title: WT rep2

city: Tuebingen

first: Marja

last: Timmermans

address: Morgenstelle 32

institute: University of Tuebingen

description:
Single cell RNA-seq libraries were prepared from fresh wild-type root protoplasts according to the 10x Genomics Single Cell 3’ Reagent Kit v2 protocol. For each replicate, 12,200 cells were loaded in the 10x Genomics Chromium single cell microfluidics device with the aim of capturing 7,000 cells. 11 cycles were used for cDNA amplification, as well as for final PCR amplification of the adapter-‐ligated libraries. Final library size and quality were checked on a DNA High Sensitivity Bioanalyzer chip (Agilent), and libraries were quantified using the NEBNext Library Quantification Kit for Illumina.
The R1 raw data files include the technical reads; the first 16 basepairs are barcode and the last 10 basepairs are UMI. The R2 raw data files include the biological reads.
processed data file: Root_single_cell_wt_datamatrix.csv

data_processing:
Cell Ranger 2.0.2 (10X Genomics) was used to process scRNA-seq data.
Bulk RNA Sequencing reads (pair-end, 75 bp) were trimmed using Trimmomatic (version 0.36), and aligned to the Arabidopsis TAIR10 reference genome with STAR. Gene expression values were calculated on uniquely mapped reads using HTSeq (version 0.7.2).
Genome_build: TAIR10
Supplementary_files_format_and_content: *_datamatrix.csv: Comma-delimited text files include UMI counts values in each cell.
Supplementary_files_format_and_content: Root_bulk_tissue_datamatrix.txt: Tab-delimited text file includes read counts and RPM values for each Sample.

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Seedlings were grown vertically on nylon mesh on ½ Murashige and Skoog 1% agar plates.

extract_protocol:
RNA extraction (for bulk RNA-seq samples) - either protoplasted (reduced to smallest possible volume) or unprotoplasted root tissue was flash-frozen in liquid nitrogen, ground to a powder and RNA extracted using the Spectrum Plant RNA Extraction Kit (Sigma). Quality and quantity were checked using Agilent Bioanalyzer chips and Nanodrop, respectively, prior to library construction.
Bulk RNA libraries were produced using the NEBNext Poly(A) mRNA Magneticb Isolation Module, and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEB Multiplex oligos. Final library size and quality were checked on a DNA High Sensitivity Bioanalyzer chip (Agilent), and libraries were quantified using the NEBNext Library Quantification Kit for Illumina. Single cell RNA-seq libraries were prepared from fresh protoplasts according to the 10x Genomics Single Cell 3’ Reagent Kit v2 protocol. For each replicate, cells were loaded in the 10x Genomics Chromium single cell microfluidics device with the aim of capturing 7,000 cells. 11 cycles were used for cDNA amplification, as well as for final PCR amplification of the adapter-‐ligated libraries. Final library size and quality were checked on a DNA High Sensitivity Bioanalyzer chip (Agilent), and libraries were quantified using the NEBNext Library Quantification Kit for Illumina.

treatment_protocol: For protoplasting: Roots of 6-day-old seedlings were cut approximately one centimetre from their tip, broadly diced with a scalpel blade, and treated with 7 ml protoplasting solution optimised for scRNA-seq from a protocol in Birnbaum et al., 2003. Immediately before use, 1.5% Cellulase R-10 and 0.1% Pectolyase (Duchefa Biochem.) were added to fresh protoplast buffer (0.1 M KCl, 0.02 M MgCl2, 0.02 M CaCl2, 0.1% BSA (Sigma Aldrich)), 0.08 M MES, and 0.6 M Mannitol adjusted to pH 5.5 with 0.1M Tris HCl) and mixed thoroughly. Root tissues were protoplasted for 2 hours at 20°C on an orbital shaker set at 200 evolutions/minute. The mixture was subsequently filtered through a 100 μm nylon filter and rinsed with 1-5 ml of root protoplast buffer. Protoplasts were then centrifuged for 10 minutes (500 g – 4°C), the supernatant gently removed, and the pellet resuspended in 10 ml root protoplast buffer containing 0.4 M Mannitol and no CaCl2. This wash procedure was repeated once more, the protoplasts centrifuged as before, and resuspended in ~500 μl or less protoplast buffer without CaCl2 and with 0.4 M Mannitol. Protoplasts were validated under a light microscope, and if necessary any excess debris or un-protoplasted tissues removed with an additional washing step. Cells were filtered through a 40 μm cell strainer (Flowmi Bel Art SP Scienceware), quantified using a haemocytometer, and adjusted to a density of approximately 800-‐900 cells per μl.

tag: strain/background

value: Col-0 pMIR166A:erGFP endodermal reporter line

value: Wild type

value: Root

tag: age

value: 6-day-old seedlings

tag: condition

value: Protoplasted


title: Lgr5eGFP+ infected

status: Public on Mar 25 2019

type: SRA

city: Berlin

first: Cornelius

last: Fischer

state: Berlin

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine (MDC)

library_source: transcriptomic

data_processing:
NextSeq data were demultiplexed using bcl2fastq v1.9
Fastq data from different lanes and appropriate indexes was merged.
Alignment, filtering, UMI counting, barcode counting and filtering and gene-barcode matrix generation performed with 10X Cell Ranger (v2.0.0, 10X Genomics).
Cell Ranger R kit version 2.0.0 and Seurat version 2.3 was used for downstream analysis. For clustering, principal-component analysis was performed for dimension reduction and t-SNE was used for clustering visualization. sSeq integrated in the Cell Ranger R kit was used for modeling the gene expression with negative binomial distribution to identify genes whose expression was enriched in specific clusters
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output:
*analysis.tar.gz: Several CSV files packed as tar.gz which contain automated secondary analysis results (Cell Ranger 2.1.0 output).
*filtered_gene_bc_matrices_h5.h5.gz: Filtered feature-barcode matrix. HDF5 Feature Barcode Matrix.
*filtered_gene_bc_matrices.tar.gz: Filtered feature-barcode matrix. Contains only detected cellular barcodes. This includes background and cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).
*metrics_summary.csv.gz: Run summary CSV.
*molecule_info.h5.gz: HDF5 file containing per-molecule information for all molecules that contain a valid cell-barcode and valid UMI and were assigned with high confidence to a gene or Feature Barcode. This HDF5 file contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.
*raw_gene_bc_matrices_h5.h5.gz: Unfiltered feature-barcode matrix. HDF5 Feature Barcode Matrix.
*raw_gene_bc_matrices.tar.gz: Unfiltered feature-barcode matrix. Contains every barcode from fixed list of known-good barcode sequences. This includes background and cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).

molecule: polyA RNA

organism: Mus musculus

source_name: Lgr5+ cells from gastric gland base

growth_protocol: Lgr5eGFP+ cells were isolated form mouse antrum, sorted and processed for single cell analysis

extract_protocol:
PolyA selection based RNA capture (Chromium Single Cell 3’ Reagent Kit , v2 Chemistry, 10X Genomics) as per the manufacturer's instructions provided by 10X Genomics platform.   RNA-Seq
Libraries were prepared as per manufacturer's insturctions provided by 10X Genomics platform (https://www.10xgenomics.com/single-cell/)

tag: strain

tag: mouse status

value: H. pylori infected

tag: tissue

value: antrum; gastric gland base

tag: cell type

value: Lgr5eGFP+ cells


title: WT rep1

molecule: total RNA

tag: genotype/variation


title: Differentiated C2C12_D6_replicate_4

status: Public on Apr 03 2019

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina's Sentrix Mouse Ref-8 v3 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.8um using the Illumina Beadstation 500 X

data_processing:
Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.
Z_VALUE = Z transformation of the natural log of the raw intensity values
Detection_Pval = Detection Pvalue from Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0.

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5 μg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: Mouse C2C12 myoblasts were cultured in growth medium (Dulbecco's Modified Eagle's Medium {DMEM, Life Technologies} containing 20% fetal bovine serum {FBS, Gibco} and antibiotics) and were maintained at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol: Total RNA from cultured cells was isolated using TRIzol (Life Technologies) following the manufacturer’s protocol. RNA quality and quantity was assessed using the RNA 6000 Nano Chip on an Agilent Bioanalyzer (Agilent, Wilmington, DE).

treatment_protocol: C2C12 cells were differentiated by replacing the growth medium with differentiation medium (DMEM with 2% horse serum) for six days.

tag: cell line

value: mouse myoblast cell line

tag: differentiation time

value: Day 6


title: Differentiated C2C12_D6_replicate_3


title: Differentiated C2C12_D6_replicate_2


title: Undifferentiated C2C12_D0_replicate_5

value: Day 0


title: Differentiated C2C12_D6_replicate_5


title: Differentiated C2C12_D6_replicate_1


title: Undifferentiated C2C12_D0_replicate_2


title: Undifferentiated C2C12_D0_replicate_1


title: Undifferentiated C2C12_D0_replicate_3


title: AAM_O_AP_rep4

status: Public on Mar 19 2019

description:
DRU1977
Gene and lncRNA expression from PBMCs.

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v3.0 (8 x 60K, Arraystar).

scan_protocol: After washing and fixing of the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Acquired array images were analyzed using the Agilent Feature Extraction software (version 11.0.1.1). Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, ComBat was used to adjust batch effects. After normalization of the raw data, lncRNAs and mRNAs that at least 8 out of 16 samples have flags in present or marginal were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs with statistical significance with Fold Change >= 2.0, P value <= 0.05 were identified through Volcano Plot filtering between two groups.

organism: Homo sapiens

source_name: PBMCs

label_protocol: lncRNA and mRNA microarrays were performed by Arraystar Inc. using the Arraystar Human LncRNA Microarray V3.0. In brief, sample preparation and microarray hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Subsequently, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

growth_protocol: Fasting blood samples are obtained from participants in the morning and collected in 8-ml Vacutainer® heparinized vials (BD, Franklin Lakes, NJ). Peripheral blood mononuclear cells were isolated within 3 hours of phlebotomy as detailed previously. After isolation, PBMCs are aliquoted and stored at -80oC.

extract_protocol: Total RNA from PBMCs was isolated using TRIzol according to manufacturer’s instructions. RNA quality and quantity were analyzed using a NanoDrop ND-1000 spectrophotometer and standard denaturing agarose gel electrophoresis.

tag: race

value: African American

tag: poverty

value: Above

tag: age group

value: O

tag: gender

value: male

value: PBMC


title: AAM_Y_BP_rep4

description:
DRU1612
Gene and lncRNA expression from PBMCs.

value: Below

value: Y


title: AAM_O_AP_rep2

description:
DRU1770
Gene and lncRNA expression from PBMCs.


title: Undifferentiated C2C12_D0_replicate_4


title: AAM_Y_BP_rep1

description:
DRU1974
Gene and lncRNA expression from PBMCs.


title: AAM_O_BP_rep2

description:
DRU0807
Gene and lncRNA expression from PBMCs.


title: AAM_Y_AP_rep1

description:
DRU1768
Gene and lncRNA expression from PBMCs.


title: AAM_Y_AP_rep3

description:
DRU1552
Gene and lncRNA expression from PBMCs.


