title: Rat_HEPATOPAC_SD_male_flutamide_30µM_6hr [US-1465620]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465620


title: adr1 triple_4h_EV_Rep2

status: Public on Jun 22 2020

type: SRA

city: Chapel Hill

first: Isai

last: Salas Gonzalez

address: 250 Bell Tower Drive, Room 4244

country: USA

institute: The University of North Carolina at Chapel Hill

library_source: transcriptomic

data_processing:
Initial quality assessment of the Illumina RNA-Seq reads was performed using FastQC version 0.11.7.
Trimmomatic version 0.36 was used to identify and discard reads containing the Illumina adaptor sequence.
The resulting high-quality reads were then mapped against the TAIR10 Arabidopsis reference genome using HISAT2 version 2.1.0 with default parameters.
The featureCounts function from the Subread package was then used to count reads that mapped to each one of the 27,206 nuclear protein-coding genes, we used these counts to construct a raw count table of expression.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Tab delimited file containing the count matrix

molecule: total RNA

organism: Arabidopsis thaliana

source_name: leaf disc

growth_protocol: Arabidopsis plants were grown at short day conditions (8-hour light/16-hour dark cycle at 21°C/18°C and 45% humidity. Arabidopsis sequence data for helper NLRs is available under the following AGI accession numbers: ADR1/At1g33560, ADR1-L1/At4g33300, ADR1-L2/At5g04720, NRG1.1/NRG1A/At5g66900, NRG1.2/NRG1B/At5g66910.

extract_protocol:
RNA was purified from plant tissue using the RNeasy 96 Kit (Qiagen). The plant “user developed protocol” was followed except for the addition of a 96% ethanol wash step after the second RPE wash to ensure removal of residual salts. Purified RNAs were kept at -80C.
Illumina-based mRNA-Seq libraries were prepared from 1 μg RNA following [61]. Briefly, mRNAs were selected using Sera-mag oligo(dT) magnetic beads (GE Healthcare Life Sciences). RNAs were washed and fragmented at 94°C for 6 minutes. First-strand cDNA synthesis was performed using random hexamers and reverse transcriptase (Superscript III reverse transcriptase, Invitrogen). Second-strand cDNA synthesis was done using DNA Polymerase I and RNAseH. Double-stranded cDNAs were end-repaired using T4 DNA polymerase, T4 polynucleotide kinase, and Klenow polymerase. The DNA fragments were then adenylated using Klenow exo-polymerase to allow the ligation of Illumina adapters (Kapa Dual-indexed adapter kit, Roche). Unless specified, reagents were purchased from Enzymatics.
Library quality control and quantification were performed using the 5200 Fragment Analyser and the NGS fragment kit (Agilent). Libraries were sequenced using Illumina HiSeq4000 sequencers to generate 50-bp single-end reads.

treatment_protocol: Plants for bacterial infiltration assays were grown for 6 weeks under short day conditions (8h light/16h dark at 21°C/18°C and 45% humidity). For bacterial growth curves, Pst DC3000 ∆hrcC and Pst DC3000 expressing either AvrRps4, AvrRpt2, EV, AvrRpm1, grown on KB plates containing appropriate antibiotics, were re-suspended in 10 mM MgCl2 to a final concentration of 5x105 (OD600 0.001).  Plants were hand-infiltrated with the bacterial suspension.

tag: genotype

value: adr1 triple

tag: time

tag: treatment

value: EV

tag: rep


title: Rat_HEPATOPAC_SD_male_MK-3207_30µM_48hr [US-1465587]

city: West Point

first: Alexei

middle: A

last: Podtelezhnikov

state: PA

address: 770 Sumneytown Pike

department: Non-clinical Drug Safety

institute: Merck & Co., Inc.

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465587

data_processing:
Genome alignment and gene quantitation was performed using OmicSoft Array Studio
Cleaned reads were aligned to the Rnor_6.0 and hg38 genome references using the OmicSoft Aligner with a maximum of 2 allowed mismatches
Gene level counts were determined by the RNA-Seq by expectation maximization algorithm as implemented in OmicSoft Array Studio and using Ensembl.R94 gene models
FPKM normalization was applied to RNA-Seq counts followed by log-transformation with smoothing, i.e., log10(FPKM+0.01)
Genome_build: Rnor_6.0 and hg38 genome
Supplementary_files_format_and_content: Count, FPKM

organism: Rattus norvegicus

growth_protocol: HEPATOPAC cells were cultured in proprietary Maintenance Medium (containing 10% serum, part number 5032C) in a  37°C humidified incubator with 10% CO2;  other cells were cultured using standard or proprietary hepatocyte procedures.

extract_protocol:
Total RNA was purified from frozen liver or cell culture samples using the MagMAX™ Express Magnetic Particle Processor using the MagMAX™-96 for Microarrays Total RNA Isolation Kit (Thermo Fisher AM1839)
Total RNA samples were converted into cDNA libraries using the KAPA RNA HyperPrep Kit with RiboErase (HMR) Kit (Roche 08098131702) for rat or the TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat Kit (Illumina 20020596) for human

treatment_protocol: HEPATOPAC cells were treated with compound-containing media on Study Days 2, 5, 7, for a total of 9 days

tag: strain

value: Sprague Dawley

tag: Sex

value: male

tag: dose

value: 30 microM

tag: time point

tag: tissue

value: HEPATOPAC


title: Rat_HEPATOPAC_SD_male_MK-3207_80µM_48hr [US-1465588]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465588

value: 80 microM


title: adr1 triple_T0_T0_Rep2


title: adr1 triple_4h_avrRpm1_Rep2


title: Rat_HEPATOPAC_SD_male_MK-3207_30µM_48hr [US-1465585]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465585


title: Rat_HEPATOPAC_SD_male_MK-3207_80µM_24hr [US-1465582]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465582


title: Rat_HEPATOPAC_SD_male_MK-3207_80µM_24hr [US-1465583]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465583


title: Rat_HEPATOPAC_SD_male_MK-3207_80µM_24hr [US-1465584]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465584


title: Rat_HEPATOPAC_SD_male_flutamide_30µM_24hr [US-1465625]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465625

value: flutamide


title: adr1 triple_4h_EV_Rep1


title: adr1 triple_T0_T0_Rep1


title: Rat_HEPATOPAC_SD_male_flutamide_30µM_6hr [US-1465621]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465621


title: Dbudc1: bud27∆ mutant chip 1

city: Jaén

first: Francisco

last: Navarro

state: Jaén

address: Campus Las Lagunillas s/n.

department: Experimental Biology

country: Spain

institute: Universidad de Jaén

description: Immunoprecipitation was performed using 200 µl of magnetic beads  Dynabeads M-280 Sheep anti-Mouse IgG (Invitrogen) mixed with 8WG16 anti-Rpb1 antibody (Santacruz), for Rpb1, and 300 µl of the sonicated sample.

library_source: genomic

data_processing:
Input DNAs were sequenced in an Illumina HiSeq 2000 instrument.
The quality metrics of the Fastq sequencing datasets were obtained with FastQC and inspected visually
Sequencing adapters were removed from raw reads with Fastx Clipper
The resulting high-quality sequences were mapped to the S. cerevisiae S288c genome (SGD R64) with Hisat2
Supplementary_files_format_and_content: RPKM-normalised coverage bigWig tracks for the individual ChIP-seq datasets.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: 200 ml of yeast culture were collected at an OD600 of about 0.6

extract_protocol:
Cell disruption was carried out by vigorously vortexing this sample in the presence of 200 µl of glass beads for 15 min. After disruption, lysis buffer was added to the cells extract to adjust 1.5 ml and then samples were subsequently sonicated by a Bioruptor sonicator (Diagenode) for 45 min at 30 s on/off intervals.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: Crosslinked by adding 1% formaldehyde to the culture, during 15 minutes.After a 15-minute incubation, 10 ml of 2.5 M glycine were added and the culture was incubated for 5 min in the presence of this solution. Cells were harvested and washed 4 times with 150 mM NaCl, 20 mM Tris-HCl, pH 7.5. Then they were resuspended in 300 µl of lysis buffer (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, pH 8, 1% (v/v) Triton-X-100, 0.1% (w/v) sodium deoxycholate, 1 mM PMSF, 0.15% (w/v) benzamidine, and protease inhibitor cocktail (Complete, Roche)).

value: bud27delta mutant in  BY4741 genetic background


title: Dbudc2: bud27∆ mutant chip 2


title: Rat_HEPATOPAC_SD_male_MK-3207_30µM_24hr [US-1465581]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465581


title: Dbudi2: bud27∆ mutant INPUT 2


title: Rat_HEPATOPAC_SD_male_MK-3207_30µM_24hr [US-1465579]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465579


title: adr1 triple_0.5h_avrRpt2_Rep2


title: Rat_HEPATOPAC_SD_male_MK-3207_80µM_6hr [US-1465578]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465578


title: Dbudi1: bud27∆ mutant INPUT 1


title: Rat_HEPATOPAC_SD_male_MK-3207_30µM_48hr [US-1465586]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465586


title: adr1 triple_0.5h_avrRpm1_Rep3


title: Rat_HEPATOPAC_SD_male_MK-3207_80µM_6hr [US-1465577]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465577


title: Rat_HEPATOPAC_SD_male_flutamide_30µM_6hr [US-1465619]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465619


title: BYc2: WT chip 2


title: Rat_HEPATOPAC_SD_male_MK-3207_80µM_6hr [US-1465576]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465576


title: adr1 triple_4h_avrRpt2_Rep2


title: BYc1: WT chip 1


title: adr1 triple_0.5h_avrRpt2_Rep3


title: adr1 triple_0.5h_avrRpt2_Rep1


title: Rat_HEPATOPAC_SD_male_MK-3207_30µM_6hr [US-1465575]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465575


title: Rat_HEPATOPAC_SD_male_MK-3207_30µM_24hr [US-1465580]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465580


title: adr1 triple_8h_EV_Rep2


title: MLL-AF4_2 d4 15µM

city: Tuebingen

first: Corina

last: Schneidawind

address: Otfried-Mueller-Str. 10

department: Hematology and Oncology

country: Germany

institute: University Hospital Tuebingen

description: rawCounts.csv (I19R038a09)

data_processing:
Single-end reads were cleaned up and trimmed with BBduk (BBMap suite v38.67) and parameters: k=13,ktrim=r,useshortkmers=t,mink=5,qtrim=r,trimq=10,minlength=20
Cleaned-up and trimmed fastq files were alined with STAR (v2.7.0a) against the Ensembl H.sapiens genome with parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD
Read counts for all genes were determined using Rsubread (v2.0.0) with parameters: GTF.featureType = "exon",GTF.attrType = "gene_id",useMetaFeatures = TRUE,allowMultiOverlap = FALSE,strandSpecific = 1,countMultiMappingReads = FALSE
Genome_build: Ensembl v95 H.sapiens
Supplementary_files_format_and_content: CVS file with raw read counts per gene identified by Ensembl gene ID

organism: Homo sapiens

source_name: CD34+ HSPCs from cord blood

growth_protocol: Cells were cultured in StemSpan II media (StemCell Technologies) including 10% fetal bovine serum (FBS, Biochrom) and 100 IU/ml penicillin-streptomycin (Lonza) supplemented with cytokines: stem cell factor (SCF), thrombopoietin (TPO), FLT3-L, interleukin-6 (IL-6), interleukin-3 (IL-3) (50 ng/mL each, PeproTech) and StemRegenin1 (SR1; 0.75 mM) and UM729 (both StemCell Technologies). Cells were maintained at a cell density of 7.5-20x105/ml, at 37°C and 5% CO2 and subcultured every second day.

extract_protocol:
Total RNA was isolated with Macherey Nagel NucleoSpin RNA Kit.
Libraries were generated using QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina.
Poly(A)-selected sequencing libraries were generated according to manufacturer instructions and sequenced on a NextSeq 500 at 75bp paired-end resolution at a depth of ~5 million reads.

treatment_protocol: The respective treatment of PF-9366 or DMSO as control was added 1:1000 to the culture medium. Cells were maintained at a cell density of 7.5-20x105/ml, at 37°C and 5% CO2 and subcultured every second day. Added medium for subculturing was supplemented with the respective treatment as well (1:1000) to avoid dilution effects.

tag: genetics


title: BYi2: WT Input 2


title: adr1 triple_0.5h_avrRps4_Rep3


title: MLL-AF4_2 d4 DMSO

description: rawCounts.csv (I19R038a07)

value: DMSO


title: Rat_HEPATOPAC_SD_male_MK-3207_30µM_6hr [US-1465574]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465574


title: adr1 triple_0.5h_avrRpm1_Rep2


title: BYi1: WT Input 1


title: adr1 triple_4h_avrRps4_Rep3


title: Rat_HEPATOPAC_SD_male_MK-3207_30µM_6hr [US-1465573]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465573


title: MLL-AF4_1 d4 15µM

description: rawCounts.csv (19R038a03)


title: adr1 triple_8h_avrRpt2_Rep3


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_100µM_48hr [US-1465572]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465572

value: β-naphthoflavone

value: 100 microM


title: MLL-AF4_1 d4 DMSO

description: rawCounts.csv (I19R038a01)


title: adr1 triple_0.5h_avrRps4_Rep2


title: adr1 triple_0.5h_avrRpm1_Rep1


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_100µM_48hr [US-1465570]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465570


