title: 883_898_H3K27ac_ChIPSeq

city: Montreal

last: Sinnett

state: Quebec

address: 3175 Cote-Sainte-Catherine

institute: CHU Sainte-Justine

description:
Pool of two patients
883_898_PrBC_ChIP_H3K27ac

data_processing:
WGBS reads were aligned to a bisulfite-converted reference genome using bwa and methylation calls were obtained using nxtgen-utils
ChIP-seq reads were aligned with bwa v.0.6.1 and peaks were called using macs2 with an input control and the ‘--broad’ option
Bigwig tracks were generated using bedtools genomeCoverageBed v2.17.0
Genome_build: hg19
Supplementary_files_format_and_content: Methylation call files are tab delimited and contain the C/T read counts and methylation levels

source_name: Childhood acute lymphoblastic leukemia

extract_protocol:
Mononuclear cells were isolated from bone marrow (BM) aspirates or peripheral blood cells at diagnosis and CD10+CD19+ cells were isolated from human cord blood
WGBS libraries were carried out using the TruSeq DNA Sample Prep Kit v2 (Illumina) with an added bisulfite conversion step.
ChIP-seq libraries were carried out using the Paired-End DNA Sample Prep Kit V1 (Illumina; PE-102-1001)

tag: subject status

value: Childhood acute lymphoblastic leukemia

tag: subject id

value: 883, 898; Pool of two patients

value: Pre-B t(12;21) [ETV6-RUNX1] acute lymphoblastic leukemia

value: Abcam; ab4729


title: 883_898_H3K4me3_ChIPSeq

status: Public on Oct 15 2018

type: SRA

first: Daniel

country: Canada

description:
Pool of two patients
883_898_PrBC_ChIP_H3K4me3

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

tag: chip antibody

value: Diagenode; pAb-003-050


title: 883_898_H3K4me1_ChIPSeq

description:
Pool of two patients
883_898_PrBC_ChIP_H3K4me1

value: Abcam; ab8895


title: 883_898_Input_ChIPSeq

description:
Pool of two patients
883_898_PrBC_ChIP_Input


title: Rif1 SG replicate 1

city: Nashville

first: Jared

last: Nordman

state: TN

address: 465 21st Ave S

department: Biological Sciences

country: USA

institute: Vanderbilt University

data_processing:
Reads were mapped to the Drosophila genome (BDGP Release 6) using BWA using default parameters
Normalized read counts (RPKM) were generated using bamCoverage using default parameters for the stage 13 samples. For salivary gland data sets (and 0-2h embryo control) normalized read counts (RPKM) were generated using bamCoverage rom Deeptools v2.5.0. Bin size 75 bases, smoothed for 225 bases. Minimum mapping quality required of 1 to only call uniquely mapped reads. Ignore duplicates flag set to true. Scaling method was RPKM, and excluded Chromosome 4 and X for normalization.
CNVnator 0.3.3 was used for the detection of underreplicated regions using a bin size of 1000
log2 ratios were generated using bamCompare from deepTool 2.5.0 by comparing stage 13 follicle cell profiles to a 0-2h embryo sample.
Genome_build: dm6

organism: Drosophila melanogaster

source_name: 3rd instar larvae

extract_protocol:
Salivary glands were extracted from wandering 3rd instar larvae. Ovaries were dissected from females fattened for 2 days on wet yeast and stage 13 egg chambers were isolated by hand dissection. Tissue was disrupted by douncing and then sonicated to fragment the genomic DNA. Genomic DNA extracted using a standard phenol chloroform extraction protocol.
Illumina libraries were prepared using NEB DNA Ultra II (New England Biolabs) following the manufacturers protocol. Barcoded libraries were sequenced using Illumina NextSeq500 platform.

tag: tissue

value: salivary gland

tag: genotype


title: plum_4wk_SUL_2

city: College Park

first: James

middle: N

last: Culver

state: MD

address: 4291 Fieldhouse Dr.

department: Plant Science and Landscape Architecture

institute: University of Maryland, College Park

description:
Prunus domestica L. 'Stanley'
Polysomal RNA from phloem leaf tissue.

library_source: transcriptomic

data_processing:
Library strategy: TRAP-seq
Reads that passed Illumina’s quality control filters were further processed. Reads were mapped to the Prunus persica v2.0 genome (Verde 2017, The International Peach Genome Initiative 2013, https://www.rosaceae.org/species/prunus_persica/genome_v2.0.a1) using the CLC Genomics Workbench v10.0.1 RNA-seq analysis tool and default parameters (Mismatch cost 2, Insertion cost 3, Deletion Cost 3, Length fraction 0.8, Similarity fraction 0.8, Max hits for a read 10 - CLC Bio, Aarhus, Denmark).
Genome_build: Prunus persica v2.0 genome (Verde 2017, The International Peach Genome Initiative 2013, https://www.rosaceae.org/species/prunus_persica/genome_v2.0.a1)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include Gene ID, Chromosome, Region, TPM, RPKM, Unique gene reads, Total gene reads, Unique exon reads and Total exon reads.

molecule: total RNA

organism: Prunus domestica

source_name: 4-week-old Prunus domestica L. leaves

growth_protocol: All transgenic plum trees expressing promoter:His6FLAG-RPL18 were maintained in a growth chamber at 25°C, 75% humidity, with a 12-hour photoperiod. After 12 weeks, plum leaves were stripped and plants were kept at 8°C for a 60 day vernalization period before being moved back to the growth chamber.

extract_protocol:
Frozen tissue was homogenized in Polysome Extraction Buffer (PEB; 200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM ethylene glycol tetraacetic acid (EGTA) pH 8.0, 35 mM MgCl2, 1% (v/v) octylphenyl-polyethylene glycol (Igepal CA-630), 1% (v/v) polyoxyethylene 10 tridecyl ether, 1% (v/v) sodium deoxycholate, 5 mM dithiothreitol (DTT), 1 mM PMSF, 50 ug/mL cycloheximide, 50 ug/mL chloramphenicol, 0.5 mg/mL heparin) using 10 mL PEB per 5 g of tissue. Homogenates were clarified by centrifugation at 16,000 g for 15 min and filtrated with cheesecloth. The supernatant was loaded onto an 8 mL 1.6 M sucrose cushion. Samples were ultracentrifuged at 170,000 g for 18 h at 4 C to pellet polysomes. 1 mL of PEB was used to resuspend the pellet. 50 μL of anti-FLAG magnetic beads (Sigma Chemical Company, St. Louis, MO USA) were added to the resuspended pellet and incubated at 4C overnight with gentle rocking. The beads were recovered using a magnet and washed four times for 5 min with 5 mL of wash buffer (200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM EGTA, 35 mM MgCl2, 5 mM DTT, 50 μg/mL cycloheximide, 50 μg/mL chloramphenicol). The complexes were eluted by treatment of the magnetic beads with 100 uL of Elution Buffer (100 uL wash buffer, 10 uL of 5mg/mL FLAG3 peptide - Sigma Chemical Company, St. Louis, MO USA, 0.5 uL of 2 U/mL RNase OUT - Thermo Fisher Scientific Cleveland, Ohio, USA). RLT buffer plus 2-Mercaptoethanol from the Qiagen RNeasy kit (Qiagen, Valencia, CA USA) was added to the eluted complexes. A 0.5 X volume of 100% ethanol was then added and the sample transferred to Qiagen RNeasy columns. Washes and RNA elutions were performed according to the manufacturer’s instructions. Isolated RNA was measured on a NanoDrop 1000 and the quality of the RNA confirmed using a 2100 Bioanalyzer Eukaryotic Total RNA Nanochip (Agilent Technologies Palo Alto, CA USA).
Library preparation and paired-end sequencing on the Illumina HiSeq system was done by Genewiz (South Plainfield, NJ, USA).

tag: cultivar

value: Stanley

tag: genotype/variation

tag: developmental stage

value: 4 weeks post vernalization

value: phloem leaf tissue


title: 898_WGBS

description:
Bisulfite treated
HI.1354.006.Index_15.898_PrBC_BS


title: plum_4wk_SUL_3


title: Rif1 st13 replicate 1

source_name: Adult females

value: ovary


title: human oocyte, biological rep2

type: RNA

city: manchester

first: Helen

middle: Louise

last: Smith

address: oxford road

country: United Kingdom

institute: The University of Manchester

description: Gene expression data from failed to fertilised oocyte i.e. before zygotic genome activation.

hyb_protocol: Labelled PolyAcRNA was hybridised to Affymetrix Human Genome U133 Plus 2.0 arrays

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Gene expression analysis and normalisation MAS 5.0 method (Affymetrix. Affymetrix Microarray Suite User Guide. Affymetrix, Santa Clara, CA, version 5 edition, 2001) were performed using Bioconductor

source_name: failed to fertilise human oocyte

label_protocol: PolyAcDNA was then subjected to a second round of amplification and biotin-16-dUTP labelling using EpiStem’s proprietary PolyAPCR based systems, EpiAmp™ (PolyAPCR based amplification) and EpiLabel™ (PolyA-PCR labelling), according to the Manufacturer’s instructions.

growth_protocol: For detailed description of the material see Shaw et.al. 2013. Embryos were cultured in G1 medium (Vitrolife, Goteborg, Sweden) covered with a thin layer of mineral oil (Ovoil, Origio, Malov, Denmark) until day 3, followed by G2 medium (Vitrolife) from day 3 to blastocyst at 37˚C, 6% CO2 in a humidified atmosphere.

extract_protocol: cDNA was prepared by polyAPCR amplification

treatment_protocol: A single embryo was transferred in a minimum volume of culture medium (<0.5 μl) to 4.5 μl complete lysis buffer. The reaction was overlaid with mineral oil, heated to 65°C for 1 min, cooled to room temperature for 3 min then placed on ice. The RNA was reverse transcribed. One volume of tailing buffer (0.33 mol/l potassium cacodylate, 6.7 mmol/l COCl2, 0.67 mmol/l DTT, 0.16 mmol/l dATP, 0.45 units/μl rTdT; Invitrogen) was then added and the reaction was incubated at 37°C for 15 min, 65°C for 10 min and then cooled on ice. This step polyadenylates the first strand cDNA allowing subsequent global amplification of cDNA using a single Not1dT24 oligonucleotide primer.

value: Oocyte

value: oocyte


title: human 4-cell stage embryo, biological rep4

description: Gene expression data from a 4-cell stage embryo, isolated on day 2

source_name: Embryos at the four-cell stage

value: Pre-implantation Embryo

value: four-cell stage


title: human oocyte, biological rep1


title: human oocyte, biological rep3


title: spermatocyte_WT_rep6

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

description: SL

hyb_protocol: Hybridization, staining and detection of cRNAs on Illumina Mouse WG-6 v2 Expression BeadChips were performed according to the manufacturer’s protocol.

scan_protocol: The Illumina I-Scan system was used to scan Expression BeadChips, according to Illumina recommendations.

data_processing: The data were normalised using quantile normalisation.

label: biotin

organism: Mus musculus

label_protocol: The starting amount of total RNA used for the reactions was 200 nanograms per sample. The Illumina Total Prep RNA Amplification Kit (Applied Biosystems / Ambion, Austin, USA) was used to generate biotinylated, amplified cRNA according to the manufacturer recommendations.

extract_protocol: Total RNA was extracted using Trizol reagent. 0.5-1 μg RNA was reverse transcribed with the SuperScriptTM III First-Strand Synthesis SuperMix (Invitrogen). Total RNA quantification was performed using the Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Incorporation, Waltham, USA). Integrity of the extracted RNAs was assessed with the Bioanalyzer 2100 and the RNA6000 Nano kit (Agilent Technologies Incorporation, Santa Clara, USA). A RNA integrity number (RIN) greater or equal to 7.00 was achieved for all samples.

