title: T4pfbA_r: dHL60_T4pfbAKOwithrPfbA_infected_1h

source_name: Neutrophil-like differentiated HL-60 cell, S. pneumoniae TIGR4 pfbA mutant strain with rPfbA-infected, 1 h


title: ATF4 overexpression rep 2

status: Public on Aug 19 2019

type: SRA

city: London

first: Joseph

middle: Matthew

last: Bateman

address: Cutcombe Road

department: Basic & Clinical Neuroscience

country: United Kingdom

institute: King's College London

library_source: transcriptomic

data_processing:
Illumina NextSeq 500 RTA v2 used for base calling.
Adaptors were automatically trimmed from the reads by the NextSeq 500, but a check for residual untrimmed adaptors was performed by FastQC (Galaxy Version 0.52), accessed via the user interface software Galaxy (UseGalaxy.org). RNA reads were then aligned to the dm6 genome using Bowtie2 (Galaxy Version 2.3.4.2) with default settings.
Raw fragment counts were compiled by FeatureCounts (Galaxy Version 1.6.3+galaxy2), accessed via the user interface software Galaxy (UseGalaxy.org), with default settings.
Differential gene expression was assessed via DESeq2 (Galaxy Version 2.11.40.6), accessed via UseGalaxy.org, with default settings.
Genome_build: dm6
Supplementary_files_format_and_content: Excel spreadsheets containing base means, log2(fold change), fold changes, standard errors, Wald statistics, p-values and adjusted p-values for each pair of samples.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Central nervous system

growth_protocol: Larvae were grown on standard fly food at 25 degrees celsius.

extract_protocol:
For each replicate, the complete CNS from 20 wandering third instar larvae were dissected in PBS and then transferred into 100ul of lysis buffer (with β-mercaptoethanol) from the Absolutely RNA Microprep kit (Stratagene) and vortexed for 5 seconds. Total RNA was then prepared using this kit. For each genotype RNA samples were prepared in quadruplicate and stored at -80 degrees celsius.
RNA samples were couriered on dry ice to the Glasgow Polyomics facility (University of Glasgow), where polyA cDNA libraries were constructed using the TruSeq Stranded mRNA Kit (Illumina).

treatment_protocol: One control and three experimental genotypes were used: Control (nsybGal4/+), Experimental group 1: TFAM3M (nsybGal4>UAS-TFAM3M), Experimental group 2: TFAM3M, ATF4 RNAi (nsybGal4>UAS-TFAM3M, UAS-ATF4 RNAi), Experimental group 3: ATF4 overexpression (nsybGal4>UAS-ATF4-HA).

tag: developmental stage

value: Late third instar larvae


title: clone3_CM_rep2

city: Atlanta

first: Greg

last: Gibson

state: Georgia

address: 950 Atlantic Drive

country: USA

institute: Georgia Institute of Technology

description:
Raw_counts_differentiation.csv
Normalized_differentiation.csv

data_processing:
RNA-Seq quality control was initiated with Trim Galore, which was used to trim the 13bp Illumina standard adapter (‘AGATCGGAAGAGC’) by default.
Reads were mapped to hg38 human reference genome by STAR with defalut parameters.
Aligned sequencing reads were counted with intersection-strict mode in HTSeq.
Scale factors of each sample were computed using the trimmed mean of M-value (TMM) algorithm in edgeR.
Raw read counts were normalized by scale factors and then transformed into log2 counts per million reads (CPM). Genes were kept if expressed in at least three samples.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include raw and normalized read counts at the gene level for each sample

organism: Homo sapiens

source_name: HL60/S4 cell line

extract_protocol: Illumina TruSeq Stranded Sample Preparation, Low Sample (LS) Protocol was used for the samples sequenced by Illumina HiSeq 2500. And NEBNext Ultra II Directional 162 RNA Library Prep Kit for Illumina was used for samples sequenced by Illumina NextSeq 550.

tag: differentiation type

value: Parental

tag: clone


title: chicken_low_lung1

city: Chengdu

first: Yao

last: Ma

state: Sichuan

address: Huiming road #211

country: China

institute: Sichuan Agricultural University

data_processing:
Small RNA libraries were constructed using the Illumina TruSeq Small RNA Sample Prep kit. Libraries were assessed using the Agilent 2200 TapeStation and sequenced on the Illumina HiSeq 2500 platforms. Initial bioinformatics analysis (base calling) was performed with CASAVA 1.8 (Illumina) to generate raw reads(in FASTQ form). Next, raw reads were subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and processed sequences were then mapped to corresponding reference genome (i.e.,chicken (Galgal4), pig (Suscrofa 10.2), cattle (UMD3.1), goat (CHIR 1.0), and sheep (Oar v3.1)) for each species with stringent criteria (less than 1 mismatch along the whole sequence) using Bowtie software. Thereafter, mappable reads were submitted to miRDeep2.0 to detect miRNAs for each species with default parameters. Notably, mature miRNA sequence of chicken and all annotated mammalian species in miRbase21 were selected as reference. miRNAs with greater than or equal to 4 reads across > 40% samples were remained for further analysis.
Genome_build: chicken (Galgal4), pig (Suscrofa 10.2), cattle (UMD3.1), goat (CHIR 1.0), and sheep (Oar v3.1); miRbase 21.0
Supplementary_files_format_and_content: Identified miRNAs in each library with reads

molecule: total RNA

organism: Gallus gallus

source_name: lung

extract_protocol:
Three adult females for each population of the five species from distinct altitudes (600 m, 2000 m, and 3000 m) were used (Table 1). Animals were humanely killed to ameliorate suffering. Upon excised from the corpse, a piece of tissue fragments from six organs including heart, liver, spleen, lung, kidney and skeletal muscle(longissimus muscle for pig, cattle, yak and sheep, and pectoral muscle for chicken) were placed immediately frozen in liquid nitrogen, and then stored at −80 °C until use. Of note, the skeletal muscle for pig, cattle, yak sheep were longissimus muscle, and the pectoral muscle for chicken. Total RNA were extracted using a standard TRIzol (Takara, Japan) protocol.
Small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: altitude

value: low

tag: tissue

value: lung

tag: age

tag: group

value: Qingyuan Partridge chicken


title: ATF4 overexpression rep 4


title: BS-Ovary

city: Hyderabad

first: Balasubramanian

last: Senthilkumaran

state: Telangana

address: School of Life Sciences Gachibowli

department: Animal Biology

country: India

institute: University of Hyderabad

data_processing:
All the 76 bp paired end raw reads (Illumina NextSeq 500) were quality checked for low quality bases and adapter sequences (Processing of raw reads). Quality check and processing was done using In-house perl scripts.
All processed reads were assembled into transcripts without any reference (De-novo) for both the samples independently using Trinity software (trinityrnaseq20140413p1)
Genome_build: No reference used, as  de novo transcriptome assembly was performed
Supplementary_files_format_and_content: tab-delimited text files include differentially expressed genes between testis and ovary of common carp

organism: Cyprinus carpio

source_name: Ovary

extract_protocol:
Total RNA was extracted from immature gonad tissue (ovary and testis) samples of juvenile carp individually using TRI-reagent
Library preparation was performed using NEB Next Ultra RNA Library Prep Kit (Cat No.: E7530S) following the manufacturers instructions

value: Juvenile

value: Ovary

tag: days post hatch


title: BS-Testis

source_name: Testis

value: Testis


title: chicken_low_spleen1

source_name: spleen

value: spleen


title: H9_NC_H3K4me3

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

institute: Tongji Hospital, Tongji University

library_source: genomic

data_processing:
Reads of RNA-seq were aligned to human reference genome (hg19) by the spliced read aligner Hisat2(vision 2.1.0) (Kim et al., 2015). The gene abundances were estimated and normalized to fragments per kilobase per million (fpkm) using stringtie (version 2.2.1) (Pertea et al., 2015) with default settings, and read counts of genes were summarized by HTSeq (vision 0.7.2) (Anders et al., 2015).
The ultrafast, memory-efficient read aligner bowtie2 (vision 2.2.6) (Langmead et al., 2009) was used to align the reads of ChIP-seq to human reference genome (hg19). The output of bowtie2 was sorted and index by SAMtools (Li et al., 2009). Peak calling was performed by MACS2 (version 2.1.1.20160309). DeepTools (Ramírez et al., 2014) was used for alignment of reads as input and normalized to RPKM (reads per kilobase and million mapped reads).
Genome_build: hg19

molecule: genomic DNA

growth_protocol: Human pluripotent stem cells (hPSCs) were cultured feeder free on Matrigel (BD Biosciences) in TeSR-E8 medium (Stem Cell Technologies), and their medium was changed daily. The hPSCs were passaged with Versene (Gibco) every 5-7 days. Culture conditions of stable CCDC144NL-AS1-KD and NC hPSCs were the same as that of hPSCs. Rock inhibitor Y27632 (Merck Millipore) was suggested to be added into the culture medium for 1 day at the final concentration of 10 μM during the first few passages of CCDC144NL-AS1-KD hPSCs.

extract_protocol:
For RNA-seq, total RNA of cells was extracted by RNAiso Plus (Takara), according to the manufactures’ instructions. For ChIP-seq, lysates were clarified from sonicated nuclei and histone-DNA complexes isolated with antibody
RNA libraries were prepared for sequencing using standard Illumina protocols. ChIP-seq libraries were prepared for sequencing using TruSeq Nano DNA Sample Prep Kit (Illumina), according to the manufacter's instructions.

treatment_protocol: Single cells of human pluripotent stem cell (hPSCs) were obtained through Accutase (Gibco) digestion, and Y27632 (10 μM) was added to the medium for 1 day after plating cells.Single cells of hPSCs were seeded at 50,000 cells per well on a 24-well plate the day before infection. Cells were infected with shCCDC144NL-AS1 or shNC viruses in TeSR-E8 medium supplemented with 2 μg/ml polybrene (Sigma-Aldrich), and the medium was renewed 6 hours after virus infection. Positively infected cells were isolated by adding 2 μg/ml puromycin (Life Technologies) into the culture medium 48 hours after virus infection. The concentrations and time of antibiotics utilized should be adjusted according to different cell viability.

tag: cell type

value: human embryonic stem cells

tag: cell line

tag: condition

value: negative control

tag: passages

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: MatureCD4SP

city: New York

first: Elham

last: Azizi

state: NY

institute: Memorial Sloan Kettering Cancer Center

data_processing:
single-cell RNA-seq data was processed from raw fastq files to count matrices with SEQC (see https://github.com/ambrosejcarr/seqc.git)
Genome_build: mm10 from ENSEMBL GRCm38
Supplementary_files_format_and_content: Cell x gene unnormalized count matrices in gzipped csv format

organism: Mus musculus

source_name: sorted thymocytes

growth_protocol: Thymus was dissociated by mechanical disruption. CD8 expressing cells were depleted and populations of interest were purified by FACS sorting.