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_30µM_48hr [US-1465569]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465569


title: adr1 triple_0.5h_EV_Rep3


title: bud27∆ rep1 [bud27rep1]

data_processing:
Input DNAs were sequenced in an Illumina HiSeq 2000 instrument
The quality metrics of the Fastq sequencing datasets were obtained with FastQC and inspected visually
Sequencing adapters were removed from raw reads with Fastx Clipper
The resulting high-quality sequences were mapped to the S. cerevisiae S288c genome (SGD R64) with Hisat2
Resulting SAM, previously obtained from the BAM,  were analyzed in the R/Bioconductor software, based on an advanced version of the DESeq package, DESeq2
Supplementary_files_format_and_content: abundance measurements

growth_protocol: Yeast strains were cultured in YPD liquid medium at 30ºC unless otherwise specified, until OD600 of about 0.8.

extract_protocol:
Sequencing cDNA libraries were performed using the QuantSeq 3' mRNA-Seq Library Prep Kit form Illumina following the manufacturer instructions; as above, they were sequenced in an Illumina HiSeq 2000 instruments.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In case of rapamycin-treated cells, cultures were incubated overnight in YPD containing 50ng/ml of rapamycin until OD600 of about 0.8.

tag: strain background

tag: genotype/variation

value: bud27{deleta} mutant


title: bud27∆ rep2 [bud27rep2]


title: WT + Ramycin rep1 [rapa11]

source_name: WT + Ramycin

value: wild type


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_30µM_48hr [US-1465568]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465568


title: adr1 triple_8h_avrRpt2_Rep2


title: Untreated TSA CD45+ infiltrating cells

city: New York

first: Aitziber

last: Buque Martinez

state: New York

address: 1300 York Avenue

department: Radiation Oncology

institute: Weill Cornell Medical College

data_processing:
10x Genomics Cell Ranger Single Cell Software suite v2.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample de-multiplexing, alignment (mm10), filtering, UMI counting, single-cell 3’end gene counting and performing quality control, using the manufacturer parameters. Unsupervised cell clustering was carried out using Seurat 2.3.456 in the R computational environment (v. 3.5.3). Cells with <1000 genes or <3000 UMIs or >10% mitochondrial genes and genes detected in <3 cells were excluded from the analysis. Gene expression raw counts were normalized following a global-scaling normalization method with a scale factor of 10,000 and a log transformation, using the Seurat NormalizeData function. The top 2775 highly variable genes were selected, followed by principal component analysis (PCA). Top 35 PCs were further used to perform harmony57 to remove the effect of confounding factors between two samples. The first 35 harmony results were used to generate 2-dimensional t-Distributed Stochastic Neighbor Embedding (RunTSNE in Seurat, perplexity=30) and unsupervised cell clustering by a shared nearest neighbor (FindClusters in Seurat, k.param=30 and resolution=0.6). A list of conserved cell-type specific genes were generated by FindAllMarkers function in Seurat. Manually use marker genes to identify cell types and confirmed by SingleR 0.2.2 (Single-cell Recognition)58 package . Gene set analysis and bar charts were generated using the ggpubr and ggplot2 packages. The scripts used for analysis and generating figures are available at https://github.com/nyuhuyang/scRNAseq-LorenzoBlood.
[Cell clustering]  Unsupervised cell clustering was carried out using Seurat 2.3.456 in the R computational environment (v. 3.5.3). Cells with <1000 genes or <3000 UMIs or >10% mitochondrial genes and genes detected in <3 cells were excluded from the analysis.
[Gene expression normalization and analysis]  Gene expression raw counts were normalized following a global-scaling normalization method with a scale factor of 10,000 and a log transformation, using the Seurat NormalizeData function. The top 2775 highly variable genes were selected, followed by principal component analysis (PCA). Top 35 PCs were further used to perform harmony57 to remove the effect of confounding factors between two samples. The first 35 harmony results were used to generate 2-dimensional t-Distributed Stochastic Neighbor Embedding (RunTSNE in Seurat, perplexity=30) and unsupervised cell clustering by a shared nearest neighbor (FindClusters in Seurat, k.param=30 and resolution=0.6). A list of conserved cell-type specific genes were generated by FindAllMarkers function in Seurat. Manually use marker genes to identify cell types and confirmed by SingleR 0.2.2 (Single-cell Recognition)58 package
[Gene set analysis and chart genaration]  Gene set analysis and bar charts were generated using the ggpubr and ggplot2 packages. The scripts used for analysis and generating figures are available at https://github.com/nyuhuyang/scRNAseq-LorenzoBlood
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files contains the counts matrix

organism: Mus musculus

source_name: mammary gland tumor

growth_protocol: For tumorigenicity assays, 0.1 x 10^6 TSA  cells were injected subcutaneously. When tumors reached 0.25cm^2 the animals were randomized to the different treatment groups.

extract_protocol:
TSA tumors were recovered from 3 mice per group, and dissociated using the Tumor Dissociation Kit and gentleMACS™ Octo Dissociator (Miltenyi Biotec), following manufacturer’s instructions. Upon pooling, samples were subjected to magnetic separation of CD45+ cells using magnetic beads and MACS separator (Miltenyi Biotec), as per manufacturer’s instructions. Upon testing viability by trypan blue exclusion using a Cellometer AutoT4 cell counter (Nexcelom Bioscience), CD45+ cells were resuspended in PBS containing 0.1% BSA.
After CD45+ cells isolation, all procedures were done by the epigenomics core at WCMC. Library preparation for Single Cell 3’ RNA-seq v.2, sequencing and post-processing of the raw data was performed at the Epigenomics Core at Weill Cornell Medicine, as follows. Single-cell RNA-seq libraries were prepared according to 10X Genomics specifications (Single Cell 3′ Reagent Kits v2 User Guide PN-120236, 10x Genomics, Pleasanton, CA, USA). Two independent cell suspensions (~60% viable) at a concentration of ~900 cells µL-1 were loaded onto to the 10x Genomics Chromium platform to generate barcoded single-cell GEMs, targeting about 3000 single cells per sample. GEM reverse transcription (53°C for 45 min, 85°C for 5 min; held at 4°C) was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad, Hercules). After reverse transcription, GEMs were broken and single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific, Waltham, MA). cDNA was amplified for 12 cycles (98 °C for 3 min; 98 °C for 15 s, 67 °C for 20 s, 72 °C for 1min) using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. Quality of the cDNA was assessed using an Agilent Bioanalyzer 2100 (Santa Clara, CA), obtaining a product of about 1693bp. This cDNA was enzymatically fragmented, end-repaired, A-tailed, subjected to a double-sided size selection with SPRIselect beads (Beckman Coulter, Indianapolis, IN) and ligated to adaptors provided in the kit. A unique sample index for each library was introduced through 13 cycles of PCR amplification using the indexes provided in the kit (98 °C for 45 s; 98 °C for 20 s, 54 °C for 30 s, and 72 °C for 20 s x 14 cycles; 72 °C for 1 min; held at 4 °C). Indexed libraries were subjected a second double-sided size selection, and libraries were then quantified using Qubit fluorometric quantification (Thermo Fisher Scientific, Waltham, MA). The quality was assessed on an Agilent Bioanalyzer 2100, obtaining an average library size of 455bp. Libraries were finally diluted to 2 nM and clustered on a HiSeq2500 high output mode at 10 pM on a pair-end read flow cell and sequenced for 26 cycles on R1 (10X barcode and the UMIs), followed by 8 cycles of I7 Index (sample Index), and 98 bases on R2 (transcript), with a coverage around 100M reads per sample. Primary processing of sequencing images was done using Illumina’s Real Time Analysis software (RTA).

treatment_protocol: 0.5 % NAM was added to the drinking water for 10 days. Drinking water was changed once a week.

value: Balb/c

value: mammary gland tumor

value: untreated


title: NAM_treated TSA CD45+ infiltrating cells

value: NAM


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_30µM_48hr [US-1465567]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465567


title: WT rep1 [BY11]

source_name: WT


title: MouseACS10

city: Cambridge

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software(version 2.1.0, 10X Genomics)
Sample alignment with the count function from Cell Ranger software(version 2.1.0, 10X Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: Csv files including gene expression matrix from all samples

source_name: P19 Mouse retina

extract_protocol:
Post-natal day 19 (P19) Chx10-cre-GFP animals were euthanized by intraperitoneal injection of Euthasol. Eyes were removed and retinas dissected in oxygenated Ames solution between 10 and 11AM. Retinas were incubated at 37°C for 10 minutes in a papain solution followed by trituration in an ovomucoid solution to quench papain activity and generate a single cell suspension. Cells were centrifuged at 450 x g for 8 minutes and the pellet was resuspended in Ames+4% BSA with rat anti-mouse CD133-APC (eBioscience) and rat anti-mouse CD73-PE (eBioscience). Following incubation for 15 minutes at room temperature, cells were washed with Ames + BSA, centrifuged again, and resuspended at a concentration appropriate for flow cytometry. Samples were sorted on a MoFlo Astrios cell sorter (Beckman) and cells triple negative for GFP, APC, and PE but positive for the cell viability marker Calcein Blue were collected.
Single cell libraries were made with Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA)

value: Chx10-cre-GFP mouse strain

value: Retina


title: MouseACS9


title: MouseACS7


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_100µM_24hr [US-1465566]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465566

value: Sprague Dawley

value: male


title: WT + Ramycin rep2 [rapa12]


title: MouseACS8


title: adr1 triple_0.5h_avrRps4_Rep1

value: adr1 triple


title: adr1 triple_8h_avrRpm1_Rep3


title: Bud27-TAP Input 2

source_name: Bud27-TAP Input

growth_protocol: 200 ml of yeast culture for a BY4147 wild-type strain containing a tap-tagged version of Bud7 were collected at an OD600 of about 0.6

extract_protocol:
Cell disruption was carried out by vigorously vortexing this sample in the presence of 200 µl of glass beads for 15 min. After disruption, lysis buffer was added to the cells extract to adjust 1.5 ml and then samples were subsequently sonicated by a Bioruptor sonicator (Diagenode) for 45 min at 30 s on/off intervals.   Immunoprecipitation was performed in duplicate using 200 µl of magnetic beads (Dynabeads Pan Mouse IgG, Invitrogen) and 300 µl of the sonicated sample. Washing and de-crosslinking followed the conventional chromatin immunoprecipitation procedure; supernatants were collected in the same tube and DNA was purified with the Nucleospin Extract II Purification kit (Macherey-Nagel). The eluted DNA was concentrated by lyophilization. Input and immunoprecipitated DNAs were sequenced in an Illumina HiSeq 2000 instrument
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

value: containing a tap-tagged version of Bud7

tag: immunopreciatation

value: input


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_100µM_48hr [US-1465571]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465571

value: HEPATOPAC


title: adr1 triple_0.5h_EV_Rep2

value: EV


title: MouseACS6


title: adr1 triple_8h_avrRpt2_Rep1


title: MouseACS5


title: WT rep2 [BY12]


title: adr1 triple_8h_avrRps4_Rep3


title: MouseACS4


title: Bud27-TAP Input 1


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_30µM_24hr [US-1465562]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465562

value: β-naphthoflavone

value: 30 microM


title: adr1 triple_8h_avrRpm1_Rep2


title: MouseACS3


title: Bud27-TAP chip 2

source_name: Bud27-TAP chip

value: magnetic beads (Dynabeads Pan Mouse IgG, Invitrogen) as the TAP epitope is recognized by the magnetic beads


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_30µM_24hr [US-1465563]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465563


title: Cord blood Nr_423

type: RNA

city: Diepenbeek

first: Michelle

last: Plusquin

address: Campus Diepenbeek Agoralaan Gebouw D

country: Belgium

institute: Hasselt University

description: excluded: missing covariates

hyb_protocol: Cyanine-3 labelled cRNA was hybridized onto Agilent Whole Human Genome 8 × 60 K microarrays

scan_protocol: Microarray signals were detected using the Agilent DNA G2505C Microarray Scanner (Agilent Technologies).Scan images were converted into TXT files using the Agilent Feature Extraction Software (Version 10.7.3.1, Agilent Technologies, Amstelveen, Netherlands).

data_processing: An in-house developed quality control pipeline in R software was used to preprocess raw data as follows: local background correction, omission of controls, flagging of bad spots and spots with too low intensity, log2 transformation and quantile normalization using arrayQC. More information about the flagging and the R-scripts of the pipeline are available at https://github.com/BiGCAT-UM/arrayQC_Module. Further preprocessing included removal of probes showing > 30% flagged data, merging of replicate probes based on the median, and imputation of missing values by means of K-nearest neighbor imputation (K = 15) resulting in 29,164 transcripts available for further analysis. Of the 200 samples, RNA extraction was not possible for 6 samples. After exclusion of samples failing preprocessing and missing covariates for denoising  gene expression levels of 165 samples were left in our analyses.