treatment_protocol:
cell enrichment protocol: Fractions enriched in spermatogenic cells at different stages of maturation, including post meiotic round/early elongating spermatids were obtained by sedimentation on a BSA gradient as detailed in a recent dedicated method publication (Buchou et al., 2017; PMID: 27761820)
samples (replicates) preparation: RNAs for transcriptomic analyses were prepared from three independent experiments corresponding to three independent cell fractionations for each genotype. For each fractionation, cell suspensions from testes from two WT mice or three Nut KO mice were used. For each genotype (WT and Nut KO), 6 samples were prepared as follows. Samples 1, 2 and 3 were directly prepared from the three above-mentioned fractionations and three additional samples were obtained by respectively mixing samples 1 with 2, 2 with 3, and 1 with 3.

tag: strain background

value: WT

tag: Sex

value: male

tag: age

value: adult

value: adult testis

value: male germ cells

tag: cell stage

value: spermatocytes


title: spermatocyte_WT_rep3

description: SI


title: SuUR^deltaSNF SG

value: SuUR [deltaSNF]


title: Rif1 SG replicate 2


title: human oocyte, biological rep4


title: spermatocyte_WT_rep2

description: SH


title: spermatocyte_WT_rep1

description: SG


title: human 4-cell stage embryo, biological rep1


title: spermatocyte_KO_rep3


title: spermatocyte_KO_rep4


title: spermatocyte_KO_rep6


title: spermatocyte_KO_rep5


title: 886_WGBS

description:
Bisulfite treated
HI.1357.005.Index_13.886_PrBC_BS

value: Childhood acute lymphoblastic leukemia

value: Pre-B t(12;21) [ETV6-RUNX1] acute lymphoblastic leukemia


title: plum_4wk_SUL_1

value: Stanley


title: SuUR SG

value: salivary gland

value: SuUR


title: spermatocyte_WT_rep4

description: SJ


title: plum_4wk_35S_3

description:
Prunus domestica L. 'President'
Polysomal RNA from whole leaf tissue.

value: President

value: 4 weeks post vernalization

value: whole leaf tissue


title: 883_WGBS

description:
Bisulfite treated
HI.1355.008.Index_12.883_PrBC_BS


title: CD10_CD19_Control _WGBS

description:
Bisulfite treated
CD10_CD19-PreBC-BS-1-3530-005_S1

source_name: Cord blood

value: CD10+ CD19+ Cord blood


title: Wild type SG

value: wildtype


title: spermatocyte_KO_rep2


title: plum_4wk_35S_2


title: treated_136181

city: Richmond

first: Amanda

last: Dickinson

state: VA

address: 1000 W. Cary St. Rm 339

department: Biology

institute: Virginia Commonwealth University

data_processing:
HiSeq v4 PE100 250 mil reads 50 GB max output with Teir 1 analysis
Reads were aligned using Xenopus laevis reference genome and STAR alignment software
counted using featureCounts software in the Subread package
The DESeq2 Bioconductor package in the R statistical computing environment to normalize count data, estimate dispersion, and fit a negative binomial model for each gene
Xenopus genes that were significantly altered (p<0.05) were converted to the human ortholog for functional and network analyses (93 unique genes).
Genome_build: ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.1/),
Supplementary_files_format_and_content: txt files containing raw counts

organism: Xenopus laevis

source_name: dissected facial tissue

growth_protocol: In vitro fertilization of X. Laevis eggs, eggs were cultured in normal growth media until stage 35,

extract_protocol:
facial region (area between the eyes from the midface to the cement gland, without eyes or brain tissue) was manually dissected from 500 embryos. Dissected regions were pooled and total RNA extracted with TriReagent following standard protocols
RNAseq was performed by Hudson Alpha Institute for Biotechnology (Huntsville, AL) where a HiSeq v4 PE100 250 mil reads 50 GB max output with Teir 1 analysis performed.
Reads were aligned using Xenopus laevis reference genome and STAR alignment software, and then counted using featureCounts software in the Subread package (http://www.xenbase.org/, RRID:SCR_003280) [29-31] The DESeq2 Bioconductor package in the R statistical computing environment to normalize count data, estimate dispersion, and fit a negative binomial model for each gene [32-34]. R Code available upon request. Data was then exported to Excel for further analysis. Xenopus genes that were significantly altered (p<0.05) were converted to the human ortholog for functional and network analyses (93 unique genes). Genetic similarity was determined to be >90% identity and similarity.

treatment_protocol: transferred to media containing control (1% DMSO) or treatment (1 micromolar BMS453 in 1% DMSO) until stage 40 (66 hpf)

value: stage 40 (66 hpf)

tag: treatment

value: 1 micromolar BMS453

value: facial


title: plum_4wk_35S_1


title: ery_input_ds_MEN1

city: London

first: Kamil

middle: R

last: Kranc

address: Charterhouse Square

institute: Queen Mary University of London

data_processing:
Alignments were performed by hisat2, v2.0.3 or v2.0.5, with the --no-spliced-alignment option
Reads were filtered by alignment to nine vertebrate genomes, including human, and assigned to the best-matching genome.
Peak calling was by MACS2, and analysis of colocalisation was by the R package ChIPpeakAnno
Normalisation and subtraction was done using the deepTools 2.5.4 bamCompare function with option string  --outFileFormat bigwig --scaleFactorsMethod readCount --ratio subtract --binSize 50 --normalizeTo1x 3100000000 --minMappingQuality 30
Genome_build: hg38
Supplementary_files_format_and_content: A bigWig graph representing difference between ChIP and input, with the difference calculated after ChIP and input had each been normalised to 1x coverage genome-wide

source_name: erythroblast

extract_protocol:
as described by Pope SH et al, Eur J Haematol 64:292-303, 2000
library construction was provided by Oxford Genomics Centre, or by Edinburgh Genomics

value: Adult erythroblasts

value: no antibody

tag: number of sonications


title: treated_136179


title: UMLILO_KO

city: Cape Town

first: Musa

middle: M

last: Mhlanga

address: Anzio Road

department: Faculty of Health Sciences

country: South Africa

institute: University of Cape Town

data_processing:
Quality control of sequence data was performed using FastQC tool (v0.11.5).
Sequencing reads were then aligned to the human GRCh38 reference genome using Hisat2 (v2.1.0).
FPKM for each sample was estimated using StringTie (v1.3.3).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

source_name: THP-1 cell line

growth_protocol: The THP-1 cell line was maintained in DMEM + 10% Foetal Bovine Serum.

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

treatment_protocol: The AAV vector construct used in this work permits co-expression of three distinct SpCas9 gRNAs from a single AAV vector backbone under the RNA polymerase III promoters U6, H1 or 7SK, respectively. The AAV vector plasmid expressing SpCas9 under the control of a cytomegalovirus (CMV) promoter was derived from pSSV9 and encoded the SpCas9 cDNA variant from the Zhang lab (Addgene plasmid #49535).

value: Monocyte-like


title: plum_2wk_SUC2_2

source_name: 2-week-old Prunus domestica L. leaves

value: 2 weeks post vernalization

value: phloem leaf tissue


title: ery_SETD1A

growth_protocol: as described by Pope SH et al, Eur J Haematol 64:292-303, 2000


title: round_spermatids_WT_rep6

description: SF

value: WT

value: male

value: adult

value: adult testis

value: male germ cells

value: round spermatids


title: control_136177

value: 1% DMSO


title: control_136178


title: plum_2wk_SUC2_1

value: Stanley


title: plum_2wk_SUL_3


title: Cas9_Control


title: ery_HCFC1

treatment_protocol: as described by Pope SH et al, Eur J Haematol 64:292-303, 2000


title: control_136176


title: plum_2wk_SUL_2


title: spermatocyte_KO_rep1

value: spermatocytes


title: ery_input_HCFC1_SETD1A


title: round_spermatids_WT_rep4

description: SD


title: treated_136180

value: stage 40 (66 hpf)


title: 8.iMT

city: TSURUMI WARD YOKOHAMA

first: Aki

last: Minoda

state: KANAGAWA

address: 230-0045, 1 CHOME-7-22 SUEHIROCHO

department: IMS

country: Japan

institute: RIKEN YOKOHAMA

description: inner region of medial tibial plateau

data_processing:
Basecalls performed using CASAVA version 1.8
FASTQ files were splitted by barcode using FASTX-Toolkit
A bioinformatics pipeline for ATAC-seq read processing, peak calling, and quality control (https://github.com/kundajelab/atac_dnase_pipelines) was implemented. Briefly, fastq files from 9 oLT (normal) samples or 9 iMT (disease) samples were grouped together and input into pipeline separately, with parameters `–true_rep –no_idr`.
Genome_build: Hg38
Supplementary_files_format_and_content: bigwig files were generated using macs2

source_name: Human knee articular cartilage

growth_protocol: Human cartilage tissues were isolated from the knee joint tibial bone.

extract_protocol: Libraries were prepared  for sequencing using standered ATAC-seq protocol.

treatment_protocol: 100 mg cartilage from both outer region of lateral tibial plateau (oLT) and inner region of medial tibial plateau (iMT) for each patient was digested with 0.2% type II collagenase (Sigma-Aldrich) at 37 °C incubator with rotation for 12 h to fully remove collagen matrix debris, and stopped by washing with chilled PBS.

value: catilage

value: chondrocyte

tag: oa stage

value: degraded

tag: tissue type

value: fresh


title: ery_MEN1

value: Adult erythroblasts


title: plum_2wk_35S_3

value: President

value: 2 weeks post vernalization

value: whole leaf tissue


title: plum_2wk_SUL_1

value: phloem leaf tissue


title: 7.iMT

description: inner region of medial tibial plateau


title: round_spermatids_WT_rep2

description: SB

value: WT

value: male

value: adult


title: plum_2wk_35S_2


title: round_spermatids_WT_rep5

description: SE

value: adult testis

value: male germ cells

value: round spermatids


title: round_spermatids_WT_rep3

description: SC


title: 7.oLT

description: outer region of lateral tibial plateau

value: normal


title: plum_2wk_35S_1


title: 6.iMT

description: inner region of medial tibial plateau


title: plum_2wk_SUC2_3

value: Stanley


title: plum_6wk_SUC2_3

source_name: 6-week-old Prunus domestica L. leaves

value: 6 weeks post vernalization


title: CD_19

city: Cambridge

first: Navpreet

last: Ranu

state: MA

address: 415 Main Street

institute: Broad Institute

description: Each sample represents 3 replicates.

data_processing:
10X cell ranger-1.3.1 to generate a UMI table and gene expression profiles from fastq
UMI counts for enriched samples were determined by bootstrapping the previous UMI table at an appropriate sequencing depth
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing UMI expression counts for enriched barcodes, key='10X'

source_name: enriched data sets

extract_protocol: Single-cell RNA-seq library preparation was performed with the Chromium Single Cell 3’ method (10X Genomics) according to the manufacturer's protocol

value: Blood


title: plum_6wk_SUC2_2


title: 8.oLT

description: outer region of lateral tibial plateau

value: catilage

value: chondrocyte


title: HLA_DR

description: Each sample represents 3 replicates.


title: 5.iMT

description: inner region of medial tibial plateau

value: degraded

value: fresh


title: round_spermatids_WT_rep1

description: SA


title: round_spermatids_KO_rep6


title: plum_6wk_SUL_3


title: plum_6wk_SUC2_1


title: BHLH OE Sultana_4

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

hyb_protocol: For microarray analysis on Sultana leaves transiently overexpressing VvBHLH075, the hybridization and washing reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

scan_protocol: Scanning and Feature Extraction were performed by using an Agilent Scanner following the settings and parameters indicated in the instruction manual.

data_processing:
A data-matrix was prepared selecting from each single sub-array outcome file the gProcessedSignalvalues, which are the raw fluorescence intensities of each probe.
The data were normalized on the 75th percentile and a correlation analysis was then performed to assess the consistency of the biological quadruplicates.