extract_protocol: 10X Genomics protocols (Chromium Single Cell 3’ Reagent Kits v2 Chemistry)

value: mature CD25- Foxp3- CD4SP thymocytes

tag: strain


title: ATF4 overexpression rep 1


title: cattle_high_kidney3

organism: Bos grunniens

source_name: kidney

value: high

value: kidney

value: > 4 year

value: Maiwa yak


title: clone3_M_rep2

value: Monocyte


title: clone3_M_rep1


title: Foxp3plus

value: Foxp3+ CD4SP thymocytes


title: H9_NC_INPUT


title: clone2_CM_rep2

value: Parental


title: H9_CCDC144NL_AS1_KD_H3K27me3

value: CCDC144NL-AS1 KD

value: H3K27me3 (ACTIVE MOTIF, 39155)


title: cattle_high_liver3

source_name: liver

value: liver


title: clone2_CM_rep1


title: chicken_low_lung3

value: low

value: lung

value: Qingyuan Partridge chicken


title: cattle_high_muscle3

source_name: muscle

value: muscle


title: H9_CCDC144NL_AS1_KD_H3K4me3

value: human embryonic stem cells


title: cattle_high_spleen3

value: spleen


title: cattle_high_muscle2


title: CD4plusCD25plus

value: CD25+ Foxp3- thymocytes


title: clone2_M_rep2


title: RNA-seq 3bKI 1

city: Gainesville

first: Rene

last: Opavsky

state: FL

address: 2033 Mowry rd, CGRC r..265

department: Anatomy and cell biology

institute: University of FLORIDA

data_processing:
The input sequences were trimmed using trimmomatic. Quality control was performed before and after trimming using FastQC. The input reads were aligned to the reference genome (mm10) using bsmap. Methylation calling was performed using Methyldackel (v 0.3.0.1). Differentially methylated regions (DMRs) were determined by Metilene. DMRs were determined based on average DMC methylation change of 30 percent or greater, p-values (MWU) < 0.05, with a minimum of three DMCs represented in a maximum distance of 200bp.
For RNA-seq, trimmed sequencing data were first aligned to mm10 reference genome using STAR aligner. RNA-seq data with minimum mapped quality 50 were quantitated using the RNA-seq quantitation pipeline in SeqMonk software. Genome version used was Mus musculus GRCm38 (08/06/2012). DeSeq2 was used to calculate differential expression. For differentially expressed genes, only genes with a fold change ≥ 2 and a p-value < 0.05 were considered to be significant.
Genome_build: mm10

source_name: whole embryo

extract_protocol:
For RRBS, genomic DNA was isolated from two independent Dnmt3b+/+, Dnmt3b-/- and Dnmt3bCI/CI embryos and tumor cell line using phenol/chloroform. For RNA-seq, total RNA was isolated by trizol from three independent  Dnmt3b+/+; Dnmt3b-/- and Dnmt3bCI/CI embryos.
The RRBS libraries were prepared and sequenced on an Illumina HiSeq2500 sequencer. RNA-seq was performed  on NovaSeq 6000 platform using paired-end 150bp runs.

tag: embryo stage

tag: genotype

value: Dnmt3b CI/CI

value: FVB


title: cattle_high_kidney2

value: high

value: kidney

value: > 4 year


title: H9_CCDC144NL_AS1_KD_INPUT2


title: RNA-seq 3bKI 2


title: H9_CCDC144NL_AS1_KD_INPUT1


title: clone2_M_rep1

value: Monocyte


title: RNA-seq 3bKI 3


title: RNA-seq 3bKO 3

value: Dnmt3b -/-


title: cattle_high_spleen2

value: Maiwa yak


title: sarF++ RNAseq S2

city: Lausanne

first: Johann

last: Mignolet

address: Biophore Quartier UNIL-SORGE

department: DMF

country: Switzerland

institute: UNIL

description:
mRNAs
processed data: Table S2.xlsx

data_processing:
Sequenced mRNAs generated several million reads that were mapped on the WT S. salivarius chromosome and processed with both bowties V0.12.9 (http://bowtie-bio.sourceforge.net/bowtie2) and samtools V0.1.18 (http://samtools.sourceforge.net/) algorithms to yield BAM files containing the read coordinates. We imported these files into SeqMonk V0.23.0 (www.bioinformatics.babraham.ac.uk/projects/) to assess the total number of reads for each coding sequence (CDS). The dataset was exported into an excel file for further analyses. First, the dataset was standardized to CDS-mapped reads per million overall reads. Then, we estimated a ratio of CDS-mapped reads in mutants vs WT.
Genome_build: Streptococcus salivarius HSISS4: CP013216.1
Supplementary_files_format_and_content: Table_S1.xlsx, Table_S2.xlsx: Excel files reporting RNAseq were generated by SeqMonk sofware. The sheet is organized in columns as follows: column 1 : gene name; column 2 : genome unit; column 3 : probe start; column 4 : probe end; column 5 : gene function; column 6 : locus tag; column 7 : old locus tag assigned in the previous genome sequencing; column 8 : orientation of the probe in regard to the associated gene; column 9 : absolute value of reads per probe in the WT; column 10 : absolute value of reads per probe in the scuR mutant (deletion in Table S1 or overexpression in Table S2); column 11 : absolute value of reads per probe in the sarF mutant (deletion in Table S1 or overexpression in Table S2); column 12 : Ratio of Normalized abundance of reads per probe in scuR mutant (deletion in Table S1 or overexpression in Table S2) versus WT background; column 13 : Ratio of normalized abundance of reads per probe in sarF mutant (deletion in Table S1 or overexpression in Table S2) versus WT background; column 14 : log10 transformation of column 12; column 15 : log10 transformation of column 13.

organism: Streptococcus salivarius

source_name: sarF++

growth_protocol: Streptococcus salivarius and derivatives were grown at 37°C in chemically defined medium supplemented with glucose (CDMG) without shaking.

extract_protocol:
S. salivarius WT, ∆scuR, ∆sarF, scuR-ST++ or sarF-ST++ strains were pre-cultured overnight in CDMG at 37°C. They were resuspended in 50 ml of fresh pre-warmed CDMG to a final OD600 of 0.05 and grown for approximately 2 h 30 min (OD600 = 0.3) at 37°C. Cells were harvested by centrifugation (10 min; 4,050 × g), the supernatants were discarded and the cell pellets were frozen with liquid nitrogen. Finally, RNA was extracted using the RiboPure bacteria kit (Ambion-Life Technologies) and the protocol provided by the manufacturer, with protocol changes to cell lysis and RNA precipitation. For lysis, cells were resuspended in RNAwiz buffer (Ambion-Life Technologies) supplemented with Zirconia beads and shaken for 40 sec (4 times) in a fastPrep homogenizer device (MP biomedicals). For RNA precipitation, a 1.25-ethanol volume (instead of 0.5) was added to partially purified RNAs. Total RNA was checked for quality on an RNA Nano chip (Agilent Technologies) and concentration was measured using Ribogreen assay (Life Technologies). rRNA depletion was performed on 2 µg total RNA with the Ribo-Zero rRNA removal kit for Gram-positive bacteria (Illumina) according to manufacturer’s instructions.
Total stranded mRNA libraries were prepped with the NEBNext Ultra Directional RNA Library Prep kit for Illumina (New England Biolabs). Library PCR was executed for 15 cycles. Quality of the libraries was evaluated with the use of a High sensitivity DNA chip (Agilent Technologies) and concentrations were determined through qPCR according to Illumina protocol. Both Libraries were equimolar pooled for sequencing on a NextSeq 500 high-throughput run with 76bp single reads. 2.3 pM of the library pool was loaded on the flowcell with a Phix spike-in of 5%.

tag: strain/background

tag: genotype/variation

value: sarF++

tag: medium

value: CDM+glucose


title: scuR++ RNAseq S2

description:
mRNAs
processed data: Table S2.xlsx

source_name: scuR++

value: scuR++


title: cattle_high_liver2

value: liver


title: cattle_high_heart1

source_name: heart

value: heart


title: RNA-seq 3bKO 1


title: RNA-seq WT 3

value: Dnmt3b +/+


title: clone3_CM_rep1

tag: differentiation type

value: Parental

tag: clone


title: cattle_high_kidney1

tag: altitude

tag: tissue


title: RNA-seq 3bKO 2


title: WT RNAseq S2

description:
mRNAs
processed data: Table S2.xlsx

source_name: WT

value: WT


title: Old NPMSCs rep2

type: RNA

city: Guangzhou

first: Cheng

last: Shi

address: Baiyun Road

institute: Guangdong General hospital

description: Old rats are difined as 25 months

hyb_protocol: 1. Prepare Hybridization Master Mix. 2. Prepare Hybridization Cocktail 3. Inject and hybridize array

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Rattus norvegicus

source_name: Old Sprague Dawley rat

label_protocol: The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of singlestranded cDNA is required for fragmentation and labeling(Whole Transcript (WT) Expression Arrays UserGuide, 2015, Affymetrix).

growth_protocol: NPMSCs was seperated from nucleus pulposus tissue,and cultured with standard MSC culture medium containing DMEM-LG, 10% FBS, and 1% penicillin-streptomycin in a humidified incubator at 37 °C and 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No special treatments

value: nucleus pulposus


title: cattle_high_spleen1

value: spleen

tag: age

tag: group


title: DsarF RNAseq S1

description:
mRNAs
processed data: Table S1.xlsx

source_name: DsarF

value: {delta}sarF


title: DscuR RNAseq S1

description:
mRNAs
processed data: Table S1.xlsx

source_name: DscuR

value: {delta}scuR


title: RNA-seq WT 1

value: FVB


title: WT RNAseq S1

description:
mRNAs
processed data: Table S1.xlsx


title: cattle_high_liver1

value: high

value: > 4 year


title: Old NPMSCs rep3

description: Old rats are difined as 26 months


title: MCF-7 cells

type: genomic

city: Lebanon

first: Todd

last: Miller

state: NH

address: DHMC One Medical Center Dr, HB-7936

institute: Geisel School of Medicine at Dartmouth

description: Parental cell line

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
Data were aligned to the hg19 reference genome.
CN5

source_name: Cells

label_protocol: Labeling, hybridization, and scanning were performed as per Affymetrix instructions.

growth_protocol: MCF-7 cells were maintained in DMEM + 10% FBS. MCF-7/FR cells were maintained in medium containing 1 uM fulvestrant

extract_protocol: DNA was extracted using Qiagen Blood and Tissue kit.


title: Old NPMSCs rep1

description: Old rats are difined as 24 months


title: Young NPMSCs rep3

description: Young rats are defined as 5months

source_name: Young Sprague Dawley rat


title: PVD_L_C_C_30h_3

status: Public on Aug 18 2019

city: Richland

first: Ryan

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

description: Gene Expression after 30 hours U937 cells Mock infected Antibody:None

hyb_protocol: Manufacturer's protocol for Whole Human Genome Oligo Microarray (4 x 44K, Agilent Technologies)

scan_protocol: Agilent Scanner G2505C

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026652_D_F_20120130)

source_name: RNA 30 hours U937 cells Mock infected Antibody:None

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer

growth_protocol: U937 and U937+DC-SIGN cells were maintained in RPMI-1640 (Gibco) at 37˚C. Growth media were supplemented with 5% fetal bovine serum (HyClone, Logan, UT), 0.1 mM nonessential amino acids (Gibco), 100 U/ml penicillin and 100 mg/ml streptomycin (Gibco). U937 and U937+DC-SIGN media was supplemented with 2 mM GlutaMAX (Gibco), 10mM HEPES (Cellgro, Manassas, VA). U937+DC-SIGN media included 2-mercaptoethanol (Sigma, St Louis, MO). All infection media contained 2% fetal bovine serum. Cells were incubated in the presence of 5% CO2

extract_protocol: Samples were sent to Arraystar (Rockville, MD) for RNA extraction using phenol chloroform (TRIzol).  RNA was quantified on a Nanodrop ND-1000 and RNA integrity was confirmed via gel electrophoresis

treatment_protocol: 1x106 U937 or U937+DC-SIGN cells were added and the infection was allowed to proceed for 2 hours at 37°C. The 2 hour time point was collected, and the rest of the cells were centrifuged for 2 minutes at 450XG and resuspended in fresh infection media. The collection timepoints were 2, 8, 16, and 24 hours post infection.  Cells were initially grown and then placed into separate wells for infection assays, with RNA and protein being collected from cells in different wells.