source_name: cord blood

label_protocol: 0.2 μg total RNA was used to synthesize fluorescent cyanine-3-labeled cRNA following the Agilent one-color Quick-Amp labeling protocol (Agilent Technologies)

extract_protocol: not provided

value: cord blood

tag: birthweight

tag: hybridization date


title: Cord blood Nr_294

description: excluded: missing covariates


title: Cord blood Nr_7

description: excluded: missing covariates


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_30µM_24hr [US-1465561]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465561


title: adr1 triple_8h_avrRpm1_Rep1


title: MouseACS1


title: MouseACS2


title: Cord blood Nr_84

description: excluded: missing covariates


title: adr1 triple_0.5h_EV_Rep1


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_100µM_6hr [US-1465560]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465560

value: 100 microM


title: Cord blood Nr_266

description: excluded: missing covariates


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_100µM_6hr [US-1465559]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465559


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_100µM_24hr [US-1465565]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465565


title: adr1 triple_8h_EV_Rep3


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_100µM_6hr [US-1465558]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465558


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_100µM_24hr [US-1465564]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465564


title: Bud27-TAP chip 1


title: miRNA T_3M_2

city: Shenzhen

first: Wen

middle: Ting

last: Li

address: No,1120,LianHua Road,FuTian District

country: China

institute: Shenzhen PKU-HKUST Medical Center

description: miRNA.expression.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 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.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

source_name: thymus

extract_protocol:
The thymuses harvested from each group were placed in cryopreservation tubes and immediately immersed in liquid nitrogen (−196°C) for preservation.Total RNA from each thymus sample was isolated using the TRIzol Reagent kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: thymus

tag: age

value: wild type


title: miRNA T_3M_1

description: miRNA.expression.txt


title: adr1 triple_8h_avrRps4_Rep1


title: Cord blood Nr_346

description: excluded: missing covariates


title: adr1 triple_4h_avrRpt2_Rep3


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_30µM_6hr [US-1465557]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465557


title: miRNA T_6W_2

description: miRNA.expression.txt


title: adr1 triple_8h_EV_Rep1


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_30µM_6hr [US-1465556]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465556


title: miRNA T_6W_1

description: miRNA.expression.txt


title: Cord blood Nr_421

description: excluded: missing covariates


title: adr1 triple_4h_avrRpm1_Rep3


title: Rat_HEPATOPAC_SD_male_β-naphthoflavone_30µM_6hr [US-1465555]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465555


title: miRNA T_2W_2

description: miRNA.expression.txt


title: Cord blood Nr_279

description: excluded: missing covariates


title: nrg1.1 nrg1.2_4h_avrRpt2_Rep1.1

value: nrg1.1 nrg1.2


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.75µM_48hr [US-1465554]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465554

value: bardoxolone

value: 0.75 microM


title: miRNA T_2W_1

description: miRNA.expression.txt


title: Cord blood Nr_28

description: excluded: missing covariates


title: Cord blood Nr_260

description: excluded: missing covariates


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.75µM_48hr [US-1465553]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465553

value: Sprague Dawley


title: nrg1.1 nrg1.2_4h_avrRps4_Rep2.1


title: nrg1.1 nrg1.2_4h_avrRpm1_Rep2.1


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.75µM_48hr [US-1465552]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465552

value: male


title: RNA-seq_mouse_CtcfcKO_2

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
RNA-seq: Reads mapped to mm10 or rn5 whole genome by Tophat with default options.
RNA-seq for mouse nerve: DESeq2 was used to generate normalized read counts, and to identify differentially expressed genes between the different comparison groups;   RNA-seq for RSCs: Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
Genome_build: RNA-seq for mouse nerve: mm10;   RNA-seq for RSCs: rn5
Supplementary_files_format_and_content: tab-delimited text file, contain the estimated expression values produced by Cufflinks and Deseq;

source_name: sciatic nerve

growth_protocol: RNA from control and Ctcf mutant sciatic nerves were extracted using TRIZOL (Life Technologies) followed by purification using an RNeasy Mini Kit (Qiagen).

extract_protocol:
RNA: RNA from control and Ctcf deficient sciatic nerves or rat Schwann cells were extracted using TRIZOL (Life Technologies) followed by purification using an RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit.

value: sciatic nerve

value: Ctcf mutant

tag: developmental stage


title: nrg1.1 nrg1.2_4h_avrRpm1_Rep1.1

tag: genotype


title: RNA-seq_mouse_control_2

value: control


title: Cord blood Nr_113

description: excluded: missing covariates


title: RNA-seq_mouse_CtcfcKO_1


title: nrg1.1 nrg1.2_4h_EV_Rep3.1

tag: time


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.2µM_48hr [US-1465551]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465551

tag: treatment

value: 0.2 microM

value: HEPATOPAC


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.2µM_48hr [US-1465550]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465550


title: Cord blood Nr_142

description: excluded: missing covariates


title: Cord blood Nr_107

description: excluded: missing covariates


title: RNA-seq_mouse_control_1


title: Cord blood Nr_281

description: excluded: missing covariates


title: nrg1.1 nrg1.2_T0_T0_Rep3.1

tag: rep


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.2µM_48hr [US-1465549]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465549

tag: strain


title: nrg1.1 nrg1.2_4h_avrRps4_Rep1


title: KP-N5-Dox

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig (coverage for mapped reads), count tables (counts per gene)

source_name: KP cells with Npm1 knockdown

growth_protocol: Mouse KP cells were transfected with pLKO.1-Tet on-shNpm1-3(N3), pLKO.1-Tet on-shNpm1-4(N4) or pLKO.1-Tet on-shNpm1-5 (N5) and then selected by using 2ug/ml puromycin, to get the 3 stable cell lines. These 3 stable cell lines (N3, N4 or N5) were treated with or without 100ng/ml Doxycline .

extract_protocol: Extract total RNA by using Rneasy Plus Mini Kit (Qiagen)

treatment_protocol: Control group includes KP-N3, KP-N4 and KP-N5 stable cell lines (Npm1 is normally expressed); Knockdown group includes KP-N3, KP-N4 and KP-N5 stall cell lines treated with Doxycycline ( Npm1 is Knockdown).

tag: transfection

value: pLKO.1-Tet on-shNpm1-5 (N5)

value: 100ng/ml Doxycline

tag: cell type

value: KP


title: KP-N5

source_name: KP cells with Npm1 WT

value: no Doxycline


title: Cord blood Nr_95

description: excluded: missing covariates

value: cord blood


title: nrg1.1 nrg1.2_4h_EV_Rep2.1

value: EV


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.75µM_24hr [US-1465547]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465547

tag: Sex

tag: dose

tag: time point


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.75µM_24hr [US-1465548]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465548

tag: tissue


title: Cord blood Nr_307

description: excluded: missing covariates


title: KP-N4


title: Cord blood Nr_127

description: excluded: missing covariates


title: nrg1.1 nrg1.2_T0_T0_Rep2.1


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.75µM_24hr [US-1465546]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465546


title: KP-N4-Dox

value: pLKO.1-Tet on-shNpm1-4(N4)


title: nrg1.1 nrg1.2_4h_EV_Rep1.1

value: nrg1.1 nrg1.2


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.2µM_24hr [US-1465545]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465545

value: bardoxolone


title: KP-N3


title: Cord blood Nr_36

description: excluded: missing covariates


title: nrg1.1 nrg1.2_0.5h_avrRpt2_Rep3.1


title: Cord blood Nr_470

description: excluded: missing covariates


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.2µM_24hr [US-1465544]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465544


title: KP-N3-Dox

value: pLKO.1-Tet on-shNpm1-3(N3)


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.2µM_24hr [US-1465543]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465543

value: Sprague Dawley


title: Cord blood Nr_416

description: excluded: missing covariates


title: nrg1.1 nrg1.2_T0_T0_Rep1.1


title: nrg1.1 nrg1.2_8h_EV_Rep2.1


title: Cord blood Nr_60

description: excluded: missing covariates


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.75µM_6hr [US-1465542]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465542

value: male

value: 0.75 microM


title: p105AA_6_1hr

city: London

first: Steve

last: Ley

address: Pond Street

department: Institute of Immunity & Inflammation

country: United Kingdom

institute: University College London

description:
p105AA_experiment
LPS (100ng/ml) for 1hrs
GEO_RSEM_normalised_data.txt.gz

data_processing:
The RSEM package (version 1.2.29) in conjunction with the STAR alignment algorithm (version 2.5.1b)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 Refseq genes downloaded from the UCSC Table Browser 15 on 14th April 2016
The “--forward-prob” parameter was set to “0” and all other parameters were kept as default
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.2.3)
Genome_build: mm10 RefSeq
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data. Rows represent Ref mouse genes and columns represent individual samples.

growth_protocol: Bone marrow cells from both femurs were cultured on non-adherent dishes for 7 days in RPMI 1640 supplemented with 20% L-cell conditioned medium, 10% FBS, 1 mM sodium pyruvate, 50 µM 2-Mercaptoethanol, 10mM HEPES, L-glutamine and pencillin/streptomycin. Cells were fed on day 4.

extract_protocol: RNA was extracted using the Rneasy kit (Qiagen) according to the manufacturers protocol. RNA was eluted in 50 µl Rnase-free water.

treatment_protocol: On day 7, cells were seeded in 6 well plates at 0.5 x 10^6 cells/ml in 2ml overnight in RPMI 1640 supplemented with 1% FBS, 1 mM sodium pyruvate, 50 µM 2-Mercaptoethanol, 10mM HEPES, L-glutamine and pencillin/streptomycin. Cells were then pre-treated with inhibitors where appropriate (PD0325901; 0.1 µM, RSKi47; 2 µM), stimulated with 100 ng/ml LPS for the indicated times or left unstimulated

value: bone marrow-derived macrophage cells


title: p105AA_5_1hr


title: Cord blood Nr_305

description: excluded: missing covariates


title: nrg1.1 nrg1.2_0.5h_avrRpt2_Rep2.1


title: Cord blood Nr_374

description: excluded: missing covariates


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.75µM_6hr [US-1465541]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465541


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.75µM_6hr [US-1465540]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465540


title: Cord blood Nr_169

description: excluded: missing covariates


title: nrg1.1 nrg1.2_0.5h_avrRpm1_Rep3.1


title: nrg1.1 nrg1.2_4h_avrRpt2_Rep2.1


title: Cord blood Nr_160

description: excluded: missing covariates


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.2µM_6hr [US-1465539]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465539


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.2µM_6hr [US-1465538]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465538


title: p105AA_3_1hr


title: p105AA_2_1hr


title: p105AA_1_1hr


title: p105AA_4_1hr


title: Rat_HEPATOPAC_SD_male_bardoxolone_0.2µM_6hr [US-1465537]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465537


title: p105AA_6_0.5hr

description:
p105AA_experiment
LPS (100ng/ml) for 0.5hrs
GEO_RSEM_normalised_data.txt.gz


title: nrg1.1 nrg1.2_0.5h_avrRps4_Rep3.1


title: Cord blood Nr_431

description: excluded: missing covariates


title: nrg1.1 nrg1.2_0.5h_avrRpm1_Rep2.1


title: p105AA_5_0.5hr


title: Rat_HEPATOPAC_SD_male_vehicle2 (DMSO/LNP)_0.2%/100 nM_48hr [US-1465618]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465618

value: vehicle2 (DMSO/LNP)


title: Cord blood Nr_117

description: excluded: missing covariates


title: nrg1.1 nrg1.2_8h_avrRpt2_Rep3.1


title: p105AA_4_0.5hr


title: Rat_HEPATOPAC_SD_male_vehicle2 (DMSO/LNP)_0.2%/100 nM_48hr [US-1465617]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465617


title: Cord blood Nr_77

description: excluded: failed preprocessing


title: Rat_HEPATOPAC_SD_male_vehicle2 (DMSO/LNP)_0.2%/100 nM_48hr [US-1465616]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465616


title: p105AA_3_0.5hr


title: nrg1.1 nrg1.2_0.5h_avrRpm1_Rep1.1


title: nrg1.1 nrg1.2_0.5h_avrRpt2_Rep1.1


title: p105AA_2_0.5hr


title: nrg1.1 nrg1.2_0.5h_EV_Rep3.1


title: p105AA_1_0.5hr


title: Rat_HEPATOPAC_SD_male_vehicle1 (DMSO)_0.2%_48hr [US-1465614]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465614

value: vehicle1 (DMSO)


title: Cord blood Nr_269

description: excluded: missing covariates


title: p105AA_6_0hr

description:
p105AA_experiment
untreated
GEO_RSEM_normalised_data.txt.gz


title: Rat_HEPATOPAC_SD_male_vehicle1 (DMSO)_0.2%_48hr [US-1465613]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465613

