title: Normal 3

city: Nan jing

first: kaixuan

last: zeng

address: Yuhuatai District, Communist Youth League Road No. 32

institute: southeast university

description:
N3
processed data file: T2.T3.N2.N3circ_expression.txt

data_processing:
For each sample, FASTQ reads were first mapped to human reference genome (GRCh37/hg19) obtained from UCSC genome database by TopHat2, and all the unmapped reads were then used to identify circRNAs.
The unmapped reads were processed to 20-nt anchors from both ends of the read. Anchors that aligned in the reversed orientation (head-to-tail) indicated a backspliced junction.
To estimate the relative expression of a circRNA, denoted as SRPBM reads, we counted the total number of reads mapped to the human reference genome in each sample and normalized the number of reads spanning the back-spliced junction to the total number of mapped reads (units in billion) and read length.
For the analyses of specific circRNAs among these tissues, we filtered circRNAs from all samples with specificity score defined in CummeRbund package (http://compbio.mit.edu/cummeRbund/) with minimum value of 0.5 and minimum level of meanþ2s.d.
The genomic regions mapping to inferred circRNA were annotated according to the RefSeq and UCSC Known Genes databases. The host genes of circRNAs were determined via a custom script. For each circRNA, we searched for the longest transcript fragment whose boundaries (5' end or 3' end) exactly matched both ends of this circRNA in the same strand and then defined the corresponding gene of this transcript fragment as the host gene of this circRNA.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: *txt: Tab-delimited text files.

source_name: breast

extract_protocol:
Breast tissues were surgically removed, flash frozen on dry ice, and total RNA was harvested using Trizol reagent and treated with the RiboMinus Eukaryote Kit (Qiagen, Valencia, CA) to remove rRNA before constructing the RNA-seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: disease state

value: triple-negative breast cancer

value: adjacent normal tissue

tag: tissue type

value: Fresh frozen


title: Normal 2

status: Public on Dec 06 2018

type: SRA

country: China

description:
N2
processed data file: T2.T3.N2.N3circ_expression.txt

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: LS-15071_S01_E1-50

city: Seattle

first: Allen

last: Institute

state: WA

address: 615 Westlake Ave N

country: USA

institute: The Allen Institute for Brain Science

description:
nuclei_exon_counts.csv.gz
nuclei_exon_counts.csv.gz

data_processing:
50-base pair paired-end reads were aligned to GRCm38 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 01/18/2016 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/). Sequence alignment was performed using STAR v2.5.3 (Dobin et al., 2013) in twopassMode. PCR duplicates were masked and removed using STAR option “bamRemoveDuplicates”. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) sumarizeOverlaps function using “IntersectionNotEmpty”.
Reads that did not map to the genome were then aligned to synthetic constructs (i.e. ERCC) sequences and the E.coli genome (version ASM584v2). Quantification was performed using summerizeOverlaps from the R package GenomicAlignments [38].
Single nucleus quality control criteria: >500,000 genome-mapped reads, >75% reads aligned, and >50% unique reads. Single cell quality control criteria: >200,000 transcriptome mapped reads and >1000 genes detected (counts > 0).
Genome_build: mm10

organism: Mus musculus

source_name: Primary Visual Cortex (VISp)

growth_protocol: All procedures were approved by the Institutional Animal Care and Use Committee at the Allen Institute for Brain Science (Protocol no. 1511). Animals were provided food and water ad libitum and were maintained on a regular 12-h day/night cycle. Mice were housed at no more than 5 adults per cage, with various enrichment materials added, including nesting materials, gnawing materials, and plastic shelters. Nutritional and foraging enrichment was provided in the form of foods such as sunflower seeds and sucrose pellets. Mice were maintained on the C57BL/6J background.

extract_protocol:
Tissue samples were obtained from adult male and female transgenic mice carrying a Cre transgene and a Cre-reporter transgene. After euthanasia, the brain was rapidly dissected and mounted for coronal slice preparation on a Compresstome VF-300 vibrating microtome (Precisionary Instruments) and sectioned at  250 μm intervals.     For whole cell dissociation, 2 mg/ml of pronase in ACSF solution was added to dissected tissues and enzymatic digestion was carried out at room temperature. After digestion,The tissue was triturated and the cell suspension was incubated on ice in preparation for fluorescence-activated cell sorting (FACS). Live cells were sorted by excluding DAPI positive events and debris, and gating to include red fluorescent events (tdTomato-positive cells). Single cells were collected into strip tubes containing 11.5μl of collection buffer (SMART-Seq v4 lysis buffer), RNase Inhibitor, and ERCCs (External RNA Controls Consortium, MIX1 at a final dilution of 1x10-8) and tubes were then stored at -80°C.    For nuclei isolation, dissected tissues were placed into a homogenization buffer (10mM Tris pH 8.0, 250mM sucrose, 25mM KCl, 5mM MgCl2, 0.1% Triton-X 100, 0.5% RNase inhibitor, 1X protease inhibitor, and 0.1mM DTT). Tissues were placed into a 1ml dounce homogenizer and homogenized using 10 strokes of the loose dounce pestle followed by 10 strokes of the tight pestle to liberate nuclei . Mouse anti-NeuN antibody (EMD Millipore, MAB377, Clone A60) was added to the nuclei at a final dilution of 1:1000 and nuclei suspensions were incubated at 4°C for 30 minutes, followed by incubation in secondary antibody (goat anti-mouse IgG (H+L), Alexa Fluor 594 conjugated, ThermoFisher Scientific, 1:5000) for 30 minutes at 4°C and staining with DAPI. Single nuclei were captured by gating on DAPI-positive events, excluding debris and doublets, and then gating on Alexa Fluor 594 (NeuN) signal. Strip tubes containing FACS isolated single nuclei were then frozen at -80°C.
The SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech #634894) was used per the manufacturer’s instructions for reverse transcription of single cell RNA and subsequent cDNA synthesis. Mouse whole cells were subjected to 18 PCR cycles after the reverse transcription step, whereas mouse nuclei were subjected to 21 PCR cycles.     Sequencing libraries were prepared using NexteraXT (Illumina, FC-131-1096) with NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT libraries were prepared at 0.5x volume, but otherwise followed the manufacturer’s instructions.

value: M

value: VISp

value: NeuN-positive

value: Pass

value: Glutamatergic

tag: molecule

value: Nuclei


title: LS-15045_S96_E1-50


title: Normal 1

description:
N1
processed data file: T1.N1.circ_expression.txt


title: ZT4_seedling_10

city: Cambridge

first: James

last: Locke

address: Bateman St

country: United Kingdom

institute: SLCU

data_processing:
The raw reads were analysed in house. We first assessed the quality of reads using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/). Potential adaptor contamination and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014), before being aligned to the TAIR10 transcriptome using Tophat (Trapnell et al., 2009). The potential optical duplicates resulted from library preparation were removed using the Picard tools (http://sourceforge.net/p/picard/wiki/Main_Page/#q-how-should-i-cite-picard-in-my-manuscript). For each gene, raw reads and TPM (Transcripts Per Million) (Wagner et al., 2012) were computed. Samples with at least 4 million reads were used for further analysis, which is between 14 and 16 samples per time-point. In order to be able to compare time-points, a total of 14 samples per time-points were used.
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Col-0 WT Arabidopsis seeds were sterilised, stratified for 3 days at 4°C in dark and transferred for germination on solid 1X Murashige and Skoog (MS) media at 22°C in long days for 24 hours. Using a binocular microscope, seeds that were at the same stage of germination were transferred into a new plate containing solid 1X MS media. In total, 16 seeds were transferred into each of the 12 individual plates. Seedlings were grown at 22°C with 12 hours of light and 12 hours of dark. After 7 days of growth, seedlings were harvested individually into a 96-well plate and flash-frozen in dry ice. Sixteen seedlings were harvested individually and flash-frozen in dry ice at each time point, every two hours over a 24 hours period. ZT2 to ZT12 corresponding to time-points harvested during the day, and ZT14 to ZT0 to time-points harvested during the night, ZT124 and ZT0 being respectively harvested just a few minutes after dusk and dawn

extract_protocol:
Total RNA was isolated from one grinded seedling using the MagMAX-96 Total RNA Isolation kit (Ambion, AM1830), following the manufacturer’s instructions. RNA quality and integrity was assessed on the Agilent 2200 TapeStation.
Library preparation was performed using the TruSeq Stranded mRNA library preparation kit a (Illumina, RS-122-2101), following manufacturer’s instruction, for 1 ug of high integrity total RNA (RIN>8) into which 2 ul of diluted 1:100e ERCC RNA Spike-In Mix (ThermoFisher, cat 4456740) was added. The libraries were sequenced on a NextSeq500 at the Sainsbuty Laboratory, Cambridge University (Cambridge, UK), using paired-end sequencing of 75 bp in length.

tag: ecotype

value: Col0 WT

value: seedlings

tag: time point

tag: individual seedling


title: LS-15071_S04_E1-50


title: ZT2_seedling_9


title: LS-15045_S95_E1-50


title: ZT2_seedling_4


title: ZT2_seedling_7


title: ZT2_seedling_3


title: 040-CB

type: RNA

city: New York

first: Ariel

last: Israel

state: NY

address: 1425 Madison Avenue

department: Department of Dermatology

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from blood

hyb_protocol: Encore Biotin Module (Nugen) and Ambion

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GC-RMA (using gcrma package from R/Bioconductor)

label: biotin

label_protocol: Encore Biotin Module (Nugen) and Ambion

extract_protocol: Cells lysed in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA).

tag: group

value: Normal

value: blood

tag: gender

tag: agegroup

value: pediatric


title: 025-AD

description: Gene expression data from blood

value: AD

value: F


title: 036-CB

description: Gene expression data from blood


title: 024-AD

description: Gene expression data from blood


title: 021-AD

description: Gene expression data from blood


title: Cancer 3

description:
T3
processed data file: T2.T3.N2.N3circ_expression.txt

value: breast cancer


title: 018-AD

description: Gene expression data from blood


title: 031-AD

description: Gene expression data from blood


title: ZT2_seedling_16


title: Cancer 2

description:
T2
processed data file: T2.T3.N2.N3circ_expression.txt

value: triple-negative breast cancer


title: LS-15045_S93_E1-50


title: LS-15045_S94_E1-50


title: ZT2_seedling_15


title: ZT2_seedling_14


title: LS-15045_S92_E1-50


title: LS-15045_S91_E1-50


title: ZT2_seedling_12


title: 008-AD

description: Gene expression data from blood


title: Cancer 1

description:
T1
processed data file: T1.N1.circ_expression.txt


title: ZT2_seedling_11


title: LS-15045_S90_E1-50


title: LS-15045_S89_E1-50


title: ZT2_seedling_10


title: 007-AD

description: Gene expression data from blood


title: ZT2_seedling_1


title: H3R17H/Carm1-/- rep4

city: Guangzhou

first: Yunbo

last: Qiao

address: Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.

institute: Guangzhou University

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads were calculated. The numbers of reads of each base were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: text files include reads number of each base for each sample.

