title: DigestiveGland_1µg/L4NP_39day_Female_rep3

description: Gene expression after 39 day exposure


title: DigestiveGland_50ng/LEE2_39day_Female_rep2

status: Public on Mar 15 2018

type: RNA

city: Boston

first: Bonnie

last: Blalock

state: MA

address: 100 Morrissey Blvd

department: School for the Environment

country: USA

institute: University of Massachusetts Boston

description: Gene expression after 39 day exposure

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 5uL 10x blocking agent and 1 uL 25x Agilent fragmentation buffer following the manufacturers instructions.  On completion of the fragmentation reaction, 25uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to our custom 60,000 sequence Mytilus edulis microarray  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), Acetonitrile for 10 seconds at room temperature, and stabilization and drying solution for 30 seconds.

scan_protocol: Microarray slides were scanned at five micron resolution using an Agilent DNA Microarray Scanner G2565CA (Agilent Technologies) at the University of Massachusetts Medical School in Worchester, MA.  Feature extraction was performed using Feature Extraction Software 11.5 (Agilent Technologies).

data_processing: Microarray intensity values were normalized by quantile normalization with median polish in Arraystar (DNAstar, Madison, Wisconsin).  Each treatment was compared to the unexposed control of the corresponding sex and DEG were selected with a 99% confidence interval and 2-fold change.

molecule: total RNA

organism: Mytilus edulis

source_name: Digestive Gland, 50ng/LEE2, Female, 39 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using Quick Amp One Color Labeling kit and One Color RNA Spike-in kit following the manufactures protocols (Agilent Technology).  Dye incorporation and cRNA yield were checked with the NanoDrop  Spectrophotometer and met Agilents recommendation of a yield of at least 825 ng and a specific activity of 6pmol prior to hybridization.

growth_protocol: Mussels (M. edulis) were kept in glass aquarium kept at 11.24 +/- 0.3 °C, 8.4 +/- 0.2 mg/L dissolved oxygen, 32.9 +/- 2.1 PSU and a 10:14-h light dark cycle.  Water was changed and treatment (control, 5ng/L EE2, 50ng/L EE2, 1ug/L 4NP, 100ug/L 4NP) was renewed twice a week.  Mussels were fed a daily mixture of Isochrysis galbana and Thalassosira weissflogii for a total of 3.0*10^7cells/mussel.

extract_protocol: Total RNA was isolated using TriReagent (Molecular Research Center, Cincinnati, OH) to each tissue sample and homogenized for 10 min at 50 vibrations/s using a Tissue Lyser bead mill (Qiagen Inc., Valencia, CA) with 3.2 mm stainless steel beads (Biospec Products, Bartlesville, OK).  Total RNA was purified and Dnase I treatment was performed using the RNeasy kit (Qiagen).  RNA concentrations were examined using a NanoDrop Spectrophotometer (Thermo Scientific, Wilmington, DE) and RNA quality was checked using 1.5% agarose gel using NorthernMax-Gly buffer (Applied Biosystems/Ambion, Austin, TX).

treatment_protocol: Treatment tanks were dosed with 100uL of the appropriate concentration of EE2 and 4NP dissolved in ethanol or 100uL of ethanol only for the control.  The amount of ethanol added represented 0.004%.  Water was changed and treatment (control, 5ng/L EE2, 50ng/L EE2, 1ug/L 4NP, 100ug/L 4NP) was renewed twice a week.  At the end of the 39 day exposure digestive gland was dissected and stored in RNA later for future analysis.

tag: gender

value: Female

tag: tissue

value: digestive gland

tag: life stage

value: adult


title: Heart at ZT12, WT mouse, SHAM, biological rep2

city: Lille

first: Lefebvre

last: Philippe

state: Nord

address: Blvd Pr. J.Leclerc

country: France

institute: Inserm

description: Heart gene expression data from WT mouse at ZT12 after short ischemia/reperfusion - reverb alpha antagonist treatment (SHAM)

hyb_protocol: Following fragmentation, 5,5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: RMA normalization

label: biotin

organism: Mus musculus

source_name: Heart from WT mouse after short ischemia/reperfusion, ZT12, -  reverb alpha antagonist (SHAM)

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: Langendorff isolated heart model were used, After txenty minutes steady state stabilisation, perfusion pump was switch off to generate no flow ischemia. Then, twenty minute later, perfusion pump was switch on for reperfusion period of twenty minutes; Heart were then flash frozen in liquid Nitrogen and RNA were extracted for affymetrix assessement

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

treatment_protocol: Reverb alpha antagonists was administrated intra peritaneously at 10 µM four hours and one hours before ischemia reperfusion protocol

value: Heart

tag: strain

tag: genotype

value: wildtype


title: Heart at ZT12, WT mouse, SHAM, biological rep1


title: Heart at ZT12, WT mouse + reverb alpha antagonist, biological rep3

description: Heart gene expression data from WT mouse at ZT12 after short ischemia/reperfusion + reverb alpha antagonist treatment

source_name: Heart from  WT mouse after short ischemia/reperfusion, ZT12, + reverb alpha antagonist treatment


title: Heart at ZT12, Reverb alpha KO mice, biological rep2

description: Heart gene expression data from Reverb alpha KO mouse after short ischemia/reperfusion at ZT12

source_name: Heart from Reverb alpha KO mouseafter short ischemia/reperfusion, ZT12

value: Reverb alpha KO mice


title: DigestiveGland_5ng/LEE2_39day_Female_rep3

description: Gene expression after 39 day exposure

source_name: Digestive Gland, 5ng/LEE2, Female, 39 days


title: Heart at ZT12, Reverb alpha KO mice, biological rep5


title: DigestiveGland_5ng/LEE2_39day_Female_rep4

description: Gene expression after 39 day exposure


title: Heart at ZT12, Reverb alpha KO mice, biological rep3


title: BiSeq_WT_ng_Pax6_2_D14

type: SRA

city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

country: Germany

institute: Max Planck Institute of Psychiatry

library_source: genomic

data_processing:
library strategy: Amplicon_BiSeq
RNA-Seq: Raw RNA-Seq reads were trimmed to a total length of 45 bp, removing 5bp from the 5’ end and removing all bases beyond bp 50 at the 3’ end using trimmomatic version 0.33 (Bolger et al., 2014). Subsequently, gene expression levels were quantified using Salmon (Patro et al., 2017) against the cDNA sequences of all ENSEMBL transcripts release 89 of genome assembly GRCh37 using default parameters.
Amplicon-BiSeq:Whole genome bisulfite sequencing and amplicon sequencing raw reads and amplicon sequencing data were aligned using bsMap version 2.7  (Xi and Li, 2009) with default parameters against the human genome build GRCh37. Next, we used the Picard suite to remove all duplicate reads. Subsequently, we carried out methylation using the mcall module implemented in the MOABS suite (Sun et al., 2014).
single cell RNA-Seq: Raw reads were then processed using the 10X Genomics cell ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) with standard settings.
WGBS: Whole genome bisulfite sequencing raw reads were aligned using bsMap version 2.7  (Xi and Li, 2009) with default parameters against the human genome build GRCh37. Next, we used the Picard suite to remove all duplicate reads. Subsequently, we carried out methylation using the mcall module implemented in the MOABS suite (Sun et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq: FPKM format output from DESeq2 (genes.fpkm.txt), tag locations of all raw reads as .bed file
WGBS: standard MOABS mcall output format (bed-like format containing chrom, start, end, ratio, totalC, methC, strand, next,  Plus,  totalC, methC, Minus, totalC, methC, localSeq columns)
scRNA-Seq: standard output from 10x Genomics pipeline: .mtx sparse matrix with UMI counts for each cell and gene, .tsv files containing the row (gene names) and column (individual cell barcodes) headers.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Stem cell cultures were maintained on Matrigel (BD Biosciences) with mTeSR1 media (Stem Cell Technologies and passaged on a weekly basis using 1mM EDTA or Accutase (Sigma). All cell cultures were maintained at 370C, 5% CO2.

extract_protocol:
RNA was purified using the Direct-zol™ RNA MiniPrep (Zymo Research Inc).
RNA-seq libraries generated using the Illumina TruSeq RNA Library Preparation Kits. Pools were sequenced on the Illumina HiSeq 2500 sequencer as 100bp paired-end reads.   WGBS:100-200 ng of genomic DNA was fragmented using a Covaris S2 for 6 min according to the following program: duty cycle 5%; intensity 10; cycle per burst 200. The sheared DNA was purified using the DNA Clean & Concentrator kit from Zymo Research per the manufacturer’s recommendations. Bisulfite conversion of DNA was then conducted using the EZ DNA Methylation-Gold kit (Zymo Research) followed the instructions, eluting to 15 µl low TE buffer. To minimize continually loss during storage, bisulfite-converted DNA was immediately processed for generating WGBS libraries using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences) followed the manufacturer’s protocol. The libraries were sequenced on an Illumina HiSeq 2500 sequencer as 100-bp paired-end reads. scRNA-Seq libraries: WT and 3A-KO cells were dissociated on days 6 and 14 of differentiation with Accutase for 10 min. Cells were collected in DMEM:F12 (day 6) or Neurobasal (day 14) + 2% FBS, and centrifuged in order to quench and remove the Accutase. Cell pellets were re-suspended in PBS + 0.04% Bovine Serum Albumin (Millipore) and filtered through a 40µm Nylon Mesh-Cell strainer (Fisher Scientific). Next, we quantified cell number and cell viability using the Nexcelom Cell Counter (Nexcelom Bioscience). To generate Cell 3’ Libraries we used a Single Cell 3’ Reagent Kit v2 (10xGenomics, Chromium). In brief, 10K cells/sample with the RT master mix were loaded in a Single Cell 3’ Chip along with the RT Single Cell 3’ Gel Beads and the Partitioning oil, and run in a Chromium Controller to generate Single Cell Gel Bead-In-Emulsions (GEMs). RT reaction of the resulting single cell-beads suspension was run in order to obtain 10x Barcoded cDNA. Silane magnetic beads were used to clean the barcoded cDNA, which was amplified by PCR to generate sufficient mass for library construction. Enzymatic Fragmentation, End Repair and A-tailing Double Sided Size Selection were used to incorporate R2, P5, P7, 10bp randomer as well as i7 index read sequences that results in Illumina-ready sequencing libraries. To QC post cDNA Amplification reaction and libraries, we loaded 1-2 µl on Us d5000 and d1000 tapes, respectively, and run in a Tapestation 4200 (Agilent Technologies). To quantify DNA concentrations in the libraries we utilized a Qubit® dsDNA High Sensitivity Assay Kit (Invitrogen). For sequencing of Single Cell 3’ libraries, we used standard Illumina sequencing primers and were run using paired-end sequencing with dual indexing following manufacturer’s recommendations. Subsequently each library was sequenced on a HiSeq4000 lane. Amplicon sequencing:  Bisulfite conversion of DNA was conducted using the EZ DNA Methylation-Gold kit (Zymo Research) following manufacturer’s instructions. Individual amplicons were PCR amplified using TaKaRa EpiTaq™ HS (Clontech). The PAX6 and ARX amplicons were amplified using the primer pairs listed in Table S7. Amplicons were sequenced on the Illumina MiSeq platform using the MiSeq Reagent Kit v2 (300-cycles). The genomic coordinates for each amplicon are: PAX6 Amplicon 1: chr11: 31,821,416-31,821,910;  PAX6 Amplicon 2: chr11: 31,840,497-31,840,800; ARX Amplicon 1: chrX: 25,011,817-25,012,198; ARX Amplicon 2: chrX: 25,017,310-25,017,775.

