title: MUT_2_input

city: La Jolla

first: David

last: Traver

state: California

address: 9500 Gilman Drive, MC 0380

department: Division of Biological Sciences

institute: UCSD

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-Seq was aligned to GRCz10 using STAR
HOMER was used to make tag directories with the the number of tags per base pair limited to 1 (-tbp1)
HOMER was also used to call and analyze peaks
Genome_build: GRCz10
Supplementary_files_format_and_content: bedGraph files generated using HOMER

organism: Danio rerio

growth_protocol: zebrafish embryos were grown at 28°C and collected at 32hpf

extract_protocol:
Approximately 1,000 of each WT and MUT supt16h embryos per treatment were collected and deyolked using the Ginzburg Fish Ringer solution. Embryos were resuspended in 1 mL PBS with 1 mM PMSF, 1X cOmplete EDTA Free Protease Inhibitor Cocktail Tablet (Roche), 1X phosSTOP Phosphatase Inhibitor Tablet (Roche) and pushed through a 21G needle. Embryos were immediately crosslinked with 4 mM DSG (ProteoChem) for 30 min, followed by 1% PFA for 8 min, and stopped with 0.125M Glycine. Fixed embryos were resuspended in 1 mL Lysis Buffer 1 (0.05M HEPES, 140 mM NaCl, 1 mM EDTA, 1% Glycerol, 0.5% NP40, 0.25% Triton-X) and subjected to the TissueRuptorII (Qiagen) for 20 sec on low. Tissue was rocked for 10 min at 4ºC, pelleted, and resuspended in 1 mL Lysis Buffer 2 (10 mM Tris,-pH 8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA). They were rocked again for 10 min at room temperature (RT), pelleted and resuspended in 1.5 mL Lysis Buffer 3 (10mM Tris-pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.05% SDS). Tissue was then sonicated on the Diagenode Bioruptor 300 (30 sec ON, 30 sec OFF, HIGH, 34 cycles). Following the addition of 0.8% Triton-X to the sonicated chromatin, cells were spun down. 20 ul of lysate was saved as input control and the remainder was incubated with Dyna Beads bound with 10 ug p53 antibody (GeneTex) overnight at 4ºC, rotating. Beads were collected on a magnet and washed 1x Wash Buffer 1 (20 mM Tris-pH 8, 150 mM NaCl, 2 mM EDTA. 0.1% SDS, 1% Triton-X), 1x Wash Buffer 2 (20mM Tris-pH 8, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton-X), 1x Wash Buffer 3 (10mM Tris-pH 8, 250 mM LiCl, 1 mM EDTA, 1% sodium deoxycholate, 1% NP40), 3x TET Buffer (1x TE, 0.2% Tween-20), and 1x TE-NaCl (1x TE, 50 mM NaCl). Beads were then resuspended in 500 ul Elution Buffer (50mM NaHCO3, 1% SDS) and incubated overnight with 0.2M NaCl at 65ºC to reverse crosslinking. Lysate was then incubated for 2 hrs at 37ºC with 5 ul RNase A (10 mg/ml) and 2 hrs at 55ºC with 5 ul Proteinase K (20 mg/ml). DNA was purified using Phenol/Chroloform/Isoamyl and resuspended in 50 ul TE (10 mM Tris-pH 8, 1 mM EDTA).
TruSeq ChIP Library Preparation Kit (Illumina) was used to construct libraries which were subsequently run at SR75 on the HiSeq4000.

tag: background strain

value: cross of AB* and WIK

value: whole embryo

tag: developmental stage

tag: chip antibody

value: none (input)


title: CSrab_head_29C_replicate 2

status: Public on Sep 01 2020

type: SRA

city: Houston

first: Richard

last: Meisel

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

country: USA

institute: University of Houston

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the housefly reference genome Musca_domestica-2.02 using HISAT2
Aligned reads were sorted with SAMtools
Sorted reads were assigned to annotated genes using htseq-count
Gene counts were analysed with DESeq2
Genome_build: Musca_domestica-2.0.2 (GCF_000371365.1)
Supplementary_files_format_and_content: CSV file with read counts for each replicate and results of a statistical test for genotype-by-environment interactions on expression

molecule: polyA RNA

organism: Musca domestica

source_name: Head

extract_protocol:
Direct-zol RNA Mini Prep (Zymo Research) was used to extract RNA from head and testis samples homogenized in TRIzol reagent (Life Technologies)
Library preparation was carried out using TruSeq Stranded mRNA Kit (Illumina). Quality of libraries were assessed using a 2100 Bioanalyzer.

tag: genotype

value: CSrab

tag: developmental temperature

tag: tissue

value: Head


title: CSrab_head_29C_replicate 3


title: MUT_1_p53-ChIP

library_source: genomic

molecule: genomic DNA

value: anti-P53 (GeneTex, Cat# GTX128135, Lot# 42263)


title: Progressive.1.2

type: RNA

city: London

first: Vitor

middle: H

last: Teixeira

address: 5 University Street

department: Medicine

country: United Kingdom

institute: University College London

hyb_protocol: Thermofisher/Affymetrix Human Clariom D GeneChip as per manufacturer's instructions [Fluidics Station 450]

scan_protocol: Affymetrix Scanner 3000 7G as per manufacturer's instructions

data_processing: Processing was performed using R and Bioconductor. Raw data in CEL format were read using the read.celfiles method from the oligo package, and normalised using RMA.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human preinvasive lung squamous cell carcinoma lesions - matched stroma

label_protocol: Thermofisher/Affymetrix WT Pico Kit Biotin labelling module as per manufacturer's instructions

extract_protocol: Laser-capture micro-dissection (LCM) was used to selectively isolate stromal regions adjacent to known CIS for molecular analysis. RNA was extracted using the High Pure FFPE RNA Kit (Roche Applied Science, West Sussex, UK) according to manufacturer’s protocol. Quantification was carried out using the Quant-iT RNA assay kit and the Qubit® 2.0 fluorometer (Life Technologies, Paisley, UK).

value: Preinvasive lung squamous cell carcinoma lesions - matched stroma

tag: lesion outcome

value: Progression

tag: matched cis lesion

value: Progressive 34


title: Regressive.5

value: Regression

value: Regressive 57


title: MUT_1_input


title: WT_input

source_name: wildtype

value: wildtype


title: Supt16h Mutant 6

data_processing:
Basecalls were performed using Illumina's CASAVA (v1.8)
Quality was assed by FastQC (v0.11.2) and samples were aligned using OLego (v1.1.7)
Peaks were called and differentially analyzed using HOMER (v4.9)
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: Excel file contains differential peak expression of wildtype and supt16h-/- as well as log2fold change and p-values. Bigwig files were generated using HOMER and represent each biological and technical replicate by strandedness.

source_name: Whole embryo

growth_protocol: Zebrafish were grown at 28°C and collected at 32hpf

extract_protocol:
Whole embryo was collected and deyolked using Ginzburg Fish Ringer solution (55mM NaCl, 1.8mM KCl, 1.25mM NaHCO3). Following trituration, 50,000 cells were collected, washed with PBS, and pelleted at 500 rcf for 5 min at 4ºC. Nuclei extracted by adding 50ul of cold lysis buffer (10 mM Tris-HCL pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630) and immediately centrifuging at 500rcf for 10 min at 4ºC.
Extracted nuclei were subjected to the transposition reaction using the Nextera Tn5 Tranposase Kit. Nuclei were incubated at 37ºC for 30 min and DNA purified using the Omega MicroElute DNA Cleanup Kit. DNA was then PCR amplified and barcoded with the NEBNext High-Fidelity 2x PCR Master Mix using the following protocol: 1. 72ºC, 5 min 2. 98ºC, 30s 3. 98ºC, 10s 4. 63ºC, 30s 5. 72ºC, 1 min; repeat steps 3-5, 5x 6. 4ºC, forever. Subsequent RT-qPCR was performed to determine additional cycles. Libraries were size selected using Mag-Bind RxnPure Plus (Omega, M1386-00) with the first selection to eliminate small products (0.4:1 ratio of beads) and the second selection (1.4:1 ratio of beads) to select desired products. Eluted samples were submitted to the BioAnalyzer to determine library size. The KAPA Library Quantification Kit (KAPA, KK4824) was used to determine library concentration prior to sequencing on the Illumina HiSeq4000.