molecule: genomic DNA

source_name: genomic DNA from E19.5 mice embryo

growth_protocol: Genomic DNA was obtained by phenol-chloroform method from E19.5 embryos

extract_protocol:
Total genomic DNA was obtained by phenol-chloroform method  from E19.5 embryos
PCR products libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: age

value: 19.5 days after microinjection

tag: genotype

value: embryo


title: 005-AD

description: Gene expression data from blood

value: M


title: Non-Lay rep1

city: Honolulu

first: Nirvay

last: Sah

state: HI

address: 1955 East-west raod

department: Human Nutrition, Food and Animal Sciences

institute: University of Hawaii at Manoa

data_processing:
Single-end reads in FASTQ format was explored using FastQC (Babraham Institute, Cambridge, UK)
Sequencing reads were cleaned using Prinseq (version 0.20.4). The cleaning procedure included trimming low quality reads from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was found and filtering out reads having mean quality score less than 30 and length below 30 nucleotides.
Cleaned reads were aligned against chicken reference genome Galgal 5.0 using Array Studio (version10)
Differential gene expression analysis in layers with respect to non-layers’ groups was performed by the DESeq2 alogrithm
Genome_build: Galgal 5.0
Supplementary_files_format_and_content: DEG data.txt: .txt file exported from DESeq2; Fold Change represent relative gene expression levels in layer compared to non-layers
Unnormalized count.txt: raw count data
RPKM Data.txt: RPKM normalized

organism: Gallus gallus

source_name: Uterus

extract_protocol:
Uterine tissues were collected and snap frozen in liquid nitrogen, and total RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA library Prep Kit (Cat#RS-122-2101) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hy-line

value: Uterus

value: 35-60 weeks

tag: egg laying status

value: non-laying


title: Non-Lay rep2


title: LS-15045_S87_E1-50

value: VISp

value: NeuN-positive

value: Pass

value: Glutamatergic

value: Nuclei


title: LS-15045_S88_E1-50


title: Lay rep3

value: 35 weeks

value: laying


title: 004-AD

description: Gene expression data from blood

value: AD

value: blood

value: pediatric


title: 009-CB

description: Gene expression data from blood

value: Normal

value: F


title: H3R17H/Carm1-/- rep3

department: Precise Genome Engineering Center, School of Life Sciences

value: 19.5 days after microinjection

value: embryo


title: Human_SI_tissue

city: Tokyo

first: Masayuki

last: Fujii

address: 35, Shinanomachi, Shinjuku-ku

country: Japan

institute: Keio University

description: Single cells from a fresh human small intestinal tissue

data_processing:
Sequence data was mapped to the human genome (GRCh38) using CellRanger (version 2.1.1). Unique molecular identifier (UMI) count matrices were imported into R (version 3.5.1) and were processed with R package Seurat (version 2.3.4).
We quantified a proportion of reads mapped to the mitochondrial genome for each cell. Then, we excluded all cells with mitochondrial reads less than 1% or more than 10% from organoid data, and excluded all cells with mitochondrial reads less than 2.5% or more than 15% from tissue data.
Log-normalized expression was obtained by NormalizeData function of the Seurat package. For tissue data, immune cells identified by the reference component analysis was excluded.
Genome_build: GRCh38
Supplementary_files_format_and_content: Log-normalized expression data for each cell in a tab-delimited text format.

source_name: Human small intestine

growth_protocol: Human small intestinal organoids were established from a terminal ileum tissue and maintained in a medium containing Wnt-3A, R-spondin, Noggin, A83-01, IGF1 and FGF2.

extract_protocol:
Crypts were released from fragmented fresh human small intestinal tissues using EDTA and further dissociated using TrypLE express. EpCAM+ live cells were FACS-sorted based on EpCAM and DAPI staining. Organoids were dissociated using TrypLE express and live cells were sorted based on DAPI staining. Single cells were partitioned into Gel Beads in emulsion using the GemCode instrument.
Libraries were constructed using Single Cell 3' Library & Gel Bead Kit v2 and the A Chip Kit (10x genomics) according to the manufacturer's instructions

treatment_protocol: The organoids were treated with IGF1/FGF2 or EGF/p38i for 10 days.

value: ileum

tag: sample type

value: tissue


title: Human_SI_organoid_ES

description: Single cells from human small intestinal organoids cultured with EGF/p38i

value: organoid

tag: treatment


title: Human_SI_organoid_IF

description: Single cells from human small intestinal organoids cultured with IGF1/FGF2


title: LS-15045_S86_E1-50

value: M

value: VISp


title: Non-Lay rep3

value: Hy-line

value: Uterus

value: 35-60 weeks

value: non-laying


title: Lay rep1

value: 35 weeks

value: laying


title: LS-15045_S84_E1-50

value: NeuN-positive

value: Pass

value: Glutamatergic

value: Nuclei


title: H3R17H/Carm1-/- rep2

value: 19.5 days after microinjection


title: LS-15045_S83_E1-50


title: 006-AD

description: Gene expression data from blood

value: AD

value: blood

value: pediatric


title: H3R17H/Carm1-/- rep1

value: embryo


title: 003-AD

description: Gene expression data from blood

value: M


title: RNAseq_C_ZF108YPETinWT_rep3

first: C. Jake

last: Harris

address: Downing Street

department: Department of Plant Sciences

institute: University of Cambridge

data_processing:
RNA-seq: 50bp single end reads were aligned using TopHat2 including the fr-firststrand option allowing for intron length of up to 10,000. bigWig tracks were generated using bamCoverage in DeepTools (https://deeptools.readthedocs.io/en/latest/).
Genome build: TAIR 10
Supplementary_files_format_and_content: RNAseq bigWig tracks are normalised reads (by mapped library size), and binned into 25bp or 50bp bins.

molecule: polyA RNA

source_name: leaf

growth_protocol: soil, 16 hour light, 8 hour dark cycle

extract_protocol:
2-3 leaves from individual plants (2-3 weeks old). Total RNA was extracted using TRIzol and Direct-zol RNA miniprep kit (Zymo, R2050) including in-column DNase treatment.
TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: leaf

tag: genotype/variation


title: RNAseq_C_ZF108YPETinWT_rep4


title: RNAseq_C_ZF108YPETinWT_rep1


title: H3R17/Carm1 WT rep3

value: H3R17/Carm1 wild type


title: LS-15045_S81_E1-50

value: VISp


title: LS-15045_S82_E1-50


title: RNAseq_C_ZF108YPETinWT_rep2


title: LS-15045_S85_E1-50


title: Lay rep2

value: Hy-line

value: Uterus


title: RNAseq_C_WTcontrol_rep3

value: wildtype


title: H3R17/Carm1 WT rep2


title: LS-15045_S79_E1-50


title: RNAseq_C_WTcontrol_rep2


title: Carm1-/- rep3

description:
Hist-13
total cDNA
processed data file: Processed_data_in_FPKM.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase Per Million (FPKM) were calculated using protocol. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Processed_data_in_FPKM.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: E4.5 embryo

extract_protocol:
Total cDNA was obtained by reverse transcription of single cell derived from E4.5 embryos cultured in vitro.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: E4.5 embryo

value: 4.5 days after microinjection


title: RNAseq_C_WTcontrol_rep1


title: H3R17/Carm1 WT rep4


title: LS-15045_S80_E1-50

value: NeuN-positive

value: Pass


title: RNAseq_C_DNAJ1inWT_rep4


title: LS-15045_S78_E1-50

value: Glutamatergic

value: Nuclei


title: Carm1-/- rep2

description:
Hist-12
total cDNA
processed data file: Processed_data_in_FPKM.txt


title: RNAseq_C_WTcontrol_rep4


title: Carm1-/- rep1

description:
Hist-3
total cDNA
processed data file: Processed_data_in_FPKM.txt


title: H3R17/Carm1 WT rep1

value: 19.5 days after microinjection


title: H3R17H rep2

description:
Carm-15
total cDNA
processed data file: Processed_data_in_FPKM.txt

value: H3R17H substitution


title: RNAseq_C_DNAJ1inWT_rep3


title: LS-15045_S76_E1-50

value: GABAergic


title: LS-15045_S75_E1-50


title: RNAseq_C_DNAJ1inWT_rep2


title: LS-15045_S74_E1-50


title: LS-15045_S77_E1-50


title: H3R17H rep1

description:
Carm-13
total cDNA
processed data file: Processed_data_in_FPKM.txt


title: RNAseq_C_DNAJ1inWT_rep1


title: LS-15045_S73_E1-50


title: ChIPseq_G_antiFLAG_ZF108DNAJ1inWT

description: ChIP DNA

data_processing:
ChIP-seq: 50bp single end reads were aligned using Bowtie2 and PCR duplicates were removed using SAMtools. bigWig tracks were generated using bamCoverage in DeepTools (https://deeptools.readthedocs.io/en/latest/).
Genome build: TAIR 10
Supplementary_files_format_and_content: ChIPseq: bigWig tracks are normalised reads (by mapped library size), and binned into 25bp or 50bp bins.

source_name: seedling

growth_protocol: 1/2x MS plates, seedling, constant light

extract_protocol:
4-8 grams of 12-14 days post germination seedling material, crosslinked in vitro and sheared using Bioruptor Plus (Diagenode).
NuGen Ovation Ultra Low System V2 1-16

tag: chip antibody

value: anti-FLAG M2 (F1804, Sigma)

value: seedling


title: H3R17H rep3

description:
Carm-16
total cDNA
processed data file: Processed_data_in_FPKM.txt

tag: tissue


title: ZT18_seedling_8

value: Col0 WT

value: seedlings


title: WT rep2

description:
C57con-3
total cDNA
processed data file: Processed_data_in_FPKM.txt

value: wild type


title: ChIPseq_G_antiFLAG_WT

description: ChIP DNA


title: LS-15045_S72_E1-50

value: M

value: VISp

tag: molecule


title: IRSI_32907_blood

type: genomic

city: Bethesda

first: Heidi

middle: G

last: Parker

state: MD

address: 50 South Dr. Rm 5347

department: CGB

institute: NHGRI

description:
Sample name: 32907
Second_half_signal.txt

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

label: CY3 and CY5

organism: Canis lupus familiaris

source_name: blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols. DNA was extracted from saliva using the DNA Genotek saliva collection kit following recommended protocol. DNA was extracted from tissue using the Qiagen DNEasy blood and tissue kits.

tag: origin

value: Italy

tag: breed

value: Irish Setter

value: blood


title: WT rep3

description:
C57con-7
total cDNA
processed data file: Processed_data_in_FPKM.txt

value: E4.5 embryo

value: 4.5 days after microinjection


title: LS-15045_S71_E1-50

description:
nuclei_exon_counts.csv.gz
nuclei_exon_counts.csv.gz

value: NeuN-positive

value: Pass


title: WT rep1

description:
C57con-1
total cDNA
processed data file: Processed_data_in_FPKM.txt


title: ChIPseq_E_antiFLAG_WT

description: ChIP DNA

tag: ecotype

value: wildtype


title: ChIPseq_E_antiFLAG_SUVH1Y277AFinsuvh1_rep2

description: ChIP DNA


title: LS-15045_S69_E1-50

value: Glutamatergic

value: Nuclei


title: ChIPseq_E_antiFLAG_SUVH1Y277AFinsuvh1_rep1

description: ChIP DNA

value: anti-FLAG M2 (F1804, Sigma)


title: LS-15045_S70_E1-50


title: ChIPseq_E_antiFLAG_SUVH1Finsuvh1_rep2

description: ChIP DNA

value: seedling


title: LEOP_33138_blood

description:
Sample name: 33138
Second_half_signal.txt

value: USA

value: Catahoula Leopard Dog


title: ChIPseq_E_antiFLAG_SUVH1Finsuvh1_rep1

description: ChIP DNA


title: LS-15045_S67_E1-50


title: LS-15045_S66_E1-50


title: LS-15045_S65_E1-50


title: LS-15045_S68_E1-50


title: IRSI_32904_blood

description:
Sample name: 32904
Second_half_signal.txt


title: ETOY_26285_whole blood

description:
Sample name: 26285
Second_half_signal.txt

source_name: whole blood

value: English Toy Spaniel

value: whole blood


title: LEOP_33137_blood

description:
Sample name: 33137
Second_half_signal.txt


title: LS-15045_S64_E1-50

value: M

value: VISp


title: RNAseq_B_ZF108DNAJ1inWT_pheno_rep4

description: polyA RNA

data_processing:
RNA-seq: 50bp single end reads were aligned using TopHat2 including the fr-firststrand option allowing for intron length of up to 10,000. bigWig tracks were generated using bamCoverage in DeepTools (https://deeptools.readthedocs.io/en/latest/).
genome build: TAIR 10
RNAseq bigWig tracks are normalised reads (by mapped library size), and binned into 25bp or 50bp bins.