title: 141403_PBMC_0

status: Public on May 26 2019

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

description:
200373830080_I
SAMPLE 20

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi in R

label: biotin

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.   Hybridization buffer from the BeadChip kit (Illumina) was mixed with 1500 ng of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip.  The BeadChips were sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours.  After the hybridization, the BeadChips were washed and stained in a series of washes and stains as outlined in the Illumina protocol.  The BeadChips were scanned on the Illumina Iscan.

extract_protocol: Total RNA from PBMC, T Cell, B Cell samples was extracted using the RNeasy mini kit (Qiagen, CA)

tag: subject status

value: Healthy Adults receiving Influenza Vaccination

value: Young

tag: blood draw date

value: day 0; prior to administration of vaccine

value: Peripheral Blood Mononuclear Cells (PBMC)


title: AAM_Y_AP_rep2

description:
DRU0933
Gene and lncRNA expression from PBMCs.


title: Undifferentiated C2C12_D0_replicate_5TR


title: AAM_O_AP_rep1

description:
DRU0724
Gene and lncRNA expression from PBMCs.


title: AAM_O_AP_rep3

description:
DRU0714
Gene and lncRNA expression from PBMCs.


title: AAM_Y_BP_rep2

description:
DRU0296
Gene and lncRNA expression from PBMCs.


title: WM_O_AP_rep1

description:
DRU1360
Gene and lncRNA expression from PBMCs.

value: White


title: AAM_Y_BP_rep3

description:
DRU0304
Gene and lncRNA expression from PBMCs.


title: WM_O_BP_rep2

description:
DRU1918
Gene and lncRNA expression from PBMCs.


title: AAM_O_BP_rep3

description:
DRU0301
Gene and lncRNA expression from PBMCs.


title: WM_O_AP_rep3

description:
DRU2355
Gene and lncRNA expression from PBMCs.


title: WM_Y_BP_rep2

description:
DRU2117
Gene and lncRNA expression from PBMCs.


title: WM_O_AP_rep2

description:
DRU1438
Gene and lncRNA expression from PBMCs.


title: WM_O_BP_rep4

description:
DRU961
Gene and lncRNA expression from PBMCs.


title: WM_Y_BP_rep3

description:
DRU996
Gene and lncRNA expression from PBMCs.


title: WM_Y_AP_rep4

description:
DRU910
Gene and lncRNA expression from PBMCs.


title: WM_Y_AP_rep2

description:
DRU1722
Gene and lncRNA expression from PBMCs.


title: AAM_O_BP_rep1

description:
DRU1489
Gene and lncRNA expression from PBMCs.


title: AAM_Y_AP_rep4

description:
DRU0710
Gene and lncRNA expression from PBMCs.


title: St5_4_b

status: Public on Mar 12 2019

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

data_processing:
Fastq files were quality controlled using FastQC (Babraham Bioinformatics) and any adapter sequences, as well as twelve bases from the five prime end, were removed and mapped to the hg19 version of the human genome using STAR (v. 2.4.0a)
The SAM files produced from STAR were de-duplicated using Samtools (v. 0.1.19) and converted to bed files.
Quantification of gene expression was then performed using the python script rpkforgenes.py  and the UCSC hg19 refGene.txt annotation file archive-2012-03-09- 03-24-41
The obtained gene counts were then analyzed using the DESeq2 bioconductor package
Prior to differential expression analysis, genes with low reads maximum read count across samples (<20) were removed. The function DESeq was used for differential expression analysis with default settings.
Differentially expressed genes with an adjusted pvalue of <0.00001 and an absolute log2 fold change of > 4 were carried forward for CLICK analysis
Genome_build: UCSC hg19 refGene.txt annotation file archive-2012-03-09- 03-24-41
Supplementary_files_format_and_content: hESC_hepat_diff_count_matrix.txt is a count matrix with gene names in the first column and sample names in the first row. The matrix is an unfiltered raw count of reads mapping to UCSC hg19 refGene.txt  annotation file archive-2012-03-09- 03-24-41.

source_name: Differentiated human embryonic stem cells

growth_protocol: Liver samples for RNAseq were collected under an approved IRB in collaboration with Planned Parenthood of the Pacific Southwest. Human fetal hepatocytes used in this study were isolated from Fetal Liver (gestation age = 17 weeks) obtained from Advanced Bioscience Resources (ABR) following a previously publish method [2]. Isolated fetal hepatocytes were then maintained in the stage 5 condition described above for the duration of the experiment. Freshly isolated adult hepatocytes (HAHs) were obtained from Samsara Sciences and cultured in DMEM (Life Technologies) supplemented with 1% ITS (Corning), 1% Antibiotic-Antimycotic solution (Life Technologies).

extract_protocol:
Total RNA was isolated using the mirVana miRNA Isolation Kit (Life Technologies, Inc.)
The RNA was quantified (Qubit RNA Assay Kit, Life Technologies, Inc.), and quality controlled (RNA6000 Nano Kit and BioAnalyzer 2100, Agilent). 500 ng of total RNA was used as input for the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc.) and sequencing libraries were generated according to the manufacturer’s protocol. Briefly, the ribosomal RNA was depleted using RiboZero Gold (Illumina, Inc.), followed by a fragmentation step. The fragmented RNA was then copied into first strand cDNA using random primers and reverse transcriptase. Next, second strand cDNA synthesis was achieved using DNA Polymerase I and RNase H. The cDNA was then ligated to Illumina supplied adapters and enriched with PCR to create the final cDNA libraries.

treatment_protocol: Differentiation conditions were as follows: Stage 1. Definitive Endoderm induction was performed as described [1] in Chemically Defined Medium (CDM) for 3 days. Briefly, hPSCs were differentiated into mesendoderm in presence of Ly294002 (10uM, Calbiochem), Activin A (100ng/ml, Stemgent), BMP4 (10ng/ml, R&D), FGF2 (25ng/ml, Biopioneer) and CHIR 99021(3uM, Tocris) for 24 hours. For the next 48 hours cells were exposed to Ly294002 (10uM), Activin A (100ng/ml), BMP4 (10ng/ml) and FGF2 (25ng/ml). Stage 2. DE cells were then committed to Posterior Foregut (PFG) Cells. We tested several combinations of factors in RPMI (Invitrogen) supplemented with B27 supplement (Invitrogen), including a range of doses of Activin A (Stemgent), Noggin (R&D) and IWR-1 (Seleckchem), as described in Fig. 2. The final condition that was identified to result in the highest yield of PFG cells, and which was used in subsequent experiments, was 1uM of IWR-1 in RPMI/B27. Stage 3. For establishment of improved hepatic commitment conditions, PFG cells were exposed for 4 days to different combinations of: TGFβ inhibitor SB431452 (10uM, Tocris), BMP4 (10ng/ml), Retinoic Acid (RA, 2uM, Sigma), and IWR-1(1uM) in RPMI medium supplemented with B27. The final condition that was identified to result in the highest yield of hepatic gut cells, and which was used in subsequent experiments, was BMP4, SB and IWR-1. Stage 4. Stage 4 conditions were established by maintaining cells during 4 days in a medium permissive for hepatic progenitors consisting of RPMI (Invitrogen) with 1% ITS (Invitrogen), 0.1% bovin serum albumin (BSA, Invitrogen), 4.5 mM nicotinamide (Sigma), 0.1 nM Zinc 3 Sulfate heptahydrate and 10-8 M hydrocortisone (Sigma), supplemented with HGF (20ng/ml, Peprotech), with the addition of combinations of: VEGF (20ng/ml, Peprotech), CHIR99001 (3uM) and TGFβ (10ng/ml, Peprotech). The final condition that was identified to result in the highest yield of proliferative hepatoblasts, and which was used in subsequent experiments, was HGF, CHIR, VEGF and TGFβ. Stage 5. Stage 5 conditions were established by maintaining hepatic progenitors 4 days in a medium permissive for hepatocytes culture (consisting of stage 4 medium complemented with 1nM triiodothyroxine 3 (T3)) in presence of HGF (20ng/ml) and different combinations of: Notch inhibitor Compound E (CE) (0.5uM, VWR), TGFβ inhibitor SB431452 (5uM) and oncostatin M (OSM) (20ng/ml, Peprotech). The final condition that was identified to result in the highest functionality of hepatocytes was HGF, CE and S

tag: developmental stage

value: Stage 5_4

tag: rnaseq protocol

value: PolyA Selection


title: WM_O_AP_rep4

description:
DRU882
Gene and lncRNA expression from PBMCs.

tag: age


title: AAM_O_BP_rep4

description:
DRU0167
Gene and lncRNA expression from PBMCs.


title: St5_4_a

value: Differentiated human embryonic stem cells


title: Prefrontal with RSD rep1

status: Public on Mar 05 2019

city: NanJing

first: Feng

last: Zhang

state: JiangSu

address: Weigang NO.1

country: China

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The transcripts with splices for each sample were screened and combined as lncRNAs using Cuffmerge according to the following criteria: FPKM ≥ 0.5 (Cuffquant), exon number ≥ 2, and length > 200 bp. In addition, with Cuffcompare Software, we excluded overlapping and potential coding transcripts located in the exon regions
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Mouse prefrontal cortex

growth_protocol: The C57BL/6 mice were housed in cohorts of three and the CD-1 mice were maintained in individual cages under a 12-h light/dark cycle at 22–24 °C with sufficient food and water. All mice were acclimated to the surroundings for 7 days before model establishment.

extract_protocol:
Total RNA was extracted with Trizol reagent (Invitrogen, Carlsbad, CA, USA). RNA purity was assessed on a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and the concentration was measured with Qubit® RNA Assay Kit on a Qubit® 2.0 fluorometer (Life Technologies, CA, USA) according to the manufacturer’s instructions. In addition, RNA integrity was assessed with RNA Nano 6000 Assay Kit (Agilent Technologies, Foster City, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The RSD-induced behavioral changes in C57/BL6 mice were evaluated with an EPM test, as a well-proven animal model for anxiety-like behaviors detection based on the aversion that rodents have for open spaces. For PFC tissue collection, eligible C57/BL6 mice were immediately decapitated after the EPM test. The brains were removed and cut coronally at the caudal border of the olfactory tubercle to remove the PFC.

value: Prefrontal cortex

value: 6-8 weeks-old


title: Prefrontal without RSD rep3


title: Prefrontal with RSD rep3


title: St5_3_b

value: Stage 5_3


title: WM_Y_AP_rep5

description:
DRU940
Gene and lncRNA expression from PBMCs.

value: Above


title: WM_Y_AP_rep1

description:
DRU1142
Gene and lncRNA expression from PBMCs.


title: WM_O_BP_rep1

description:
DRU1295
Gene and lncRNA expression from PBMCs.

value: O


title: Prefrontal without RSD rep2


title: Prefrontal without RSD rep1


title: WM_Y_AP_rep3

description:
DRU21
Gene and lncRNA expression from PBMCs.

value: male


title: 141397_PBMC_0

description:
200373830108_I
SAMPLE 16

value: Older


title: WM_Y_BP_rep1

description:
DRU1157
Gene and lncRNA expression from PBMCs.

value: Below

value: PBMC


title: Prefrontal with RSD rep2


title: HFD_Low_DSF_replicate_2

status: Public on Feb 28 2019

description: Male C57BL/6J mice were obtained from the NIA Aging colony (Charles Rivers, Bethesda, MD) at 8 weeks of age. Mice were grouped into cages of four and were fed house chow (2018 Teklad Global 18% Protein Rodent Diet 2018S, Harlan Teklad, Indianapolis, IN) until they reached 16 weeks of age.