tag: time point

value: 30 hours

tag: cell type

tag: infection

value: Mock

tag: antibody


title: PVD_L_D1_Ab_30h_4

description: Gene Expression after 30 hours U937 cells DENV-1 infected Antibody:4G2

source_name: RNA 30 hours U937 cells DENV-1 infected Antibody:4G2


title: PVD_L_C_C_30h_4


title: Young NPMSCs rep2

description: Young rats are defined as 4months


title: PVD_L_C_DCS_30h_1

description: Gene Expression after 30 hours U937+DC-SIGN cells Mock infected Antibody:None

source_name: RNA 30 hours U937+DC-SIGN cells Mock infected Antibody:None


title: PVD_L_C_DCS_30h_4


title: PVD_L_C_C_30h_1


title: PVD_L_C_DCS_30h_3


title: Young NPMSCs rep1

description: Young rats are defined as 3months


title: PVD_L_C_DCS_30h_2


title: PVD_L_D1_DCS_30h_1

description: Gene Expression after 30 hours U937+DC-SIGN cells DENV-1 infected Antibody:None

source_name: RNA 30 hours U937+DC-SIGN cells DENV-1 infected Antibody:None


title: PVD_L_D1_Ab_30h_5


title: PVD_L_D1_DCS_30h_4


title: PVD_L_D1_Ab_30h_3


title: PVD_L_D1_Ab_30h_2


title: PVD_L_C_C_24h_2

description: Gene Expression after 24 hours U937 cells Mock infected Antibody:None

source_name: RNA 24 hours U937 cells Mock infected Antibody:None

value: 24 hours


title: PVD_L_D1_Ab_30h_1


title: PVD_L_C_C_24h_3


title: PVD_L_C_C_24h_5


title: PVD_L_D1_DCS_30h_2


title: PVD_L_C_DCS_30h_6


title: PVD_L_C_C_24h_4


title: PVD_L_C_C_30h_2


title: MCF-7/FR cells

description: Fulvestrant-resistant cell line

tag: cell line


title: PVD_L_C_C_30h_5


title: PVD_L_D1_Ab_24h_4

description: Gene Expression after 24 hours U937 cells DENV-1 infected Antibody:4G2

source_name: RNA 24 hours U937 cells DENV-1 infected Antibody:4G2


title: PVD_L_D1_Ab_24h_5


title: H9_NC_H3K27me3

value: human embryonic stem cells

tag: condition

value: negative control

tag: passages

tag: chip antibody

value: H3K27me3 (ACTIVE MOTIF, 39155)


title: PVD_L_C_C_18h_3

description: Gene Expression after 18 hours U937 cells Mock infected Antibody:None

source_name: RNA 18 hours U937 cells Mock infected Antibody:None

value: 18 hours


title: PVD_L_D1_DCS_24h_5

description: Gene Expression after 24 hours U937+DC-SIGN cells DENV-1 infected Antibody:None

source_name: RNA 24 hours U937+DC-SIGN cells DENV-1 infected Antibody:None


title: PVD_L_C_C_18h_2


title: PVD_L_C_C_18h_4


title: PVD_L_C_C_18h_1


title: PVD_L_D1_Ab_24h_1


title: PVD_L_C_DCS_24h_4

description: Gene Expression after 24 hours U937+DC-SIGN cells Mock infected Antibody:None

source_name: RNA 24 hours U937+DC-SIGN cells Mock infected Antibody:None


title: PVD_L_C_DCS_24h_5


title: PVD_L_D1_Ab_18h_2

description: Gene Expression after 18 hours U937 cells DENV-1 infected Antibody:4G2

source_name: RNA 18 hours U937 cells DENV-1 infected Antibody:4G2


title: PVD_L_D1_DCS_24h_1


title: PVD_L_C_DCS_24h_2


title: PVD_L_C_DCS_24h_3


title: PVD_L_C_DCS_24h_1


title: PVD_L_C_DCS_18h_4

description: Gene Expression after 18 hours U937+DC-SIGN cells Mock infected Antibody:None

source_name: RNA 18 hours U937+DC-SIGN cells Mock infected Antibody:None


title: PVD_L_D1_DCS_24h_4


title: PVD_L_D1_Ab_18h_3


title: PVD_L_C_C_18h_5


title: PVD_L_C_DCS_18h_5


title: PVD_L_D1_DCS_24h_3


title: PVD_L_D1_Ab_18h_1


title: PVD_L_D1_Ab_18h_5


title: PVD_L_D1_DCS_18h_3

description: Gene Expression after 18 hours U937+DC-SIGN cells DENV-1 infected Antibody:None

source_name: RNA 18 hours U937+DC-SIGN cells DENV-1 infected Antibody:None


title: PVD_L_C_DCS_18h_2


title: PVD_L_C_DCS_18h_1


title: RNA-seq WT 2

source_name: whole embryo

tag: embryo stage

tag: genotype

value: Dnmt3b +/+

tag: strain


title: PVD_L_C_C_10h_3

description: Gene Expression after 10 hours U937 cells Mock infected Antibody:None

source_name: RNA 10 hours U937 cells Mock infected Antibody:None

value: 10 hours


title: PVD_L_C_C_10h_2


title: PVD_L_D1_Ab_10h_2

description: Gene Expression after 10 hours U937 cells DENV-1 infected Antibody:4G2

source_name: RNA 10 hours U937 cells DENV-1 infected Antibody:4G2


title: PVD_L_C_C_10h_5


title: PVD_L_D1_DCS_18h_5


title: PVD_L_D1_DCS_18h_2


title: PVD_L_D1_DCS_18h_1


title: PVD_L_D1_DCS_18h_4


title: PVD_L_C_C_10h_1


title: PVD_L_D1_Ab_10h_1


title: PVD_L_D1_Ab_10h_3


title: PVD_L_D1_Ab_10h_4


title: PVD_L_D1_Ab_10h_5


title: PVD_L_C_DCS_10h_1

description: Gene Expression after 10 hours U937+DC-SIGN cells Mock infected Antibody:None

source_name: RNA 10 hours U937+DC-SIGN cells Mock infected Antibody:None


title: PVD_L_C_DCS_10h_5


title: PVD_L_C_DCS_10h_4


title: PVD_L_C_DCS_10h_3


title: PVD_L_C_C_10h_4


title: PVD_L_D1_DCS_10h_4

description: Gene Expression after 10 hours U937+DC-SIGN cells DENV-1 infected Antibody:None

source_name: RNA 10 hours U937+DC-SIGN cells DENV-1 infected Antibody:None


title: PVD_L_D1_DCS_10h_2


title: PVD_L_D1_DCS_10h_1


title: PVD_L_C_C_6h_5

description: Gene Expression after 6 hours U937 cells Mock infected Antibody:None

source_name: RNA 6 hours U937 cells Mock infected Antibody:None

value: 6 hours


title: PVD_L_C_C_6h_4


title: PVD_L_C_DCS_10h_2


title: PVD_L_C_C_6h_3


title: PVD_L_C_C_6h_2


title: PVD_L_D1_DCS_10h_5


title: PVD_L_C_C_6h_1


title: PVD_L_D1_DCS_6h_3

description: Gene Expression after 6 hours U937+DC-SIGN cells DENV-1 infected Antibody:None

source_name: RNA 6 hours U937+DC-SIGN cells DENV-1 infected Antibody:None


title: PVD_L_C_DCS_6h_5

description: Gene Expression after 6 hours U937+DC-SIGN cells Mock infected Antibody:None

source_name: RNA 6 hours U937+DC-SIGN cells Mock infected Antibody:None


title: PVD_L_D1_Ab_6h_4

description: Gene Expression after 6 hours U937 cells DENV-1 infected Antibody:4G2

source_name: RNA 6 hours U937 cells DENV-1 infected Antibody:4G2


title: PVD_L_D1_Ab_6h_3


title: PVD_L_C_DCS_6h_2


title: PVD_L_D1_Ab_6h_2


title: PVD_L_D1_DCS_6h_4


title: PVD_L_D1_Ab_6h_1


title: PVD_L_D1_DCS_6h_2


title: PVD_L_C_C_2h_3

description: Gene Expression after 2 hours U937 cells Mock infected Antibody:None

source_name: RNA 2 hours U937 cells Mock infected Antibody:None

value: 2 hours


title: PVD_L_D1_DCS_6h_5


title: PVD_L_D1_Ab_6h_5


title: PVD_L_C_C_2h_4


title: PVD_L_C_C_2h_2


title: PVD_L_C_DCS_2h_3

description: Gene Expression after 2 hours U937+DC-SIGN cells Mock infected Antibody:None

source_name: RNA 2 hours U937+DC-SIGN cells Mock infected Antibody:None


title: PVD_L_C_DCS_2h_5


title: PVD_L_D1_Ab_2h_3

description: Gene Expression after 2 hours U937 cells DENV-1 infected Antibody:4G2

source_name: RNA 2 hours U937 cells DENV-1 infected Antibody:4G2


title: PVD_L_D1_DCS_6h_1


title: PVD_L_C_DCS_6h_1


title: PVD_L_PVD_L_C_C_2h_1


title: PVD_L_D1_Ab_2h_4


title: PVD_L_C_DCS_6h_3


title: PVD_L_C_DCS_6h_4


title: PVD_L_D1_Ab_2h_1


title: PVD_L_C_DCS_2h_4


title: PVD_L_D1_Ab_2h_2


title: PVD_L_D1_Ab_2h_5


title: PVD_L_C_DCS_2h_1


title: PVD_L_C_C_2h_5


title: PVD_L_C_DCS_2h_2


title: PVD_L_D1_DCS_2h_3

description: Gene Expression after 2 hours U937+DC-SIGN cells DENV-1 infected Antibody:None

source_name: RNA 2 hours U937+DC-SIGN cells DENV-1 infected Antibody:None


title: PVD_L_D1_DCS_2h_1


title: PVD_C_C_C_1_24Hr_RNA

description: Gene Expression after 24 hours U937 cells Mock infected Antibody:None

source_name: RNA 24 hours U937 cells Mock infected Antibody:None


title: PVD_C_C_C_4_24Hr_RNA


title: PVD_L_D1_DCS_2h_4


title: PVD_L_D1_DCS_2h_2


title: PVD_C_C_C_5_16Hr_RNA

description: Gene Expression after 16 hours U937 cells Mock infected Antibody:None

source_name: RNA 16 hours U937 cells Mock infected Antibody:None

value: 16 hours


title: PVD_C_C_C_3_24Hr_RNA


title: PVD_C_C_C_2_24Hr_RNA


title: PVD_C_C_C_4_16Hr_RNA


title: PVD_C_C_C_4_8Hr_RNA

description: Gene Expression after 8 hours U937 cells Mock infected Antibody:None

source_name: RNA 8 hours U937 cells Mock infected Antibody:None

value: 8 hours


title: PVD_C_C_C_3_2Hr_RNA


title: PVD_C_C_C_3_16Hr_RNA


title: PVD_L_D1_DCS_2h_5


title: PVD_C_D4_AbC_3_24Hr_RNA

description: Gene Expression after 24 hours U937 cells DENV-4 infected Antibody:3E8

source_name: RNA 24 hours U937 cells DENV-4 infected Antibody:3E8


title: PVD_C_D4_AbC_5_24Hr_RNA


title: PVD_C_C_C_5_24Hr_RNA


title: PVD_C_C_C_5_8Hr_RNA


title: PVD_C_C_C_2_8Hr_RNA


title: PVD_C_C_C_1_16Hr_RNA


title: PVD_C_C_C_3_8Hr_RNA


title: PVD_C_C_C_1_8Hr_RNA


title: PVD_C_C_C_5_2Hr_RNA


title: PVD_C_C_C_4_2Hr_RNA


title: PVD_C_C_C_1_2Hr_RNA


title: PVD_C_C_C_2_2Hr_RNA


title: PVD_C_D4_AbC_2_24Hr_RNA


title: PVD_C_D4_AbC_4_24Hr_RNA


title: PVD_C_D4_AbC_1_24Hr_RNA


title: C646-rep3-H3K27ac

city: Wuhan City

first: Qinglan

last: Li

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

data_processing:
All ChIP-seq raw fastq data was cleaned by removing adaptor sequence.
Cleaned reads were aligned to mouse reference genome (mm10) using BWA (v 0.7.15)
Peaks calling was finished by MACS2 (v 2.1.1) with the parameters --nomodel --keep-dup all -p 1E-10 --broad --broad-cutoff 1E-10 --extsize 147.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using MACS2 (v 2.1.1); Scores represent the ratio of ChIP RPM / Input RPM.

