title: MK-801+CLO group_3

city: Guangzhou

first: hui

middle: Wen

last: Huang

address: Huang pu da dao West 601

institute: Jinan University

data_processing:
Illumina Casava1.7 software used for basecalling.
After removing low-quality reads and reads without the 3’ adaptor and 5’adaptor-contaminant by Cutadapt (Version 1.14) software, keep Q20 reads (>80%) according to fastx_toolkit (Version 0.0.13) software, removing the reads with N bases according to NGSQCToolkit (Version 2.3.3) software.
Subsequently, the remaining clean reads counted and analyzed by software (such as fastx_toolkit, bowtie, OE reads Statistical tool, DESeq). The clean reads were compared against the Rfam, GeneBank and Repbase databases to remove rRNAs, tRNAs, small nuclear RNA (snRNA) and other non-coding RNAs.
The remnant reads were searched against miRbase (version21; http://www.mirbase.org/) to identify known miRNAs for further analysis. After identifying the known miRNAs, unannotated sequences that were not assigned to any above databases were used for the prediction of novel miRNAs by miRDeep2.
Additionally, their hairpin structures were then analyzed using the RNAfold software. We predicted differentially expressed miRNA target genes according to TargetScan, miRDB, RNAhybrid and Miranda algorithms in miRwalk2.0 online website.
To assess the prospective functions of the most significant differently miRNAs, we discharged GO-term functional enrichment analysis of biological processes and KEGG pathways using DAVID (Database for Annotation, Visualization, and Integrated Discovery).
Genome_build: Rnor_6.0 (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000001895.5_Rnor_6.0/GCF_000001895.5_Rnor_6.0_genomic.fna.gz)
Supplementary_files_format_and_content: tab-delimited text file includes raw and  TPM values for each Sample

source_name: MK-801+CLO group

growth_protocol: Rats were housed two or three to a clear polycarbonate cages under a controlled 12/12-h light-dark cycle (light from 7:00 AM to 7:00 PM), with room temperature at 23±1 °C and humidity at 55±5% in Guangdong Medical University Experimental Animal Center. The rats were continuously given free access to food and water. After 14 days of habituation to the age 5 weeks (120-140 g), rats were used in the subsequent drug treatment and experiments.

extract_protocol:
Brains were rapidly removed and each hippocampus was dissected, frozen immediately in liquid nitrogen, then stored at -80°C refrigerator until needed. Total RNA was extracted from the frozen tissues using the AMBION RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s protocol. Subsequent RNA purification was performed using the Qiagen RNeasy® Kit (Qiagen, Mainz, Germany). RNA quality was confirmed using the Agilent 2100 Bioanalyzer system after purification (Agilent Technologies, Inc., Santa Clara, CA).
miRNA libraries were prepared for sequencing using standard Illumina protocols
Small RNA next generation sequencing

treatment_protocol: This study used 3 groups (10 rats/group) Sprague-Dawley rats. Thirty rats were randomly assigned to three groups, VEH control group (n = 10), MK-801 group (n = 10) and MK-801+CLO group (n = 10). Rat model of schizophrenia was induced by MK-801 intraperitoneal injection. Each rat in the MK-801 and MK-801+CLO groups received an intraperitoneal injection of 0.2 mg/kg of MK-801 once a day for 14 consecutive days. 0.2 mg/kg MK-801 has been demonstrated to induce schizophrenia-like structural changes in rat hippocampus and regulate multiple steps of hippocampal neurogenesis. Ten control animals received an equal volume of sterile saline for 14 and 7 days. After treating with MK-801 for 14 consecutive days, MK-801 group were intraperitoneally in an equal volume of sterile saline for additional 7 days, the third group (MK-801+CLO) rats were administered intraperitoneally in 10mg/kg dose for additional 7 days.

value: hippocampus

value: Sprague-Dawley

value: post natal day 21


title: splenic CD4+ T cells, Het_GFP_pos_replicate_1

status: Public on Oct 01 2020

type: SRA

city: Freiburg

first: Ekaterina

last: Lupar

address: Stuebeweg 51

department: Department of Cellular & Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

library_source: transcriptomic

data_processing:
Raw data from the Illumina HiSeq 2500 sequencing machine was demultiplexed and converted into FASTQ files using Illumina bcl2fastq2 (version 1.8.4, http://support.illumina.com/downloads/bcl2fastq_conversion_software_184.html).
Screening for contamination with fastq_screen (version 0.5.1, (http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
Automatic detection and trimming of adaptors, quality control and mapping was performed with an rna-seq-qc pipeline (https://github.com/maxplanck-ie/rna-seq-qc).
Reads alignment against mouse genome was done with TopHat2 (version 2.0.13).
Reads were counted with featureCounts (version 1.5.0-p1).
Differential gene expression analysis was performed using the DESeq2 (version 1.6.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include non-normalized feature counts, differentially expressed genes

molecule: total RNA

organism: Mus musculus

source_name: splenic CD4+ T cells, Het_GFP_pos

growth_protocol: FACS-Sorted splenic CD45RBhi CD25- naïve CD4+ T cells from Eomes-Het-GFP or Eomes-KO-GFP reporter mice were adoptively transferred into adult male Rag2-/- recipients. 3 weeks later recipient mice were killed and GFP+ and GFP- CD4+ cells were sorted from their spleens for RNAseq analysis.

extract_protocol:
Total RNA was extracted with TRI reagent (Sigma-Aldrich, Munich, Germany).
Depletion of the ribosomal RNA and library preparation was performed with the TruSeq® Stranded Total RNA Gold kit (former name TruSeq® Stranded Total RNA LT - (with Ribo-Zero TM GOLD), Illumina, San Diego, USA).

tag: donor genotype

value: Eomes flox/GFP; no cre

tag: gfp expression

value: positive

tag: activation condition

value: 3 weeks in Rag2-/- recipient

tag: cell type

value: splenic CD4+ T cells

tag: number of cells in sample


title: genomic DNA from old PBMCs 14

type: genomic

city: Boulder

first: Christopher

middle: R

last: Martens

state: CO

address: 354 UCB

department: Integrative Physiology

country: USA

institute: University of Colorado Boulder

description:
O-SED
OS14

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

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

data_processing: R (v3.2.2)/Bioconductor Package 'minfi' package (minfi_1.14.0) was used to pre-process data: RGset was processed using the function preprocessRaw.  Failed probes (p>0.05 in at least 1% of samples) were removed and data were normalized using SWAN normalization.  Methylation loci on sex chromosomes or containing random or known SNPs were removed.  Beta values were extracted using getBeta function.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMCs old sedentary

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from PBMCs using the Qiagen Mini DNA isolation kit, following the manufacturer's instructions.

treatment_protocol: Sedentary was defined as not having performed regular exercise (<30 min/day, <2 days/week) during the previous 2 years; Exercise Trained was defined as performing ≥4 sessions/week of vigorous aerobic/endurance exercise for ≥45 minutes/session.

tag: age

tag: Sex

value: M

tag: training status

value: sedentary


title: RNA-seq_3591T

city: Kunming

first: Ming

last: Li

state: Yunnan

address: NO 32 Jiao-Chang Donglu

country: China

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

data_processing:
For RNA-Seq, trimmomatic v0.32 were used to examine the sequencing quality and trim reads. Clean paired-end reads were aligned to the reference genome using Hisat2.We quantified gene-level reads counts using htseq-count. DESeq2 was used to analyze the expression differences between experimental groups.
For ATAC-Seq, the raw 150-bp paired-end reads of the ATAC-Seq libraries from HiSeq X Ten sequencer underwent quality control processes using FastQC and trimmomatic-0.36.Bowtie2 (-X 2000 --sensitive-local --dovetail) was used to align trimmed reads to the GRCh37.p13 build of the human genome. Potential PCR duplicate reads were marked using MarkDuplicates program from the Picard tool. Reads from mitochondrial DNA and the Y chromosome were filtered using SAMtools. Peaks were called in the each sample using MACS2 with parameters: --nomodel --shift -100 --extsize 200. Narrow peaks mapped to the blacklisted regions were excluded using bedtools. Peaks called from different samples were then merged using the mergePeaks program (-d 2000) in the HOMER tool. The reads counts of each peak were quantified using featureCounts based on the chromosome position of merged peaks. The Wald test in DESeq2 was used to identify differently accessible peaks between groups.
Genome_build: For RNA-Seq, GRCh38. For ATAC-Seq, hg19.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of each gene in RNA-Seq analysis and reads counts of each peak in ATAC-Seq analysis for each sample

source_name: Monocolony HEK293T cell carrying [A/A] genotype at rs4420550.

growth_protocol: HEK293T cells were cultured in a humidified 5% CO2 incubator at 37 °C in Dulbecco’s Modified Eagle’s Medium (DMEM) basic (Gibco) supplemented with 10% fetal bovine serum (FBS) (Biological Industries), 1% non-essential amino acids, 1% Sodium pyruvate and 1% penicillin-streptomycin (Life Technologies). PCR detection was regularly performed to ensure there were no mycoplasma contamination.

extract_protocol:
For RNA-Seq, total RNAs were extracted from cultured cells using the TRIzol Reagent (Life Technologies) according to standard protocol. For ATAC-Seq, 3×104 HEK293T cells were lysed in lysis buffer [10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.1% (v/v) Igepal CA-630] on ice for 10 minutes to release the nuclei. The mixture was centrifuged at 4 °C at 500× g for 5 minutes and the supernatant was discarded as much as possible. The nuclei pellet was then incubated with a reaction mix containing Tn5 transposome at 37 °C for 30 minutes. DNA was purified immediately after transposition by using a Qiagen MinElute
For RNA-Seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. For ATAC-Seq, the transposed DNA fragments were PCR-amplified using the following conditions: 72 °C for 3 minutes, 98 °C for 30 seconds, and thermocycling for 15 cycles at 98 °C for 15 seconds, 60 °C for 30 seconds and 72 °C for 30 seconds, followed by 72 °C for 5 minutes. The PCR products were immediately purified with 1.2×AMPure (Beckman) beads to obtain ATAC-Seq libraries.

treatment_protocol: The [A/A] genotype at rs4420550 in wild-type HEK293T cells were precisely edited by CRISPR/cas9 to [G/G] genotype. Briefly, the pL-CRISPR-E.EFS.GFP construct targeting rs4420550 and the ssODN carrying C allele at rs4420550 were transiently co-transfected into wild-type HEK293T cells and cells positive for GFP fluorescence were sorted with a flow cytometer, and cultured for 5-7 days to form distinct colonies derived from single cells. Genomic DNA was then extracted from each colony for amplifying the target region containing rs4420550, and Sanger sequencing was performed to confirm the genomic editing. Overall, eight single cell colonies were selected after flow cytometry for subsequent analysis. Four colonies carried the [A/A] genotype at rs4420550, and the other four carried the [G/G] genotype.

tag: cell line

tag: snp

tag: genotype

value: A/A


title: MK-801+CLO group_2

organism: Rattus norvegicus

tag: tissue

tag: strain

tag: treatment


title: MK-801 group_3

source_name: MK-801 group


title: MK-801+CLO group_1


title: splenic CD4+ T cells, Het_GFP_neg_replicate_1

source_name: splenic CD4+ T cells, Het_GFP_neg

value: negative


title: genomic DNA from old PBMCs 8

description:
O-SED
OS8


title: RNA-seq_3589T


title: genomic DNA from old PBMCs 11

description:
O-SED
OS11


title: splenic CD4+ T cells, Het_GFP_neg_replicate_2


title: genomic DNA from old PBMCs 10

description:
O-SED
OS10


title: MK-801 group_2


title: RNA-seq_3015T


title: single cell RNA sequencing of dissected mouse mandibular prominence at embryonic day 13.5

city: Cincinnati

first: Samantha

last: Brugmann

state: OH

address: Department of Developmental Biology, DK 1 BLDG R, 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Raw scRNA-Seq data was processed using cellranger (v2.0.0 10xGenomics) (https://github.com/10XGenomics/cellranger). Reads were aligned to mouse genome [mm10] to produce counts of genes across barcodes. Barcodes with less than ~5k UMI counts were not included in downstream analysis. Percentage of reads mapped to transcriptome was ~70% each sample. QC, Filtering, Normalization and Clustering was carried out using Seurat [v2.3.4]
Genome_build: mm10
Supplementary_files_format_and_content: Processed Data files consists of counts matrixs of counts of genes across all cells and metadata providing information of each cells cluster definition.

growth_protocol: Mice were maintained in specified pathogen free condition in accordance with institutional guidance.