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina's Sentrix Mouse Ref-8 v2 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. The arrays were rinsed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.53 um using an Illumina iScan scanner.

source_name: Liver

extract_protocol: Total RNA was isolated from mouse liver with Trizol® (Invitrogen) as per the manufacturers recommendations. RNA quality and quantity was assessed using the RNA 6000 Nano Chip on an Agilent Bioanalyzer (Agilent, Wilmington, DE).

treatment_protocol: Mice were then randomized to one of six study diets: standard diet (SD) of AIN-93G (carbohydrate:protein:fat ratio of 64:19:17 percent of kcal), a SD supplemented with low dose of disulfiram (DSF) (SD-DSF-L; 100 mg/kg/day), a SD supplemented with high dose of DSF (SD-DSF-H; 200 mg/kg/day), a high fat diet consisting of AIN-93G modified to provide 60% of calories from fat (HFD; carbohydrate:protein:fat ratio of 16:23:61), a HFD supplemented with low dose of DSF (HFD-DSF-L; 100 mg/kg/day), or a HFD supplemented with high dose of DSF (HFD-DSF-H; 200 mg/kg/day). DSF was included in diets at a concentration of 1 g/kg (SD-DSF-L) and 2 g/kg (SD-DSF-H), as well as 2.33 g/kg (HFD-DSF-L) and 2.67 g/kg (HFD-DSF-H), respectively, which was formulated to provide mice with approximate daily doses of 100 mg/kg and 200 mg/kg (drug/kg body weight). Study diets were purchased from Dyets, Inc. (Bethlehem, PA). DSF was purchased from Sigma-Aldrich (St-Louis, MO). All groups had ad libitum access to their prescribed diet and water throughout the study. Body weight and food intake were monitored bi-weekly. Animal rooms were maintained at 20–220C with 30–70% relative humidity and a 12-hour light/dark cycle. All animal protocols were approved by the Animal Care and Use Committee (444-TGB-2016) of the National Institute on Aging.  Unless otherwise indicated, a subset of mice was euthanized at 58 weeks of age, 40 weeks on the diet, and tissues were collected for further analysis. For euthanasia and subsequent tissue collection, mice were on their normal feeding cycle (study diet ad libitum) and not fasted. The animal procedures were approved by the Laboratory Animal Care and Use Committee of the National Institute on Aging, NIH (444-TGB-2016). Seven-month-old retired breeder male and female C57BL/6J mice were obtained from the Jackson’s Laboratory (Bar Harbor, ME) and single housed under temperature-controlled conditions with 12 h light/12 h dark cycle with ad libitum access to food (2018S, see above) and water. Beginning at 9 months of age (defined as baseline), mice were maintained on high-fat diet (see above for composition) for the next 12 weeks (defined as HFD period) with bodyweight and food consumption measured bi-weekly.  After the HFD period, 6 mice of both sexes were sacrificed and the remaining animals were randomly divided into four groups (n=12/group per sex) for the intervention leg of the study, which consisted of: 1) HFD diet alone; 2) HFD supplemented with 100 mg.kg-1 DSF (HFDL); 3) HFD supplemented with 200 mg.kg-1 DSF (HFDH) and; 4) Standard diet (SD, see above for composition). All animals were sacrificed after an additional 12 weeks of treatment and tissues were collected for further analysis.

value: Male

value: 56 weeks

tag: diet

value: High-fat

tag: disulfiram

value: 100 mg/kg/day


title: HFD_Low_DSF_replicate_4

tag: strain


title: HFD_High_DSF_replicate_1

value: 200 mg/kg/day


title: HFD_replicate_4

value: 0 mg/kg/day


title: HFD_Low_DSF_replicate_1


title: HFD_High_DSF_replicate_3


title: HFD_replicate_2_REPEAT


title: HFD_replicate_5


title: SD_High_DSF_replicate_4

value: Standard


title: SD_High_DSF_replicate_2


title: WM_O_BP_rep3

description:
DRU856
Gene and lncRNA expression from PBMCs.

value: White


title: SD_Low_DSF_replicate_3


title: SD_Low_DSF_replicate_2


title: SD_Low_DSF_replicate_1


title: HFD_Low_DSF_replicate_3


title: SD_Low_DSF_replicate_4


title: HFD_High_DSF_replicate_2


title: SD_High_DSF_replicate_1


title: SD_High_DSF_replicate_5


title: HFD_High_DSF_replicate_4


title: SD_High_DSF_replicate_3


title: HFD_replicate_1


title: HFD_High_DSF_replicate_5


title: SD_Low_DSF_replicate_5


title: HFD_replicate_2


title: SD_replicate_5


title: Hb_pellet_polyp_1

status: Public on Feb 21 2019

city: Irapuato

first: Cei

last: Abreu-Goodger

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: Langebio - Cinvestav

data_processing:
All libraries were quality checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), reaper v16-098 (https://www.ebi.ac.uk/~stijn/reaper/reaper.html) was used to remove the Illumina small RNA Adapter sequences, and PullSeq 1.0.2 (https://github.com/bcthomas/pullseq) to keep reads that were at least 16 nucleotides long.
Tally v16-098 (https://www.ebi.ac.uk/~stijn/reaper/tally.html) was used to collapse all reads to a single occurrence in a FASTA file, keeping the counts of each read in the header. These are provided as processed files.
The alignment component of ShortStack 3.8.3 was used, with parameters: --nostitch, --mismatches 2, --mmap u, --bowtie_m 500 and --ranmax 500.
All the sRNA-seq results for each genome were used to predict novel ncRNA producing regions or clusters. All libraries for each genome were combined as a single input, and ShortStack 3.8.3 was used with the following parameters: --pad 10, --mincov 10, --dicermin 18, --dicermax 32. All the clusters were then split at exon-intron boundaries.
In order to obtain a level of expression for each sRNA-producing cluster, mapped reads were counted using the findOverlaps function from GenomicRanges R package with parameters minoverlap=16 and ignore.strand=TRUE. Only reads between 20-25nt were counted. Count tables were produced for each genome, where each cluster is a row and each library a column. These are provided as supplementary files.
Genome_build: The reference genome assembly for H. bakeri genome was nHp_v2.0 from http://parasite.wormbase.org/Heligmosomoides_polygyrus_prjeb15396 and for C. elegans WBcel235 from http://parasite.wormbase.org/Caenorhabditis_elegans_prjna13758.
Supplementary_files_format_and_content: Contains all reads of at least 16 nucleotides collapsed to a unique occurrences and saved in FASTA format. Read count is included in the tab files.

organism: Heligmosomoides polygyrus bakeri

source_name: Input pellet

growth_protocol: CBA x C57BL/6 F1 (CBF1) mice were infected with L3 infective-stage H. bakeri larvae by gavage and adult nematodes were collected from the small intestine 14 days post infection. The nematodes were washed and maintained in serum-free media in vitro.

extract_protocol:
Total RNA was treated with RNA 5' Polyphosphatase (Epicenter) following manufacturer's instructions, before library preparation.
Total RNA was extracted using a miRNAeasy mini kit (Qiagen) following manufacturer's instructions. RNA was treated with Turbo DNA-free kit (Thermo Fisher) to remove residual DNA.
Libraries were prepared using the CleanTag small RNA library prep kit according to manufacturer’s instructions, using total RNA from adult worms (30 ng), and sucrose-gradient purified EVs (equivalent 1E10 EVs measured by Nanosight, Malvern). For all samples, 1:12 dilutions of both adapters were used with 18 amplification cycles (TriLink BioTechnologies). Fragments between 140-170bp were size selected and sequenced on an Illumina HiSeq high output v4 50bp SE in Edinburgh Genomics.

tag: tissue

value: Input pellet

tag: agent

value: polyphosphatase

tag: treatment protocol

value: Nematodes were disrupted in 700 µl of Qiazol (Qiagen) using mechanical disruption with 5 mm stainless steel beads (Qiagen) on a Tissue Lyser II (30hz for 2 min twice; Qiagen)


title: Hb_pellet_polyp_2


title: Hb_EV_polyp_1

source_name: Extracellular vesicles

value: Extracellular vesicles


title: WT_rep1

status: Public on Feb 05 2019

city: Ann Arbor

first: John

last: Schiefelbein

state: Michigan

address: 830 North University Avenue

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

data_processing:
Single-cell raw fastq files were processed by 10X Chromium cell ranger pipeline v2.1.1
only UMI count data was used for downstream analysis
Genome_build: TAIR10
Supplementary_files_format_and_content: 5way_merge_raw.tsv contains the raw count for all 5 samples; The  barcodes are included in the column header line in the format of 'sample_sample_cellBarcode'.
Supplementary_files_format_and_content: The tar archive on the series record contains Cell Ranger (Ver. 2.1.1) output from sequence reads, separated by batch (TSV, MTX).

source_name: WT_protoplasts from roots

growth_protocol: Plants grow on MS media for 5 DAG (day after germination).

extract_protocol:
After Isolating protoplasts from roots, load into 10X Genomics unit for single-cell cDNA library construction.
Libraries were prepared for sequencing using 10X Genomics protocols; R1 is technical and R2 contains the real biological information.

tag: ecotype background

tag: genotype/varaition

value: wild type

tag: development stage

value: 5 day after germination

value: root

tag: cell type

value: protoplasts


title: Hb_EV_polyp_2


title: Hb_EV_monop_2

extract_protocol:
Total RNA was used directly for library preparation.
Total RNA was extracted using a miRNAeasy mini kit (Qiagen) following manufacturer's instructions. RNA was treated with Turbo DNA-free kit (Thermo Fisher) to remove residual DNA.
Libraries were prepared using the CleanTag small RNA library prep kit according to manufacturer’s instructions, using total RNA from adult worms (30 ng), and sucrose-gradient purified EVs (equivalent 1E10 EVs measured by Nanosight, Malvern). For all samples, 1:12 dilutions of both adapters were used with 18 amplification cycles (TriLink BioTechnologies). Fragments between 140-170bp were size selected and sequenced on an Illumina HiSeq high output v4 50bp SE in Edinburgh Genomics.


title: Hb_EV_monop_1


title: HFD_replicate_3


title: SD_replicate_3


title: SD_replicate_2


title: SD_replicate_4


title: SD_replicate_1


title: SD_replicate_1_REPEAT


title: HFD_Low_DSF_replicate_5


title: Liver_KO_FED2X_HF_replicate_3

status: Public on Jan 22 2019

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v1 gene expression microarrays (G4852-60510) 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) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray hybridization intensity data from four separate experiments were log-transformed.  Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: Male C57BL/6 (WT) mice were purchased from The Jackson Laboratory (Bar Harbor, ME, USA) and kept under constant temperature and humidity in a 12 h controlled dark/light cycle. Generation of miR-33-/- mice was accomplished with the assistance of Cyagen Biosciences Inc. CRISPR/Cas9 mediated excision of miR-33 was accomplished using targeted guide sequences toward intron 16 of the Srebp-2 gene.  All mice were fed a standard chow diet for 8-10 weeks after which were either switched to a high fat diet (60% calories from fat: Research Diets D12492) for 20 weeks or maintained on chow diet. For fasting-refeeding experiments mice were fasted for 24 h beginning at 8:00am or fasted for 24 h beginning at 8:00pm followed by 12 h of feeding overnight. All of the experiments were approved by the Institutional Animal Care Use Committee of Yale University School of Medicine.