value: leaf


title: LS-15045_S63_E1-50


title: RNAseq_B_ZF108DNAJ1inWT_pheno_rep3

description: polyA RNA


title: IRSI_32906_blood

description:
Sample name: 32906
Second_half_signal.txt

value: Italy

value: Irish Setter

value: blood


title: SMFX_33294_blood

description:
Sample name: 33294
Second_half_signal.txt

value: Smooth Fox Terrier


title: RNAseq_B_ZF108DNAJ1inWT_pheno_rep2

description: polyA RNA


title: RNAseq_B_ZF108DNAJ1inWT_pheno_rep5

description: polyA RNA


title: LS-15045_S62_E1-50

value: NeuN-positive

value: Pass


title: SMFX_33295_saliva

description:
Sample name: 33295
Second_half_signal.txt

source_name: saliva

value: saliva


title: ETOY_06354_blood

description:
Sample name: 6354
Second_half_signal.txt


title: RNAseq_B_ZF108DNAJ1inWT_pheno_rep1

description: polyA RNA


title: RNAseq_B_ZF108DNAJ1inWT_NophenoControl_rep3

description: polyA RNA


title: RNAseq_B_ZF108DNAJ1inWT_pheno_rep6

description: polyA RNA


title: LS-15045_S58_E1-50

value: GABAergic

value: Nuclei


title: LS-15045_S59_E1-50


title: LS-15045_S60_E1-50

value: Glutamatergic


title: LS-15045_S57_E1-50


title: LAKE_33293_saliva

description:
Sample name: 33293
Second_half_signal.txt

value: USA

value: Lakeland Terrier


title: RNAseq_B_ZF108DNAJ1inWT_NophenoControl_rep1

description: polyA RNA


title: RNAseq_B_WTcontrol_rep3

description: polyA RNA

value: wildtype


title: RNAseq_B_ZF108DNAJ1inWT_NophenoControl_rep2

description: polyA RNA


title: SMFX_33296_saliva

description:
Sample name: 33296
Second_half_signal.txt


title: RNAseq_B_WTcontrol_rep2

description: polyA RNA


title: LAKE_33292_saliva

description:
Sample name: 33292
Second_half_signal.txt


title: ETOY_33218_saliva

description:
Sample name: 33218
Second_half_signal.txt

value: English Toy Spaniel


title: SKYE_33240_saliva

description:
Sample name: 33240
Second_half_signal.txt

value: Skye Terrier


title: LS-15045_S56_E1-50

value: M

value: VISp


title: MUDI_33170_blood

description:
Sample name: 33170
Second_half_signal.txt

value: Mudi


title: RNAseq_B_WTcontrol_rep1

description: polyA RNA

value: leaf


title: RNAseq_A_WT_rep3

description: polyA RNA

source_name: floral bud

extract_protocol:
2-3 bunches of unopened floral bud tissue from individual plants. Total RNA was extracted using TRIzol and Direct-zol RNA miniprep kit (Zymo, R2050) including in-column DNase treatment
TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: floral bud


title: MUDI_33180_blood

description:
Sample name: 33180
Second_half_signal.txt

value: blood


title: LS-15045_S53_E1-50

description:
nuclei_exon_counts.csv.gz
nuclei_exon_counts.csv.gz

value: NeuN-positive


title: LS-15045_S54_E1-50

value: Pass


title: LS-15045_S55_E1-50


title: RNAseq_A_WT_rep2

description: polyA RNA


title: SKYE_33239_saliva

description:
Sample name: 33239
Second_half_signal.txt

value: saliva


title: LS-15045_S61_E1-50


title: RNAseq_A_WT_rep1

description: polyA RNA


title: RNAseq_A_suvh3_rep3

description: polyA RNA


title: IRSI_32903_blood

description:
Sample name: 32903
Second_half_signal.txt

value: Italy

value: Irish Setter


title: RNAseq_A_suvh3_rep2

description: polyA RNA


title: RNAseq_A_suvh3_rep1

description: polyA RNA


title: LAKE_33222_saliva

description:
Sample name: 33222
Second_half_signal.txt


title: LAKE_33318_saliva

description:
Sample name: 33318
Second_half_signal.txt


title: RNAseq_A_suvh1_rep3

description: polyA RNA


title: LS-15045_S48_E1-50

value: GABAergic

value: Nuclei


title: LS-15045_S52_E1-50

value: Glutamatergic


title: LS-15045_S49_E1-50


title: LS-15045_S50_E1-50


title: LS-15045_S47_E1-50


title: MUDI_33142_blood

description:
Sample name: 33142
Second_half_signal.txt

value: USA


title: RNAseq_A_suvh1_rep2

description: polyA RNA


title: RNAseq_A_suvh1_rep1

description: polyA RNA


title: LS-15045_S45_E1-50


title: IRSI_32905_blood

description:
Sample name: 32905
Second_half_signal.txt


title: LS-15045_S46_E1-50


title: THAI_33134_blood

description:
Sample name: 33134
Second_half_signal.txt

value: Thai Ridgeback


title: RNAseq_A_dnaj2_rep2

description: polyA RNA


title: RNAseq_A_suvh1_3_rep1

description: polyA RNA

value: suvh1, suvh3


title: RNAseq_A_suvh1_3_rep3

description: polyA RNA


title: RNAseq_A_suvh1_3_rep2

description: polyA RNA


title: RNAseq_A_dnaj2_rep3

description: polyA RNA


title: LS-15045_S32_E1-50

value: M


title: LS-15045_S43_E1-50

value: VISp


title: LS-15045_S44_E1-50


title: LS-15045_S41_E1-50


title: RNAseq_A_dnaj2_rep1

description: polyA RNA


title: RNAseq_A_dnaj1_rep3

description: polyA RNA


title: LS-15045_S29_E1-50


title: LS-15045_S30_E1-50


title: THAI_33135_saliva

description:
Sample name: 33135
Second_half_signal.txt


title: MANN_31442_blood

description:
Sample name: 31442
Second_half_signal.txt

value: Mannera


title: RNAseq_A_dnaj1_rep2

description: polyA RNA


title: RNAseq_A_dnaj1_rep1

description: polyA RNA


title: FONN_31395_blood

description:
Sample name: 31395
Second_half_signal.txt

value: Fonni's Dog


title: LS-15045_S28_E1-50


title: LS-15045_S26_E1-50


title: LS-15045_S27_E1-50


title: THAI_33133_Saliva

description:
Sample name: 33133
Second_half_signal.txt

source_name: Saliva

value: Saliva


title: LS-15045_S25_E1-50


title: RNAseq_A_dnaj1_2_rep3

description: polyA RNA

value: floral bud

value: dnaj1, dnaj2


title: ITCC_31343_blood

description:
Sample name: 31343
Second_half_signal.txt

value: Cane Corso

value: blood


title: RNAseq_A_dnaj1_2_rep2

description: polyA RNA


title: RNAseq_A_dnaj1_2_rep1

description: polyA RNA


title: LS-15045_S24_E1-50

value: NeuN-positive

value: Pass


title: LS-15045_S23_E1-50


title: BOLO_31301_blood

description:
Sample name: 31301
Second_half_signal.txt

value: Italy

value: bolognese


title: ChIPseq_F_antiH3K9me2_WT

description: ChIP DNA

data_processing:
ChIP-seq: 50bp single end reads were aligned using Bowtie2 and PCR duplicates were removed using SAMtools. bigWig tracks were generated using bamCoverage in DeepTools (https://deeptools.readthedocs.io/en/latest/).
genome build: TAIR 10
ChIPseq: bigWig tracks are normalised reads (by mapped library size), and binned into 25bp or 50bp bins.

extract_protocol:
4-8 grams of 12-14 days post germination seedling material, crosslinked in vitro and sheared using Bioruptor Plus (Diagenode).
NuGen Ovation Ultra Low System V2 1-26

value: anti-H3K9me2 = ab1220 (abcam)

value: seedling

value: wildtype


title: LS-15045_S22_E1-50

value: GABAergic

value: Nuclei


title: LS-15045_S20_E1-50

value: M

value: VISp

value: Glutamatergic


title: ChIPseq_F_antiH3K9me2_suvh1_3

description: ChIP DNA

extract_protocol: 4-8 grams of 12-14 days post germination seedling material, crosslinked in vitro and sheared using Bioruptor Plus (Diagenode).

value: suvh1, suvh3


title: ITCC_31342_blood

description:
Sample name: 31342
Second_half_signal.txt


title: MARM_31469_blood

description:
Sample name: 31469
Second_half_signal.txt

value: Maremma


title: LS-15045_S19_E1-50


title: BERG_31484_blood

description:
Sample name: 31484
Second_half_signal.txt

value: Bergamasco


title: LUPO_31367_blood

description:
Sample name: 31367
Second_half_signal.txt

value: Lupo Italiano


title: ChIPseq_D_antiFLAG_SUVH1Finsuvh1_rep2

description: ChIP DNA

extract_protocol:
4-8 grams of 12-14 days post germination seedling material, crosslinked in vitro and sheared using Bioruptor Plus (Diagenode). Samples are each from two technical replicates (rep1 and rep2) as chromatin was split into two before the addition of antibody
NuGen Ovation Ultra Low System V2 1-23

value: anti-FLAG M2 (F1804, Sigma)


title: MANN_31449_whole blood

description:
Sample name: 31449
Second_half_signal.txt

value: Mannera

value: whole blood


title: ITCC_31338_whole blood

description:
Sample name: 31338
Second_half_signal.txt

value: Italy

value: Cane Corso


title: ITCC_31337_whole blood

description:
Sample name: 31337
Second_half_signal.txt


title: CIRN_31391_whole blood

description:
Sample name: 31391
Second_half_signal.txt

value: Cirneco dellEtna


title: SIPF_31526_whole blood

description:
Sample name: 31526
Second_half_signal.txt

value: Segugio Italiano pelo forte


title: SVAL_08343_whole blood

description:
Sample name: 8343
First_half_signal.txt

value: USA

value: Swedish Vallhund


title: ChIPseq_D_antiFLAG_WT_rep2

description: ChIP DNA

extract_protocol:
4-8 grams of 12-14 days post germination seedling material, crosslinked in vitro and sheared using Bioruptor Plus (Diagenode). Samples are each from two technical replicates (rep1 and rep2) as chromatin was split into two before the addition of antibody
NuGen Ovation Ultra Low System V2 1-24

value: seedling

value: wildtype


title: CLSP_02588_buccal cells

description:
Sample name: 2588
First_half_signal.txt

source_name: buccal cells

value: Clumber Spaniel

value: buccal cells


title: SPII_31566_whole blood

description:
Sample name: 31566
Second_half_signal.txt

value: Spinoni Italiano


title: GSMD_31264_saliva

description:
Sample name: 31264
First_half_signal.txt

value: Greater Swiss Mountain Dog

value: saliva


title: SIPR_31546_whole blood

description:
Sample name: 31546
Second_half_signal.txt

value: Segugio Italiano pelo raso


title: ChIPseq_D_antiFLAG_SUVH1Finnrpe1_rep2

description: ChIP DNA

extract_protocol:
4-8 grams of 12-14 days post germination seedling material, crosslinked in vitro and sheared using Bioruptor Plus (Diagenode). Samples are each from two technical replicates (rep1 and rep2) as chromatin was split into two before the addition of antibody
NuGen Ovation Ultra Low System V2 1-22