treatment_protocol: hESC colonies were dissociated using Accutase and plated at a density of 74,000 cells/cm2 with 10µM ROCK inhibitor (Y-27632, DNSK International) in mTeSR1 for 48 hours. Media was replaced on day 0 with N2B27 medium (50% DMEM:F12, 50% Neurobasal, supplemented with  NEAA, Glutamax, N2 and B27; Gibco, Life Technologies) containing 10µM SB431542 (DNSK International), 100nM LDN-193189 (DNSK International), 1 µM Retinoic Acid (RA, Sigma) and 1µM of Smoothened-Agonist (SAG, DNSK International). Culture medium was changed daily for 6 days and then was switched to N2B27 medium supplemented with 1µM RA, 1µM SAG, 5µM DAPT (DNSK International) and 4µM SU5402 (DNSK International). Cells were fed daily until day 14 of differentiation. On day 14 MNs were dissociated using TrypLE Express (Gibco, Life Technologies) supplemented with DNase I (Worthington) and plated onto pre-coated Poly-D-Lysine/Laminin surfaces (BD Biosciences) and cultured in Neurobasal medium supplemented with NEAA, Glutamax, N2, B27, Ascorbic acid (0.2 µg/ml) and BDNF, CNTF and GDNF (10ng/mL, R&D systems).

tag: cell line

tag: cell type

value: human embryonic stem cells

tag: genotype/variation

value: WT

tag: stage/time point

tag: modification


title: BiSeq_WT_ng_Arx_1_D6


title: BiSeq_WT_ng_Arx_2_D6


title: Heart at ZT12, WT mouse + reverb alpha antagonist, biological rep1


title: DigestiveGland_50ng/LEE2_39day_Female_rep1

description: Gene expression after 39 day exposure


title: DigestiveGland_5ng/LEE2_39day_Female_rep1

description: Gene expression after 39 day exposure


title: DigestiveGland_1µg/L4NP_39day_Female_rep1

description: Gene expression after 39 day exposure

source_name: Digestive Gland, 1µg/L4NP, Female, 39 days


title: Heart at ZT12, WT mice, biological rep6

description: Heart gene expression data from WTmouse after short ischemia/reperfusion at ZT12

source_name: Heart from WT mouse after short ischemia/reperfusion, ZT12


title: DigestiveGland_1µg/L4NP_39day_Female_rep4

description: Gene expression after 39 day exposure


title: DigestiveGland_control_39day_Female_rep4

description: Gene expression after 39 day exposure

source_name: Digestive Gland, control, Female, 39 days


title: BiSeq_WT_ng_Arx_2_D14


title: Heart at ZT12, Reverb alpha KO mice, biological rep4


title: Heart at ZT12, Reverb alpha KO mice, biological rep1


title: DigestiveGland_5ng/LEE2_39day_Female_rep2

description: Gene expression after 39 day exposure


title: BiSeq_KO3A_ng_PAX6_2_D6


title: B2-1-TSA-RNA.rep2

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

library_source: transcriptomic

data_processing:
Basecalls performed by BGI, Shenzhen.
Data were filtered using samtools to remove potential PCR duplicates
MeDIP sequencing reads were mapped to the Human genome (hg19) using Bowtie2.
Sequencing qualities were evaluated with FASTQC software and then the reads were aligned to hg19 genome sequences with a maximum of 2 mismatches allowed. Only the uniquely mapped reads were kept, and duplicate reads were removed. Mapped reads were extended to the average fragment sizes. Genome profile files were generated with IGV tools and linearly normalized to the same depth of 10 million reads.
RNA-Seq data were mapped by TopHat and quantitified by Crosslinks.
Genome_build: hg19
Supplementary_files_format_and_content: The transcription levels (RPKM) were quantified with Cufflinks (v2.0.2) software. Bigwig files were generated with IGV tools followed by UCSC utilities.

source_name: TSA treated B2-1 cells

extract_protocol:
Genomic DNA was isolated by conventional phenol extraction and proteinase K treatment. For sperm samples, 40 mM DTT were added during cell lysis.
According to standard protocols provided by Illumina Kits.

tag: parental cell line

value: somatic cell line

value: B2-1 treated with TSA

value: embryonic kidney

tag: developmental stage

value: fetus


title: BiSeq_KO3A_ng_Arx_2_D6


title: BiSeq_KO3A_ng_PAX6_1_D6


title: Heart at ZT12, WT mice, biological rep5


title: B2-1-TSA-RNA.rep1


title: Heart at ZT12, WT mice, biological rep7


title: B2-1-siKpnb1-RNA.rep2

source_name: siKpnb1 treated B2-1 cells

value: siKpnb1 in B2-1


title: BiSeq_KO3A_ng_Arx_1_D6


title: BiSeq_WT_ng_Pax6_1_D14


title: DigestiveGland_50ng/LEE2_39day_Female_rep3

description: Gene expression after 39 day exposure


title: Heart at ZT12, WT mouse + reverb alpha antagonist, biological rep2


title: DigestiveGland_control_39day_Female_rep3

description: Gene expression after 39 day exposure


title: BiSeq_WT_ng_Arx_1_D14


title: Heart at ZT12, WT mice, biological rep4


title: Heart at ZT12, WT mice, biological rep3


title: Heart at ZT12, WT mice, biological rep1


title: Heart at ZT12, WT mice, biological rep2


title: B2-1-siKpnb1-RNA.rep1


title: DigestiveGland_control_39day_Female_rep1

description: Gene expression after 39 day exposure


title: DigestiveGland_control_39day_Female_rep2

description: Gene expression after 39 day exposure


title: BiSeq_KO3A_ng_PAX6_2_D14


title: Heart at ZT0, WT mice, biological rep6

description: Heart gene expression data from WTmouse after short ischemia/reperfusion at ZT0

source_name: Heart from WT mouse after short ischemia/reperfusion, ZT0


title: B2-1-siCse1l-RNA.rep2

source_name: siCse1l treated B2-1 cells

value: siCse1l in B2-1


title: BiSeq_KO3A_ng_PAX6_1_D14


title: BiSeq_KO3A_ng_Arx_2_D14


title: BiSeq_KO3A_ng_Arx_1_D14


title: B2-1-SAHA-RNA.rep1

source_name: SAHA treated B2-1 cells

value: B2-1 treated with SAHA


title: B2-1-SAHA-RNA.rep2


title: WGBS_hESC_KO3A_D0_R1

data_processing:
library strategy: WGBS
RNA-Seq: Raw RNA-Seq reads were trimmed to a total length of 45 bp, removing 5bp from the 5’ end and removing all bases beyond bp 50 at the 3’ end using trimmomatic version 0.33 (Bolger et al., 2014). Subsequently, gene expression levels were quantified using Salmon (Patro et al., 2017) against the cDNA sequences of all ENSEMBL transcripts release 89 of genome assembly GRCh37 using default parameters.
Amplicon-BiSeq:Whole genome bisulfite sequencing and amplicon sequencing raw reads and amplicon sequencing data were aligned using bsMap version 2.7  (Xi and Li, 2009) with default parameters against the human genome build GRCh37. Next, we used the Picard suite to remove all duplicate reads. Subsequently, we carried out methylation using the mcall module implemented in the MOABS suite (Sun et al., 2014).
single cell RNA-Seq: Raw reads were then processed using the 10X Genomics cell ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) with standard settings.
WGBS: Whole genome bisulfite sequencing raw reads were aligned using bsMap version 2.7  (Xi and Li, 2009) with default parameters against the human genome build GRCh37. Next, we used the Picard suite to remove all duplicate reads. Subsequently, we carried out methylation using the mcall module implemented in the MOABS suite (Sun et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq: FPKM format output from DESeq2 (genes.fpkm.txt), tag locations of all raw reads as .bed file
WGBS: standard MOABS mcall output format (bed-like format containing chrom, start, end, ratio, totalC, methC, strand, next,  Plus,  totalC, methC, Minus, totalC, methC, localSeq columns)
scRNA-Seq: standard output from 10x Genomics pipeline: .mtx sparse matrix with UMI counts for each cell and gene, .tsv files containing the row (gene names) and column (individual cell barcodes) headers.


title: B2-1-5Aza-RNA.rep2

source_name: 5-Aza treated B2-1 cells

value: B2-1 treated with 5-Aza


title: B2-1-5Aza-RNA.rep1


title: B2-1-RNA.rep2

source_name: B2-1 ctrl cells

value: HEK-293 integrated with methylCMV-GFP


title: B2-1-RNA.rep1


title: WGBS_hESC_WT_D0_R2


title: B2-1-siCse1l-RNA.rep1


title: H3K9ac_ChipSeq_Input

city: Orsay

first: Maria Victoria

last: Gomez-Roldan

address: bat 630

institute: CNRS

data_processing:
Preprocessing of sequenced reads for quality was performed using FASTQC
libraries were cleaned and trimmed with trim_galore (mean Phred quality score greater than 20 ; read length greater than 10 after trimming ; retain unpaired reads)
ChipSeq were aligned onto RcHzRDP12 or RchiOBHm genome with bowtie2 with a maximum mismatch of 1bp and unique mapping
H3K9Aac peaks were called with MACS2 software ( number of duplicate reads at a location:1; nandwidth:300; mfold of 5:30; q-value cutoff:0.05)
SICER was used to detect H3K27me3 modification regions SICER was used (window size:200, gap size:600)
Genome_build: RcHzRDP12 GenBank accession number pending
Genome_build: RchiOBHm GenBank accession number pending
Supplementary_files_format_and_content: H3K9ac peaks calling results files are in a BED (6 col +4 )format file
Supplementary_files_format_and_content: H3K27me3 peaks calling results file are in BED (6 col) format file

organism: Rosa chinensis

source_name: petal

extract_protocol:
ChIP assays were performed using anti-H3K9ac (Millipore, ref. 07-352) or anti-H3K27me3 (Millipore, ref. 07-449) antibodies.  petals at the onset of flower opening were fixed in 1% (v/v) formaldehyde. Petal tissues were homogenized and nuclei were isolated and lyzed
Ten nanograms of IP or input DNA was used for ChIP-Seq library construction using NEB-Next Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s recommendations. Ten PCR cycles were used for all libraries. The library quality was assessed with Agilent 2100 Bioanalyzer (Agilent), and the libraries were subjected to high-throughput sequencing by NextSeq 500 (Illumina).

tag: genome

tag: chip antibody

value: petals at the onset of flower opening


title: H3K27me3_ChipSeq

description: H3K37me3 peaks calling on RcHzRDP12 genome and on RchiOBHm homozygous genome

value: H3K27me3 (Millipore, ref. 07-449, lot number 2686928)


title: H3K27me3_ChipSeq_Input


title: H3K9ac_ChipSeq

description: H3K9AC peaks calling on RcHzRDP12 genome and on RchiOBHm homozygous genome

value: H3K9ac (Millipore, ref. 07-352, lot number 2325091)


title: Heart at ZT0, WT mice, biological rep7

value: Heart


title: Heart at ZT0, WT mice, biological rep5

value: wildtype


title: Father

status: Public on Mar 14 2018

city: Taipei

first: Hsien-Sung

last: Huang

address: Rm: 1547, 15th Floor, No.1, Sec.1, Ren-ai Rd.

country: Taiwan

institute: National Taiwan University

data_processing:
ConDeTri was implemented to trim or remove the reads according to the quality score. Qualified reads after filtering low-quality data were analyzed using TopHat/Cufflinks for gene expression estimation. The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). For differential expression analysis, CummeRbund was employed to perform statistical analyses of gene expression profiles.
Genome_build: hg19
Supplementary_files_format_and_content: Gene ID, gene, locus, sample 1, sample 2, value 1, value 2, ratio, p value, q value.The ASE (allele-specific expression) means the  RNA-Seq data  were processed with allele-specific expression analysis. The gene means the RNA-Seq data were processed with gene expression analysis. The isoform means the RNA-Seq data were processed with gene isoform expression analysis.  .