extract_protocol: Total RNA from tissue was isolated using TRIzol reagent (Invitrogen) according to the manufacturers protocol.

treatment_protocol: Male mice were fed a standard chow diet for 8-10 weeks, after which they were either switched to a high fat diet (HF, 60% calories from fat: Research Diets D12492) for 20 weeks, or maintained on chow diet (CHOW). For fasting-refeeding experiments, mice were either sacrificed at 8:00am after overnight feeding (FED), after being fasted for 24 h beginning at 8:00am (FAST), or after being fasted for 24 h beginning at 8:00pm followed by 12 h of feeding overnight (FED2X).

tag: strain background

tag: genotype/variation

value: miR-33 KO

value: 7 month

tag: Sex

value: male

value: High fat diet

tag: treatment

value: Fasted, re-fed

value: Liver


title: Liver_KO_FED2X_HF_replicate_2

tag: developmental stage


title: Liver_KO_FED_HF_replicate_1

value: Fed


title: Liver_KO_FED_HF_replicate_2


title: Liver_KO_FED2X_HF_replicate_4


title: Liver_WT_FED2X_HF_replicate_1

value: Wildtype


title: Liver_WT_FED2X_HF_replicate_2


title: Liver_KO_FED_HF_replicate_4


title: Liver_WT_FED2X_HF_replicate_3


title: Liver_WT_FAST_HF_replicate_4

value: Fasted


title: Liver_KO_FED_HF_replicate_3


title: Liver_KO_FAST_HF_replicate_1


title: Liver_KO_FAST_HF_replicate_3


title: Liver_KO_FAST_HF_replicate_4


title: Liver_KO_FAST_HF_replicate_2


title: Liver_KO_FED2X_HF_replicate_1


title: Liver_WT_FAST_HF_replicate_3


title: Liver_WT_FED2X_HF_replicate_4


title: Liver_WT_FAST_HF_replicate_1


title: Liver_WT_FAST_HF_replicate_2


title: Liver_WT_FED_HF_replicate_3


title: Liver_WT_FED_HF_replicate_4


title: Liver_WT_FED_HF_replicate_1


title: Liver_KO_FED2X_CHOW_replicate_4

value: Chow


title: Liver_KO_FAST_CHOW_replicate_4


title: Liver_KO_FED2X_CHOW_replicate_3


title: Liver_KO_FAST_CHOW_replicate_3


title: Liver_KO_FED2X_CHOW_replicate_1


title: Liver_WT_FED_HF_replicate_2


title: Liver_KO_FED2X_CHOW_replicate_2


title: Liver_KO_FED_CHOW_replicate_2


title: Liver_WT_FAST_CHOW_replicate_2


title: Liver_WT_FED_CHOW_replicate_4


title: Liver_WT_FAST_CHOW_replicate_4


title: Liver_WT_FED_CHOW_replicate_2


title: Liver_WT_FED2X_CHOW_replicate_1


title: Liver_WT_FAST_CHOW_replicate_1


title: Liver_WT_FED2X_CHOW_replicate_3


title: Liver_KO_FAST_CHOW_replicate_1


title: Liver_WT_FED_CHOW_replicate_1


title: Liver_KO_FAST_CHOW_replicate_2


title: Liver_WT_FED2X_CHOW_replicate_4


title: Liver_KO_FED_CHOW_replicate_4


title: Liver_WT_FAST_CHOW_replicate_3


title: Liver_WT_FED2X_CHOW_replicate_2


title: Liver_KO_FED_CHOW_replicate_3


title: Liver_KO_FED_CHOW_replicate_1


title: Lhx8_KO_P7_Replicate_3

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Human-Ref8 v3 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has ~22,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.

data_processing: Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.

label: Streptavidin-Cy3 bound to biotin labeled cRNA.

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5ug of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: Lhx8 mutant mice were obtained from Dr. Heiner Westphal at the National Institute of Child Health and Human Development (Bethesda, MD), and were maintained on a mixed 129, C57BL/6, SF1 genetic background. Mice were euthanized ethically according to ACUC-approved NIA Standard Operation Procedures.

extract_protocol: For each genotype, ovaries from three animals were processed, providing biological replicates. Total RNA was extracted from ovaries using a Precellys 24 homogenizer (Bertin Technologies, France), followed by an RNeasy isolation. RNA concentration and purity were determined using Nanodrop ND-1000 spectrophotometer, and confirming ratios A260:230 and A260:280 greater than 1.8. RNA integrity was assessed using an Agilent BioAnalyzer.

treatment_protocol: Gonads were collected from pups at 0 and 7 days postnatum (P0 and P7).

value: Oocytes

tag: genotype

value: Lhx8 knockout


title: Lhx8_WT_P7_Replicate_3

tag: age

value: Lhx8 wildtype


title: Lhx8_KO_P7_Replicate_2


title: Lhx8_KO_P7_Replicate_1


title: Lhx8_WT_P7_Replicate_2


title: Lhx8_WT_P0_Replicate_3


title: Lhx8_KO_P0_Replicate_2


title: Lhx8_WT_P0_Replicate_2


title: Input 7

status: Public on Dec 31 2018

library_source: genomic

data_processing:
Basecalls performed using Illumina's SCS software (v2.50) and Illumina's GAPipeline software v1.5.1
First 35 to 41 bases of the ChIP-seq reads were aligned to the mm9 genome assembly using ELAND software
Peaks were called using CisGenome v1.2 with the following setting: 2 sample anaylsis, input as negative control, FDR <0.01, Cut-Off of 6 tags (with 3 tags per strand), window size of 1000 and boundary refinement.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are in BEDGRAPH format containg both the genomic coordinates and tag frequency.

molecule: genomic DNA

extract_protocol:
Respective cells were purified by FACS and average 100,000 cells were subjected to micro-chromatin immunoprecipitation (micro-ChIP) using antibodies directed against H3K4me3 and H3K27me3
Briefly, the ends of the fragments were repaired using T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase), and T4 polynucleotide kinase (PNK) and A’s were added to the 3’ end. Adapters were ligated to the DNA fragments and a 18-cycle PCR amplification was performed before size selection (250-300 bases) on a 2% agarose gel, followed by cluster generation and sequencing with Solexa/Illumina Genome Analyzer (GA-II).

value: double negative 2

value: Thymus

tag: chip anibody


title: Lhx8_WT_P0_Replicate_1


title: Liver_WT_FED_CHOW_replicate_3

tag: diet


title: Lhx8_KO_P0_Replicate_1

tag: strain


title: Input 3

source_name: CLP

value: common lymphoid progenitors

tag: tissue

value: Bone marrow


title: Input 4

source_name: ETP

value: early thymic precursors


title: Lhx8_KO_P0_Replicate_3


title: Input 2

source_name: LMPP

value: lymphoid-primed multipotent progenitors


title: Input 5


title: Input 6

value: double negative 3


title: Input 1

source_name: HSC

value: hematopoietic stem cells


title: Common lymphoid progenitors (CLP)-K27me3 micro-ChIP

description: 2 biological reps

value: Anti-H3K27me3 antibody (Active Motif)


title: Double negative 2 (DN2)-K27me3 ChIP

description: 2 biological reps


title: Double negative 3 (DN3-K27me3 ChIP

description: 2 biological reps


title: Early thymic precursors (ETP)-K27me3 micro-ChIP

description: 2 biological reps


title: Double negative 2 (DN2)-K4me3 micro-ChIP

description: 2 biological reps

value: Anti-H3K4me3 antibody (Active Motif)


title: Common lymphoid progenitors (CLP)-K4me3 micro-ChIP

description: 2 biological reps


title: Early thymic precursors (ETP)-K4me3 micro-ChIP

description: 2 biological reps


title: Double negative 3 (DN3-K4me3 micro-ChIP

description: 2 biological reps


title: Hematopoietic stem cells (HSC)-K27me3 micro-ChIP

description: 2 biological reps


title: Lymphoid-primed multipotent progenitors (LMPP)-K4me3 micro-ChIP

description: 2 biological reps


title: Hematopoietic stem cells (HSC)-K4me3 micro-ChIP

description: 2 biological reps


title: Lymphoid-primed multipotent progenitors (LMPP)-replicate1

description: Gene expression data from Lymphoid-primed multipotent progenitors from bone marrow of C57BL/6J mice

hyb_protocol: Hybridized for 16 h at 45 °C on Affymetrix Mouse Gene 1.0 ST Array

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000 7G

data_processing: Data were normalized by RMA (robust multi-array average) normalization

label_protocol: Affymetrix WT Terminal Labelling kit was used according to the manufacturers’ instructions

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

value: Lymphoid-primed multipotent progenitors


title: Double negative 3 (DN3)-replicate2

description: Gene expression data from Double negative 3 from bone marrow of C57BL/6J mice

value: Double negative 3 from bone marrow


title: UACC62P_2

status: Public on Dec 30 2018

city: East Lansing

first: Sean

middle: Alexander

last: Misek

state: MI

address: 1355 Bogue Street

institute: Michigan State University

data_processing:
Basecalls performed with Illumina Real Time Analysis, RTA_v2.7.7
Demultiplexing and FastQ conversion with Illumina Bcl2fastq v2.19.0
Quality Control with FastQC v0.11.5
Read Trimming with Trimmomatic v0.33
Read Mapping with HISAT2 v2.1.0
Read Counting/Analysis with HTSeq v0.6.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include raw HTSeq counts for each sample

source_name: Parental Cancer Cell Line

growth_protocol: Cells were grown in DMEM + 10% FBS + 1% Anti/Anti. Vemurafenib-resistant variants were selected in 2 uM Vemurafenib for 2 months, and were continuously cultured in 2 uM Vemurafenib.

extract_protocol:
Total cellular RNA was harvested from the cell lines using the Qiagen Rneasy Mini Kit (Cat# 74104)
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit on a Perkin Elmer Sciclone G3 robot following manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Caliper LabChipGX HS DNA assays. Libraries were pooled and run on two lanes, and sequencing was performed in a 1x50bp single end read format using HiSeq 4000 SBS reagents.