extract_protocol:
Mandibles from e11.5 or e13.5 wildtype CD1 mouse embryos were quickly dissected in ice-cold PBS and minced to a fine paste. 12.5mg of tissue was placed in a sterile 1.5mL tube containing 0.5mL protease solution containing 125 U/ml DNase and Bacillus Licheniformis (3mg/ml for e11.5 sample and 5mg/ml for e13.5 sample). The samples were incubated at 4C for at total of 10 minutes, with trituration using a wide boar pipette tip every minute after the first two. Protease was inactivated using ice-cold PBS containing 0.02% BSA and filtered using 30µM filter. The cells were pelleted by centrifugation at 200G for 4 minutes and resuspended in 0.02% BSA in PBS. Cell number and viability were assessed using a hemocytometer and trypan blue staining. 9,600 cells were loaded onto a well on a 10x Chromium Single Cell instrument (10X Genomics) to target sequencing of 6,000 cells.
RNA libraries were prepared for sequencing using standard 10X Genomics protocols

treatment_protocol: Timed mating between CD1 mice were performed and the date when a plug was detected was considered embryonic day 0.5.

tag: cell source

value: micro-dissected mandibular tissues

tag: embryo age

value: embryonic day 13.5

value: epithelium and mesenchyme of mandibular prominence including developing tongue and skeletal elements


title: genomic DNA from old PBMCs 5

description:
O-SED
OS5


title: MK-801 group_1


title: genomic DNA from old PBMCs 9

description:
O-SED
OS9

value: F


title: genomic DNA from old PBMCs 6

description:
O-SED
OS6


title: single cell RNA sequencing of dissected mouse mandibular prominence at embryonic day 11.5

value: micro-dissected mandibular prominence

value: embryonic day 11.5

value: epithelium and mesenchyme of mandibular prominence including developing tongue bud.


title: RNA-seq_3010T


title: Input

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

institute: Nanjing University

description: skeletal muscle DNA input control

library_source: genomic

data_processing:
Illumina RTA used for base calling and converting into raw FASTQ files with Bcl2Fastq conversion software.
quality control using fastQC version 0.11.3
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 version 2.2.5 with the default parameters.
peaks were called using macs2 version 2.2.1 with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph and excel files including tag density and peak information were generated using macs2.

source_name: skeletal muscle

extract_protocol:
Lysates were clarified from sonicated nuclei and MLL4-DNA complexes were isolated with antibody.
NEBNext® UNEBNext DNA Library Prep Master Mix Set for Illumina (cat# E6040L) was used with ChIP-DNA for the construction of sequencing libraries. ChIP libraries were prepared for sequencing using standard Illumina protocols

value: skeletal muscle

value: Wild-type

tag: chip antibody


title: RNA-seq_3612C

source_name: Monocolony HEK293T cell edited by CRISPR/cas9 carrying [G/G] genotype at rs4420550.

value: G/G


title: VEH control group_3

source_name: VEH control group

value: hippocampus

value: Sprague-Dawley

value: post natal day 21

value: VEH control


title: VEH control group_2


title: MLL4_ChIPSeq_Mll4-MKO

description: skeletal muscle DNA from Mll4 muscle specific knockout mouse

source_name: skeletal muscle from Mll4-MKO mouse

value: Mll4 knockout

value: homemade MLL4 antibody


title: splenic CD4+ T cells, KO_GFP_neg_replicate_3

source_name: splenic CD4+ T cells, KO_GFP_neg

tag: donor genotype

value: Eomes flox/GFP; Lck-cre

value: negative

value: 3 weeks in Rag2-/- recipient

value: splenic CD4+ T cells


title: genomic DNA from old PBMCs 7

description:
O-SED
OS7

value: F

value: sedentary


title: VEH control group_1


title: RNA-seq_3602C


title: genomic DNA from old PBMCs 4

description:
O-SED
OS4


title: splenic CD4+ T cells, Het_GFP_neg_replicate_3

value: Eomes flox/GFP; no cre

tag: gfp expression


title: MLL4_ChIPSeq_WT

description: skeletal muscle DNA from wild-type mouse - control mouse for muscle specific knockout Mll4

source_name: skeletal muscle from wild-type mouse


title: RNA-seq_3546C


title: WGS-HCT116

city: Bethesda

first: Andre

last: Nussenzweig

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

description: Whole Genome Sequencing

data_processing:
Data was aligned to hg19 human refernce genome
Supplementary_files_format_and_content: bigwig files were made for plus (*.pos.bw) and minus (*.neg.bw) strand separately using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

growth_protocol: Cell lines containing doxycycline-inducible shWRN cassette (KM12, HCT116, SW837, RPE-1) were generated as previously described 3. Cell lines were grown in medium supplemented with 10% fetal bovine serum (FBS), penicillin (100 µg/mL) / streptomycin (100 µg/mL), and L- glutamine (Gibco, 292 µg/mL) unless stated otherwise.

extract_protocol: none provided by the submitter


title: genomic DNA from young PBMCs 12

description:
Y-SED
YS12

source_name: PBMCs young

value: M


title: genomic DNA from old PBMCs 2

description:
O-SED
OS2


title: genomic DNA from young PBMCs 11

description:
Y-SED
YS11


title: genomic DNA from old PBMCs 3

description:
O-SED
OS3


title: WGS-KM12

description: Whole Genome Sequencing


title: AR3368_03

type: RNA

city: Nagoya

first: Tetsuro

last: Taki

state: Aichi

address: 65 Tsuromai Showa

department: Pathology

country: Japan

institute: Nagoya University

description: Gene expression in lung tumors after intratracheal administration of adenoviral Cre recombinase

hyb_protocol: Fragmentation of Cy3-labeled cRNA and hybridization to SurePrint G3 Mouse GE Microarray 8×60K Ver.2.0 were performed by CDM Center (Takara Bio Inc., Kusatsu, Japan).

scan_protocol: One color scan setting for SurePrint G3 Mouse GE Microarray 8×60K Ver.2.0.

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

source_name: Lung tumors of CD109-/- KP mouse, replicate 1

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 100 ng total RNA using a Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies).

extract_protocol: Total RNA was extracted from the lung tumors of CD109+/+ and CD109-/- KP mice using TRIzol (Thermo Fisher Scientific) and an RNeasy Mini Kit (Qiagen).

treatment_protocol: Intratracheal administration of adenoviral Cre recombinase was performed 88-92 days before RNA extraction.

value: lung tumors

tag: cd109 genotype

tag: gender

value: male


title: genomic DNA from old PBMCs 13

description:
O-SED
OS13


title: AR3368_04

source_name: Lung tumors of CD109-/- KP mouse, replicate 2

value: female


title: genomic DNA from old PBMCs 1

description:
O-SED
OS1


title: T476_patient_sample_1

city: Luxembourg

first: Ann-Christin

last: Hau

address: 1, Rue Louis Rech

department: National Center of Pathology

country: Luxembourg

institute: Laboratoire National de sante

hyb_protocol: Similarly treated amounts of reference; Female or Male gDNA pool (Promega) were processed as sample genomic DNAs and hybridized with the Agilent Oligo aCGH Hybridization Kit to the corresponding platform array at 65°C for 24h or 48h respectively.

scan_protocol: Microarray slides were scanned using an Agilent 2565C DNA scanner

data_processing:
The tif images were analyzed with Agilent Feature Extraction version 12.5, using default settings
normalised log ratio Cy5/Cy3 representing test/reference; transformed logratio matrix with 0 - unaltered, 1 - gain, -1 - loss, 2 - amplification, -2 - deletion

source_name: Primary patient sample

label_protocol: For Agilent-021529 platform 2µg, for Agilent-021850 and Agilent-028081 platform 1µg, for Agilent-030587 platform 500ng and for Agilent-021924 platform 250ng of genomic DNA  were digested with RSA1 and Alu1 (Agilent) to generate 200-500bp large fragments. The BioPrime aCGH Genomic labeling Kit (Life Technologies) and Cy3 and Cy5 dyes (GE Healthcare) were used following standard protocols for Agilent aCGH (CGH enzymatic protocol v6.2; Ref # G4410-90010).

growth_protocol: patient specimen were: 1) flash frozen on dry ice after surgical removal or 2) mechanically cut, seeded on agar coated flasks (0.85%) and allowed to form spheroids for up to 2 weeks at 37°C under 5% CO2 and atmospheric oxygen in DMEM medium, 10% FBS, 2mM L-Glutamine, 0.4mM NEAA and 100U/ml Pen-Strep (all from Lonza).  Spheroids (generation 0) with a diameter of 300-1000 µm were then implanted in the brain of immunodeficient mice (NOD/Scid, Nude or NSG; 6 spheroids per mice). Cell lines were derived from xenotransplanted mice by papain-based enzymatic digestion of PDOX tissue and cultured in serum-free medium based on  Neurobasal® base medium (Life Technologies) supplemented with 1 x B27 (Life Technologies) 2 mM L-Glutamine, 30 U/ml Pen-Step, 1 U/ml Heparin (Sigma), 20 ng/ml bFGF (Miltenyi, 130-093-841) and 20 ng/ml EGF (Provitro, 1325950500).

extract_protocol: Genomic DNA was isolated from patient tissue, spheroid cultures or cell lines using the AllPrep DNA/RNA Mini Kit® (Qiagen) following manufacturer’s instructions for “Simultaneous purification of genomic DNA and total RNA from animal tissues”.

tag: sample type

value: Primary patient sample

value: Male

source_name: Reference DNA

value: Reference DNA

tag: catalog no


title: T386_patient_sample_1


title: T407_patient_sample_1

value: Female


title: genomic DNA from young PBMCs 8

description:
Y-SED
YS8

tag: age

tag: Sex


title: AR3368_02

source_name: Lung tumors of CD109+/+ KP mouse, replicate 2


title: AR3368_01

source_name: Lung tumors of CD109+/+ KP mouse, replicate 1


title: Wistar_scRNAseq

city: Oxford

first: David

last: Paterson

address: Parks Road

department: Department of Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

description:
sc-RNA-seq
processed data file: Differential_Expression.csv

data_processing:
Cell Ranger (v3.0.2) for alignment and abundance measurements. Seurat (v3) for filtering, clustering and differential expression (via DESeq2).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Wistar_NeuronCluster_Expression.csv: Comma-separated text file of neuron cluster expression values in Wistar.
Supplementary_files_format_and_content: SHR_NeuronCluster_Expression.csv: Comma-separated text file of neuron cluster expression values in SHR.
Supplementary_files_format_and_content: Differential_Expression.csv: Comma-separated text file of differential expression between Wistar and SHR neuron clusters.

source_name: Stellate Ganglia

extract_protocol:
1mg/ml Collagenase IV for 25 minutes, 2mg/ml Trypsin for 30 minutes. Followed by mechanical disruption.
10x Genomics, Single cell 3' v3. Hiseq 4000.

value: Wistar

value: 5-6 weeks

tag: cell type

value: Stellate ganglia

tag: phenotype

value: Normotensive


title: SKMEL28_Ctrl

status: Public on Sep 30 2020

city: Epalinges

first: Soumitra

last: Ghosh

state: Choose State/Province

address: Chemin des Boveresses 155

department: Biochemistry

country: Switzerland

institute: University of Lausanne, Switzerland

hyb_protocol: Following fragmentation, 5.2 ug of cRNA were hybridized for 16 hr at 45 °C on GeneChip Human Clariom D arrays with rotation 60 rpm in GeneChip Hybridization Oven 645. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with SST-RMA algorithm ss normalization method using Transcriptome Analysis Console (TAC) software V4.0.

label: Biotin

source_name: SKMEL28 cells transfected with control shRNA

label_protocol: 100 ng of total RNA were used as input for the preparation of biotinylated sense-stranded DNA targets using the WT PLUS reagent kit from Thermofisher Scientific. Targets were then fragmented and labeled with the Affymetrix GeneChip WT terminal Labeling Kit and hybridized on Human Clariom D arrays accroding to recommendations.

growth_protocol: Melanoma cell lines were maintained in Dulbecco's modified Eagle's medium (DMEM)  supplemented with 10% (v/v) fetal bovine serum (Thermo Fisher Scientific) and 1% Pen-Strep. Cells were cultured at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Extraction of total RNA was performed using directZol  RNA miniprep kit  (Zymo Research) according to the manufacturer's instructions.

treatment_protocol: Melanoma cells were infected for 2 hours with high-titer lentiviruses sufficient to infect the majority of cells. 48 hours after infection, cells were selected with 1 μg/ml of Puromycin for 3 days. The selected cells were subjected for RNA isolation.