organism: Vitis vinifera

source_name: BHLH overexpressing plantlet of Vitis vinifera cv. Sultana_line 4

label_protocol: For microarray analysis on Sultana leaves transiently overexpressing VvBHLH075, the cDNA synthesis and labeling reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

growth_protocol: For the transient overexpression of VvBHLH075 in grapevine, plantlets of Vitis vinifera cv. Sultana were in vitro micropropagated and cultivated in growth chamber at 25°C with a 16-h photoperiod.

extract_protocol: Total RNA was isolated from ~100 mg of young and well expanded ground leaves using SpectrumTM Plant Total RNA kit (Sigma-Aldrich) according to the manufacturer's instructions.

treatment_protocol: For transient transformation of Vitis vinifera cv. Sultana, the 35S:VvBHLH075 construct was transferred to Agrobacterium tumefaciens strain C58C1 by electroporation. As control, Agrobacterium was also transformed with an empty GoldenBraid 2.0 vector (pDGBΩ1). Seven in vitro six-week-old plants of grapevine cv. Sultana were immersed in each bacterial suspension and vacuum infiltrated (2 X 2 min at 90kPa).

value: Sultana

value: BHLH overexpressing

value: young leaves


title: round_spermatids_KO_rep4


title: plum_6wk_SUL_2

value: phloem leaf tissue


title: round_spermatids_KO_rep2

value: male


title: round_spermatids_KO_rep3

value: adult


title: BHLH OE Sultana_1

source_name: BHLH overexpressing plantlet of Vitis vinifera cv. Sultana_line 1


title: 4.iMT

description: inner region of medial tibial plateau


title: 4.oLT

description: outer region of lateral tibial plateau


title: 5.oLT

description: outer region of lateral tibial plateau


title: 3.iMT

description: inner region of medial tibial plateau


title: plum_6wk_SUL_1


title: 6.oLT

description: outer region of lateral tibial plateau


title: NRVM-ETV1_3

city: New York

first: Akshay

last: Shekhar

state: NY

address: 564 1st Ave Apt 11S

department: Medicine - Cardiology

institute: NYU School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.4
Calculating insert size and standard deviation performed using Picard v.1.126
Reads were mapped to Rnor6 using the STAR aligner (v2.5.0c)
read counting performed using HT-seq v0.6.0
Normalization and Deferential expression analysis performed using DEseq2 v3.0
BAM to bedgraph performed using bedtools v2.17.0
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.1.1
Genome_build: Rnor6
Supplementary_files_format_and_content: BigWig (coverage for mapped reads), count tables (read counts for genomic features) and normalized count tables

organism: Rattus norvegicus

extract_protocol:
Cells were harvested and total RNAs were extracted using the RNeasy kit (Qiagen) according to the manufacture's protocol.
Sequencing  libraries  were  prepared  using  the  TruSeq  RNALibrary  Prep  Kit  v2  (Illumina) according to the manufacture's protocol.

treatment_protocol:
Plate isolated and purified neonatal rat ventricular myocytes (NRVMs) into 6-well plates at 3,000,000 cells/well. Twenty-four hours post plating, NRVMs were transduced with either Ad-Etv1-EGFP (Etv1 vector; multiplicity of infection 5:1; Vector Biolabs) or Ad-EGFP (control vector; multiplicity  of  infection  5:1;  Vector  Biolabs) overnight. Next morning, viruses were removed by replacing virus-containing media with fresh media. 4 days post transduction, harvest RNA.
Plating media: DMEM plus 10% FBS plus supplements (3 mM pyruvic acid, 2 g/l BSA, 0.5 mg/ml primocin,  15  mM HEPES,  4 ug/ml  transferrin,  0.7  ng/ml  sodium  selenite,  5 ug/ml linoleic  acid,  10 uM ascorbic  acid). Media 24 hrs after plating: Serum-free  DMEM  with  supplements.

value: Sprague-Dawley

value: Postnatal day 1

value: Neonatal rat ventricular myocytes (NRVM)

tag: cell subtype

value: enriched primary cardiomyocytes

tag: adenovirus viral transgenes

value: Ad-Etv1 (5 MOI)

tag: harvest time

value: day 4 post transduction


title: 3.oLT

description: outer region of lateral tibial plateau

tag: cell type

value: normal


title: NRVM-ETV1_2


title: BHLH OE Sultana_3

source_name: BHLH overexpressing plantlet of Vitis vinifera cv. Sultana_line 3

tag: tissue


title: plum_6wk_35S_2

value: President

value: 6 weeks post vernalization

value: whole leaf tissue


title: Control Sultana_2 [BHLH OE]

source_name: Control plantlet of Vitis vinifera cv. Sultana _line 2

value: control


title: 2.iMT

description: inner region of medial tibial plateau

value: catilage

value: chondrocyte

value: degraded

value: fresh


title: Control Sultana_1 [BHLH OE]

source_name: Control plantlet of Vitis vinifera cv. Sultana _line 1

value: Sultana

value: young leaves


title: round_spermatids_KO_rep1

value: male

value: adult

value: adult testis

value: male germ cells

value: round spermatids


title: BHLH OE Sultana_2

source_name: BHLH overexpressing plantlet of Vitis vinifera cv. Sultana_line 2

value: BHLH overexpressing


title: Control Sultana_3 [BHLH OE]

source_name: Control plantlet of Vitis vinifera cv. Sultana _line 3


title: plum_6wk_35S_1


title: WRKY19 OE Sultana_4

hyb_protocol: For microarray analysis on Sultana leaves transiently overexpressing VvWRKY19, the hybridization and washing reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

source_name: WRKY19 overexpressing plantlet of Vitis vinifera cv. Sultana_line 4

label_protocol: For microarray analysis on Sultana leaves transiently overexpressing VvWRKY19, the cDNA synthesis and labeling reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

growth_protocol: For the transient overexpression of VvWRKY19 in grapevine, plantlets of Vitis vinifera cv. Sultana were in vitro micropropagated and cultivated in growth chamber at 25°C with a 16-h photoperiod.

treatment_protocol: For transient transformation of Vitis vinifera cv. Sultana, the 35S:VvWRKY19 construct was transferred to Agrobacterium tumefaciens strain C58C1 by electroporation. As control, Agrobacterium was also transformed with an empty GoldenBraid 2.0 vector (pDGBΩ1). Seven in vitro six-week-old plants of grapevine cv. Sultana were immersed in each bacterial suspension and vacuum infiltrated (2 X 2 min at 90kPa).

value: WRKY19 overexpressing


title: NRVM-ETV1_1

value: Sprague-Dawley

value: Postnatal day 1

value: Neonatal rat ventricular myocytes (NRVM)

value: enriched primary cardiomyocytes

value: Ad-Etv1 (5 MOI)

value: day 4 post transduction


title: WRKY19 OE Sultana_2

source_name: WRKY19 overexpressing plantlet of Vitis vinifera cv. Sultana_line 2


title: WRKY19 OE Sultana_3

source_name: WRKY19 overexpressing plantlet of Vitis vinifera cv. Sultana_line 3


title: Control Sultana_4 [BHLH OE]

source_name: Control plantlet of Vitis vinifera cv. Sultana _line 4

value: control


title: NRVM-GFP_3

source_name: NRVM-GFP

value: Ad-GFP (5 MOI)


title: Control Sultana_4 [WRKY19 OE]

value: Sultana


title: plum_6wk_35S_3

value: President

value: 6 weeks post vernalization

value: whole leaf tissue


title: 1.iMT

description: inner region of medial tibial plateau

value: catilage

value: chondrocyte

value: degraded

value: fresh


title: plum_4wk_SUC2_2

source_name: 4-week-old Prunus domestica L. leaves

value: Stanley

value: 4 weeks post vernalization

value: phloem leaf tissue


title: NRVM-GFP_2

value: Sprague-Dawley

value: Postnatal day 1

value: Neonatal rat ventricular myocytes (NRVM)


title: NRVM-GFP_1

value: enriched primary cardiomyocytes

value: day 4 post transduction


title: plum_4wk_SUC2_1


title: Control Sultana_3 [WRKY19 OE]

value: control

value: young leaves


title: Control Sultana_2 [WRKY19 OE]

value: Sultana


title: plum_4wk_SUC2_3


title: PPARG+PPARGD5

status: Public on Oct 14 2018

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

institute: National Research Council

description:
Cells co-expressing PPARG+PPARGD5
PolyA RNA
processed data file: UQUA_normalized_counts.txt

data_processing:
FastQC was used for quality check of sequenced reads (fastq files). Mapping on human genome (hg19 release) and transcriptome (GENCODE v19) were carried out using TopHat (version 2.0.10) with default parameters. Uniquely mapped reads were extracted using custom script from command line (grep -w).
SAMTools and BEDTools were used to convert file formats (.sam/.bam/.bed) and generate wig files for visualization on UCSC Genome Browser.
RNASeqGUI software was used to measure gene expression on raw counts (SummarizeOverlaps option), to filter low count genes (Proportion Test), normalize expression data (Counts per Million, CPM) and to identify differentially expressed genes (R Bioconductor package, NOISeq-sim function).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: UQUA_normalized_counts.txt: Tab-delimited; upper quartile normalized read counts.

source_name: HEK293 cell line

growth_protocol: Human Embryonic Kidney 293 cells (HEK239) were cultured in DMEM supplemented with 10% South American FBS, glutamine and antibiotics. Media, sera and antibiotics for cell culture were purchased from Thermo Fisher Scientific (Waltham, Massachusetts, USA).

extract_protocol:
Total RNA was isolated from cells by TRIzol Reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instructions. RNA quantity and quality were evaluated using Qubit (Life Technologies, Carlsbad, CA, USA) and Experion system (Bio-Rad, Hercules, CA, USA).
Paired-end cDNA libraries were prepared using Agilent SureSelect Strand Specific RNA library prep for sequencing on Illumina Hi-Seq 2000 platform at high coverage (100x2 bp reads) according to previous analysis.

treatment_protocol: HEK293 cells were transfected with PPARG and PPARGD5 expression vectors (1ug/ml) in by Lipofectamine 3000 (Life Technologies, Carlsbad, CA, USA), in culture medium without antibiotics and serum, according to manufacturer's instructions (transfection efficiency ≈ 95%). After 6 hours, transfected cells were fed with medium supplemented with 10% FBS and further treated.

tag: cell line

value: human embryonic kidney cell line

value: Troglitazone + co-expression of PPARG and PPARGD5


title: PPARG

description:
Cells over-expressing PPARG
PolyA RNA
processed data file: UQUA_normalized_counts.txt

value: Troglitazone + over-expression of PPARG


title: Control

description:
Control cells
PolyA RNA
processed data file: UQUA_normalized_counts.txt

value: Troglitazone


title: round_spermatids_KO_rep5

value: male

value: adult

value: adult testis

value: male germ cells

value: round spermatids


title: LR-V-EL38-C_FPKM

city: Beijing

first: Lei

last: He

address: No. 17 Tsinghua east road

country: China

institute: China Agricultural University

description: variety: Cabernet Sauvignon

data_processing:
The original image data was transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
The dirty raw reads including reads with adaptors, reads in which unknown bases are more than 10% and low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) were removed to get the clean reads.
Clean reads were mapped to reference grapevine genome V2 using Bowtie. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level was calculated by using FPKM method.
Genome_build: http://genomes.cribi.unipd.it/DATA/V2/V2.1/
Supplementary_files_format_and_content: Results include length, excepted_count and FPKM and the description of gene for each sample were shown in xlsx table files.