tag: cell line name

value: melanoma

tag: treatment time (h)


title: Early thymic precursors (ETP)-replicate2

description: Gene expression data from Early thymic precursors from bone marrow of C57BL/6J mice


title: Double negative 3 (DN3)-replicate1


title: Double negative 2 (DN2)-replicate1

description: Gene expression data from Double negative 2 from bone marrow of C57BL/6J mice

value: Double negative 2 from bone marrow


title: Lymphoid-primed multipotent progenitors (LMPP)-replicate2


title: UACC62P_1


title: Common lymphoid progenitors (CLP)-replicate1

description: Gene expression data from Common lymphoid progenitors from bone marrow of C57BL/6J mice


title: Hematopoietic stem cells (HSC)-replicate 2

description: Gene expression data from Hematopoietic stem cells from bone marrow of C57BL/6J mice

value: Hematopoietic stem cells


title: UACC62R_1

source_name: Vemurafenib-resistant Cancer Cell Line


title: Common lymphoid progenitors (CLP)-replicate2


title: CBMS1_ESC_single_75perS_35

status: Public on Dec 20 2018

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

data_processing:
BrdUIP, Population early-S, 100-cells, Single-cell data: sequence reads were trimmed to remove adapter sequences using the cutadapt program before mapping. For WGA samples, we performed a two-step adapter trimming, first removing the Illumina adapter based on the index of each NGS library and then removing the SEQXE adapter. As the SEQXE adapter sequence was not available, we empirically estimated it as the sequence that repeatedly appeared near the 5’ end.
BrdUIP, Population early-S, 100-cells, Single-cell data: trimmed reads were mapped into mm9, hg19, CBMS1-specific (CBA/MsM) diploid genome based on mm9 genome by using bwa (ver: 0.7.10-r789, command: bwa aln => bwa samse). CBMS1-specific diploid genome was constructed as described in Sakata et al. Development (2017) with minor modifications using CBA or MsM strain genomic reads. Duplicated reads mapped into mm9 or hg19 were removed by using picard tool and the reads overlapped with mm9, hg19 black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered out. The mapped reads with MAQP>10 were used for the further analysis. For the diploid genome mapping, we defined MAPQ>16 as the allele specific reads and used the liftover tool (UCSC Genome Browser) to convert to the mm9 genome coordinates. After this, duplicate reads identified as an identical chromosome start position and strand information were filtered out.
BrdUIP data: we counted the reads of early and late S-phase BrdU-IP samples in sliding windows of 200 kb at 40-kb or 80-kb intervals (written in the processed data file as “w200sk40k” or “w200ks80k”, respectively) in non-overlapping 400-kb windows (“400k”) and performed rpm (reads per million) normalization. Then, the ratio of early-S to total read counts [(Early-S reads)/(Early-S reads + Late-S reads)] was calculated for each bin and their distribution converted to fit within a ± 1 scale, and this value was defined as the BrdU-IP RT score of each bin. We filtered out bins whose total read counts were within the bottom 5% of all bins.
Population early-S data: we counted the reads of early-S and G1 in sliding windows of 200 kb at 40-kb intervals, performed rpm normalization in a manner identical to BrdU-IP data processing, and defined Log2[(Early-S reads)/(G1 reads)] as the population early-S RT score.
100-cells data: we counted the reads of 100 mid-S and G1 cells in sliding windows of 200 kb at 40-kb intervals and used the correctMappability command in the R package AneuFinder (http://bioconductor.org/packages/release/bioc/html/AneuFinder.html) for normalizing mid-S data based on G1 data. From the mappability corrected mid-S read counts, the genome-wide median was obtained and used to generate Log2[(Mappability corrected Mid-S reads)/median] scores, which we defined as the 100-cell mid-S RT score.
Single-cell data (hTERT-RPE1): For the analysis of single mid-S cells, we counted the reads in sliding windows of 200 kb at 40-kb intervals, and used the AneuFinder’s correctMappability command sfor normalizing mid-S data based on the merged G1 control. From the mappability corrected mid-S read counts, the genome-wide median was obtained and was used to generate Log2[(Mappability corrected Mid-S reads)/median] scores, which we defined as the single-cell mid-S RT score.
Single-cell data (CBMS1 un-resolved): first, we counted the reads in non-overlapping 80-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the merged G1 control. Binarization was performed using the Mappability corrected 25per-S (25% S-phase) , Mid-S (50% S-phase), 75per-S (75% S-phase) reads described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy"; options for Mid-S, 75per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"; 1-somy, unreplicated; 2-somy, replicated]. In the processed data files, replicated bin was shown as 1, unrelicated bin was shown as -1, and no-data was shown as 0. “Repliscore” was calculated as a percentage of replicated bins in the total number of replicated and unreplicated bins.
Single-cell haplotype-resolved data: after the specific filtering steps for haplotype-resolved data, we counted the reads in non-overlapping 400-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the filtered merged G1 control. Binarization was performed as described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy" ; options for Mid-S, 75per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy" ].
Binarized unresolved data: Sample_Name_80k_100S_MAP_2HMM2_eps0.01.binary.bedGraph, Binarized CBA data: Sample_name_cba_400k_100S_MAP_HMM2_eps0.01.binary.bedGraph, Binarized MsM data: Sample_name_msm_400k_100S_MAP_HMM2_eps0.01.binary.bedGraph
For paired-end reads, only "R1" (Fwd) reads were used for the analysis.
RNA-seq: allele-specific RNA-seq analysis was performed using CBA/MsM diploid genome as described in Sakata et al. Development 2017. We defined genes with allelic expression imbalance as those with the percentage of either MsM- or CBA-specific reads above 60% (or >70%) among genes that show ≥10 total reads (i.e. CBA+MsM read numbers combined) and >0.1 FPKM (fragments per kilobase of exon per million fragments mapped, in a non-allelic manner) in three biological replicates (CBMS1_allele_specific_genetable.txt).
Genome_build: hg19 / mm9 / CBMS1 diploid genome
Supplementary_files_format_and_content: bedGraph, bigWig

source_name: CBMS1 ESC

growth_protocol: hTERT-RPE1 cells were grown in MEM-alpha supplemented with 10% FBS and penicillin/streptomycin. CBMS1 mESCs have been described (Murakami et al. Development, 2011) and were grown in 2i/LIF medium as described (Hayashi K et al., Nat. Protoc., 2013).

extract_protocol:
For BrdU-IP samples, we followed our routine protocol as described (Ryba et al., Nat. Protoc. 2011). A Sony SH800 cell sorter was used in the ultra-purity mode, fractionating early and late S-phase populations. The BrdU-IP protocol has been described in detail (Ryba et al., Nat. Protoc. 2011), except that we used a Bioruptor UCD-250 (Sonic Bio) for gDNA sonication in high output mode, with ON/OFF pulse times of 30 sec/30 sec for 6 minutes. After BrdU-IP, immunoprecipitated DNA samples were subject to WGA with a SeqPlex kit (Sigma, SEQXE).   For early S-phase population samples, 200,000 cells from the first half of S-phase were sorted by Sony SH800 cell sorter, and gDNA was isolated using a Qiagen kit (Qiagen #69504, DNeasy Blood & Tissue Kit) and fragmented to 200–300 bp with a Covaris ultrasonciator (model: S220, tube: microTUBE snap-cap) according to the manufacturer’s instructions (peak incident power: 175, duty factor: 10%, cycles per burst: 200, treatment time: 120), followed by cleanup and size selection via Agencourt AMPure XP SPRI beads (Beckman Coulter).  For single or 100 cells samples, cells were sorted with a Sony SH800 cell sorter using the single-cell mode. Sample preparations were based on the previous study (Baslan et al., Genome Res. 2015). Extracted gDNA samples were subjected to WGA with a SeqPlex kit (Sigma, SEQXE). Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu).  For RNA-seq samples, cells were lysed in TRI Reagent (Molecular Research Center, Inc. cat. TR 118) to extract total RNA.
NGS libraries were constructed with a NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions, with slight modifications based on the previous study (Kadota et al., Sci. Rep. 2017). For a multi-plex NGS run, a SeqCap adapter kit A/B (Roche, 07141530001/ 07141548001) and NEXTflex DNA barcode (Bio Scientific, NOVA) were used. The samples were subjected to NGS on an Illumina Hiseq 1500 system (80, 84, 127-bp length, single-read or paired-end read). For NGS on Ion Proton system, libraries were constructed using Ion Plus Core Module for AB Library Builder System (Thermo Fisher Scientific, #4477683) with Ion Xpress Barcode Adapters 1-16 Kit (Thermo Fisher Scientific, #4477683).  For RNA-seq, NGS library preparation was performed using 500ng of total RNA following the standard protocol of TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: For differentiation, CBMS1 mESCs were differentiated to EpiLCs for 2 days and then switched to aggregation culture (EB/embryoid body culture) in Nunclon Sphera 96U-well plates (ThermoFisher, #174925), starting from 2,000 EpiLCs per well exactly as described (Hayashi K et al. Nat. Protoc., 2013), except for the use of plain GK15 medium (Hayashi K et al. Nat. Protoc., 2013) without any additional factors added during the aggregation culture. This process is practically identical to the SFEBq neural method of mESC differentiation (serum-free floating culture of EB-like aggregates with quick reaggregation) (Eiraku et al. Nat. Protoc., 2012) except that we started from EpiLCs instead of mESCs. In our hands, this resulted in efficient formation of neurectoderm cells based on gene expression after 7 days of differentiation (2 days to EpiLCs and then 5 additional days of EB culture).

