processing:
Raw sequencing reads were quality controlled with Illumina chastity filter and fastqc v0.11.3.
Illumina adapters were trimmed from them using Trimmomatic v0.32.
The resulting reads were aligned to the Aspergillus fumigatus A1163 CADRE genome from Ensemble fungi, version 28 using Bowtie2 v2.2.3.
Peak calling was carried out using a Model-based Analysis for ChIP-Sequencing (MACS2) version 2.1.0.20140616 with a q-value cutoff of 0.01.
Genome_build: Aspergillus fumigatus A1163 CADRE genome from Ensemble fungi, version 28
Supplementary_files_format_and_content: bigWig file were generated using bedGraphToBigWig v305

organism: Aspergillus fumigatus

source_name: Mycelia

growth_protocol: 1x10e6 spores/ml of the S-tagged NctA expressing strain was grown in 50 ml of Vogel’s minimal medium for 18 h at 37 °C with constant shaking at 180 rpm. The mycelia were harvested by filtration, washed twice with distilled water, and were transferred into 50 ml of RPMI 1640 medium containing 2.0 % glucose and 165mM MOPS buffer (pH7.0). The cells were incubated for 4 hours in the absence and the presence (0.5 mg/mL) of itraconazole at 37 °C under shaking.

extract_protocol:
Cross-linked mycelia were ground to a fine powder under liquid nitrogen. Samples were suspended in a ChIP lysis buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Deoxycholate (Sigma D6750), 0.1% SDS, 1 mM PMSF, and fungal proteinase inhibitor cocktail (Sigma)), and then sonicated with a Q125 sonicator (Qsonica, USA). The sheared chromatin was immunoprecipitated with a GFP-polyclonal antibody (A-11122, Thermo Fischer Scientific) on Dynabeads Protein A magnetic beads (Thermo Fischer Scientific). Immunoprecipitated DNA was reverse cross-linked, treated with RNase A (Sigma), and then purified using a MinElute PCR purification kit (QIAGEN).
Libraries were constructed following the manufacture's instractions for Illumina TruSeq ChIP-seq samplepreparation kit.

treatment_protocol: Cross-linking was carried out by the addition of formaldehyde to a final concentration of 1.0 % followed by incubation at 37°C for 20 min. Fixation was stopped by adding glycine to a final concentration of 125 mM and continuing shaking for 10 min at 37 °C. Mycelia were then collected by filtration, washed twice with distilled water and immediately frozen with liquid nitrogen and kept frozen at -80 ˚C until used

tag: condition

value: itraconazole

value: Mycelia


title: NctA-S_0.5mg/mL_Itra_ChIP_Rep2

value: Anti-S tag polyclonal antibody (abcam, ab18588)


title: NctA-S_NoDrug_Input_Rep2

value: control


title: NctA-S_0.5mg/mL_Itra_Input_Rep1


title: Parent - High (JPF67)

value: MDCKI

value: High dose of light


title: NctA-S_0.5mg/mL_Itra_ChIP_Rep1


title: NctA-S_NoDrug_ChIP_Rep2


title: HapC_GFP_Fe_minus_Input_Rep2

data_processing:
Raw sequencing reads were quality controlled with Illumina chastity filter and fastqc v0.11.3.
Illumina adapters were trimmed from them using Trimmomatic v0.32.
The resulting reads were aligned to the Aspergillus fumigatus A1163 CADRE genome from Ensemble fungi, version 28 using Bowtie2 v2.2.3.
Peak calling was carried out using a Model-based Analysis for ChIP-Sequencing (MACS2) v2.1.0.20150420 with a q-value cutoff of 0.01.
Genome_build: Aspergillus fumigatus A1163 CADRE genome from Ensemble fungi, version 28
Supplementary_files_format_and_content: bigWig file were generated using bedGraphToBigWig v305

growth_protocol: 1x10e6 spores/ml of the HapC-GFP expressing strain were grown in 50 ml of Aspergillus minimal medium (AMM) in the presence (and the absence of iron for 24 h at 37 °C with constant shaking at 180 rpm.

treatment_protocol: Cross-linking was carried out by the addition of formaldehyde to a final concentration of 1.0 % followed by incubation at 37°C for 20 min. Fixation was stopped by adding glycine to a final concentration of 125 mM and continuing shaking for 10 min at 37 °C.

value: A1160 pyrG+, {delta}hapC::ble, hapC-gfp, hph


title: HapC_GFP_Fe_plus_Input_Rep2


title: HapC_GFP_Fe_minus_ChIP_Rep2

value: GFP Tag polyclonal antibody (ThermoFischerScientific, A-11122)


title: HapC_GFP_Fe_plus_ChIP_Rep2


title: NctA-S_NoDrug_Input_Rep1


title: HapC_GFP_Fe_plus_ChIP_Rep1


title: HapC_GFP_Fe_plus_Input_Rep1


title: NctA-S_NoDrug_ChIP_Rep1


title: 2.0M_NaCl 1

source_name: Mycelium

value: 7 days


title: HapC_GFP_Fe_minus_Input_Rep1


title: Carotid artery_test-3

city: Guangzhou

first: Yu

last: Zhou

state: Guangdong

address: No 58, Zhongshan 2nd street

department: Division of Vascular Surgery

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

description: Gene expression in carotid artery 14 days after balloon-injury

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
Scanned images were then imported into Agilent Feature Extraction (FE) software for grid alignment and data extraction.
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). Normalized Intensity of each group was shown as averaged normalized intensities of replicate samples(log2 transformed). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (?All Targets Value?) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

organism: Rattus norvegicus

source_name: Carotid artery,14days after injury,replicate 3

label_protocol: The Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) was used according to the manufacturer’s guideline for labelling