source_name: grape berry

growth_protocol: The sunlight exposure treatments were performed in a commercial vineyard of V. vinifera L. Cabernet Sauvignon located in Manas Country (44°17ˊ N, 86°12ˊ E), Xinjiang, China. This region was characterized by alkaline soil of pH 8.0, annual sunshine time of 3749.9 hours, annual precipitation of 117.2 mm and annual effective accumulated temperature of 3725.0°C. The own-rooted vines were planted in the year 2000 and arranged in north-south rows with 2.5 m × 1 m vine spacing. A modified Vertical-Shoot-Positioned (M-VSP) trellis system with a spur-pruned cordon retaining 15 nodes per linear meter, was trained to all the vines. Nutrition and pest management was carried out following local industry standards as described in previous publications

extract_protocol:
Three biological replicates for each sample were performed. A sub-sample of 50 berries were randomly selected from each biological replicate for RNA extraction. Total RNA was extracted from the frozen deseeded berries (whole pericarp) using a SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, CA, USA).  RNA integrity and quality were assessed by analysis with the Aglient 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: leaf removal treatment was carried out by stripping the first one to six basal leaves from the shoot with clusters at berry pepper-corn size (E-L 29; named as LR-PS) and veraison (E-L 35; LR-V), respectively. Half-leaf removal referred to removing three basal leaves from the first, third and fifth of each shoot with clusters and this treatment was implemented at veraison (abbreviated as HLR-V). Leaf moving treatment was carried out at veraison (abbreviated as LM-V) by carefully moving away the one to six basal leaves to a different position with nylon zipties to completely expose the cluster to sunlight. The grapevines without any treatment was take as the control. Both control and various treatments were arranged in a completely randomized experimental design with three biological replicates. And 15 vines with 15 fruiting shoots each vine and one cluster each shoot were selected for each replicate. The grape berry samples were collected at the stages of E-L 31, E-L 36, E-L 37 and E-L 38, respectively.

tag: cultivar

value: Cabernet Sauvignon

tag: Stage

value: LR-V


title: 1.oLT

description: outer region of lateral tibial plateau

source_name: Human knee articular cartilage

value: catilage

value: chondrocyte

value: normal

value: fresh


title: Control Sultana_1 [WRKY19 OE]

tag: genotype/variation

value: control

value: young leaves


title: WRKY19 OE Sultana_1

source_name: WRKY19 overexpressing plantlet of Vitis vinifera cv. Sultana_line 1

value: Sultana

value: WRKY19 overexpressing


title: LR-V-EL38-B_FPKM

description: variety: Cabernet Sauvignon


title: daf-16 500 mM NaCl replicate 3

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

description:
D17-2272
mRNA
processed data file: nburton_fpkm.txt

data_processing:
RSEM v. 1.2.15, with Bowtie v. 1.0.1 for read alignment (flags --paired-end -p 6 --bowtie-chunkmbs 1024 --forward-prob 0, for strand-specific libraries).
Genome_build: ce10 with 2015 Ensembl gene annotation.
Supplementary_files_format_and_content: nburton_fpkm.txt: Text file containing FPKM values generated by RSEM.

organism: Caenorhabditis elegans

source_name: embryos

growth_protocol: Wild-type, ssu-1(fc73), and daf-16(m26) embryos were placed on standard NGM plates.

extract_protocol:
After 3 hrs, embryos were collected in M9, lysed using a BeadBug microtube homogenizer (Sigma) and 0.5 mm Zirconium beads (Sigma), and RNA was extracted using the RNeasy Mini kit (QIAGEN).
Illumina NeoPrep.

treatment_protocol: 50 mM or 500mM NaCl.

tag: strain

value: embryos

tag: growth condition

value: 500 mM NaCl in media


title: LR-V-EL38-A_FPKM

description: variety: Cabernet Sauvignon


title: LR-V-EL37-C_FPKM

description: variety: Cabernet Sauvignon


title: LR-V-EL37-B_FPKM

description: variety: Cabernet Sauvignon


title: daf-16 500 mM NaCl replicate 2

description:
D17-2271
mRNA
processed data file: nburton_fpkm.txt


title: genomic DNA from healthy control  C17

type: genomic

city: Suzhou

first: Xingbo

last: Mo

address: Renai Road

institute: Soochow University

description:
healthy control
SAMPLE 42

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: female

value: peripheral blood mononuclear

tag: disease state

value: healthy control


title: LR-V-EL37-A_FPKM

description: variety: Cabernet Sauvignon

tag: treatment


title: LR-V-EL36-C_FPKM

description: variety: Cabernet Sauvignon


title: genomic DNA from healthy control  C15

description:
healthy control
SAMPLE 40


title: genomic DNA from healthy control  C14

description:
healthy control
SAMPLE 39


title: 2.oLT

description: outer region of lateral tibial plateau


title: daf-16 500 mM NaCl replicate 1

description:
D17-2270
mRNA
processed data file: nburton_fpkm.txt


title: daf-16 50 mM NaCl replicate 3

description:
D17-2269
mRNA
processed data file: nburton_fpkm.txt

value: 50 mM NaCl in media


title: MacaqueCochlea_MacaqueArray_rep2

city: Tokyo

first: Hideki

last: Mutai

address: 2-5-1 Higashigaoka, Meguro-ku

department: National Institute of Sensory Organs Div Hearing and Balance Research

institute: National Hospital Organization Tokyo Medical Center

hyb_protocol: Ten microgram of aRNA was hybridized on GeneChip for 16 hours at 45 C.

scan_protocol: The microarrays were washed and stained in the Affymetrix Fluidcs Station 450. The stained GeneChips were scanned using the Affymetris Scanner 3000-7G. The images were digitalized using GeneChip Operating Software (GCOS) v1.3 (Affymetrix)

data_processing: The data were normalized using the MAS5 algorithm (Affymetrix). The intensities were converted to a logarithmic scale (base 2). To correct for bias between arrays, we then performed quantile normalization to all array data using R software (“affy” and “limma” packages). The signal reliability of each probe was determined based on the MAS5 Call algorithm (Affymetrix)

organism: Macaca fascicularis

source_name: crab-eating macaque, whole right cochlea at Tsukuba Primate Research Center, National Institute of Biomedical Innovation.

label_protocol: Preparation of biotinylated aRNA from 250 ng total RNA was according to the manufacturer’s protocols (Affiymetrix, CA, USA).

extract_protocol: Whole cochlear tissues were dissected within 30 minutes after euthanatizing the animal,  and homogenized in acidic phenol (ISOGEN-II, Nippon-gene, Toyama, Japan). Extracted RNA was purified using RNeasy Mini kit (QIAGEN, Humburg, Germany).

tag: age

value: 5 years old

tag: Sex

value: male

value: cochlea


title: genomic DNA from healthy control  C16

description:
healthy control
SAMPLE 41


title: genomic DNA from healthy control  C02

description:
healthy control
SAMPLE 27


title: LR-V-EL36-A_FPKM

description: variety: Cabernet Sauvignon

value: Cabernet Sauvignon

value: LR-V


title: genomic DNA from healthy control  C18

description:
healthy control
SAMPLE 43


title: genomic DNA from healthy control  C09

description:
healthy control
SAMPLE 34


title: daf-16 50 mM NaCl replicate 2

description:
D17-2268
mRNA
processed data file: nburton_fpkm.txt


title: genomic DNA from healthy control  C10

description:
healthy control
SAMPLE 35


title: genomic DNA from healthy control  C08

description:
healthy control
SAMPLE 33


title: LM-V-EL38-C_FPKM

description: variety: Cabernet Sauvignon

value: LM-V


title: genomic DNA from healthy control  C05

description:
healthy control
SAMPLE 30


title: genomic DNA from healthy control  C12

description:
healthy control
SAMPLE 37


title: genomic DNA from healthy control  C04

description:
healthy control
SAMPLE 29


title: daf-16 50 mM NaCl replicate 1

description:
D17-2267
mRNA
processed data file: nburton_fpkm.txt


title: genomic DNA from healthy control  C06

description:
healthy control
SAMPLE 31


title: genomic DNA from healthy control  C13

description:
healthy control
SAMPLE 38


title: genomic DNA from healthy control  C01

description:
healthy control
SAMPLE 26


title: genomic DNA from healthy control  C03

description:
healthy control
SAMPLE 28


title: N2 500 mM NaCl replicate 6

description:
D17-2266
mRNA
processed data file: nburton_fpkm.txt

value: Bristol strain N2


title: genomic DNA from RA patient A22

description:
rheumatoid arthritis
SAMPLE 22

value: rheumatoid arthritis


title: LM-V-EL38-B_FPKM

description: variety: Cabernet Sauvignon


title: LR-V-EL36-B_FPKM

description: variety: Cabernet Sauvignon


title: LM-V-EL38-A_FPKM

description: variety: Cabernet Sauvignon


title: MacaqueCochlea_MacaqueArray_rep1

source_name: crab-eating macaque, whole left cochlea at Tsukuba Primate Research Center, National Institute of Biomedical Innovation.


title: N2 500 mM NaCl replicate 5

description:
D17-2265
mRNA
processed data file: nburton_fpkm.txt


title: MacaqueCochlea_HumanArray_rep2


title: SUZ12

first: Martin

last: Allday

state: London

address: Norfolk Place

department: Medicine

institute: Imperial College London

description: Chromatin immunoprecipitated DNA with anti SUZ12

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
Sequence reads were mapped to the human genome (vhg19) downloaded from UCSC using BWA
Binding regions were identified using the MACS v2.1.0 peak-calling algorithm comparing the sample to a control input sample. Peaks were defined as significant with a q value cut-off of 5.00e-02. For SUZ12 --broad -- nomodel parameters were used
Genome_build: hg19
Supplementary_files_format_and_content: bed files with called peaks

source_name: LCL

growth_protocol: Lymphoblastoid cell lines (LCLs) were created by recombinant EBV infection of isolated CD19 +ve B cells from buffy coat from a blood donor (D11)

extract_protocol:
15 x 10^6 cells were fixed for 10 mins in 1% formaldehyde at room temperature and then washed, resuspended in swelling buffer (25 M HEPES, pH 7.8; 1.5 mM MgCl2; 10 mM KCl, 0.1% NP-40; 1 mM DTT; 1 mM PMSF; 1 μg/ml aprotinin; 1 μg/ml pepstatin A) and incubated at 4oC for 20 mins with rotation. The swelling buffer was aspirated after centrifugation. Τhe pelleted nuclei were resuspended in 1 ml sonication buffer (50 mM HEPES pH 7.9; 140 mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% sodium deoxycholate; 0.1% SDS; 1 mM PMSF; 1 μg/ml aprotinin; 1 μg/ml pepstatin A), incubated on ice for 30 mins and then sonicated for 1 hour with a Covaris M220 Focused-ultrasonicator with milliTUBE holder (peak power 75; duty factor 26; cycles/burst 200; temperature 6oC). The lysate was centrifuged at 10,000g for 10 mins at 4oC and the 1 ml supernatant was diluted with 3.2 ml sonication buffer. 200 μl of the sonicated lysate were taken for input control. Lysates were incubated overnight with 16µg of the relevant antibody and 120µl of ChIP-grade protein G magnetic beads (NEB, #9006) at 4oC in a 15ml Falcon tube on rollers. The following day the beads were washed with standard ChIP wash buffers, 4ml buffer for each wash for 15 minutes at 4oC on rollers. Precipitated chromatin was eluted in 400µl of elution buffer, the eluate was treated with RNase, formaldehyde cross-links were reversed before proteinase K treatment and DNA was cleaned with a Qiagen PCR purification MinElute kit, for ChIP sample and input control.
DNA from ChIP was run on a 2% agarose gel (Bio-Rad Low Range Ultra, #161-3107) and DNA between 100-500bp was excised and purified using the Qiagen MinElute gel purification kit, according to manufacturing instructions. At least 5ng of DNA for each sample was then sent to the Harvard Biopolymers facility for library construction (ChIP-Seq Wafergen) and sequencing (Illumina HiSeq 2500, 50bp single-reads).