source_name: Blood

extract_protocol:
RNA was extracted using a NucleoSpin miRNAKit (Macherey-Nagel, 740971). Genomic DNA was extracted using NucleoSpin Tissue (Macherey-Nagel, 740952)
Library for RNA-Seq was built up using a SureSelect Strand-Specific RNA Library Prep Kit (Agilent Technologies, G9691A).

tag: subject status

value: Father

value: Blood

tag: ngs id


title: Mother

value: Mother


title: WGBS_hESC_WT_D0_R1

value: human embryonic stem cells

value: WT


title: Offspring without autism

description:
processed data file:
Sample_6640-Sample_7827_isoform.xls
Sample_6640-Sample_7827_isoform.xls

source_name: Prefrontal cortex

value: Offspring without autism

value: Prefrontal cortex


title: Offspring with autism

description:
processed data file:
Sample_6640-Sample_7827_gene.xls
Sample_6640-Sample_7827_gene.xls

value: Offspring with autism


title: Heart at ZT0, WT mice, biological rep4


title: Heart at ZT0, WT mice, biological rep2


title: Heart at ZT0, WT mice, biological rep3


title: Heart at ZT0, WT mice, biological rep1


title: Jmjd1a- and Jmjd1b- double KO ES cells, biological replicate2

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with Factor Analysis for Robust Microarray Summarization (FARMS), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

source_name: Jmjd1b-conditional knockout induced in Jmjd1a-deficient ES cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA.

growth_protocol: ES cells were maintained in Dulbecco’s modified Eagle’s medium, containing 10% knockout SR (Invitrogen), 1% fetal calf serum, and leukemia-inhibiting factor (103 U/ml).

extract_protocol: Total RNA was isolated and purified using RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: To delete the conditional allele of Jmjd1b, ES cells were cultured in the presence of 800 nM OHT.

value: murine embryonic stem cells

value: (Jmjd1adelta/delta; Jmjd1bdelta/delta)


title: Jmjd1a-KO ES cells, biological replicate1

source_name: Jmjd1a-deficient ES cell line

value: (Jmjd1adelta/delta; Jmjd1b+/+)


title: WT ES cells, biological replicate2

source_name: embryonic stem cells from WT mice


title: Jmjd1b-KO ES cells, biological replicate1

source_name: embryonic stem cells from Jmjd1b-deficient mice

value: (Jmjd1a+/+; Jmjd1bdelta/delta)


title: Jmjd1a- and Jmjd1b- double KO ES cells, biological replicate1


title: Jmjd1b-KO ES cells, biological replicate2


title: WT ES cells, biological replicate1


title: Jmjd1a-KO ES cells, biological replicate2


title: LTKO-FST288-1

city: boston

first: rongya

last: tao

address: 300 Longwood Ave

institute: boston children's hospital

description: Gene expression files from liver from LTKO infected with Fst288-aav-tbg

hyb_protocol: Following labeling, 3.5 ug of ssDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene ST 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix Expression Console(Build 1.3.1.187) using Affymetrix default RMA analysis settings.

source_name: Liver from LTKO infected with Fst288-aav-tbg

label_protocol: Biotinylated ssDNA were prepared according to the standard GeneChip WT Plus Reagents Kit Affymetrix protocol from 500ng total RNA (User manual P/N 703174 Rev 1, 2013, Affymetrix). Fragmentation and labeling prepared using 5.5ug of ssDNA.

growth_protocol: All mice were housed in plastic cages on a 12:12 h light–dark photo-cycle with free access to water and food. We performed animal experiments according to procedures approved by the Boston Children’s Hospital Institutional Animal Care and Use Committee.

extract_protocol: RNA was extracted with TRI regent and then subjected to a cleanup step using an RNeasy Mini Kit with on-column DNase digestion (Qiagen)

treatment_protocol: Mice were infected with aav-tbg virus around two weeks and were fasting before tissue collection

value: male

value: liver


title: HFD-FST288-2

description: Gene expression files from liver from wild type mice maintainted on high fat diet infected with Fst288-aav-tbg

source_name: Liver from wild type mice maintainted on high fat diet infected with Fst288-aav-tbg


title: HFD-GFP3

description: Gene expression files from liver from wild type mice maintainted on high fat diet infected with GFP-aav-tbg

source_name: Liver from wild type mice maintainted on high fat diet infected with GFP-aav-tbg


title: LTKO-FST288-2


title: LTKO-GFP-2

description: Gene expression files from liver from LTKO mice infected with GFP-aav-tbg

source_name: Liver from LTKO mice infected with GFP-aav-tbg


title: LTKO-GFP-1


title: HFD-FST288-1


title: HFD-GFP1


title: HFD-FST288-3


title: LTKO-EPI

description: Gene expression data from epigonadal white adipose tissue of Irs1/2:FoxO1-flox: Albumin cre mice

treatment_protocol: Mice were fasting before tissue collection

value: epigonadal white adipose


title: Cntr-EPI

description: Gene expression data from epigonadal white adipose tissue of Irs1/2-flox mice


title: fad_rep2

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

hyb_protocol: Biotinylated cRNA was hybridized on GeneChip® Mouse Gene 2.0 ST Arrays , that were stained, washed and scanned following standard procedures.

data_processing: Background correction and normalization was performed using RMA as implemented in BRB-Tools

source_name: fad, microglia cells

label_protocol: Total RNA was amplified using the Ovation PicoSL WTA System V2 and further processed using the Encore Biotin Module according to the instructions supplied by the manufacturer (NuGen).

growth_protocol: All animals were maintained in SPF condition

extract_protocol: Animals were killed by transcardial perfusion in anasthesia. Microglia cells were isolated from the brain by FACS sorting. Total RNA was extracted from sorted microglia by Pico Pure RNA extraction kit (Life Technologies) according to manufacturer’s protocol.

treatment_protocol: All animals were injected with 8 mg Tamoxifen (20mg/ml Tamoxifen in corn oil) at 6 weeks of age to induce Hdac1 and 2 knock out in microglia.

value: Brain

value: Microglial cell

value: female

tag: age

value: 24-28 weeks

value: FAD Hdac1/2fl/fl


title: HFD-GFP2

tag: gender


title: fad_dko_rep1

scan_protocol: Biotinylated cRNA was hybridized on GeneChip® Mouse Gene 2.0 ST Arrays , that were stained, washed and scanned following standard procedures.

source_name: fad_dko, microglia cells

tag: tissue

value: FAD Hdac1/2fl/fl Cx3cr1CreERT2


title: LDKO-EPI

description: Gene expression data from epigonadal white adipose tissue of Irs1/2-flox: Albumin cre mice


title: Cntr3-EPI

description: Gene expression data from epigonadal white adipose tissue of Irs1/2:FoxO1-flox mice


title: fad_dko_rep2


title: fad_rep3


title: wt_rep3

source_name: wt, microglia cells

value: Wildtype


title: fad_rep1


title: fad_dko_rep3


title: wt_rep1


title: gastric cancer tissue_rep5

first: Taotao

last: Han

state: Beijing

address: NO.5 Dong Dan San Tiao, Dongcheng District

department: Department of Biochemistry and Molecular Biology

institute: Peking Union Medical College & Chinese Academy of Medical Sciences

description:
cancer-5
This sample is cancer tissue from a patient with gastric cancer

hyb_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was  fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 14 out of 16 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: gastric cancer tissue

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: patient with gastric cancer

value: gastric cancer tissues


title: gastric cancer tissue_rep4

description:
cancer-4
This sample is cancer tissue from a patient with gastric cancer


title: atrophic gastritis_rep3

description:
Inflammation-3
This sample is  gastritis tissue from a patient with atrophic gastritis

source_name: atrophic gastritis

value: patient with atrophic gastritis

value: atrophic gastritis


title: atrophic gastritis_rep2

description:
Inflammation-2
This sample is  gastritis tissue from a patient with atrophic gastritis


title: atrophic gastritis_rep5

description:
Inflammation-5
This sample is  gastritis tissue from a patient with atrophic gastritis


title: atrophic gastritis_rep6

description:
Inflammation-6
This sample is  gastritis tissue from a patient with atrophic gastritis


title: wt_rep2


title: gastric cancer tissue_rep2

description:
cancer-2
This sample is cancer tissue from a patient with gastric cancer


title: normal mucosa_rep4

description:
normal-4
This sample is normal mucosa tissue.

source_name: normal mucosa

value: normal mucosa


title: normal mucosa_rep3

description:
normal-3
This sample is normal mucosa tissue.


title: normal mucosa_rep1

description:
normal-1
This sample is normal mucosa tissue.


title: myc-R495X replicate 2

city: Baltimore

first: Jiou

last: Wang

state: MD

address: 615 N. Wolfe St.

institute: Johns Hopkins University

hyb_protocol: Total Affymetrix  Hyb Cocktail plus labeled sample were incubated on miRNA_2.0 arrays for 16hr at 48°C at 60RPM.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing: MicroRNA array CEL files were processed with Partek Genomics Suite 6.4 software. The RMA algorithm was used for summarization and normalization. Library files used in this analysis included: miRNA-2_0.cdf (Chip Layout Information), miRNA-2_0.annotations.20101222.csv (Chip Annotation).

source_name: HEK 293T

label_protocol: Affymetrix FlashTag Biotin HSR RNA Labeling kit following manufacturer's standard protocol.

growth_protocol: 6x106 HEK293T cells were plated onto 100mm2 plates prior to transfection with either myc-FUS or mutant myc-R495X and pMax-EGFP (Amaxa) marker with Lipofectamine 2000 (Life Technologies).

extract_protocol: Twenty-four hours after transfection, cells were trypsinized and resuspended in FACS Buffer (1X PBS, 100mM EDTA, 1% FBS) and sorted based upon GFP fluorescence. RNA was immediately isolated from sorted cells using phenol-chloroform extraction with TRIzol reagent (Invitrogen) according to manufacturer’s instructions. RNA was then submitted for the Agilent microRNA microarray analysis.

treatment_protocol: Not applicable

value: HEK 293T


title: myc-FUS replicate 2

value: myc-FUS


title: myc-FUS replicate 1


title: myc-FUS replicate 3


title: myc-R495X replicate 1


title: Sample_Zc3h13_RIP_Input

city: Shanghai

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

institute: Institutes of Biomedical Sciences Fudan University

data_processing:
Basecalls performed using CASAVA version 1.4
m6A-seq:
m6A-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf --max-multihits 1 --prefilter-multihits -o m6A_thout mm9_assemblies m6A.fq
m6A peaks were called by exomePeak 2.13 package of of Bioconductor under default parameters.
Mapped m6A reads were transfer to bedgraph files for visualization using bedtools.
RNA-seq:
RNA-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
Transcriptome is assemblied using cufflinks;differential expressed genes were identified by cuffdiff.
FPKM value of Ensembl genes were calculated by cufflinks.
RIP-seq:
RIP-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
Zc3h13 protein RIP signal was calculated as FPKM by FPKM_count.
FPKM value of Ensembl genes were calculated by FPKM_count.
Genome_build: mm9
Supplementary_files_format_and_content:
bed files include m6A peak lists identified by exomePeaks; bedGraph files include the averaged m6A enriched density.
tab-delimited text file include the FPKM values of Refseq genes in Mus musculus genome;
tab-delimited text file include the genes with Zc3h13 binding on mRNA transcripts.

growth_protocol: E14 murine embryonic stem cell was cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum, 1% none essential amino acid, 0.1% beta-mercaptoethanol, 100u/ml penicillin/ Streptomycin and 1000u LIF.