tag: strain

value: MUT


title: Supt16h Mutant 5


title: Supt16h Mutant 2


title: Supt16h Mutant 4


title: Wildtype Sibling 2

value: WT


title: MUT_2_p53-ChIP


title: Wildtype Sibling 1


title: Supt16h Mutant 1


title: WT_p53-ChIP


title: Wildtype Sibling 4


title: Wildtype Sibling 6


title: Mouse muscle 24

city: Madison

first: Nicole

middle: Elise

last: Richardson

state: WI

address: 2500 Overlook Terr VA Hospital C3127 Research 151

institute: University of Wisconsin Madison

data_processing:
Expected counts were calculated
Genes with 0-read or very low expression transcripts were removed
Counts were log2 normalized
Trimmed mean of-M values (TMM) normalization factors were calculated to scale library sizes.
Constrasts were made between each group of interest using the generalised linear model quasi-likelihood ratio test
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: quadriceps muscle

extract_protocol:
RNA was isolated using TRI Reagent (Sigma-Aldrich), following the protocol provided by manufacturer
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were fed Control or Low BCAA diets, were the branched-chain amino acids were restricted by two-thirds, from weaning until 16 months of age. After an overnight fast, mice were sacrificed by cervical dislocation and quadriceps muscle was isolated and snap frozen in liquid nitrogen

tag: diet

value: Low BCAA

tag: Sex

value: Female

tag: age

value: 16 mo


title: Mouse muscle 23


title: Wildtype Sibling 3


title: Mouse muscle 21


title: Supt16h Mutant 3


title: Mouse muscle 22


title: Mouse muscle 20


title: Mouse muscle 19


title: Mouse muscle 17

value: Control


title: Mouse muscle 16


title: Mouse muscle 15


title: Mouse muscle 18


title: Mouse muscle 14


title: Mouse muscle 13


title: Wildtype Sibling 5

value: whole embryo


title: Mouse muscle 12

value: Male


title: Mouse muscle 11


title: Mouse muscle 9


title: Mouse muscle 8


title: Mouse muscle 7


title: Mouse muscle 10


title: Mouse muscle 5


title: Mouse muscle 4


title: Mouse muscle 2


title: Mouse muscle 3


title: Mouse muscle 1


title: Mouse muscle 6


title: LungRep5

city: New York

first: Donna

middle: L

last: Farber

state: NY

address: 650 West 168th Street, BB1701

department: Surgery

institute: Columbia University

data_processing:
Read mapping to annotated transcriptome was done using kallisto (version 0.44). Mouse transcriptome Mus_musculus.GRCm38.cdna.all.fa.gz (Ensembl Relsease 94) was donwloaded from https://useast.ensembl.org/index.html
quant function of kallisto was used with arguments '--single -l 180 -s 20' for the single-end sequenced batch
Estimated counts generated with tximport(countsFromAbundance="lengthScaledTPM") for protein-coding genes
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated text file includes estimated counts for each sample

source_name: lung-resident influenza-specific mouse CD4+ T cells

extract_protocol:
After sorting using a BD Influx (BD Biosciences) sorter, cells were centrifuged and transferred into microcentrifuge tubes for extraction of RNA. Pellets of sorted cells were resuspended in 700ul of QIAzol Lysis Reagent (QIAGEN) and vortexed. Lysed samples were homogenated in the TissueLyser LT (QIAGEN) by shaking for 5min at 50Hz. Samples were left to rest for additional 5min at room temperature for complete dissociation of nucleoprotein complexes. Homogenized lysates were centrifuged through QIAshredder filters (QIAGEN). 100ul of gDNA eliminator solution was added. Samples received 140μl of chloroform followed by vortexing. Finally, samples were spun at 12,000 x g for 15min at 4°C. After centrifugation, the two phase solution contains RNA in the top transparent phase. The RNA phase was collected and transferred into a new microcentrifuge tube. An equivalent volume of 70% ethanol was added to the RNA-containg solution. The RNA/ethanol solution was transferred to an RNeasy MinElute spin column (QIAGEN) and washed with Buffer RWT and two rounds of Buffer RPE (QIAGEN). Following a final wash of the column with 80% ethanol, the RNA was eluted using RNase-Free water and stored at -80°C. Quality and quantity of total RNA was determined using the RNA 6000 Pico chip run on 2100 Bioanalyzer (Agilent Technologies).
Library preparation and RNA sequencing was performed by the Columbia University Genome Center. Total RNA samples were submitted and enriched for mRNA using a poly-A pull down strategy.

treatment_protocol: Lung tissue was mechanically disrupted using the gentleMACS tissue dissociator (Milteny Biotech). Tissue homogenates were then incubated for 30-60min at 37°C with digestion medium RPMI (Thermo Fisher) containing 10% fetal bovine serum (FBS) (Thermo Fisher), L-glutamate (Thermo Fisher), sodium pyruvate (Thermo Fisher), nonessential amino acids (Thermo Fisher), penicillin-streptomycin (Thermo Fisher), collagenase D (1 mg/ml, Roche), trypsin inhibitor (1 mg/ml, Thermo Fisher) and DNase I (0.1 mg/ml, Roche). After digestion, samples were once again mechanically disrupted using the gentleMACS dissociator, followed by a passing through a 100μm filter. After centrifugation, samples were depleted for red blood cells using ACK Lysing Buffer (Thermo Fisher) for 5min at room temperature. After washing and resuspending in RPMI containing 5% FBS, samples are filtered through a 70μm filter and kept on ice in the dark.   Lymphocytes from spleens were isolated by first pressing the tissues through a 100μm filter with a plunger of a 1mL syringe to generate cell suspensions in RPMI containing 5% FBS. Spleen cell suspensions were further depleted for red blood cells using ACK Lysing Buffer as described above. Cells were then washed, resuspended, filtered through a 70μm filter and kept on ice until processing for flow cytometric analysis.

value: Lung

tag: cell type

value: CD4+ OT-II T cell


title: LungRep3


title: LungRep4


title: SpleenRep4

source_name: spleen influenza-specific mouse CD4+ T cells

value: Spleen


title: SpleenRep3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E7_AD002_indexed

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: MOp

value: male


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E7_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E8_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A4_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A1_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E3_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E3_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G9_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C2_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E2_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A6_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A3_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C6_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A11_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A8_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H9_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H9_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H9_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H9_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H9_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H9_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H8_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H8_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H8_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H7_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H8_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H8_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H7_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H7_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H7_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A11_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H5_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H6_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H7_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H6_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H6_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H5_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A10_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H6_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H6_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H7_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H7_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H6_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H6_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H5_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H5_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H5_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H4_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H4_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H4_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H8_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H5_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H3_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H1_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H3_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H5_AD002_indexed


title: TPC-1_siCOPZ1_72h_rep3

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip Gene 2.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Normalized expression values were obtained using Robust Multi Array Average (RMA) procedure. A custom annotation pipeline was applied that combined GENCODE v25 (Ensembl v87) annotations with the CDF (Chip Definition File) version 21 for gene annotations freely available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/genecodeg.asp, in order to withdraw probes that map to regions where ambiguous detection due to transcript overlap might occur. Therefrom, the expression levels of  18642 Ensembl specific genes were obtained.

source_name: TPC-1 cell line transfected with siRNA oligos directed to COPZ1 gene, collected 72h after transfection, replicate 3

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100-250 nanograms of total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

growth_protocol: TPC-1 cells were maintained in DMEM (Gibco, Life Technologies, Carlsbad, CA, USA) medium containing 10% heat-inactivated fetal bovine serum (FBS) (EuroClone, Pero, Italy), 2 mM glutamine, penicillin (100 U/ml) and streptomycin (100 mg/ml).Nhy-ori 3-1 cells were cultured in RPMI 1640 medium (Gibco Life Technologies, Carlsbad, CA, USA). All cell lines were cultured as monolayer at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol: Total RNA extraction by means of NucleoSpin RNA kit (Macherey-Nagel)

treatment_protocol: siRNA transfection was performed using 20 nM of the following siRNA oligos siCOPZ1:MISSION esiRNA EHU1040461, siRNA  Universal Negative Control #1 SIC001 (non-targeting: siNT) (Sigma-Aldrich, St. Louis, MO, USA) and the Lipofectamine RNAiMAX reagent (Invitrogen Life Technologies, Carlsbad, CA, USA)), according to manufacturer's instruction.