value: CBA/MsM

value: embryonic stem cell

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase


title: CBMS1_ESC_single_75perS_34

tag: cell type


title: Hematopoietic stem cells (HSC)-replicate 1


title: CBMS1_ESC_single_75perS_33


title: UACC62R_2

tag: treatment


title: Lymphoid-primed multipotent progenitors (LMPP)-K27me3 micro-ChIP


title: CBMS1_ESC_single_75perS_30


title: CBMS1_ESC_single_75perS_29


title: CBMS1_ESC_single_75perS_27


title: CBMS1_ESC_single_75perS_26


title: CBMS1_ESC_single_75perS_28


title: CBMS1_ESC_single_75perS_31


title: CBMS1_ESC_single_75perS_23


title: CBMS1_ESC_single_75perS_21


title: CBMS1_ESC_single_25perS_36


title: CBMS1_ESC_single_25perS_41


title: CBMS1_ESC_single_25perS_39


title: CBMS1_ESC_single_25perS_35


title: CBMS1_ESC_single_75perS_20


title: CBMS1_ESC_single_25perS_42


title: CBMS1_ESC_single_25perS_40


title: CBMS1_ESC_single_25perS_37


title: CBMS1_ESC_single_25perS_38


title: CBMS1_ESC_single_25perS_32


title: Early thymic precursors (ETP)-replicate1

value: Thymus


title: CBMS1_ESC_single_25perS_30


title: CBMS1_ESC_single_75perS_25


title: CBMS1_ESC_single_25perS_43


title: CBMS1_ESC_single_75perS_19


title: CBMS1_ESC_single_75perS_24


title: CBMS1_ESC_single_75perS_18


title: CBMS1_ESC_single_75perS_22


title: CBMS1_ESC_single_25perS_31


title: CBMS1_ESC_single_75perS_14


title: CBMS1_ESC_single_75perS_15


title: CBMS1_ESC_single_75perS_16


title: CBMS1_ESC_single_75perS_13


title: CBMS1_ESC_single_25perS_34


title: Lhx8_WT_P7_Replicate_1

value: Oocytes

value: Lhx8 wildtype


title: CBMS1_ESC_single_25perS_33


title: CBMS1_ESC_single_75perS_11


title: CBMS1_ESC_single_75perS_06


title: CBMS1_ESC_single_75perS_08


title: CBMS1_ESC_single_25perS_23


title: CBMS1_ESC_single_25perS_18


title: CBMS1_ESC_single_25perS_17


title: CBMS1_ESC_single_25perS_27


title: CBMS1_ESC_single_75perS_09


title: CBMS1_ESC_single_25perS_22


title: CBMS1_ESC_single_25perS_15


title: CBMS1_ESC_single_25perS_19


title: CBMS1_ESC_single_75perS_07


title: CBMS1_ESC_single_25perS_25


title: CBMS1_ESC_single_25perS_26


title: CBMS1_ESC_single_25perS_29


title: CBMS1_ESC_single_G1_12


title: CBMS1_ESC_single_25perS_28


title: CBMS1_ESC_single_25perS_24


title: CBMS1_ESC_single_G1_11


title: CBMS1_ESC_single_25perS_14


title: CBMS1_ESC_single_75perS_10


title: CBMS1_ESC_single_G1_10


title: CBMS1_ESC_single_75perS_12


title: CBMS1_ESC_single_75perS_17


title: CBMS1_ESC_single_25perS_20


title: CBMS1_ESC_single_25perS_13


title: CBMS1_ESC_single_25perS_21


title: CBMS1_ESC_single_25perS_16


title: CBMS1_ESC_single_25perS_12


title: CBMS1_ESC_single_G1_09


title: CBMS1_ESC_single_25perS_11


title: CBMS1_ESC_single_25perS_08


title: CBMS1_ESC_single_25perS_06


title: CBMS1_ESC_single_25perS_10


title: CBMS1_ESC_single_25perS_09


title: CBMS1_ESC_single_25perS_05


title: CBMS1_ESC_single_25perS_07


title: CBMS1_ESC_single_25perS_01


title: CBMS1_ESC_single_MidS_50

value: MidS


title: CBMS1_ESC_single_MidS_48


title: CBMS1_ESC_single_25perS_04


title: CBMS1_ESC_single_MidS_47


title: CBMS1_ESC_single_MidS_46


title: CBMS1_ESC_single_25perS_03


title: CBMS1_ESC_single_MidS_49


title: CBMS1_ESC_single_MidS_44


title: CBMS1_ESC_single_MidS_43


title: CBMS1_ESC_single_MidS_42


title: CBMS1_ESC_single_MidS_41


title: CBMS1_ESC_single_MidS_40


title: CBMS1_ESC_single_MidS_39


title: CBMS1_ESC_single_MidS_37


title: CBMS1_ESC_single_MidS_36


title: CBMS1_ESC_single_MidS_38


title: CBMS1_ESC_single_MidS_51


title: CBMS1_ESC_single_MidS_35


title: CBMS1_ESC_single_MidS_45


title: CBMS1_ESC_single_75perS_04


title: CBMS1_ESC_single_75perS_02


title: CBMS1_ESC_single_75perS_03


title: CBMS1_ESC_single_75perS_05


title: CBMS1_ESC_single_75perS_01


title: CBMS1_ESC_single_G1_06


title: CBMS1_Day7Diff_ESC_single_MidS_37

status: Public on Dec 13 2018

source_name: Day7 Differentiated CBMS1 ESC

value: day7 differentiated ESCs

value: XX

value: CBA

value: MsM

value: FALSE


title: CBMS1_Day7Diff_ESC_single_MidS_32

value: XO(ΔCBA-X(Trancation))

value: TRUE


title: CBMS1_Day7Diff_ESC_single_MidS_38


title: CBMS1_Day7Diff_ESC_single_MidS_27


title: CBMS1_Day7Diff_ESC_single_MidS_34


title: CBMS1_Day7Diff_ESC_single_MidS_36


title: CBMS1_Day7Diff_ESC_single_MidS_35

value: XO(ΔMsM-X)


title: CBMS1_Day7Diff_ESC_single_MidS_29

value: XO(ΔCBA-X)


title: CBMS1_Day7Diff_ESC_single_MidS_26


title: CBMS1_Day7Diff_ESC_single_MidS_21


title: CBMS1_ESC_single_25perS_02


title: CBMS1_Day7Diff_ESC_single_MidS_23


title: CBMS1_Day7Diff_ESC_single_MidS_18


title: CBMS1_Day7Diff_ESC_single_MidS_16


title: CBMS1_Day7Diff_ESC_single_MidS_17


title: CBMS1_Day7Diff_ESC_single_MidS_14


title: CBMS1_Day7Diff_ESC_single_MidS_13

description: Binarization in haplotype-resolved analysis was failed


title: CBMS1_ESC_single_G1_08


title: CBMS1_Day7Diff_ESC_single_MidS_12


title: CBMS1_ESC_single_G1_07


title: CBMS1_Day7Diff_ESC_single_MidS_40


title: CBMS1_Day7Diff_ESC_single_MidS_09


title: CBMS1_Day7Diff_ESC_single_MidS_08


title: CBMS1_ESC_single_MidS_17


title: CBMS1_ESC_single_MidS_23


title: CBMS1_Day7Diff_ESC_single_MidS_11


title: CBMS1_Day7Diff_ESC_single_MidS_02


title: CBMS1_Day7Diff_ESC_single_MidS_03


title: CBMS1_ESC_single_MidS_03

description: High read depth


title: CBMS1_ESC_single_MidS_01

description: High read depth


title: CBMS1_ESC_single_MidS_02

description: High read depth


title: CBMS1_Day7Diff_ESC_single_MidS_04


title: CBMS1_Day7Diff_ESC_single_MidS_01


title: CBMS1_Day7Diff_ESC_single_MidS_07


title: CBMS1_ESC_single_MidS_13


title: CBMS1_Day7Diff_ESC_single_MidS_06


title: CBMS1_ESC_single_75perS_32


title: WT_VEH_replicate_6

status: Public on Nov 26 2018

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays 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) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following post-hybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray hybridization intensity data were log-transformed. Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

source_name: Hippocampus, WT, vehicle

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: All animal experiments were performed and approved by NIA Animal Care and Use Committee. The APP/PS1 mouse strain (#004462, Jackson's laboratory) was from Prof. Mark Mattson's laboratory. APP/PS1 mice and their WT littermates were used for experiments. All the animals were maintained at the National Institute on Aging under standard conditions and fed standard animal chow.

extract_protocol: RNA was purified from hippocampal tissue using the Nucleospin RNA isolation kit (Macherey-Nagel, #740955.250) according to the manufacturer's instructions.

treatment_protocol: APP/PS1 mice were treated with Urolithin A (200 mg/kg/day) in vehicle (DMSO) by gavage starting from 6 months (the age at which Aβ plaques appear) to 8 months, and subsequently evaluated for behavioral and molecular endpoints.

tag: genotype/variation

value: WT

value: 8 months

value: Brain

tag: region

value: Hippocampus

value: Vehicle


title: WT_VEH_replicate_4

tag: age


title: WT_VEH_replicate_1


title: HIPP_APP_PS1_VEH_replicate_4

source_name: Hippocampus, APP/PS1, vehicle


title: WT_VEH_replicate_3


title: WT_VEH_replicate_5


title: HIPP_APP_PS1_VEH_replicate_6


title: WT_VEH_replicate_2


title: HIPP_APP_PS1_VEH_replicate_7


title: HIPP_APP_PS1_VEH_replicate_2


title: HIPP_APP_PS1_ULA_replicate_6

source_name: Hippocampus, APP/PS1, Urolithin A

value: Urolithin A


title: HIPP_APP_PS1_VEH_replicate_5


title: HIPP_APP_PS1_VEH_replicate_3


title: HIPP_APP_PS1_VEH_replicate_1


title: HIPP_APP_PS1_ULA_replicate_4


title: HIPP_APP_PS1_ULA_replicate_3


title: HIPP_APP_PS1_ULA_replicate_1


title: HuR IP_control siRNA_replicate_3

status: Public on Oct 22 2018

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina's HumanHT-12 V4.0 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.54 μm using the Illumina iScan scanner.

source_name: HuR IP_control siRNA

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: U2OS cells were grown in DMEM containing high glucose, supplemented with Penicillin-Streptomycin (Corning) and 10% fetal bovine serum (FBS) (HyClone, GE). Cell synchronization was performed as described previously. Briefly, to collect mitotic cells, U2OS cells were treated with 50 ng/ml Nocodazole for 12-16 hours. To synchronize cells in G1, the mitotic cells were washed again with PBS and grown in fresh medium for 5-6 hours. The cells were synchronized to S-phase by double thymidine block and release. Briefly, cells were grown in 2 mM thymidine for 24 hours. After the first block, thymidine was removed and cells were released for 12 hours in fresh medium. Further, 2 mM thymidine was added again for 24 hours to synchronize cells at G1/S. The cells were released in fresh medium for 4 hours to collect them in S phase and 8 hours for G2 phase.

extract_protocol: Total RNA was prepared using Trizol (Trizol Reagent, Invitrogen) and acidic phenol (Ambion, Waltham, MA) according to manufacturer’s instructions.

treatment_protocol: U2OS cells were treated for 48 hours using either a siRNA targeting mIR-110HG exon 4 to deplete lnc-MIR100HG (IGM and IPM) or with a control siRNA (IGC and IHC. cells were then lysed in 20 mM Tris-HCl at pH 7.5, 100 mM KCl, 5 mM MgCl2 and 0.5% NP-40 for 10 min on ice, and centrifuged at 10,000 × g for 15 min at 4°C. The supernatants were incubated with protein A-Sepharose beads coated with antibodies that recognized HuR (Santa Cruz Biotechnology) for 1 h at 4°C.  After the beads were washed with NT2 buffer (50 mM Tris-HCl at pH 7.5, 150 mM NaCl, 1 mM MgCl2 and 0.05% NP-40), the complexes were incubated with 20 units of RNase-free DNase I (15 min at 37°C), and then further incubated with 0.1% SDS/0.5 mg/ml Proteinase K (15 min at 55 °C) to remove the DNA and proteins, respectively.

tag: cell line

value: osteosarcoma cells

tag: transfected with

value: Control siRNA

tag: immunoprecipitate

value: HuR IP


title: HuR IP_control siRNA_replicate_4


title: HIPP_APP_PS1_ULA_replicate_5

tag: tissue


title: IgG IP_miR-100HG siRNA_replicate_4

source_name: IgG IP_miR-100HG siRNA

value: miR-100HG siRNA

value: IgG IP


title: HuR IP_control siRNA_replicate_1


title: HuR IP_miR-100HG siRNA_replicate_2

source_name: HuR IP_miR-100HG siRNA


title: HIPP_APP_PS1_ULA_replicate_2


title: HuR IP_miR-100HG siRNA_replicate_1


title: IgG IP_miR-100HG siRNA_replicate_2


title: IgG IP_control siRNA_replicate_4

source_name: IgG IP_control siRNA


title: HuR IP_miR-100HG siRNA_replicate_4


title: HuR IP_control siRNA_replicate_2


title: IgG IP_miR-100HG siRNA_replicate_3


title: IgG IP_miR-100HG siRNA_replicate_1


title: HuR IP_miR-100HG siRNA_replicate_3


title: POLII4h1

status: Public on Sep 17 2018

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2((v2.2.9)) with the defaut parameters
further processed using samtools (v0.1.19)
peaks were called using MACS2 (v2.1.0) with the defaut setting except --nomodel  --extsize 250  -q 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using homer: makeUCSCfile

source_name: BJAB cell line

growth_protocol: BJAB cells were cultured in RPMI 1640 medium supplemented with 10% FBS (HyClone), Penicillin-Streptomycin-Glutamine (Invitrogen), and 2-mercaptoethanol.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
For sequencing, adapters were ligated to the precipitated DNA fragments or the input DNA to construct a sequencing library according to the manufacturer’s protocol (Illumina, San Diego, CA).  Adapters with a T overhang were ligated to the DNA fragments and size selected (~200 - 350 bases) on a 4.5% agarose gel. 18-cycles PCR amplification were performed to enrich for fragments with an adaptor on both ends.  These samples were bound to an Illumina single-read Flowcell, followed by cluster generation on the Illumina Cluster Station, and sequencing with Illumina Genome Analyzer (GA-II).