value: anti-FLAG M2 (F1804, Sigma)


title: ChIPseq_D_antiFLAG_SUVH1Finsuvh1_rep1

description: ChIP DNA

extract_protocol: 4-8 grams of 12-14 days post germination seedling material, crosslinked in vitro and sheared using Bioruptor Plus (Diagenode). Samples are each from two technical replicates (rep1 and rep2) as chromatin was split into two before the addition of antibody


title: CAAN_30658_whole blood

description:
Sample name: 30658
First_half_signal.txt

value: Canaan Dog


title: ITCC_31336_whole blood

description:
Sample name: 31336
Second_half_signal.txt

value: whole blood


title: BIEW_31254_saliva

description:
Sample name: 31254
First_half_signal.txt

value: Biewer Terrier


title: LS-15045_S16_E1-50

description:
nuclei_exon_counts.csv.gz
nuclei_exon_counts.csv.gz

extract_protocol:
Tissue samples were obtained from adult male and female transgenic mice carrying a Cre transgene and a Cre-reporter transgene. After euthanasia, the brain was rapidly dissected and mounted for coronal slice preparation on a Compresstome VF-300 vibrating microtome (Precisionary Instruments) and sectioned at  250 μm intervals.     For whole cell dissociation, 2 mg/ml of pronase in ACSF solution was added to dissected tissues and enzymatic digestion was carried out at room temperature. After digestion,The tissue was triturated and the cell suspension was incubated on ice in preparation for fluorescence-activated cell sorting (FACS). Live cells were sorted by excluding DAPI positive events and debris, and gating to include red fluorescent events (tdTomato-positive cells). Single cells were collected into strip tubes containing 11.5μl of collection buffer (SMART-Seq v4 lysis buffer), RNase Inhibitor, and ERCCs (External RNA Controls Consortium, MIX1 at a final dilution of 1x10-8) and tubes were then stored at -80°C.    For nuclei isolation, dissected tissues were placed into a homogenization buffer (10mM Tris pH 8.0, 250mM sucrose, 25mM KCl, 5mM MgCl2, 0.1% Triton-X 100, 0.5% RNase inhibitor, 1X protease inhibitor, and 0.1mM DTT). Tissues were placed into a 1ml dounce homogenizer and homogenized using 10 strokes of the loose dounce pestle followed by 10 strokes of the tight pestle to liberate nuclei . Mouse anti-NeuN antibody (EMD Millipore, MAB377, Clone A60) was added to the nuclei at a final dilution of 1:1000 and nuclei suspensions were incubated at 4°C for 30 minutes, followed by incubation in secondary antibody (goat anti-mouse IgG (H+L), Alexa Fluor 594 conjugated, ThermoFisher Scientific, 1:5000) for 30 minutes at 4°C and staining with DAPI. Single nuclei were captured by gating on DAPI-positive events, excluding debris and doublets, and then gating on Alexa Fluor 594 (NeuN) signal. Strip tubes containing FACS isolated single nuclei were then frozen at -80°C.
The SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech #634894) was used per the manufacturer’s instructions for reverse transcription of single cell RNA and subsequent cDNA synthesis. Mouse whole cells were subjected to 18 PCR cycles after the reverse transcription step, whereas mouse nuclei were subjected to 21 PCR cycles.     Sequencing libraries were prepared using NexteraXT (Illumina, FC-131-1096) with NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT libraries were prepared at 0.5x volume, but otherwise followed the manufacturer’s instructions.

value: M

value: VISp

value: NeuN-positive

value: Pass

value: Glutamatergic

value: Nuclei


title: SVAL_08407_whole blood

description:
Sample name: 8407
First_half_signal.txt

value: USA

value: Swedish Vallhund


title: ChIPseq_D_antiFLAG_SUVH1Finnrpe1_rep1

description: ChIP DNA

value: seedling


title: LAGO_31430_whole blood

description:
Sample name: 31430
Second_half_signal.txt

value: Italy

value: Lagotto Romagnolo


title: ChIPseq_D_antiFLAG_SUVH1Finnrpd1_rep2

description: ChIP DNA

extract_protocol:
4-8 grams of 12-14 days post germination seedling material, crosslinked in vitro and sheared using Bioruptor Plus (Diagenode). Samples are each from two technical replicates (rep1 and rep2) as chromatin was split into two before the addition of antibody
NuGen Ovation Ultra Low System V2 1-21


title: SILA_31513_whole blood

description:
Sample name: 31513
Second_half_signal.txt

value: Sila's Shepherd


title: LEOP_07705_buccal cells

description:
Sample name: 7705
First_half_signal.txt

value: Catahoula Leopard Dog

value: buccal cells


title: SPII_31560_whole blood

description:
Sample name: 31560
Second_half_signal.txt

value: Spinoni Italiano


title: LS-15045_S14_E1-50


title: LS-15045_S18_E1-50


title: CPBR_00888_whole blood

description:
Sample name: 888
First_half_signal.txt

value: Chesapeake Bay Retriever

value: whole blood


title: ChIPseq_D_antiFLAG_WT_rep1

description: ChIP DNA

value: anti-FLAG M2 (F1804, Sigma)

value: wildtype


title: LS-15045_S12_E1-50

value: M

value: VISp

value: NeuN-positive


title: ChIPseq_D_antiFLAG_SUVH1Finnrpd1_rep1

description: ChIP DNA


title: LS-15045_S13_E1-50

value: Pass

value: Glutamatergic

value: Nuclei


title: ChIPseq_D_antiFLAG_SUVH1Findrm1_2_rep2

description: ChIP DNA

extract_protocol:
4-8 grams of 12-14 days post germination seedling material, crosslinked in vitro and sheared using Bioruptor Plus (Diagenode). Samples are each from two technical replicates (rep1 and rep2) as chromatin was split into two before the addition of antibody
NuGen Ovation Ultra Low System V2 1-20

value: seedling

value: drm1, drm2


title: LS-15045_S11_E1-50


title: ChIPseq_D_antiFLAG_SUVH1Findrm1_2_rep1

description: ChIP DNA


title: LS-15045_S10_E1-50


title: ChIPseq_C_antiFLAG_WT

description: ChIP DNA

extract_protocol:
4-8 grams of 12-14 days post germination seedling material, crosslinked in vitro and sheared using Bioruptor Plus (Diagenode).
NuGen Ovation Ultra Low System V2 1-19


title: CARO_29687_whole blood

description:
Sample name: 29687
First_half_signal.txt

value: USA

value: Carolina Dog


title: SILA_31512_whole blood

description:
Sample name: 31512
Second_half_signal.txt

value: Italy

value: Sila's Shepherd


title: ChIPseq_C_antiFLAG_DNAJ2Findnaj2

description: ChIP DNA


title: LS-15045_S09_E1-50


title: LS-15045_S08_E1-50


title: ChIPseq_C_antiFLAG_DNAJ1Findnaj1

description: ChIP DNA

extract_protocol:
4-8 grams of 12-14 days post germination seedling material, crosslinked in vitro and sheared using Bioruptor Plus (Diagenode).
NuGen Ovation Ultra Low System V2 1-18


title: ChIPseq_A_antiFLAG_WT

description: ChIP DNA


title: ChIPseq_A_antiFLAG_SUVH1Finsuvh1

description: ChIP DNA


title: LS-15045_S07_E1-50


title: LS-15045_S06_E1-50


title: LS-15045_S17_E1-50


title: LS-15045_S05_E1-50


title: LS-15045_S04_E1-50


title: LS-15045_S02_E1-50

value: GABAergic


title: LS-15045_S03_E1-50


title: LS-15045_S01_E1-50


title: LEOP_07702_buccal cells

description:
Sample name: 7702
First_half_signal.txt

value: Catahoula Leopard Dog

value: buccal cells


title: WGBS_dnaj2_rep2

description:
bisulfite treated genomic DNA
The libraries were multiplexed then sequenced on multiple lanes including both a HiSeq 2500 and HiSeq 4000. Thus every library has reads from both instruments.

data_processing:
WGBS: 50bp single end reads were aligned using BSMAP, allowing 2 mismatches with unique mapping. The methyratio_alt.py script was used to determine coverage and methylation ratio for each cytosine in the genome, including options to remove duplicates and reads with three methylated CHH in a row (the latter indicating incomplete bisulfite conversion). wig files were generated using a perl script (bsmap2wiggle.pl) and were further converted to bigWig using wigToBigWig from UCSC (https://genome.ucsc.edu/goldenpath/help/bigWig.html)
Genome build: TAIR 10
Supplementary_files_format_and_content: WGBS bigWig tracks show fraction methylation level at each cytosine (between 0 and 1) for cytosines covered by at least 4 reads. If a cytosine position has less than 4 reads, this is flagged by a -0.2 score.

extract_protocol:
2-3 bunches of unopened floral bud tissue from individual plants. Genomic DNA was extracted with DNeasy Plant Mini Kit (QIAGEN, 69106) and was sheared using Covaris sonicator (500ng genomic DNA starting material from each)
~200ng of sheard genomic DNA used as input for KAPA hyper prep kit (KAPA #KK8502), bisulfite converted using EZ DNA methylation lightning kit (ZYMO #D5030), MyTAq HS mix was used for amplification.

value: floral bud


title: MANT_12926_whole blood

description:
Sample name: 12926
First_half_signal.txt

value: Manchester Terrier

value: whole blood


title: WGBS_dnaj1_rep2


title: WGBS_dnaj2_rep1


title: LS-15045_S15_E1-50

value: M

value: VISp


title: WGBS_dnaj1_rep1


title: WGBS_dnaj1_2_rep2

value: dnaj1, dnaj2


title: CARO_29684_whole blood

description:
Sample name: 29684
First_half_signal.txt


title: WGBS_dnaj1_2_rep1


title: AKBH_06286_whole blood

description:
Sample name: 6286
First_half_signal.txt

value: Akbash


title: WGBS_WT_rep2

data_processing:
WGBS: 50bp single end reads were aligned using BSMAP, allowing 2 mismatches with unique mapping. The methyratio_alt.py script was used to determine coverage and methylation ratio for each cytosine in the genome, including options to remove duplicates and reads with three methylated CHH in a row (the latter indicating incomplete bisulfite conversion). wig files were generated using a perl script (bsmap2wiggle.pl) and were further converted to bigWig using wigToBigWig from UCSC (https://genome.ucsc.edu/goldenpath/help/bigWig.html)
genome build: TAIR 10
WGBS bigWig tracks show fraction methylation level at each cytosine (between 0 and 1) for cytosines covered by at least 4 reads. If a cytosine position has less than 4 reads, this is flagged by a -0.2 score.

value: wildtype


title: INCA_25399_whole blood

description:
Sample name: 25399
First_half_signal.txt

value: Peruvian Inca Orchid


title: XOLO_30509_saliva

description:
Sample name: 30509
First_half_signal.txt

value: Xoloitzcuinte

value: saliva


title: BIEW_31246_saliva

description:
Sample name: 31246
First_half_signal.txt

value: USA

value: Biewer Terrier


title: WGBS_suvh3_rep2


title: WGBS_WT_rep1


title: CLSP_02314_buccal cells

description:
Sample name: 2314
First_half_signal.txt

value: Clumber Spaniel


title: WGBS_suvh3_rep1


title: CARO_29866_whole blood

description:
Sample name: 29866
First_half_signal.txt

value: Carolina Dog


title: 1629_SM

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

description:
1629
8691758029_G

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalized using quantile normalization with BeadStudio software v3.8

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Illumina MicroRNA Expression Profiling Assay Guide).