tag: cell line

value: human papillary thyroid carcinoma cell line

tag: genotype/variation

value: siRNA oligos directed to COPZ1 gene

tag: time point

value: collected 72h after transfection


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H3_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H2_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H2_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H4_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H3_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H1_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H2_AD004_indexed


title: TPC-1_siCOPZ1_72h_rep2

source_name: TPC-1 cell line transfected with siRNA oligos directed to COPZ1 gene, collected 72h after transfection, replicate 2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H2_AD010_indexed


title: TPC-1_siNegativeControl_72h_rep2

source_name: TPC-1 cell line transfected with siRNA Universal Negative Control, collected 72h after transfection, replicate 2

value: siRNA Universal Negative Control


title: TPC-1_siNegativeControl_72h_rep1

source_name: TPC-1 cell line transfected with siRNA Universal Negative Control, collected 72h after transfection, replicate 1


title: TPC-1_siCOPZ1_48h_rep3

source_name: TPC-1 cell line transfected with siRNA oligos directed to COPZ1 gene, collected 48h after transfection, replicate 3

value: collected 48h after transfection


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H1_AD012_indexed


title: TPC-1_siNegativeControl_72h_rep3

source_name: TPC-1 cell line transfected with siRNA Universal Negative Control, collected 72h after transfection, replicate 3


title: TPC-1_siCOPZ1_72h_rep1

source_name: TPC-1 cell line transfected with siRNA oligos directed to COPZ1 gene, collected 72h after transfection, replicate 1


title: TPC-1_siNegativeControl_48h_rep3

source_name: TPC-1 cell line transfected with siRNA Universal Negative Control, collected 48h after transfection, replicate 3


title: TPC-1_siCOPZ1_48h_rep1

source_name: TPC-1 cell line transfected with siRNA oligos directed to COPZ1 gene, collected 48h after transfection, replicate 1


title: TPC-1_siNegativeControl_48h_rep2

source_name: TPC-1 cell line transfected with siRNA Universal Negative Control, collected 48h after transfection, replicate 2


title: TPC-1_siCOPZ1_48h_rep2

source_name: TPC-1 cell line transfected with siRNA oligos directed to COPZ1 gene, collected 48h after transfection, replicate 2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H3_AD006_indexed


title: Nthy-ori 3-1_siNegativeControl_72h_rep3

source_name: Nthy-ori 3-1 cell line transfected with siRNA Universal Negative Control, collected 72h after transfection, replicate 3

value: Nthy-ori 3-1

value: human normal thyroid follicular epithelial cell line


title: TPC-1_siNegativeControl_48h_rep1

source_name: TPC-1 cell line transfected with siRNA Universal Negative Control, collected 48h after transfection, replicate 1


title: Nthy-ori 3-1_siCOPZ1_72h_rep3

source_name: Nthy-ori 3-1 cell line transfected with siRNA oligos directed to COPZ1 gene, collected 72h after transfection, replicate 3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H4_AD012_indexed


title: Nthy-ori 3-1_siCOPZ1_72h_rep2

source_name: Nthy-ori 3-1 cell line transfected with siRNA oligos directed to COPZ1 gene, collected 72h after transfection, replicate 2


title: Nthy-ori 3-1_siCOPZ1_72h_rep1

source_name: Nthy-ori 3-1 cell line transfected with siRNA oligos directed to COPZ1 gene, collected 72h after transfection, replicate 1


title: Nthy-ori 3-1_siNegativeControl_72h_rep2

source_name: Nthy-ori 3-1 cell line transfected with siRNA Universal Negative Control, collected 72h after transfection, replicate 2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H3_AD007_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H2_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H4_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H1_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H11_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H2_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H3_AD002_indexed


title: Nthy-ori 3-1_siCOPZ1_48h_rep2

source_name: Nthy-ori 3-1 cell line transfected with siRNA oligos directed to COPZ1 gene, collected 48h after transfection, replicate 2


title: Nthy-ori 3-1_siCOPZ1_48h_rep1

source_name: Nthy-ori 3-1 cell line transfected with siRNA oligos directed to COPZ1 gene, collected 48h after transfection, replicate 1


title: Nthy-ori 3-1_siNegativeControl_72h_rep1

source_name: Nthy-ori 3-1 cell line transfected with siRNA Universal Negative Control, collected 72h after transfection, replicate 1


title: Nthy-ori 3-1_siCOPZ1_48h_rep3

source_name: Nthy-ori 3-1 cell line transfected with siRNA oligos directed to COPZ1 gene, collected 48h after transfection, replicate 3


title: Nthy-ori 3-1_siNegativeControl_48h_rep3

source_name: Nthy-ori 3-1 cell line transfected with siRNA Universal Negative Control, collected 48h after transfection, replicate 3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H11_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H11_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H11_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H10_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H1_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H11_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H11_AD001_indexed


title: mimic_451a_3: SNU478 mimic-451a 3

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: SNU478 mimic-451a transfected

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Clariom D type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, Kernel Surface background correction and Medianpolish Probeset Summary

source_name: CCA cell line SNU478 mimic-451a transfected

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol.

growth_protocol: SNU478 cells were cultivated in RPMI 1640 medium (Sigma-Aldrich) supplemented with 10% fetal bovine serum (ThermoFisher) and 1% penicillin/streptomycin (Thermo Fisher).

extract_protocol: Total RNA from cell lines was isolated with TRIzol Reagent (ThermoFisher).

treatment_protocol: Cells were transfected with miRNA mimics of miR-451a (5'AAACCGUUACCAUUACUGAGUU3´) or AllStars control both provided by Qiagen using Lipofectamine RNAiMAX (ThermoFisher).

value: cholangiocarcinoma


title: mimic_451a_4: SNU478 mimic-451a 4

description: SNU478 mimic-451a transfected


title: Nthy-ori 3-1_siNegativeControl_48h_rep2

source_name: Nthy-ori 3-1 cell line transfected with siRNA Universal Negative Control, collected 48h after transfection, replicate 2


title: mimic_451a_2: SNU478 mimic-451a 2

description: SNU478 mimic-451a transfected


title: AllStar_2: SNU478 AllStars rep2

description: SNU478 control

source_name: CCA cell line SNU478 AllStars transfected


title: TS/A_A-Nfe2_rep01

city: Kanazawa

first: Soichiro

last: Sasaki

address: Kakuma-machi

country: Japan

institute: Cancer Research Institute, Kanazawa University

data_processing:
We used TruSeq RNA Library Preparation Kit v2.
Sequencing was performed by NextSeq 500/550, High output 75 bp.
total gene reads' for analysis generated by CLC Genomics Wrokbench (20.0.4).
Genome_build: Mus-musclus-2019-04-08-19-53

growth_protocol: RPMI supplemented with 10% FCS

extract_protocol:
Total RNAs were extracted by using RNeasy Mini Kit (Qiagen).
We used TruSeq RNA Library Preparation Kit v2.

treatment_protocol: 4T1 or TS/A cells which were transduced Nfe2 expressing vector or empty vector

tag: strain background

value: BALB/c

value: TS/A

value: Mouse breast cancer cell line

tag: transduced vector

value: Nfe2 expressing vector


title: AllStar_1: SNU478 AllStars rep1

description: SNU478 control

value: Control


title: mimic_451a_1: SNU478 mimic-451a 1

description: SNU478 mimic-451a transfected


title: Nthy-ori 3-1_siNegativeControl_48h_rep1

source_name: Nthy-ori 3-1 cell line transfected with siRNA Universal Negative Control, collected 48h after transfection, replicate 1


title: AllStar_3: SNU478 AllStars rep3

description: SNU478 control


title: AllStar_4: SNU478 AllStars rep4

description: SNU478 control


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H10_AD010_indexed


title: 4T1_Nfe2_rep02


title: TS/A_A-Emp_rep01

value: Empty vector


title: 4T1_Nfe2_rep01


title: 4T1_Control_rep02


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H10_AD006_indexed


title: 4T1_Control_rep01


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H10_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H10_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H10_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H10_AD004_indexed


title: Eumyc rep2

city: Esch-sur-Alzette

first: Takumi

last: Kobayashi

address: 29, rue Henri Koch

department: Department of Infections and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

data_processing:
Reads were mapped to the mm10 genome with STAR v2.5.2 (Dobin et al 2013) using Ensembl gene annotation (GRCm38, release 88).
Gene level read counts were obtained with HTSeq-count v0.6.1 (Anders et al, 2015) using the attribute gene_id from the Ensembl GTF file Mus musculus GRCm38 release 88 as feature ID.
Genes were filtered for downstream analysis if they failed to achieve an FPM (fragments per million mapped fragments) value of at least 3 in at least three samples. We also excluded T-cell receptor and immunoglobulin genes, pseudogenes, rRNA genes and Gm annotated genes from Ensembl.
Differential gene expression analysis was performed with the Bioconductor package DESeq2 v1.10.1 (Love et al 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated values text file include gene-level raw counts of sequencing reads from HTSeq-count and differential expression results from DESeq2

source_name: NK cells

extract_protocol:
B cell depletion using 1D3 antibody followed by anti-rat beads (negative selection) followed by positive selection for NK cells with CD49b beads (Miltenyi)*. Then stained and sorted as NK1.1+TCRb-. Washed in PBS and resuspended in RLT+ buffer for RNA isolation.
TruSeq Illumina - RNA was purified and fragmented , cDNA was synthesised. Libraries were prepared (end repair, A-tailing and adaptor ligation) and enriched.
*for Eumyc samples, NK positive selection was not as efficient, so both positive and negative fractions from CD49b purification were used for sorting.