treatment_protocol: For activation, cells were exposed to 50ng/ml PMA and 2µM ionomycin (Sigma-Aldrich) for 1 and 4 hours.

value: b cell lymphoma cell line

tag: passages

value: BJAB

tag: chip antibody

value: RNA polymerase II (Covance Cat # MMS-126R)


title: POLII1h2


title: POLII1h1


title: POLII0h1


title: POLII0h2


title: IgG IP_control siRNA_replicate_3


title: RELA4h2

value: RelA (sc-372, Santa Cruz)


title: Monocyte_PBS_Replicate_2

description: PBS or PKH26-labeled extracellular vesicles (EVs) from diabetic or euglycemic individuals were pooled together and incubated with PBMCs (female, 38 yr old with no allergies) for 24 hours. Following the incubation, monocytes were isolated using the Monocyte Isolation Kit II (Myltenyi Biotec).

data_processing:
Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.
ID_REF = Unique identifiers from GPL10558
Detection_Pval = Detection Pvalue from Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0.

extract_protocol: RNA was isolated with Trizol (Thermo Fisher Scientific) according to manufacturer’s instructions, and followed by an additional phenol-chloroform extraction. RNA concentration and integrity was evaluated by Nanodrop and Agilent Bioanalyzer RNA 6000 Chip (Agilent, Santa Clara, CA).

tag: cells

value: Primary human PBMC monocytes

value: PBS


title: Monocyte_PBS_Replicate_3


title: IgG IP_control siRNA_replicate_1


title: RELA1h2


title: RELA1h1


title: Monocyte_Diabetic EVs_Replicate_1

source_name: Monocyte_Diabetic EVs

value: Diabetic EVs


title: IgG IP_control siRNA_replicate_2


title: RELA0h1


title: Monocyte_PBS_Replicate_1


title: chip input1

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2((v2.2.9)) with the defaut parameters
further processed using samtools (v0.1.19)
peaks were called using MACS2 (v2.1.0) with the defaut setting except -q 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using homer: makeUCSCfile


title: chip input2


title: BJAB4h2

data_processing:
Basecalls performed using NextSeq 500 RTA 2.4.11
 RSEM (https://github.com/deweylab/RSEM) was used to align RNA-Seq reads to the human genome and to quantify transcript abundance .
the differentially expressed genes were identified by EBseq  under the criteria of  FDR≤0.05.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated from aligned BAM files using the bamCoverage tool within the Galaxy platform

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit (Qiagen Inc).
Libraries were prepared according to the manufacturer’s protocol of TruSeq stranded mRNA sample preparation kit(20020595)

treatment_protocol: For activation, cells were exposed to 50ng/ml PMA and 2µM ionomycin (Sigma-Aldrich) for 1 and 4 hours.  To inhibit ERK signaling, cells were pre-treated with 0.33nM PD0325901 (Selleckchem) for 1h before PMA and ionomycin stimulation.


title: Monocyte_Euglycemic EVs_Replicate_1

source_name: Monocyte_Euglycemic EVs

value: Euglycemic EVs


title: BJAB4h1


title: Monocyte_Euglycemic EVs_Replicate_2


title: Monocyte_Euglycemic EVs_Replicate_1TR


title: POLII4h2


title: Monocyte_Diabetic EVs_Replicate_1TR


title: Monocyte_Diabetic EVs_Replicate_2TR


title: Monocyte_Diabetic EVs_Replicate_2


title: BJAB1h1


title: RELA4h1


title: BJAB0h2


title: BJAB0h1


title: RELA0h2


title: BJAB1h2


title: clone2 -Tet 4h1


title: clone2 -Tet 1h2


title: clone2 -Tet 1h1


title: clone2 -Tet 0h2


title: clone2 -Tet 0h1


title: clone2 +Tet 4h1


title: clone2 +Tet 1h1


title: clone2 +Tet 1h2


title: clone2 +Tet 0h2


title: clone2 -Tet 4h2


title: clone2 +Tet 4h2


title: clone2 +Tet 0h1


title: clone1 -Tet 4h2


title: clone1 +Tet 4h1


title: clone1 +Tet 4h2


title: clone1 -Tet 1h1


title: clone1 -Tet 1h2


title: clone1 +Tet 1h2


title: polymerase II 0h ChIA-PET1

data_processing:
Basecalls performed using NextSeq 500 RTA 2.4.11
The ChIA-PET sequence data were  analyzed using ChIA-PET Tool (https://github.com/GuoliangLi-HZAU/ChIA-PET_Tool). The linker sequences are  GTTGGATAAGATATCGC and  GTTGGAATGTATATCGC.  Interaction clusters with Span < 8Kb are filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: the loop txt files were generated using ChIA-PET Tool.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Chromatin was isolated and subjected to ChIA-PET protocol as described in Fullwood et al (Fullwood et al: An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 2009, 462(7269):58-64).   BJAB cells were treated with 1.5mM EGS (Pierce Cat # 21565) for 30 min, followed 1% formaldehyde at room temperature for 15 min, and then neutralized using 0.2M glycine.  Chromatin was sheared by sonication, and anti-Pol II monoclonal antibody 8WG16 (Covance, MMS-126R) was used to enrich Pol II-bound fragments.  A portion of ChIP DNA was eluted from antibody-coated beads for quantitation using Picogreen fluorimetry, and for enrichment analysis using quantitative PCR.  Two biological replicate ChIP samples were used for ChIA-PET library construction.

treatment_protocol: no activation


title: clone1 +Tet 0h1


title: Act-Top3bdRGG_HP1ChIP_complementation_input

status: Public on Sep 12 2018

data_processing:
CHIP SEQ fastq files are first passed fastqc to remove potentially low quality bases
After cleaning, the fastq files are mapped to Drosophila dm6 genome by Bowtie2.v2-2.3.4 by using command  "bowtie2 --very-sensitive-local -p 16 --no-unal -k 20 --rdg 10,6 " as parameters, and then piplined  with  the tool box samtools v1.8 as "samtools view -T  -q30 -S -b"  to generate mapped bam files.
The bam files are sorted by samtools.v1.9 sort and index, and then converted to bed format files by bamtools.v1.8 with convert function
The bed files are used to find significant peaks by SICER.v1.1 under PYTHON.v2.7 by using "SICER.sh dm6 1 100 100 0.692 600 .05" to obtain significant island peaks between the sample bed files and its control (input) bed files for ChIP assays. The island.bed files are used for studies of the peak binding sites for indicated proteins on chromatin.
Comparing peaks between different genotypes are genearted by SICER.  We can study the differences between different genotypes by using the bedtools.v1.8 intersect.
Genome_build: Drosophila dm6
Supplementary_files_format_and_content: bed file

organism: Drosophila melanogaster

source_name: Drosophila head

growth_protocol: Drosophila were cultured on corn syrup-soy recipe food from Archon Scientific at 25±1°C and 60±5% humidity, under a 12h/12hr light/dark cycle

extract_protocol:
The homogenized and cleared fly heads were sonicated to a length between 200~500 bp. The sheared chromatin was precleared with Protein A beads then incubated with 5ml of antibody and 30ml of Protein A beads at 4°C for 3 hours. After thorough washing, the samples were eluted by 10% SDS and Protease K at 65°C for 8 hours. The eluted chromatin was extracted by phenol-chloroform clean-up followed by ethanol precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 100ml of fly heads were isolated from fast freeze and sieving

tag: antibody for chip

value: n/a (input chromatin)

value: adult (1-2 weeks)


title: polymerase II 0h ChIA-PET2


title: clone1 -Tet 0h1


title: clone1 +Tet 1h1


title: Act-Top3bWT_HP1ChIP_complementation_input


title: Top3b26_HP1ChIP_complementation_input


title: Act-Top3bY332F_HP1ChIP_complementation_input


title: clone1 -Tet 4h1


title: w1118_HP1ChIP_complementation_input


title: w1118_input_Top3brp1_H3K9me23

description: w1118_input_H3K9me23 and Top3b rpeat1                   (Used for multiple ChIP samples)


title: w1118_Top3bChIP_repeat3_input


title: FLAGAGO2_FLAGChIP_input_repeat2


title: w1118_Top3bChIP_repeat2_input


title: w1118_FLAGChIP_input


title: Top3b26_AGO21-1-7_HP1ChIP_repeat2_input


title: Top3b26_AGO21-1-7_HP1ChIP_repeat1_input


title: FLAGAGO2_FLAGChIP_input_repeat1


title: Top3b26_HP1ChIP_repeat2_input


title: w1118_HP1ChIP_repeat3_input


title: AGO2_1-1-7_HP1ChIP_input_repeat2


title: Top3b26_HP1ChIP_repeat1_input


title: AGO2_1-1-7_HP1ChIP_input_repeat1


title: w1118_HP1ChIP_repeat2_input


title: Act-Top3bdRGG_HP1ChIP_complementation

description: HP1 ChIP in Top3b26;Act>Top3bDRGG mutant complementation


title: Act-Top3bWT_HP1ChIP_complementation

description: HP1 ChIP in Top3b26;Act>Top3bWT complementation


title: w1118_HP1ChIP_repeat1_input


title: Top3b26_HP1ChIP_complementation

description: HP1 ChIP in Top3b26 mutant


title: w1118_HP1ChIP_complementation

description: HP1 ChIP in w1118


title: Top3b26_H3K9me3ChIP_repeat3

description: H3K9me3 ChIP in Top3b 26 mutant (repeat3)     (Compared to Top3b26_input_H3K9me23)


title: Top3b26_H3K9me3ChIP_repeat2

description: H3K9me2 ChIP in Top3b 26 mutant (repeat2)     (Compared to Top3b26_input_H3K9me23)


title: Top3b26_input_H3K9me23

description: Top3b26_input_H3K9me23                 (Used for multiple ChIP samples)


title: clone1 -Tet 0h2


title: Top3b26_H3K9me3ChIP_repeat1

description: H3K9me3 ChIP in Top3b 26 mutant (repeat1)     (Compared to Top3b26_input_H3K9me23)


title: Top3b26_H3K9me2ChIP_repeat2


title: Top3b26_H3K9me2ChIP_repeat3

description: H3K9me2 ChIP in Top3b 26 mutant (repeat3)     (Compared to Top3b26_input_H3K9me23)


title: Top3b26_H3K9me2ChIP_repeat1

description: H3K9me2 ChIP in Top3b 26 mutant (repeat1)     (Compared to Top3b26_input_H3K9me23)


title: w1118_H3K9me2ChIP_repeat3

description: H3K9me2 ChIP in w1118 (repeat3)     (Compared to  w1118_input_Top3brp1_H3K9me23)


title: w1118_H3K9me3ChIP_repeat3

description: H3K9me3 ChIP in w1118 (repeat3)     (Compared to  w1118_input_Top3brp1_H3K9me23)