extract_protocol:
Total RNAs from mESCs were isolated using Trizol reagent according to the manufacturer’s instruction (Life technology, 15596018). Polyadenylated RNAs were extracted by oligodT beads (NEB, S1419S), followed by removal of contaminated rRNA with RiboMinus transcriptome isolation kit (Life technologies, A15026).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
m6A-seq: RNA was fragmented and subject to immunoprecipitation with a m6A specific antibody.
RNA-seq: RNAs were isolated from Zc3h13 knockdown, scramble knockdown and Zc3h13 rescue mouse ESCs. Polyadenylated RNA was extracted for library generation and sequencing.
RIP-seq: RNA was fragmented and subject to immunoprecipitation with a anti-Zc3h13 specific antibody.

value: Zc3h13 over-expression

value: murine embryonic stem cell

tag: molecule subtype

value: total RNA


title: Sample_Zc3h13_RIP_control

tag: antibody

value: Rabbit Normal IgG (Santa cruz, sc-2027)


title: Sample_Zc3h13_RIP_IP

value: Rabbit anti-Zc3h13 (bethyl, A300-748A)


title: Scid.adh.2c2_Satb1_RNA-rep2

city: Isehara

first: Hiroyuki

last: Hosokawa

state: Kanagawa

address: 143 Shimokasuya

department: Department of Immunology

institute: Tokai University School of Medicine

data_processing:
RNA-sequenced reads were trimmed with Trimmomatic (v.033; http://www.usadellab.org/cms/?page=trimmomatic) (Bolger et al., 2014) for removal of adapter –and low quality sequences (settings: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).  Resulting reads were then mapped onto the mouse genome build NCBI37/mm9 with STAR (v2.4.0) (Dobin et al., 2013) and post-processed with RSEM (v1.2.25; http://deweylab.github.io/RSEM/) (Li and Dewey, 2011) according to the settings in the ENCODE long-rna-seq-pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh) with the minor modifications that settings “--output-genome-bam --sampling-for-bam” was added to rsem-calculate-expression. STAR and RSEM reference libraries were created from genome build NCBI37/mm9 together with the Ensembl gene model file Mus_musculus.NCBIM37.66.gtf.  The resulting bam-files were used to create HOMER (Heinz et al., 2010) tag directories (makeTagDirectory with –keepAll setting).  For analysis of statistical significance among differentially expressed genes the raw gene counts were derived from each tag directory with analyzeRepeats.pl with the –noadj -condenseGenes options followed by the getDiffExpression.pl command using EdgeR (v3.6.8; http://bioconductor.org/packages/release/bioc/html/edgeR.html) (Robinson et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: Scid.adh.2c2_Runx1_WT_DN_Satb1_RNA-seq_RPKM_table.xlsx

source_name: Scid.adh.2c2 cells

extract_protocol:
Total RNA was isolated from 300,000 cells using an RNAeasy MicroKit (Qiagen).
Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) from ~1 μg of total RNA following manufacturer’s instructions.  Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

treatment_protocol: Scid.adh.2c2 cells were infected with either mock control, Runx1 WT, Runx1 DN or Satb1-containing retrovirus. Two days after infection, infected Scid.adh.2c2 cells were sorted and total RNA was isolated using an RNAeasy MicroKit (Qiagen).

tag: treatment

value: Transduced with Satb1-GFP


title: atrophic gastritis_rep1

description:
Inflammation-1
This sample is  gastritis tissue from a patient with atrophic gastritis

value: male


title: gastric cancer tissue_rep3

description:
cancer-3
This sample is cancer tissue from a patient with gastric cancer


title: myc-R495X replicate 3

tag: cell line

tag: genotype


title: atrophic gastritis_rep4

description:
Inflammation-4
This sample is  gastritis tissue from a patient with atrophic gastritis


title: Scid.adh.2c2_Runx1_DN_RNA-rep2

value: Transduced with Runx1 DN-GFP


title: Scid.adh.2c2_Runx1_WT_RNA-rep1

value: Transduced with Runx1 WT-GFP


title: Scid.adh.2c2_Runx1_WT_RNA-rep2


title: Scid.adh.2c2_Satb1_RNA-rep1


title: Scid.adh.2c2_Mock_RNA-rep2

value: Transduced with Mock-GFP


title: E13.5WL_5_02

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

description:
Single-cell_RNA-seq_Gene_Read_Count.txt.gz
Single-cell_RNA-seq_Gene_RPKM.txt.gz

data_processing:
The sequencing reads were aligned to the Mus musculus genome (mm10) using TopHat (v2.1.0) with the parameters “-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq”.
Reads aligned to genes were counted using HTSeq (v0.6.0) with the parameters “htseq-count -f bam -r pos -s no -a 30 input_bam gtf”.
Gene expression levels were quantified as reads per kilobase of the longest transcript per million mapped reads (RPKM).
genome build: mm10
processed data files format and content: values tab-delimited text files include read count and RPKM values for each sample

source_name: Pancreas

extract_protocol:
cDNA synthesis was performed following the Smart-seq2 method described by Picelli et al. 0.1 ul ERCC spike-in RNA (1:1,000,000 dilution, Life, 4456740) was added to the 4 ul lysis buffer in single cell RNA-seq.
2.5 ng of cDNA was used to conduct library using “TruePrep DNA Library Prep Kit” (Vazyme, TD502).

tag: embryonic day

tag: cell type

value: dorsal pancreas; E13.5 WT; Ngn3-low


title: E13.5WL_5_01


title: E13.5WL_5_03


title: E13.5WL_5_04


title: E13.5WH_6_16

value: dorsal pancreas; E13.5 WT; Ngn3-high


title: E13.5WH_6_14


title: E13.5WH_6_13


title: E13.5WH_6_15


title: E13.5WL_5_05


title: E13.5WH_6_08


title: E13.5WH_6_07


title: E13.5WH_6_09


title: E13.5WH_6_12


title: E13.5WH_6_10


title: E13.5WH_6_05


title: DLD-1α-Cat_3D_96h_rep2

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Hybridization and washing was performed according to manufacturers instructions.

data_processing: The data were analyzed with the Affymetrix Expression console using standard values, quantile normalization and RMA procedure.

label: Biotin

source_name: DLD-1 subpopulations, cultivated for 96h in collagen type I

label_protocol: Biotinylated cRNA were prepared according to manufacturers instructions.

growth_protocol: DLD-1 subpopulations were cultivated for 96h in 3D collagen type I (1 mg/ml)

extract_protocol: mRNA was isolated according to the manufacturer's instructions using NucleoSpin RNA II Kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: no treatment applied

value: subclone derived from DLD-1 cell line


title: DLD-1α-Cat_3D_96h_rep1


title: E13.5WH_6_11


title: DLD-1Δα-Cat_3D_96h_rep1


title: DLD-1α-Cat_3D_96h_rep3


title: DLD-1Δα-Cat_3D_96h_rep2


title: DLD-1Δα-Cat_3D_96h_rep3


title: E13.5WH_5_15


title: E13.5WH_6_02


title: E13.5WH_6_03


title: E13.5WH_5_14


title: E13.5WH_6_01


title: E13.5WH_5_11


title: E13.5WH_5_06


title: E13.5WH_5_16


title: E13.5WH_6_04


title: E13.5WH_5_01


title: E13.5WH_1_24


title: E13.5WH_1_23


title: E13.5WH_5_10


title: E13.5WH_5_08


title: E13.5WH_5_09


title: E13.5WH_1_20


title: E13.5WH_5_05


title: E13.5WH_5_04


title: E13.5WH_1_27


title: E13.5WH_1_26


title: E13.5WH_1_25


title: E13.5WH_1_22


title: E13.5WH_1_11


title: E13.5WH_1_13


title: E13.5WH_5_13


title: E13.5WH_1_09


title: E13.5WH_5_12


title: E13.5WH_5_07


title: E13.5WH_1_19


title: E13.5WH_1_18


title: E13.5WH_5_03


title: E13.5WH_1_06


title: E13.5WH_1_05


title: E13.5WH_1_17


title: E13.5WH_5_02


title: E13.5WH_1_16


title: E13.5WH_1_14


title: E13.5WH_1_03


title: E13.5WH_1_02


title: E13.5WH_1_21


title: E13.5WH_1_12


title: E13.5WH_1_01


title: E13.5WH_1_10


title: E13.5KL_5_14

value: dorsal pancreas; E13.5 Pdx1-Cre; Jmjd3 fl/fl ; Ngn3-low


title: E13.5WH_1_08


title: E13.5WH_1_07


title: E13.5WH_1_15


title: E13.5KL_5_15


title: E13.5KL_5_10


title: E13.5KL_5_11


title: E13.5WH_1_04


title: E13.5KL_5_12


title: E13.5KL_5_08


title: E13.5KL_5_13


title: E13.5KL_5_09


title: E13.5KL_5_04


title: E13.5KL_5_05


title: E13.5KL_5_03


title: E13.5KH_6_06

value: dorsal pancreas; E13.5 Pdx1-Cre; Jmjd3 fl/fl ; Ngn3-high


title: E13.5KH_6_05


title: E13.5KH_6_04


title: E13.5KL_5_01


title: E13.5KH_6_01


title: E13.5KH_5_13


title: E13.5KH_6_02


title: E13.5KL_5_02


title: E13.5KH_5_14


title: E13.5KH_5_12


title: E13.5KL_5_07


title: E13.5KH_5_15


title: E13.5KH_5_10


title: E13.5KH_5_09


title: E13.5KH_5_11


title: E13.5KH_5_03


title: E13.5KH_5_06


title: E13.5KH_5_07


title: E13.5KL_5_06


title: E13.5KH_5_05


title: E13.5KH_5_08


title: E13.5KH_5_04


title: E13.5KH_5_02


title: E13.5KH_6_03


title: E13.5KH_1_22


title: E13.5KH_1_23


title: E13.5KH_5_01


title: E13.5KH_1_18


title: E13.5KH_1_19


title: E13.5KH_1_20


title: E13.5KH_1_21


title: E13.5KH_1_08


title: E13.5KH_1_09


title: E13.5KH_1_17


title: E13.5KH_1_11


title: E13.5KH_1_06


title: E13.5KH_1_14


title: E13.5KH_1_15


title: E13.5KH_1_07


title: E13.5KH_1_10


title: E13.5KH_1_16


title: 34_5xFAD_HDAC1-2lox-HDAC2-2lox-Cx3cr1-CreERT2_H3K27ac

data_processing:
bcl2fastq version: 2.17.1.14 was used to convert RTA files generated from a Hiseq3000 run to Fastq files.
STAR 2.5.2b was used to align sequences to the mouse genome with parameters  --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --alignIntronMax 1 --seedSearchStartLmax 30 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10
Picard Tools 2.7.1 markDuplicates was performed with standard settings to remove duplicate reads
Deeptools 2.4.0 bamCoverage was used to generate bigWig files with parameters --normalizeTo1x (mm10 genome size) --normalizeUsingRPKM -e -bs 10 --smoothLength 50
Genome_build: GRCm38
Supplementary_files_format_and_content: bigWig files containing coverage information for ChIP and input DNA samples respectively.

source_name: FACS sorted microglia

growth_protocol: A microglia specific inducible knockout mouse line was generated by crossing Hdac1-2lox, Hdac2-2lox and Cx3cr1-CreERT2 mice. Mice were then crossed to the 5xFAD mouse line.

extract_protocol:
Mice were sacrificed at an age of 12 months and microglia were isolated by FACS sorting of brain homogenate for CD11bhi CD45lo cells.
Sequencing library preparation was performed using the KAPA Library Preparation Kit with Real-time PCR Library Amplification for Illumina Platforms Kit (Kapa Biosystems) as per the manufacturer’s protocol.

treatment_protocol: HDAC1 and HDAC2 knockout was induced at an age of 6 weeks and animals tehreafter aged to 12 months prioor to FACS sorting of microglia.