treatment_protocol: Eumyc lymphoma was inoculated i.v. into C57BL/6J mice. Spleens were harvested from healthy or Emyc lymphoma-bearing mice at day 14 post-inoculation, and splenic NK cells were purfied using flow cytometry.

value: splenic NK cells


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G9_AD010_indexed

value: MOp


title: Eumyc rep3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G9_AD004_indexed

value: male


title: Eumyc rep1


title: WT rep3

value: wild type


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G8_AD010_indexed


title: WT rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G9_AD006_indexed


title: WT rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G8_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G8_AD008_indexed


title: PBMC_HC_rep47

city: milan

first: massimo

last: acquaviva

state: mi

address: Via Olgettina, 60

institute: San Raffaele Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Microarray raw data originating from Illumina HumanRef-8 v2 and HumanHT-12 v4 arrays were pre-processed and normalized independently using the limma package and then merged into a single integrated dataset according to the common probes. Raw intensities were background subtracted and filtered according to detection pvalues (p<0.05 in at least 20% of samples) and then normalized using quantile normalization. Pre-processed data were log2 transformed and inspected for the presence of hidden batch effects using DASC. Batch correction and cross-platform integration of the two independently normalized datasets was performed using Combat.
[Matrix-merged-normalized-batch.corrected.txt]  quantile normalized and batch corrected signals.

source_name: blood

label_protocol: Reverse transcription and biotinylated cRNA synthesis were performed using the Illumina TotalPrep RNA Amplification Kit (Ambion), according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted using Trireagent (Ambion) and stored at -80°C. Quantification and quality analyses of RNA were performed at a Bioanalyzer 2100 (Agilent).

treatment_protocol: Peripheral blood mononuclear cells were collected from healthy subjects, untreated MS and CIS individuals and other neurological diseases.

tag: disease

tag: disease staging

value: healthy control

tag: illumina chip

value: HumanRef-8 v2

tag: dataset partition

value: Independent Test set

value: blood

value: PBMC


title: PBMC_HC_rep46

tag: tissue


title: PBMC_HC_rep49


title: PBMC_HC_rep45


title: PBMC_HC_rep48


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G9_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G8_AD012_indexed


title: PBMC_HC_rep43


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G9_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G8_AD001_indexed


title: PBMC_HC_rep32

value: Training Set


title: PBMC_HC_rep29


title: PBMC_HC_rep30


title: PBMC_HC_rep31


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G7_AD012_indexed


title: PBMC_HC_rep27


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G7_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G9_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G7_AD010_indexed


title: PBMC_HC_rep26


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G7_AD001_indexed


title: PBMC_HC_rep25


title: PBMC_HC_rep28


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G9_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G5_AD001_indexed


title: PBMC_HC_rep44


title: PBMC_HC_rep24


title: PBMC_HC_rep23


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G5_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_H11_AD002_indexed


title: PBMC_HC_rep21


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G5_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G7_AD006_indexed


title: PBMC_HC_rep22


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G7_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G5_AD007_indexed


title: PBMC_HC_rep20


title: PBMC_HC_rep19.1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G7_AD007_indexed


title: PBMC_HC_rep18


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G5_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G6_AD006_indexed


title: PBMC_HC_rep19


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G7_AD004_indexed


title: PBMC_HC_rep16


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G5_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G6_AD001_indexed


title: PBMC_HC_rep13


title: PBMC_HC_rep14


title: PBMC_HC_rep15


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G4_AD012_indexed


title: PBMC_HC_rep12


title: PBMC_HC_rep11


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G4_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G3_AD012_indexed


title: PBMC_HC_rep9


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G4_AD006_indexed


title: PBMC_HC_rep10


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G3_AD008_indexed


title: PBMC_HC_rep8


title: PBMC_HC_rep7


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G4_AD007_indexed


title: PBMC_HC_rep17


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G5_AD002_indexed


title: PBMC_HC_rep5


title: PBMC_HC_rep4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G6_AD010_indexed


title: PBMC_HC_rep3


title: PBMC_HC_rep2


title: PBMC_SP_rep24

value: multiple sclerosis

value: Independent test set


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G3_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G2_AD010_indexed


title: PBMC_SP_rep23


title: PBMC_HC_rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G2_AD006_indexed


title: PBMC_HC_rep6


title: PBMC_SP_rep22


title: PBMC_SP_rep21


title: PBMC_SP_rep20


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G3_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G2_AD004_indexed


title: PBMC_SP_rep19


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G3_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G1_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G2_AD012_indexed


title: PBMC_SP_rep15


title: PBMC_SP_rep13


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G1_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G1_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G2_AD007_indexed


title: PBMC_SP_rep12


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G3_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G1_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G3_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G2_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G2_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G1_AD010_indexed


title: PBMC_SP_rep14


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G11_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G11_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G11_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G11_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G11_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G11_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G11_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G10_AD004_indexed


title: PBMC_SP_rep8


title: PBMC_SP_rep9


title: PBMC_SP_rep5


title: PBMC_SP_rep10


title: PBMC_SP_rep6


title: PBMC_SP_rep7


title: PBMC_SP_rep11


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G10_AD008_indexed


title: PBMC_SP_rep4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G10_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G10_AD001_indexed


title: PBMC_SP_rep2


title: PBMC_SP_rep1


title: PBMC_SP_rep3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G11_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G10_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_G10_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F9_AD010_indexed


title: PBMC_PP_rep16

value: primary-progressive multiplle sclerosis


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F9_AD012_indexed


title: PBMC_PP_rep17


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F9_AD007_indexed


title: PBMC_PP_rep29

value: Independent Test Set


title: PBMC_PP_rep28


title: PBMC_PP_rep26


title: PBMC_PP_rep25


title: PBMC_PP_rep30


title: PBMC_PP_rep27


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F9_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F8_AD008_indexed


title: PBMC_PP_rep14


title: PBMC_PP_rep12


title: PBMC_PP_rep11


title: PBMC_PP_rep13


title: PBMC_PP_rep10


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F9_AD006_indexed


title: PBMC_PP_rep8


title: PBMC_PP_rep9


title: PBMC_PP_rep7


title: PBMC_PP_rep6


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F8_AD010_indexed


title: PBMC_PP_rep5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F9_AD004_indexed


title: PBMC_PP_rep15


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F7_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F8_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F8_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F7_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F9_AD002_indexed


title: PBMC_PP_rep3


title: PBMC_RR_rep79

value: relapse-remitting multiple sclerosis


title: PBMC_PP_rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F8_AD001_indexed


title: PBMC_RR_rep76


title: PBMC_RR_rep77


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F8_AD007_indexed


title: PBMC_RR_rep78


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F8_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F7_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F7_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F6_AD008_indexed


title: PBMC_PP_rep4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F7_AD006_indexed


title: PBMC_RR_rep75


title: PBMC_PP_rep1


title: PBMC_RR_rep74


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F6_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F6_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F7_AD007_indexed


title: PBMC_RR_rep38


title: PBMC_RR_rep41


title: PBMC_RR_rep39


title: PBMC_RR_rep37


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F6_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F6_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F6_AD004_indexed


title: PBMC_RR_rep35


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F6_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F6_AD007_indexed


title: PBMC_RR_rep36


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F5_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F5_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F5_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F5_AD004_indexed


title: PBMC_RR_rep34


title: PBMC_RR_rep30


title: PBMC_RR_rep33


title: PBMC_RR_rep31


title: PBMC_RR_rep32.1


title: PBMC_RR_rep32


title: PBMC_RR_rep40


title: PBMC_RR_rep29


title: PBMC_RR_rep28


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F3_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F3_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F3_AD006_indexed


title: PBMC_RR_rep27


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F3_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F3_AD004_indexed


title: PBMC_RR_rep25


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F5_AD008_indexed


title: PBMC_RR_rep24


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F4_AD007_indexed


title: PBMC_RR_rep23


title: PBMC_RR_rep22


title: PBMC_RR_rep21


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F4_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F2_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F2_AD007_indexed


title: PBMC_RR_rep19


title: PBMC_RR_rep20


title: PBMC_RR_rep16


title: PBMC_RR_rep18


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F5_AD001_indexed


title: PBMC_RR_rep26


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F3_AD007_indexed


title: PBMC_RR_rep17


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F2_AD006_indexed


title: PBMC_RR_rep19.1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F1_AD001_indexed


title: PBMC_RR_rep15


title: PBMC_RR_rep14


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F1_AD002_indexed


title: PBMC_RR_rep13.1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F3_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F1_AD004_indexed