value: HEPATOPAC


title: nrg1.1 nrg1.2_0.5h_EV_Rep2.1


title: p105AA_5_0hr


title: nrg1.1 nrg1.2_8h_avrRpt2_Rep2.1


title: p105AA_4_0hr


title: Rat_HEPATOPAC_SD_male_vehicle2 (DMSO/LNP)_0.2%/100 nM_24hr [US-1465611]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465611


title: Cord blood Nr_465


title: nrg1.1 nrg1.2_0.5h_avrRps4_Rep2.1


title: Rat_HEPATOPAC_SD_male_vehicle2 (DMSO/LNP)_0.2%/100 nM_24hr [US-1465610]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465610


title: nrg1.1 nrg1.2_8h_avrRpt2_Rep1.1


title: nrg1.1 nrg1.2_8h_avrRps4_Rep3.1


title: p105AA_3_0hr


title: Rat_HEPATOPAC_SD_male_vehicle1 (DMSO)_0.2%_24hr [US-1465609]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465609


title: Rat_HEPATOPAC_SD_male_vehicle1 (DMSO)_0.2%_48hr [US-1465615]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465615


title: Cord blood Nr_287


title: Cord blood Nr_44


title: p105AA_2_0hr


title: nrg1.1 nrg1.2_8h_avrRpm1_Rep2.1


title: Rat_HEPATOPAC_SD_male_vehicle1 (DMSO)_0.2%_24hr [US-1465608]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465608


title: nrg1.1 nrg1.2_8h_avrRpm1_Rep3.1


title: Rat_HEPATOPAC_SD_male_vehicle2 (DMSO/LNP)_0.2%/100 nM_24hr [US-1465612]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465612


title: Cord blood Nr_120


title: Cord blood Nr_93


title: Cord blood Nr_8


title: nrg1.1 nrg1.2_0.5h_EV_Rep1.1


title: Rat_HEPATOPAC_SD_male_vehicle1 (DMSO)_0.2%_24hr [US-1465607]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465607


title: stim_RSKi47.4_2h

description:
RISKi47_experiment
10min RSKi47  pre-treatment + LPS (100ng/ml) for 2hrs
GEO_RSEM_normalised_data.txt.gz

value: WT


title: nrg1.1 nrg1.2_8h_avrRps4_Rep2.1


title: Cord blood Nr_414


title: stim_RSKi47.3_2h


title: Cord blood Nr_380


title: Rat_HEPATOPAC_SD_male_vehicle2 (DMSO/LNP)_0.2%/100 nM_6hr [US-1465606]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465606


title: nrg1.1 nrg1.2_8h_avrRpm1_Rep1.1


title: Rat_HEPATOPAC_SD_male_vehicle2 (DMSO/LNP)_0.2%/100 nM_6hr [US-1465605]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465605


title: Cord blood Nr_9


title: stim_RSKi47.2_2h


title: nrg1.1 nrg1.2_8h_EV_Rep3.1


title: stim_RSKi47.1_2h


title: Rat_HEPATOPAC_SD_male_vehicle2 (DMSO/LNP)_0.2%/100 nM_6hr [US-1465604]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465604


title: stim_RSKi47.4_1h

description:
RISKi47_experiment
10min RSKi47  pre-treatment + LPS (100ng/ml) for 1hrs
GEO_RSEM_normalised_data.txt.gz


title: Rat_HEPATOPAC_SD_male_vehicle1 (DMSO)_0.2%_6hr [US-1465603]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465603


title: p105AA_1_0hr


title: nrg1.1 nrg1.2_8h_avrRps4_Rep1.1


title: Cord blood Nr_288


title: Rat_HEPATOPAC_SD_male_vehicle1 (DMSO)_0.2%_6hr [US-1465602]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465602


title: Rat_HEPATOPAC_SD_male_vehicle1 (DMSO)_0.2%_6hr [US-1465601]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465601


title: stim_RSKi47.2_1h


title: Cord blood Nr_463


title: stim_RSKi47.3_1h


title: nrg1.1 nrg1.2_4h_avrRpm1_Rep3.1


title: Cord blood Nr_303


title: Cord blood Nr_3


title: stim_RSKi47.1_1h


title: nrg1.1 nrg1.2_4h_avrRpt2_Rep1


title: nrg1.1 nrg1.2_4h_avrRpt2_Rep3.1


title: ATAC-seq_siCtcf-2

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
ATAC-seq: Reads mapped to rn5 whole genome by Bowtie2 with default options.
ATAC-seq: Peak calling was performed using Model-based analysis of MACS with special parameter: --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01, to call peak.
Genome_build: rn5
Supplementary_files_format_and_content: wig files were generated by MACS

source_name: rat Schwann cell

growth_protocol: Rat Schwann cells from sciatic nerves of newborn rats (1–2 days-old) were isolated. Schwann cells were grown routinely in DMEM/10% FBS (Life Technologies), supplemented with 10 ng/ml Neuregulin 1 (Nrg1; R&D Systems), and 5 μM forskolin (Sigma), plus L-glutamine and penicillin/streptomycin, hereafter denoted as SC proliferation medium. Cells between passages 2 and 6 were used in all experiments. >95% SC purity was achieved, assessed by positive SOX10 and S100β immunoreactivity.

extract_protocol:
DNA for ATAC-seq: We isolated nuclei of 50,000 cells from the siControl and siCtcf rat Schwann cells in a cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) by exclude GFP- and 7-AAD+ cells. After spinning down at 500 × g for 10 min at 4 °C, nuclei were resuspended in transposition mix containing TD (2× reaction buffer), TDE1 (Nextera Tn5 Transposase) at 37°C for 30 min. The samples were purified using a Qiagen MinElute kit. Transposed DNA fragments were subsequently amplified and purified using Qiagen MinElute PCR Purification Kit. Libraries were generated using the Ad1_noMX and Ad2.1-2.4 barcoded primers and were amplified for 11 total cycles. Libraries were purified with AMPure beads (Agencourt) to remove contaminating primer dimers. All libraries were sequenced on the Illumina HiSeq 2500 with 75 bp single-end reads.
ATAC-seq libraries were purified with AMPure beads (Agencourt) to remove contaminating primer dimers. All libraries were sequenced on the Illumina HiSeq 2500 with 75 bp single-end reads.

value: siCtcf

value: differentiation for 9h

value: Schwann cell


title: nrg1.1 nrg1.2_4h_avrRps4_Rep3


title: Cord blood Nr_31

value: cord blood


title: Cord blood Nr_13


title: ATAC-seq_control-2

value: control


title: stim_RSKi47.3_0.5h

description:
RISKi47_experiment
10min RSKi47  pre-treatment + LPS (100ng/ml) for 0.5hrs
GEO_RSEM_normalised_data.txt.gz


title: Cord blood Nr_188


title: nrg1.1 nrg1.2_8h_EV_Rep1.1

value: EV


title: ATAC-seq_siCtcf-1


title: stim_RSKi47.1_0.5h


title: nrg1.1 nrg1.2_4h_avrRps4_Rep2

value: nrg1.1 nrg1.2


title: ATAC-seq_control-1


title: ChIPseq_H3K27ac_siCtcf

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
ChIP-seq: Reads mapped to rn5 whole genome by Bowtie2 with default options.
ChIP-seq: Peak calling was performed using MACS1.4 with a default p value cut off.
Genome_build: rn5
Supplementary_files_format_and_content: wig files were generated by MACS14

extract_protocol:
DNA for ChIP-seq:Purified rat SCs (∼20 million cells) were fixed for 10 min at room temperature with 1% formaldehyde-containing medium. Nuclei were isolated and sonicated in sonication buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.5 mM EGTA, and protease inhibitor cocktail). Sonicated chromatin (∼300 μg) was used for immunoprecipitation by incubation with anti-CTCF, anti-H3K27ac antibody overnight at 4°C.
ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB catalogue number E6240L) and then run on the Illumina sequencer HiSeq 2000.


title: stim_RSKi47.2_0.5h


title: Cord blood Nr_50


title: unstim_RSKi47.4_0h

description:
RISKi47_experiment
10min RSKi47 treatment
GEO_RSEM_normalised_data.txt.gz


title: Cord blood Nr_118


title: ChIPseq_H3K27ac_control


title: unstim_RSKi47.3_0h


title: nrg1.1 nrg1.2_4h_avrRpm1_Rep1


title: Cord blood Nr_178


title: Cord blood Nr_324


title: ChIP-seq_CTCF_pro

value: proliferation


title: nrg1.1 nrg1.2_4h_EV_Rep3


title: nrg1.1 nrg1.2_T0_T0_Rep3


title: nrg1.1 nrg1.2_4h_avrRpm1_Rep2


title: ChIP-seq_CTCF_diff

value: differentiation


title: Cord blood Nr_11


title: nrg1.1 nrg1.2_T0_T0_Rep2


title: RNA-seq_rsc_siCtcf_2

description: siCtcf vs siControl gene_rep_matix_anno_diff.txt.gz


title: unstim_RSKi47.2_0h


title: unstim_RSKi47.1_0h


title: nrg1.1 nrg1.2_4h_EV_Rep2


title: Cord blood Nr_35


title: PD6_LPS_1hr

description:
PD_experiment
10min PD0325901 pre-treatment + LPS (100ng/ml) for 1hrs
GEO_RSEM_normalised_data.txt.gz


title: Cord blood Nr_240


title: nrg1.1 nrg1.2_4h_EV_Rep1


title: RNA-seq_rsc_control_3


title: PD5_LPS_1hr


title: PD3_LPS_1hr


title: RNA-seq_rsc_control_2


title: Cord blood Nr_372


title: Cord blood Nr_57


title: nrg1.1 nrg1.2_0.5h_avrRpt2_Rep3


title: nrg1.1 nrg1.2_T0_T0_Rep1


title: PD2_LPS_1hr


title: RNA-seq_rsc_siCtcf_1


title: nrg1.1 nrg1.2_8h_EV_Rep2


title: RNA-seq_rsc_siCtcf_3


title: RNA-seq_rsc_control_1


title: Cord blood Nr_32


title: PD1_LPS_1hr


title: Cord blood Nr_289


title: PD4_LPS_1hr


title: nrg1.1 nrg1.2_0.5h_avrRpm1_Rep3


title: nrg1.1 nrg1.2_0.5h_avrRpt2_Rep2


title: Cord blood Nr_92


title: PD6_LPS_0.5hr

description:
PD_experiment
10min PD0325901 pre-treatment + LPS (100ng/ml) for 0.5hrs
GEO_RSEM_normalised_data.txt.gz


title: Cord blood Nr_129


title: PD5_LPS_0.5hr


title: nrg1.1 nrg1.2_4h_avrRpt2_Rep2


title: nrg1.1 nrg1.2_0.5h_avrRpt2_Rep1


title: nrg1.1 nrg1.2_0.5h_avrRps4_Rep3


title: Cord blood Nr_434


title: Cord blood Nr_447


title: 8h_2

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

hyb_protocol: Affymetrix GeneChip® Rat Gene 2.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.3.1.187

label: Biotin

source_name: rat cardiomyocytes wt treated with SIN-1 , 8h

label_protocol: 100ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Catalog Number 902281, Affymetrix, Santa Clara, CA)

growth_protocol: Primary rat cardiomyocytes were grown in DMEM/F12 medium supplemented with FBS (20%), horse serum (5%),  L-glutamine (2 mM), Na pyruvate (3 mM), non-essential amino acids (0.1 mM), penicillin (100 U/mL) and streptomycin (100 µg/mL).

