title: ISCH LVAD_K

first: Mark

middle: Emile

last: Pepin

address: 870 Quarry Road

department: Cardiovascular Medicine

data_processing:
Illumina bcl2fastq version 1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using TrimGalore version 0.4.0 with parameters: --paired, --trim1
Trimmed reads were then aligned with TopHat version 2.0.12 (Bowtie2 version 2.2.3) to UCSC hg19 reference genome with parameters: -r 150, --library-type fr-firststrand, --keep-fasta-order, --transcriptome-index, --rg-id, --rg-sample, --rg-library, --rg-platform-unit, --rg-platform, -o
Cufflinks version 2.2.1 estimated transcript abundances with parameters: --library-type fr-firststrand, -o, -g, -L, -b, -u
Cuffmerge, Cuffquant, Cuffdiff, and Cuffquant were then run to get to final differential expression results
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: Left Ventricle Endocardium

extract_protocol:
Endocardial samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human Samples taken from left ventricle of patients with end-stage heart failure during Ventricular Assist Device implantation.

tag: race

value: CAU

tag: ischemia

value: ISCH


title: ISCH LVAD_J

status: Public on Aug 22 2018

type: SRA

city: Stanford

state: CA

country: USA

institute: Stanford University

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: age

tag: Sex

value: Male


title: BLA-214

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequencing reads obtained from mouse brain cells were mapped to mm10 using TopHat2v2.1.0. Counts of reads mapping to genes were obtained using HTSeq-count against Ensembl v75 annotation. Differential expression analysis was done using the voom-limma R package at FDR cutoff of 0.05 (5% False Discovery Rate) and a log fold change cutoff of < -0.05 or > 0.05 was applied.
Genome_build: mm10
Supplementary_files_format_and_content: Counts in tab delimited text file generated using HTSeq-count against Ensembl v75 annotation

molecule: polyA RNA

organism: Mus musculus

source_name: Brain

growth_protocol: Male C57BL/6J mice were obtained from The Jackson Laboratory.

extract_protocol:
RNA from mouse brain samples was extracted using an RNeasy micro kit using Trizol, followed by DNase 1 treatment, as described by the manufacturer (Qiagen). RNA integrity number (RIN) and concentration were assessed using a Bioanalyzer (Agilent).
Libraries were constructed using the ScriptSeq Complete Gold Kit (Epicentre, Illumina) preceded by ribosomal RNA depletion.

treatment_protocol: C57BL/6J male mice underwent cocaine or saline SA followed by 24 hr or 30 d of WD. At the 30 d WD time-point, animals were challenged with a single IP injection of cocaine or saline within the drug SA and transcriptional analysis was conducted on tissue collected 1 hr later.

tag: tissue

value: Brain

tag: region

value: Basolateral amygdala

tag: self-administration

value: Cocaine

tag: challenge

tag: strain


title: ISCH LVAD_I


title: sc.iRBC.3

city: Stockholm

first: Rickard

last: Sandberg

address: Solnavägen 9  Solna

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

data_processing:
Aligned reads with STAR version 2.3 to combined genomes of P.falciparum(Pf3D7v3) and human (hg19) with the outSAMstrandField  set to 'intronMotif'.
Calculated expression values with rpkmforgenes.py (available at https://github.com/danielramskold/S3_species-specific_sequencing) with options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendceil and gene annotation for the UCSC genome browser Ensembl track and Plasmodb release 11.1 annotation for P.falciparum (Pf3D7v3).
Principal component analysis done using prcomp function and t-stochastic neighbour embedding performed using tsne version 0.1-3 in R.
Single-cell differential expression analysis done using SCDE version 2.8.0.
Genome_build: Combined Pf3D7v3 (Plasmodb release 11.1) and hg19 (UCSF Human Genome Assembly)
Supplementary_files_format_and_content: Tab-delimited text with each row and column corresponding to P. falciparum genes and samples respectively. The first 208 fields represent the read counts and the next 208 are the normalized gene expression measurements (RPKM).