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: SM

value: tumor nodule


title: WGBS_suvh1_rep1

value: floral bud


title: CLSP_01009_whole blood

description:
Sample name: 1009
First_half_signal.txt


title: CLSP_01008_whole blood

description:
Sample name: 1008
First_half_signal.txt


title: MANT_27149_saliva

description:
Sample name: 27149
First_half_signal.txt

value: Manchester Terrier


title: CLSP_27422_whole blood

description:
Sample name: 27422
First_half_signal.txt

value: whole blood


title: NGSD_13227_whole blood

description:
Sample name: 13227
First_half_signal.txt

value: New Guinea Singing Dog


title: 1631_un

description:
1631
8691758029_H

source_name: 1631, untreated

value: un


title: LEOP_10791_whole blood

description:
Sample name: 10791
First_half_signal.txt

value: Catahoula Leopard Dog


title: TIBT_10792_whole blood

description:
Sample name: 10792
First_half_signal.txt

value: Tibetan Terrier


title: BIEW_31256_saliva

description:
Sample name: 31256
First_half_signal.txt


title: WGBS_suvh1_3_rep1

value: suvh1, suvh3


title: AKBH_06285_whole blood

description:
Sample name: 6285
First_half_signal.txt

value: Akbash


title: BIEW_31253_saliva

description:
Sample name: 31253
First_half_signal.txt


title: BIEW_31248_saliva

description:
Sample name: 31248
First_half_signal.txt


title: CAAN_30657_whole blood

description:
Sample name: 30657
First_half_signal.txt

value: Canaan Dog


title: 1627_SM

description:
1627
8691758029_F


title: ChIPseq_B_antiFLAG_SUVH3Finsuvh3

description: ChIP DNA

extract_protocol:
4-8 grams of 12-14 days post germination seedling material, crosslinked in vitro and sheared using Bioruptor Plus (Diagenode).
NuGen Ovation Ultra Low System V2 1-17

value: anti-FLAG M2 (F1804, Sigma)

value: seedling


title: 1624_un

description:
1624
8691758029_C

source_name: 1624, untreated


title: ChIPseq_B_antiFLAG_WT

description: ChIP DNA

value: wildtype


title: ATACseq_WT_rep2

description: transposase accessible chromatin

data_processing:
ATACseq: 50bp paired end reads were aligned using Bowtie1, allowing 2 mismatches with unique mapping and including –k 2000 option.
genome build: TAIR 10
ATACseq bigWig tracks are normalised reads (by mapped library size), and binned into 25bp or 50bp bins.

extract_protocol:
1g of 12-14 days post germination seedling material from two biological replicates each of WT or suvh1/3 mutant genotypes as input. Briefly, seedling tissue was chopped on glass using a razor blade in 5 ml of ice-cold Lysis buffer (15mM Tris-Cl pH 7.5, 0.5mM spermine-4HCl, 80mM KCl, 20mM NaCl, 0.25 % Triton X-100, 5mM β-mercaptoethanol), filtered through 40µM strainer (Falcon) into 5ml Sucrose buffer (20mM Tris-Cl pH 8.0, 1.7M Sucrose, 5mM MgCl2, 0.25 % Triton X-100, 2mM EDTA, 5mM β-mercaptoethanol), and spun at 20,000xg, for 30mins at 4oC. Pellets were resuspended in 1ml of Lysis buffer and stained with DAPI (0.5µg/ml final concentration) and 50k nuclei were collected by FACS into 0.5ml of Lysis buffer.
Tn5 transposase reaction followed by NEBNext High-Fidelity Master-Mix amplification.


title: AKBH_06283_whole blood

description:
Sample name: 6283
First_half_signal.txt

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols. DNA was extracted from saliva using the DNA Genotek saliva collection kit following recommended protocol. DNA was extracted from tissue using the Qiagen DNEasy blood and tissue kits.

value: USA


title: 1625_un

description:
1625
8691758029_D

source_name: 1625, untreated


title: BIEW_31247_saliva

description:
Sample name: 31247
First_half_signal.txt

value: Biewer Terrier

value: saliva


title: ATACseq_WT_rep1

description: transposase accessible chromatin


title: INCA_25400_whole blood

description:
Sample name: 25400
First_half_signal.txt

value: Peruvian Inca Orchid


title: 1623_un

description:
1623
8691758029_B

source_name: 1623, untreated

value: tumor nodule


title: ATACseq_suvh1_3_rep2

description: transposase accessible chromatin


title: LEOP_07703_buccal cells

description:
Sample name: 7703
First_half_signal.txt

value: buccal cells


title: 1622_SM

description:
1622
8691758029_A

value: SM


title: RTVB_31258_saliva

description:
Sample name: 31258
First_half_signal.txt

value: Russian Tsvetnaya Bolonka


title: Inland treatment Rep2

city: CHARLOTTE

first: HENGYOU

last: ZHANG

state: NORTH CAROLINA

address: 9201 University City Blvd

department: Biological Sciences

institute: Univ. of North Carolina at Charlotte

description: Pooled root tissues from 3h, 24h, and 7d supplied with NaCl solution

data_processing:
QC was assesed with FastQC and controlled with Trimmomatic v0.36
Filtered data were aligned against common bean (Phaseolus vulgaris) reference genome Pvulgaris_218_v1.0 (https://phytozome.jgi.doe.gov) using RNA-seq aligner STAR software
Abandance of transcripts were estimated using featureCounts
Difference expression analyses was conducted using EdgeR
Genome_build: Pvulgaris_218_v1.0 (https://phytozome.jgi.doe.gov)
Supplementary_files_format_and_content: STAR generated .bam files; featureCount generated a tab-delimited text files containing raw counts of sequencing reads; EdgeR output lists of differentially expressed genes in tab-delimited text format

organism: Strophostyles helvola

source_name: Whole roots

growth_protocol: The seeds were germinated in a growth chamber (Percival Scientific Inc., Perry, IA, USA) and the healthy seedlings were transplanted into flats filled with soil. Briefly, seed coat was sliced to facilitate germination and placed on moist filter paper on a petri dish. 3-day post germination, the seedlings were transplanted in 3×6 flat (3.10" x 3.10" x 2.33") (Greenhouse MegaStore, US) filled with potting mix soil

extract_protocol:
We used pooled root tissues that were collected at 3h, 24h, and 7d for the following study. Total RNA was isolated with RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). Purified RNA was quantified using a Quant-iT™ RiboGreen™ RNA Assay Kit (Invitrogen Carlsbad, CA, USA) and its integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
One microgram of RNA samples with RNA integrity number (RIN) ≥ 7.0 (Table 1) from three independent biological replicates of each condition was used to generate cDNA libraries using a TruSeq RNA Library Prep Kit from Illumina.

treatment_protocol: We used 200 Mm and 400 Mm of NaCl solution as a final concentration to stress Inland and Beach beans, respectively. For treatment, the plants were supplied with 50 mL NaCl solution per day.  In parallel, plants supplied with the same amount of water were used as controls. Whole roots were sliced off from the treatment and control plants at 3h, 24h and 7d, respectively, after the concentration of NaCl was reached as designed and flash frozen in liquid nitrogen.

value: Whole roots

value: 10-d seedings

value: NaCl soultion

value: USA Missouri


title: Inland treatment Rep1


title: NGSD_13226_whole blood

description:
Sample name: 13226
First_half_signal.txt

value: New Guinea Singing Dog

value: whole blood


title: Inland control Rep3

description: Pooled root tissues from 3h, 24h, and 7d supplied with water

value: Water


title: ATACseq_suvh1_3_rep1

description: transposase accessible chromatin

value: seedling

value: suvh1, suvh3


title: RTVB_31259_saliva

description:
Sample name: 31259
First_half_signal.txt

value: USA


title: DMSO21H2

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

description: DMSO 21 hrs replicate 2

data_processing:
Segemehl V0.18 used for mapping.
Read counts were calculated using custom made perl script.
Reads were normalised using VOOM approach from Limma package in R.
Differential gene expression was calculated using Limma in R.
Mapped reads were transformed into graphical "GR" files for visualisation using IGB.
Genome_build: Klebsiella pneumoniae MGH 78578
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include VOOM transformed log2CPM values (normalised abundance measurements) for each Sample.

organism: Klebsiella pneumoniae MGH 78578

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina HiSeq2500 RNA Sample Prep Kit was used with total RNA for the construction of sequencing libraries.

value: DMSO control

tag: time

value: 21 hr


title: CPBR_00889_whole blood

description:
Sample name: 889
First_half_signal.txt

value: Chesapeake Bay Retriever


title: DMSO21H1

description: DMSO 21 hrs replicate 1


title: Inland control Rep2


title: Beach treatment Rep3

value: USA Beach in Wilmington, NC


title: NMP21H2

description: NMP 21 hrs replicate 2

value: NMP


title: GORD_28456_saliva

description:
Sample name: 28456
First_half_signal.txt

value: Gordon Setter

value: saliva


title: Beach treatment Rep1

value: Whole roots


title: WGBS_suvh1_rep2

description:
bisulfite treated genomic DNA
The libraries were multiplexed then sequenced on multiple lanes including both a HiSeq 2500 and HiSeq 4000. Thus every library has reads from both instruments.

value: floral bud


title: Static4

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

data_processing:
Transcript-level quantitation with Salmon
Gene level summarization with txImport
Normalization with DESeq2
Differential expression with DESeq2
Genome_build: Ensembl Mmul 8.0.1
Supplementary_files_format_and_content: raw gene level counts for each Mmul Ensembl gene ID

organism: Macaca mulatta

source_name: RF/6A cells from ATCC

growth_protocol: We used RF/6A purchased in August 2017 from American Type Culture Collection (ATCC), Lot #700791. RF/6A were grown in Dulbecco's Modified Eagle Media supplemented with 10% heat inactivated fetal bovine serum and 100 U/mL penicillin and 100 U/mL streptomycin.

extract_protocol:
Total RNA was isolated from RF/6A using the RNeasy Micro Kit (Thermo Fisher) according to the manufacturer's specifications.
BGISEQ-500

treatment_protocol: All cells were maintained in a sterile humidified incubator at 37C in 5% atmospheric CO2.

tag: cell line

tag: cell type

value: chorioretinal cells


title: AKBH_15287_whole blood

description:
Sample name: 15287
First_half_signal.txt

value: Akbash


title: CPBR_12347_whole blood

description:
Sample name: 12347
First_half_signal.txt


title: NGSD_13228_whole blood

description:
Sample name: 13228
First_half_signal.txt

value: New Guinea Singing Dog


title: Human small intestinal organoids cultured with EGF and p38i

hyb_protocol: Standard Affymetrix procedures

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: Raw expression data were normalized by RMA together with human healthy colonic organoid data from GSE74843. Batch effects were compensated using the ComBat algorithm.

source_name: Human small intestinal organoids

label_protocol: Standard Affymetrix procedures

extract_protocol: Total RNA was extracted using the Rneasy Plus Mini Kit according to the manufacturer's instructions.