tag: genotype/variation

value: BRAF mutation

tag: tumor stage

value: Met

tag: cell line

value: transfected with control shRNA

value: melanoma cell line


title: WM115_shAR2

source_name: WM115 cells transfected with shRNA2 against AR

value: VGP

tag: treatment

value: transfected with shRNA2 against AR


title: SKMEL28_shAR1

source_name: SKMEL28 cells transfected with shRNA1 against AR

value: transfected with shRNA1 against AR


title: WM115_Ctrl

source_name: WM115 cells transfected with control shRNA


title: genomic DNA from young PBMCs 2

description:
Y-SED
YS2

value: M

tag: training status

value: sedentary


title: genomic DNA from young PBMCs 4

description:
Y-SED
YS4


title: RNA-seq_3531C

source_name: Monocolony HEK293T cell edited by CRISPR/cas9 carrying [G/G] genotype at rs4420550.

tag: snp

tag: genotype

value: G/G


title: genomic DNA from young PBMCs 10

description:
Y-SED
YS10


title: genomic DNA from young PBMCs 5

description:
Y-SED
YS5

value: F


title: genomic DNA from young PBMCs 9

description:
Y-SED
YS9


title: WM1366_Ctrl

source_name: WM1366 cells transfected with control shRNA

value: NRAS mutation

value: Male


title: SKMEL28_shAR2

source_name: SKMEL28 cells transfected with shRNA2 against AR


title: genomic DNA from young PBMCs 6

description:
Y-SED
YS6


title: WM115_shAR1

source_name: WM115 cells transfected with shRNA1 against AR

value: Female


title: genomic DNA from young PBMCs 7

description:
Y-SED
YS7


title: WM1366_shAR2

source_name: WM1366 cells transfected with shRNA2 against AR


title: genomic DNA from young PBMCs 1

description:
Y-SED
YS1

source_name: PBMCs young


title: genomic DNA from young PBMCs 3

description:
Y-SED
YS3


title: Normal kidney parenchyma (NKP_24)

city: Manchester

first: Caroline

last: Dive

address: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road

institute: Cancer Research UK Manchester Institute

description: Normal kidney parenchyma

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Illumina HiScan

data_processing: Raw 450k array data was extracted using GenomeStudio. Methylation data preprocessing was performed using the minfi R package (15). CpGs with missing data in more than ten percent of patient samples (n= 2371 CpG sites) were discarded.

label: Cy5 and Cy3

source_name: Normal kidney parenchyma (tumor-adjacent)

extract_protocol: DNA was extracted from fresh frozen tissue samples using the Qiagen DNA Mini kit

value: normal kidney parenchyma

tag: race

value: white

tag: patient

tag: pathologic stage

tag: pathologic grade

value: IV


title: Normal kidney parenchyma (NKP_16)

description: Normal kidney parenchyma

tag: gender

tag: sample type


title: Hybrid oncocytic renal neoplasm (Hybrid_onc_RN_16)

description: Hybrid oncocytic renal neoplasm

source_name: Hybrid oncocytic renal neoplasm

value: hybrid oncocytic renal neoplasm

tag: age


title: Clear cell RCC (ccRCC_24)

description: Clear cell RCC

source_name: Clear cell RCC

value: clear cell renal cell carcinoma


title: Oncocytoma (oncocytoma_23)

description: Oncocytoma

source_name: Oncocytoma

value: oncocytoma

tag: tumor size


title: RCC-Chromophobe (chRCC_7)

description: RCC-Chromophobe

source_name: RCC-Chromophobe

value: renal cell carcinoma-chromophobe


title: RCC-Chromophobe (chRCC_17)

description: RCC-Chromophobe


title: Normal kidney parenchyma (NKP_6)

description: Normal kidney parenchyma

value: black


title: WM1366_shAR1

source_name: WM1366 cells transfected with shRNA1 against AR

value: VGP

tag: cell type

value: melanoma cell line


title: RCC-Chromophobe (chRCC_9)

description: RCC-Chromophobe

value: hispanic


title: Clear cell RCC (ccRCC_25)

description: Clear cell RCC

value: III


title: Normal kidney parenchyma (NKP_19)

description: Normal kidney parenchyma


title: Oncocytoma (oncocytoma_18)

description: Oncocytoma


title: Normal kidney parenchyma (NKP_18)

description: Normal kidney parenchyma


title: Oncocytoma (oncocytoma_20)

description: Oncocytoma


title: Normal kidney parenchyma (NKP_12)

description: Normal kidney parenchyma


title: RCC-Chromophobe (chRCC_4)

description: RCC-Chromophobe


title: Oncocytoma (oncocytoma_19)

description: Oncocytoma


title: Oncocytoma (oncocytoma_21)

description: Oncocytoma


title: RCC-Chromophobe (chRCC_2)

description: RCC-Chromophobe


title: Oncocytoma (oncocytoma_15)

description: Oncocytoma


title: Normal kidney parenchyma (NKP_4)

description: Normal kidney parenchyma


title: Hybrid oncocytic/Chromophobe type (Hybrid_onc_chRCC_type_6)

description: Hybrid oncocytic/Chromophobe type

source_name: Hybrid oncocytic/Chromophobe type

value: hybrid oncocytic/chromophobe type


title: Dam-Esg replicate 3

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

hyb_protocol: Hybridisation has been done with HX1 mixer following NimbleGen's procedures.

scan_protocol: Arrays were scanned on an Axon 4000B scanner following NimbleGen guidelines.

data_processing:
The Dam-Esg/Dam log2 ratios were median normalised using NimbleScan software (v.2.6, Nimblegen).
Dam-Esg_testes_rel6_*.gff: Log2 ratios of Dam-Esg/Dam.
GATC_bin_for_Esg_testes_*.gff: GFF files with the data binned to GATC fragments (between each GATC site).

organism: Drosophila melanogaster

source_name: UAS-Dam-Esg processed DNA from Drosophila testes

label_protocol: Labeling has been done using the NimbleGen Dual-Color Labeling Kit based on a Klenow enzymatic reaction following manufacturer's protocol.

growth_protocol: Flies were grown at 25oC.

extract_protocol: Tissues were dissected and placed in 180ul of PBS with 100mM EDTA before samples were processed as previously described (Choksi et al., 2006).

value: w-; UAS-Dam-Esg

tag: Sex

tag: tissue

value: Testes

source_name: UAS-Dam processed DNA from Drosophila testes

value: w-; UAS-Dam


title: Dam-Esg replicate 2

tag: genotype/variation

value: Male


title: Oncocytoma (oncocytoma_12)

description: Oncocytoma


title: Hybrid oncocytic/Chromophobe type (Hybrid_onc_chRCC_type_13)

description: Hybrid oncocytic/Chromophobe type

value: II


title: Dam-Esg replicate 1


title: Normal kidney parenchyma (NKP_1)

description: Normal kidney parenchyma

value: normal kidney parenchyma

value: white


title: Oncocytoma (oncocytoma_22)

description: Oncocytoma

value: Female


title: RCC-Chromophobe (chRCC_3)

description: RCC-Chromophobe


title: Normal kidney parenchyma (NKP_9)

description: Normal kidney parenchyma


title: Normal kidney parenchyma (NKP_10)

description: Normal kidney parenchyma


title: Oncocytoma (oncocytoma_11)

description: Oncocytoma


title: H_1

city: Tarragona

first: Mercè

last: Sunyer-Figueres

state: Catalunya

address: C/ Marcel·lí Domingo, 1

department: Departament de Bioquímica i Biotecnologia

country: Spain

institute: Universitat Rovira i Virgili

description: Gene expression of cells without melatonin treatment after 1h in 2mM H2O2

hyb_protocol: The Agilent One-Color Microarray-Based Exon Analysis-Low Input Quick Amp WT Labeling Kit protocol version 2.0 (Agilent Technologies) was followed according manufacter instructions. The hibridization step was performed during 17h at 65oC.

scan_protocol: An Agilent scan control in version A.8.5.1 software was used to scan the 3-µM resolution slides using the Agilent G2565CA microarray scanner system with sure scan high resolution technology. Slides were scanned after washing.

data_processing: Feature extraction version 12.0.1.1 software (Agilent Technologies) was used for data extraction. The protocol applied was GE1_1200_Jun14, the grid was 016322_D_F_20150202 and the metrics was GE1_QCMT_Jun14. The protocol of extraction GE1_1200_Jun14 uses by defaut the following parameters: No Background, BagkgroundDetrend ON and Global Background Adjust OFF. The BG corrected signal corresponds to the MeanSignal-BG Used and according to theses parameters the BG Used Corresponds to the Spatial Detrend Sufrace Value that refers to the surface created by the union of the lowintensity spots distributed through the entire array.

organism: Saccharomyces cerevisiae

source_name: Yeast, 2 mM H2O2, 0µM Mel. Replicate 1

label_protocol: The Agilent One-Color Microarray-Based Exon Analysis-Low Input Quick Amp WT Labeling Kit protocol version 2.0 (Agilent Technologies) was followed according manufacter instructions. Each sample was labeled with Cy3 and hybridize in a single array.

growth_protocol: Cells of S. cerevisiae were grown in YPD broth (2% (w/v) glucose, 2% (w/v) peptone and 1% (w/v) yeast extract) incubated at 28oC  with orbital shaking (120 rpm)

extract_protocol: RNA from 107 cells was isolated using a Trizol® Plus RNA urification Kit (Ambion Life Technologies, Woburn, MA, United States) following the manufacturer's recommendations, with some modifications: the step with chloroform was repeated twice before transferring the upper phase containing the RNA into a fresh tube, and a DNAse (Qiagen, Barcelona, Spain) incubation step at 37o for 15 min was included to remove the remaining DNA. RNA was quantified using a NanoDrop-1000 sectrophotometer (Thermo Scientific, USA), and integrity was analyzed with an RNA 2100 Bioanalyzer (Agilent Technologies Inc), using the RNA 6000 Nano kit and the Plant RNA Nano protocol in the Agilent 2100 Expert software.

treatment_protocol: Cells were supplemented with or without melatonin (5 or 25 µM) when they were growth in YPD, and when they arrived at mid-exponential phase (OD 0.5-0.6) oxidative stress (2 mM H2O2) was induced during 1h, when cells were harvested by centrifugation, fast-frozen and stored at -80oC.

tag: strain

tag: melatonin concentration

value: 0 microM melatonin

tag: h2o2 concentration

value: 2 mM H2O2


title: 5Mel_2

description: Gene expression of cells with 5 µM melatonin treatment after 1h in 0mM H2O2

source_name: Yeast, 0 mM H2O2, 5 µM Mel. Replicate 2

value: 5 microM melatonin

value: 0 mM H2O2


title: Normal kidney parenchyma (NKP_11)

description: Normal kidney parenchyma

value: black


title: H_2

source_name: Yeast, 2 mM H2O2, 0µM Mel. Replicate 2


title: Oncocytoma (oncocytoma_5)

description: Oncocytoma

value: oncocytoma


title: H_3

source_name: Yeast, 2 mM H2O2, 0µM Mel. Replicate 3


title: Control_3

description: Gene expression of cells without melatonin treatment after 1h in 0mM H2O2

source_name: Yeast, 0 mM H2O2, 0 µM Mel. Replicate 3


title: 5MelH_2

description: Gene expression of cells with 5 µM melatonin treatment after 1h in 2mM H2O2

source_name: Yeast, 2 mM H2O2, 5 µM Mel. Replicate 2


title: Normal kidney parenchyma (NKP_8)

description: Normal kidney parenchyma


title: 5MelH_1

source_name: Yeast, 2 mM H2O2, 5 µM Mel. Replicate 1


title: Control_1

source_name: Yeast, 0 mM H2O2, 0 µM Mel. Replicate 1


title: Oncocytoma (oncocytoma_14)

description: Oncocytoma

value: unknown


title: RCC-Chromophobe (chRCC_1)

description: RCC-Chromophobe

value: renal cell carcinoma-chromophobe


title: 14-3-3-zeta_shRNA_H1975 cells, biological rep3

city: Harbin

first: Hailing

last: Lu

address: 150 Haping Road

institute: Harbin Medical University Cancer Hospital

description: Gene expression data from H1975 cells infected with a lentivirus expressing 14-3-3ζ-shRNA.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the FS450-0002.

data_processing: The data were analyzed with R.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA.

growth_protocol: H1975 cells were cultured in RPMI 1640 media with 10% fetal bovine serum and 1% penicillin/streptomycin.