title: PBMC_RR_rep13


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F1_AD012_indexed


title: PBMC_RR_rep12.1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F3_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F1_AD007_indexed


title: PBMC_RR_rep12


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F2_AD002_indexed


title: PBMC_RR_rep11.1


title: PBMC_RR_rep15.1


title: PBMC_RR_rep11


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F2_AD001_indexed


title: PBMC_RR_rep10


title: PBMC_RR_rep9


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F1_AD008_indexed


title: PBMC_RR_rep8


title: PBMC_RR_rep7


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F1_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F10_AD001_indexed


title: PBMC_RR_rep6


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F11_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F11_AD012_indexed


title: PBMC_RR_rep5


title: PBMC_RR_rep3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F11_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F11_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F10_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E9_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E9_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E9_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F10_AD007_indexed


title: PBMC_CIS_rep49

value: clinically isolated syndrome


title: PBMC_CIS_rep50


title: PBMC_CIS_rep51


title: PBMC_CIS_rep52


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E9_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F10_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E9_AD002_indexed


title: PBMC_CIS_rep38

value: Training set


title: PBMC_CIS_rep41


title: PBMC_RR_rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F11_AD006_indexed


title: PBMC_CIS_rep39


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F11_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E9_AD007_indexed


title: PBMC_RR_rep1


title: PBMC_CIS_rep37


title: PBMC_CIS_rep36


title: PBMC_CIS_rep35


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E7_AD001_indexed


title: PBMC_CIS_rep34


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E8_AD006_indexed


title: PBMC_CIS_rep33


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E7_AD007_indexed


title: PBMC_CIS_rep31


title: PBMC_CIS_rep30


title: PBMC_CIS_rep32


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E9_AD001_indexed


title: PBMC_CIS_rep29


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E8_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E8_AD001_indexed


title: PBMC_RR_rep4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F10_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F10_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_F11_AD002_indexed


title: PBMC_CIS_rep28


title: PBMC_CIS_rep42


title: PBMC_CIS_rep27


title: PBMC_CIS_rep40


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E8_AD002_indexed


title: PBMC_CIS_rep25


title: PBMC_CIS_rep26


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E8_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E7_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E7_AD006_indexed


title: PBMC_CIS_rep24


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E8_AD010_indexed


title: PBMC_CIS_rep23


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E6_AD008_indexed


title: PBMC_CIS_rep22


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E7_AD012_indexed


title: PBMC_CIS_rep21


title: PBMC_CIS_rep20


title: PBMC_CIS_rep19


title: PBMC_CIS_rep17


title: PBMC_CIS_rep18


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E6_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E8_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E5_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E5_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E4_AD007_indexed


title: PBMC_CIS_rep15


title: PBMC_CIS_rep14


title: PBMC_CIS_rep16


title: PBMC_CIS_rep13


title: PBMC_CIS_rep12


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E4_AD008_indexed


title: PBMC_CIS_rep11


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E4_AD010_indexed


title: PBMC_CIS_rep10


title: PBMC_CIS_rep9


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E5_AD004_indexed


title: PBMC_CIS_rep8


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E5_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E4_AD012_indexed


title: PBMC_CIS_rep7


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E6_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E4_AD006_indexed


title: PBMC_CIS_rep6


title: PBMC_CIS_rep6.1


title: PBMC_CIS_rep5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E5_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E3_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E6_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E5_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E5_AD001_indexed


title: PBMC_CIS_rep3


title: PBMC_CIS_rep5.1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E4_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E3_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E4_AD001_indexed


title: PBMC_CIS_rep3.1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E5_AD012_indexed


title: PBMC_CIS_rep2


title: PBMC_CIS_rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E3_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E3_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E2_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E2_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E2_AD007_indexed


title: PBMC_CIS_rep4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E1_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E3_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E1_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E1_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E1_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E1_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E1_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E11_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E11_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E2_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E10_AD012_indexed


title: Ex-TAQed diploid strain ExTQ002

type: genomic

city: Nagakute

first: Hidenori

last: Tanaka

state: Aichi

address: 41-1 Yokomichi

department: Genome Engineering Program

institute: Toyota Central R&D Labs., Inc

description: Ex-TAQing treated strain ExTQ001. Leaves from progeny of Ex-TAQing treated plant

hyb_protocol: Hi-RPM Gene Expression Hybridization Kit and Gene Expression Wash Buffer Kit (Buffer1 and Buffer2) was used according to manufacturer instruction,

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1). gProcessedSignal value and SystematicName were used to get normalized signal intensities. Data were normalized using the quantile-method (limma package).

organism: Arabidopsis thaliana

source_name: leaves from progeny of Ex-TAQing treated plant

label_protocol: 200 ng of total RNA was fluorescently labeled using Quick Amp Labeling Kit One color (Agilent). Synthesis of Cy3-labeled cRNA was performed according to the manufacturer’s recommendations.

growth_protocol: Plants were grown in corner dishes on germinaton medium (MS medium containing 1% sucrose and 0.8% agar) for 4weeks under a 16 h light/8 h dark regime.

extract_protocol: Total RNA was isolated using RNeasy plant Mini Kit according to the manufacturer instructions (Qiagen).

treatment_protocol: Progeny of Ex-TAQing treated plant. Ex-TAQing treated plant was introduced of Mse I reatriction enzyme gene, and the heat treatment for activation of Mse I incubated for 3 hours at 33ºC.

value: leaves

tag: progeny

value: progeny of Ex-TAQing treated plant


title: Ex-TAQed diploid strain ExTQ013

description: Ex-TAQing treated strain ExTQ002. Leaves from progeny of Ex-TAQing treated plant


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E11_AD012_indexed

value: MOp

value: male

tag: strain


title: Ex-TAQed diploid strain ExTQ015

description: Ex-TAQing treated strain ExTQ003. Leaves from progeny of Ex-TAQing treated plant


title: Ex-TAQed diploid strain ExTQ016

description: Ex-TAQing treated strain ExTQ006. Leaves from progeny of Ex-TAQing treated plant


title: Ex-TAQed diploid strain ExTQ018

description: Ex-TAQing treated strain ExTQ007. Leaves from progeny of Ex-TAQing treated plant


title: Ex-TAQed diploid strain ExTQ003

description: Ex-TAQing treated strain ExTQ004. Leaves from progeny of Ex-TAQing treated plant


title: HDAC4/5/7_Combi_5nM_Replicate_2

city: Frankfurt am Main

first: Daniel

last: Margerie

address: Industrial Park Hoechst, Building H831

department: R&D, Digital Data Sciences

institute: Sanofi-Aventis Deutschland GmbH

description:
SAMPLE 14
human hepatocytes (Upcyte Technologies)

hyb_protocol: 15 µg cRNA samples were fragmented at 94 degree Celsius for 35 min in 40 mM Tris/acetate pH 8.1, 100 mM KOAc and 30 mM MgOAc, added to hybridisation buffer and hybridised to Affymetrix GeneChip for 16-18 hours at 45 degree Celsius and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Array Studio (Omicsoft Corp., Cary, NC, USA) using default settings and RMA as normalization method.

label_protocol: Biotin-UPT and -CTP labelled cRNA was transcribed in vitro using Enzo BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, NY, NY) and purified by RNeasy cleanup and ethanol precipitation.

growth_protocol: Human hepatocytes were seeded in a density of 17,000 cells/cm2 in either precoated collagen type 1 96-well plates, for siRNA screening or 6-well plates for Affymetrix gene expression profiling.

extract_protocol: Isolation of RNA from cell lysates was performed using the SV 96 RNA Isolation System (Promega) following the manufacturers’ instructions.

treatment_protocol: Transfection was performed using the Lipofectamine RNAiMAX Transfection Reagent (Invitrogen) following the manufacturers’ protocol. In total, 1, 5 or 25nM of non-silencing or HDAC 4, 5 or 7 siRNA either individually or in combination was delivered. After 48h, cells were synchronized by replacing the standard medium by a serum- and BSA-free MEM (Thermo Fisher Scientific) for 4h. Plates were then washed with pre-warmed PBS, and freshly prepared gluconeogenesis induction medium (MEM containing 15 mM fructose, 10mM lactate, 1mM pyruvate, 5mM L-alanine, 2mM L-glutamine, 100nM dexamethasone, 10nM glucagon, 5mM dibutyryl-cAMP, and 300nM forskolin) was added to each well for additional 20h. Transfected cells were harvested after 72h and subsequently processed for RNA isolation.