tag: chip antibody

value: anti-SUZ12; Abcam; ab12073

value: lymphoblastoid cell line


title: genomic DNA from RA patient A25

description:
rheumatoid arthritis
SAMPLE 25


title: genomic DNA from healthy control  C11

description:
healthy control
SAMPLE 36


title: genomic DNA from RA patient A21

description:
rheumatoid arthritis
SAMPLE 21


title: genomic DNA from RA patient A20

description:
rheumatoid arthritis
SAMPLE 20


title: genomic DNA from RA patient A23

description:
rheumatoid arthritis
SAMPLE 23


title: BMI1

description: Chromatin immunoprecipitated DNA with anti BMI1

value: anti-BMI1; Bethyl Laboratories; A301-694A


title: genomic DNA from RA patient A24

description:
rheumatoid arthritis
SAMPLE 24


title: LM-V-EL37-C_FPKM

description: variety: Cabernet Sauvignon


title: genomic DNA from healthy control  C07

description:
healthy control
SAMPLE 32


title: N2 500 mM NaCl replicate 4

description:
D17-2264
mRNA
processed data file: nburton_fpkm.txt

value: embryos


title: LM-V-EL37-B_FPKM

description: variety: Cabernet Sauvignon


title: Input2

description: Second input control


title: LM-V-EL36-C_FPKM

description: variety: Cabernet Sauvignon


title: LM-V-EL37-A_FPKM

description: variety: Cabernet Sauvignon


title: N2 50 mM NaCl replicate 4

description:
D17-1629
mRNA
processed data file: nburton_fpkm.txt


title: genomic DNA from RA patient A19

description:
rheumatoid arthritis
SAMPLE 19


title: MacaqueCochlea_HumanArray_rep1


title: N2 50 mM NaCl replicate 3

description:
D17-1628
mRNA
processed data file: nburton_fpkm.txt


title: LM-V-EL36-B_FPKM

description: variety: Cabernet Sauvignon


title: ssu-1 500 mM NaCl replicate 3

description:
D16-11319
mRNA
processed data file: nburton_fpkm.txt

value: 500 mM NaCl in media


title: N2 50 mM NaCl replicate 5

description:
D17-2263
mRNA
processed data file: nburton_fpkm.txt


title: LM-V-EL36-A_FPKM

description: variety: Cabernet Sauvignon


title: L1_reference_6

first: David

last: Miller

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

description:
AVK_RPKM
processed_data_column_header: CTRL_edgeR-2983-DMM-19_1_sequence

data_processing:
Reads were mapped and analyzed using CLC Genomics Workbench Version 11. Mapping done with CLC Genomics Workbench reference genome for C. elegans
The Empirical analysis of DGE tool was used to analyze differential expression between AVK and L1 reference groups.
EdgeR Bioconductor package and Exact Test for two-group comparisons are both incorporated for the EDGE test (see CLC Genomics Workbench Vesion 11 description).
A Principle Component Analysis was performed on all datasets to verify quality of RNA seq data and to determine variability between groups.
Genome_build: C. elegans reference genome
Supplementary_files_format_and_content: excel file includes RPKM for AVK enriched genes

source_name: Whole L1 worm reference

growth_protocol: Embryos were obtained by hypochlorite treatment of adult hermaphrodites were allowed to hatch overnight in M9 buffer as L1 larvae.

extract_protocol:
Dissociated larval cells and RNA extractions were generated as described (Spencer et al., PLoS ONE, 2014). Reference RNA samplesfrom all larval cells were obtained from synchronized L1 larvae quick froizen in liquid nitrogen. cDNA synthesis was prepared using Clonetech Smart-Seq V3 Ultra Low Input RNA Kit
RNA libraries were prepared for sequencing using standard Illumina HiSeq 2500

treatment_protocol: A truncated flp-1 promoter [flp-1(trc)] was used to limit AVK expression. AVK::mCherry expression is limited to AVK neurons. mCherry-labeled AVK neurons were isolated by FACS and collected in Trizol

value: L1 synchronized animals

tag: cell isolation strategy

value: All cells, frozen over LN2


title: L1_reference_5

description:
AVK_RPKM
processed_data_column_header: CTRL_edgeR-2983-DMM-18_1_sequence


title: ssu-1 500 mM NaCl replicate 2

description:
D16-11318
mRNA
processed data file: nburton_fpkm.txt


title: Control-EL38-B_FPKM

description: variety: Cabernet Sauvignon

value: Control


title: L1_reference_4

description:
AVK_RPKM
processed_data_column_header: CTRL_edgeR-2983-DMM-17_1_sequence


title: Input1

description: Input control


title: genomic DNA from RA patient A18

description:
rheumatoid arthritis
SAMPLE 18

value: female

value: peripheral blood mononuclear


title: ssu-1 50 mM NaCl replicate 1

description:
D16-11315
mRNA
processed data file: nburton_fpkm.txt

value: 50 mM NaCl in media


title: L1_reference_2

description:
AVK_RPKM
processed_data_column_header: CTRL_edgeR-2983-DMM-15_1_sequence


title: L1_reference_3

description:
AVK_RPKM
processed_data_column_header: CTRL_edgeR-2983-DMM-16_1_sequence


title: ssu-1 50 mM NaCl replicate 2

description:
D16-11316
mRNA
processed data file: nburton_fpkm.txt


title: L1_reference_1

description:
AVK_RPKM
processed_data_column_header: CTRL_edgeR-2983-DMM-14_1_sequence


title: ssu-1 500 mM NaCl replicate 1

description:
D16-11317
mRNA
processed data file: nburton_fpkm.txt


title: Control-EL38-C_FPKM

description: variety: Cabernet Sauvignon


title: AVK_L1_5

description:
AVK_RPKM
processed_data_column_header: AVK_edgeR-2983-DMM-41_1_sequence

source_name: Isolated L1 AVK neurons

value: FACS sorting to isolate AVK


title: Control-EL37-B_FPKM

description: variety: Cabernet Sauvignon

value: Cabernet Sauvignon


title: N2 500 mM NaCl replicate 3

description:
D16-11313
mRNA
processed data file: nburton_fpkm.txt


title: genomic DNA from RA patient A16

description:
rheumatoid arthritis
SAMPLE 16


title: genomic DNA from RA patient A12

description:
rheumatoid arthritis
SAMPLE 12


title: genomic DNA from RA patient A14

description:
rheumatoid arthritis
SAMPLE 14


title: genomic DNA from RA patient A17

description:
rheumatoid arthritis
SAMPLE 17


title: Control-EL37-C_FPKM

description: variety: Cabernet Sauvignon


title: genomic DNA from RA patient A15

description:
rheumatoid arthritis
SAMPLE 15


title: genomic DNA from RA patient A13

description:
rheumatoid arthritis
SAMPLE 13


title: N2 500 mM NaCl replicate 2

description:
D16-11312
mRNA
processed data file: nburton_fpkm.txt


title: Control-EL37-A_FPKM

description: variety: Cabernet Sauvignon


title: AVK_L1_4

description:
AVK_RPKM
processed_data_column_header: AVK_edgeR-2983-DMM-40_1_sequence


title: N2 500 mM NaCl replicate 1

description:
D16-11311
mRNA
processed data file: nburton_fpkm.txt


title: AVK_L1_1

description:
AVK_RPKM
processed_data_column_header: AVK_edgeR-2983-DMM-10_1_sequence


title: Control-EL36-C_FPKM

description: variety: Cabernet Sauvignon


title: genomic DNA from RA patient A09

description:
rheumatoid arthritis
SAMPLE 9


title: N2 50 mM NaCl replicate 2

description:
D16-11310
mRNA
processed data file: nburton_fpkm.txt


title: Control-EL36-B_FPKM

description: variety: Cabernet Sauvignon


title: Control-EL36-A_FPKM

description: variety: Cabernet Sauvignon


title: Control-EL38-A_FPKM

description: variety: Cabernet Sauvignon


title: genomic DNA from RA patient A08

description:
rheumatoid arthritis
SAMPLE 8


title: genomic DNA from RA patient A11

description:
rheumatoid arthritis
SAMPLE 11


title: genomic DNA from RA patient A06

description:
rheumatoid arthritis
SAMPLE 6


title: 16h_4

status: Public on Oct 13 2018

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, Mainz

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with STAR_2.4.0h to the BDGP6 reference genome
Secondary alignments were filtered with samtools 1.2
Counts for every gene were calculated with HTSeq-0.6.1p1 using the gene model provided with Ensembl version 79 for BDGP6
Genome_build: dm6
Supplementary_files_format_and_content: tab separated file containing counts per gene

molecule: polyA RNA

source_name: whole embryo_16h

growth_protocol: Population cages of wild-type Oregon R flies containing only fertilized females were maintained at 25°C.

extract_protocol:
Embryos were dechorionated using 7.5% hypochlorite for 2 min and rinsed with water. At this point, approximately 30% of the embryos (20 µl embryo pellets) were transferred to PBS buffer. Total RNA was extracted from approximately 20 µl embryo pellets with the RNeasy Mini Kit (Qiagen) and RNA integrity checked by Bioanalyzer.
NGS library prep was performed with Illumina’s TruSeq stranded mRNA LT Sample Prep Kit following Illumina’s standard protocol (Part #15031047 Rev. E). Libraries were prepared with a starting amount of 500 ng and amplified in 11 PCR cycles. All 68 embryo samples were pooled in equimolar ratio and sequenced on 8 HiSeq 2500 lanes, SR for 1x 51 cycles plus 7 cycles for the index read.

value: whole embryo

tag: developmental stage


title: 18h_3

source_name: whole embryo_18h


title: 20h_4

source_name: whole embryo_20h


title: genomic DNA from RA patient A05

description:
rheumatoid arthritis
SAMPLE 5


title: 16h_1


title: 16h_2


title: 20h_2


title: 20h_1


title: 18h_2


title: 18h_4


title: AVK_L1_2

description:
AVK_RPKM
processed_data_column_header: AVK_edgeR-2983-DMM-12_1_sequence


title: genomic DNA from RA patient A04

description:
rheumatoid arthritis
SAMPLE 4


title: genomic DNA from RA patient A03

description:
rheumatoid arthritis
SAMPLE 3


title: 20h_3


title: 16h_3


title: 14h_3

source_name: whole embryo_14h


title: genomic DNA from RA patient A10

description:
rheumatoid arthritis
SAMPLE 10


title: 18h_1


title: genomic DNA from RA patient A07

description:
rheumatoid arthritis
SAMPLE 7


title: 12h_2

source_name: whole embryo_12h


title: 12h_1


title: genomic DNA from RA patient A02

description:
rheumatoid arthritis
SAMPLE 2


title: 10h_4

source_name: whole embryo_10h


title: 10h_2


title: 10h_1


title: 14h_2


title: 14h_4


title: 14h_1


title: genomic DNA from RA patient A01

description:
rheumatoid arthritis
SAMPLE 1


title: 12h_4


title: 08h_1

source_name: whole embryo_08h


title: 12h_3


title: 06h_4

source_name: whole embryo_06h


title: 08h_2


title: 08h_4


title: 10h_3


title: 06h_3


title: 08h_3


title: 06h_1


title: 06h_2


title: 05h_2

source_name: whole embryo_05h


title: 05h_4


title: 05h_1


title: 05h_3


title: 04h_4

source_name: whole embryo_04h


title: 04h_3


title: 03h_4

source_name: whole embryo_03h


title: 04h_1


title: 03h_2


title: 03h_3


title: 02h_4

source_name: whole embryo_02h


title: 02h_2


title: 01h_4

source_name: whole embryo_01h


title: 02h_1


title: 02h_3


title: 00h_4

source_name: whole embryo_00h


title: 01h_3


title: 01h_1


title: 00h_1


title: 00h_3


title: 00h_2


title: TenxNuc_healthy

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

description:
single nucleus RNA-seq
Processed data file: Healthy.combined.dge.txt.gz

data_processing:
We used a newly developed pipeline, zUMIs (Parekh et al., 2018), to process the single cell and single nucleus sequencing data from mouse kidney. In brief, we first filtered out the low-quality barcodes or UMIs based on sequence with the internal read filtering algorithm built in zUMIs. We then used zUMIs to map the filtered reads to mouse reference genome (mm10) using STAR 2.5.3a (two-pass mapping mode). Next, zUMIs quantified the reads uniquely mapped to exonic or intronic reads and inferred the true barcodes that mark cells by fitting a k-dimensional multivariate normal distribution with mclust package. Finally, a UMI count table utilizing both exonic and intronic reads were generated for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: The .txt files report gene-level raw UMI count matrices.  The .txt files' column headers contain barcode sequences.