value: Ileum

value: EGF and p38i


title: Beach treatment Rep2

value: 10-d seedings

value: NaCl soultion


title: Beach control Rep2

value: Water


title: NMP21H1

description: NMP 21 hrs replicate 1


title: NMP15M2

description: NMP 15" replicate 2

value: 15 min


title: Beach control Rep3


title: RTVB_31262_saliva

description:
Sample name: 31262
First_half_signal.txt

value: USA

value: Russian Tsvetnaya Bolonka


title: Human small intestinal organoids cultured with IGF1 and FGF2

value: IGF1 and FGF2


title: NMP15M1

description: NMP 15" replicate 1

value: NMP


title: RATT_24735_whole blood

description:
Sample name: 24735
First_half_signal.txt

value: Rat Terrier

value: whole blood


title: Static3


title: Static1


title: Static2


title: GREE_26335_muscle

description:
Sample name: 26335
First_half_signal.txt

source_name: muscle

value: Switzerland

value: Greenland Dog

value: muscle


title: P. aeruginosa_vehicle (EtOH)_mRNA (duplicate)

status: Public on Dec 05 2018

city: Birmingham

first: Javier

last: Campos-Gomez

state: Alabama

address: 2000 Ninth Ave South

department: Infectious Diseases

institute: Southern Research

description:
Ribosomal RNA-depleted total RNA
Emp_20

data_processing:
Illumina bcl2fastq version 2.18.0.12 software used for basecalling.
EDGE-Pro version 1.3.1 was used to align the raw fastq files to the reference genome with parameters -g -p -r -u -t -o
EDGE-Pro version 1.3.1 Perl script edgeToDeseq.pl was used to convert the intensity values to counts for DESeq2
DESeq2 version 1.20.0 was used in R version 3.4.3 following their vignette
Genome_build: NC_002516
Supplementary_files_format_and_content: tab delmiited Excel file of genes and intensity values for each sample

organism: Pseudomonas aeruginosa

source_name: PAO1 ΔPA2076 (ΔodsR)

extract_protocol:
Bacterial cells were recovered and used to isolate total RNA using a QIAGEN RNeasy Plus Mini Kit (cat. no. 74134). Concentration and purity of RNA samples were determined by measuring the absorbance (A260:A280) using a NanoDrop 2000 spectrophotometer (ThermoFisher Scientific). Total RNA samples were then processed for the depletion of ribosomal RNA (rRNA) following the manufacturer’s user manual for Ribo-Zero rRNA removal kit for bacteria from Illumina (Document # 15066012 V02).
RNA libraries were prepared following the Lexogen’s user manual of Sense Total RNA-seq library preparation kit (cat.no. 009.24, 020.24, 022.24). Briefly, 10 ng of rRNA-depleted RNA was used as the starting material for the generation of libraries. The library generation started with the random hybridization of the starter/stopper heterodimer mix to the rRNA-depleted RNA. These starter/stopper heterodimers contained Illumina-compatible linker sequences. A single-tube reverse transcription and ligation reaction was then performed to extend the starter to the next hybridized heterodimer, where the newly synthesized cDNA insert was ligated to the stopper. The second strand synthesis was then performed to hydrolyze the RNA and then the library was converted to double-stranded DNA, which was purified using magnetic beads to adjust the library length and to ensure the complete removal of second strand synthesis reaction components. The library amplification was then performed to add the complete adaptor sequences required for cluster generation and to produce sufficient material for quality control and sequencing; i7 indices were added during this step in order to uniquely multiplex the samples for the sequencing run. The resulting RNA libraries were then purified using magnetic beads to get rid of PCR components, which could interfere with quantification and sequenced on an Illumina MiSeq instrument.

treatment_protocol: P. aeruginosa PAO1 ΔPA2076 strain was grown in quadruplicates in M63 complete medium (3 ml) up to an OD600 = 1 at 30⁰C and shaking (240 rpm). The cultures were then treated with 0.1 mg/ml of OA, 10-HOME or 7,10-DiHOME or treated with the vehicle only (ethanol) as baseline control and incubated 30 additional min at 30⁰C and shaking (240 rpm). This was done in duplicates.

value: vehicle (EtOH)

tag: genotype/strain

value: PAO1 deltaPA2076 (delta-odsR)

tag: phenotype

value: mutant unable to produce oxylipins


title: P. aeruginosa_vehicle (EtOH)_mRNA

description:
Ribosomal RNA-depleted total RNA
Emp_20_2


title: P. aeruginosa_7-HOME_mRNA (duplicate)

description:
Ribosomal RNA-depleted total RNA
Emp20_monohydroxy


title: GREE_26334_muscle

description:
Sample name: 26334
First_half_signal.txt


title: P. aeruginosa_7-HOME_mRNA

description:
Ribosomal RNA-depleted total RNA
Emp20_monohydroxy_2


title: P. aeruginosa_oleic acid_mRNA (duplicate)

description:
Ribosomal RNA-depleted total RNA
Emp20_Oleic_acid

value: oleic acid


title: GORD_26995_saliva

description:
Sample name: 26995
First_half_signal.txt

value: Gordon Setter

value: saliva


title: P. aeruginosa_7,10-DiHOME_mRNA

description:
Ribosomal RNA-depleted total RNA
Emp20_Dihydroxy_2


title: WGBS_suvh1_3_rep2

value: floral bud

value: suvh1, suvh3


title: P. aeruginosa_oleic acid_mRNA

description:
Ribosomal RNA-depleted total RNA
Emp20_Oleic_acid_2


title: DMSO15M1

description: DMSO 15" replicate 1

value: DMSO control

value: 15 min


title: P. aeruginosa_7,10-DiHOME_mRNA (duplicate)

description:
Ribosomal RNA-depleted total RNA
Emp20_Dihydroxy


title: GREE_26333_muscle

description:
Sample name: 26333
First_half_signal.txt


title: Inland treatment Rep3

description: Pooled root tissues from 3h, 24h, and 7d supplied with NaCl solution

value: Whole roots

tag: age

value: 10-d seedings

value: NaCl soultion

value: USA Missouri


title: Liver-PPARaKO_HFD-Rep8

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

description: 20 weeks old mice

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 39 out of 48 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 35469 spots out of 62976 were selected.  The mean signal of the 24 first samples and 24 last ones were substracted to individuals signals to correct the batch effect of the 2 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 32816 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Liver

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: WT, PPARα LKO and PPARα KO male mice (C57Bl6J) were used for this liver gene expression analysis

extract_protocol: Standard RNA extraction with TriZol was used.

treatment_protocol: Mice were treated with either control diet (CTRL) or high fat diet (HFD) containing 60% of fat for 12 weeks

tag: genotype

value: PPARaKO

tag: diet

value: HFD

tag: washbatch


title: DMSO15M2

description: DMSO 15" replicate 2

tag: treatment


title: Inland control Rep1

description: Pooled root tissues from 3h, 24h, and 7d supplied with water

value: Water


title: Liver-PPARaKO_CTRL-Rep8

description: 20 weeks old mice

value: CTRL


title: Liver-PPARaLKO_HFD-Rep2

description: 20 weeks old mice

value: PPARaLKO


title: Liver-PPARaLKO_HFD-Rep6

description: 20 weeks old mice


title: Liver-PPARaWT_HFD-Rep8

description: 20 weeks old mice

value: PPARaWT


title: Beach control Rep1

value: USA Beach in Wilmington, NC


title: Liver-PPARaLKO_CTRL-Rep2

description: 20 weeks old mice


title: 1626_SM

description:
1626
8691758029_E

value: SM

value: tumor nodule


title: Liver-PPARaLKO_CTRL-Rep8

description: 20 weeks old mice


title: Liver-PPARaLKO_CTRL-Rep6

description: 20 weeks old mice


title: Liver-PPARaWT_CTRL-Rep5

description: 20 weeks old mice


title: Liver-PPARaWT_CTRL-Rep1

description: 20 weeks old mice


title: Liver-PPARaWT_HFD-Rep3

description: 20 weeks old mice


title: Liver-PPARaKO_HFD-Rep1

description: 20 weeks old mice


title: Liver-PPARaLKO_CTRL-Rep5

description: 20 weeks old mice


title: Liver-PPARaKO_HFD-Rep5

description: 20 weeks old mice


title: Liver-PPARaWT_HFD-Rep1

description: 20 weeks old mice


title: Liver-PPARaLKO_CTRL-Rep3

description: 20 weeks old mice


title: Liver-PPARaKO_HFD-Rep7

description: 20 weeks old mice


title: Liver-PPARaKO_CTRL-Rep6

description: 20 weeks old mice


title: Liver-PPARaKO_CTRL-Rep1

description: 20 weeks old mice


title: Liver-PPARaWT_CTRL-Rep2

description: 20 weeks old mice


title: Liver-PPARaWT_CTRL-Rep8

description: 20 weeks old mice


title: Liver-PPARaLKO_CTRL-Rep1

description: 20 weeks old mice


title: Liver-PPARaKO_CTRL-Rep3

description: 20 weeks old mice


title: Liver-PPARaKO_HFD-Rep3

description: 20 weeks old mice


title: Liver-PPARaKO_CTRL-Rep2

description: 20 weeks old mice


title: Liver-PPARaWT_HFD-Rep5

description: 20 weeks old mice


title: RATT_25647_whole blood

description:
Sample name: 25647
First_half_signal.txt

value: USA

value: Rat Terrier

value: whole blood


title: Liver-PPARaWT_CTRL-Rep7

description: 20 weeks old mice


title: Liver-PPARaKO_CTRL-Rep4

description: 20 weeks old mice


title: Liver-PPARaKO_HFD-Rep2

description: 20 weeks old mice


title: Liver-PPARaLKO_HFD-Rep5

description: 20 weeks old mice


title: Liver-PPARaKO_HFD-Rep6

description: 20 weeks old mice


title: Liver-PPARaLKO_HFD-Rep1

description: 20 weeks old mice


title: Liver-PPARaWT_HFD-Rep4

description: 20 weeks old mice


title: Liver-PPARaWT_CTRL-Rep4

description: 20 weeks old mice


title: Liver-PPARaWT_HFD-Rep6

description: 20 weeks old mice


title: MMA041-1511

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description: Sample 215

data_processing:
Raw sequencing intensities were obtained on a NextSeq500 instrument and converted to base calls using bcl2fastq software (Illumina)
TruSeq Small RNA adapters were trimmed using cutadapt in Partek Flow (Partek), with minimum length set to 19
Alignment to miRbase 21 index of hg38 was performed using Shrimp2 in Partek Flow (Partek)
Quantification was performed in Partek Flow (Partek)
Normalization was performed to total read counts
Genome_build: hg38
Supplementary_files_format_and_content: a single data matrix of raw count abundance is provided as a comma separated value (CSV) file for the combined set of 218 samples

source_name: Serum

extract_protocol:
Saliva was collected in an RNA stabilizing container (Oragene RNA RE-100, DNA Genotek) and RNA was harvested using Qiazol reagent followed by RNeasy (Qiagen).
llumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 250-500 nanograms of total RNA for the construction of sequencing libraries.