extract_protocol: RNA was extracted with TriFast Reagent (VWR International, Radnor, PA) and subsequent RNA cleanup and concentration was performed using the Rneasy MinElure Cleanup Kit (Qiagen, Venlo, Netherlands)

treatment_protocol: Primary rat cardiomyocytes were treated with the peroxynitrite donor 3-morpholinosydnoimine (SIN-1) for 70 min, 4 and 8 h

value: cardiomyocytes


title: nrg1.1 nrg1.2_8h_avrRpt2_Rep3


title: nrg1.1 nrg1.2_0.5h_avrRpm1_Rep2


title: Cord blood Nr_124


title: 8h_3


title: PD3_LPS_0.5hr


title: PD1_LPS_0.5hr


title: PD4_LPS_0.5hr


title: PD2_LPS_0.5hr


title: nrg1.1 nrg1.2_0.5h_avrRps4_Rep2


title: PD3_1hr

description:
PD_experiment
70min PD0325901 treatment
GEO_RSEM_normalised_data.txt.gz


title: 4h_2

source_name: rat cardiomyocytes wt treated with SIN-1 , 4h


title: PD2_1hr


title: Cord blood Nr_407


title: nrg1.1 nrg1.2_0.5h_avrRpm1_Rep1

source_name: leaf disc


title: Cord blood Nr_166


title: PD1_1hr


title: Cord blood Nr_183


title: 4h_1


title: 8h_1


title: Cord blood Nr_97


title: Cord blood Nr_411


title: Cord blood Nr_167


title: 70'_3

source_name: rat cardiomyocytes wt treated with SIN-1 , 70minutes


title: 4h_3


title: 70'_2


title: nrg1.1 nrg1.2_0.5h_EV_Rep3


title: 70'_1


title: PD3_0.5hr

description:
PD_experiment
40min PD0325901 treatment
GEO_RSEM_normalised_data.txt.gz


title: PD2_0.5hr


title: nrg1.1 nrg1.2_8h_avrRpt2_Rep2


title: nrg1.1 nrg1.2_8h_avrRpm1_Rep3


title: PD1_0.5hr


title: Rat_hepatoma H4IIE_strain_sex_untreated_0µM_120hr [H4IIE_Day2_UTC_3]

description:
Rat_Models.tar.gz
H4IIE_Day2_UTC_3

tag: donor

value: hepatoma H4IIE

value: male

value: untreated

value: 0 microM


title: Cord blood Nr_500


title: Cord blood Nr_131


title: nrg1.1 nrg1.2_0.5h_EV_Rep2


title: PD3_0hr

description:
PD_experiment
10min PD0325901 treatment
GEO_RSEM_normalised_data.txt.gz

value: bone marrow-derived macrophage cells


title: ctrl_3

source_name: rat cardiomyocytes wt


title: Rat_hepatoma H4IIE_strain_sex_untreated_0µM_120hr [H4IIE_Day2_UTC_2]

description:
Rat_Models.tar.gz
H4IIE_Day2_UTC_2


title: nrg1.1 nrg1.2_0.5h_avrRps4_Rep1


title: PD2_0hr


title: PD_DMSO3

description:
PD_experiment
10min DMSO treatment
GEO_RSEM_normalised_data.txt.gz


title: Rat_hepatoma H4IIE_strain_sex_untreated_0µM_120hr [H4IIE_Day2_UTC_1]

description:
Rat_Models.tar.gz
H4IIE_Day2_UTC_1


title: ctrl_1


title: nrg1.1 nrg1.2_8h_avrRpt2_Rep1


title: Cord blood Nr_73


title: nrg1.1 nrg1.2_8h_avrRps4_Rep3


title: Cord blood Nr_432


title: nrg1.1 nrg1.2_8h_avrRpm1_Rep2


title: Rat_primary hepatocytes_Wistar(Han)_male_untreated_0µM_120hr [Day_5_Hepatocyte_7]

description:
Rat_Models.tar.gz
Day_5_Hepatocyte_7

value: Wistar(Han)

value: primary hepatocytes


title: PD_DMSO1

value: WT


title: Rat_primary hepatocytes_Wistar(Han)_male_untreated_0µM_120hr [Day_5_Hepatocyte_8]

description:
Rat_Models.tar.gz
Day_5_Hepatocyte_8


title: PD1_0hr


title: Rat_primary hepatocytes_Wistar(Han)_male_untreated_0µM_120hr [Day_5_Hepatocyte_9]

description:
Rat_Models.tar.gz
Day_5_Hepatocyte_9


title: Cord blood Nr_275


title: Cord blood Nr_318


title: Cord blood Nr_109


title: ctrl_2


title: Cord blood Nr_53


title: Cord blood Nr_88


title: Rat_primary hepatocytes_Wistar(Han)_male_untreated_0µM_48hr [Day_2_Hepatocyte_6]

description:
Rat_Models.tar.gz
Day_2_Hepatocyte_6


title: 2hr_dKO4_elksap

description:
dKO_ELKSAP_experiment
LPS (100ng/ml) for 2hrs
GEO_RSEM_normalised_data.txt.gz


title: 2hr_dKO3_elksap


title: nrg1.1 nrg1.2_8h_avrRpm1_Rep1


title: nrg1.1 nrg1.2_8h_avrRps4_Rep2


title: Cord blood Nr_323


title: PD_DMSO2


title: nrg1.1 nrg1.2_0.5h_EV_Rep1


title: Rat_primary hepatocytes_Wistar(Han)_male_untreated_0µM_48hr [Day_2_Hepatocyte_4]

description:
Rat_Models.tar.gz
Day_2_Hepatocyte_4


title: nrg1.1 nrg1.2_8h_EV_Rep3


title: Rat_primary hepatocytes_Wistar(Han)_male_untreated_0µM_0hr [Day_0_Hepatocyte_3]

description:
Rat_Models.tar.gz
Day_0_Hepatocyte_3


title: 2hr_dKO2_elksap


title: Cord blood Nr_436


title: nrg1.1 nrg1.2_8h_avrRps4_Rep1


title: 1hr_dKO4_elksap

description:
dKO_ELKSAP_experiment
LPS (100ng/ml) for 1hrs
GEO_RSEM_normalised_data.txt.gz


title: Cord blood Nr_301


title: Rat_primary hepatocytes_Wistar(Han)_male_untreated_0µM_0hr [Day_0_Hepatocyte_2]

description:
Rat_Models.tar.gz
Day_0_Hepatocyte_2


title: nrg1.1 nrg1.2_4h_avrRpt2_Rep3


title: 2hr_dKO1_elksap


title: nrg1.1 nrg1.2_8h_EV_Rep1


title: 1hr_dKO3_elksap


title: nrg1.1 nrg1.2_4h_avrRpm1_Rep3


title: 1hr_dKO2_elksap


title: Rat_primary hepatocytes_Wistar(Han)_male_untreated_0µM_48hr [Day_2_Hepatocyte_5]

description:
Rat_Models.tar.gz
Day_2_Hepatocyte_5


title: Rat_primary hepatocytes_Wistar(Han)_male_untreated_0µM_0hr [Day_0_Hepatocyte_1]

description:
Rat_Models.tar.gz
Day_0_Hepatocyte_1


title: Rat_HEPATOPAC_Wistar(Han)_male_untreated_0µM_216hr [RatHepatoPac_D9_3]

description:
Rat_Models.tar.gz
RatHepatoPac_D9_3

value: HEPATOPAC


title: Cord blood Nr_479


title: herlperless_4h_avrRpt2_Rep1.1

value: herlperless


title: herlperless_4h_avrRps4_Rep3.1


title: 1hr_dKO1_elksap


title: Rat_HEPATOPAC_Wistar(Han)_male_untreated_0µM_216hr [RatHepatoPac_D9_2]

description:
Rat_Models.tar.gz
RatHepatoPac_D9_2


title: Cord blood Nr_63

value: cord blood


title: 0.5hr_dKO4_elksap

description:
dKO_ELKSAP_experiment
LPS (100ng/ml) for 0.5hrs
GEO_RSEM_normalised_data.txt.gz


title: Rat_HEPATOPAC_Wistar(Han)_male_untreated_0µM_168hr [RatHepatoPac_D7_3]

description:
Rat_Models.tar.gz
RatHepatoPac_D7_3


title: herlperless_4h_avrRpm1_Rep2.1


title: 0.5hr_dKO3_elksap


title: Rat_HEPATOPAC_Wistar(Han)_male_untreated_0µM_168hr [RatHepatoPac_D7_2]

description:
Rat_Models.tar.gz
RatHepatoPac_D7_2


title: Rat_HEPATOPAC_Wistar(Han)_male_untreated_0µM_216hr [RatHepatoPac_D9_1]

description:
Rat_Models.tar.gz
RatHepatoPac_D9_1


title: Cord blood Nr_75


title: Cord blood Nr_326


title: 0.5hr_dKO2_elksap


title: Rat_HEPATOPAC_Wistar(Han)_male_untreated_0µM_120hr [RatHepatoPac_D5_3]

description:
Rat_Models.tar.gz
RatHepatoPac_D5_3


title: unstim_dKO4_elksap

description:
dKO_ELKSAP_experiment
untreated
GEO_RSEM_normalised_data.txt.gz


title: Cord blood Nr_478


title: herlperless_4h_avrRpm1_Rep1.1


title: Cord blood Nr_419


title: herlperless_4h_EV_Rep3.1


title: Rat_HEPATOPAC_Wistar(Han)_male_untreated_0µM_120hr [RatHepatoPac_D5_2]

description:
Rat_Models.tar.gz
RatHepatoPac_D5_2


title: herlperless_T0_T0_Rep3.1


title: 0.5hr_dKO1_elksap


title: herlperless_4h_avrRps4_Rep1.1


title: unstim_dKO3_elksap


title: unstim_dKO2_elksap


title: Rat_HEPATOPAC_Wistar(Han)_male_untreated_0µM_120hr [RatHepatoPac_D5_1]

description:
Rat_Models.tar.gz
RatHepatoPac_D5_1


title: herlperless_4h_avrRps4_Rep2.1


title: Cord blood Nr_168


title: Rat_HEPATOPAC_Wistar(Han)_male_untreated_0µM_48hr [RatHepatoPac_D2_3]

description:
Rat_Models.tar.gz
RatHepatoPac_D2_3


title: Rat_HEPATOPAC_Wistar(Han)_male_untreated_0µM_168hr [RatHepatoPac_D7_1]

description:
Rat_Models.tar.gz
RatHepatoPac_D7_1


title: unstim_dKO1_elksap


title: Cord blood Nr_206


title: Cord blood Nr_337


title: Cord blood Nr_334


title: Cord blood Nr_228


title: herlperless_4h_EV_Rep2.1


title: Rat_HEPATOPAC_Wistar(Han)_male_untreated_0µM_48hr [RatHepatoPac_D2_2]

description:
Rat_Models.tar.gz
RatHepatoPac_D2_2


title: herlperless_T0_T0_Rep2.1


title: 2hr_TPL6

description:
TPL_experiment
LPS (100ng/ml) for 2hrs
GEO_RSEM_normalised_data.txt.gz


title: 2hr_TPL5


title: herlperless_4h_EV_Rep1.1


title: Rat_liver_Wistar(Han)_male_vehicle (14.85% L-Arginine HCl)_5ml/kg_120hr [TT19-2532_19-0008_L]

description:
Rat_Models.tar.gz
TT19-2532_19-0008_L

value: vehicle (14.85% L-Arginine HCl)

value: liver


title: Cord blood Nr_115


title: herlperless_T0_T0_Rep1.1


title: herlperless_0.5h_avrRpt2_Rep3.1


title: Rat_HEPATOPAC_Wistar(Han)_male_untreated_0µM_48hr [RatHepatoPac_D2_1]

description:
Rat_Models.tar.gz
RatHepatoPac_D2_1


title: 2hr_TPL3


title: Cord blood Nr_443


title: Cord blood Nr_247


title: Rat_liver_Wistar(Han)_male_vehicle (14.85% L-Arginine HCl)_5ml/kg_120hr [TT19-2532_19-0006_L]

description:
Rat_Models.tar.gz
TT19-2532_19-0006_L


title: herlperless_8h_EV_Rep2.1

value: EV


title: 2hr_TPL4


title: Cord blood Nr_145


title: Cord blood Nr_236


title: Rat_liver_Wistar(Han)_male_vehicle (14.85% L-Arginine HCl)_5ml/kg_120hr [TT19-2532_19-0002_L]

description:
Rat_Models.tar.gz
TT19-2532_19-0002_L


title: 2hr_TPL2


title: Rat_liver_Wistar(Han)_male_vehicle (14.85% L-Arginine HCl)_5ml/kg_120hr [TT19-2532_19-0004_L]

description:
Rat_Models.tar.gz
TT19-2532_19-0004_L


title: herlperless_0.5h_avrRpt2_Rep2.1


title: herlperless_4h_avrRpt2_Rep2.1


title: 2hr_TPL1


title: Rat_liver_Wistar(Han)_male_vehicle (10% Tween 80)_5ml/kg_120hr [TT17-3500_17-9466_L]

description:
Rat_Models.tar.gz
TT17-3500_17-9466_L

value: vehicle (10% Tween 80)


title: herlperless_0.5h_avrRpm1_Rep3.1


title: Rat_liver_Wistar(Han)_male_vehicle (10% Tween 80)_5ml/kg_120hr [TT17-3500_17-9467_L]

description:
Rat_Models.tar.gz
TT17-3500_17-9467_L


title: 1hr_TPL6

description:
TPL_experiment
LPS (100ng/ml) for 1hrs
GEO_RSEM_normalised_data.txt.gz


title: 1hr_TPL5


title: Cord blood Nr_310


title: herlperless_0.5h_avrRpt2_Rep1.1


title: Rat_liver_Wistar(Han)_male_vehicle (10% Tween 80)_5ml/kg_120hr [TT17-3500_17-9465_L]

description:
Rat_Models.tar.gz
TT17-3500_17-9465_L


title: 1hr_TPL4


title: herlperless_0.5h_avrRps4_Rep3.1


title: 1hr_TPL3


title: 1hr_TPL2


title: Cord blood Nr_466


title: herlperless_0.5h_avrRpm1_Rep2.1


title: herlperless_8h_avrRpt2_Rep3.1


title: Cord blood Nr_199


title: 1hr_TPL1


title: Cord blood Nr_56


title: Cord blood Nr_1


title: herlperless_0.5h_avrRps4_Rep2.1


title: Subject 4 - low DNA input (<300ng)

city: New Haven

first: Ke

last: Xu

state: CT

institute: Yale University

description: Methylation capture bisulfite sequencing

data_processing:
Library strategy: MC-seq
Signal intensities were converted to individual base calls during a run using the system's Real Time Analysis (RTA) software. Sample de-multiplexing and alignment to the human genome was performed using Illumina's CASAVA 1.8.2 software suite. The sample error rate was required to be less than 1% and the distribution of reads per sample in a lane was required to be within reasonable tolerance.
Quality control (QC) on MC-seq was conducted following standard procedure as previously described. Quality of sequence data was examined by using FastQC (ver. 0.11.8). Adapter sequences and fragments at 5’ and 3’ (phred score <30) with poor quality were removed by Trim_galore (ver. 0.6.3_dev). We used Bismark pipelines (ver. v0.22.1_dev) to align the reads to the bisulfite human genome (hg19) with default parameters(17). Quality-trimmed paired-end reads were transformed into a bisulfite converted forward strand version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand). Duplicated reads were removed from the Bismark mapping output and CpG, CHG and CHH (where H = A, T or C) were extracted.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.bismark.cov: Tab-delimited text files: chromosome, start position, end position, percentage of methylation, methylated intensity, unmethylated intensity.