source_name: Kidney

extract_protocol:
[Single cell dissociation protocol] Kidney from a C57BL/6 mouse was minced into 1 mm pieces with a razor blade and incubated at 37 ˚C in enzyme dissociation buffer containing 250 U/ml Liberase (Roche) and 40 U/ml DNase I. After 10 min, the solution was transferred to a Miltenyi C-tube and the gentleMACS D1 program was run (Miltenyi). Cells were further digested for additional 10 min with trituration, and the reaction was stopped by adding 10% fetal bovine serum. The dissociated cells were pelleted by centrifugation (500 g, 5 min), washed twice, passed through a 35 µM FACS tube (Falcon) and pelleted again by centrifugation (500 g, 5 min). Cells were resuspended in PBS+1%BSA and purified by FACS with optimal gates set for side scatter and forward scatter.
[Nuclei extraction protocol] Nuclei were isolated with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with protease inhibitor (Roche #5892791001) and RNase inhibitor (Promega #N2615, Life Technologies #AM2696). Samples were cut into <2 mm pieces and homogenized using a Dounce homogenizer (Kimble Chase #885302-0002) in 2ml of ice-cold Nuclei EZ Lysis buffer and incubated on ice for 5 min with an additional 2ml of lysis buffer. The homogenate was filtered through a 40-µm cell strainer (pluriSelect #43-50040-51) and then centrifuged at 500 x for 5 min at 4 ºC. The pellet was resuspended and washed with 4 ml of the buffer and incubated on ice for 5 min. After another centrifugation, the pellet was resuspended with Nuclei Suspension Buffer (1x PBS, 0.07% BSA, 0.1% RNase inhibitor), filtered through a 20-µm cell strainer (pluriSelect 43-50020-50) and counted. We used the inDrops protocol developed by Klein et al to generate single nucleus transcriptome.
[Dropseq protocol] We used the DropSeq protocol described by Mackosco et al to generate the single cell transcriptomes
[sNuc-Dropseq protocol] We adapted the DropSeq platform to profile single nucleus with the methods reported by Hu et al  (Mol Cell, 2017)
[DroNcSeq protocol] We used soft lithography techniques to fabricate the DroNc-seq silicon master microfluidic devices. DroNc was performed as previously described by Habib et al (Nature Methods, 2017)
[sNuc-10x protocol] We followed the guideline provided by the manufacturer (10x Genomics) to generate single nucleus transcriptomes
RNA libraries were prepared for sequencing using standard Dropseq and 10X Chromium procedure
single cell/nucleus RNA-seq

tag: protocol

value: Single nucleus isolation

tag: disease state (group)

value: Healthy

tag: platform

value: TenxNuc


title: TenxNuc_UUO

description:
single nucleus RNA-seq
Processed data file: UUO.dge.txt.gz

value: Day14 UUO


title: 03h_1

tag: tissue


title: DroNcSeq_healthy

value: DroNcSeq


title: 04h_2


title: 01h_2


title: RiboTag Affinity Purification D2-MSN, Male, Rep 6

city: New York City

first: Felix

last: Richter

address: 1470 Madison Ave, New York, NY 10029

institute: Icahn School of Medicine at Mount Sinai

data_processing:
HISAT2 (2.0.5)
Rsubread (1.26.1), Mus_musculus.GRCm38.90, featurecounts settings strandSpecific=0 allowMultiOverlap=T, countMultiMappingReads=F, isPairedEnd=T, GTF.featureType = "gene"
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file with counts per gene per sample

source_name: D2 medium spiny neurons

growth_protocol: Mice used for nuclear isolation heterozygously expressed a nuclear GFP label under the promoter of either Drd1 or Drd2 (Drd1-cre x Thy1-loxPSTOPloxP-EGFP-F; Drd2-cre x Thy1-loxPSTOPloxP-EGFP-F). Mice used for whole cell isolation heterozygously expressed a cytoplasmic fluorophore under the promoter of either Drd1 or Drd2. Mice used for RiboTag affinity purification expressed an HA-tagged ribosomal subunit under the control of Drd1 and Drd2 (Drd1-cre x Rpl22-loxPexon4loxP-exon4-HA; Drd2-cre x Rpl22-loxPexon4loxP-exon4-HA).

extract_protocol:
Each sample represents tissue from a unique mouse. Nuclear samples were obtained from frozen tissue. This tissue was mechanically dissociated and nuclei lysed using a glass douncer in ice-cold lysis buffer (10.94% w/v sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 0.1 mM EDTA, 10 mM Tris-HCl pH 8, 1 mM DTT, in H2O). Samples were centrifuged and supernatant removed and placed on top of a 60% sucrose solution (60% w/v sucrose, 3 mM Mg(CH3COO)2, 10 mM Tris-HCl pH 8, 1 mM DTT, in H2O). The sucrose gradient was centrifuged at 24,400 rcf for an hour, and nuclei at the bottom of the gradient were resuspended in PBS. DAPI was added at a concentration of 0.5 μg/mL. Whole cell samples were obtained from fresh tissue, which was rotated at 37°C for 45 minutes in 1 mg/mL papain suspended in digestion buffer (5% w/v D-trehalose, 0.05 mM APV, 0.0125 mg/mL DNAse, in HibernateTM-A (Thermofisher, A1247501)). Tissue was then placed in FACS buffer (0.58 mg/mL albumin inhibitor (Worthington Biochemical, LK003182), 5% w/v D-trehalose, 0.05 mM APV, 0.0125 mg/mL DNAse, in HibernateTM-A) and triturated using progressively smaller pipette tips. Samples were passed through a 70 µm filter and placed on top of a layer of 10 mg/mL ovomucoid-albumin in FACS buffer. The pellet was resuspended in FACS buffer and DAPI was added at a concentration of 0.5 μg/mL. RiboTag samples were obtained from fresh tissue as previously described (see PMID 25995477, 29268097).
All isolated RNA was prepared using the Clontech SMARTer® Stranded library preparation kit (cat. no. 634838). Briefly, samples were ribo-depleted, and total RNA was reversed transcribed, classified using Illumina indices and amplified with 8 cycles of PCR. Samples were sequenced to a minimum depth of 30 million reads using paired-end reads with V4 chemistry on an Illumina Hi-Seq machine.

value: brain

tag: molecule

value: ribosomal RNA


title: RiboTag Affinity Purification D2-MSN, Male, Rep 5


title: RiboTag Affinity Purification D2-MSN, Male, Rep 4


title: RiboTag Affinity Purification D2-MSN, Male, Rep 2


title: sNucDropseq_healthy

value: sNucDropseq


title: RiboTag Affinity Purification D2-MSN, Male, Rep 1


title: RiboTag Affinity Purification D2-MSN, Female, Rep 5


title: RiboTag Affinity Purification D2-MSN, Female, Rep 4


title: RiboTag Affinity Purification D2-MSN, Female, Rep 3


title: RiboTag Affinity Purification D2-MSN, Female, Rep 2


title: Mouse 13.5 Tgfbr2_Knockout Tgfbr2 Maxilla Distal Replicate 2

city: Los Angeles

first: Michael

last: Kesling

address: 2250 Alcazar Street

institute: University of Southern California

description: Gene Expression

hyb_protocol: Following fragmentation, 12 µg of cRNA was hybridized for 16hr on Affymetrix Mouse 430_2 (gene version) as recommended by the manufacturer.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The probe level data was summarized to gene level and was analyzed with PGS 6.6. RMA (Robust Multi array average) normalization was used.

source_name: mouse embryo stage 13.5

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Qiagen Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturer's instructions.

extract_protocol: RNA was extracted from tissues using RNeasy kit (Qiagen Valenica, CA).

tag: strain/background

value: Maxilla

tag: tissue compartment

value: Distal

value: Tgfbr2 Knockout


title: Mouse 13.5 Tgfbr2_Knockout Tgfbr2 Mandible Proximal Replicate 3

description: Gene Expression

value: Mandible

value: Proximal

tag: genotype/variation


title: RiboTag Affinity Purification D2-MSN, Male, Rep 3

tag: strain


title: Mouse 13.5 Tgfbr2_Knockout Tgfbr2 Mandible Distal Replicate 3

description: Gene Expression


title: Mouse 13.5 Tgfbr2_Knockout Tgfbr2 Maxilla Proximal Replicate 2

description: Gene Expression


title: RiboTag Affinity Purification D2-MSN, Female, Rep 1


title: Mouse 13.5 Tgfbr2_Knockout Tgfbr2 Mandible Distal Replicate 1

description: Gene Expression


title: Mouse 13.5 Tgfbr2_Knockout Tgfbr2 Mandible Proximal Replicate 1

description: Gene Expression


title: Mouse 13.5 Tgfbr2_Knockout Tgfbr2 Maxilla Distal Replicate 3

description: Gene Expression


title: Mouse 13.5 Tgfbr2_Knockout Tgfbr2 Maxilla Proximal Replicate 1

description: Gene Expression


title: Mouse 13.5 Tgfbr2_Knockout Tgfbr2 Mandible Distal Replicate 2

description: Gene Expression


title: Mouse 13.5 Tgfbr2_Knockout Tgfbr2 Mandible Proximal Replicate 2

description: Gene Expression


title: RiboTag Affinity Purification D1-MSN, Male, Rep 5

source_name: D1 medium spiny neurons


title: RiboTag Affinity Purification D1-MSN, Male, Rep 6


title: Mouse 13.5 Control Tgfbr2 Mandible Proximal Replicate 3

description: Gene Expression

value: Control


title: Mouse 13.5 Control Tgfbr2 Maxilla Proximal Replicate 3

description: Gene Expression


title: Mouse 13.5 Tgfbr2_Knockout Tgfbr2 Maxilla Distal Replicate 1

description: Gene Expression


title: RiboTag Affinity Purification D1-MSN, Male, Rep 4


title: Mouse 13.5 Tgfbr2_Knockout Tgfbr2 Maxilla Proximal Replicate 3

description: Gene Expression


title: Mouse 13.5 Control Tgfbr2 Maxilla Distal Replicate 3

description: Gene Expression


title: RiboTag Affinity Purification D1-MSN, Male, Rep 3


title: RiboTag Affinity Purification D1-MSN, Male, Rep 2


title: RiboTag Affinity Purification D1-MSN, Male, Rep 1


title: AVK_L1_3

city: Nashville

description:
AVK_RPKM
processed_data_column_header: AVK_edgeR-2983-DMM-39_1_sequence

source_name: Isolated L1 AVK neurons

value: L1 synchronized animals

value: FACS sorting to isolate AVK


title: FGR, rep20

city: Toronto

first: Brian

last: Cox

state: Ontario

address: 1 King's College Circle

department: Physiology

institute: University of Toronto

description:
Sample_21922
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

hyb_protocol: Hybridization was performed by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrix protocols.

scan_protocol: Scanning was performed by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrix protocols.

data_processing: Data was processed, normalized, converted into log2 values, and batch corrected in R using the oligo, virtualArray, and sva libraries from Bioconductor. Genes with mean expression values in the bottom quartile across all placentas were removed to avoid confounding with background noise.

label: Biotin

source_name: Human placenta associated with an SGA infant with suspected FGR

label_protocol: Biotinylated cDNA was prepared by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrix protocols.

extract_protocol: A 100 mg aliquot was used to prepare an mRNA extract using Trizol followed by RNeasy spin columns. RNA purity and integrity were determined using 28S to 18S rRNA ratio (Agilent Bioanalyzer).

treatment_protocol: Four tissue biopsies (one sample/quadrant, excluding the chorionic plate) are collected per placenta, rinsed in PBS to remove contaminating maternal blood, pooled, snap-frozen in liquid nitrogen, and crushed into a powder.