source_name: Mammary tumor tissue

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND604).

value: MMTV-PyVT

value: Mammary tumor tissue

tag: treatment

value: 1mg/kg C646 injection


title: C646-rep3-Input


title: C646-rep2-Input


title: PVD_C_D4_AbC_2_16Hr_RNA

description: Gene Expression after 16 hours U937 cells DENV-4 infected Antibody:3E8

source_name: RNA 16 hours U937 cells DENV-4 infected Antibody:3E8


title: dorsal pallium at E16.5

city: Kyoto

first: Tadashi

last: Sunohara

address: 53 Kawahara-cho, Shogoin, Sakyo-ku,

department: Dept. of clinical application

country: Japan

institute: Center for iPS cell research and application

description:
miRNA expression data from dorsal pallium at E16.5.
mmu_E16 dp_us

hyb_protocol: Following fragmentation, 4 ug of cRNA were hybridized for 17 hr at 48C on GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrics GeneChip Scanner 3000.

data_processing: affymetrix-algorithm-name = rma : dabg

source_name: dorsal pallium at E16.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng/8uL total RNA (Expression Analysis Technical Manual, miRNA 4.0 ARRAY & FLASHTAGTM BUNDLES, Affymetrix).

growth_protocol: Bcl11b-IRES-EGFP knock-in mice were established by Red/ET BAC recombination technology. F2 mice embryo were confirmed the coexpression of Bcl11b and EGFP in microscope.

treatment_protocol: At E14.5 and E16.5, embryo were dissected gently in cold water to collect dorsal pallium under microscope. After enzymatically separation to single cell, cells were separated to two population based on GFP emission by cell sorter(AriaIII).

value: dorsal pallium


title: PVD_C_D4_AbC_1_16Hr_RNA


title: CFuPN at E16.5

description:
miRNA expression data from Corticofugal projection neuron at E16.5.
mmu_E16 dp_Ctip2+

source_name: corticofugal projection neurons at E16.5

value: corticofugal projection neuron (CFuPN) from dorsal pallium


title: PVD_C_D4_AbC_3_16Hr_RNA


title: dorsal pallium at E14.5

description:
miRNA expression data from dorsal pallium at E14.5.
mmu_E14 dp_us

source_name: dorsal pallium at E14.5


title: PVD_C_D4_AbC_1_8Hr_RNA

description: Gene Expression after 8 hours U937 cells DENV-4 infected Antibody:3E8

source_name: RNA 8 hours U937 cells DENV-4 infected Antibody:3E8


title: dorsal pallium without CFuPN at E14.5 ofdp

description:
miRNA expression data from dorsal pallium without corticofugal projection neuron at E14.5.
mmu_E14 dp_Ctip2-

source_name: dorsal pallium without corticofugal projection neurons at E14.5

value: dorsal pallium without corticofugal projection neuron (CFuPN)


title: CFuPN at E14.5

description:
miRNA expression data from Corticofugal projection neuron at E14.5.
mmu_E14 dp_Ctip2+

source_name: corticofugal projection neurons at E14.5


title: dorsal pallium without CFuPN at E16.5 ofdp

description:
miRNA expression data from dorsal pallium without corticofugal projection neuron at E16.5.
mmu_E16 dp_Ctip2-

source_name: dorsal pallium without corticofugal projection neurons at E16.5


title: PVD_C_D4_AbC_2_8Hr_RNA


title: PVD_C_D4_AbC_4_16Hr_RNA


title: PVD_C_D4_AbC_5_2Hr_RNA

description: Gene Expression after 2 hours U937 cells DENV-4 infected Antibody:3E8

source_name: RNA 2 hours U937 cells DENV-4 infected Antibody:3E8


title: PVD_C_D4_Ab_1_24Hr_RNA

description: Gene Expression after 24 hours U937  cells DENV-4 infected Antibody:4G2

source_name: RNA 24 hours U937  cells DENV-4 infected Antibody:4G2

value: 24 hours


title: PVD_C_D4_AbC_3_2Hr_RNA


title: PVD_C_D4_AbC_4_8Hr_RNA


title: PVD_C_D4_Ab_5_16Hr_RNA

description: Gene Expression after 16 hours U937  cells DENV-4 infected Antibody:4G2

source_name: RNA 16 hours U937  cells DENV-4 infected Antibody:4G2


title: PVD_C_D4_Ab_4_24Hr_RNA


title: PVD_C_D4_AbC_5_8Hr_RNA


title: PVD_C_D4_Ab_5_24Hr_RNA


title: PVD_C_D4_AbC_3_8Hr_RNA


title: PVD_C_D4_AbC_5_16Hr_RNA


title: PVD_C_D4_AbC_1_2Hr_RNA


title: PVD_C_D4_Ab_2_24Hr_RNA


title: PVD_C_D4_Ab_4_16Hr_RNA


title: PVD_C_D4_AbC_2_2Hr_RNA


title: C646-rep2-H3K27ac


title: C646-rep1-Input


title: C646-rep1-H3K27ac


title: PVD_C_C_C_2_16Hr_RNA

value: Mock


title: DMSO-rep3-Input

value: 1mg/kg DMSO injection


title: DMSO-rep2-Input


title: DMSO-rep3-H3K27ac


title: DMSO-rep2-H3K27ac


title: DMSO-rep1-Input


title: DMSO-rep1-H3K27ac


title: Tumor-rep3-Input-2

description: Input for Tumor-rep3 H4K8ac

value: No treatment


title: Tumor-rep3-Input-1

description: Input for Tumor-rep3 H3K4me3, H3K27ac and H3K27me3


title: Tumor-rep3-H4K8ac


title: Tumor-rep3-H3K4me3


title: PVD_C_D4_Ab_2_16Hr_RNA


title: PVD_C_D4_Ab_3_16Hr_RNA


title: Tumor-rep3-H3K27me3


title: Tumor-rep3-H3K27ac


title: Tumor-rep2-Input-2

description: Input for Tumor-rep2 H4K8ac


title: PVD_C_D4_Ab_4_8Hr_RNA

description: Gene Expression after 8 hours U937  cells DENV-4 infected Antibody:4G2

source_name: RNA 8 hours U937  cells DENV-4 infected Antibody:4G2


title: PVD_C_D4_Ab_1_16Hr_RNA


title: PVD_C_D4_Ab_1_8Hr_RNA


title: Tumor-rep2-Input-1

description: Input for Tumor-rep2 H3K4me3, H3K27ac and H3K27me3


title: PVD_C_D4_Ab_3_8Hr_RNA


title: PVD_C_C_DCS_4_24Hr_RNA

description: Gene Expression after 24 hours U937+DC-SIGN cells Mock infected Antibody:None

source_name: RNA 24 hours U937+DC-SIGN cells Mock infected Antibody:None


title: Tumor-rep2-H48ac


title: PVD_C_D4_Ab_2_8Hr_RNA


title: PVD_C_D4_Ab_4_2Hr_RNA

description: Gene Expression after 2 hours U937  cells DENV-4 infected Antibody:4G2

source_name: RNA 2 hours U937  cells DENV-4 infected Antibody:4G2


title: PVD_C_D4_Ab_5_8Hr_RNA


title: Tumor-rep2-H3K4me3


title: PVD_C_C_DCS_5_24Hr_RNA


title: PVD_C_D4_Ab_5_2Hr_RNA


title: Tumor-rep2-H3K27me3


title: Tumor-rep2-H3K27ac


title: Tumor-rep1-Input-3

description: Input for Tumor-rep1 H4K8ac


title: PVD_C_D4_Ab_1_2Hr_RNA


title: PVD_C_D4_Ab_3_2Hr_RNA


title: Tumor-rep1-Input-1

description: Input for Tumor-rep1 H3K4me3 and H3K27ac


title: Tumor-rep1-H48ac


title: Tumor-rep1-H3K4me3


title: PVD_C_C_DCS_3_24Hr_RNA


title: PVD_C_C_DCS_1_24Hr_RNA


title: PVD_C_C_DCS_2_16Hr_RNA

description: Gene Expression after 16 hours U937+DC-SIGN cells Mock infected Antibody:None

source_name: RNA 16 hours U937+DC-SIGN cells Mock infected Antibody:None


title: PVD_C_C_DCS_5_16Hr_RNA


title: PVD_C_C_DCS_5_8Hr_RNA

description: Gene Expression after 8 hours U937+DC-SIGN cells Mock infected Antibody:None

source_name: RNA 8 hours U937+DC-SIGN cells Mock infected Antibody:None


title: Tumor-rep1-Input-2

description: Input for Tumor-rep1 H3K27me3

source_name: Mammary tumor tissue


title: PVD_C_C_DCS_4_8Hr_RNA


title: PVD_C_C_DCS_3_16Hr_RNA


title: Tumor-rep1-H3K27ac


title: PVD_C_C_DCS_4_16Hr_RNA


title: PVD_C_C_DCS_2_24Hr_RNA


title: Normal-rep3-Input

source_name: Normal mammary gland tissue

value: FVB wild type

value: Normal mammary gland tissue


title: PVD_C_C_DCS_1_16Hr_RNA


title: Normal-rep3-H3K27ac


title: Sfmbt2 genetrap rep2

city: Toronto

first: Susannah

last: Varmuza

state: Ontario

address: 25 Harbord Street

country: Canada

institute: University of Toronto

data_processing:
cDNA library was subject to paired-end sequencing on a Illumina HiSeq 2500 platform to generate paired-end reads of 126 bp in length.
Paired end reads were mapped to the mm10 genome using Tophat2.
Aligned reads were then analysed using Cufflinks and Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: FPKM tracking is .txt format.  FPKM tracking files and .GTF are generated from Cufflinks.

source_name: Extraembryonic tissue

extract_protocol:
Extraembryonic tissues were dissected from e7.5 embryos.  Embryonic portions were used for genotyping and RNA was extracted from extraembryonic tissues of homozygous wild-type and mutant embryos using Trizol.
RNA libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Preparation protocol with rRNA depletion performed using Ribo-Zero Gold rRNA removal kit.

value: Sfmbt2 gt on CD1 genetic background

value: extraembryonic

value: Sfmbt2 gt/gt


title: Tumor-rep1-H3K27me3


title: PVD_C_C_DCS_1_8Hr_RNA


title: Normal-rep2-Input


title: Normal-rep3-H3K4me3


title: Normal-rep3-H4K8ac


title: Sfmbt2 genetrap rep1


title: Normal-rep3-H3K27me3


title: Normal-rep2-H3K4me3


title: Normal-rep2-H4K8ac


title: Normal-rep2-H3K27ac


title: PVD_C_C_DCS_3_8Hr_RNA


title: WT rep2

value: wild type


title: PVD_C_C_DCS_4_2Hr_RNA

description: Gene Expression after 2 hours U937+DC-SIGN cells Mock infected Antibody:None

source_name: RNA 2 hours U937+DC-SIGN cells Mock infected Antibody:None

value: 2 hours


title: PVD_C_C_DCS_5_2Hr_RNA


title: PVD_C_D4_DCS_5_24Hr_RNA

description: Gene Expression after 24 hours U937+DC-SIGN cells DENV-4 infected Antibody:None

source_name: RNA 24 hours U937+DC-SIGN cells DENV-4 infected Antibody:None


title: PVD_C_C_DCS_3_2Hr_RNA


title: PVD_C_C_DCS_2_2Hr_RNA


title: WT rep1

description: Submitter indicates R1 fastq file is not available.