value: human hepatocytes

value: HDAC4/5/7 Combi


title: Ex-TAQed diploid strain ExTQ005

description: Ex-TAQing treated strain ExTQ005. Leaves from progeny of Ex-TAQing treated plant


title: Ex-TAQed diploid strain ExTQ019


title: HDAC5_s19464_5nM_Replicate_1

description:
SAMPLE 9
human hepatocytes (Upcyte Technologies)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E11_AD008_indexed


title: HDAC4/5/7_Combi_5nM_Replicate_4

description:
SAMPLE 16
human hepatocytes (Upcyte Technologies)


title: HDAC5_s19464_5nM_Replicate_3

description:
SAMPLE 11
human hepatocytes (Upcyte Technologies)


title: HDAC4_s18339_5nM_Replicate_4

description:
SAMPLE 8
human hepatocytes (Upcyte Technologies)


title: HDAC5_s19464_5nM_Replicate_4

description:
SAMPLE 12
human hepatocytes (Upcyte Technologies)


title: HDAC4/5/7_Combi_5nM_Replicate_3

description:
SAMPLE 15
human hepatocytes (Upcyte Technologies)


title: HDAC4/5/7_Combi_5nM_Replicate_1

description:
SAMPLE 13
human hepatocytes (Upcyte Technologies)


title: HDAC4_s18339_5nM_Replicate_2

description:
SAMPLE 6
human hepatocytes (Upcyte Technologies)


title: HDAC4_s18339_5nM_Replicate_1

description:
SAMPLE 5
human hepatocytes (Upcyte Technologies)


title: HDAC4_s18339_5nM_Replicate_3

description:
SAMPLE 7
human hepatocytes (Upcyte Technologies)


title: LV3_5nM_Replicate_4

description:
SAMPLE 4
human hepatocytes (Upcyte Technologies)

value: LV3 Control


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E10_AD007_indexed


title: LV3_5nM_Replicate_3

description:
SAMPLE 3
human hepatocytes (Upcyte Technologies)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E10_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E11_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E11_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E10_AD010_indexed


title: LV3_5nM_Replicate_2

description:
SAMPLE 2
human hepatocytes (Upcyte Technologies)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E10_AD006_indexed


title: HDAC5_s19464_5nM_Replicate_2

description:
SAMPLE 10
human hepatocytes (Upcyte Technologies)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E10_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E10_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D9_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D9_AD010_indexed


title: LV3_5nM_Replicate_1

description:
SAMPLE 1
human hepatocytes (Upcyte Technologies)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D9_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D8_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D9_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D8_AD004_indexed


title: HDMB03 DMSO-3, technical replicate 3

city: Heidelberg

first: Venu

last: Thatikonda

address: Technologiepark III, Im Neuenheimer Feld

institute: German Cancer Research Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with affy R/bioconductor package by employing log2 GC-RMA normalization.

source_name: HDMB03 cells

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

value: MYC amplified Group3 Medulloblastoma

tag: treatment

value: DMSO


title: HDMB03 MS275, technical replicate 2

value: 5uM entinostat for 6 hours


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D8_AD008_indexed

tag: Sex


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D8_AD007_indexed

tag: age


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D9_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_E10_AD002_indexed


title: HDMB03 DMSO-2, technical replicate 2

tag: cell type


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D6_AD012_indexed

tag: brain region


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D6_AD006_indexed


title: HDMB03 DMSO-1, technical replicate 1


title: HDMB03 MS275, techincal replicate 3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D6_AD004_indexed


title: HDMB03 MS275, technical replicate 1


title: Breast tumor tissue_H-CICs_1

city: Beijing

first: Xiaochen

last: Yu

address: Fengtai District, Beijing Fengtai East Street on the 20th

country: China

institute: Institute of Biotechnology

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix Hybridization Cocktail. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250 - Antibody Amplification for Eukaryotic Targets.

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

data_processing: The data were analyzed with GeneChip Command Console Software using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Human breast cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA according to Affymetrix eukaryotic gene expression profile).

growth_protocol: Following biopsy, tissues were divided into multiple copies around 0.5 cm x 0.5 cm x 0.5 cm and stored at −80 °C/ liquid nitrogen in a frozen tube until required.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.Briefly, added 0.2 ml of chloroform used for homogenization and shaked tube vigorously by hand for 15 sec. Incubated for 2–3 min at room temperature followed by centrifuged at 12,000 ×g for 15 min at 4°C. Attained the aqueous phase of the sample by pipetting the solution out and added 0.5 ml of 100% isopropanol to the aqueous phase, incubated at room temperature for 10 min, centrifuged at 12,000 ×g for 10 min at 4°C. Removed the supernatant from the tube and washed the RNA pellet with 1 ml of 75% ethanol, then centrifuge at 7500 × g for 5 min at 4°C. Discarded the wash and air dry the RNA pellet for  10 min. At last, resuspended the RNA pellet in RNase-free water and stored at -80℃.

treatment_protocol: Tissue samples were cut into small pieces, and transfered into 1.5 ml tube containing 1 ml TRIzol on ice.

value: breast cancer tumor

tag: group

value: high cell-in-cell structure


title: Breast tumor tissue_H-CICs_4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D6_AD008_indexed


title: Breast tumor tissue_H-CICs_2


title: Breast tumor tissue_H-CICs_7


title: Breast tumor tissue_H-CICs_5


title: Breast tumor tissue_H-CICs_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D8_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D9_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D5_AD010_indexed


title: Breast tumor tissue_H-CICs_6


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D5_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D6_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D8_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D4_AD012_indexed


title: Breast tumor tissue_L-CICs_2

value: low cell-in-cell structure


title: Breast tumor tissue_L-CICs_3


title: Breast tumor tissue_L-CICs_5


title: B tumor cells from FL 121

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

country: France

institute: Rennes University Hospital

hyb_protocol: Following fragmentation, cARN were hybridized on GeneChip Human U133Plus2 arrays

scan_protocol: GeneChips were scanned using the Genechip Scanner Affymetrix 3000

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC). Normalization was performed by using the RMA algorithm using GC content from the Partek Genomics Suite software (Partek, St Louis, MO). Dataset was then filtering by eliminating PS with no expression in all dataset and/or no gene symbol annotations.

source_name: B tumor cells from FL

label_protocol: Biotinylated cRNA were amplified according to the small sample labeling protocol (Affymetrix, Santa Clara, CA)

growth_protocol: B  lymphocytes were purified by FACSARIA sorting strategy from FL lymph nodes or non tumoral tonsils using CD20hiCD44loCD38posIgDnegCD138neg phenotype.

extract_protocol: RNA extraction was  performed using Qiazol (Qiagen, Valencia, CA) according to the manufacturer's instructions.

tag: status

value: FL patient

value: Lymph node

value: B tumor cells purified from follicular lymphoma lymph node


title: B tumor cells from FL 125


title: B tumor cells from FL 122


title: Breast tumor tissue_L-CICs_7


title: B tumor cells from FL 124


title: B tumor cells from FL 123


title: Breast tumor tissue_L-CICs_1


title: Breast tumor tissue_L-CICs_6


title: Breast tumor tissue_L-CICs_4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D4_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D6_AD002_indexed


title: B tumor cells from FL 120


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D5_AD008_indexed


title: B tumor cells from FL 117


title: B tumor cells from FL 118


title: B tumor cells from FL 119


title: B tumor cells from FL 116


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D4_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D4_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D5_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D4_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D4_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D5_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D3_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D3_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D5_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D3_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D3_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D2_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D3_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D3_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D2_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D3_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D3_AD006_indexed


title: N463 non-CAV test

city: Vancouver

first: Bruce

middle: Maxwell

last: McManus

state: BC

address: 1081 Burrard Street

department: UBC James Hogg Research Centre

country: Canada

institute: PROOF Centre of Excellence

description: non-CAV, test

hyb_protocol: Following fragmentation, the cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. Equilibrate probe array to room temperature immediately before use.  Then, heat the hybridization cocktail to 99°C for 5 minutes in heatblock.  Next, wet the array by filling it through one of the septa with appropriate volume of 1X MES Hybridization Buffer using a micropipettor and appropriate tips. Last, incubate the probe array for 10 minutes at 45°C in the hybridization oven with rotation.

scan_protocol: The Probe Array is scanned using the Affymetrix System.  The scanner is controlled by the GeneChip software.  The probe array is scanned after the wash protocols are complete

data_processing: RMA

source_name: whole blood, week 104 post-transplant

label_protocol: Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA.