source_name: peripheral blood mononuclear cells

extract_protocol:
DNA was extracted from de-identified PBMC collected from four individuals. Genomic DNA quality was determined by estimating the A260/A280 and A260/A230 ratios by spectrophotometry and concentration by fluorometry. DNA integrity and fragment size were confirmed using a microfluidic chip run on an Agilent Bioanalyzer. To assess the reproducibility of MC-seq by DNA quantity, DNA samples from each participant were profiled in triplicate times with high (>1000ng), medium (300-1000ng) and low (150-300ng) DNA input. In total, 12 DNA samples were measured by MC-seq.
Indexed paired-end whole genome sequencing libraries were prepared using the SureSelect XT Methyl-Seq kit (Agilent, part#G9651B). Genomic DNA was sheared to a fragment length of 150-200 bp using focused acoustic energy delivered by the Covaris E220 system (Covaris, part#500003). Fragmented sample size distribution was determined using the Caliper LabChip GX system (PerkinElmer, Part#122000). Fragmented DNA ends were repaired with T4 DNA Polymerase and Polynucleotide Kinase and “A” base was added using Klenow fragment in a single reaction followed by AMPure XP bead-based purification (Beckman Coulter, part#A63882). The methylated adapters were ligated using T4 DNA ligase followed by AMPure XP bead purification. Quality and quantity of adapter-ligated DNA were assessed using the Caliper LabChip GX system. Samples yielding >350 ng were enriched for targeted methylation sites by using the custom SureSelect Methyl-Seq Capture Library. Hybridization was performed at 65°C for 16 hours using a C1000 Thermal Cycler (BIO-RAD, part# 1851197). Once the enrichment was completed the samples were mixed with streptavidin-coated beads (Thermo Fisher Scientific, part#65602) and washed with a series of buffers to remove non-specific bound DNA fragments. DNA fragments were eluted from beads with 0.1 M NaOH. Unmethylated C residues of enriched DNA were modified by bisulfite conversion using the EZ DNA Methylation-Gold Kit (Zymo Research, part#D5005). The SureSelect enriched, bisulfite-converted libraries were PCR amplified using custom-made indexed primers (IDT, Coralville, Iowa). Dual-indexed libraries were quantified by quantitative polymerase chain reaction (qPCR) using the Library Quantification Kit (KAPA Biosystems, Part#KK4854) and inserts size distribution was assessed using the Caliper LabChip GX system. Samples with a yield of ≥2 ng/ul were proceeded to sequencing.

value: Peripheral blood mononuclear cells

tag: dna input

value: Low DNA input

tag: dna input quantity

tag: subject


title: Subject 2 - low DNA input (<300ng)


title: Subject 3 - low DNA input (<300ng)


title: herlperless_0.5h_avrRpm1_Rep1.1

extract_protocol:
RNA was purified from plant tissue using the RNeasy 96 Kit (Qiagen). The plant “user developed protocol” was followed except for the addition of a 96% ethanol wash step after the second RPE wash to ensure removal of residual salts. Purified RNAs were kept at -80C.
Illumina-based mRNA-Seq libraries were prepared from 1 μg RNA following [61]. Briefly, mRNAs were selected using Sera-mag oligo(dT) magnetic beads (GE Healthcare Life Sciences). RNAs were washed and fragmented at 94°C for 6 minutes. First-strand cDNA synthesis was performed using random hexamers and reverse transcriptase (Superscript III reverse transcriptase, Invitrogen). Second-strand cDNA synthesis was done using DNA Polymerase I and RNAseH. Double-stranded cDNAs were end-repaired using T4 DNA polymerase, T4 polynucleotide kinase, and Klenow polymerase. The DNA fragments were then adenylated using Klenow exo-polymerase to allow the ligation of Illumina adapters (Kapa Dual-indexed adapter kit, Roche). Unless specified, reagents were purchased from Enzymatics.
Library quality control and quantification were performed using the 5200 Fragment Analyser and the NGS fragment kit (Agilent). Libraries were sequenced using Illumina HiSeq4000 sequencers to generate 50-bp single-end reads.


title: 0.5hr_TPL6

description:
TPL_experiment
LPS (100ng/ml) for 0.5hrs
GEO_RSEM_normalised_data.txt.gz


title: Cord blood Nr_200

tag: birthweight

tag: hybridization date


title: Cord blood Nr_302


title: 0.5hr_TPL5

tag: genotype


title: Cord blood Nr_401


title: Subject 1 - low DNA input (<300ng)


title: Cord blood Nr_430


title: Subject 3 - medium DNA input (300-1000ng)

value: Medium DNA input


title: Cord blood Nr_163


title: 0.5hr_TPL3


title: Cord blood Nr_373


title: herlperless_0.5h_EV_Rep3.1

tag: time


title: herlperless_8h_avrRpm1_Rep3.1

tag: treatment


title: Rat_liver_Wistar(Han)_male_vehicle (10% Tween 80)_5ml/kg_120hr [TT17-3500_17-9464_L]

description:
Rat_Models.tar.gz
TT17-3500_17-9464_L

extract_protocol:
Total RNA was purified from frozen liver or cell culture samples using the MagMAX™ Express Magnetic Particle Processor using the MagMAX™-96 for Microarrays Total RNA Isolation Kit (Thermo Fisher AM1839)
Total RNA samples were converted into cDNA libraries using the KAPA RNA HyperPrep Kit with RiboErase (HMR) Kit (Roche 08098131702) for rat or the TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat Kit (Illumina 20020596) for human

value: male


title: Subject 2 - medium DNA input (300-1000ng)


title: herlperless_8h_avrRpt2_Rep2.1

tag: rep


title: Subject 4 - medium DNA input (300-1000ng)


title: Subject 1 - medium DNA input (300-1000ng)


title: 0.5hr_TPL2

tag: strain


title: 0.5hr_TPL1


title: herlperless_0.5h_avrRps4_Rep1.1


title: herlperless_8h_avrRpt2_Rep1.1


title: Subject 3 - high DNA input (>1000ng)

value: High DNA input


title: 0.5hr_TPL4


title: Subject 4 - high DNA input (>1000ng)


title: herlperless_0.5h_EV_Rep2.1


title: herlperless_8h_avrRps4_Rep3.1


title: unstim_TPL5

description:
TPL_experiment
untreated
GEO_RSEM_normalised_data.txt.gz


title: Subject 2 - high DNA input (>1000ng)


title: unstim_TPL6


title: Cord blood Nr_420


title: Cord blood Nr_138


title: Cord blood Nr_182


title: Cord blood Nr_104


title: herlperless_8h_avrRpm1_Rep2.1


title: Cord blood Nr_204


title: Cord blood Nr_226


title: Cord blood Nr_149


title: unstim_TPL3


title: herlperless_0.5h_EV_Rep1.1


title: Cord blood Nr_89


title: herlperless_8h_avrRpm1_Rep1.1


title: herlperless_8h_EV_Rep3.1


title: unstim_TPL1


title: herlperless_8h_avrRps4_Rep1.1


title: 2hr_WT6


title: unstim_TPL4


title: 2hr_WT7


title: Cord blood Nr_157


title: herlperless_4h_avrRpt2_Rep3.1


title: 2hr_WT4


title: 2hr_WT5


title: herlperless_4h_avrRpm1_Rep3.1


title: Subject 1 - high DNA input (>1000ng)


title: herlperless_4h_avrRpt2_Rep1


title: unstim_TPL2


title: 1hr_WT8


title: Cord blood Nr_238


title: 1hr_WT7


title: herlperless_4h_avrRpm1_Rep2


title: herlperless_4h_avrRps4_Rep3


title: Cord blood Nr_46


title: Cord blood Nr_358


title: Cord blood Nr_391


title: herlperless_4h_avrRps4_Rep2


title: Cord blood Nr_384


title: Cord blood Nr_389


title: Cord blood Nr_336


title: 1hr_WT6


title: herlperless_4h_avrRpm1_Rep1


title: herlperless_4h_EV_Rep3


title: herlperless_T0_T0_Rep3


title: iPSC-derived cerebral organoids, 164SZ

city: Boston

first: Annie

last: Kathuria

address: 185 cambridge street

institute: Mass Gen Hospital

data_processing:
Analysis was performed by DNA Link USA, Inc.
Sequence quality was assessed using FASTQC
Sequences were trimmed using cutadapt v 1.18, paired-end reads mode -u 7 -u -3 -U 7 -U -3
Trimmed reads were aligned to the reference genome using TopHat v2.1.1 (--no-coverage-search, -G refseqhg38p9.gtf)
Bam files were merged using samptools v 1.9 for samples with techincal replicates.
FPKM calculation done using cufflinks v2.2.1 using annotation from RefSeq assembly hg38 p9 which was modified according UCSC-style-name
Pairwise differential expression analysis was performed using cuffdiff v2.2.1
Genome_build: Homo sapiens hg38 (UCSC tophat version as downloaded May 2017)
Supplementary_files_format_and_content: tab-delimited file w/ the following columns: tracking_id, gene_id, gene_short_name, locus, FPKM for each sample

source_name: cerebral organoids

extract_protocol:
Tissue was dissolved in Trizol and RNA was extracted using qiagen rneasy kit
Truseq Stranded Total RNA H/M/R Prep Kit

tag: disease state

value: schizophrenia

value: Human iPSC derived cerebral organoids

tag: age

value: 6 months of differentiation


title: 1hr_WT9

value: bone marrow-derived macrophage cells


title: Cord blood Nr_194


title: 0.5hr_WT9

value: WT


title: iPSC-derived cerebral organoids, 250SZ

tag: cell type


title: herlperless_4h_avrRps4_Rep1

data_processing:
Initial quality assessment of the Illumina RNA-Seq reads was performed using FastQC version 0.11.7.
Trimmomatic version 0.36 was used to identify and discard reads containing the Illumina adaptor sequence.
The resulting high-quality reads were then mapped against the TAIR10 Arabidopsis reference genome using HISAT2 version 2.1.0 with default parameters.
The featureCounts function from the Subread package was then used to count reads that mapped to each one of the 27,206 nuclear protein-coding genes, we used these counts to construct a raw count table of expression.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Tab delimited file containing the count matrix


title: herlperless_4h_EV_Rep2


title: 0.5hr_WT8


title: iPSC-derived cerebral organoids, 40SZ.2


title: 0.5hr_WT7


title: herlperless_T0_T0_Rep2


title: 1hr_WT5


title: 1hr_WT4


title: Cord blood Nr_2


title: Cord blood Nr_410


title: Cord blood Nr_458


title: iPSC-derived cerebral organoids, 40SZ.1


title: Cord blood Nr_376


title: Cord blood Nr_413


title: Cord blood Nr_271


title: Cord blood Nr_475


title: 0.5hr_WT6


title: herlperless_4h_EV_Rep1


title: 0.5hr_WT5


title: iPSC-derived cerebral organoids, 141SZ


title: iPSC-derived cerebral organoids, 233SZ


title: herlperless_0.5h_avrRpt2_Rep3


title: iPSC-derived cerebral organoids, 123SZ


title: herlperless_T0_T0_Rep1


title: herlperless_8h_EV_Rep2


title: unstim_WT9


title: 0.5hr_WT4


title: iPSC-derived cerebral organoids, 67SZ.2


title: iPSC-derived cerebral organoids, 33SZ


title: herlperless_0.5h_avrRpt2_Rep2


title: Cord blood Nr_496


title: unstim_WT7


title: Cord blood Nr_139


title: unstim_WT8


title: unstim_WT6


title: herlperless_0.5h_avrRpm1_Rep3


title: Cord blood Nr_23


title: iPSC-derived cerebral organoids, 292CON

value: control


title: iPSC-derived cerebral organoids, 67SZ.1


title: herlperless_4h_avrRpt2_Rep2

value: herlperless


title: Cord blood Nr_33

value: cord blood


title: unstim_WT5


title: Cord blood Nr_277


title: Cord blood Nr_446


title: herlperless_0.5h_avrRpt2_Rep1


title: iPSC-derived cerebral organoids, 22CON.2


title: Cord blood Nr_354


title: herlperless_0.5h_avrRpm1_Rep2


title: iPSC-derived cerebral organoids, 22CON.1


title: iPSC-derived cerebral organoids, 27CON


title: herlperless_8h_avrRpt2_Rep3


title: herlperless_0.5h_avrRps4_Rep2


title: herlperless_0.5h_avrRpm1_Rep1


title: iPSC-derived cerebral organoids, 135CON.2


title: iPSC-derived cerebral organoids, 135CON.1


title: Cord blood Nr_361


title: iPSC-derived cerebral organoids, 56CON


title: herlperless_0.5h_avrRps4_Rep3


title: herlperless_0.5h_EV_Rep3


title: iPSC-derived cerebral organoids, 51CON


title: unstim_WT4


title: herlperless_8h_avrRpt2_Rep2


title: Cord blood Nr_15


title: TOF PVR 08

first: Daniel

last: Brayson

address: 125 Coldharbour Lane

department: School of Cardiovascular Sciences and Medicine

institute: King's College London

description: total RNA-SPIA DNA

hyb_protocol: Hybridization cocktails were prepared from the fragmented labeled-cDNA according to Nugen’s recommendations and hybridized to the microarrays at 45°C for 18 hours