title: Normal-rep1-Input


title: Normal-rep1-H3K4me3


title: Normal-rep1-H4K8ac


title: Normal-rep2-H3K27me3


title: Normal-rep1-H3K27me3


title: PVD_C_D4_DCS_3_24Hr_RNA


title: PVD_C_D4_DCS_4_24Hr_RNA


title: Normal-rep1-H3K27ac


title: hMYC-13

city: Oklahoma City

first: John

middle: Kimble

last: Frazer

state: Oklahoma

address: 941 Stanton L Young Blvd

department: Pediatrics

institute: University of Oklahoma Health Sciences Center

data_processing:
Illumina bcl2fastq2 was used for basecalling.
RNA-Seq data were processed as previously described in Garcia et al., 2018 (PMID 29749398).  Briefly, reads were aligned using STAR (Dobin et al., 2013) to GRCz10.  Picard was used to filter out potential PCR duplicates.  Counts were assigned to each gene using featureCounts (Liao et al., 2014).
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text file includes count matrix for all samples

organism: Danio rerio

source_name: GFP+_FACS purified ALL from total body

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit (Cat#FC-122-1001) was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: rag2:hMYC;lck:eGFP double transgenic line


title: hMYC-14


title: MN_FLAG-SFMBT2_2

description:
Micrococcal nuclease-digested FLAG-SFMBT2 ChIP-seq
bnm_bowtie2-W200-G1000-FDR1E-2-islandfiltered-normalized.bw
bnm_bowtie2-W200-normalized.bw

data_processing:
ChIP and associated input DNA libraries were subject to paired-end sequencing on a Illumina HiSeq 2500 platform to generate paired-end reads of 100 bp or 126 bp in length.
Raw sequences were assessed by FastQC for quality checking, identification of adapter sequences, and identification of non-adapter overrepresented sequences.  Adaptor sequences were trimmed using TrimGalore and CutAdapt.  Quality of reads trimmed reads were then reassessed to ensure removal of adaptor sequences.
Adapter-trimmed sequences were then aligned to the mm10 genome via Bowtie2 with the quality-check filter implemented.
Peaks were called using SICER v1.1 using a FDR of 0.01, a window of 200 bp and a gap of 1000 bp.
Genome_build: mm10
Supplementary_files_format_and_content: .bw

source_name: Trophoblast stem cell

growth_protocol: Trophoblast stem cells (TSCs) were grown in media comprised of 30% standard media (RPMI 1640, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 100 μM β-mercaptoethanol, 2 mM L-glutamine, 20% FBS and 1% penicillin-streptomycin) and 70% MEF-conditioned media, supplemented with 25 ng/ml FGF4, and 1 μg/ml heparin.  Cells were grown at 37C with 5% CO2.

extract_protocol:
[library prep] NEB Ultra DNA
Cell lysis and genomic fragmentation methods varied according to the intended fragmentation method -- sonication or micrococcal nuclease digestion.  Briefly, cells were sonicated to an average size of 75 bp to 400 bp using a total processing time of 5 mins with an amplitude of 40, pulse duration of 10 s, and cooling duration of 30 s.  Samples fragmented by micrococcal nuclease digestion were on average 175 bp in size.  DNA crosslinked with endogenous SFMBT2 was immunoprecipitated using magnetic Protein G beads coated with anti-SFMBT2 antibody produced in house.  FLAG-SFMBT2 complexes were immunoprecipitated with magnetic FLAG-conjugated beads.  Immunoprecipitation was performed at 4C for 2 hrs and subsequently washed 5X with cold RIPA buffer and once with cold TE supplemented with 50 mM NaCl.  Complexes were decrosslinked in 1% SDS and 0.1 M NaHCO3 overnight at 65C.  DNA was subsequently extracted through phenol-chloroform extraction and purified by ethanol-based precipitation.  DNA was reconstituted in water and quantified using PicoGreen.
Sonicated endogenous SFMBT2 ChIP and input DNA libraries were generated using the Illumina TruSeq protocol.  Sonicated FLAG-SFMBT2 and all micrococcal nuclease-digested ChIP and input DNA libraries were prepared using the NEB Ultra DNA library preparation protocol.

treatment_protocol: TSCs were washed 3X with cold PBS and fixed with 1% formaldehyde for 10 mins at room temperature.  Formaldehyde was quenched by adding glycine to a final concentration of 0.125 M.  Cells were then washed 3X with cold PBS and harvested in PBS supplemented with protease inhibitor and PMSF.  Cells were pelleted and flash frozen for a total weight of 0.23 g.  Pellets were stored at -80C until required for processing.

value: stably transfected FLAG-SFMBT2 TSC line

tag: fragmentation

value: Micrococcal nuclease-digested

value: FLAG-conjugated magnetic beads (Sigma Aldrich #M8823, lot# SLBM0090V)


title: MN_FLAG-SFMBT2_input

description:
Micrococcal nuclease-digested FLAG-SFMBT2 input
bnm_bowtie2-W200-G1000-FDR1E-2-islandfiltered-normalized.bw
bnm_bowtie2-W200-normalized.bw


title: MN_FLAG-SFMBT2_1


title: hMYC-12


title: hMYC-11


title: MN_SFMBT2_2

description:
Micrococcal nuclease-digested endogenous SFMBT2 ChIP-seq
bsm_bowtie2-W200-G1000-FDR1E-2-islandfiltered-normalized.bw
bsm_bowtie2-W200-normalized.bw

value: TSC line

value: protein G Dynabeads (ThermoFisher Scientific #100009D) coated with anti-SFMBT2 generated inhouse (Miri K et al., 2013)


title: MN_SFMBT2_1


title: PVD_C_D4_DCS_5_16Hr_RNA

description: Gene Expression after 16 hours U937+DC-SIGN cells DENV-4 infected Antibody:None

source_name: RNA 16 hours U937+DC-SIGN cells DENV-4 infected Antibody:None

value: 16 hours


title: C646-rep2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat  v2.1.1 with default  parameters.
The gene expression level was calculated by Cufflinks (v 2.2.1).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

extract_protocol:
For both normal mammary gland and tumor samples, 20 mg tissue was used for RNA extraction. Total RNA was extracted by using EASYspin RNA Mini Kit (Aidlab RN07).
RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111).

value: MMTV-PyVT

value: Mammary tumor tissue

value: 1mg/kg C646 injection

value: 12 weeks old


title: C646-rep1


title: PVD_C_D4_DCS_1_24Hr_RNA

value: 24 hours


title: PVD_C_D4_DCS_2_24Hr_RNA


title: MN_SFMBT2_input

description:
Micrococcal nuclease-digested endogenous SFMBT2 input
bsm_bowtie2-W200-G1000-FDR1E-2-islandfiltered-normalized.bw
bsm_bowtie2-W200-normalized.bw


title: DMSO-rep3

value: 1mg/kg DMSO injection


title: hMYC-9


title: S_FLAG-SFMBT2_2

description:
Sonicated FLAG-SFMBT2 ChIP-seq
bss_bowtie2-W200-G1000-FDR1E-2-islandfiltered-normalized.bw
bss_bowtie2-W200-normalized.bw

value: Sonicated


title: PVD_C_D4_DCS_4_16Hr_RNA


title: PVD_C_D4_DCS_3_16Hr_RNA


title: PVD_C_D4_DCS_2_16Hr_RNA


title: DMSO-rep2


title: C646-rep3


title: PVD_C_D4_DCS_5_8Hr_RNA

description: Gene Expression after 8 hours U937+DC-SIGN cells DENV-4 infected Antibody:None

source_name: RNA 8 hours U937+DC-SIGN cells DENV-4 infected Antibody:None

value: 8 hours


title: hMYC-8


title: S_FLAG-SFMBT2_1


title: DMSO-rep1


title: hMYC-6


title: PVD_C_D4_DCS_4_8Hr_RNA


title: hMYC-10


title: S_FLAG-SFMBT2_input

description:
Sonicated FLAG-SFMBT2 input
bss_bowtie2-W200-G1000-FDR1E-2-islandfiltered-normalized.bw
bss_bowtie2-W200-normalized.bw


title: Tumor-rep3

value: No treatment


title: hMYC-5


title: S_SFMBT2_2

description:
Sonicated endogenous SFMBT2 ChIP-seq
bns_bowtie2-W200-G1000-FDR1E-2-islandfiltered-normalized.bw
bns_bowtie2-W200-normalized.bw

extract_protocol:
[library prep] llumina TruSeq
Cell lysis and genomic fragmentation methods varied according to the intended fragmentation method -- sonication or micrococcal nuclease digestion.  Briefly, cells were sonicated to an average size of 75 bp to 400 bp using a total processing time of 5 mins with an amplitude of 40, pulse duration of 10 s, and cooling duration of 30 s.  Samples fragmented by micrococcal nuclease digestion were on average 175 bp in size.  DNA crosslinked with endogenous SFMBT2 was immunoprecipitated using magnetic Protein G beads coated with anti-SFMBT2 antibody produced in house.  FLAG-SFMBT2 complexes were immunoprecipitated with magnetic FLAG-conjugated beads.  Immunoprecipitation was performed at 4C for 2 hrs and subsequently washed 5X with cold RIPA buffer and once with cold TE supplemented with 50 mM NaCl.  Complexes were decrosslinked in 1% SDS and 0.1 M NaHCO3 overnight at 65C.  DNA was subsequently extracted through phenol-chloroform extraction and purified by ethanol-based precipitation.  DNA was reconstituted in water and quantified using PicoGreen.
Sonicated endogenous SFMBT2 ChIP and input DNA libraries were generated using the Illumina TruSeq protocol.  Sonicated FLAG-SFMBT2 and all micrococcal nuclease-digested ChIP and input DNA libraries were prepared using the NEB Ultra DNA library preparation protocol.


title: hMYC-4


title: S_SFMBT2_1


title: Tumor-rep1


title: hMYC-3


title: S_SFMBT2_input

description:
Sonicated endogenous SFMBT2 input
bns_bowtie2-W200-G1000-FDR1E-2-islandfiltered-normalized.bw
bns_bowtie2-W200-normalized.bw


title: hMYC-2


title: PVD_C_D4_DCS_2_8Hr_RNA


title: Normal-rep2

value: FVB wild type

value: Normal mammary gland tissue


title: hMYC-1

value: rag2:hMYC;lck:eGFP double transgenic line


title: Cl_RSA

city: Tianjin

first: feiyu

last: fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

department: Key Laboratory of Systems Microbial Biotechnology

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences.