value: Serum

tag: timepoint

value: 0d post

tag: hits to the head

tag: subject


title: MMA042-1711

description: Sample 217

tag: tissue


title: MMA038-1361

description: Sample 210

value: 0d pre


title: MMA040-1411

description: Sample 214


title: MMA039-1211

description: Sample 212


title: MMA039-1111

description: Sample 211


title: MMA038-1296

description: Sample 209


title: MMA037-2182

description: Sample 208


title: Liver-PPARaLKO_HFD-Rep7

description: 20 weeks old mice


title: Liver-PPARaWT_CTRL-Rep6

description: 20 weeks old mice


title: MMA042-1811

description: Sample 218


title: MMA037-2021

description: Sample 207


title: Liver-PPARaLKO_CTRL-Rep7

description: 20 weeks old mice


title: Liver-PPARaLKO_HFD-Rep4

description: 20 weeks old mice


title: Liver-PPARaWT_HFD-Rep7

description: 20 weeks old mice


title: Liver-PPARaWT_CTRL-Rep3

description: 20 weeks old mice


title: MMA036-1778

description: Sample 205


title: MMA040-1311

description: Sample 213


title: MMA035-2559

description: Sample 204


title: Liver-PPARaKO_CTRL-Rep7

description: 20 weeks old mice


title: Liver-PPARaLKO_HFD-Rep8

description: 20 weeks old mice


title: SLOU_24408_saliva

description:
Sample name: 24408
First_half_signal.txt

tag: origin

value: Sloughi

value: saliva


title: Liver-PPARaKO_CTRL-Rep5

description: 20 weeks old mice

value: PPARaKO


title: Liver-PPARaLKO_HFD-Rep3

description: 20 weeks old mice

value: HFD


title: Liver-PPARaKO_HFD-Rep4

description: 20 weeks old mice


title: Liver-PPARaWT_HFD-Rep2

description: 20 weeks old mice


title: MMA035-3231

description: Sample 203


title: MMA033-2360

description: Sample 199


title: MMA032-2089

description: Sample 197


title: MMA034-1282

description: Sample 202


title: MMA032-3145

description: Sample 198


title: MMA033-2075

description: Sample 200


title: MMA031-1896

description: Sample 195


title: MMA031-2702

description: Sample 196


title: MMA036-2276

description: Sample 206


title: MMA030-1988

description: Sample 194


title: MMA029-2321

description: Sample 192


title: MMA030-1647

description: Sample 193


title: MMA029-1453

description: Sample 191


title: MMA027-3227

description: Sample 187


title: MMA026-2117

description: Sample 185


title: MMA028-1719

description: Sample 190


title: MMA025-3198

description: Sample 184


title: MMA026-3169

description: Sample 186


title: MMA025-2037

description: Sample 183


title: MMA034-3013

description: Sample 201


title: MMA028-3176

description: Sample 189


title: MMA024-1489

description: Sample 182

value: Saliva

value: 1wk post


title: Liver-PPARaLKO_CTRL-Rep4

description: 20 weeks old mice

value: PPARaLKO

value: CTRL


title: MMA024-2850

description: Sample 181


title: MMA023-1767

description: Sample 174


title: MMA024-2285

description: Sample 178


title: MMA023-1813

description: Sample 170

value: 1wk pre


title: MMA024-2388

description: Sample 179


title: MMA023-1624

description: Sample 173

source_name: serum

value: serum

value: 2-3d post


title: MMA023-1682

description: Sample 172


title: MMA024-2126

description: Sample 177


title: MMA024-1888

description: Sample 180


title: MMA023-1263

description: Sample 175


title: MMA024-2484

description: Sample 176


title: MMA023-3159

description: Sample 171


title: MMA027-1117

description: Sample 188


title: MMA023-1223

description: Sample 166


title: MMA022-3038

description: Sample 160


title: MMA022-1975

description: Sample 165


title: MMA023-2091

description: Sample 167


title: MMA023-1301

description: Sample 169


title: MMA022-3185

description: Sample 163


title: MMA022-3196

description: Sample 161


title: MMA021-2737

description: Sample 159


title: MMA022-2775

description: Sample 162


title: MMA023-2413

description: Sample 168


title: MMA021-3222

description: Sample 157


title: MMA021-3136

description: Sample 155


title: MMA021-1650

description: Sample 156


title: MMA022-2445

description: Sample 164


title: MMA021-1686

description: Sample 154


title: MMA021-3128

description: Sample 153


title: MMA021-2044

description: Sample 158


title: MMA020-2912

description: Sample 148


title: MMA019-2424

description: Sample 144


title: MMA019-1772

description: Sample 143


title: MMA019-1494

description: Sample 146


title: MMA019-1289

description: Sample 142


title: MMA020-2724

description: Sample 149


title: MMA019-2823

description: Sample 145


title: MMA021-2690

description: Sample 152


title: MMA019-2939

description: Sample 141


title: MMA018-2054

description: Sample 140


title: MMA017-2341

description: Sample 137


title: MMA018-2666

description: Sample 139


title: MMA017-2914

description: Sample 138


title: MMA017-1765

description: Sample 136


title: MMA017-3267

description: Sample 133


title: MMA016-1284

description: Sample 127


title: MMA017-2108

description: Sample 135


title: MMA017-2038

description: Sample 132


title: MMA016-3134

description: Sample 129


title: MMA017-1536

description: Sample 134


title: MMA016-1889

description: Sample 128


title: MMA019-1316

description: Sample 147


title: MMA016-1167

description: Sample 131


title: MMA016-2495

description: Sample 126


title: MMA021-1898

description: Sample 150


title: MMA021-1607

description: Sample 151


title: MMA016-1123

description: Sample 130


title: MMA015-1149

description: Sample 124

value: 3+ wks post


title: MMA015-1824

description: Sample 122


title: MMA015-2833

description: Sample 118


title: MMA015-1527

description: Sample 119


title: MMA016-2027

description: Sample 125


title: MMA015-2966

description: Sample 123


title: MMA015-2103

description: Sample 121


title: MMA015-2913

description: Sample 117


title: MMA015-2062

description: Sample 120


title: MMA015-2959

description: Sample 115


title: MMA014-2394

description: Sample 113


title: MMA014-3097

description: Sample 112


title: MMA015-1764

description: Sample 114


title: MMA014-1769

description: Sample 105


title: MMA014-1482

description: Sample 106


title: MMA014-2036

description: Sample 104


title: MMA014-1237

description: Sample 103


title: MMA014-3051

description: Sample 111


title: MMA014-1661

description: Sample 110


title: MMA014-1370

description: Sample 109


title: MMA013-2723

description: Sample 99


title: MMA014-1678

description: Sample 101


title: MMA014-2567

description: Sample 108


title: MMA015-1939

description: Sample 116


title: MMA014-1138

description: Sample 102


title: MMA014-1199

description: Sample 107


title: MMA013-2570

description: Sample 93


title: MMA012-2040

description: Sample 90


title: MMA013-2160

description: Sample 98


title: MMA013-1434

description: Sample 94


title: MMA013-1544

description: Sample 96


title: MMA013-3316

description: Sample 92


title: MMA012-2941

description: Sample 89


title: MMA012-2965

description: Sample 88


title: MMA014-1124

description: Sample 100


title: MMA013-2946

description: Sample 97


title: MMA012-1805

description: Sample 91


title: MMA011-1712

description: Sample 87


title: MMA041-1611

description: Sample 216


title: MMA013-2153

description: Sample 95


title: MMA011-3084

description: Sample 83


title: MMA010-2449

description: Sample 75


title: MMA010-1756

description: Sample 77


title: MMA011-2531

description: Sample 79


title: MMA011-2306

description: Sample 78


title: MMA010-2631

description: Sample 73


title: MMA010-2177

description: Sample 72


title: MMA011-1785

description: Sample 86


title: MMA010-1216

description: Sample 65


title: MMA010-2128

description: Sample 61


title: MMA010-2181

description: Sample 63


title: MMA010-1541

description: Sample 66


title: MMA011-2994

description: Sample 84


title: MMA011-2184

description: Sample 81


title: MMA010-1308

description: Sample 76


title: MMA011-2708

description: Sample 85


title: MMA011-1567

description: Sample 80


title: MMA011-3180

description: Sample 82


title: MMA010-1121

description: Sample 69


title: MMA010-2669

description: Sample 70


title: MMA010-1623

description: Sample 71


title: MMA010-1470

description: Sample 64


title: MMA010-1637

description: Sample 68


title: MMA010-2099

description: Sample 62


title: MMA010-2064

description: Sample 58


title: MMA009-3233

description: Sample 56


title: MMA010-1236

description: Sample 74


title: MMA008-2915

description: Sample 50


title: MMA009-1919

description: Sample 53


title: MMA010-2636

description: Sample 60


title: MMA010-1642

description: Sample 59


title: MMA009-2591

description: Sample 57


title: MMA009-2121

description: Sample 55


title: MMA009-1852

description: Sample 52


title: MMA009-1528

description: Sample 54


title: MMA008-1502

description: Sample 51


title: MMA010-1992

description: Sample 67


title: MMA008-1608

description: Sample 48


title: MMA008-2997

description: Sample 49


title: MMA008-1456

description: Sample 47


title: MMA008-3253

description: Sample 46


title: MMA007-1169

description: Sample 44


title: MMA008-1552

description: Sample 45


title: MMA007-2155

description: Sample 43


title: MMA007-3153

description: Sample 42


title: MMA006-1771

description: Sample 41


title: MMA006-3123

description: Sample 40


title: MMA006-1264

description: Sample 39


title: MMA005-2679

description: Sample 37


title: MMA005-2790

description: Sample 36


title: MMA005-1340

description: Sample 35


title: MMA005-1876

description: Sample 34


title: MMA005-1626

description: Sample 33


title: 51558_D28_BCG

city: Oxford

first: Julius

last: Muller

state: Oxfordshire

address: ORCRB, Roosevelt Drive

department: Nuffield Department of Medicine

institute: The Jenner Institute, University of Oxford

data_processing: Probes were background corrected using negative control probes followed by quantile normalization using the neqc method of Shi et al. (2010) [PMID:20929874].

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared with the Ambion Total Prep RNA amplification kit

growth_protocol: Rested PBMC (1 x 106 ) were resuspended in single wells of 200ul RPMI supplemented with 10% FBS and L-glutamine.

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions with the following modification; in the first step an equal volume of 80% ethanol was added to cells lysed in RLT buffer, mixed and total volume transferred to an RNeasy column.  RNA was quantified by Nanodrop and stored at -80°C until use.

treatment_protocol: Cells were stimulated for 12 hours at 37°C in single wells containing BCG SSI from pooled vaccine vials (~2 × 105  CFU/ml) or media only.  After 12 hours of stimulation cells were pelleted and lysed in RNA lysis buffer (RLT, Qiagen).