extract_protocol: Isolation begins with a centrifugation step to pellet nucleic acids in the PAXgene Blood RNA Tube. The pellet is washed, resuspended, and incubated in optimized buffers containing Proteinase K to digest proteins. A second centrifugation step is carried out to remove residual cell debris, and the supernatant is transferred to a fresh microcentrifuge tube. Ethanol is added to adjust binding conditions, and the lysate is applied to a PAXgene RNA spin column. During a brief centrifugation, RNA is selectively bound to the silica-gel membrane of the spin column as contaminants pass through. Remaining contaminants are removed in three wash steps, and pure RNA is then eluted in Buffer BR5. Generally, DNase digestion is not required for RNA purified with the PAXgene Blood RNA Kit, since PAXgene silica-gel–membrane technology efficiently removes most of the DNA without DNase treatment. However, further DNA removal is recommended for RNA applications that are sensitive to DNA contamination. In these cases, residual DNA can be removed either by using the RNase-Free DNase Set for on-column DNase digestion, or by treating the eluted RNA with DNase.

tag: gender

value: M

tag: age at transplant

tag: race

value: Caucasian

tag: original disease

value: Ischemic heart disease

value: whole blood


title: N461 non-CAV test

description: non-CAV, test

source_name: whole blood, week 78 post-transplant


title: N473 CAV test

description: CAV, test

source_name: whole blood, week 105 post-transplant

value: Other


title: N472 CAV test

description: CAV, test

source_name: whole blood, week 248 post-transplant

value: Non-ischemic cardiomyopathy


title: N460 CAV test

description: CAV, test


title: Shoot apices, tfl1 24hr FRP rep3 RNA-Seq

city: Philadelphia

first: Doris

last: Wagner

state: PA

address: 103G Carolyn Lynch Laboratory

department: Department of Biology

institute: University of Pennsylvania

data_processing:
Base-calling was performed automatically in Illumina BaseSpace
Trimmed reads were mapped to Arabidopsis thaliana genome using STAR v2.5.3a
Read counts at each gene for each sample and replicate was calculated with HT-Seq v0.7.2
Genes were count-normalized and differentially-expressed genes were identified in each genotype (adjusted p-value ≤ 0.005) using default methods in Deseq2 for photoperiord shift (24 hr FRP) comparet to untreated (0hr FRP) plants.
Genome_build: TAIR10 release 31
Supplementary_files_format_and_content: StarAligned_htseq.txt.gz file

source_name: 42-day old short-day-grown shoot apices

growth_protocol: Plants were grown in short days (8hr light, 16 hr dark ) for 42 days with a light intensity of 120 μMol/m2s

extract_protocol:
total RNAs were extracted by trizol and chloroform and further purified by Qiagen RNA cleanup kit
TruSeq RNA Sample Prep Kit (Illumina, RS-122-2001).

treatment_protocol: 24-hour FRP

tag: ecotype

tag: genotype

value: shoot apices

value: 24-hour FRP

tag: deseq2 analyzed for differential expression

value: yes


title: L527 non-CAV training

description: non-CAV, training

source_name: whole blood, week 52 post-transplant

tag: tissue


title: N470 CAV training

description: CAV, training


title: L528 CAV test

description: CAV, test

value: F


title: L537 CAV training

description: CAV, training

source_name: whole blood, week 51 post-transplant


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D1_AD008_indexed

city: La Jolla

source_name: C57BL/6J Male P56 Mouse Brain

value: MOp

value: male


title: L533 non-CAV training

description: non-CAV, training


title: N450 non-CAV test

description: non-CAV, test


title: N452 CAV test

description: CAV, test


title: L532 non-CAV training

description: non-CAV, training


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D2_AD010_indexed


title: N453 non-CAV test

description: non-CAV, test


title: I400 non-CAV training

description: non-CAV, training


title: N462 non-CAV test

description: non-CAV, test


title: N471 non-CAV training

description: non-CAV, training


title: L525 non-CAV training

description: non-CAV, training


title: N459 CAV training

description: CAV, training


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D2_AD007_indexed


title: Shoot apices, tfl1 24hr FRP rep1 RNA-Seq


title: L531 CAV training

description: CAV, training

source_name: whole blood, week 96 post-transplant


title: L530 CAV training

description: CAV, training


title: I403 CAV training

description: CAV, training


title: Shoot apices, tfl1 24hr FRP rep2 RNA-Seq

value: no


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D2_AD001_indexed


title: Shoot apices, tfl1 0hr FRP rep3 RNA-Seq

treatment_protocol: No Treatment

value: No Treatment


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D1_AD010_indexed


title: enGFP

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

data_processing:
Basecalls performed using CASAVA version 1.4
Cluster generation was performed with Illumina TruSeq cluster kit v2-cBot-HS
Single-read 50 bp sequencing was completed with Illumina TruSeq SBS kit v3-HS.
Reads were aligned using Tophat2 v2.0.12
RPKM expression values from different conditions were extracted and compared by cuffdiff v2.2.1 using Refseq gene models [2].
Genome_build: dm6 Drosophila

organism: Drosophila melanogaster

source_name: Larval wing disc cells

growth_protocol: Drosophila of the relevant genotypes were cultured under standard conditions at 25 degrees Celsius in humidity-controlled incubators with 12hr light:dark cycles

extract_protocol:
Wandering stage (L3 instar) larvae were sorted for GFP expression under a dissecting microscope equipped with a Zeiss HBO lamp and a GFP filter. Larvae were rinsed in 1x PBS and then dissected to remove wing discs, which were then immediately dissolved in Trizol (TM) kept on ice. Disc+Trizol mixtures from one 2hr dissection session were frozen at -80 degrees Celsius. This was repeated until 80-100 total discs per genotype (en>GFP or en>GFP,Tai) had been collected. Discs were then pooled within genotypes, and total RNA was extracted according the manufacturer's instructions and depleted for rRNA prior to analysis.
4 µg of total RNA was rRNA depleted and utilized for library construction with the Illumina TruSeq RNA Sample Preparation Kit v2 following the manufacturer's instructions. Libraries were sequenced with an Illumina HiScan platform.

tag: Stage

value: L3 instar

tag: expression

value: enGFP


title: enGFP+Yki+Tai-IR

value: enGFP+Yki+Tai-IR


title: Shoot apices, tfl1 0hr FRP rep1 RNA-Seq

tag: treatment


title: Shoot apices, tfl1 0hr FRP rep2 RNA-Seq


title: enGFP+Yki+Tai

value: enGFP+Yki+Tai


title: Shoot apices, WT 24hr FRP rep3 RNA-Seq

value: WT


title: Nup98IR_p35_rep3

city: Ann Arbor

first: Laura

last: Buttitta

state: MI

address: 5218 Biological Sciences Bldg., 1105 North University Ave.

department: Molecular, Cellular, Developmental Biology

institute: University of Michigan

data_processing:
Sequencing was performed with the Illumina HiSeq 2000 platform
High read quality was confirmed using FastQC
Reads were aligned to the D. melanogaster genome using Rsubread (v1.21.5) and featureCounts
Counts per million (cpm) were determined with edgeR (v3.13.4)
Transcripts with low expression were identified and removed using the data-based Jaccard similarity index determined with HTSFilter (v1.11.0)
The cpm were TMM normalized (calcNormFactors), voom transformed, then fit to a linear model (lmFit)
differential gene expression calls were made with eBayes
Genome_build: BDGP6.82
Supplementary_files_format_and_content: Raw counts of the sequencing reads per annotated gene were generated using Rsubread and FeatureCounts. The Microsoft Excel file contains counts for each biological replicate in separate columns.

source_name: wandering 3rd instar larval wing

growth_protocol: The genotypes are: UAS-P35/+; ap-Gal4, UAS-GFP/+ ; tub-Gal80TS/ UAS-Nup98 RNAi HM05048 or UAS-white RNAi JF01540.  Embryos were collected on grape plates overnight and transferred to vials as newly hatched larvae to synchronize developmental stages.  Animals were kept in un-crowded vials (70 animals/vial) prior to their dissection

extract_protocol:
Twenty wing discs were dounce homogenized in TRIzol with ten strokes of a tight pestle. Samples were vortexed at speed 10 for 1min, incubated for 5mins at room temperature then frozen in liquid nitrogen. Samples were kept at -80°C until they were pooled to make a total of 40 wing discs per replicate of each condition and genotype. The pooled RNA was phase separated with chloroform and RNA was precipitated in isopropanol at -30°C overnight prior to 20min 4°C centrifugation at 12,000x g. The RNA pellet was resuspended in 30μL of RNase-Free water.
Using PolyA selection, the University of Michigan's Sequencing Core generated directional barcoded libraries for each sample and confirmed the quality via the Bioanalyzer and qPCR.