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

treatment_protocol: H1975 cells were infected with a lentivirus expressing either scrambled shRNA or 14-3-3ζ-shRNA, MOI 20.

tag: cell line

tag: phenotype

value: Lung adenocarcinoma

tag: cell line phenotype

value: EGFR-TKI-resistant

tag: knockdown

value: 14-3-3-zeta shRNA


title: Normal kidney parenchyma (NKP_14)

description: Normal kidney parenchyma

source_name: Normal kidney parenchyma (tumor-adjacent)

tag: race

tag: patient

tag: pathologic stage


title: 25MelH_1

description: Gene expression of cells with 25 µM melatonin treatment after 1h in 2mM H2O2

source_name: Yeast, 2 mM H2O2, 25 µM Mel. Replicate 1

value: 25 microM melatonin


title: 5Mel_1

source_name: Yeast, 0 mM H2O2, 5 µM Mel. Replicate 1


title: 25MelH_2

source_name: Yeast, 2 mM H2O2, 25 µM Mel. Replicate 2


title: 5MelH_3

source_name: Yeast, 2 mM H2O2, 5 µM Mel. Replicate 3


title: 25MelH_3

source_name: Yeast, 2 mM H2O2, 25 µM Mel. Replicate 3


title: 14-3-3-zeta_shRNA_H1975 cells, biological rep1

source_name: H1975 cells infected with a lentivirus expressing 14-3-3ζ-shRNA


title: 14-3-3-zeta_shRNA_H1975 cells, biological rep2


title: Normal kidney parenchyma (NKP_3)

description: Normal kidney parenchyma

tag: gender

tag: sample type

tag: pathologic grade


title: scrambled_shRNA_H1975 cells, biological rep3

description: Gene expression data from H1975 cells infected with a lentivirus expressing scrambled shRNA.

value: scrambled shRNA


title: Oncocytoma (oncocytoma_8)

description: Oncocytoma

source_name: Oncocytoma

tag: age


title: Clas-infected psyllid_5 dpi rep1

city: Lake Alffred

first: Xu

last: Wei

state: FL

address: 700 Experiment Station Rd. Lake Alfred, FL

institute: University of Florida

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the reference Citrus clementina v1.0 genome using v2.2.5, and calculate geneex pression level with RSEM.
The gene expression level analysis of RNA-seq data was estimated by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) (Trapnell et al., 2010). Data normalization and call of differentially expressed genes (DEGs) was implemented with EBseq by setting the algorithms with |log2ration| ≥ 1 and false discovery rate (FDR) ≤ 0.05, and enabling independent filtering.
Genome_build: Citrus_clementina_v1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

organism: Citrus sinensis

source_name: leaf

growth_protocol: Budwoods of Valencia sweet orange were collected at greenhouse repository of citrus budwood program of Florida Department of Agriculture and Consumer Services. The certified repository greenhouses were guaranteed that collected budwoods were clean without any infected disease. The size of budwood was about 2-3 inch. Budwoods were sterilized in 20% Clorox® regular bleach (3% sodium hypochlorite, v:v) for 5 min, followed by 70% ethanol for 10s, and washing with sterilized water for 10 s in three times. After briefly dried, they were transferred to 25 × 100-mm test tubes containing MS culture media under condition of 25 ± 1 ºC, 16:8 h photoperiod and 60 µmol-2 s-1 cool-white light.

extract_protocol:
TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA)was used following the manufacturer’s protocol. Extracted RNA was further purified using the TURBO DNA-free™ kit to eliminate genomic DNA. ANanoDrop™ One Spectrophotometer (Thermo Scientific™) and gel electrophoresis were used to assess RNA quality and quantity. RNA quality was further assessed using an Agilent 2100 Bioanalyzer (Aglient Technologies Inc, Waldbronn, Germany). mRNAs were isolated from total RNA with oligo(dT) method.
After fragmented, the first strand cDNA and second strand cDNA are synthesized. cDNA fragments were purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. Then cDNA fragments were linked with adapters. Those cDNA fragments with suitable size are selected for the PCR amplification. Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of those libraries. 17 cDNA libraries were constructed using an Illumina kit and sequenced on an Illumina HiSeqTM 2000 platform employing paired-end technology at BGI Genomics Co., Ltd (Shenzhen, China), including three biological replicates of No_psyllid_1dpi, No psyllid_5dpi, Healthy_psyllid_1dpi, Healthy_psyllid_5dpi, CaLas-infected_psyllid_1dpi, respectively; and two biological replicates of CaLas-infected_psyllid_5dpi.

treatment_protocol: Feeding experiment of Diaphorina citri was carried out when leaves of budwood were unfolded. Colonies of D. citri were reared on HLB-free curry leaf plants (Bergera [Murraya] koenigii) in a growth room maintained at 28 ± 1 ºC and 60 ± 5% relative humidity, and with a 16:8 h (L:D) photoperiod. Infected psyllids were collected from citrus grove at Citrus Research and Education Center of University of Florida. Five adult psyllids were released to each tube for feeding test. Leaf samples of budwood cultured in media were collected after psyllid feeding at 1 and 5 days (dpi).Three feeding treatments were set up for leaf sample collection: no psyllid, heathy psyllid and psyllid infected with CaLas. Three biological replicates were used except two replicationsfor 5 dpi with CaLas-infected psyllids.

tag: cultivar

value: Valencia sweet orange

value: leaf

tag: treatment

value: Fed by Clas-infected psyllid at 5 dpi


title: Healthy psyllid_5 dpi rep2

tag: tissue

value: Fed by healthy psyllid at 5 dpi


title: Healthy psyllid_5 dpi rep1


title: No psyllid_5 dpi_rep1

value: untreated at 5 dpi


title: Clas-infected psyllid_1 dpi rep1

value: Fed by Clas-infected psyllid at 1 dpi


title: Clas-infected psyllid_1 dpi rep2


title: Clas-infected psyllid_1 dpi rep3


title: No psyllid_1 dpi_rep3

value: untreated at 1 dpi


title: Healthy psyllid_5 dpi rep3


title: Clas-infected psyllid_5 dpi rep2


title: Healthy psyllid_1 dpi rep2

value: Fed by healthy psyllid at 1 dpi


title: No psyllid_1 dpi_rep2


title: Extracellular Vesicles_treated_Replicate_3

city: Fort Collins

first: Samuel

middle: Gebremedhn

last: Etay

address: 1683 Campus Delivery

department: Biomedical Sciences

institute: Colorado State University

data_processing:
Trimming was performed using Cutadapt (1.11) to extract information of adapter and UMI in raw reads, and output from Cutadapt is used to remove adapter sequences and to collapse reads by UMI with in-house script.
Bowtie2 (2.2.2) was used used for mapping the reads. The mapping criteria for aligning reads to spike-ins,abundant sequence and miRBase are the reads have to have perfect match to the reference sequences. For mapping to the genome, not more than one mismatch was allowed in the first 32 basesof the read. No indels are allowed in mapping.
Differential expression analysis is performed using the EdgeR statistical software package (Bioconductor, http://bioconductor.org/). For normalization, the trimmed mean of M-values method. based on log-fold and absolute gene-wise changes in expression levels between samples (TMM normalization) was used. The isomiR analysis and putative miRs are done with in-house scripts (exq_ngs_mircount and exq_ngs_mirpred using the MiRPara tool)
Genome_build: UMD3.1
Supplementary_files_format_and_content: CSV with normalized expression value of each microRNA

organism: Bos taurus

source_name: Granulosa cells

extract_protocol:
Total RNA enriched with miRNAs was isolated from the purified EVs using Norgen exosomes RNA kit (Norgen, Canada) according to the manufacturer´s instruction.
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN). A total of 100ng total RNA was converted into miRNA NGS libraries. Adapters containing UMIs were ligated to the RNA. Then RNA was converted to cDNA. The cDNA was amplified using PCR (16 cycles) and during the PCR indices were added. After PCR the samples were purified. Library preparation QC was performed using either Bioanalyzer 2100 (Agilent) or TapeStation 4200 (Agilent). Based on quality of the inserts and the concentration measurements the libraries were pooled in equimolar ratios. The library pool(s) were quantified using qPCR. The library pool were then sequenced on a NextSeq550 sequencing instrument according to the manufacturer instructions. Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina inc.). FASTQ data were checked using the FastQC tool.

tag: incubation temperature

value: EVs_Treated_incubated_at_42 OC

tag: developmental stage of follilces

value: Evs from granulosa cells of Small antral follicles


title: scrambled_shRNA_H1975 cells, biological rep2

source_name: H1975 cells infected with a lentivirus expressing scrambled shRNA


title: 5Mel_3

source_name: Yeast, 0 mM H2O2, 5 µM Mel. Replicate 3

tag: strain

tag: melatonin concentration

value: 5 microM melatonin

tag: h2o2 concentration

value: 0 mM H2O2


title: No psyllid_5 dpi_rep2


title: Normal kidney parenchyma (NKP_5)

description: Normal kidney parenchyma

value: Male

value: normal kidney parenchyma

value: white


title: No psyllid_5 dpi_rep3


title: scrambled_shRNA_H1975 cells, biological rep1

tag: cell line

tag: phenotype

value: Lung adenocarcinoma

tag: cell line phenotype

value: EGFR-TKI-resistant


title: Healthy psyllid_1 dpi rep1

value: Valencia sweet orange


title: No psyllid_1 dpi_rep1

value: leaf


title: Healthy psyllid_1 dpi rep3


title: RCC-Chromophobe (chRCC_10)

description: RCC-Chromophobe

source_name: RCC-Chromophobe

value: Female

value: renal cell carcinoma-chromophobe

tag: race

value: hispanic

tag: patient


title: Extracellular Vesicles_treated_Replicate_2


title: Extracellular vesicles_control_Replicate_3

value: Evs_Control_incubated_at_37 OC


title: Extracellular vesicles_control_Replicate_2


title: SKO_Dnmt1_KO_BS_seq

city: Beijing

first: Wei

last: Xie

address: Haidian District

institute: Tsinghua University

data_processing:
Library strategy: MethylC-seq
MethylC-seq reads were mapped to the mm9 reference genome using Bsmap with parameters -r 0 -w 100 -v 0.1. Adaptor sequences were removed with parameter -A. PCR duplicates were also removed. Pair-end reads with a flag equal 177 or 129 were also removed from this data. Only samples with bisulfite conversion rates greater than 99% were accepted. 200bp bins were used for most analyses and those with total CG coverage less than 5 were removed. Methylation ratio was calculated using methylated CG versus total CG for each bin.
Genome_build: mm9
Supplementary_files_format_and_content: Bisulfite-seq processed data files: methylated and unmethylated C are counted at watson and crick strand seperately
Supplementary_files_format_and_content: *mcG.txt column headers: chr, pos, mCwatson, Cwatson, mCcrick, Ccrick

source_name: mESC

growth_protocol: Mouse ES cells were cultured on 0.1% gelatin of porcine skin in DMEM (Gibco Cat. 11995-065) containing 15% FBS (Hyclone Cat. SH30396.03), leukemia inhibiting factor (LIF) (Millipore Cat. GSE1107), penicillin/streptomycin (Millipore Cat. TMS-AB2-C), GlutaMAX (Gibco Cat. 35050-061), nucleotides (Millipore Cat. ES-008-D), β-mercaptoethanol (Gibco Cat. 21985-023), and non-essential amino acids (Gibco Cat. 25-025-CIR).

extract_protocol:
Cells were digested using Cell Lysis Solution (Qiagen, Cat. 1045723) and proteins were removed using Protein Precipitation Solution (Qiagen, Cat. 1045701). Genome DNA was precipitated by isopropyl alcohol and cleaned by wash with 75% ethanol.
A total amount of 6ug genomic DNA was mixed with 25ng lambda DNA and sonicated to 200-500bp.DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Bisulfite treatment is performed using commercial kit (Zymo research, Cat. D5005). DNA was amplified and 200-500bp fragments were gel selected.