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G

data_processing: CEL files were QC assessed in the Expression Console software package (Affymetrix, ThermoFisher Scientific) by using standard metrics and guidelines for the Affymetrix microarray system

label: biotin

source_name: Human heart right ventricle

label_protocol: SPIA cDNA was fragmented and biotin-labeled using the Encore Biotin Module

growth_protocol: human tissue samples

extract_protocol: RNA was extracted directly from tissue using Direct-zol according to manufacturers instructions

value: right ventricle

tag: tissue source

value: TOF PVR


title: TOF PVR 09

description: total RNA-SPIA DNA


title: TOF PVR 06

description: total RNA-SPIA DNA


title: Cord blood Nr_290


title: Cord blood Nr_242


title: Cord blood Nr_452


title: TOF PVR 07

description: total RNA-SPIA DNA


title: Cord blood Nr_175


title: Cord blood Nr_83


title: Cord blood Nr_469


title: Cord blood Nr_220


title: TOF PVR 03

description: total RNA-SPIA DNA


title: TOF PVR 05

description: total RNA-SPIA DNA


title: iPSC-derived cerebral organoids, 300CON.1


title: herlperless_0.5h_avrRps4_Rep1


title: herlperless_0.5h_EV_Rep2

value: EV


title: TOF PVR 01

description: total RNA-SPIA DNA


title: iPSC-derived cerebral organoids, 15CON


title: herlperless_8h_avrRpm1_Rep3


title: herlperless_8h_avrRpt2_Rep1


title: iPSC-derived cerebral organoids, 300CON.2


title: herlperless_8h_avrRps4_Rep3


title: herlperless_8h_avrRpm1_Rep2


title: herlperless_0.5h_EV_Rep1


title: Cord blood Nr_347


title: herlperless_8h_avrRps4_Rep2


title: Biopsy_CIT2_EVLP48

city: Toronto

first: Ricardo

last: Zamel

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

hyb_protocol: According to manufacturer guidelines

scan_protocol: According to manufacturer guidelines

data_processing: Affymetrix CEL files were imported and processed using RMA in R version 3.5.1 with the affy package. We used an alternative CDF probset description file from Brainarray at the University of Michigan (Nucleic Acid Research 33 (20), e175; http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp): clariomdhumanhsentrezgcdf_22.0.0.zip

source_name: Biopsy_timepoint end of second cold ischemia

label_protocol: According to manufacturer guidelines

extract_protocol: RNA was extracted from snap frozen samples using the RNeasy Mini Kit (Qiagen; Hilden, Germany). RNA quality was assessed using Nanodrop spectrophotometer (VWR; Radnor, PA) and Bioanalyzer (Agilent; Santa Clara, CA)

tag: paired samples

tag: timepoint

value: lung


title: Cord blood Nr_209

tag: tissue


title: Cord blood Nr_428


title: Cord blood Nr_335


title: Biopsy_CIT2_EVLP49


title: herlperless_8h_avrRpm1_Rep1


title: Biopsy_CIT1_EVLP49

source_name: Biopsy_timepoint end of cold ischemia


title: Cord blood Nr_144


title: Cord blood Nr_211


title: RV 7060

description: total RNA-SPIA DNA

value: RV Donor


title: RV 7012

description: total RNA-SPIA DNA


title: RV 7040

description: total RNA-SPIA DNA


title: Cord blood Nr_140


title: STR26

type: genomic

city: Nanjing

first: Félix

last: Picazo

state: Jiangsu

address: 22#, 18, North Linshan Road, Qixia

department: Nanjing Institute of Geography and Limnology

institute: Chinese Academy of Sciences

hyb_protocol: Each dried and labelled DNA sample was resuspended in 42 µL of hybridization solution. This solution consisted of 1 x HI-RPM hybridization buffer, 1 x comparative genome hybridization blocking agent, 0.05 µg・µL-1 Cot-1 DNA, 10 pM universal standard, and 10% formamide (final concentrations). The solution was later denatured by remaining at 95 ℃ for 3 min. To remove the bubbles created during the denaturation process, the conditions were maintained at 37 ℃ for 30 min. The hybridizations were carried out at 67 ℃ for 24 h

scan_protocol: The scanned images of the GeoChip hybridizations were obtained and converted by means of the Agilent Feature Extraction 11.5 software (Agilent Technologies, California, USA)

data_processing: The signal intensities, used as a proxy of abundances, were quantified and processed based on previous pipelines48 as follows: (i) removing probes with a signal-to-noise ratio of less than 2.0; (ii) normalizing the signal intensity of each probe by dividing the total signal intensity of a sample and multiplying by a constant; iii) removing singletons, i.e., genes detected only once on each mountain; and (iv) selecting those genes involved in the carbon (C), nitrogen (N), phosphorus (P), and sulphur (S) cycles and stress-related (St) processes

organism: biofilm metagenome

source_name: biofilm

label_protocol: The DNA from each sample (500 ng) was labelled with the fluorescent dye Cy-3 (GE Healthcare, California, USA) by random priming (He et al. 2010)). The DNA was purified as explained above and dried in a SpeedVac (Thermo Savant, New York, USA)

extract_protocol: Microbial DNA was extracted from the biofilm samples using the phenol chloroform method (Zhou, 1996) and purified using the QIAquick Gel Extraction Kit (QIAGEN Sciences, Germantown, MD, USA). The purified DNA was then quantified with a PicoGreen Kit (Eugene, OR, USA) and used for the GeoChip 4.0 hybridization

tag: latitude

tag: longitude


title: Biopsy_CIT1_EVLP48


title: RV 5090

description: total RNA-SPIA DNA


title: RV 3168

description: total RNA-SPIA DNA


title: Biopsy_CIT2_EVLP47


title: RV 7004

description: total RNA-SPIA DNA


title: STR25


title: herlperless_8h_avrRps4_Rep1

first: Isai

last: Salas Gonzalez

institute: The University of North Carolina at Chapel Hill


title: STR24


title: Biopsy_CIT1_EVLP47


title: herlperless_8h_EV_Rep1


title: herlperless_4h_avrRpt2_Rep3


title: Cord blood Nr_193

source_name: cord blood


title: herlperless_4h_avrRpm1_Rep3


title: Biopsy_CIT2_EVLP46


title: Cord blood Nr_222


title: STR21


title: STR22


title: Col-0_4h_avrRpt2_Rep1.1

value: wildtype (Col-0)