title: Top3b26_HP1ChIP_repeat3_input


title: w1118_H3K9me3ChIP_repeat2

description: H3K9me3 ChIP in w1118 (repeat2)     (Compared to  w1118_input_Top3brp1_H3K9me23)


title: w1118_Top3bChIP_repeat3

description: Top3b ChIP in w1118 (repeat3)


title: w1118_H3K9me2ChIP_repeat1

description: H3K9me2 ChIP in w1118 (repeat1)     (Compared to  w1118_input_Top3brp1_H3K9me23)


title: clone1 +Tet 0h2


title: w1118_H3K9me2ChIP_repeat2

description: H3K9me2 ChIP in w1118 (repeat2)     (Compared to  w1118_input_Top3brp1_H3K9me23)


title: FLAGAGO2_FLAGChIP_repeat1

description: FLAG ChIP in FLAG-AGO2 flies (repeat1)

value: FLAG


title: w1118_Top3bChIP_repeat2

description: Top3b ChIP in w1118 (repeat3)


title: FLAGAGO2_FLAGChIP_repeat2

description: FLAG ChIP in FLAG-AGO2 flies (repeat2)


title: w1118_Top3bChIP_repeat1

description: Top3b ChIP in w1118 (repeat1)      (Compared to w1118_input_Top3brp1_H3K9me23)


title: Act-Top3bY332F_HP1ChIP_complementation

description: HP1 ChIP in Top3b26;Act>Top3bY332F mutant complementation


title: w1118_FLAGChIP

description: FLAG ChIP in w1118 flies


title: Top3b26_AGO21-1-7_HP1ChIP_repeat2

description: HP1 ChIP in Top3b 26;AGO2 1-1-7 double mutant (repeat2)


title: Top3b26_AGO21-1-7_HP1ChIP_repeat1

description: HP1 ChIP in Top3b 26;AGO2 1-1-7 double mutant (repeat1)


title: Top3b26_HP1ChIP_repeat3

description: HP1 ChIP in Top3b 26 mutant (repeat3)


title: Top3b26_HP1ChIP_repeat2

description: HP1 ChIP in Top3b 26 mutant (repeat2)


title: Top3b26_HP1ChIP_repeat1

description: HP1 ChIP in Top3b 26 mutant (repeat1)


title: AGO2_1-1-7_HP1ChIP_repeat2

description: HP1 ChIP in AGO2 1-1-7 mutant (repeat2)


title: AGO2_1-1-7_HP1ChIP_repeat1

description: HP1 ChIP in AGO2 1-1-7 mutant (repeat1)


title: w1118_HP1ChIP_repeat2

description: HP1 ChIP in w1118 (repeat2)


title: w1118_HP1ChIP_repeat3

description: HP1 ChIP in w1118 (repeat3)


title: w1118_HP1ChIP_repeat1

description: HP1 ChIP in w1118 (repeat1)


title: Top3b26_RNAseq_repeat4

description: RNA-seq of Top3b26 mutant (repeat4)

data_processing:
RNA SEQ fastq files are first passed fastqc to remove potentially low quality bases
After cleaning, the fastq files are mapped to Drosophila dm6 genome by Tophat v2.1.1 by using command  "tophat2  --b2-very-sensitive-local -p 16 --segment-length=15 --max-intron-length=200000 --min-intron-length=5 --max-segment-intron=200000 --min-coverage-intron=5 --max-coverage-intron=200000 --min-anchor-length=3 --splice-mismatches=2 --coverage-search  --transcriptome-only " as parameters, and then piplined  with  the tool box samtools v1.8 as "samtools view -T  -q30 -S -b"  to generate mapped bam files.
The bam files are sorted by samtools.v1.9 sort and index, and then converted to bed format files by bamtools.v1.8 with convert function
The bam files are used to do further gene expression differential analysis by Tuxedo Suite  v2.2.1 pipleline to do genome structrte mapping, merging and gei siginificant defferential gene lists for each comparison.
The bed files are used to get gene raw counts data and fpkm normalized data for further analyses.
Genome_build: Drosophila dm6
Supplementary_files_format_and_content: raw counts files

extract_protocol:
Total RNA was extracted using TRIzol reagent, and cDNAs were synthesized by reverse transcription
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 200ml of Drosophila heads/per sample were collected by fast freezing and sieving

value: head

value: Top3b26 mutant


title: Top3b26_RNAseq_repeat3

description: RNA-seq of Top3b26 mutant (repeat3)


title: Top3b26_RNAseq_repeat2

description: RNA-seq of Top3b26 mutant (repeat2)


title: w1118_H3K9me3ChIP_repeat1

description: H3K9me3 ChIP in w1118 (repeat1)     (Compared to  w1118_input_Top3brp1_H3K9me23)


title: Top3b26_RNAseq_repeat1

description: RNA-seq of Top3b26 mutant (repeat1)


title: w1118_RNAseq_repeat4

description: RNA-seq of w1118 (repeat4)


title: w1118_RNAseq_repeat1

description: RNA-seq of w1118 (repeat1)


title: w1118_RNAseq_repeat3

description: RNA-seq of w1118 (repeat3)


title: w1118_RNAseq_repeat2

description: RNA-seq of w1118 (repeat2)


title: Hydroxyurea_replicate_3

status: Public on Sep 10 2018

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays 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) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

data_processing: Raw microarray hybridization intensity data were log-transformed.  Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

growth_protocol: All studies were approved by the National Institute of Aging Institute of Animal Care and Use Committee and all procedures followed the NIH Guide for the Care and Use of Laboratory Animals. All mice were female nontransgenic control littermates of APPswe695/PSEN1dE9 mice [B6.Cg-Tg(APPswe,PSEN1dE9)85Dbo/J].  Original breeding pairs were purchased from the Jackson Laboratory, and were maintained on a C57BL/6J background in the National Institute of Aging vivarium under a 12-hour light/12-hour dark cycle on a C57BL/6 background. There were two to four mice per cage.

extract_protocol: RNA was purified from hippocampal tissue using Trizol (Thermo Fisher Scientific) according to the manufacturer's instructions.

treatment_protocol: Four nontransgenic control littermates of APP/PS1 mice were treated with HU (45 mg/kg/day) in their drinking water, starting  at 9-14 weeks of age, and lasting for  for 2.5 month.  THeir hippocampi were removed, flash frozen, and stored at -80oC along with four untreated control animals.

value: Brain

value: Hippocampus

tag: age at end of treatment

value: 19 weeks

value: hydroxyurea (45 mg/kg/day

tag: treatment time

value: 10 weeks


title: Hydroxyurea_replicate_1

value: 24 weeks


title: Soleus_EX_AF_replicate5

growth_protocol: Thirty-five 6 month old male C57 BL/6J mice (Jackson Laboratories, Bar Harbor, ME) were housed individually with ad libitum access to water.  Animal rooms were maintained at 20-22°C with 30%-70% relative humidity and a 12 hour light/12 hour dark cycle. Blood samples were collected via eye bleeds and a VO2max test was performed prior to the initiation of dietary and exercise interventions.

extract_protocol: RNA extraction was performed using Qiagen RNeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA), as per the manufacturers instructions, using the fibrous tissue protocol for soleus muscle.

treatment_protocol: Mice were randomly assigned to one of four groups: sedentary ad libitum fed control (CTRL; n=9); sedentary alternate day fasting (AF; n=8); daily treadmill exercise fed ad libitum (EX; n=9); and daily treadmill exercise alternate-day fasting (EXAF; n=9). All other mice completed all tests in the study, except for the maximum endurance test in which one mouse in the CTRL group and one mouse in the EXAF group refused to run on the treadmill.  For AF and EXAF groups, food (standard mouse chow: NIH-07 diet from Harlan-Teklad, Indianapolis, IN) was alternatively provided or removed every day at 17:00. Body weights were recorded weekly.  Average weekly food/energy consumption was calculated (the weight of food provided minus the weight of food remaining uneaten) x kcal/gram of food.  Blood glucose measurements were made at baseline, and every two weeks on consecutive feeding and fasting days, before and after exercise using a Freestyle Lite® Abbott meter. On the fourth week of training blood ketone levels were measured on consecutive feeding and fasting days, before and after exercise using a StatSite® M B-HB meter. After 8 weeks of training the animals were anesthetized and decapitated. AF and EXAF mice were euthanized on a fasting day and EX mice were sacrificed 18 hours after the last exercise session.  All mice were sacrificed between the hours of 9:00 and 12:00. Trunk blood, liver and soleus muscle tissues were collected and immediately flash frozen and stored at -80 C.

value: Exercised_Alternate day fasting

value: Soleus

tag: developmental stage

value: 6 month old

tag: Sex

value: male

tag: strain


title: Soleus_EX_AF_replicate1

tag: treatment


title: Soleus_EX_replicate3

value: Exercised


title: Soleus_EX_replicate7


title: Soleus_EX_replicate4


title: Control_replicate_2

value: Control


title: Soleus_AF_replicate4

value: Alternate day fasting


title: Control_replicate_3


title: Soleus_EX_AF_replicate4


title: Soleus_EX_replicate1


title: Soleus_EX_replicate6


title: Monocyte_Euglycemic EVs_Replicate_3

description: PBS or PKH26-labeled extracellular vesicles (EVs) from diabetic or euglycemic individuals were pooled together and incubated with PBMCs (female, 38 yr old with no allergies) for 24 hours. Following the incubation, monocytes were isolated using the Monocyte Isolation Kit II (Myltenyi Biotec).

value: Primary human PBMC monocytes

value: Euglycemic EVs


title: Hydroxyurea_replicate_4


title: Soleus_AF_replicate5


title: Control_replicate_4


title: Soleus_EX_replicate2


title: Soleus_AF_replicate6


title: Soleus_EX_AF_replicate3


title: Soleus_AF_replicate2


title: Hydroxyurea_replicate_2


title: Soleus_EX_AF_replicate2


title: Soleus_AF_replicate8


title: Soleus_AF_replicate7


title: Soleus_EX_replicate5


title: Soleus_CTRL_replicate7


title: Soleus_AF_replicate3


title: Soleus_AF_replicate1


title: Control_replicate_1


title: Soleus_CTRL_replicate6


title: Liver_EX_AF_replicate7

value: Liver


title: Soleus_CTRL_replicate2


title: Soleus_CTRL_replicate3


title: Soleus_CTRL_replicate5


title: Liver_EX_replicate3


title: Liver_EX_AF_replicate5


title: Soleus_CTRL_replicate4


title: Liver_EX_replicate2


title: Liver_AF_replicate8


title: Liver_EX_replicate7


title: Soleus_CTRL_replicate1


title: Liver_EX_AF_replicate4


title: Liver_EX_AF_replicate8


title: Liver_EX_replicate6


title: Liver_EX_AF_replicate1


title: Liver_EX_AF_replicate6


title: Liver_EX_replicate5


title: Liver_EX_replicate1


title: Liver_EX_AF_replicate2


title: Liver_AF_replicate6


title: Liver_AF_replicate7


title: Liver_EX_replicate8


title: Liver_EX_AF_replicate3


title: Liver_AF_replicate1


title: Liver_AF_replicate2


title: Liver_EX_replicate4


title: Liver_AF_replicate4


title: Liver_AF_replicate5


title: Liver_AF_replicate3


title: Liver_CTRL_replicate5