tag: genotype/variation

value: Tet1-/- Tet2-/- Tet3-/- Dnmt3a-/- Dnmt3b-/- Dnmt3c-/- Dnmt1-/-

tag: cell type

value: mESC


title: Granulosa cells_treated_Replicate_1

data_processing:
Trimming was performed using Cutadapt (1.11) to extract information of adapter and UMI in raw reads, and output from Cutadapt is used to remove adapter sequences and to collapse reads by UMI with in-house script.
Bowtie2 (2.2.2) was used used for mapping the reads. The mapping criteria for aligning reads to spike-ins,abundant sequence and miRBase are the reads have to have perfect match to the reference sequences. For mapping to the genome, not more than one mismatch was allowed in the first 32 basesof the read. No indels are allowed in mapping.
Differential expression analysis is performed using the EdgeR statistical software package (Bioconductor, http://bioconductor.org/). For normalization, the trimmed mean of M-values method. based on log-fold and absolute gene-wise changes in expression levels between samples (TMM normalization) was used. The isomiR analysis and putative miRs are done with in-house scripts (exq_ngs_mircount and  exq_ngs_mirpred using the MiRPara tool)
Genome_build: UMD3.1
Supplementary_files_format_and_content: CSV with normalized expression value of each microRNA

extract_protocol:
miRNA enriched total RNA was extracted using miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN). A total of 100ng  total RNA was converted into miRNA NGS libraries. Adapters containing UMIs were ligated to the  RNA. Then RNA was converted to cDNA. The cDNA was amplified using PCR (16 cycles) and  during the PCR indices were added. After PCR the samples were purified. Library preparation QC  was performed using either Bioanalyzer 2100 (Agilent) or TapeStation 4200 (Agilent).  Based on quality of the inserts and the concentration measurements the libraries were pooled in  equimolar ratios. The library pool(s) were quantified using qPCR. The library pool were then  sequenced on a NextSeq550 sequencing instrument according to the manufacturer instructions. Raw  data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq  software (Illumina inc.). FASTQ data were checked using the FastQC tool.

value: Treated_incubated_at_42 OC

value: Small antral follicles


title: Extracellular vesicles_control_Replicate_1

value: Evs from granulosa cells of Small antral follicles


title: Granulosa cells_treated_Replicate_3


title: Granulosa cells_treated_Replicate_2


title: Granulosa cells_control_Replicate_3

value: Control_incubated_at_37 OC


title: Granulosa cells_control_Replicate_1


title: Lung_endothelial _cell_Day3_post_LPS

city: Chicago

first: Jalees

last: Rehman

state: IL

address: 909 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

data_processing:
Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files.
Alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting were performed using Cell Ranger v1.2.
Genome_build: mm10

source_name: Lung_endothelial _cell

growth_protocol: tdTOMATO fl/fl:CDH5CreERT2(+)  transgenic mice (2-4 months) were given Tamoxifen ( i.p.) to induce tdTOMATO expression in vascular endothelial cells for one month.

extract_protocol:
Three lungs were harvested at each time points - baseline, LPS treatment 6 hours, 1 day, 2 days, 3 days and 7 days. After perfusing with PBS 20 ml through left and right ventricular chamber, the mouse lungs were minced and digested with 3 ml collagenase A at 1 mg/ml in PBS (Roche, REF#:10103586001) at 37ºC water bath for 1 hour. Mixtures were titrated with #18 needles and then pipetted through a 40 μm disposable cell strainer. After centrifuge 500 g for 5 minutes and wash with PBS, the Isolated cells were treated with red blood cell lysis buffer (Biolegend, Cat: 420301) for 5 minutes to lyse red blood cells. After washing with PBS twice, cells were incubated with DAPI (1 mg/ml) in suspension buffer (Ca2+ and Mg2+ free PBS, 5% BSA, 2mM EDTA) at 4 ºC for 30 mins with gentle tilting. After centrifuge, the lung cells from three mice of each time point were mixed and incubated in buffer (Ca2+ and Mg2+ free PBS,10% BSA, 2mM EDTA).  Seven samples at seven time points were subjected to single-cell fluorescence-activated cell sorting (FACS) in the MoFlow Astrios machine for TdTOMATO+/DAPI- cell.
tdTOMATO+/DAPI- Cells were loaded into a 10x Genomics microfluidics chip and encapsulated with barcoded oligo-dT-containing gel beads using the 10x Genomics Chromium controller according to the manufacturer’s instructions. The viabilities of cells at each time points were checked (>80%). 5000 cells at each time point were targeted. Single-cell libraries were constructed using v2 kit according to the manufacturer’s instructions. cDNA quality of each time points was checked (high quality). Libraries from individual samples were multiplexed into two lanes for sequencing on NovaSeq 6000 S4 (~100k reads per cell and per lane 2x150bp Paired-Read) at a depth of ~200,000 reads per cell.

treatment_protocol: The mice were injected with bacterial endotoxin lipopolysaccharide (LPS)

tag: strains

tag: genotyping

value: tdTOMATO fl/fl :Cdh5-ERT2 +

value: Lung

tag: cells

value: Vascular endothelial cells

value: 2-4 months


title: Lung_endothelial _cell_Day7_post_LPS

tag: age


title: Lung_endothelial _cell_Day1_post_LPS

tag: tissue


title: Granulosa cells_control_Replicate_2

tag: incubation temperature


title: Extracellular Vesicles_treated_Replicate_1

value: EVs_Treated_incubated_at_42 OC

tag: developmental stage of follilces


title: Lung_endothelial _cell_Hour6_post_LPS


title: Lung_endothelial _cell_Basal


title: Lung_endothelial _cell_Day2_post_LPS


title: Cardiac endothelial cells, het3

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava.
Illumina and SMARTer adaptor contaminations were removed from reads using Cutadapt.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM and summarized at gene level.
Genome_build: GRCm38 assembly, Ensembl genebuild 76
Supplementary_files_format_and_content: ALL.GRCm38_76.rsem.genes.results.txt contains ENSEMBL gene and transcript identifiers, and RSEM estimated raw counts for each gene and sample.

source_name: Cardiac endothelial cells

extract_protocol:
Total RNA from sorted endothelial cells of embryonic hearts were isolated using the RNEasy Micro Kit (Qiagen). Briefly cells were sorted directly to RLT Buffer containing BMeOH and extraction was done following the kit instructions. We also performed the DNAseI on column Kit  (Qiagen) extra steps as recommended.
cDNA were amplified with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara), and libraries then prepared with the Nextera XT DNA library preparation kit (Illumina).
Paired end next generation sequencing (Illumina HiSeq 2500)

tag: genotype

value: Cardiac endothelial cell


title: Cardiac endothelial cells, Ko2


title: Cardiac endothelial cells, wt4

value: WT


title: Cardiac endothelial cells, wt5


title: Cardiac endothelial cells, Ko1


title: HIFU treated tumor at 72 hrs 1

city: Washington

first: Avinash

last: Eranki

state: DC

address: 111 Michigan Avenue, NW, 6th Floor - SZI

institute: Children's National Medical Center

description: Gene expression data in murine neuroblastoma tumors

hyb_protocol: ss-cDNA was hybridized for 16 hr at 45C on the GeneChip Mouse Clariom S arrays.  The arrays were hybridized in the  genechip hybridization oven 645.   GeneChips were washed and stained using the Affymetrix Fluidics 450 station.

scan_protocol: Gene chips were scanned on Affymetrix GeneChip scanner

data_processing: The data were assessed and visualized using Transcriptome Analysis Console (4.0) using default settings.

source_name: HIFU treated tumor at 72 hrs

label_protocol: cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Tumors were grown by inoculating neuroblastoma cells in A/J mice

extract_protocol: The tumor tissue was disrupted using a mortar and pestle, the tissue was frozen in liquid nitrogen and ground up in liquid nitrogen.  The tissue powder suspension was decanted into liquid nitrogen cooled 1.5 ml tubes.

treatment_protocol: Tumors were treated using HIFU

value: neuroblastoma tumor

tag: treatment

value: high intensity focused ultrasound (HIFU) for 72hrs

tag: sample type

value: frozen tissue


title: HIFU treated tumor at 48 hrs 2

source_name: HIFU treated tumor at 48 hrs

value: high intensity focused ultrasound (HIFU) for 48hrs


title: Pre-graft_6_TA_500cells_Exp2_BSseq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Adapter sequences and poor-quality calls were removed from the raw sequencing files using Trim galore (version 0.4.2). Reads were then mapped to mouse genome GRCm38 and deduplicated using Bismark (version 0.16.3).
Adapter sequences and poor-quality calls were removed from the raw sequencing files using Trim galore (version 0.4.4). Reads were then mapped to mouse genome GRCm38 using HISAT2 (version 2.1.0). Log2 transformed counts were generated using Seqmonk (v1.47.0).
Genome_build: GRCm38
The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>
The RNA-seq QC report examines the proportion of reads found in different genomic features. It is tab-delimited and in the following format: <DataStore> <Percent in Gene> <Percent in exons> <Percent in rRNA> <Percent Genes Measured> <Percent in MT> <Percent on sense strand>
The summary report contains the metrics of the RNA-seq samples such as the number of reads. It is tab-delimited and in the following format: <DataStore> <Total Read Count> <Forward Read Count> <Reverse Read Count> <Unknown Read Count> <Mean Read Length> <Total Read Length> <Fold Coverage> <Total Quantitation> <Median Quantitation> <Mean Quantitation> <Valid Quantitations>
A tab delimited text report generated by SeqMonk (v1.47.0) with log2 RPM values for each gene.

source_name: Tibialis anterior muscles

extract_protocol:
Tibialis anterior and extraocular muscles were dissected and placed into cold DMEM (ThermoFisher, 31966). Muscles were then manually chopped with scissors and put into a 15 ml Falcon tube containing 10 ml of DMEM, 0.08% collagenase D (Sigma, 11 088 882 001), 0.1% trypsin (ThermoFisher, 15090), 10 µg/ml DNase I (Sigma, 11284932) at 37°C under gentle agitation for 25 min. Digests were allowed to stand for 5 min at room temperature and the supernatants were added to 5 ml of foetal bovine serum (FBS; Gibco) on ice. The digestion was repeated 3 times until complete digestion of the muscle. The supernatants were filtered through a 70-µm cell strainer (Miltenyi, 130-098-462). Cells were spun for 15 min at 515g at 4°C and the pellets were resuspended in 1 ml cold freezing medium (10% DMSO (Sigma, D2438) in FBS) for long term storage in liquid nitrogen or processed directly through FACS-isolation for transplantations. Before isolation by FACS, samples were thawed in 50 ml of cold DMEM, spun for 15 min at 515g at 4°C. Pellets were resuspended in 300 µl of DMEM 2% FBS 1 µg/mL propidium iodide (Calbiochem, 537060) and filtered through a 40-µm cell strainer (BD Falcon, 352235). Viable muscle stem cells were isolated based on size, granulosity and GFP intensity using a MoFlo Astrios cell sorter (Beckmann Coulter). Cells were collected in 5 µl cold RLT Plus buffer (Qiagen, 1053393) containing 1U/µl RNAse inhibitor (Ambion, AM2694), flash-frozen on dry ice and stored at -80°C, or in cold DMEM 2% FBS.
RNA was separated from cell lysates and processed into libraries using the G&T method as described in Macaulay et al., 2016. DNA was also processed into libraries using the bulk protocol described in Clark et al., 2017. Bisulfite-seq libraries were sequenced on an Illumina HiSeq-2500 with 125bp paired end reads and RNA-seq libraries were sequenced on an Illumina HiSeq-2500 with 75bp paired end reads.