description: RNA sample prepared as the following description: Germinated young mycelia of A. coerulea after 22-24 pre-culture in PDB medium were harvested and transferred into a new 30 ml potassium phosphate buffer supplement with 170 mg/L RSA dissolved in N, N-dimethylformamide. Additional two-hour cultivations were performed to induction of the 11β-hydroxylase gene expression.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then the clean reads were used to create a  de novo transcriptome assembly using the Trinity pipeline (v2.4.0)
The abundance for each of the resulted transcripts was calculated by RSEM (v1.2.0) using the Fragments Per Kilobase per Million (FPKM) measure
Detailed parameters for de novo trscripts assambly using Trinity: perl ../trinityrnaseq-Trinity-v2.4.0/Trinity --seqType fq --max_memory 50G --left Cl_all_1.fq --right Cl_all_2.fq --trimmomatic --full_cleanup
Detailed parameters for abundance measurements: perl ../trinityrnaseq-Trinity-v2.4.0/util/align_and_estimate_abundance.pl --transcripts ./AC.Trinity.fasta --seqType fq --left Cl_RSA_1.fq --right Cl_RSA_2.fq --prep_reference --est_method RSEM --thread_count 8 --aln_method bowtie2 --output_dir ./Cl_RSA_res
Supplementary_files_format_and_content: The file named “CL.Trinity.fasta”  records the complete assembled transcript sequences of our de novo transcriptome assembly. The other two txt files record the tab-delimited RSEM results include FPKM values for each Sample .

organism: Curvularia lunata

source_name: Mycelia of C. lunata

extract_protocol:
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: Wild-type

value: 100 mg/L 11-deoxycortisol 21-acetate (RSA) dissolved in N, N-dimethylformamide

value: mycelia


title: PVD_C_D4_DCS_3_8Hr_RNA


title: Normal-rep1

tag: tissue


title: Cl_Mock

description: RNA sample prepared as the following description: Germinated young mycelia of A. coerulea after 22-24 pre-culture in PDB medium were harvested and transferred into a new 30 ml potassium phosphate buffer supplement with an equal volume of N, N-dimethylformamide as mock. Additional two-hour cultivations were performed to induction of the 11β-hydroxylase gene expression.

value: Equal volume of N, N-dimethylformamide (DMF)


title: PVD_C_D4_DCS_1_8Hr_RNA


title: Tumor-rep2

tag: age


title: spleen WT PCB rep3

status: Public on Aug 17 2019

city: Irvine

first: Riann

middle: Jenay

last: Egusquiza

state: CA

address: 4311 Natural Sciences II

institute: University of California, Irvine

description:
WP3-GCCAAT-Sequences
processed data file:
norm_spleen_counts.txt
spleen_WPvsWD_alpha0.05.txt
spleen_KPvsWP_alpha0.05.txt

data_processing:
raw sequencing files were checked for sequence quality using FastQC then aligned to the mm10 genome using the STAR 2.6.0 aligner
unsorted BAM files were checked for mapping quality using FastQC. Reads were counted using Rsubread 3.8/featureCounts (R, Bioconductor) using the parameters TF.featureType = "exon GTF.attrType = "gene_name", allowMultiOverlap = TRUE, isPairedEnd = FALSE, nthreads = 24, countMultiMappingReads = TRUE, StrandSpecific = 0)
Differentially expressed genes (DEGs) and normalized counts were obtained using DESeq2 3.8 for each comparision using the parameters: alpha= 0.05
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing DEGs (between the indicated samples in the file name), mean values per group, fold changes, and p-values; txt file containing normalized counts from liver dataset (output of DESeq2)

source_name: spleen WT PCB

extract_protocol:
tissues were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 4 weeks old

tag: exposure

value: spleen tissue


title: spleen WT DMSO rep4

description:
WD4-AGTTCC-Sequences
processed data file:
norm_spleen_counts.txt
spleen_KDvsWD_alpha0.05.txt
spleen_WPvsWD_alpha0.05.txt

source_name: spleen WT DMSO

value: DMSO


title: spleen WT PCB rep1

description:
WP1-TTAGGC-Sequences
processed data file:
norm_spleen_counts.txt
spleen_WPvsWD_alpha0.05.txt
spleen_KPvsWP_alpha0.05.txt


title: spleen WT PCB rep5

description:
WP5-ACTTGA-Sequences
processed data file:
norm_spleen_counts.txt
spleen_WPvsWD_alpha0.05.txt
spleen_KPvsWP_alpha0.05.txt


title: spleen WT DMSO rep5

description:
WD5-ATGTCA-Sequences
processed data file:
norm_spleen_counts.txt
spleen_KDvsWD_alpha0.05.txt
spleen_WPvsWD_alpha0.05.txt


title: spleen WT PCB rep4

description:
WP4-CAGATC-Sequences
processed data file:
norm_spleen_counts.txt
spleen_WPvsWD_alpha0.05.txt
spleen_KPvsWP_alpha0.05.txt


title: Normal-rep3


title: spleen WT PCB rep2

description:
WP2-TGACCA-Sequences
processed data file:
norm_spleen_counts.txt
spleen_WPvsWD_alpha0.05.txt
spleen_KPvsWP_alpha0.05.txt


title: spleen WT DMSO rep3

description:
WD3-ACAGTG-Sequences
processed data file:
norm_spleen_counts.txt
spleen_KDvsWD_alpha0.05.txt
spleen_WPvsWD_alpha0.05.txt


title: PVD_C_D4_DCS_4_2Hr_RNA

description: Gene Expression after 2 hours U937+DC-SIGN cells DENV-4 infected Antibody:None

source_name: RNA 2 hours U937+DC-SIGN cells DENV-4 infected Antibody:None

tag: time point

value: 2 hours


title: spleen KO DMSO rep4

description:
KD4-GTCCGC-Sequences
processed data file:
norm_spleen_counts.txt
spleen_KDvsWD_alpha0.05.txt
spleen_KPvsKD_alpha0.05.txt

source_name: spleen KO DMSO

value: SXR knockout


title: spleen KO DMSO rep5

description:
KD5-GTGAAA-Sequences
processed data file:
norm_spleen_counts.txt
spleen_KDvsWD_alpha0.05.txt
spleen_KPvsKD_alpha0.05.txt


title: PVD_C_D4_DCS_5_2Hr_RNA

tag: cell type


title: spleen KO PCB rep3

description:
KP3-AGTCAA-Sequences
processed data file:
norm_spleen_counts.txt
spleen_KPvsKD_alpha0.05.txt
spleen_KPvsWP_alpha0.05.txt

source_name: spleen KO PCB


title: spleen KO PCB rep1

description:
KP1-GGCTAC-Sequences
processed data file:
norm_spleen_counts.txt
spleen_KPvsKD_alpha0.05.txt
spleen_KPvsWP_alpha0.05.txt


title: spleen KO PCB rep2

description:
KP2-CTTGTA-Sequences
processed data file:
norm_spleen_counts.txt
spleen_KPvsKD_alpha0.05.txt
spleen_KPvsWP_alpha0.05.txt


title: spleen KO PCB rep5

description:
KP5-GTTTCG-Sequences
processed data file:
norm_spleen_counts.txt
spleen_KPvsKD_alpha0.05.txt
spleen_KPvsWP_alpha0.05.txt


title: spleen WT DMSO rep1

description:
WD1-ATCACG-Sequences
processed data file:
norm_spleen_counts.txt
spleen_KDvsWD_alpha0.05.txt
spleen_WPvsWD_alpha0.05.txt


title: PVD_C_D4_DCS_3_2Hr_RNA

tag: infection


title: PVD_C_D4_DCS_1_2Hr_RNA

tag: antibody


title: spleen KO DMSO rep2

description:
KD2-TAGCTT-Sequences
processed data file:
norm_spleen_counts.txt
spleen_KDvsWD_alpha0.05.txt
spleen_KPvsKD_alpha0.05.txt


title: spleen KO DMSO rep3

description:
KD3-CCGTCC-Sequences
processed data file:
norm_spleen_counts.txt
spleen_KDvsWD_alpha0.05.txt
spleen_KPvsKD_alpha0.05.txt


title: spleen KO DMSO rep1

description:
KD1-GATCAG-Sequences
processed data file:
norm_spleen_counts.txt
spleen_KDvsWD_alpha0.05.txt
spleen_KPvsKD_alpha0.05.txt


title: PVD_C_D4_DCS_2_2Hr_RNA


title: Liver WT PCB rep4

description:
WP4-GTTTCG-Sequences
processed data file:
norm_liver_counts.txt
liver_WPvsWD_alpha0.05.txt
liver_KPvsWP_alpha0.05.txt

source_name: Liver WT PCB

value: liver tissue


title: Liver WT PCB rep3

description:
WP3-GTGGCC-Sequences
processed data file:
norm_liver_counts.txt
liver_WPvsWD_alpha0.05.txt
liver_KPvsWP_alpha0.05.txt


title: Liver WT PCB rep2

description:
WP2-ACTTGA-Sequences
processed data file:
norm_liver_counts.txt
liver_WPvsWD_alpha0.05.txt
liver_KPvsWP_alpha0.05.txt


title: Liver WT DMSO rep4

description:
WD4-GGCTAC-Sequences
processed data file:
norm_liver_counts.txt
liver_KDvsWD_alpha0.05.txt
liver_WPvsWD_alpha0.05.txt

source_name: Liver WT DMSO


title: Liver WT PCB rep1

description:
L-WP1-TTAGGC-Sequences
processed data file:
norm_liver_counts.txt
liver_WPvsWD_alpha0.05.txt
liver_KPvsWP_alpha0.05.txt


title: Liver WT DMSO rep5

description:
WD5-CTTGTA-Sequences
processed data file:
norm_liver_counts.txt
liver_KDvsWD_alpha0.05.txt
liver_WPvsWD_alpha0.05.txt


title: Liver KO PCB rep5

description:
KP5-GTGAAA-Sequences
processed data file:
norm_liver_counts.txt
liver_KPvsKD_alpha0.05.txt
liver_KPvsWP_alpha0.05.txt

source_name: Liver KO PCB


title: Liver WT DMSO rep1

description:
L-WD1-ATCACG-Sequences
processed data file:
norm_liver_counts.txt
liver_KDvsWD_alpha0.05.txt
liver_WPvsWD_alpha0.05.txt


title: Liver WT DMSO rep2

description:
WD2-GATCAG-Sequences
processed data file:
norm_liver_counts.txt
liver_KDvsWD_alpha0.05.txt
liver_WPvsWD_alpha0.05.txt


title: spleen KO PCB rep4

description:
KP4-GTGGCC-Sequences
processed data file:
norm_spleen_counts.txt
spleen_KPvsKD_alpha0.05.txt
spleen_KPvsWP_alpha0.05.txt


title: Liver KO PCB rep2

description:
KP2-GCCAAT-Sequences
processed data file:
norm_liver_counts.txt
liver_KPvsKD_alpha0.05.txt
liver_KPvsWP_alpha0.05.txt


title: Liver KO DMSO rep4

description:
KD4-AGTCAA-Sequences
processed data file:
norm_liver_counts.txt
liver_KDvsWD_alpha0.05.txt
liver_KPvsKD_alpha0.05.txt

source_name: Liver KO DMSO


title: Liver KO DMSO rep3

description:
KD3-ATTCCT-Sequences
processed data file:
norm_liver_counts.txt
liver_KDvsWD_alpha0.05.txt
liver_KPvsKD_alpha0.05.txt


title: Liver KO DMSO rep2

description:
KD2-ACTGAT-Sequences
processed data file:
norm_liver_counts.txt
liver_KDvsWD_alpha0.05.txt
liver_KPvsKD_alpha0.05.txt


title: Liver KO DMSO rep5

description:
KD5-CCGTCC-Sequences
processed data file:
norm_liver_counts.txt
liver_KDvsWD_alpha0.05.txt
liver_KPvsKD_alpha0.05.txt


title: Liver KO PCB rep4

description:
KP4-GTCCGC-Sequences
processed data file:
norm_liver_counts.txt
liver_KPvsKD_alpha0.05.txt
liver_KPvsWP_alpha0.05.txt