value: Placenta

tag: maternal age (years)

tag: maternal ethnicity

tag: maternal blood type

value: B

tag: maternal pre-pregnancy weight (kg)

tag: maternal height (cm)

tag: maternal bmi

tag: gestational age at delivery (weeks)

tag: gestational age at delivery (days)

tag: placental weight (g)

tag: mode of delivery

value: c-section

tag: fetal sex

value: M

tag: newborn weight z-score

tag: apgar at 1min

tag: apgar at 5min

tag: max left uterine artery pi

tag: max right uterine artery pi

tag: max umbilical artery pi

tag: placental thickness (cm)

tag: cord diameter (cm)

tag: max systolic blood pressure (mmhg)

tag: max diastolic blood pressure (mmhg)


title: Mouse 13.5 Control Tgfbr2 Maxilla Proximal Replicate 2

description: Gene Expression

tag: strain/background

tag: tissue

tag: tissue compartment

tag: genotype/variation

tag: developmental stage


title: Mouse 13.5 Control Tgfbr2 Maxilla Distal Replicate 2

description: Gene Expression


title: FGR, rep15

description:
Sample_11620
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: maternal age (years)

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

value: A

tag: maternal pre-pregnancy weight (kg)

tag: maternal height (cm)

tag: maternal bmi

tag: gestational age at delivery (weeks)

tag: gestational age at delivery (days)

tag: placental weight (g)

tag: mode of delivery

value: vaginal


title: FGR, rep18

description:
Sample_13795
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: fetal sex

tag: newborn weight z-score

tag: apgar at 1min

tag: apgar at 5min

tag: max left uterine artery pi

tag: max right uterine artery pi

tag: max umbilical artery pi

tag: placental thickness (cm)

tag: cord diameter (cm)

tag: max systolic blood pressure (mmhg)


title: FGR, rep19

description:
Sample_14071
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: tissue

tag: maternal age (years)

tag: maternal ethnicity

tag: maternal blood type

tag: maternal pre-pregnancy weight (kg)

value: F

tag: max diastolic blood pressure (mmhg)


title: FGR, rep17

description:
Sample_13452
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

value: O

tag: maternal height (cm)

tag: maternal bmi

tag: gestational age at delivery (weeks)

tag: gestational age at delivery (days)

tag: placental weight (g)

tag: mode of delivery


title: RiboTag Affinity Purification D1-MSN, Female, Rep 3

tag: strain

value: brain

tag: molecule

value: ribosomal RNA


title: RiboTag Affinity Purification D1-MSN, Female, Rep 5


title: Mouse 13.5 Control Tgfbr2 Maxilla Proximal Replicate 1

description: Gene Expression

tag: strain/background

value: Maxilla

tag: tissue compartment

tag: genotype/variation

tag: developmental stage


title: RiboTag Affinity Purification D1-MSN, Female, Rep 4

tag: tissue


title: Mouse 13.5 Control Tgfbr2 Mandible Distal Replicate 3

description: Gene Expression

value: Mandible

value: Distal


title: FGR, rep16

description:
Sample_11945
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: maternal age (years)

tag: maternal ethnicity

value: Black

tag: fetal sex

tag: newborn weight z-score

tag: apgar at 1min

tag: apgar at 5min

tag: max left uterine artery pi

tag: max right uterine artery pi

tag: max umbilical artery pi

tag: placental thickness (cm)

tag: cord diameter (cm)

tag: max systolic blood pressure (mmhg)


title: FGR, rep13

description:
Sample_10601
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: maternal blood type

tag: maternal pre-pregnancy weight (kg)

tag: maternal height (cm)

tag: maternal bmi

tag: gestational age at delivery (weeks)

tag: gestational age at delivery (days)

tag: placental weight (g)

tag: mode of delivery

tag: max diastolic blood pressure (mmhg)


title: Mouse 13.5 Control Tgfbr2 Mandible Proximal Replicate 2

description: Gene Expression

tag: strain/background

tag: tissue

tag: tissue compartment

value: Proximal

tag: genotype/variation

value: Control

tag: developmental stage


title: RiboTag Affinity Purification D1-MSN, Female, Rep 2

tag: strain

tag: molecule


title: FGR, rep11

description:
Sample_10462
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

value: Placenta

tag: maternal age (years)

tag: maternal ethnicity

tag: fetal sex

tag: newborn weight z-score

tag: apgar at 1min

tag: apgar at 5min

tag: max left uterine artery pi

tag: max right uterine artery pi

tag: max umbilical artery pi

tag: placental thickness (cm)

tag: cord diameter (cm)

tag: max systolic blood pressure (mmhg)


title: FGR, rep14

description:
Sample_11425
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: tissue

tag: maternal blood type

tag: maternal pre-pregnancy weight (kg)

tag: maternal height (cm)

tag: maternal bmi

tag: gestational age at delivery (weeks)

tag: gestational age at delivery (days)

tag: placental weight (g)

tag: mode of delivery

tag: max diastolic blood pressure (mmhg)


title: FGR, rep12

description:
Sample_10525
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: maternal age (years)

tag: maternal ethnicity

tag: fetal sex

tag: newborn weight z-score

tag: apgar at 1min

tag: apgar at 5min


title: FGR, rep10

description:
Sample_9821
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

value: East Asian

tag: max left uterine artery pi

tag: max right uterine artery pi

tag: max umbilical artery pi

tag: placental thickness (cm)

tag: cord diameter (cm)

tag: max systolic blood pressure (mmhg)


title: FGR, rep9

description:
Sample_9583
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: tissue

value: East Indian

tag: maternal blood type

value: B

tag: maternal pre-pregnancy weight (kg)

tag: maternal height (cm)

tag: maternal bmi

tag: gestational age at delivery (weeks)


title: RiboTag Affinity Purification D1-MSN, Female, Rep 1

tag: strain

tag: molecule


title: Mouse 13.5 Control Tgfbr2 Maxilla Distal Replicate 1

description: Gene Expression

tag: strain/background

tag: tissue compartment

tag: genotype/variation

tag: developmental stage


title: Mouse 13.5 Control Tgfbr2 Mandible Distal Replicate 2

description: Gene Expression


title: N2 50 mM NaCl replicate 1

description:
D16-11309
mRNA
processed data file: nburton_fpkm.txt

source_name: embryos

value: Bristol strain N2

value: embryos

tag: growth condition

value: 50 mM NaCl in media


title: Mouse 13.5 Control Tgfbr2 Mandible Distal Replicate 1

description: Gene Expression


title: Mouse 13.5 Control Tgfbr2 Mandible Proximal Replicate 1

description: Gene Expression


title: Mouse E13.5 Alk5_Knockout Alk5 Maxilla Proximal Replicate 4

description: Gene Expression

source_name: mouse embryo stage E13.5

value: Alk5 Knockout


title: FGR, rep8

description:
Sample_9535
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: maternal age (years)

tag: maternal ethnicity

value: Caucasian

value: O

tag: gestational age at delivery (days)

tag: placental weight (g)

tag: mode of delivery

value: vaginal

tag: fetal sex

value: F

tag: newborn weight z-score

tag: apgar at 1min

tag: apgar at 5min

tag: max left uterine artery pi

tag: max right uterine artery pi

tag: max umbilical artery pi

tag: max diastolic blood pressure (mmhg)


title: Nuclear D2-MSN FACS, Male, Rep 5

molecule: nuclear RNA

tag: strain

tag: tissue

value: brain

tag: molecule

value: nuclear RNA


title: Nuclear D2-MSN FACS, Male, Rep 3


title: FGR, rep5

description:
Sample_8717
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: maternal blood type

tag: maternal pre-pregnancy weight (kg)

tag: maternal height (cm)

tag: maternal bmi

tag: gestational age at delivery (weeks)

value: c-section

value: M

tag: placental thickness (cm)

tag: cord diameter (cm)

tag: max systolic blood pressure (mmhg)


title: Nuclear D2-MSN FACS, Male, Rep 2


title: FGR, rep3

description:
Sample_7656
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: maternal age (years)

tag: maternal ethnicity

tag: gestational age at delivery (days)

tag: placental weight (g)

tag: mode of delivery

tag: fetal sex

tag: newborn weight z-score

tag: apgar at 1min


title: FGR, rep1

description:
Sample_7375
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: tissue

tag: apgar at 5min

tag: max left uterine artery pi

tag: max right uterine artery pi

tag: max umbilical artery pi

tag: max diastolic blood pressure (mmhg)


title: FGR, rep6

description:
Sample_9201
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: maternal blood type

value: A

tag: maternal pre-pregnancy weight (kg)

tag: maternal height (cm)

tag: maternal bmi

tag: gestational age at delivery (weeks)

tag: placental thickness (cm)


title: FGR, rep2

description:
Sample_7523
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

value: Placenta

tag: maternal age (years)

tag: maternal ethnicity

value: Black

tag: gestational age at delivery (days)

tag: placental weight (g)

tag: cord diameter (cm)

tag: max systolic blood pressure (mmhg)


title: FGR, rep7

description:
Sample_9328
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: tissue

value: East Indian

tag: mode of delivery

tag: fetal sex

tag: newborn weight z-score

tag: apgar at 1min

tag: apgar at 5min


title: Nuclear D2-MSN FACS, Male, Rep 4

tag: strain

tag: molecule


title: Nuclear D1-MSN FACS, Male, Rep 6


title: TAU_WT_Y_12 [miRNA-Seq]

city: Leuven

first: Bart

last: De Strooper

address: O&N4 Herestraat 49

department: Centre for Brain and Disease research

country: Belgium

institute: VIB - KU Leuven

description: nm.miRNA.mmu.txt

data_processing:
Raw reads were trimmed with Flexbar (version 2.5.35, (22)) and filtered to remove unwanted adaptors, low-quality reads and reads with ambiguous nucleotides. Reads with ≥15 nucleotides were mapped to the mm10/GRCm38 Mus musculus assembly using Bowtie2 (version 2.2.1, (23)) allowing 1 mismatch. Stranded miRNA read counts were produced by FeatureCounts from the Subread package (version 1.4.4, (24)) using the miRBase gff3 annotation file (version 20, (25)).
We found in 2 of the 12 mice in the APPtg-O group a 46% lower expression levels of hsa-APPswe, a 26% lower expression of hsa-Psen1L166p and a 24% reduction in mmu-Thy1 gene, whose promoter drives the expression of the transgenes, compared to the other APPtg-O mice. In the absence of an explanation, these two mice were excluded from all further analyses (data not shown).
miRNAs with an average of raw read counts <5 were discarded, leaving 644 miRNAs for differential expression (DE) analysis. Non-biological variation was removed by the removeBatchEffect function from limma package 3.22.7 Bioconductor/R, preserving biological variation of genotype, age and their interactions in a generalized linear model for the APPtg and TAUtg dataset combined, as well as separately, while removing technical effects such as batch effect, RNA extraction group effects, RNA concentration effects. DE analysis was conducted using a 2-way interaction model (age, genotype, age*genotype) and performing Benjamini-Hochberg p-value adjustment for multiple testing.
Genome_build: mm10/GRCm38 Mus musculus reference genome
Supplementary_files_format_and_content: tab-delimited text file containing read counts after Limma Voom normalisation for all Samples

source_name: hippocampus

growth_protocol: Mice were co-housed and had ad libitum access to food and water.