value: Tibialis anterior muscles

tag: strain

value: Pre grafting TA satellite cells

value: 7 weeks


title: Pre-graft_5_TA_500cells_Exp1_BSseq

value: 7.6 weeks


title: Pre-graft_6_EOM_500cells_Exp2_BSseq

source_name: Extra ocular muscles

value: Extra ocular muscles

value: Pre grafting EOM satellite cells


title: Control Tumor-2

source_name: Control Tumor

value: none (control)


title: Cardiac endothelial cells, het2


title: HIFU treated tumor at 24 hrs 1

source_name: HIFU treated tumor at 24 hrs

value: high intensity focused ultrasound (HIFU) for 24hrs


title: HIFU treated tumor at 24 hrs 2


title: HIFU treated tumor at 24 hrs 3


title: Pre-graft_5_TA_500cells_Exp2_BSseq


title: HIFU treated tumor at 72 hrs 3


title: HIFU treated tumor at 72 hrs 2


title: C2C12 cells_si-lncMGPF_rep3

city: Wuhan

first: lvwei

middle: jian

last: jun

state: Hubei

address: shizishan street, NO.1

department: College of Animal science and technology

institute: huazhong agriculture university

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: standard Agilent protocol

source_name: si-lncMGPF

label_protocol: standard Agilent protocol

extract_protocol: none provided by the submitter

treatment_protocol: We further transfected the siRNA to knock down lncMGPF gene (si-lncMGPF) and induced cells to differentiate for 2 days

tag: cell line


title: C2C12 cells_si-lncMGPF_rep1


title: HIFU treated tumor at 48 hrs 1


title: HIFU treated tumor at 48 hrs 3


title: C2C12 cells_si-NC_rep3

source_name: si-NC


title: Control Tumor-3


title: Control Tumor-1


title: C2C12 cells_si-lncMGPF_rep2


title: C2C12 cells_si-NC_rep2


title: Pre-graft_5_EOM_500cells_Exp2_BSseq


title: Pre-graft_5_EOM_500cells_Exp1_BSseq


title: Pre-graft_3_TA_500cells_Exp2_BSseq


title: Pre-graft_4_TA_500cells_Exp1_BSseq


title: Pre-graft_1_EOM_500cells_Exp2_BSseq


title: Pre-graft_1_TA_500cells_Exp2_BSseq


title: Pre-graft_4_EOM_500cells_Exp1_BSseq


title: Pre-graft_4_EOM_500cells_Exp2_BSseq


title: Pre-graft_1_TA_500cells_Exp1_BSseq


title: Pre-graft_1_EOM_500cells_Exp1_BSseq


title: Pre-graft_3_TA_500cells_Exp1_BSseq


title: Pre-graft_3_EOM_500cells_Exp1_BSseq


title: Graft_5_TA_D21_1_36cells_Exp1_BSseq

value: Grafted TA satellite cells


title: Graft_4_EOM_D21_1_103cells_Exp1_BSseq

value: Grafted EOM satellite cells


title: Graft_3_TA_D21_A_16cells_Exp2_BSseq


title: Graft_5_EOM_D21_A_60cells_Exp2_BSseq


title: Graft_5_EOM_D21_1_105cells_Exp1_BSseq


title: Graft_6_TA_D21_A_16cells_Exp2_BSseq


title: Control_2

source_name: Yeast, 0 mM H2O2, 0 µM Mel. Replicate 2

tag: melatonin concentration

value: 0 microM melatonin

tag: h2o2 concentration

value: 0 mM H2O2


title: Graft_4_EOM_D21_A_9cells_Exp2_BSseq


title: Pre-graft_3_EOM_500cells_Exp2_BSseq


title: Graft_4_TA_D21_1_28cells_Exp1_BSseq


title: Graft_4_TA_D21_A_66cells_Exp2_BSseq


title: Graft_3_TA_D21_1_24cells_Exp1_BSseq


title: Pre-graft_4_TA_500cells_Exp2_BSseq


title: Pre-graft_2_EOM_500cells_Exp2_BSseq


title: Graft_5_TA_D21_A_67cells_Exp2_BSseq


title: Graft_3_EOM_D21_1_100cells_Exp1_BSseq


title: Graft_3_EOM_D21_A_16cells_Exp2_BSseq


title: Graft_2_TA_D21_A_67cells_Exp2_BSseq


title: Graft_1_TA_D21_2_43cells_Exp1_BSseq


title: Graft_1_EOM_D21_2_100cells_Exp1_BSseq


title: Pre-graft_2_TA_500cells_Exp2_BSseq


title: Graft_2_EOM_D21_A_35cells_Exp2_BSseq


title: L-28-3

city: Stockholm

first: Sourav

middle: Prasanna

last: Mukherjee

address: IMM, Karolinska Institutet

country: Sweden

institute: KI

description:
merged_gene_counts.txt
P8861_136

data_processing:
bcl2fastq_v2.19.1.403 from Illumina CASAVA software suite for Bcl to FastQ conversion
the preprocessed sequencing reads were aligned against the Homo sapiens (GRCh37) reference genome using STAR version 2.5.1b
the read-counts to genes were generated using a software featureCounts version 1.5.1
Full-length transcripts representing multiple splice variants for each gene locus were assembled and quantitated using StringTie version 1.3.3
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample and one tab-delimited text file include the merged read counts for each gene provided in the reference gtf file for all samples

source_name: Lung

growth_protocol: Six to 8-week old female C57BL/6 mice (Envigo, UK) were allowed to acclimatise for 7 days prior to any experiment. Animals were kept in groups of 5 with free access to water and food, under a regular 12 h light/dark cycle between 7 am and 7 pm, at a temperature of 19°C–22°C and relative humidity of 45%–65%. All procedures were conducted after ethical approval from the UK Home Office, under Project License no. 70/7763, in accordance with the ARRIVE guidelines for animal research (https://doi.org/10.3390/ani4010035).

extract_protocol:
Mice were sacrificed at days 1, 7, 28 or 90 days after exposure by overdose via intraperitoneal injection of 2 mL pentobarbitone. At all considered time points, the lungs were carefully dissected from the large airways and small portions of each lobe were extracted for RNA extraction. Tissue samples were placed in RNAlater (Invitrogen, Thermo Fisher Scientific, UK), and placed immediately on ice. Samples in RNAlater solution were incubated overnight at 4 degree Celsius prior to storage at -20 degree Celsius, until further processing. Tissue samples in RNAlater solution (Invitrogen, Thermo Fisher Scientific, UK) were homogenised using a TissueLyser LT (QIAGEN, UK). Homogenised samples were then loaded onto spin cartridges containing silica membranes, for extraction of total RNA performed using a PureLink RNA Mini kit (Invitrogen, Thermo Fisher Scientific, UK) according to the manufacturer’s instructions. Total RNA concentration and purity were calculated by measuring the optical density at 230, 260 and 280 nm, using a Biophotometer Plus spectrophotometer (Eppendorf AG, Germany). RNA quantity and RNA integrity number (RIN) were assessed by Agilent 2200 bioanalyzer. Sample RNA with RIN values below 8 was discarded. The isolated RNA samples were stored at -80°C until RNA sequencing was carried out.
Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc., San Diego, CA, USA) was used to prepare mRNA sequencing libraries. Briefly, 1000 ng of total RNA was used for mRNA isolation using poly dT-coated beads.

treatment_protocol: Experiments were carried out using 4-5 animals per group. All GO materials were dispersed in an aqueous solution of 5% (m/v) dextrose in ultrapure water (5% dextrose), at a concentration of 1 mg/mL, about 30 min before administration. MWCNTs were dispersed at the same concentration in an aqueous solution of 0.9% (m/v) sodium chloride supplemented with 0.5% (m/v) bovine serum albumin (BSA), followed by bath sonication for 10 min at 80 W (VWR, UK). Both dispersants were sterile filtered (Merck Millipore, PES membrane, 0.2 μm, 33 mm) prior to use. Animals were anesthesised by inhalation of 2.5% isoflurane in 100% oxygen flowing at 2 L/min. Mice in experimental groups were instilled with 50 μL of the respective nanomaterial dispersions (i.e., 50 μg/mouse), which were equally distributed in each nostril. The same volume of 5% dextrose solution was given to the control group. During administration, the animals were held in a supine position, tilted to about 60°, in order to effectively introduce the full dose. Mice were observed until full recovery, which occurred within 5 min after instillation.

value: Lung

tag: gender

value: Female

value: 13 weeks

value: wild type

tag: exposure time

value: 28 days

value: 50 μg GO/mouse


title: S-28-3

description:
merged_gene_counts.txt
P8861_133


title: C2C12 cells_si-NC_rep1


title: L-28-1

description:
merged_gene_counts.txt
P8861_134


title: S-28-2

description:
merged_gene_counts.txt
P8861_132


title: D-28-3

description:
merged_gene_counts.txt
P8861_127

value: 0 μg GO/mouse


title: US-28-2

description:
merged_gene_counts.txt
P8861_129


title: L-7-1

description:
merged_gene_counts.txt
P8861_122

value: 10 weeks

value: 7 days


title: L-28-2

description:
merged_gene_counts.txt
P8861_135


title: L-7-2

description:
merged_gene_counts.txt
P8861_123


title: D-28-2

description:
merged_gene_counts.txt
P8861_126


title: S-28-1

description:
merged_gene_counts.txt
P8861_131


title: US-28-1

description:
merged_gene_counts.txt
P8861_128


title: US-28-3

description:
merged_gene_counts.txt
P8861_130


title: Graft_6_EOM_D21_A_33cells_Exp2_BSseq

value: Extra ocular muscles

tag: cell type

value: 7 weeks


title: S-7-3

description:
merged_gene_counts.txt
P8861_121


title: US-7-3

description:
merged_gene_counts.txt
P8861_118


title: S-7-1

description:
merged_gene_counts.txt
P8861_119


title: Graft_1_EOM_D21_A_46cells_Exp2_BSseq


title: Graft_1_TA_D21_A_26cells_Exp2_BSseq

value: Tibialis anterior muscles


title: S-7-2

description:
merged_gene_counts.txt
P8861_120


title: US-7-1

description:
merged_gene_counts.txt
P8861_116


title: US-7-2

description:
merged_gene_counts.txt
P8861_117


title: D-7-2

description:
merged_gene_counts.txt
P8861_114


title: D-7-3

description:
merged_gene_counts.txt
P8861_115


title: L-7-3

description:
merged_gene_counts.txt
P8861_124


title: D-28-1

description:
merged_gene_counts.txt
P8861_125


title: L-1-3

description:
merged_gene_counts.txt
P8861_112

value: 9 weeks

value: 1 day


title: D-7-1

description:
merged_gene_counts.txt
P8861_113


title: L-1-2

description:
merged_gene_counts.txt
P8861_111


title: US-1-3

description:
merged_gene_counts.txt
P8861_106


title: S-1-1

description:
merged_gene_counts.txt
P8861_107


title: L-1-1

description:
merged_gene_counts.txt
P8861_110


title: D-1-3

description:
merged_gene_counts.txt
P8861_103


title: US-1-1

description:
merged_gene_counts.txt
P8861_104


title: S-1-2

description:
merged_gene_counts.txt
P8861_108


title: D-1-2

description:
merged_gene_counts.txt
P8861_102


title: E-100nM-rep2

first: Kevin

middle: Richard

last: Costello

state: Cambridgeshire

address: Genetics Building Downing St.

department: Department of Genetics

institute: Univerity of Cambridge

data_processing:
Basecalls performed using CASAVA version 1.4
Read were aligned using to the mm10 reference genome using hisat2 version 2.1.0 with the refseq annotated splice sites
Gene expression was found using bedtools coverageBed -counts on annotated Refseq genes
E-10nM-rep1, E-10nM-rep2, E-1nM-rep1, and  E-1nM-rep2 were sequenced in a different run. Limma was used to correct  batch effects
Differentail expression analsysis was preformed using DEseq2. Genes which an FDR < 0.05 were selected as differentially expressed.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: bigwig

molecule: polyA RNA

source_name: ST2 cell line

growth_protocol: RPMI 1640  supplemented with 10% Fetal Bovine Serum (FBS).  Prior to and during treatment with E2, ral and las, cells were cultured for 2 days in the respective phenol-free medium supplemented with 10% charcoal-stripped FBS

extract_protocol:
RNA was extracted using Aurum total RNA minikit
Library preperation was preformed using KAPA bioscience kit, KK8420. Reads were sequenced using Illumia 2500 Hiseq

treatment_protocol: ST2 cells were treated in duplicate with beta-Estradiol, Raloxifene or Lasofoxifene, each at the concentrations of 0.1 nM, 1, nM 10 nM and 100 nM

tag: agent


title: D-1-1

description:
merged_gene_counts.txt
P8861_101


title: E-100nM-rep1


title: Las-10nM-rep2


title: Las-1nM-rep1


title: Las-1nM-rep2


title: Las-10nM-rep1


title: Ral-0.1nM-rep2


title: Las-100nM-rep1


title: Ral-1nM-rep1


title: Ral-1nM-rep2


title: Ral-0.1nM-rep1


title: S-1-3

description:
merged_gene_counts.txt
P8861_109


title: Ral-100nM-rep1


title: Ral-10nM-rep2


title: US-1-2

description:
merged_gene_counts.txt
P8861_105


title: Ral-10nM-rep1


title: Las-100nM-rep2


title: Ral-100nM-rep2


title: E-0.1nM-rep1


title: E-1nM-rep1


title: Las-0.1nM-rep2


title: Control-rep2

value: Control


title: Las-0.1nM-rep1


title: E-1nM-rep2


title: E-10nM-rep1


title: E-0.1nM-rep2


title: E-10nM-rep2


title: C_03_7 days post IR

city: Berlin

first: Marina

last: Kolesnichenko

address: Robert Roessle str 10

institute: Max Delbrueck Center for Molecular Medicine

data_processing:
Sequencing output (in BCL format) were demultiplexed using Illumina’s bcl2fastq conversion software (version v2.17.1.14)
The raw reads were further trimmed to remove low quality reads and adapter sequences using Trimmomatic.
The reads were aligned using STAR (v2.4.2a) to human genome (version hg19).
Gene-wise expression was quantified using QuasR (R package) in a strand-aware fashion.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: TSV (tab-separated) file for gene-wise read counts measured using QuasR (R package)

source_name: U2OS_7 days post IR

growth_protocol: DMEM with 10 percent FCS

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols using HiSeq2000 platform

treatment_protocol: IR 20 Gy at time points indicated. NFKBIA knockdown using shRNA.