title: E13.5KH_1_03


title: E13.5KH_1_04


title: E13.5KH_1_02


title: E13.5KH_1_01


title: Scid.adh.2c2_Runx1_DN_RNA-rep1


title: 34_5xFAD_HDAC1-2lox-HDAC2-2lox-Cx3cr1-CreERT2_Input

value: Input DNA


title: 35_5xFAD_HDAC1-2lox-HDAC2-2lox_H3K9ac


title: Scid.adh.2c2_Mock_RNA-rep1


title: 35_5xFAD_HDAC1-2lox-HDAC2-2lox_Input


title: 34_5xFAD_HDAC1-2lox-HDAC2-2lox-Cx3cr1-CreERT2_H3K9ac


title: 35_5xFAD_HDAC1-2lox-HDAC2-2lox_H3K27ac


title: E13.5KH_1_12


title: E13.5KH_1_13


title: E13.5KH_1_05


title: 60_5xFAD_HDAC1-2lox-HDAC2-2lox_H3K9ac


title: 60_5xFAD_HDAC1-2lox-HDAC2-2lox_Input


title: 61_5xFAD_HDAC1-2lox-HDAC2-2lox-Cx3cr1-CreERT2_Input


title: 61_5xFAD_HDAC1-2lox-HDAC2-2lox-Cx3cr1-CreERT2_H3K27ac


title: E13.5WH_6_06


title: 62_5xFAD_HDAC1-2lox-HDAC2-2lox-Cx3cr1-CreERT2_H3K9ac


title: 61_5xFAD_HDAC1-2lox-HDAC2-2lox-Cx3cr1-CreERT2_H3K9ac


title: 62_5xFAD_HDAC1-2lox-HDAC2-2lox-Cx3cr1-CreERT2_Input


title: 69_5xFAD_HDAC1-2lox-HDAC2-2lox_H3K9ac


title: 69_5xFAD_HDAC1-2lox-HDAC2-2lox_H3K27ac


title: 62_5xFAD_HDAC1-2lox-HDAC2-2lox-Cx3cr1-CreERT2_H3K27ac


title: 69_5xFAD_HDAC1-2lox-HDAC2-2lox_Input


title: 60_5xFAD_HDAC1-2lox-HDAC2-2lox_H3K27ac


title: Sample_shZc3H13_m6A_Input_rep1

data_processing:
Library strategy: m6A-seq
Basecalls performed using CASAVA version 1.4
m6A-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf --max-multihits 1 --prefilter-multihits -o m6A_thout mm9_assemblies m6A.fq
RNA-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
m6A peaks were called by exomePeak 2.13 package of of Bioconductor under default parameters.
Transcriptome is assemblied using cufflinks;differential expressed genes were identified by cuffdiff.
Mapped m6A reads were transfer to bedgraph files for visualization using bedtools.
FPKM value of Ensembl genes were calculated by cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content:
bed files include m6A peak lists identified by exomePeaks;and bg files include the averaged m6A enriched density.
tab-delimited text file include the FPKM values of Ensembl genes in Mus musculus genome;

source_name: murine embryonic stem cell

treatment_protocol: RNA was fragmented and subject to immunoprecipitation with a m6A specific antibody.

tag: genotype/variation

value: Zc3H13 knock-down


title: Sample_shZc3H13_m6A_rep1

value: Rabbit anti-m6A (Synaptic, 202003)


title: Sample_shZc3H13_m6A_rep2


title: Sample_scr_m6A_Input_rep1

value: scr


title: Sample_WT_m6A_rep2


title: Sample_WT_m6A_rep1


title: DL145

type: genomic

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

description: Cytoscan HD

hyb_protocol: Samples were hybridized onto Cytoscan HD arrays Cytoscan HD and were washed and stained with GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
Nexus biodiscovery 7.5 edition Software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

source_name: Lymph Node

label_protocol: CytoScan™ Reagent Kit / 901808,t/GPL16131

extract_protocol: DNAs from frozen tissues samples were extracted using the QIAamp DNA Mini Kit.

tag: type of sample

value: Diffuse Large B-cell Lymphoma

value: frozen tissue


title: DLD-1α-Cat_3D_96h_rep1

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

data_processing: Affymetrix Chromosome Analysis Suite (ChAS) software was used for data processing and copy number aberration detection using the manufacturers standard settings and array annotation database build 32.3

label_protocol: The CytoScanHD kit and Reagent kit from Affymetrix was used following maufacturers instructions.

extract_protocol: genomic DNA was isolated according to the manufacturer's instructions using Macherey-Nagel Kit (Düren, Germany).


title: DLD-1Δα-Cat_3D_96h_rep1


title: DL138

description: Cytoscan HD

value: female


title: DL146

description: Cytoscan HD


title: DLD-1Δα-Cat_3D_96h_rep2


title: DL141

description: Cytoscan HD


title: DL143

description: Cytoscan HD


title: DL139

description: Cytoscan HD


title: DLD-1α-Cat_3D_96h_rep2


title: DLD-1α-Cat_3D_96h_rep3


title: DL142

description: Cytoscan HD


title: DL154

description: Cytoscan HD


title: DL136

description: Cytoscan HD


title: DL157

description: Cytoscan HD


title: DL159

description: Cytoscan HD


title: DLD-1Δα-Cat_3D_96h_rep3


title: DL140

description: Cytoscan HD


title: DL149

description: Cytoscan HD


title: DL134

description: Cytoscan HD


title: DL158

description: Cytoscan HD


title: DL155

description: Cytoscan HD


title: DL132

description: Cytoscan HD


title: DL152

description: Cytoscan HD


title: DL148

description: Cytoscan HD


title: DL131

description: Cytoscan HD


title: DL147

description: Cytoscan HD


title: DL151

description: Cytoscan HD


title: DL153

description: Cytoscan HD


title: DL133

description: Cytoscan HD


title: Mesocosm growth with Riboflavin, day 7, Replicate 2

city: Bayreuth

first: Alfons

middle: R

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

institute: University of Bayreuth

description: Biological replicate 1 of 2, Riboflavin treatment, harvest day 7, dye-swap

hyb_protocol: Hybridization and washing if the Microarrays was perfomed as described in the Low Input Quick Amp Labeling Kit (Agilent Technologies)

scan_protocol: Microarrays were scanned using a high-resolution scanner G2505C (Agilent Technologies) and Agilent's Feature Extraction software (v. 11.5.1.1) was used to quantify hybridization signals;

data_processing: Data were processed using LIMMA: background correction (normexp), normalized within arrays (loess), normalized between arrays (Aquantile);

organism: Agaricus bisporus

source_name: mycelia, drought, Riboflavin addition, day 7

label_protocol: RNA was labelled using the Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA);

growth_protocol: Agaricus bisporus hyphae on agar medium were placed on hay in gas-tight mesocosms and irrigated for three weeks with water or water containing 50 µM Riboflavin;

extract_protocol: Total RNA was extracted using the Rneasy Microarray Tissue Kit (Qiagen GmbH, Hilden, Germany);

treatment_protocol: Drought treatment was applied by stopping irrigation; samples were taken after 3 and 7 days, respectively;

tag: strain

value: var bisporus (H97)

value: mycelia

tag: stress

value: drought

value: Riboflavin-supplemented

source_name: mycelia, irrigated, Riboflavin addition, day 7

value: irrigated


title: DL128

description: Cytoscan HD


title: DL127

description: Cytoscan HD

value: male


title: DL123

description: Cytoscan HD


title: DL118

description: Cytoscan HD


title: DL125

description: Cytoscan HD


title: DL129

description: Cytoscan HD


title: Mesocosm growth with Riboflavin, day 7, Replicate 1

description: Biological replicate 1 of 2, Riboflavin treatment, harvest day 7


title: Mesocosm growth with Riboflavin, day 3, Replicate 2

description: Biological replicate 1 of 2, Riboflavin treatment, harvest day 3, dye-swap

source_name: mycelia, drought, Riboflavin addition, day 3

source_name: mycelia, irrigated, Riboflavin addition, day 3


title: Mesocosm growth with Riboflavin, day 3, Replicate 1

description: Biological replicate 1 of 2, Riboflavin treatment, harvest day 3


title: DL99

description: Cytoscan HD


title: DL117

description: Cytoscan HD


title: DL119

description: Cytoscan HD


title: DL113

description: Cytoscan HD


title: DL112

description: Cytoscan HD


title: Mesocosm growth, day 7, Replicate 2

description: Biological replicate 1 of 2, harvest day 7, dye-swap

source_name: mycelia, drought, day 7

source_name: mycelia, irrigated, day 7


title: DL124

description: Cytoscan HD


title: DL111

description: Cytoscan HD


title: DL107

description: Cytoscan HD


title: DL126

description: Cytoscan HD


title: DL122

description: Cytoscan HD


title: Mesocosm growth, day 7, Replicate 1

description: Biological replicate 1 of 2, harvest day 7


title: DL108

description: Cytoscan HD


title: aNP rep3

city: Rijeka

first: Tihana

last: Lenac Rovis

address: B. Branchetta 20

department: Center for Proteomics

country: Croatia

institute: University of Rijeka Faculty of Medicine

data_processing:
basecalls performed using bcl2fastq2 v2.15.0
trimming off adaptors
Sequenced reads were mapped to the Zv9 zebrafish genome using TopHat2 with following parameters tophat--segmentlength20--segment-mismatches 1-p 4 -o output.sam ref.fasta R1_001_egal.fastq R2_001.egal.fastq
Genome_build: Zv9
Supplementary_files_format_and_content: delimited text files include raw read counts.

organism: Danio rerio

source_name: telencephalon

extract_protocol:
The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish, to recover RFP-positive qRGs, RFP/GFP-double positive aRGs and GFP-positive aNPs
RNA libraries were prepared for sequencing using standard Illumina protocols

value: telencephalon

value: 3 months

value: WT

tag: cell types

value: activated Neural Progenitors


title: aNP rep2


title: DL115

description: Cytoscan HD


title: DL100

description: Cytoscan HD


title: DL104

description: Cytoscan HD


title: Mesocosm growth, day 3, Replicate 1

description: Biological replicate 1 of 2, harvest day 3

source_name: mycelia, irrigated, day 3

source_name: mycelia, drought, day 3


title: aNP rep1


title: aRG rep3

value: activated Radial Glia


title: Mesocosm growth, day 3, Replicate 2

description: Biological replicate 1 of 2, harvest day 3, dye-swap


title: DL103

description: Cytoscan HD


title: DL98

description: Cytoscan HD


title: aRG rep1


title: qRG rep3

value: quiescent Radial Glia


title: DL114

description: Cytoscan HD


title: aRG rep2


title: qRG rep2


title: qRG rep1


title: notch-neg rep3

source_name: head, without eyes

value: head, without eyes

value: Notch3 mutant

value: radial glia


title: DL116

description: Cytoscan HD

value: Diffuse Large B-cell Lymphoma

value: frozen tissue


title: notch-neg rep1


title: notch-pos rep2


title: DL102

description: Cytoscan HD

value: female


title: notch-pos rep3


title: DL97

description: Cytoscan HD


title: notch-pos rep1


title: Wild-type replicate 2

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
NextSeq v2 reagents
Genome sequence and annotation were downloaded from Ensembl (Mus_musculus.GRCm38.91.gtf.gz and Mus_musculus.GRCm38.dna.primary_assembly.fa.gz)
UMI-tools version: 0.5.3 (PMID:28100584)  was used to whitelist and extract cell barcodes
Skewer v0.2.2 was used to trim low quality bases from the end of read 2 containing the transcript sequence
STAR version 2.5.2b was used to map read2 to the
featureCounts v1.6.0  was used to assign reads to genes using the Ensembl v91 annotation in gtf format.
UMI-tools version: 0.5.3 was used to tabulate the gene counts for each cell barcode
Our custom script is available from Zenodo https://doi.org/10.5281/zenodo.1195057
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene-wise raw read counts of gene expression per cell in tsv format
Supplementary_files_format_and_content: 3 column table gene /cell barcode/count

source_name: Renal cortex

growth_protocol: C57BL/6-Ins2Akita/J mice and their wild-type counterparts were obtained from The Jackson Laboratory, USA. The  water and feed (standard lab chow) were provided ad libitum. Mice were housed in specific pathogen-free conditions with exposure to 12:12-h light-dark cycles for 24 weeks (n=8/group). All animal studies were performed in accordance with the guidelines of the AMREP Animal Ethics Committee and the NHMRC of Australia.