treatment_protocol: Animals were kept at 18oC for four days to keep the Gal4 expression off, followed by a shift to 28°C to activate Gal4 expression for 72 hours prior to dissection as wandering L3 larvae

value: larval wing


title: whiteIR_p35_rep3

value: UAS-P35/+; ap-Gal4, UAS-GFP/+ ; tub-Gal80TS/ UAS-white RNAi JF01540


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D11_AD012_indexed

tag: Sex

tag: strain


title: Nup98IR_p35_rep2

value: UAS-P35/+; ap-Gal4, UAS-GFP/+ ; tub-Gal80TS/ UAS-Nup98 RNAi HM05048


title: Nup98IR_p35_rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D1_AD006_indexed

tag: age


title: whiteIR_p35_rep1


title: whiteIR_p35_rep2


title: Shoot apices, WT 24hr FRP rep2 RNA-Seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D1_AD004_indexed

tag: brain region


title: enGFP+Yki

value: enGFP+Yki


title: PBMC2

city: Tuebingen

first: Ludger

last: Schöls

address: Hoppe-Seyler-Strasse 3

department: Department of Neurology and Hertie Institute for Clinical Brain Research

institute: University of Tübingen

data_processing:
For adapter sequence trimming in FASTQ files, ngs-bits SeqPurge version 2018_06 was used.
Cleaned read sequences were aligned with STAR version 2.5.4a
Read counting for exonic regions was performed with subread featureCounts version 1.6.0.
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw count data in featureCounts default output format, see description at http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf

source_name: peripheral blood mononuclear cellc

extract_protocol:
Cells were lysed with RLT buffer (Qiagen). RNA was isolated with RNeasy Mini kit (Qiagen) according to the manufacturer's instructions. 20 ng/ul used for making libraries.
TruSeq mRNA v2Kit (polyA)

tag: cell type

value: peripheral blood mononuclear cellc


title: Shoot apices, WT 24hr FRP rep1 RNA-Seq

value: shoot apices

value: 24-hour FRP


title: LB1

source_name: lymphoblasts

value: lymphoblasts


title: iPSC2

source_name: Induced pluripotent stem cells

value: Induced pluripotent stem cells


title: PBMC1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D1_AD012_indexed

value: MOp

value: male


title: Shoot apices, WT 0hr FRP_rep3 RNA-Seq

value: No Treatment

value: yes


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D1_AD001_indexed


title: iPSC1


title: F2

source_name: fibroblasts

value: fibroblasts


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D1_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D11_AD007_indexed


title: Shoot apices, WT 0hr FRP_rep1 RNA-Seq

value: no


title: CN1

source_name: iPSC-derived cortical neurons

value: iPSC-derived cortical neurons


title: CN2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D11_AD010_indexed


title: Shoot apices, ft 24hr FRP Rep3 RNA-Seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D2_AD002_indexed


title: LB2


title: Shoot apices, ft 24hr FRP Rep2 RNA-Seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D1_AD007_indexed


title: GEN220 Quiescent

city: NEDLANDS

first: David

last: Martino

state: Western Australia

address: Perth Childrens Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute

description: primary cells

data_processing:
Data were processed using the ENCODE data processing pipeline for ChiP-seq and ATAC-seq data v1.4. Complete details of each step are available here (https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit)
Genome_build: hg38
Supplementary_files_format_and_content: peaks called using MACS2 caller, adapters trimmed, blacklisted regions and duplicates removed.

source_name: naïve CD4+ T-cell

growth_protocol: naïve CD4+T cells were enriched from cryopreserved peripheral blood mononuclear cells using a negative selection magnetic bead protocol to yield untouched T cells

extract_protocol:
At 72 hours cells were harvested and nuclei were isolated for transposition using the omni-ATAC method of Corces et al (https://www.nature.com/articles/nmeth.4396)
Library amplification was performed using Nextera DNA library prep kit (Illumina, cat. no. FC-121-1030) with Nextera Index Kit (Illumina, cat. no. FC-121-1011) as per manufacturers instructions

treatment_protocol: Cells were plated in 96 well plates in RPMI+10% HI FCS for 72 hours in the presence of anti-CD3 + anti-CD28 beads (Activated) or with medial alone (Quiescent)

value: Quiescent

value: Female

tag: ancestry

value: caucasian


title: IFO189 Quiescent

description: primary cells

value: Male


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D11_AD006_indexed

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: IFO139 Quiescent

description: primary cells


title: GEN170 Quiescent

description: primary cells


title: IFO139 Activated

description: primary cells

value: Activated


title: Shoot apices, WT 0hr FRP_rep2 RNA-Seq

value: WT


title: GEN157 Quiescent

description: primary cells


title: F1


title: Shoot apices, ft 24hr FRP Rep1 RNA-Seq

value: shoot apices


title: Shoot apices, ft 0hr FRP Rep3 RNA-Seq


title: IFO001 Quiescent

description: primary cells


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D7_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D11_AD008_indexed


title: GEN220 Activated

description: primary cells


title: IFO189 Activated

description: primary cells


title: Shoot apices, ft 0hr FRP Rep2 RNA-Seq


title: GEN157 Activated

description: primary cells


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D11_AD004_indexed


title: Shoot apices, ft 0hr FRP Rep1 RNA-Seq


title: GEN170 Activated

description: primary cells


title: Shoot apices, Control input ChIP-Seq

data_processing:
Base-calling was performed automatically in Illumina BaseSpace
Trimmed sequencing reads were aligned to the Arabidopsis thaliana genome using Bowtie2 v2.3.1 with the `--no-unal` parameter and further processed as per ENCODE guidelines (Landt et al 2012)
For narrowPeak files, significant peaks were identified using MACS2 2.1.1 callpeak on ChIP samples relative to relevant control ChIPs performed in non epitope containing plants using 224 bp read extension and summit q-value ≤ 10^-10.
For bigwig files, reads were extended to 224 bp using bedtools v.2.26.0, normalized to 10 million reads mapped per million reads sequenced (10RPM) and coverage was averaged using bedtools.
Genome_build: TAIR10
Supplementary_files_format_and_content:
bigwig normalized to 10RPKM for single replicates
bigwig normalized to 10RPKM for the mean of three replicates for each sample
bigwig normalized to 10RPKM for the mean of three replicates for each sample after subtracting the relevant background sample
bed file (narrowPeak format) containing peaks called by MACS v2.1.0.20151222 filtered by Q-value < 1e-10

extract_protocol:
ChIP assay was performed according to Yamaguchi et al., 2014. N. Yamaguchi et al., PROTOCOLS: Chromatin Immunoprecipitation from Arabidopsis Tissues. Arabidopsis Book 12, e0170 (2014).
DNA libraries were generated using the ThruPLEX DNA-seq kit (RUBICON GENOMICS, cat. R400406) and quantified by the NEBNext Library Quant Kit (cat. E7630L). Equal amounts of DNA were pooled from each library with different dual indexing primers and sequenced on a Next seq

tag: transgenics

tag: chip antibody


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D11_AD002_indexed


title: PAIVS 2 - hCTS

city: Hong Kong

first: Yin Yu

last: Lam

address: 102 Pokfulam Road

department: Department of Paediatrics and Adolescent Medicine

institute: The University of Hong Kong

data_processing:
Raw sequencing reads filtered and aligned with Cell Ranger 2.0
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx (RNA expression levels)
Supplementary_files_format_and_content: barcodes.tsv (Cell identification code)
Supplementary_files_format_and_content: features.tsv (List of genes)

source_name: Human induced pluripotent stem cell derived cardiomyocytes

extract_protocol:
hiPSC-CMs and hCAS were dissociated with 1X TrypLE and hCTS were dissociated with collagenase IV. Dissociated cells were resuspended in RPMI/B27 for cell encapsulation.
Constructed with Chromium Single Cell 3' Reagent Kit according to manufacturer's protocol
scRNA-seq

tag: disease state

value: PAIVS


title: PAIVS 1 - hCTS

value: Human induced pluripotent stem cell derived cardiomyocytes


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D11_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D10_AD012_indexed


title: Shoot apices, TFL1B input  ChIP-Seq


title: Control 2 - hiPSC-CM

value: Normal


title: Control 1 - hCAS


title: PAIVS 1 - hCAS


title: Shoot apices, TFL1 Input Rep2 ChIP-Seq


title: PAIVS 1 - hiPSC-CM


title: Shoot apices, TFL1 Input Rep1 ChIP-Seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D10_AD010_indexed

value: MOp


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D10_AD006_indexed

value: male


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C9_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D10_AD008_indexed


title: Shoot apices, Control Rep2 ChIP-Seq

value: anti-GFP Thermo Fisher, A-11122


title: Shoot apices, Control for fd_gTFL1_GFP Rep1 ChIP-Seq


title: Shoot apices, Control for fd_gTFL1_GFP Rep2 ChIP-Seq


title: IFO001 Activated

description: primary cells


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D10_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C9_AD010_indexed


title: Shoot apices, Control Rep1 ChIP-Seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D10_AD007_indexed