title: Liver WT PCB rep5

description:
WP5-CGTACG-Sequences
processed data file:
norm_liver_counts.txt
liver_WPvsWD_alpha0.05.txt
liver_KPvsWP_alpha0.05.txt


title: PVD_C_D4_DCS_1_16Hr_RNA

description: Gene Expression after 16 hours U937+DC-SIGN cells DENV-4 infected Antibody:None

value: 16 hours


title: Liver WT DMSO rep3

description:
WD3-TAGCTT-Sequences
processed data file:
norm_liver_counts.txt
liver_KDvsWD_alpha0.05.txt
liver_WPvsWD_alpha0.05.txt


title: Liver KO DMSO rep1

description:
KD1-GAGTGG-Sequences
processed data file:
norm_liver_counts.txt
liver_KDvsWD_alpha0.05.txt
liver_KPvsKD_alpha0.05.txt


title: Liver KO PCB rep1

description:
KP1-TGACCA-Sequences
processed data file:
norm_liver_counts.txt
liver_KPvsKD_alpha0.05.txt
liver_KPvsWP_alpha0.05.txt


title: Liver KO PCB rep3

description:
KP3-CAGATC-Sequences
processed data file:
norm_liver_counts.txt
liver_KPvsKD_alpha0.05.txt
liver_KPvsWP_alpha0.05.txt


title: Peripheral Blood Mononuclear Cells, Healthy control 41

city: Beijing

first: Lin

state: Beijing

address: Xicheng District, No.167 Beilishi Road

department: Department of Epidemiology

institute: Department of Epidemiology, State Key Laboratory of Cardiovascular Disease

description: Gene expression

hyb_protocol: cDNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Human lncRNA+mRNA Array V4.0 (4×180 K) were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 45℃. After hybridization, microarrays were washed  6 minutes at 42℃ with GE Wash Buffer 1 (0.2% SDS，2×SSC) and 4 minutes with 42°C GE Wash buffer 2 (0.2% SDS，2×SSC), then dried immediately by brief centrifugation.

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Agilent genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Peripheral Blood Mononuclear Cells

label_protocol: 14μl cDNA labeled with a 1μl fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using the WT Expression Kit (No. A24696C, Thermo Fisher Scientific)for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Overnight fasting blood samples were drawn by venipuncture from all patients and stored at -80 ℃ prior to use. PBMCs were isolated from the middle white monolayer by density gradient centrifugation using lymphocyte separation medium (TBD, Tianjin, China).

value: whole blood

tag: gender

value: male


title: Peripheral Blood Mononuclear Cells, Healthy control 45

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 47

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 43

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 40

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 32

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 39

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 42

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 48

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 34

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 38

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 44

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 35

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 30

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 36

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 28

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 24

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 31

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 37

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 33

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 27

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 25

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 26

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 29

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 23

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 20

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 22

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 17

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 15

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 16

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 18

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 19

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 21

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 10

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 12

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 9

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 14

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 11

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 7

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 8

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 6

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 13

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 4

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 2

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 46

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 93

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 1

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 5

description: Gene expression


title: Peripheral Blood Mononuclear Cells, Healthy control 3

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 85

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 87

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 92

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 91

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 83

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 79

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 90

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 88

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 77

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 75

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 81

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 86

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 73

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 89

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 84

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 71

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 80

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 82

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 76

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 70

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 69

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 68

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 78

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 72

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 74

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 64

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 65

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 63

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 67

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 60

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 62

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 61

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 59

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 57

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 55

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 53

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 66

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 58

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 51

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 52

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 56

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 54

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 50

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 46

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 48

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 47

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 44

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 49

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 42

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 43

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 45

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 41

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 40

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 39

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 38

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 36

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 34

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 35

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 37

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 33

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 31

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 32

description: Gene expression


title: 21-029

city: Atlanta

first: Suresh

last: Venkateswaran

address: 1760 Haygood Drive, HSRB, Room No: E-250

institute: Emory University

hyb_protocol: HumanMethylationEPIC BeadChip standard protocol

scan_protocol: BeadStudio

data_processing: non-normalized, background subtracted

source_name: non-IBD control_Ileal biopsies

extract_protocol:
peripheral blood DNA extraction protocol: AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA)
bisulfite conversion protocol: EZ DNA Methylation-GoldTM Kit (Zymo Research, Irvine, CA)

value: Male

tag: diagnosis

value: non-IBD control

tag: baseline vs follow-up

value: BL

tag: disease stage at diagnosis

value: Ileal biopsies


title: 04-128

source_name: Crohn's disease_Ileal biopsies

label_protocol: HumanMethylationEPIC BeadChip standard protocol

value: Crohn's disease

value: B1 inflammatory


title: 03-171

value: Female


title: Peripheral Blood Mononuclear Cells,CAD patient 29

description: Gene expression


title: 22-012


title: Peripheral Blood Mononuclear Cells,CAD patient 30

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 28

description: Gene expression


title: 03-165


title: 12-014


title: 06-094


title: 03-178


title: 03-032


title: 07-004


title: 15-013


title: Peripheral Blood Mononuclear Cells,CAD patient 26

description: Gene expression


title: 03-168


title: Peripheral Blood Mononuclear Cells,CAD patient 25

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 24

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 23

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 27

description: Gene expression


title: 27-038


title: 05-097


title: 03-127


title: Peripheral Blood Mononuclear Cells,CAD patient 22

description: Gene expression


title: 21-025


title: 03-170


title: Peripheral Blood Mononuclear Cells,CAD patient 21

description: Gene expression


title: 03-076


title: Peripheral Blood Mononuclear Cells,CAD patient 20

description: Gene expression


title: 18-022


title: 04-096


title: 09-035


title: monocyte_Donor4

city: Leiden

first: Koen

last: Dekkers

country: Netherlands

institute: Leiden University Medical Center

description:
3999840096_R06C02
monocyte

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450 Beadchip using standard Illumina protocol

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

source_name: monocyte

label_protocol: not provided

growth_protocol: Monocytes were differentiated to macrophages in the presence of M-CSF

extract_protocol: genomic DNA was purified from CD14+ monocytes and macrophages using the QIAamp DNA blood mini Kit

treatment_protocol: Macrophages were treated with LPS+IFNγ, IL-4, oxidized LDL, acetylated LDL or left unstimulated

tag: donor id

value: monocyte


title: M(acLDL)_Donor1

description:
3999840096_R05C02
M(acLDL)

source_name: macrophage activated with acetylated LDL

value: macrophage


title: Peripheral Blood Mononuclear Cells,CAD patient 18

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 16

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 15

description: Gene expression


title: 14-010


title: M(oxLDL)_Donor2

description:
3999840096_R04C02
M(oxLDL)

source_name: macrophage activated with oxidized LDL


title: 04-117


title: Sample 4

city: Chongqing

first: Zhong

last: Jianjun

address: NO.1 Youyi Road, Yuzhong District, Chongqing

department: Neurosurgery Department

institute: The first Affiliated Hospital of Chongqing Medical University

description: cultured in a condition which was deprived of oxygen and glucose (OGD)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat2 with parameters read-mismatches=2，read-gap-length=2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10

source_name: infected with targeted lentivirus against Neat1

growth_protocol: DMEM/F12 + 10%FBS or OGD

extract_protocol:
The RNA was isolated by TRIzol according to the manufacturer's protocol, and its purity as well as integrity also were assessed.
Total RNA was harvested from HT22 cells and RNA integrity was assessed and judged by A260/A280. Then the total RNA was fragmented into ~200 base pair (bp) units. RNA fragments were used to generate double-stranded cDNA, and then single strand of cDNA labeled by deoxy-UTP, which was enriched by PCR for 12 cycles.

treatment_protocol: infected with control negative lentivirus or targeted lentivirus against Neat1

tag: cell line

value: hippocampal neurons


title: Peripheral Blood Mononuclear Cells,CAD patient 19

description: Gene expression


title: 10-023


title: M(LPS+IFNγ)_Donor2

description:
3999840096_R02C02
M(LPS+IFNγ)

source_name: macrophage activated with LPS + IFNγ


title: Peripheral Blood Mononuclear Cells,CAD patient 17

description: Gene expression


title: M(IL-4)_Donor4

description:
3999840096_R03C02
M(IL-4)

source_name: macrophage activated with IL-4


title: 14-008


title: Peripheral Blood Mononuclear Cells,CAD patient 12

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 13

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 11

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 14

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 10

description: Gene expression


title: Sample 2

description: cultured in DMEM/F12 + 10%FBS

tag: strain


title: macrophage_Donor1

description:
3999840096_R01C02
macrophage

source_name: macrophage


title: 11-052


title: HT-64

city: Palmerston North

first: rubina

last: jibran

address: Tennent Drive

country: New Zealand

institute: Plant and Food Research

data_processing:
Each sample was run over 2 lanes, raw reads were merged prior to processing
illumina RTA was used for base calling on the NovaSeq instrument computer
Read sequences of low quality, ribosomal RNA, as well as adaptors were filtered out using Trimmomatic (Bolger et al., 2014) and SortMeRna (Kopylova et al., 2012).
RNAseq reads were aligned to the R. occidentalis reference gene models (VanBuren et al., 2018) using Spliced Transcripts Alignment to a Reference (STAR).
Differential expression analysis was performed using DESeq2 (Love et al., 2014).
Significant DEG were selected using a threshold of α< -0.005 with an adjusted p value of < 0.01 and a |log2 fold change | > 1. Arabidopsis orthologues were determined by BLAST against the TAIR database.
Genome_build: R. occidentalis genome assembly ORUS 4115-3 v3.0 (VanBuren et al., 2018)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Rubus idaeus

source_name: axillary buds, 5-10 nodes below apex

growth_protocol: Plants were grown in the field under standard conditions

extract_protocol:
Bud samples were collected on November 5th (spring/early summer). Tissue was snap-frozen in liquid nitrogen and total RNA was extracted from three biological replicates of each cultivar as described in Janssen et al. (2008). The quality and concentration of the RNA samples were assessed using a Fragment Analyzer (Agilent, Santa Clara, CA, USA) and only samples with an RNA Integrity Number higher than 8 were sequenced.
Library preparation was completed at the Australian Genome Research Facility using the TruSeq Stranded kit and subsequent paired-end Illumina® sequencing employed the NovaSeq6000 platform, with the S2 flow cell.

tag: ecotype

value: Heritage

value: axillary buds, 5-10 nodes below apex

tag: phenotype

value: annual-fruiting


title: 03-189


title: macrophage_Donor2

description:
3999840096_R06C01
macrophage


title: Peripheral Blood Mononuclear Cells,CAD patient 8

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 7

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 9

description: Gene expression


title: monocyte_Donor3

description:
3999840096_R05C01
monocyte


title: M(acLDL)_Donor3

description:
3999840096_R04C01
M(acLDL)


title: Sample 3

source_name: infected with control negative lentivirus


title: Sample 1

description: cultured in DMEM/F12 + 10%FBS


title: 01-077

value: B2 stricturing


title: M(oxLDL)_Donor1

description:
3999840096_R03C01
M(oxLDL)


title: 04-129


title: HT-63


title: M(IL-4)_Donor3

description:
3999840096_R02C01
M(IL-4)


title: 03-182


title: HT-62


title: Peripheral Blood Mononuclear Cells,CAD patient 6

description: Gene expression


title: Peripheral Blood Mononuclear Cells,CAD patient 5

description: Gene expression


title: WA-59

value: Wakefield

value: biennial-fruiting


title: Peripheral Blood Mononuclear Cells,CAD patient 4

description: Gene expression

value: whole blood

value: male


title: Peripheral Blood Mononuclear Cells,CAD patient 3

description: Gene expression


title: 16-009


title: WA-60


title: Peripheral Blood Mononuclear Cells,CAD patient 2

description: Gene expression


title: LY1 cells, 1-VD-9-19

city: Jinan

first: Juan

last: Yang

address: No. 324 Jingwu Road

institute: Shandong Provincial Hospital Affiliated to Shandong University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files.xlsx (FPKMs)

growth_protocol: Cells are cultured using IMDM basic medium

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: LY1 cells were infected with lentivirus vectors that encoded either shSirt6 or an empty vector (control) according to the manufacturers’ instruction

value: DLBCL cell line LY1

tag: genotype

value: Control


title: M(IL-4)_Donor1

description:
3999840113_R06C02
M(IL-4)


title: STIM1 KO rep3

first: Huakan

last: Zhao

state: State...