extract_protocol:
Renal cortex was collected from one harvested kidney and minced with a scalpel then pushed through a 70 micron sieve followed by digestion with collagenase IV for 30 mins at 37 C. Cells were pelleted by centrifugation for 3 mins at 300g, followed by two washes with PBS.
Cell suspensions underwent drop-seq according to the protocol of Macosko et al (PMID: 26000488). Cell barcode is the first 12 nt of read 1. UMI is position 13 to 20 of read 1.

tag: age (days)

value: Wild-type


title: DL101

description: Cytoscan HD


title: DL91

description: Cytoscan HD


title: Wild-type replicate 1


title: DL106

description: Cytoscan HD


title: DL109

description: Cytoscan HD


title: Akita replicate 1


title: notch-neg rep2


title: DL87

description: Cytoscan HD


title: DL86

description: Cytoscan HD


title: sample185: brief 60m rep3, u0126, eRNA

city: Boston

first: Kelsey

last: Tyssowski

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
Base-calling with Illumina RTA v2 (default NextSeq settings)
Alignment was done using STAR with the following settings: --alignSJDBoverhangMin 3 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMax 100000 --clip3pAdapterSeq GATCGGAAGAGCACACGTCTGAACTCCAGT --limitBAMsortRAM 117874660630 --outSAMtype SAM SortedByCoordinate --seedSearchStartLmax 25 --seedPerReadNmax 100000
Resulting SAM files were converted to BAM files then to BED files using samtools and bedtools. Reads were mapped to genes using the bedtools map function with the strand consideration setting turned on.
Normalization was performed using both ERCC spike ins or the genometric mean of control genes/enhancers.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file with control-normalized values for regions of interest

source_name: Primary Cutlure Mouse Cortical Neurons

growth_protocol: Sample from mouse cortical neurons dissected at E16.5 and cultured for 7-8 days in vitro

extract_protocol:
RNA was extracted using the Qiagen Rneasy kit with the DNase step according to instructions of the manufacturer.
Libraries were constructed using the Illuminia LT or HT TruSeq Stranded Total RNA kit according to the instructions of the manufacturer except that all volumes were reduced to 1/3 of their recommended amount.
For captured libraries, 250ng of pooled libraries were heated to 95C to denature DNA and then incubated with 250ng ARG-seq or eRNA-seq RNA baits overnight at 65C in hybridization buffer (2.5ug Cot1 DNA (ThermoFisher), 2.5ug Salmon Sperm DNA (ThermoFisher), 15mM p5 blocking primers, 15mM p7 blocking primers, 5X SSPE (ThermoFisher), 5X Denhardt’s Solution (ThermoFisher), 0.133% SDS). Blocking primers are: p5-AATGATACGGCGACCACCGAGATCTACAC, ACACTCTTTCCCTACACGACGCTCTTCCGATC/3InvdT/ p7-CAAGCAGAAGACGGCATACGAGAT, GTGACTGGAGTTCAGACGTGT GCTCTTCCGATC/3InvdT/ Primers for amplification are: p5-AATGATACGGCGACCACCGAGA, p7-CAAGCAGAAGACGGCATACGAG. Hybridized samples were incubated with MyOne Streptavadin T1 Dynabeads (Invitrogen) in binding buffer (1M NaCl, 10mM Tris-HCl pH 7.5, 1mM EDTA). Beads were washed once in 1x SCC, 0.1% SDS at room temperature and three times in 0.1x SCC 0.1% SDS at 65C. Captured libraries were eluted with 0.1M NaOH and neutralized with 1M Tris-HCl pH 7.5. Libraries were then purified using the Qiagen MinElute PCR cleanup kit and re-amplified using Herculase II Fusion polymerase (Agilent).

tag: mouse strain

value: Primary Cutlure Mouse Cortical Neurons

tag: capture

value: eRNA

tag: activation

value: brief

tag: time point

tag: drug

tag: molecule

value: captured total RNA


title: sample186: brief 60m rep4, u0126, eRNA

tag: tissue


title: DL85

description: Cytoscan HD

tag: gender

value: male


title: DL82

description: Cytoscan HD


title: Akita replicate 2


title: sample184: brief 60m rep2, u0126, eRNA


title: sample183: brief 60m rep1, u0126, eRNA


title: sample182: brief 20m rep4, u0126, eRNA


title: DL81

description: Cytoscan HD


title: sample181: brief 20m rep3, u0126, eRNA


title: DL74

description: Cytoscan HD


title: sample180: brief 20m rep2, u0126, eRNA


title: DL75

description: Cytoscan HD


title: DL72

description: Cytoscan HD


title: sample179: brief 20m rep1, u0126, eRNA


title: DL73

description: Cytoscan HD


title: DL59

description: Cytoscan HD


title: DL71

description: Cytoscan HD


title: sample178: brief 60m rep4, veh, eRNA

value: DMSO


title: DL69

description: Cytoscan HD


title: sample177: brief 60m rep3, veh, eRNA


title: sample176: brief 60m rep2, veh, eRNA


title: DL64

description: Cytoscan HD


title: DL66

description: Cytoscan HD


title: sample175: brief 60m rep1, veh, eRNA


title: DL61

description: Cytoscan HD


title: sample174: brief 20m rep4, veh, eRNA


title: DL60

description: Cytoscan HD


title: sample173: brief 20m rep3, veh, eRNA


title: sample172: brief 20m rep2, veh, eRNA


title: DL55

description: Cytoscan HD


title: DL47

description: Cytoscan HD


title: DL63

description: Cytoscan HD


title: DL57

description: Cytoscan HD


title: DL48

description: Cytoscan HD


title: DL79

description: Cytoscan HD


title: sample170: sustained 60m rep 5, u0126, eRNA

value: sustained


title: sample169: sustained 60m rep3, u0126, eRNA


title: DL53

description: Cytoscan HD


title: DL70

description: Cytoscan HD


title: DL50

description: Cytoscan HD


title: sample168: sustained 60m rep2, u0126, eRNA


title: sample167: sustained 60m rep1, u0126, eRNA


title: sample166: sustained 20m rep4, u0126, eRNA


title: sample165: sustained 20m rep3, u0126, eRNA


title: sample171: brief 20m rep1, veh, eRNA


title: sample163: sustained 20m rep1, u0126, eRNA


title: sample164: sustained 20m rep2, u0126, eRNA


title: DL68

description: Cytoscan HD


title: sample162: sustained 60m, rep4, veh, eRNA


title: sample161: sustained 60m rep3, veh, eRNA


title: sample160: sustained 60m rep2, veh, eRNA


title: sample159: sustained 60m rep1, veh, eRNA


title: sample158: sustained 20m rep4, veh, eRNA


title: sample157: sustained 20m rep3, veh, eRNA


title: DL42

description: Cytoscan HD


title: DL45

description: Cytoscan HD


title: sample156: sustained 20m rep2, veh, eRNA


title: DL37

description: Cytoscan HD


title: DL40

description: Cytoscan HD


title: DL38

description: Cytoscan HD


title: DL39

description: Cytoscan HD


title: DL36

description: Cytoscan HD


title: sample154: unstim 4.2, u0126, eRNA

description: sample154 (technical replicate of sample 153, from same dissection, grown separately)


title: sample153: unstim, 4.1, u0126, eRNA

description: sample153 (technical replicate of sample 154, from same dissection, grown separately)


title: DL46

description: Cytoscan HD


title: sample155: sustained 20m rep1, veh, eRNA


title: DL29

description: Cytoscan HD


title: sample152: unstim 3.2, u0126, eRNA

description: sample152 (technical replicate of sample 151, from same dissection, grown separately)


title: sample151: unstim, 3.1, u0126, eRNA

description: sample151 (technical replicate of sample 152, from same dissection, grown separately)


title: DL30

description: Cytoscan HD


title: DL33

description: Cytoscan HD


title: DL26

description: Cytoscan HD


title: sample149: unstim, rep2.1, u0126, eRNA

description: sample149 (technical replicate of sample 150, from same dissection, grown separately)


title: DL27

description: Cytoscan HD


title: DL18

description: Cytoscan HD


title: DL44

description: Cytoscan HD


title: sample148: unstim, rep 1.2, u0126, eRNA

description: sample148 (technical replicate of sample 147, from same dissection, grown separately)


title: DL25

description: Cytoscan HD


title: DL34

description: Cytoscan HD


title: sample147: unstim, rep1.1, u0126, eRNA

description: sample147 (technical replicate of sample 148, from same dissection, grown separately)


title: DL23

description: Cytoscan HD


title: rep6_wt_aPDL1 [Lexogen_48]

city: Innsbruck

first: Dietmar

last: Rieder

address: Innrain 80

department: Biocenter

country: Austria

institute: Medical University of Innsbruck

description:
therapy_normalized_counts.txt
Lexogen_48

data_processing:
The reads were first preprocessed through a high stringency quality control pipeline consisting of adapter removal with Cutadapt and quality trimming with Trimmomatic to remove bases with bad quality scores. All reads shorter than 22 nucleotides were removed.
The quality-trimmed reads were mapped to the mm10 reference genome using a two-step alignment method; alignment with STAR followed by alignment of the unmapped reads with Bowtie2.
Gene-specific read counts were calculated using HTSeq-count. Differential expression analyses were performed using the R package DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix with normalized counts, where rows are genes and columns are samples

source_name: Tumour infiltrating lymphocytes

growth_protocol: 5×10^5 B16-OVA tumor cells were injected s.c. into wild-type or Nr2f6-deficient mice.

extract_protocol:
RNA was isolated using the RNeasy® Mini Kit.  (205113, Qiagen). RNA integrity was verified with the Agilent Bioanalyzer. Ion TorrentTM compatible libraries were generated from 20 ng total RNA input
QuantSeq 3' mRNA-Seq Library Prep Kit from Lexogen was used for library construction

treatment_protocol: Ab treatment with 0.5 mg anti-mouse PD-L1 (Clone10F.9G2; BE0101) or control Ab IgG2b (LTF-2; BE0090) was injected i.p. starting on d3 twice a week.