value: PBMC

tag: day

tag: stimulus

value: BCG

tag: risk for tb

value: Control

tag: cmv status

value: CMVn

tag: vaccine

value: Candin


title: 50421_D0_uns

value: unstimulated


title: 50919_D0_BCG

value: CMVp


title: MMA004-2343

description: Sample 32

value: 0d pre


title: 53264_D28_BCG


title: MMA004-2798

description: Sample 31

value: 0d post


title: 51986_D0_BCG


title: 50246_D0_BCG

value: Case


title: 52378_D28_uns


title: MMA003-3003

description: Sample 30

value: Serum


title: MMA005-2273

description: Sample 38

value: Saliva


title: 52546_D28_uns


title: MMA003-2230

description: Sample 29


title: 51841_D28_BCG


title: 50551_D0_BCG


title: 51373_D28_BCG


title: MMA003-1814

description: Sample 27


title: MMA003-1585

description: Sample 26


title: MMA003-2170

description: Sample 25

value: 1wk post


title: 52218_D0_BCG


title: 52218_D28_BCG


title: 52044_D28_BCG


title: 50245_D28_uns


title: 53416_D0_uns


title: 53305_D28_uns


title: 53207_D28_BCG


title: MMA003-1592

description: Sample 24


title: 50245_D0_uns


title: MMA003-1784

description: Sample 23


title: 51566_D0_BCG


title: MMA003-2837

description: Sample 21


title: MMA003-3268

description: Sample 22


title: MMA003-3041

description: Sample 19


title: MMA003-3079

description: Sample 28


title: MMA003-1531

description: Sample 18


title: 51626_D0_BCG


title: 50421_D28_BCG


title: 53153_D0_BCG


title: MMA003-2928

description: Sample 20


title: 30044_D0_BCG


title: 51986_D0_uns


title: 53109_D28_uns


title: MMA002-1113

description: Sample 14


title: MMA002-2862

description: Sample 15


title: MMA001-2152

description: Sample 13


title: MMA003-2982

description: Sample 17


title: MMA001-2532

description: Sample 12

value: 1wk pre


title: MMA002-2895

description: Sample 16


title: 52687_D0_BCG


title: 52546_D0_uns


title: 51914_D0_uns


title: 51901_D0_BCG


title: MMA001-1863

description: Sample 10

value: serum


title: 52546_D0_BCG


title: MMA001-1872

description: Sample 9


title: MMA001-1918

description: Sample 7

value: 2-3d post


title: MMA001-1734

description: Sample 8


title: MMA001-1232

description: Sample 6


title: MMA001-1636

description: Sample 4


title: MMA001-2973

description: Sample 11


title: 51708_D0_uns


title: 53257_D28_uns


title: 52640_D28_BCG


title: 53430_D0_BCG


title: 53042_D28_uns


title: MMA001-2784

description: Sample 2


title: MMA001-1425

description: Sample 5


title: MMA001-2719

description: Sample 3


title: MMA001-2533

description: Sample 1


title: 53748_D0_BCG


title: 51708_D0_BCG


title: 53169_D0_BCG


title: FI#3

city: Vienna

first: Philip

last: Kienzl

state: Vienna

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

data_processing:
Trimmomatic v0.36
FastQC v0.11.7
HISAT2 v2.1
Stringtie v1.3.4c
Ballgown v2.10.0
Genome_build: grch38_snp_tran
Supplementary_files_format_and_content: Excel file include FPKM values for each sample

source_name: skin

growth_protocol: 4 week cultured T cells were isolated from skin explant cultures and freshly isolated cells by collagenase P digestion and CD2 magnetic bead enrichment

extract_protocol:
E.Z.N.A. MicroElute Total RNA Kit (Omega Bio-tek, USA) with DNase I on-column digestion
NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: IL-2, IL-4, TGF-b - TH9-PC; IL-2, IL-15 - SC; all cells were anti-CD3/28 activated and PMA/ionomycin restimulated before lysis

tag: medium

value: Medium only

tag: cell type

value: T cell

tag: culture

value: freshly isolated cells


title: 52956_D28_BCG

value: PBMC

value: BCG

value: Control


title: 52884_D0_uns

value: unstimulated

value: CMVn


title: FI#4


title: SC#3

value: 4 weeks


title: FI#5


title: 51124_D0_BCG

value: Candin


title: SC#1


title: 53120_D28_uns


title: 50245_D28_BCG

value: Case


title: 52640_D0_uns


title: 51374_D28_uns


title: 51083_D0_BCG


title: TH9-PC#5

value: IL-2, IL-4, TGF-beta


title: 52512_D0_uns


title: 51914_D0_BCG

value: CMVp


title: TH9-PC#4


title: SC#5


title: 51777_D0_uns


title: 53298_D28_uns


title: TH9-PC#3


title: 52210_D28_uns


title: FI#1


title: SC#4


title: TH9-PC#1


title: FI#2


title: SC#2


title: 50832_D0_BCG


title: Lymph node met (CA054)

city: Hospitalet de Llobregat

first: Alvaro

last: Aytes

state: Catalonia

address: Granvia 199

department: ProCURE

country: Spain

institute: IDIBELL

data_processing:
RNA-seq pipeline description:
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Mouse: UCSC/mm9) using Tophat [1] (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.  We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings. We test for differentially expressed genes under various conditions using DEseq [3]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Raw RNAseq counts were normalized (variance stabilization) using DESeq2 package in R-studio Version 0.99.484
Genome_build: Mouse: UCSC/mm9
Supplementary_files_format_and_content: Tab-delimited text includes DESeq normalized values for each Sample

source_name: Prostate cancer metastasis

extract_protocol:
RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser 2100
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

tag: strain

value: hybrid 129/SvImJ and C57Bl/6J strain

value: Lymph node metastasis

tag: genotype


title: Lymph node met (CA055)


title: Lymph node met (CA024)


title: TH9-PC#2


title: Lymph node met (CA053)


title: 53042_D28_BCG


title: 51498_D0_BCG


title: Lymph node met (CA052)


title: 50821_D0_uns


title: 51863_D0_BCG


title: 53215_D0_uns


title: Lymph node met (CA017)


title: 52764_D28_BCG


title: 53457_D0_BCG


title: 51914_D28_uns


title: 50967_D0_BCG


title: 53794_D0_BCG


title: 50307_D0_uns


title: 53298_D0_uns


title: 51196_D28_uns


title: Lymph node met (CA021)


title: 50543_D28_uns


title: 51768_D0_BCG


title: Liver met (CA030)

value: Liver metastasis


title: 30044_D0_uns


title: Lung met (CA049)

value: Lung metastasis


title: Liver met (CA050)


title: 51991_D0_uns


title: 50263_D28_uns


title: Lung met (CA048)


title: Liver met (CA051)


title: Lung met (CA033)


title: Lung met (CA047)


title: 51093_D0_uns


title: Liver met (CA031)


title: Liver met (CA026)


title: 52378_D28_BCG


title: Lung met (CA022)


title: Lung met (CA029)


title: Lung met (CA025)


title: Lung met (CA018)


title: Primary tumor (CA065)

source_name: Prostate tissue

value: Primary tumor premet


title: Primary tumor (CA063)


title: 53302_D0_BCG


title: Primary tumor (CA060)


title: Primary tumor (CA061)


title: 51863_D0_uns


title: Primary tumor (CA046)

value: Primary tumor postmet


title: 53307_D0_BCG


title: 51270_D28_uns


title: 53457_D0_uns


title: Primary tumor (CA044)


title: 51238_D0_BCG


title: Primary tumor (CA043)


title: 50246_D0_uns


title: 51789_D28_BCG


title: 50842_D28_BCG


title: 51201_D0_uns


title: 53264_D28_uns


title: 51776_D28_BCG


title: Primary tumor (CA041)


title: Primary tumor (CA040)


title: 51373_D28_uns


title: 52850_D0_BCG


title: 53430_D0_uns


title: 50833_D0_uns


title: 53471_D0_uns


title: 50919_D0_uns


title: 52117_D0_BCG


title: Primary tumor (CA045)


title: Primary tumor (CA023)


title: Primary tumor (CA011)

value: Primary tumor NP


title: Primary tumor (CA036)


title: Primary tumor (CA008)


title: 53472_D0_uns

value: PBMC


title: Primary tumor (CA016)


title: Primary tumor (CA004)


title: Primary tumor (CA020)


title: WTadultK3

city: Würzburg

first: Kai

last: Kretzschmar

address: Josef-Schneider-Str. 2

country: Germany

institute: University Hospital Würzburg

description:
Adult murine hearts
barcode file: CEL-Seq_UMI_barcodes.csv.gz

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: coutb files contain UMI barcode normalised abundance counts

source_name: Extracted RNA from living cells of the ventricles of hearts of adult wildtype mice, replicate 2 [K3]

extract_protocol:
Live single cells were sorted in 384- well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: strain background

tag: genotype/variation

value: wildtype

tag: time point

value: adult

value: Heart

tag: heart region

value: ventricles


title: WTadultK2

source_name: Extracted RNA from living cells of the ventricles of hearts of adult wildtype mice, replicate 2 [K2]


title: WTadultK1

source_name: Extracted RNA from living cells of the ventricles of hearts of adult wildtype mice, replicate 2 [K1]


title: WTadultK4

source_name: Extracted RNA from living cells of the ventricles of hearts of adult wildtype mice, replicate 2 [K4]


title: Primary tumor (CA042)


title: 52970_D0_BCG

tag: subject

value: BCG

value: Control

value: CMVn


title: Primary tumor (CA005)

tag: tissue


title: 52586_D28_BCG

value: Candin


title: 51901_D28_BCG


title: 51373_D0_uns

value: unstimulated

value: Case

value: CMVp


title: WTadultJ3

source_name: Extracted RNA from living cells of the ventricles of hearts of adult wildtype mice, replicate 1 [J3]


title: WTadultJ1

source_name: Extracted RNA from living cells of the ventricles of hearts of adult wildtype mice, replicate 1 [J1]


title: 51116_D28_uns


title: WTadultJ2

source_name: Extracted RNA from living cells of the ventricles of hearts of adult wildtype mice, replicate 1 [J2]


title: 51462_D0_uns


title: 50879_D0_uns


title: WTneoI

description:
Neonatal murine hearts
barcode file: CEL-Seq_UMI_barcodes.csv.gz

source_name: Extracted RNA from living cells of the ventricles of hearts of neonatal wildtype mice [I]

value: Neonatal


title: 52117_D0_uns


title: 51116_D0_uns


title: 52549_D0_BCG


title: 52586_D0_uns


title: 53472_D0_BCG


title: 53748_D28_BCG


title: 51239_D0_BCG


title: 52889_D0_uns


title: RFPadultH2

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the ventricles of hearts of adult Ki67TagRFP mice, replicate 2 [H2]


title: RFPadultH3

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the ventricles of hearts of adult Ki67TagRFP mice, replicate 2 [H3]


title: RFPadultH4

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the ventricles of hearts of adult Ki67TagRFP mice, replicate 2 [H4]


title: RFPadultH1

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the ventricles of hearts of adult Ki67TagRFP mice, replicate 2 [H1]


title: 52889_D28_BCG


title: 51705_D0_BCG


title: 51346_D28_uns


title: 52864_D28_BCG


title: RFPMIRemF4

description:
Murine hearts 14 days after myocardial infarction
barcode file: CEL-Seq_UMI_barcodes.csv.gz

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the remote area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 2 [F4]

value: 14 days post-MI

value: remote area


title: RFPMIRemF3

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the remote area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 2 [F3]


title: 50015_D0_uns

source_name: PBMC


title: 51156_D28_BCG


title: RFPadultG1

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the ventricles of hearts of adult Ki67TagRFP mice, replicate 1 [G1]


title: RFPadultG2

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the ventricles of hearts of adult Ki67TagRFP mice, replicate 1 [G2]


title: 52797_D0_BCG


title: RFPMIRemF1

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the remote area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 2 [F1]


title: RFPMIRemF2

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the remote area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 2 [F2]


title: RFPMIInfE4

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the infarcted area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 2 [E4]

value: infarcted area


title: RFPMIInfE3

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the infarcted area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 2 [E3]


title: 50967_D0_uns


title: 53091_D0_BCG


title: RFPMIInfE2

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the infarcted area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 2 [E2]


title: 52210_D28_BCG


title: RFPSHInfD4

description:
Murine hearts 14 days after sham surgery
barcode file: CEL-Seq_UMI_barcodes.csv.gz

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the apex area (corresponding area in control to infarcted area in infarcted mice) area of hearts of Ki67TagRFP mice 14 days post-sham surgery, replicate 1 [D4]

value: 14 days after sham surgery

value: apex area


title: RFPSHInfD3

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the apex area (corresponding area in control to infarcted area in infarcted mice) area of hearts of Ki67TagRFP mice 14 days post-sham surgery, replicate 1 [D3]


title: RFPMIInfE1

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the infarcted area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 2 [E1]


title: RFPSHInfD2

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the apex area (corresponding area in control to infarcted area in infarcted mice) area of hearts of Ki67TagRFP mice 14 days post-sham surgery, replicate 1 [D2]


title: RFPSHInfD1

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the apex area (corresponding area in control to infarcted area in infarcted mice) area of hearts of Ki67TagRFP mice 14 days post-sham surgery, replicate 1 [D1]