extract_protocol:
Total RNA was extracted by homogenizing the left hippocampus in TRIzol (Invitrogen, Carlsbad, CA, USA) using 1ml syringes and 22G/26G needles and purified on mirVana spin columns according to the manufacturer’s instructions (Ambion, Austin, TX, USA). RNA purity (260/280 and 260/230 ratios) and integrity was assessed using  Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer with High Sensitivity chips (Agilent Technologies, Inc., Santa Clara, CA, USA) and Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA), respectively.
The miRNA library was prepared by the Genomics Core (UZ Leuven) using Illumina TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA, USA), adding 2µl of 50% PEG8000 in the 3’ ligation and with 13 cycles of cDNA amplification. Library construction of 96 samples was performed in 4 different batches of 24 samples, with 1-5 samples per experimental group within each batch. Three libraries were pooled and all RNAs between 5 and 40 bps in length were selected using the BluePippin (Sage Science, Beverly, MA, USA). Equimolar concentrations of 8 pools of 3 samples were loaded per lane and 4 lanes in total were used to sequence 50 bps single-end reads using the Illumina HiSeq 2500 (Illumina, San Diego, CA, USA).

treatment_protocol: Mice were sacrificed by cervical dislocation and the hippocampus was microdissected. Brain samples were snap frozen in liquid nitrogen and stored in -80°C until use.

value: hippocampus

tag: age (months)

tag: genotype

value: Wildtype


title: TAU_WT_Y_10 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_WT_Y_11 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E13.5 Alk5_Knockout Alk5 Mandible Proximal Replicate 4

description: Gene Expression

tag: strain/background

value: Mandible

tag: tissue compartment

value: Proximal

tag: genotype/variation

tag: developmental stage


title: TAU_WT_Y_09 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: FGR, rep4

description:
Sample_7731
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada).

tag: maternal age (years)

tag: maternal ethnicity

tag: maternal blood type

tag: maternal pre-pregnancy weight (kg)

tag: maternal height (cm)

tag: maternal bmi

tag: gestational age at delivery (weeks)

tag: gestational age at delivery (days)

tag: placental weight (g)

tag: max left uterine artery pi

tag: max right uterine artery pi

tag: max umbilical artery pi

tag: placental thickness (cm)

tag: max diastolic blood pressure (mmhg)


title: Nuclear D1-MSN FACS, Male, Rep 5

tag: strain

tag: tissue

tag: molecule


title: Nuclear D2-MSN FACS, Male, Rep 1


title: TAU_WT_Y_08 [miRNA-Seq]

description: nm.miRNA.mmu.txt

tag: age (months)

tag: genotype


title: Nuclear D1-MSN FACS, Male, Rep 4


title: Nuclear D1-MSN FACS, Male, Rep 3


title: TAU_WT_Y_05 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_WT_Y_07 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_WT_Y_06 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_WT_Y_04 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E13.5 Control Alk5 Maxilla Distal Replicate 4

description: Gene Expression

tag: strain/background

value: Maxilla

tag: tissue compartment

value: Distal

tag: genotype/variation

value: Control

tag: developmental stage


title: Mouse E13.5 Control Alk5 Mandible Proximal Replicate 4

description: Gene Expression


title: Mouse E13.5 Alk5_Knockout Alk5 Maxilla Distal Replicate 4

description: Gene Expression

value: Alk5 Knockout


title: Mouse E13.5 Alk5_Knockout Alk5 Mandible Distal Replicate 4

description: Gene Expression


title: Mouse E13.5 Control Alk5 Maxilla Proximal Replicate 4

description: Gene Expression


title: Nuclear D1-MSN FACS, Male, Rep 1


title: TAU_WT_Y_02 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E13.5 Alk5_Knockout Alk5 Maxilla Proximal Replicate 3

description: Gene Expression


title: TAU_WT_Y_03 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_WT_Y_01 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E13.5 Control Alk5 Mandible Distal Replicate 4

description: Gene Expression


title: Mouse E13.5 Alk5_Knockout Alk5 Maxilla Distal Replicate 3

description: Gene Expression


title: CA/CA HSPCs

city: Kyoto

first: Masahiro

middle: Marshall

last: Nakagawa

address: Yoshidakonoecho, Sakyo-ku, Kyoto,

institute: Kyoto University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The images are analyzed using Illumina Beadstudio software. Quality control and data analysis are carried out according to the instructions provided by Illumina.

source_name: Flt3low LSK cells

label_protocol: RNA was amplified and labeled with Illumina total prep RNA amplification kit.

extract_protocol: RNA was extracted with Qiagen RNeasy micro kit. RNA Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: Flt3 low Lin-Sca1+c-Kit+ (LSK)

value: CA/CA


title: Mouse E13.5 Alk5_Knockout Alk5 Mandible Distal Replicate 3

description: Gene Expression


title: Mouse E13.5 Alk5_Knockout Alk5 Mandible Proximal Replicate 3

description: Gene Expression


title: TAU_WT_O_13 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_WT_O_12 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Nuclear D1-MSN FACS, Male, Rep 2

value: brain

value: nuclear RNA


title: Control HSPCs

value: control


title: TAU_WT_O_11 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E13.5 Control Alk5 Maxilla Distal Replicate 3

description: Gene Expression


title: Mouse E13.5 Control Alk5 Maxilla Proximal Replicate 3

description: Gene Expression


title: Whole cell D2-MSN FACS, Male, Rep 6

value: total RNA


title: Whole cell D2-MSN FACS, Male, Rep 8


title: Whole cell D2-MSN FACS, Male, Rep 5


title: TAU_WT_O_06 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_WT_O_05 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Whole cell D2-MSN FACS, Male, Rep 7


title: TAU_WT_O_04 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_WT_O_03 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_WT_O_02 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Whole cell D2-MSN FACS, Male, Rep 3


title: Whole cell D2-MSN FACS, Male, Rep 2


title: Mouse E13.5 Control Alk5 Mandible Proximal Replicate 3

description: Gene Expression


title: Mouse E13.5 Control Alk5 Mandible Distal Replicate 3

description: Gene Expression


title: TAU_TG_Y_12 [miRNA-Seq]

description: nm.miRNA.mmu.txt

value: Transgenic


title: TAU_TG_Y_11 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_WT_O_09 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E13.5 Alk5_Knockout Alk5 Maxilla Proximal Replicate 2

description: Gene Expression


title: TAU_TG_Y_10 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Whole cell D2-MSN FACS, Male, Rep 1


title: TAU_WT_O_08 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E13.5 Alk5_Knockout Alk5 Maxilla Distal Replicate 2

description: Gene Expression


title: Mouse E13.5 Alk5_Knockout Alk5 Mandible Distal Replicate 2

description: Gene Expression


title: TAU_TG_Y_09 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_TG_Y_08 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_TG_Y_07 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Whole cell D1-MSN FACS, Male, Rep 8


title: Whole cell D2-MSN FACS, Male, Rep 4


title: Mouse E13.5 Control Alk5 Maxilla Proximal Replicate 2

description: Gene Expression


title: TAU_WT_O_01 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Whole cell D1-MSN FACS, Male, Rep 7


title: TAU_TG_Y_06 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E13.5 Control Alk5 Mandible Proximal Replicate 2

description: Gene Expression


title: TAU_TG_Y_05 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_TG_Y_04 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_TG_Y_03 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Whole cell D1-MSN FACS, Male, Rep 6


title: TAU_TG_Y_02 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E13.5 Control Alk5 Maxilla Distal Replicate 2

description: Gene Expression


title: Mouse E13.5 Alk5_Knockout Alk5 Mandible Proximal Replicate 2

description: Gene Expression


title: TAU_TG_O_13 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_TG_Y_01 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_TG_O_11 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_TG_O_12 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Whole cell D1-MSN FACS, Male, Rep 3


title: Whole cell D1-MSN FACS, Male, Rep 4


title: Mouse E13.5 Control Alk5 Mandible Distal Replicate 2

description: Gene Expression


title: Mouse E13.5 Alk5_Knockout Alk5 Maxilla Proximal Replicate 1

description: Gene Expression


title: TAU_TG_O_09 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E13.5 Alk5_Knockout Alk5 Maxilla Distal Replicate 1

description: Gene Expression


title: TAU_TG_O_08 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_TG_O_07 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_TG_O_05 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_TG_O_06 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Whole cell D1-MSN FACS, Male, Rep 1


title: Whole cell D1-MSN FACS, Male, Rep 5


title: Whole cell D1-MSN FACS, Male, Rep 2


title: Mouse E13.5 Alk5_Knockout Alk5 Mandible Distal Replicate 1

description: Gene Expression


title: Mouse E13.5 Alk5_Knockout Alk5 Mandible Proximal Replicate 1

description: Gene Expression


title: TAU_TG_O_03 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_TG_O_02 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: TAU_TG_O_01 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_WT_Y_12 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_WT_Y_10 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Dropseq_healthy

description:
single cell RNA-seq
Processed data file: Healthy.combined.dge.txt.gz

tag: protocol

value: Single cell dissociation

tag: disease state (group)

value: Healthy

tag: platform

value: DropSeq


title: TAU_TG_O_04 [miRNA-Seq]

description: nm.miRNA.mmu.txt

value: hippocampus


title: APP_WT_Y_09 [miRNA-Seq]

description: nm.miRNA.mmu.txt

value: Wildtype


title: APP_WT_Y_08 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_WT_Y_06 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_WT_Y_07 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Jukat-TET-On_Tax-B_Dox+_#2

city: Kurashiki

first: Tadasuke

last: Naito

state: Okayama

address: 577 Matsushima

department: Microbiology

institute: Kawasaki Medical School

description: Jurkat-TET-On cells were transfected with pTRE3G-Tax-B, and then were treated with Dox for protein induction

hyb_protocol: 0.6 ?g of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ?l containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ?l of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Jukat-TET-On cell line

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 ?g Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNAeasy Mini Kit column purification (QIAGEN) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with Agilent 4200 TapeStation.

tag: transfected plasmid

tag: induced protein

value: HTLV-1 Tax-B

tag: doxycycline

value: Treated


title: APP_WT_Y_04 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_WT_Y_05 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E13.5 Control Alk5 Maxilla Distal Replicate 1

description: Gene Expression

value: Maxilla

value: Distal


title: APP_WT_Y_03 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_WT_Y_11 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_WT_Y_02 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Jukat-TET-On_Tax-B_Dox+_#3


title: Mouse E13.5 Control Alk5 Maxilla Proximal Replicate 1

description: Gene Expression

value: Proximal

value: Control


title: Jukat-TET-On_Tax-A_Dox+_#3

description: Jurkat-TET-On cells were transfected with pTRE3G-Tax-A, and then were treated with Dox for protein induction

value: HTLV-1 Tax-A


title: APP_WT_Y_01 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_WT_O_12 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Jukat-TET-On_Tax-A_Dox+_#2


title: APP_WT_O_11 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E12.5 Tgfbr2_Knockout Tgfbr2 Maxilla Distal Replicate 3

description: Gene Expression

source_name: mouse embryo stage E12.5

value: Tgfbr2 Knockout


title: Mouse E12.5 Tgfbr2_Knockout Tgfbr2 Maxilla Proximal Replicate 3

description: Gene Expression


title: APP_WT_O_09 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Jukat-TET-On_empty_Dox+_#3

description: Jurkat-TET-On cells were transfected with pTRE3G-IRES-empty, and then were treated with Dox for non-induction control


title: APP_WT_O_08 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Jukat-TET-On_Tax-B_Dox+_#1


title: APP_WT_O_05 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_WT_O_06 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_WT_O_10 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E12.5 Tgfbr2_Knockout Tgfbr2 Mandible Distal Replicate 3

description: Gene Expression

value: Mandible


title: Jukat-TET-On_Tax-A_Dox+_#1


title: Jukat-TET-On_empty_Dox+_#2


title: Mouse E13.5 Control Alk5 Mandible Proximal Replicate 1

description: Gene Expression


title: Mouse E12.5 Control Tgfbr2 Maxilla Distal Replicate 3

description: Gene Expression


title: APP_WT_O_03 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_WT_O_04 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Jukat-TET-On_empty_Dox+_#1


title: APP_WT_O_07 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E12.5 Control Tgfbr2 Mandible Proximal Replicate 3

description: Gene Expression


title: APP_WT_O_02 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E12.5 Control Tgfbr2 Mandible Distal Replicate 3

description: Gene Expression