value: Tumour infiltrating lymphocytes

tag: genotype

value: wild type

tag: treatment


title: rep5_wt_aPDL1 [Lexogen_47]

description:
therapy_normalized_counts.txt
Lexogen_47

tag: cell type


title: sample145: unstim, rep 4.1, veh, eRNA

description: sample145 (technical replicate of sample 146, from same dissection, grown separately)


title: sample150: unstim, rep 2.2, u0126, eRNA

description: sample150 (technical replicate of sample 149, from same dissection, grown separately)


title: DL17

description: Cytoscan HD


title: DL43

description: Cytoscan HD


title: rep6_Nr2f6_aPDL1 [Lexogen_45]

description:
therapy_normalized_counts.txt
Lexogen_45


title: rep4_wt_aPDL1 [Lexogen_46]

description:
therapy_normalized_counts.txt
Lexogen_46


title: DL24

description: Cytoscan HD


title: sample143: unstim rep 3.1, veh, eRNA

description: sample143 (technical replicate of sample 144, from same dissection, grown separately)


title: DL20

description: Cytoscan HD


title: rep5_Nr2f6_aPDL1 [Lexogen_44]

description:
therapy_normalized_counts.txt
Lexogen_44


title: DL15

description: Cytoscan HD


title: DL16

description: Cytoscan HD


title: DL28

description: Cytoscan HD


title: DL35

description: Cytoscan HD


title: DL21

description: Cytoscan HD


title: rep4_Nr2f6_aPDL1 [Lexogen_43]

description:
therapy_normalized_counts.txt
Lexogen_43


title: sample146: unstim, rep 4.2 veh, eRNA

description: sample146 (technical replicate of sample 145, from same dissection, grown separately)


title: sample141: unstim rep 2.1, veh, eRNA

description: sample141 (technical replicate of sample 142, from same dissection, grown separately)


title: DL31

description: Cytoscan HD


title: rep3_wt_aPDL1 [Lexogen_39]

description:
therapy_normalized_counts.txt
Lexogen_39


title: rep1_wt_aPDL1 [Lexogen_37]

description:
therapy_normalized_counts.txt
Lexogen_37


title: sample138: 150m light, sl327, brief

source_name: Visual Cortex

growth_protocol: Sample from visual cortex of adult male mouse

value: Visual Cortex

value: ARG


title: sample140: unstim, rep1.2, veh, eRNA

description: sample140 (technical replicate of sample 139, from same dissection, grown separately)


title: sample139: unstim, rep 1.1 veh, eRNA

description: sample139 (technical replicate of sample 140, from same dissection, grown separately)


title: rep3_wt_IgG2b [Lexogen_36]

description:
therapy_normalized_counts.txt
Lexogen_36


title: sample137: 150m light, sl327, brief


title: sample142: unstim rep 2.2, veh, eRNA

description: sample142 (technical replicate of sample 141, from same dissection, grown separately)


title: sample144: unstim, rep 3.2, veh, eRNA

description: sample144 (technical replicate of sample 143, from same dissection, grown separately)


title: rep2_wt_aPDL1 [Lexogen_38]

description:
therapy_normalized_counts.txt
Lexogen_38


title: DL14

description: Cytoscan HD


title: rep2_wt_IgG2b [Lexogen_35]

description:
therapy_normalized_counts.txt
Lexogen_35


title: sample136: 150m dark, sl327


title: rep3_Nr2f6_aPDL1 [Lexogen_33]

description:
therapy_normalized_counts.txt
Lexogen_33


title: sample135: 150m dark, sl327


title: sample134: 150m light, corn oil, brief

value: Corn Oil


title: rep1_wt_IgG2b [Lexogen_34]

description:
therapy_normalized_counts.txt
Lexogen_34


title: rep2_Nr2f6_aPDL1 [Lexogen_32]

description:
therapy_normalized_counts.txt
Lexogen_32


title: DL11

description: Cytoscan HD


title: sample133: 150m light, corn oil, brief


title: rep1_Nr2f6_aPDL1 [Lexogen_31]

description:
therapy_normalized_counts.txt
Lexogen_31


title: sample132: 150m dark, corn oil


title: rep3_Nr2f6_IgG2b [Lexogen_30]

description:
therapy_normalized_counts.txt
Lexogen_30


title: sample131: 150m dark, corn oil


title: sample130: 30m light, sl327, brief


title: rep2_Nr2f6_IgG2b [Lexogen_29]

description:
therapy_normalized_counts.txt
Lexogen_29


title: rep1_Nr2f6_IgG2b [Lexogen_28]

description:
therapy_normalized_counts.txt
Lexogen_28


title: sample129: 30m light, sl327, brief


title: ML1_sample_0090

city: Saint Augustine

first: Alexandra

last: Hernandez

state: FL

address: 9505 OCEAN SHORE BLVD

department: Biology

institute: Whitney Laboratory for Marine Bioscience, University of Florida

data_processing:
Libraries were sequenced on the Illumina HiSeq2000 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 10. trimming of read2 to 35 bases - not required).
CEL-Seq (Hashimshony, et a. 2012l) demultiplexing of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0, against MlScaffold09
Read counting with htseq-count version 0.5.4p3. on annotations evm2.2
Genome_build: MlScaffold09 [http://research.nhgri.nih.gov/mnemiopsis/download/download.cgi?dl=genome; http://research.nhgri.nih.gov/mnemiopsis/download/proteome/ML2.2.gff3.gz (http://www.sciencemag.org/content/342/6164/1242592.full.pdf?keytype=ref&siteid=sci&ijkey=yaMBwY%2FafqQpk)]
Supplementary_files_format_and_content: tabular Expression matrix containing read counts

organism: Mnemiopsis leidyi

source_name: single embryo_20hr

extract_protocol:
Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps.
The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. A slightly different set of barcodes was used that includes Unique Molecular Identifier.

tag: sample id

value: single embryo 90

tag: developmental time (hours)


title: ML1_sample_0089

source_name: single embryo_19hr

value: single embryo 89


title: ML1_sample_0088

source_name: single embryo_18hr

value: single embryo 88


title: sample126: 30m dark, sl327


title: ML1_sample_0087

source_name: single embryo_17hr

value: single embryo 87


title: sample128: 30m light, sl327, brief


title: sample125: 30m light, corn oil, brief


title: sample127: 30m dark, sl327


title: ML1_sample_0086

source_name: single embryo_16hr

value: single embryo 86


title: sample123: 30m light, corn oil, brief


title: sample124: 30m light, corn oil, brief


title: ML1_sample_0085

source_name: single embryo_15hr

value: single embryo 85


title: ML1_sample_0084

source_name: single embryo_14hr

value: single embryo 84


title: DL12

description: Cytoscan HD

source_name: Lymph Node

tag: type of sample

value: Diffuse Large B-cell Lymphoma

value: frozen tissue


title: sample122: 30m dark, corn oil

value: captured total RNA


title: DL10

description: Cytoscan HD

value: male


title: ML1_sample_0083

value: single embryo 83


title: sample120: 30m dark, corn oil


title: ML1_sample_0081

value: single embryo 81


title: sample119: 150m light, sl327, sustained

value: sustained


title: sample121: 30m dark, corn oil

value: Visual Cortex


title: sample118: 150m light, sl327, sustained

value: ARG


title: ML1_sample_0079

value: single embryo 79


title: ML1_sample_0078

value: single embryo 78


title: sample117: 150m light, sl327, sustained


title: ML1_sample_0082

value: single embryo 82


title: ML1_sample_0080

value: single embryo 80


title: sample116: 150m dark, sl327


title: ML1_sample_0077

value: single embryo 77


title: sample115: 150m dark, sl327


title: ML1_sample_0076

source_name: single embryo_13hr

value: single embryo 76


title: sample114: 30m light, sl327, sustained


title: DL5

description: Cytoscan HD

value: female


title: ML1_sample_0074

value: single embryo 74


title: sample112: 30m light, sl327, sustained


title: sample113: 30m light, sl327, sustained


title: ML1_sample_0072

value: single embryo 72


title: sample110: 30m dark, sl327


title: ML1_sample_0073

value: single embryo 73


title: ML1_sample_0071

value: single embryo 71


title: ML1_sample_0070

value: single embryo 70


title: sample107: 150m light, corn oil, sustained

value: Corn Oil

value: captured total RNA


title: sample106: 150m dark, corn oil


title: sample111: 30m dark, sl327


title: ML1_sample_0068

value: single embryo 68


title: DL4

description: Cytoscan HD

value: Diffuse Large B-cell Lymphoma

value: male

value: frozen tissue


title: sample105: 150m dark, corn oil

value: Visual Cortex

value: ARG


title: sample108: 150m light, corn oil, sustained

value: sustained


title: ML1_sample_0067

value: single embryo 67


title: DL8

description: Cytoscan HD


title: sample102: 30m light, corn oil, sustained


title: ML1_sample_0065

value: single embryo 65


title: ML1_sample_0064

value: single embryo 64


title: DL9

description: Cytoscan HD

value: female


title: sample103: 30m light, corn oil, sustained


title: ML1_sample_0069

value: single embryo 69


title: sample109: 150m light, corn oil, sustained


title: ML1_sample_0063

value: single embryo 63


title: ML1_sample_0062

value: single embryo 62


title: sample101: dark 30m, corn oil


title: ML1_sample_0066

value: single embryo 66


title: sample104: 30m light, corn oil, sustained

value: Corn Oil


title: sample100: dark 30m, corn oil

value: captured total RNA


title: ML1_sample_0060

value: single embryo 60


title: ML1_sample_0061

value: single embryo 61


title: sample99: 360m rep 6, u0126, brief

value: Primary Cutlure Mouse Cortical Neurons

value: brief


title: sample98: 360m rep 7, u0126, brief


title: ML1_sample_0059

value: single embryo 59


title: DL6

description: Cytoscan HD

value: Diffuse Large B-cell Lymphoma

value: frozen tissue


title: sample96: 60m rep 6, u0126, brief

value: ARG


title: sample97: 60m rep 7, u0126, brief


title: ML1_sample_0057

source_name: single embryo_11hr

value: single embryo 57


title: sample95: 60m rep 5, u0126, brief


title: ML1_sample_0055

source_name: single embryo_9hr

value: single embryo 55


title: ML1_sample_0056

source_name: single embryo_10hr

value: single embryo 56


title: DL3

description: Cytoscan HD

value: male


title: sample94: 20m rep 7, u0126, brief


title: sample93: 20m rep 6, u0126, brief


title: ML1_sample_0058

source_name: single embryo_12hr

value: single embryo 58


title: ML1_sample_0053

source_name: single embryo_8hr

value: single embryo 53


title: sample92: 20m rep 5, u0126, brief

source_name: Primary Cutlure Mouse Cortical Neurons


title: sample91: 360m rep 6, u0126, sustained

value: sustained


title: ML1_sample_0054

source_name: single embryo_8.5hr

value: single embryo 54


title: DL2

description: Cytoscan HD

value: female


title: sample90: 360m rep 7, u0126, sustained

value: captured total RNA


title: ML1_sample_0051

source_name: single embryo_7hr

value: single embryo 51


title: sample89: 60m rep 7, u0126, sustained

value: Primary Cutlure Mouse Cortical Neurons


title: ML1_sample_0050

source_name: single embryo_6.5hr

value: single embryo 50


title: ML1_sample_0049

source_name: single embryo_6hr

value: single embryo 49


title: sample88: 60m rep 6, u0126, sustained


title: sample87: 60m rep 5, u0126, sustained


title: ML1_sample_0048

source_name: single embryo_5.5hr

value: single embryo 48


title: sample86: 20m rep 7, u0126, sustained


title: sample85: 20m rep 6, u0126, sustained


title: ML1_sample_0046

source_name: single embryo_4.5hr

value: single embryo 46


title: ML1_sample_0047

source_name: single embryo_5hr

value: single embryo 47


title: sample84: 20m rep 5, u0126, sustained

value: ARG


title: sample83: 0m rep 7.2, u0126, sustained

description: sample083 (technical replicate of sample 82, from same dissection, grown separately)


title: ML1_sample_0044

source_name: single embryo_3hr

value: single embryo 44


title: ML1_sample_0045

source_name: single embryo_4hr

value: single embryo 45


title: sample82: 0m rep 7.1, u0126, sustained

description: sample082 (technical replicate of sample 83, from same dissection, grown separately)


title: ML1_sample_0042

source_name: single embryo_1hr

value: single embryo 42


title: ML1_sample_0043

source_name: single embryo_2hr

value: single embryo 43


title: sample81: 0m rep 6.2, u0126, sustained

description: sample081 (technical replicate of sample 80, from same dissection, grown separately)


title: sample80: 0m rep 6.1, u0126, sustained

description: sample080 (technical replicate of sample 81, from same dissection, grown separately)


title: ML1_sample_0041

source_name: single embryo_0hr

value: single embryo 41


title: ML1_sample_0052

source_name: single embryo_7.5hr

value: single embryo 52


title: sample79: 0m, rep 5.2, u0126, sustained

description: sample079 (technical replicate of sample 78, from same dissection, grown separately)


title: sample76: 360m rep 7, veh, brief

value: brief

value: DMSO


title: sample75: 360m rep 4, veh, sustained

value: sustained

value: captured total RNA


title: sample74: 360m rep 3, veh, brief

value: Primary Cutlure Mouse Cortical Neurons


title: sample72: 360m rep 1, veh, brief


title: sample73: 360m rep 2, veh, brief


title: sample68: 60m rep 4, veh, brief


title: sample70: 60m rep 6, veh, brief


title: sample71: 60m rep 7, veh, brief


title: sample78: 0m, rep 5.1, u0126, sustained

description: sample078 (technical replicate of sample 79, from same dissection, grown separately)


title: sample66: 60m rep 2, veh, brief


title: sample65: 60m rep 1, veh, brief


title: sample62: 20m rep , veh, brief


title: sample63: 20m rep 6, veh, brief


title: sample64: 20m rep 7, veh, brief


title: sample77: 360m rep 6, veh, brief


title: sample61: 360m rep 6, veh, sustained


title: sample60: 360m rep 7, veh, sustained


title: sample59: 360m rep 4, veh, sustained


title: GES-1

city: Beijing

description:
GES-1
This sample is of Homo sapiens  normal gastric epithelial cell line GES-1.