value: osteosarcoma cells

tag: treatment/time point

value: 7 days post IR


title: D_03_NFKBIA knockdown

source_name: U2OS_NFKBIA knockdown

value: NFKBIA knockdown


title: Control-rep1


title: D_04_NFKBIA knockdown


title: B_03_90 minutes post IR

source_name: U2OS_90 minutes post IR

value: 90 minutes post IR


title: B_04_90 minutes post IR


title: C_04_7 days post IR


title: C_02_7 days post IR


title: B_05_90 minutes post IR


title: C_01_7 days post IR


title: C_05_7 days post IR


title: D_01_NFKBIA knockdown


title: D_05_NFKBIA knockdown


title: 4T1 shYTHDF3 2

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with R package Olig using default analysis settings and RMA as normalization method.

source_name: 4T1 shYTHDF3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: 4T1Br cells were cultured in the same medium with 5% FBS and 1% penicillin-streptomycin. Cells were grown in a 5% CO2 cell culture incubator at 37℃.

treatment_protocol: 4T1Br cells were transduced with shControl and shYTHDF3 lentivirus and selected by puromycin.

value: Breast Cancer Cell Line

tag: genotype/variation

value: YTHDF3 knockdown


title: A_04_untreated

value: untreated


title: A_05_untreated


title: A_02_untreated


title: MDA-MB-231 shYTHDF3 2

source_name: MDA-MB-231 shYTHDF3

growth_protocol: MDA-MB-231Br cells were grown in DMEM medium with 10% FBS and 1% penicillin-streptomycin. Cells were grown in a 5% CO2 cell culture incubator at 37℃.

treatment_protocol: MDA-MB231Br cells were transduced with shControl and shYTHDF3 lentivirus and selected by puromycin.


title: D_02_NFKBIA knockdown


title: B_01_90 minutes post IR


title: B_02_90 minutes post IR


title: 4T1 shControl 2

source_name: 4T1 shControl

value: control


title: MDA-MB-231 shYTHDF3 1


title: MDA-MB-231 shControl 2

source_name: MDA-MB-231 shControl


title: 4T1 shYTHDF3 1


title: A_01_untreated


title: MDA-MB-231 shControl 1


title: 4T1 shControl 1


title: AC16_18d5h37d90min_N2

first: Harry

last: Fischl

address: Babraham Research Campus

institute: Storm Therapeutics

description: Quantseq

data_processing:
Sequences were aligned using the Ion Torrent Server TMAP aligner to genome build hg19 or, for spiked in samples, to a combined hg19 and dm6 genome build.
Mapped reads were narrowed to their 3’ most nucleotide and converted to bigwig files for positive and negative strands
Genome_build: hg19 or combined hg19 and dm6
Supplementary_files_format_and_content: bigwig files of reads narrowed to their 3’ most nucleotide for positive and negative strands. Full length bigwig files are not narrowed but are normalised to counts per million aligned counts (CPM).

growth_protocol: The AC16 cardiomyocyte cell line is derived from fusion of primary cells from human ventricular tissues with SV40-transformed fibroblasts (Davidson et al., 2005). AC16 cells were cultured in Dulbecco’s Modified Eagle’s Medium: Nutrient Mixture F-12 (DMEM/F-12) containing 10 % (v/v) Foetal Bovine Serum (FBS), 2.5 mM L-Glutamine and 1 % Penicillin/Streptomycin solution. The U2OS osteosarcoma cells were cultured in DMEM containing 10 % (v/v) FBS, 2.5 mM L-Glutamine 1 % Penicillin/Streptomycin solution

extract_protocol:
Subcellular fractionation into nuclear and cytoplasmic fractions followed by RNA isolation using Triazol reagent (Neve et al., 2015). For spiked in samples, cells were spiked with a known ratio of D. melanogaster S2 cells prior to subcellular fractionation.
The 3’ ends of extracted RNA were generated into libraries using the QuantSeq 3’mRNA-Seq library kit (Lexogen). Full length RNA libraries were generated using the using the Ion Total RNA-seq Kit v2 (ThermoFisher). For this full-length RNA-seq polyadenylated RNAs were first purified from total RNA from each fraction using the NEBNext Poly(A) mRNA Isolation Module.

treatment_protocol: Cells were cultured in a 37°C incubator with 5 % CO2 to 80-90 % confluency before harvesting, passaging or transfer to incubators set at 8°C, 18°C or 28°C (also with 5 % CO2) for the temperature exposure conditions indicated

tag: subcellular fraction

value: Nuclear

tag: temperature treatment

value: 18°C for 5 h, then 37°C for 90 min

tag: spike


title: AC16_18d5h37d90min_C1

description: Quantseq

value: Cytoplasmic


title: AC16_18d5h37d90min_C2

description: Quantseq


title: A_03_untreated


title: AC16_37d_FullLength Nuclear

description: Full-length RNAseq


title: AC16_18d24h_FullLength Nuclear

description: Full-length RNAseq

value: 18°C for 24 h


title: AC16_37d_FullLength Cytoplasmic

description: Full-length RNAseq


title: U2OSWT_37d_C2

description: Quantseq


title: AC16_18d24h_FullLength Cytoplasmic

description: Full-length RNAseq


title: U2OSWT_18d24h_N2

description: Quantseq


title: U2OSWT_18d5h_N1

description: Quantseq

value: 18°C for 5 h


title: U2OSWT_37d_C1

description: Quantseq


title: U2OSWT_37d_N2

description: Quantseq


title: U2OSWT_18d24h_N1

description: Quantseq


title: U2OSWT_18d5h_C1

description: Quantseq


title: U2OSWT_18d24h_C2

description: Quantseq


title: U2OSWT_18d24h37d2h_C1

description: Quantseq

value: 18°C for 24 h, then 37°C for 2 h


title: U2OSWT_18d24h37d2h_C2

description: Quantseq


title: U2OSWT_37d_N1

description: Quantseq


title: U2OSWT_18d5h_C2

description: Quantseq


title: U2OSWT_18d24h37d2h_N2

description: Quantseq


title: U2OSWT_18d24h_C1

description: Quantseq


title: AC16_8d24h_N3

description: Quantseq

value: 8°C for 24 h


title: AC16_8d24h_N4

description: Quantseq


title: AC16_8d24h_N6

description: Quantseq


title: AC16_8d24h_N5

description: Quantseq


title: AC16_8d24h_N2

description: Quantseq


title: AC16_18d5h37d90min_N1

description: Quantseq


title: U2OSWT_18d5h_N2

description: Quantseq


title: AC16_8d24h_N1

description: Quantseq


title: AC16_8d24h_C6

description: Quantseq


title: AC16_8d24h_C3

description: Quantseq


title: U2OSWT_18d24h37d2h_N1

description: Quantseq


title: AC16_8d24h_C4

description: Quantseq


title: AC16_37d_N2

description: Quantseq


title: AC16_8d24h_C2

description: Quantseq


title: AC16_37d_N4

description: Quantseq


title: AC16_37d_N3

description: Quantseq


title: AC16_37d_N7

description: Quantseq


title: AC16_37d_N6

description: Quantseq


title: AC16_37d_C2

description: Quantseq


title: AC16_37d_C3

description: Quantseq


title: AC16_28d24h_N1

description: Quantseq

value: 28°C for 24 h


title: AC16_28d24h_N4

description: Quantseq


title: AC16_28d24h_N6

description: Quantseq


title: AC16_37d_C4

description: Quantseq


title: AC16_37d_C6

description: Quantseq


title: AC16_37d_C5

description: Quantseq


title: AC16_28d24h_N5

description: Quantseq


title: AC16_28d24h_C6

description: Quantseq


title: AC16_8d24h_C5

description: Quantseq


title: AC16_28d24h_N2

description: Quantseq


title: AC16_28d24h_C4

description: Quantseq


title: AC16_28d24h_C5

description: Quantseq


title: AC16_28d24h_C2

description: Quantseq


title: AC16_28d24h37d2h_N1

description: Quantseq

value: 28°C for 24 h, then 37°C for 2 h


title: AC16_28d24h_C3

description: Quantseq


title: AC16_8d24h_C1

description: Quantseq


title: AC16_37d_N5

description: Quantseq


title: AC16_37d_N1

description: Quantseq


title: AC16_28d24h37d2h_N2

description: Quantseq


title: AC16_28d24h_C1

description: Quantseq


title: AC16_37d_C1

description: Quantseq


title: AC16_28d24h_N3

description: Quantseq


title: AC16_18d24h_N6

description: Quantseq


title: AC16_28d24h37d2h_C2

description: Quantseq


title: AC16_18d5h_N2

description: Quantseq


title: AC16_18d5h_N4

description: Quantseq


title: AC16_18d5h_C1

description: Quantseq


title: AC16_18d5h_C2

description: Quantseq


title: AC16_18d5h_C3

description: Quantseq


title: AC16_18d5h_C4

description: Quantseq


title: AC16_18d5h_N3

description: Quantseq


title: AC16_18d24h_N3

description: Quantseq


title: AC16_28d24h37d2h_C1

description: Quantseq


title: AC16_18d24h_C5

description: Quantseq


title: AC16_18d24h_N1

description: Quantseq


title: AC16_18d24h_N5

description: Quantseq


title: AC16_18d24h_N4

description: Quantseq


title: AC16_18d24h_C4

description: Quantseq


title: AC16_18d24h_C6

description: Quantseq


title: AC16_18d24h_C2

description: Quantseq


title: AC16_18d5h_N1

description: Quantseq


title: AC16_18d24h_C1

description: Quantseq


title: AC16_18d24h_N2

description: Quantseq


title: AC16_18d24h_C3

description: Quantseq


title: AC16_18d24h37d5h_N2

description: Quantseq

value: 18°C for 24 h, then 37°C for 5 h


title: AC16_18d24h37d5h_N1

description: Quantseq


title: AC16_18d24h37d5h_C2

description: Quantseq


title: AC16_18d24h37d2h_N3

description: Quantseq


title: AC16_18d24h37d2h_N4

description: Quantseq


title: AC16_18d24h37d5h_C1

description: Quantseq


title: AC16_18d24h37d2h_N1

description: Quantseq


title: AC16_18d24h37d2h_N2

description: Quantseq


title: AC16_18d24h37d2h_C4

description: Quantseq


title: AC16_18d24h37d24h_N2

description: Quantseq

value: 18°C for 24 h, then 37°C for 24 h


title: AC16_18d24h37d2h_C1

description: Quantseq


title: AC16_18d24h37d2h_C3

description: Quantseq


title: AC16_18d24h37d2h_C2

description: Quantseq


title: AC16_18d24h37d24h_C1

description: Quantseq


title: AC16_18d24h37d10h_N1

description: Quantseq

value: 18°C for 24 h, then 37°C for 10 h


title: AC16_18d24h37d24h_N1

description: Quantseq


title: AC16_18d24h37d10h_N2

description: Quantseq


title: AC16_18d10h_C4

description: Quantseq

value: 18°C for 10 h


title: AC16_18d10h_N2

description: Quantseq


title: AC16_18d24h37d10h_C1

description: Quantseq


title: AC16_18d24h37d10h_C2

description: Quantseq


title: AC16_18d10h_C3

description: Quantseq


title: AC16_18d10h_C2

description: Quantseq


title: AC16_18d10h_N4

description: Quantseq


title: AC16_18d10h_N1

description: Quantseq


title: AC16_18d10h_C1

description: Quantseq


title: AC16_18d24h37d24h_C2

description: Quantseq


title: AC16_18d10h_N3

description: Quantseq


title: Cells treated with 500µg Cissampelos pareira replicate 2

city: Delhi

first: Mitali

last: Mukerji

address: Mathura Road

country: India

institute: CSIR-IGIB

hyb_protocol: 5.2 µg of fragmented and labelled ss cDNA were hybridized on Affymetrix HTA 2.0 Cartridge arrays for 16hrs at 45°C at 60rpm in Affymetrix hybridization oven. Arraya were stained and washed in the Affymetrix Fluidics Station 450

scan_protocol: The stained chips were then scanned using GeneChip™ Scanner 3000

data_processing: CEL files were processed using Oligo package of Bioconductior. The intensity values were background corrected, normalised and summarised based on probe level information using Robust multi-array (RMA) normalization.