title: STR23


title: Col-0_4h_avrRps4_Rep3.1


title: Biopsy_CIT1_EVLP46


title: STR20


title: Biopsy_CIT2_EVLP45


title: Cord blood Nr_69


title: Biopsy_CIT1_EVLP45


title: Col-0_4h_avrRpm1_Rep2.1


title: Cord blood Nr_268


title: Cord blood Nr_90


title: Biopsy_CIT2_EVLP44


title: Col-0_4h_avrRps4_Rep2.1


title: STR16


title: Col-0_4h_avrRpm1_Rep1.1


title: STR17


title: Col-0_4h_EV_Rep3.1


title: STR14


title: STR15


title: Cord blood Nr_125


title: Col-0_T0_T0_Rep3.1


title: Biopsy_CIT1_EVLP44


title: STR13


title: Cord blood Nr_122


title: Col-0_4h_avrRps4_Rep1.1


title: STR12


title: Biopsy_CIT2_EVLP43


title: Cord blood Nr_276


title: Cord blood Nr_218


title: STR11


title: Biopsy_CIT1_EVLP43


title: Cord blood Nr_400


title: Biopsy_CIT1_EVLP42


title: Cord blood Nr_461


title: Biopsy_CIT2_EVLP42


title: Cord blood Nr_55


title: Biopsy_CIT2_EVLP40


title: STR10


title: Col-0_T0_T0_Rep2.1


title: Col-0_4h_EV_Rep1.1


title: Col-0_4h_EV_Rep2.1


title: Biopsy_CIT2_EVLP41


title: Cord blood Nr_155


title: Col-0_8h_EV_Rep2.1


title: Col-0_0.5h_avrRpt2_Rep2.1


title: herlperless_8h_EV_Rep3


title: PY20


title: STR01


title: Col-0_T0_T0_Rep1.1


title: Cord blood Nr_385


title: Biopsy_CIT2_EVLP39


title: PY21


title: STR06


title: Cord blood Nr_249


title: PY18


title: Cord blood Nr_340


title: Biopsy_CIT1_EVLP40


title: Cord blood Nr_213


title: Cord blood Nr_20


title: Biopsy_CIT2_EVLP36


title: Col-0_0.5h_avrRpm1_Rep3.1


title: Biopsy_CIT2_EVLP38


title: Cord blood Nr_126


title: Biopsy_CIT1_EVLP38


title: PY16


title: Biopsy_CIT1_EVLP37


title: Biopsy_CIT1_EVLP39


title: Col-0_4h_avrRpt2_Rep2.1


title: Col-0_0.5h_avrRpt2_Rep1.1


title: PY15


title: Col-0_0.5h_avrRps4_Rep3.1


title: Cord blood Nr_284


title: Cord blood Nr_64


title: Cord blood Nr_379


title: PY17


title: Biopsy_CIT2_EVLP37


title: Cord blood Nr_492


title: Col-0_8h_avrRpt2_Rep3.1


title: Col-0_0.5h_avrRpm1_Rep2.1


title: Biopsy_CIT1_EVLP35


title: PY13


title: PY14


title: PY11


title: Col-0_0.5h_avrRps4_Rep2.1


title: PY10


title: Biopsy_CIT1_EVLP36


title: Biopsy_CIT2_EVLP33


title: Biopsy_CIT1_EVLP34


title: Biopsy_CIT2_EVLP35


title: Biopsy_CIT1_EVLP41


title: PY09


title: Cord blood Nr_344


title: PY08


title: Cord blood Nr_375


title: Cord blood Nr_49


title: Cord blood Nr_150


title: Biopsy_CIT2_EVLP34


title: Col-0_0.5h_EV_Rep3.1


title: Col-0_8h_avrRpt2_Rep2.1


title: Biopsy_CIT1_EVLP33


title: Cord blood Nr_474


title: PY06


title: Cord blood Nr_47


title: Col-0_0.5h_avrRpm1_Rep1.1


title: Col-0_8h_avrRpm1_Rep3.1


title: Col-0_0.5h_avrRps4_Rep1.1


title: PY05


title: Biopsy_CIT2_EVLP32


title: PY07


title: Col-0_0.5h_EV_Rep2.1


title: PY04


title: Biopsy_CIT2_EVLP31


title: Biopsy_CIT1_EVLP32


title: PY01


title: Cord blood Nr_223


title: Col-0_8h_avrRpt2_Rep1.1


title: Col-0_8h_avrRps4_Rep3.1


title: N119


title: Cord blood Nr_263


title: N118


title: Col-0_8h_avrRpm1_Rep2.1


title: Cord blood Nr_219


title: Cord blood Nr_333


title: Biopsy_CIT1_EVLP31


title: Biopsy_CIT2_EVLP30


title: Cord blood Nr_230


title: N117


title: Col-0_0.5h_EV_Rep1.1


title: Col-0_8h_avrRps4_Rep2.1


title: STR09


title: Biopsy_CIT2_EVLP29


title: Biopsy_CIT1_EVLP29


title: Biopsy_CIT1_EVLP30


title: Col-0_8h_avrRpm1_Rep1.1


title: Cord blood Nr_365


title: N115


title: Cord blood Nr_176


title: N114


title: N116


title: Col-0_8h_EV_Rep3.1


title: lncRNA T_3M_2

description:
lncRNA.expression.txt
mRNA.expression.txt
circRNA.expression.txt

source_name: thymus

value: thymus

value: wild type


title: Cord blood Nr_212


title: Cord blood Nr_448


title: Col-0_0.5h_avrRpt2_Rep3.1


title: Col-0_8h_avrRps4_Rep1.1


title: Biopsy_CIT2_EVLP28


title: N113


title: Biopsy_CIT2_EVLP27


title: Biopsy_CIT1_EVLP27


title: Cord blood Nr_76


title: N112


title: Col-0_4h_avrRpt2_Rep3.1


title: lncRNA T_3M_1


title: Biopsy_CIT2_EVLP26


title: N111


title: Biopsy_CIT1_EVLP28


title: Cord blood Nr_499


title: lncRNA T_6W_2


title: Col-0_8h_EV_Rep1.1


title: N110


title: lncRNA T_6W_1


title: Biopsy_CIT2_EVLP25


title: Col-0_4h_avrRpm1_Rep3.1


title: N109


title: lncRNA T_2W_1


title: Col-0_4h_avrRpt2_Rep1


title: lncRNA T_2W_2


title: Col-0_4h_avrRps4_Rep3


title: S2_HA-ZKSCAN4_ChIP_Input_genomic_DNA

city: Marseille

first: Andrew

middle: J

last: Saurin

address: Campus de Luminy

country: France

institute: IBDM / CNRS

description:
S2-ZKSCAN4 ChIP Input gDNA
ZKSCAN4_S2_peaks.bed

data_processing:
Basecalls performed using RTA (Illumina)
RNA-seq reads were aligned to the dm6 genome assembly using subread-align
Gene exon counts were made using featureCounts
RNA-Seq differentially expressed genes were called using DESeq2 using a false discovery rate (FDR;padj) cut-off of 0.001
ChIP-Seq peak calling was performed using MACS2 using low stringency on individual replicates. Final peaks were called using an Irreproducible Discovery Rate (IDR) of 0.1% according to guidelines set out by the ENCODE consortium.
Genome_build: dm6
Supplementary_files_format_and_content: DGE files show the DESeq output of differentially expressed genes of L3W versus L3F or L3F M1BP RNAi versus L3F at FDR 0.1% (padj <0.001)
Supplementary_files_format_and_content: Bed files were prepared using MACS2 and represent peaks called in both replicates having an IDR of 0.1%.

organism: Drosophila melanogaster

source_name: S2-HA::ZKSCAN4 Cell line

growth_protocol:
WT or cgGal4 crossed to WT or M1BP RNAi larvae were reared at 25oC and fed only normal Drosophila media
Cells were grown in T-flasks to a density of not more than 7x10^6 cells/ml in Schneider Medium supplemented with 10% FBS

extract_protocol:
RNA was extracted with Qiagen Rneasy kit; Chromatin was prepared according to the modENCODE procedure
DNA and mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
cgGal4 crossed to WT or M1BP RNAi larvae were reared at 25oC and fed only normal Drosophila media
Cells were treated with 10 microMolar Copper Sulphate for 24 h prior to chromatin preparation

tag: developmental stage

value: late embryo-derived cell line stably transfected with HA::ZKSCAN4

value: S2-DRSC-HA::ZKSCAN4 cell line

value: 10 microMolar Cu2SO4


title: N108


title: Biopsy_CIT1_EVLP25


title: S2_HA-ZKSCAN4_ChIPSeq_Rep2

description:
HA ChIP-Seq of S2-ZKSCAN4 cells Rep2
ZKSCAN4_S2_peaks.bed

tag: chip antibody

value: HA (AbCam ab9110)


title: Col-0_4h_avrRps4_Rep2

city: Chapel Hill

address: 250 Bell Tower Drive, Room 4244


title: Biopsy_CIT2_EVLP24


title: Biopsy_CIT1_EVLP26


title: S2_HA-ZKSCAN4_ChIPSeq_Rep1

description:
HA ChIP-Seq of S2-ZKSCAN4 cells Rep1
ZKSCAN4_S2_peaks.bed


title: N106


title: Biopsy_CIT2_EVLP23


title: Col-0_4h_avrRpm1_Rep1


title: Biopsy_CIT1_EVLP23


title: S2_HA-ZKSCAN3_ChIP_Input_genomic_DNA

description:
S2-ZKSCAN3 ChIP Input gDNA
ZKSCAN3_S2_peaks.bed

source_name: S2-HA::ZKSCAN3 Cell line

value: late embryo-derived cell line stably transfected with HA::ZKSCAN3

value: S2-DRSC-HA::ZKSCAN3 cell line


title: Biopsy_CIT1_EVLP24


title: Col-0_4h_EV_Rep3


title: N104


title: S2_HA-ZKSCAN3_ChIPSeq_Rep2

description:
HA ChIP-Seq of S2-ZKSCAN3 cells Rep2
ZKSCAN3_S2_peaks.bed


title: N102


title: N107


title: Col-0_T0_T0_Rep3


title: Col-0_4h_avrRpm1_Rep2


title: Biopsy_CIT2_EVLP22


title: Biopsy_CIT1_EVLP22


title: N101


title: S2_HA-ZKSCAN3_ChIPSeq_Rep1

description:
HA ChIP-Seq of S2-ZKSCAN3 cells Rep1
ZKSCAN3_S2_peaks.bed


title: MN32

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

institute: TAmiRNA GmbH

description:
control
SAMPLE 29

data_processing:
Cq-values were called using the second-derivate maximum method. Data quality was assessed using spike-in controls to determine RNA extraction efficiency, enzymatic inhibition, and overall variability. Data normalization was performed using the global mean (i.e. average Cq-value for all endogenous microRNAs with Cq<35) to obtain delta Cq-values.
normalized data file contains global-mean normalized delta Cq-value (dCqs)
Log2 Fold Change = log2 (PLS3 MP vs MN)

label: SYBR Green

source_name: serum

growth_protocol: We have previously identified four Finnish families with X-linked PLS3 osteoporosis due to different mutations in PLS3 . The first family (Family A) has an intronic splice site mutation c.73–24T>A (p.Asp25Alafs*17) identified by exome sequencing as previously described. The second family (Family B) includes three subjects with an intragenic tandem duplication within PLS3 as identified by genomic hybridization array (array-CGH). The third family (Family C) consists of a single subject with a de novo heterozygous missense mutation c.1424A>G (p.AsnN446Ser )  in exon 12 identified by Sanger sequencing of the whole PLS3 gene as previously described. The fourth family (Family D) includes two subjects with a nonsense mutation c.766C>T (p.Arg256*) in exon 8, also identified by conventional Sanger sequencing of the whole PLS3 gene.

extract_protocol: Serum was thawed at room temperature and centrifuged at room temperature for 5 minutes at 12,000 x g in order to remove cellular debris. RNA extraction was performed using precisely 200 µl serum as previously described (8,15) using the miRNeasy Mini Kit (Qiagen, Germany) with the following modification: synthetic, non-human oligonucleotides (Qiagen, Germany) were added to the Qiazol lysis buffer, glycogen was added to the precipitation at a final concentration of 0.5 mg/mL to enhance precipitation, and columns were washed three times with Ethanol before elution in 30 µl nuclease-free water. Eluted total RNA was stored at -80°C until further analysis.

treatment_protocol: We collected serum samples from all subjects during the summer months (June–August) in 2017 to avoid seasonal bias from variable sunlight exposure. We collected all samples after an overnight fast, in the morning between 8 and 9 a.m. First, we collected venous peripheral blood to normal serum tubes, let them stand and clot in room temperature for 30–60 minutes and then centrifuged them at 2500 x g for 10 minutes. The supernatants were then transferred to 1.5 ml tubes in 250 µl aliquots and stored immediately at -80 °C until analysis.

value: serum

tag: diagnosis

value: control

tag: pls3 mutation status

value: PLS3 mutation-negative

tag: gender

value: M


title: Col-0_4h_avrRps4_Rep1

tag: genotype

tag: time

tag: treatment


title: Biopsy_CIT2_EVLP21


title: LI_R3

city: ottawa

first: Chanchal

last: Yadav

address: 1125 colonel by drive

department: Biology

institute: Carleton University

data_processing:
150bp Paired end RNA seq generated by NextSeq500 at StemCore Sequencing Facility, Ottawa, ON, Canada
Raw sequences trimmed were by Trimmomatic-0.36, followed by quality check by FastQC v0.11.7
De novo transcriptome was assembled using Trinity v2.4.0  with default parameters; this transcriptome (Darcuata.fasta) was the used as reference for expression analysis
Abundance estimation conducted using RSEM, followed by differential expression analysis by edgeR
Genome_build: Darcuata.fasta
Supplementary_files_format_and_content: De novo assembled sequences used as reference for abundance estimation; Tab-delimited text files generated by RSEM that include FPKM values for each sample and replicates

organism: Drepana arcuata

source_name: Whole larva

growth_protocol: Drepana arcuata larvae used in this study were reared from the eggs laid by same  female captured at ultraviolet lights near Ottawa, ON, Canada (45.4215 °N, 75.6972 °W). Larave were reared on paper birch (Betula papyrifera) leaves held in water-filled vials contained in glass jars at room temperature (21–23°C) on a 16 h: 8 h light: dark cycle

extract_protocol:
Whole larvae were frozen in liquid nitrogen, followed by RNA extraction using Norgen Biotek RNA extraction kit (Norgen Biotek Corp, Thorold, ON, Canada). Quality of RNA samples was assessed using Agilent Bioanalyser (Santa Clara, CA, United States) , and   then used for paired-end Illumina sequencing using NextSeq 500 at the StemCore sequencing facility (Ottawa Hospital Research Institute, ON, Canada).
Libraries were generated using standard Illumina paired-end sequencing protocols

treatment_protocol: Three biological replicates for each of early instars (I, II; N= 20 larvae per replicate) and late instars (IV,V; N = 5 larvae per replicate) were frozen separately in liquid nitrogen and kept at -80C prior to RNA isolation (see below) for sequencing.

value: Late instar

value: whole body


title: Col-0_4h_EV_Rep2

value: EV

tag: rep


title: Biopsy_CIT1_EVLP21

value: lung


title: MN26

description:
control
SAMPLE 27

value: F


title: Biopsy_CIT2_EVLP20


title: LI_R2


title: MP31

description:
case
SAMPLE 26

value: PLS3 osteoporosis

value: PLS3 mutation-positive


title: Col-0_T0_T0_Rep2

value: wildtype (Col-0)


title: Biopsy_CIT1_EVLP20


title: MP29

description:
case
SAMPLE 25


title: Col-0_4h_EV_Rep1


title: LI_R1


title: MP32

description:
case
SAMPLE 28


title: E1_R3

value: Early instar


title: Biopsy_CIT2_EVLP19


title: Col-0_T0_T0_Rep1


title: EI_R2


title: Biopsy_CIT1_EVLP19


title: MN21

description:
control
SAMPLE 24


title: Col-0_8h_EV_Rep2


title: Cord blood Nr_398

data_processing: An in-house developed quality control pipeline in R software was used to preprocess raw data as follows: local background correction, omission of controls, flagging of bad spots and spots with too low intensity, log2 transformation and quantile normalization using arrayQC. More information about the flagging and the R-scripts of the pipeline are available at https://github.com/BiGCAT-UM/arrayQC_Module. Further preprocessing included removal of probes showing > 30% flagged data, merging of replicate probes based on the median, and imputation of missing values by means of K-nearest neighbor imputation (K = 15) resulting in 29,164 transcripts available for further analysis. Of the 200 samples, RNA extraction was not possible for 6 samples. After exclusion of samples failing preprocessing and missing covariates for denoising  gene expression levels of 165 samples were left in our analyses.

extract_protocol: not provided

value: cord blood

tag: birthweight

tag: hybridization date


title: Col-0_0.5h_avrRpt2_Rep3


title: MP28

description:
case
SAMPLE 23


title: Biopsy_CIT1_EVLP18


title: Biopsy_CIT2_EVLP18


title: Col-0_0.5h_avrRpm1_Rep3


title: Biopsy_CIT2_EVLP17


title: MN34

description:
control
SAMPLE 22


title: Biopsy_CIT1_EVLP17


title: MP34

description:
case
SAMPLE 19


title: MP23

description:
case
SAMPLE 20


title: Biopsy_CIT2_EVLP16


title: EI_R1


title: Col-0_0.5h_avrRpt2_Rep1


title: Col-0_0.5h_avrRps4_Rep3


title: MP26

description:
case
SAMPLE 21


title: Col-0_0.5h_avrRpt2_Rep2


title: C2

city: changsha

first: Fangwen

last: Zou

state: hunan

institute: Central south univ

description:
circRNA expression data from Homo sapiens carcinoma tissues.
circRNA

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software. A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated in detail with the circRNA/miRNA interaction information.

source_name: Gastrointestinal stromal tumor tissue from terminal cancer patient

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing random primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: Gastrointestinal stromal tumor and matched non-tumor tissues.

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

treatment_protocol: Tissues from gastrointestinal stromal tumor surgery and promptly frozen in liquid nitrogen.

value: Gastrointestinal stromal tumor

value: Male

tag: age

value: 61 years


title: C3

value: Female

value: 43 years


title: C1

value: 55 years