source_name: GES-1 cells

growth_protocol: Homo sapiens normal gastric epithelial cell line GES-1 was grown to Logarithmic phase phase (5% CO2,at 37°C ) in RPMI1640 (Gibco, Eggenstein, Germany) supplemented with 10% (vol) fetal bovine serum (10106078, Gibco) and 100U/ml penicillin.

treatment_protocol: GES-1  cell is infected with cultured H.pylori. The cultures were incubated for 24 or 72 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

value: normal gastric epithelial cell line

tag: infected with

value: none (uninfected control)


title: GES1-Hp72h

description:
GES1-72h
This sample is of Homo sapiens  normal gastric epithelial cell line GES-1 infected with cultured H.pylori for 72 hours.

source_name: GES-1, 72hr, H.pylori infected

value: H. pylori


title: sample58: 360m rep 3, veh, sustained


title: sample57: 360m rep 2, veh, sustained


title: GES1-Hp24h

description:
GES1-24h
This sample is of Homo sapiens  normal gastric epithelial cell line GES-1 infected with cultured H.pylori for 24 hours.

source_name: GES-1, 24hr, H.pylori infected


title: DPC2-STK2

city: Hiroshima

first: katsumi

last: Fujimoto

address: 1-2-3 Kasumi, Minami-ku

institute: Hiroshima University

hyb_protocol: cRNA fragmentation and hybridization were preformed using the Gene Expression Hybridization Kit (Agilent) according to the manufacturer's instructions. 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes. The fragmentation mixture was hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash buffer 2 (Agilent) according to the manufacturer's instructions.

scan_protocol: The arrays were then scanned using the Agilent DNA Microarray Scanner (G2505C).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol: GE1_107_Sep09 and Grid: 028004_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: dental pulp cell, cultured with STK2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the Low Input Quick Amp Labeling Kit, one color (Agilent) according to the manufacturer's instructions.

growth_protocol: Dental pulp cells were exposed to DMEM with 10% FBS or serum-free medium STK2 for 7 days.

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

value: permanent molar

value: female

tag: age

value: 24 years old


title: DPC3-STK2

value: 25 years old


title: DPC2-DMEM/FBS

source_name: dental pulp cell, cultured with DMEM/10% FBS


title: sample56: 360m rep 1, veh, sustained

source_name: Primary Cutlure Mouse Cortical Neurons

tag: mouse strain

value: ARG


title: DPC4-STK2


title: DPC3-DMEM/FBS


title: DPC4-DMEM/FBS


title: sample67: 60m rep 3, veh, brief

tag: capture


title: sample55: 60m rep 7, veh, sustained

tag: activation


title: sample54: 60m rep 6, veh, sustained

tag: time point


title: sample69: 60m rep 5, veh, brief

tag: drug


title: sample53: 60m rep 5, veh, sustained

tag: molecule


title: sample48: 20m rep 7, veh, sustained

tag: tissue


title: sample50: 60m rep 2, veh, sustained


title: sample47: 20m rep 6, veh, sustained


title: sample52: 60m rep 4, veh, sustained


title: sample51: 60m rep 3, veh, sustained


title: sample46: 20m rep 5, veh, sustained


title: sample49: 60m rep 1, veh, sustained


title: sample44: 0h rep 7.1, veh, sustained

description: sample044 (technical replicate of sample 45, from same dissection, grown separately)


title: sample45: 0h rep 7.2, veh, sustained

description: sample045 (technical replicate of sample 44, from same dissection, grown separately)


title: sample43: 0h rep 6.2, veh, sustained

description: sample043 (technical replicate of sample 42, from same dissection, grown separately)


title: sample42: 0h rep 6.1, veh, sustained

description: sample042 (technical replicate of sample 43, from same dissection, grown separately)


title: sample41: 0h rep 5, veh, sustained


title: sample40: 0h rep 4.2, veh, sustained

description: sample040 (technical replicate of sample 39, from same dissection, grown separately)


title: sample39: 0h rep 4.1, veh, sustained

description: sample039 (technical replicate of sample 40, from same dissection, grown separately)


title: sample38: 0h rep 3.2, veh, sustained

description: sample038 (technical replicate of sample 37, from same dissection, grown separately)


title: sample37: 0h rep 3.1, veh, sustained

description: sample037 (technical replicate of sample 38, from same dissection, grown separately)


title: sample36: 0h rep 2.2, veh, sustained

description: sample036 (technical replicate of sample 35, from same dissection, grown separately)


title: sample35: 0h rep 2.1, veh, sustained

description: sample035 (technical replicate of sample 36, from same dissection, grown separately)


title: sample33: 0h rep 1.1, veh, sustained

description: sample033 (technical replicate of sample 34, from same dissection, grown separately)


title: sample34: 0h rep 1.2, veh, sustained

description: sample034 (technical replicate of sample 33, from same dissection, grown separately)


title: sample32: 6h sustained stim, CHX, rep 2, CHXexpt

value: CHX


title: sample31: 6h sustained stim, CHX, rep 1, CHXexpt


title: ML1_sample_0075

source_name: single embryo_19hr

value: single embryo 75


title: Pat3_Bb_WT

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

institute: CIC bioGUNE

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalised using quantile normalisation with lumi in R
After background correction with GenomeStudio and log2 transformation, probes with a detection p-value greater than 0.01 for all samples were discarded, using the detectionCall function in the lumi R package.

source_name: Buffy coat

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre)

growth_protocol: Human monocytes were purified from buffy coats of healthy blood donors by positive selection using a human CD14 purification kit (Miltenyi Biotec).

extract_protocol: Total RNA was extracted using the NucleoSpin® RNA kit (Macherey-Nagel, Düren, GE)

treatment_protocol: Stimulation was carried out at a multiplicity of infection of 25. The monocytes were stimulated with Borrelia burgdorferi strain B31 for 20 h.

value: Normal human monocytes

value: Stimulated with Borrelia burgdorferi


title: Pat1_Ctrol

value: non-stimulated


title: Pat2_Bb_WT


title: sample30: 6h sustained stim, vehicle, rep 2, CHXexpt

value: DMSO


title: Pat3_Ctrol


title: Pat2_Ctrol


title: Pat1_Bb_WT


title: sample29: 6h sustained stim, vehicle, rep 1, CHXexpt

value: sustained


title: AorticValve_241

city: Quebec

first: Yohan

last: Bossé

state: Quebec

address: 2725, chemin Sainte-Foy

country: Canada

institute: Laval University

data_processing: Data was processed by log2-transformation and quantile normalized using the lumi package in R (Du et al 2008)

label_protocol: IlluminaTotalPrep™-96 RNA Amplification Kit (Ambion)

extract_protocol: RNA was extracted from valve leaflets using RNeasy Plus Universal Mini kit (Qiagen)

value: aortic valve


title: AorticValve_242


title: AorticValve_237


title: AorticValve_240


title: AorticValve_239


title: AorticValve_243


title: AorticValve_238


title: AorticValve_235


title: sample27: unstim, CHX, rep 1, CHXexpt

value: Primary Cutlure Mouse Cortical Neurons

value: captured total RNA


title: AorticValve_234


title: AorticValve_232


title: AorticValve_231


title: sample26: unstim, vehicle, rep 2, CHXexpt


title: sample23: brief, 60m, rep 1, u0126, total RNA

value: brief

value: total RNA


title: sample22: sustained 60m, rep 2, u0126, total RNA


title: sample20: brief, 20m, rep 2, u0126, total RNA


title: sample25: unstim, vehicle, rep 1, CHXexpt


title: sample18: sustained 20m, rep 2, u0126, total RNA


title: sample28: unstim, CHX, rep 2, CHXexpt


title: sample19: brief, 20m, rep 1, u0126, total RNA


title: sample24: brief, 60m, rep 2, u0126, total RNA


title: sample21: sustained 60m, rep 1, u0126, total RNA


title: AorticValve_236


title: sample17: sustained 20m, rep 1, u0126, total RNA


title: sample16: unstim rep 2.2, u0126, total RNA

description: sample016 (technical replicate of sample 14, from same dissection, grown separately)


title: sample15: unstim rep 1.2, u0126, total RNA

description: sample015 (technical replicate of sample 13, from same dissection, grown separately)


title: sample14: unstim rep 2.1, u0126, total RNA

description: sample014 (technical replicate of sample 16, from same dissection, grown separately)


title: AorticValve_228


title: AorticValve_230


title: sample13: unstim rep 1.1, u0126, total RNA

description: sample013 (technical replicate of sample 15, from same dissection, grown separately)


title: AorticValve_233


title: sample11: brief, 60m, rep 1, veh, total RNA


title: AorticValve_225


title: AorticValve_220


title: sample10: sustained 60m, rep 2, veh, total RNA


title: sample9: sustained 60m, rep 1, veh, total RNA


title: AorticValve_224


title: AorticValve_218


title: AorticValve_226


title: AorticValve_217


title: AorticValve_223


title: sample7: brief, 20m, rep 1, veh, total RNA


title: AorticValve_229


title: AorticValve_221


title: AorticValve_227


title: AorticValve_219


title: sample12: brief, 60m, rep 2, veh, total RNA


title: AorticValve_222


title: AorticValve_213


title: AorticValve_215


title: AorticValve_216


title: AorticValve_211


title: AorticValve_210


title: AorticValve_214


title: sample6: sustained 20m, rep 2, veh, total RNA


title: AorticValve_212


title: sample8: brief, 20m, rep 2, veh, total RNA


title: AorticValve_209


title: sample2: unstim rep 2.1, veh, total RNA

description: sample002 (technical replicate of sample 4, from same dissection, grown separately)


title: sample3: unstim rep 1.2, veh, total RNA

description: sample003 (technical replicate of sample 1, from same dissection, grown separately)


title: sample4: unstim rep 2.2, veh, total RNA

description: sample004 (technical replicate of sample 2, from same dissection, grown separately)


title: sample5: sustained 20m, rep 1, veh, total RNA


title: sample1: unstim rep 1.1, veh, total RNA

description: sample001 (technical replicate of sample 3, from same dissection, grown separately)


title: AorticValve_208


title: AorticValve_204


title: AorticValve_206


title: AorticValve_203


title: AorticValve_207


title: AorticValve_201