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: Adult male Sprague-Dawley rats (weight 250-300 g) were randomized to common carotid artery balloon injury group or uninjured group. The rats were anesthetized by injection of phenobarbital sodium (50 mg/kg) and then a 2F Fogarty catheter was applied to damage the intima of the right common carotid artery. A dissecting microscope was used to monitor the procedure. After 2 weeks, the rats were anesthetized and the common arteries were isolated ad stored at -80°C for microarray,

value: Sprague-Dawley

value: Carotid artery

tag: gender

value: Male

tag: weight


title: Carotid artery_control-3

description: Gene expression in normal carotid artery

source_name: Carotid artery, sham,replicate3

tag: strain


title: HapC_GFP_Fe_minus_ChIP_Rep1

tag: genotype


title: Carotid artery_test-2

source_name: Carotid artery,14days after injury,replicate 2


title: Carotid artery_control-2

source_name: Carotid artery, sham,replicate2


title: SHEE_DMSO_rep2

city: Shantou

first: Caixia

last: Liu

address: Xinling Road, No.22, Shantou

department: Department of Preventive Medicine

institute: Shantou University Medical College

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: gilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

label_protocol: RNA was labeled using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) following the manufacturer's recommendations.    Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNasey Mini Kit(Qiagen p/n 74104) following the manufacturer's recommendations.

value: SHEE

value: immortal esophageal cell line

value: DMSO for  48hrs

tag: passage

value: 30 passages


title: SHEE_CSE_rep2

value: cigarette smoking extract (15µg/ml) for 48hrs


title: Carotid artery_control-1

source_name: Carotid artery, sham,replicate1


title: anp1_TONO_7dai

city: Tsukuba

first: Yoshikazu

last: Shimoda

state: Ibaraki

address: 3-1-1 Kannondai

country: Japan

institute: National Agriculture and Food Research Organization

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Obtained Fastq sequences were subjected to four steps of quality filtering and trimming by FastX-toolkit. Step1: select the reads with more than QV10 accounting for more than 10% (fastq_quality_filter). Step2: trim the sequence less than QV10 and select the reads of more than 30bp (fastq_quality_trimmer). Step3: remove the repetitive sequences (fastx_artifacts_filter). Step4: Remove the adaptor sequences if the read contains more than 5 characters of the adapter sequence from the 3’ end and select the reads of more than 30bp (fastx_clipper).
Selected reads were mapped to Lotus japonicus coding sequence (build 2.5) including 5' UTR and 3' UTR using Bowtie2 (ver. 2.0.2).
Normalization of mapped read counts was performed using DEseq with iDEGES/DESeq (Sun et al., BMC Bioinformatics, 2013).
Genome_build: build 2.5
Supplementary_files_format_and_content: tab-delimited text files include original mapped read count and DESeq normalized count.

organism: Lotus japonicus

source_name: nodule

growth_protocol: Lotus japonicus was planted in vermiculite soil supplemented with nitrogen-free B&D medium and was grown in a growth chamber under 16 h/8 h light/dark cycle at 25°C/23°C.

extract_protocol:
Nodule primordias and developing nodules were excised from roots. Total RNA was isolated using Cetyltrimethylammonium Bromide (CTAB) and LiCl. Total RNA was treated with DNase (Qiagen) and Ribo-Zero kit for plant seed/root and for gram-negative bacteria (Epicentre) to remove genomic and ribosomal DNA. 50 ng of RNA was used for library preparation.
RNA libraries were prepared using Scriptseq Ver2 library preparation kit (Epicentre) by following manufacture's instructions

treatment_protocol: Mesorhizobium loti was inoculated at 7 days after planting into vermiculite.

tag: plant genotype

value: Fix- mutant

tag: inoculation (rhizobial strain)

value: Mesorhizobium loti TONO

tag: time

value: nodule


title: Carotid artery_test-1

source_name: Carotid artery,14days after injury,replicate 1

tag: tissue


title: anp1_MAFF_10dai

value: Mesorhizobium loti MAFF303099


title: SHEE_CSE_rep1

tag: treatment


title: genomic DNA from normal colon sample 129

city: Seattle

first: Ting

last: Wang

address: 1100 Fairview Ave. N.

institute: Fred Hutchinson Cancer Research Center

description: normal colon sample

data_processing: Raw IDAT files of the two methylation arrays were read into R with the minfi package separately, the combineArrays function was utilized to combine the two arrays’ data together. Then the data was preprocessed with background and dye bias correction using the Noob method, following by the Functional normalization. CpG probes that were SNP-associated, cross-reactive, located on sex chromosomes and unreliably detected (>10% of samples with detection P-value > 0.01), with the exception of those epigenetic clock CpGs, were excluded from the analysis

extract_protocol: Genomic DNA samples were extracted from the fresh frozen normal colon mucosa tissue samples using the DNeasy Blood and Tissue Kit (Qiagen). Genomic DNA quantification was performed using the Quant-iT PicoGreen DNA assay kit (Life Technologies). 500 ng of DNA from each sample was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research, Irvine, USA)

tag: source

value: ColoCare

tag: array platform_id

value: EPIC

tag: run date

tag: age

value: M

tag: crc risk

value: High


title: anp1_TONO_10dai


title: anp1_MAFF_7dai


title: WT(MG20)_TONO_10dai

value: wild type


title: WT(MG20)_MAFF_5dai


title: WT(MG20)_TONO_5dai


title: SHEE_DMSO_rep1

tag: cell line

tag: cell type


title: anp1_MAFF_5dai


title: anp1_TONO_5dai


title: WT(MG20)_TONO_7dai


title: WT(MG20)_MAFF_7dai