source_name: Breast cancer

label_protocol: Fragmented and biotin labelled Second cycle single stranded cDNA were prepared from 250ng total RNA following the manufacturers protocol (GeneChip WT plus reagent kit user manual)

growth_protocol: MCF7 cells were grown in DMEM high glucose supplemented with 10% FBS and 1% Anti Anti, at normal conditions (37°C, 5% CO2)

extract_protocol: Total RNA was extracted using Trizol according to manufacturers instructions

treatment_protocol: Cells were treated with mentioned doses of reconstituted aqeuous extract of Cissampelos pareira (water was used as vehicle) and incubated for 24 hours

value: 500ug Cissampelos pareira


title: Cells treated with 100µg Cissampelos pareira replicate 2

value: 100ug Cissampelos pareira


title: Cells treated with 1µg Cissampelos pareira replicate 1

value: 1ug Cissampelos pareira


title: Cells treated with 100µg Cissampelos pareira replicate 1


title: Cells treated with 1000µg Cissampelos pareira replicate 2

value: 1000ug Cissampelos pareira


title: Cells treated with 1µg Cissampelos pareira replicate 2


title: Cells treated with 1000µg Cissampelos pareira replicate 3


title: Vehicle treated cells Replicate 3

value: Vehicle treated


title: all brain_NuGEN_rep2

city: Oklahoma City

first: Susan

middle: Kasko

last: Munster

state: OK

address: 6500 S. MacArthur Blvd.

department: Office of Aerospace Medicine

institute: Federal Aviation Admininistration

description: all-brain NuGEN B

hyb_protocol: All samples were fragmented and biotin labeled using GeneChip® Hybridization, Wash, and Stain Kit and hybridized onto GeneChip® Human Transcriptome Array 2.0 microarrays

scan_protocol: Affymetrix 7G GeneChip® Scanner 3000

data_processing:
QC was performed in R using arrayQualityMetrics package. Samples were normalized using the oligo and pd.hta.2.0 packages in R.  All non-core probesets were removed using genefilter in R. Differential expression analysis was carried out using the limma package in R.
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.na36.hg19.transcript.csv

source_name: brain, NuGEN

label_protocol: Samples were amplified using GeneChip® WT PLUS or Ovation® PICO WTA system kits to produce cDNA.

extract_protocol: Blood: extracted using a Paxgene® Blood RNA Kit, Brain: N/A

treatment_protocol: Blood: samples collected in Paxgene blood RNA tubes, Brain: RNA purchased from Life Technologies

tag: tissue

value: all brain

tag: amplification method

value: NuGEN Ovation® Pico WTA System V2


title: Cells treated with 1000µg Cissampelos pareira replicate 1

tag: treatment


title: all blood_NuGEN_rep1

description: all-blood NuGEN A

source_name: blood, NuGEN

value: all blood


title: Cells treated with 500µg Cissampelos pareira replicate 1


title: all brain_Affymetrix_rep2

description: all-brain Affymetrix B

source_name: brain, Affymetrix

label_protocol: Samples were amplified using GeneChip® WT PLUS

value: Affymetrix GeneChip® WT PLUS


title: all blood_Affymetrix_rep1

description: all-blood Affymetrix A

source_name: blood, Affymetrix


title: Cells treated with 500µg Cissampelos pareira replicate 3


title: Cells treated with 100µg Cissampelos pareira replicate 3


title: all brain_Affymetrix_rep1

description: all-brain Affymetrix A


title: 2/3 blood 1/3 brain_NuGEN_rep2

description: 2/3-blood NuGEN B

source_name: blood/brain, NuGEN

value: 2/3 blood, 1/3 brain


title: all brain_NuGEN_rep1

description: all-brain NuGEN A


title: 2/3 blood 1/3 brain_NuGEN_rep1

description: 2/3-blood NuGEN A


title: all blood_Affymetrix_rep2

description: all-blood Affymetrix B


title: Cells treated with 1µg Cissampelos pareira replicate 3


title: Vehicle treated cells Replicate 1


title: Cells treated with 10µg Cissampelos pareira replicate 2

value: 10ug Cissampelos pareira


title: Vehicle treated cells Replicate 2


title: all blood_NuGEN_rep2

description: all-blood NuGEN B


title: Cells treated with 10µg Cissampelos pareira replicate 3


title: 1/3 blood 2/3 brain_NuGEN_rep1

description: 1/3-blood NuGEN A

value: 1/3 blood, 2/3 brain


title: 1/3 blood 2/3 brain_NuGEN_rep2

description: 1/3-blood NuGEN B


title: Cells treated with 10µg Cissampelos pareira replicate 1


title: 2/3 blood 1/3 brain_Affymetrix_rep2

description: 2/3-blood Affymetrix B

source_name: blood/brain, Affymetrix


title: Control_48h_rep2

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: SAMPLE 5

hyb_protocol: 16 h to Affymetrix Human Transcriptome 2.0 ST arrays

scan_protocol: Affymetrix Scanner 3000 7G using AGCC software.

data_processing: CEL files were summarized using the SST RMA algorithm in Transcriptome Analysis Console v4.0.1.36 (Affymetrix) and the normalized data were subjected to one-way ANOVA with a Benjamin Hochberg False Discovery Rate correction included (p<0.05). A 2-fold change was used to select entities that were statistically and differentially expressed between the two conditions.

growth_protocol: U87 celles were grown in EMEM containing 10% FBS and 1 mM sodium pyruvate for 48 h before treatment

extract_protocol: Total RNA was extrcated using trizol followed by an RNeasy column cleanup that included a Dnase step. The quality and the concentrations of total RNA were assessed using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). Total RNA (100 ng) deemed to be of good quality (RNA integrity number (RIN) greater than 8) was processed according to the standard Affymetrix Whole Transcript Sense Target labeling protocol (Affymetrix, Santa Clara, CA).

treatment_protocol: U87 cells were treated with EMEM media containing 1 mM carborane bearing compound and incubated in a dish for 48 h before extraction.

value: Glioblastoma cells

value: none (control)


title: 1/3 blood 2/3 brain_Affymetrix_rep2

description: 1/3-blood Affymetrix B


title: Treated_48h_rep3

description: SAMPLE 3

label_protocol: Affymetrix Whole Transcript Sense Target labeling protocol

value: 1 mM carborane bearing amino acid


title: Treated_48h_rep1

description: SAMPLE 1


title: 2/3 blood 1/3 brain_Affymetrix_rep1

description: 2/3-blood Affymetrix A


title: Control_48h_rep3

description: SAMPLE 6


title: 1/3 blood 2/3 brain_Affymetrix_rep1

description: 1/3-blood Affymetrix A


title: IMSA094_EPI_S

city: Pittsburgh

first: Anuradha

last: Ray

state: PA

address: 3459 Fifth Ave, MUH 628 NW

department: Medicine/Pulmonary

institute: University of Pittsburgh

description: Human Bronchial Brushings

data_processing:
Quality control for raw FASTQ files was performed using FastQC, and the lowquality reads and 3’ adapters were trimmed with Trim Galore! (Babraham Bioinformatics, Cambridge, United Kingdom)
The RNA sequence aligner STAR was used to align the trimmed reads to the reference human genome (hg19)
Gene expression was quantified  from mapped genes using featureCounts
Quantified gene expression was normalized using the rlog package from DESeq2
Samples were controlled for batch effect using the COMBAT algorithm
Genome_build: hg19

source_name: Bronchial Epithelial RNA Extraction

extract_protocol:
Frozen RNA samples were purified removing DNA and rRNA with standard procedures.
cDNA libraries were prepared for sequencing using Illumina protocols. (Illumina Document #1000000040499v00 and Illumina Kit #20020596).

value: lung

value: Bronchial Epithelial Cells

tag: diagnosis

value: Severe Asthma

tag: steroid

value: yes

value: male

tag: batch

tag: age


title: Control_48h_rep1

description: SAMPLE 4

tag: cell line


title: BS_drm2 cmt23

city: Bunkyo-ku

first: Taiko

middle: Kim

last: To

state: Tokyo

address: 7-3-1 Hongo

department: Biological Science

institute: University of Tokyo

data_processing:
WGBS: The adaptor sequences and low quality regions were trimmed using Trimmomatic (Bolger et al. 2014). Mapping to the reference genome (TAIR10), deduplication, and methylation extraction were performed using Bismark version 0.10.1 (Krueger and Andrews, 2011). The parameters used for mapping is -n 1 –l 20 –e 90. Uniquely aligned reads were used and reads with more than one alignment with same read quality were removed.
RNA-seq: The adaptor sequences and low quality regions were trimmed using Trimmomatic (Bolger et al. 2014). The quality filtered reads were mapped to genes (TAIR10) were counted through STAR algorithm (Dobin et al., 2013).
ChIP-seq: The reads were quality-filtered using Trimmomatic (Bolger et al. 2014) and mapped to TAIR10 genome using Bowtie (Langmead et al., 2009) with option -M 1 --best.
Genome_build: TAIR10
Supplementary_files_format_and_content: WGBS: CX_report file
Supplementary_files_format_and_content: RNA-seq: STAR ReadsPerGene output file
Supplementary_files_format_and_content: ChIP-seq: bowtie output file

organism: Arabidopsis thaliana

source_name: Rosette leaves

growth_protocol: WGBS: Plants were grown on soil.

extract_protocol:
WGBS: Genomic DNA was isolated from rosette leaves using the Nucleon Phytopure genomic DNA extraction kit (GE Healthcare).
WGBS: Genomic DNA was fragmented using Covaris S220, and the size between 300-450bp were gel-purified. The libraries were prepared using TruSeq DNA LT Sample Prep Kit (Illumina) and subjected to bisulfite conversion using MethylCode Bisulfite Conversion Kit (Life Technologies). Bisulfite-treated DNA were amplified with KAPA HiFi HotStart Uracil ReadyMix (Kapa Biosystems), and then purified with Agencourt AMPure XP (Beckman Coulter).

tag: genotype

value: drm2 cmt2 cmt3

value: Leaves


title: BS_F1(met1-6 X vim123)_rep1


title: BS_drm2 suvh456

value: drm2 suvh4 suvh5 suvh6


title: BS_Col

value: Wild-type


title: Treated_48h_rep2

description: SAMPLE 2


title: BS_(suvh456 X cmt23 F1)


title: BS_met1-6


title: BS_cmt23

value: cmt2 cmt3


title: BS_suvh456

value: suvh4 suvh5 suvh6


title: BS_F1(drm2 cmt23 X drm2 suvh456)_rep2


title: BS_F1(drm2 cmt23 X drm2 suvh456)_rep1


title: BS_F1(met1-6 X vim123)_rep2


title: BS_F2(met1-6 X vim123)_rep1


title: BS_(cmt23 X suvh456 F1)


title: BS_vim123

value: vim1 vim2 vim3


title: IMSA093_EPI_H

description: Human Bronchial Brushings

value: Healthy Control

value: no

tag: gender


title: IMSA091_EPI_H

description: Human Bronchial Brushings

tag: cell type


title: IMSA087_EPI_S

description: Human Bronchial Brushings


title: IMSA086_EPI_H

description: Human Bronchial Brushings

value: female


title: IMSA085_EPI_H

description: Human Bronchial Brushings


title: IMSA090_EPI_H

description: Human Bronchial Brushings


title: IMSA098_EPI_H

description: Human Bronchial Brushings


title: IMSA083_EPI_H

description: Human Bronchial Brushings


title: IMSA080_EPI_S

description: Human Bronchial Brushings


title: IMSA078_EPI_S

description: Human Bronchial Brushings


title: IMSA077_EPI_S

description: Human Bronchial Brushings


title: IMSA069_EPI_H

description: Human Bronchial Brushings


title: IMSA068_EPI_S

description: Human Bronchial Brushings


title: IMSA067_EPI_M

description: Human Bronchial Brushings

value: M/M Asthma


title: IMSA070_EPI_S

description: Human Bronchial Brushings


title: IMSA071_EPI_S

description: Human Bronchial Brushings


title: IMSA075_EPI_H

description: Human Bronchial Brushings


title: IMSA065_EPI_S

description: Human Bronchial Brushings