address: Xinqiao Street 183, Shapingba district

department: Clinical Medicine Research Center

institute: Xinqiao Hospital, Third Military Medical University

data_processing: For the normalization in this study, we useed ACTB as the housekeeping gene. Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].

label: SYBR Green II

source_name: SMMC7721 cell line

label_protocol: Reverse transcription was performed from 1μg total RNA using PrimeScript™ RT reagent Kit with gDNA Eraser (TAKARA).3 ng cDNA was added into each 20μL reaction mix. mRNA expression was assessed by RT-quantitative PCR using TB Green® Premix Ex Taq™ II (TAKARA) on BioRad CFX386 (Bio-Rad, CA) with 40 cycles at 95 °C for 10 seconds, 59 °C for 20 seconds and 72 °C for 30 seconds.

growth_protocol: Cells were cultured in DMEM supplemented with 10% (v/v) FBS at 37°C in 5% CO2.

extract_protocol: When the cells grow to 60~70% confluent, Total RNA was extracted by using Trizol (TAKARA, Japan).

treatment_protocol: STIM1knockout- (STIM1 KO)SMMC7721 cells were constructed by CRISPR/Cas9.

value: STIM1-Knockout SMMC7721 generated by CRISPR-Cas9


title: LY1 cells, 1-VD-9-17


title: WA-61

tag: tissue


title: M(LPS+IFNγ)_Donor4

description:
3999840096_R01C01
M(LPS+IFNγ)


title: 05-105

value: Male

tag: age

value: Crohn's disease

value: BL

value: Ileal biopsies


title: M(LPS+IFNγ)_Donor3

description:
3999840113_R05C02
M(LPS+IFNγ)

value: macrophage


title: 06-104

value: non-IBD control


title: LY1 cells, 1-VA-9-25


title: M(acLDL)_Donor4

description:
3999840113_R02C02
M(acLDL)


title: macrophage_Donor4

description:
3999840113_R04C02
macrophage


title: WT rep3

value: SMMC7721 without any gene editing


title: WT rep2


title: Brain TDAG51 KO Tg vs TDAG51 KO

city: Daejeon

first: Hyeongseok

last: Yun

address: 99, Daehak-ro, Yuseong-gu

country: South Korea

institute: Chungnam national university

hyb_protocol: Each 825 ng of cyanine 3-labeled and cyanine 5-labeled cRNA target were mixed and the fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 °C for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent Mouse whole genome 44K microarray. The arrays hybridized at 65 °C for 17 h using Agilent Hybridization oven (Agilent Technology, USA). The hybridized miroarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by Agilent DNA microarray Scanner G2505C (Agilent Technology, USA). Data quantification was performed using Agilent Feature Extraction software 9.3.2.1 (Agilent Technology, USA).

data_processing: The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3.1 (Agilent Technology, USA).

source_name: TDAG51 KO P0 brain

label_protocol: The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1 M DTT, NTP mix, 50 % PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was performed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 °C for 2 hours.

growth_protocol: Mice were maintained in a pathogen-free facility and animal study was approved by the Animal Experiment Ethics Committee of Chungnam National University (approval No. CNU-00114).

extract_protocol: Total RNA extracted using TRIzol reagent following manufacturer's instructions.

value: TDAG51 knockout (KO)

value: female

value: 8 weeks

tag: parturition

value: postpartum day 0

value: brain

value: TDAG51 knockout (KO) and TDAG51 transgenic (Tg)

source_name: TDAG51 KO Tg P0 brain


title: M(oxLDL)_Donor3

description:
3999840113_R01C02
M(oxLDL)


title: LY1 cells, 1-VA-9-17


title: LY1 cells, 1-VD-6-12


title: monocyte_Donor2

description:
3999840113_R03C02
monocyte

value: monocyte


title: LY1 cells, 1-VA-6-18

value: DLBCL cell line LY1


title: 05-079

value: Female

value: B1 inflammatory


title: WT rep1


title: 14-006

value: Male


title: 06-053

value: Crohn's disease


title: Peripheral Blood Mononuclear Cells,CAD patient 1

description: Gene expression

value: whole blood

value: male


title: STIM1 KO rep2

value: STIM1-Knockout SMMC7721 generated by CRISPR-Cas9


title: lung121 biopsy

status: Public on Aug 16 2019

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: lung biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

growth_protocol: All human lung biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

value: lung transplant transbronchial biopsy (TBB)

tag: high surfactant (yes or no)

value: no


title: M(LPS+IFNγ)_Donor1

description:
3999840113_R03C01
M(LPS+IFNγ)

tag: cell type

value: macrophage


title: STIM1 KO rep1


title: lung59 biopsy

value: yes


title: 13-028

value: BL

value: Ileal biopsies


title: M(acLDL)_Donor2

description:
3999840113_R06C01
M(acLDL)


title: monocyte_Donor1

description:
3999840113_R01C01
monocyte


title: lung76 biopsy


title: lung232 biopsy


title: lung194 biopsy


title: M(oxLDL)_Donor4

description:
3999840113_R05C01
M(oxLDL)


title: lung39 biopsy


title: lung72 biopsy


title: 03-043

value: non-IBD control


title: lung58 biopsy


title: lung140 biopsy


title: lung35 biopsy


title: M(IL-4)_Donor2

description:
3999840113_R04C01
M(IL-4)


title: lung62 biopsy


title: lung52 biopsy


title: lung219 biopsy


title: lung154 biopsy


title: lung2 biopsy


title: 04-132


title: 09-008


title: lung70 biopsy


title: lung60 biopsy


title: lung50 biopsy


title: lung128 biopsy


title: lung163 biopsy


title: lung30 biopsy


title: lung198 biopsy


title: lung137 biopsy


title: lung214 biopsy


title: lung67 biopsy


title: macrophage_Donor3

description:
3999840113_R02C01
macrophage


title: lung18 biopsy


title: lung211 biopsy


title: lung144 biopsy


title: lung205 biopsy


title: lung196 biopsy


title: lung91 biopsy


title: lung81 biopsy


title: lung63 biopsy


title: lung102 biopsy


title: lung95 biopsy


title: 03-056


title: lung227 biopsy


title: lung199 biopsy


title: lung159 biopsy


title: lung131 biopsy


title: lung125 biopsy


title: lung185 biopsy


title: lung1 biopsy


title: lung83 biopsy


title: lung48 biopsy


title: Brain TDAG51 WT vs TDAG51 KO

value: TDAG51 knockout (KO)

value: female

value: 8 weeks

value: postpartum day 0

value: brain

value: TDAG51 wild-type (WT)

source_name: TDAG51 WT P0 brain


title: lung103 biopsy


title: lung179 biopsy


title: lung51 biopsy


title: lung201 biopsy


title: lung169 biopsy


title: lung45 biopsy


title: lung65 biopsy


title: lung215 biopsy


title: lung136 biopsy


title: lung111 biopsy


title: lung141 biopsy


title: lung75 biopsy


title: lung104 biopsy


title: lung158 biopsy


title: lung68 biopsy


title: lung228 biopsy


title: lung217 biopsy


title: lung118 biopsy


title: lung96 biopsy


title: lung105 biopsy


title: lung124 biopsy


title: lung139 biopsy


title: lung134 biopsy


title: lung11 biopsy


title: lung21 biopsy


title: lung120 biopsy


title: lung230 biopsy


title: lung82 biopsy


title: lung187 biopsy


title: lung171 biopsy


title: lung90 biopsy


title: lung161 biopsy


title: lung107 biopsy


title: lung109 biopsy


title: lung202 biopsy


title: lung181 biopsy


title: lung189 biopsy


title: lung89 biopsy


title: lung231 biopsy


title: lung218 biopsy


title: lung177 biopsy


title: lung138 biopsy


title: lung38 biopsy


title: lung212 biopsy


title: lung110 biopsy


title: lung22 biopsy


title: lung114 biopsy


title: lung172 biopsy


title: lung13 biopsy


title: lung153 biopsy


title: lung225 biopsy


title: lung46 biopsy


title: lung180 biopsy


title: lung195 biopsy


title: lung57 biopsy


title: lung20 biopsy


title: lung101 biopsy


title: lung235 biopsy


title: lung27 biopsy


title: lung36 biopsy


title: lung229 biopsy


title: lung112 biopsy


title: lung148 biopsy


title: lung100 biopsy


title: lung26 biopsy


title: lung99 biopsy


title: lung206 biopsy


title: lung34 biopsy


title: lung167 biopsy


title: lung233 biopsy


title: lung71 biopsy


title: lung8 biopsy


title: lung5 biopsy


title: lung208 biopsy


title: lung115 biopsy


title: lung221 biopsy


title: lung84 biopsy


title: lung203 biopsy


title: lung33 biopsy


title: lung178 biopsy


title: lung241 biopsy


title: lung66 biopsy


title: lung239 biopsy


title: lung149 biopsy


title: lung117 biopsy


title: lung29 biopsy


title: lung73 biopsy


title: lung226 biopsy


title: lung193 biopsy


title: lung145 biopsy


title: lung126 biopsy


title: lung74 biopsy


title: lung92 biopsy


title: lung133 biopsy


title: lung175 biopsy


title: lung197 biopsy


title: lung17 biopsy


title: lung28 biopsy


title: lung170 biopsy


title: lung19 biopsy


title: lung164 biopsy


title: lung16 biopsy


title: lung79 biopsy


title: lung168 biopsy


title: lung7 biopsy


title: lung106 biopsy


title: lung78 biopsy


title: lung132 biopsy


title: lung142 biopsy


title: lung119 biopsy


title: lung183 biopsy


title: lung155 biopsy


title: lung113 biopsy


title: lung150 biopsy


title: lung122 biopsy


title: lung55 biopsy


title: lung4 biopsy


title: lung88 biopsy


title: lung224 biopsy


title: lung87 biopsy


title: lung147 biopsy


title: lung40 biopsy


title: lung25 biopsy


title: lung64 biopsy


title: lung190 biopsy


title: lung123 biopsy


title: lung24 biopsy


title: lung97 biopsy


title: lung94 biopsy


title: lung200 biopsy


title: lung49 biopsy


title: lung54 biopsy


title: lung32 biopsy


title: lung237 biopsy


title: lung6 biopsy


title: lung127 biopsy


title: lung41 biopsy


title: lung69 biopsy


title: lung165 biopsy


title: lung98 biopsy


title: lung77 biopsy


title: lung9 biopsy


title: lung15 biopsy


title: lung3 biopsy


title: lung192 biopsy


title: lung156 biopsy


title: lung85 biopsy


title: lung151 biopsy


title: lung56 biopsy


title: lung223 biopsy


title: lung173 biopsy


title: lung12 biopsy


title: lung236 biopsy


title: lung207 biopsy


title: lung129 biopsy


title: lung14 biopsy


title: lung143 biopsy


title: lung234 biopsy


title: lung220 biopsy