organism: Plasmodium falciparum

extract_protocol: SmartSeq2 (Picelli S, Nat Methods. 2013, PubMed PMID: 24056875)

value: A

tag: library quality

value: high

tag: group

value: single-cell

tag: sub-population

tag: batch

value: one


title: NICM LVAD_H

value: NICM


title: BLA-205

value: Saline


title: BLA-204


title: NICM LVAD_G


title: NICM LVAD_F


title: PDA_tumor_41

type: RNA

city: Brussels

first: Sylvain

last: Brohée

address: Boulevard de Waterloo 127

country: Belgium

institute: Institut Jules Bordet

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

label: biotin

source_name: pancreatic tumor

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by submitter

tag: death


title: BLA-193


title: BLA-194


title: BLA-191


title: PDA_tumor_42


title: PDA_tumor_40


title: NICM LVAD_D

value: AA


title: PDA_tumor_39


title: BLA-185


title: ISCH LVAD_E


title: ISCH LVAD_C


title: PDA_tumor_36


title: BLA-183


title: NICM LVAD_B


title: PDA_tumor_37


title: BLA-182


title: PDA_tumor_35


title: PDA_tumor_38


title: PDA_tumor_33


title: PDA_tumor_34


title: PDA_tumor_32


title: PDA_tumor_31


title: NICM LVAD_A


title: BLA-162


title: BLA-161


title: BLA-171


title: PDA_tumor_30


title: BLA-151


title: PDA_tumor_29


title: BLA-144


title: BLA-145


title: BLA-143


title: PDA_tumor_28


title: BLA-175


title: BLA-125


title: BLA-122


title: BLA-091


title: BLA-111


title: PDA_tumor_26


title: PDA_tumor_27


title: BLA-105


title: PDA_tumor_25


title: PDA_tumor_21


title: PDA_tumor_23


title: PDA_tumor_24


title: BLA-115


title: PDA_tumor_22


title: BLA-085


title: BLA-083


title: PDA_tumor_20


title: PDA_tumor_17


title: PDA_tumor_18


title: BLA-074


title: PDA_tumor_19


title: PDA_tumor_16


title: BLA-073


title: BLA-065


title: BLA-072


title: PDA_tumor_15


title: PDA_tumor_14


title: BLA-052


title: PDA_tumor_10


title: PDA_tumor_12


title: PDA_tumor_11


title: BLA-043


title: BLA-031


title: BLA-035


title: BLA-011


title: BLA-014


title: BLA-012


title: PDA_tumor_9


title: PDA_tumor_13


title: PDA_tumor_8


title: PDA_tumor_6


title: PDA_tumor_7


title: TPC1115_shPRMT2_1_RNAseq

city: Tianjin

first: xudong

last: Wu

address: Qixiangtai Road

country: China

institute: Tianjin medical university

data_processing:
RNA-seq analysis was completed by BGI company(Shenzhen,China). For ChIP-seq, Clean reads were obtained from sequencing company.
Clean reads were aligned to human reference genome (hg19) using Bowtie2 version 2.2.9. Only unique mapped reads were used in further analysis.
Peak calling and annotation were performed using MACS version 1.4.2. and ChIPseeker package respectively.
Heatmaps and average profiles were generated by deepTools V2.4.0.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include FPKM values for each sample. For ChIP-seq, bigwig files were generated using deepTools V2.4.0, score represents the normalized coverage of  DNA fragments at a given genomic coordinate.

growth_protocol: The glioblastoma cell lines U87 was cultured in DMEM containing 10% fetal bovine serum (FBS). TPC1115 was obtained from fresh surgical specimens of human primary GBMs and cultured as either monolayer or tumorspheres in DMEM/F12 medium supplemented with N2, B27 (Gibco), 20 ng/ml human Fibroblast Growth Factor-basic (bFGF, Sino Biological, Beijing, China), 20 ng/ml Epidermal Growth Factor-basic (EGF, Sino Biological, Beijing, China).

extract_protocol:
Total RNA isolated using Trizol reagent (Ambion)
Construction of RNA-seq library was completed by BGI company (Shenzhen,China).

treatment_protocol: U87 cells were infected with shPRMT2 lentivirus

tag: cell line

tag: cell type

value: glioblastoma cells

tag: transfected with

value: shPRMT2 lentivirus


title: PDA_tumor_4


title: PDA_tumor_3


title: PDA_tumor_5


title: PDA_tumor_2


title: TPC1115_scramble_RNAseq

value: scramble control


title: U87_shPRMT2_2_RNAseq


title: PDA_tumor_1


title: KW_ab_ZK rep1

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Illumina basespace used for basecalling.
Reads acquired from the illumina NextSeq 500 sequencing platform were cleaned up with the Cutadapt program to trim off sequencing adaptors and low quality bases with a quality phred-like score<20.  Reads <40 bases were excluded from RNA-seq analysis.
ICBR scripts along with SAMtools and the DESeq, EdgeR, and Bayseq (DEB) computational applications were applied to generate the gene expression data, including fold changes and p-values, to remove duplicates or artifacts from PCR, and choose uniquely mapped reads for gene expression analysis. Digital gene expression was assessed by counting the number of transcripts that mapped to a gene sequence.
Genome_build: Aedes-aegypti-Liverpool_TRANSCRIPTS_AaegL3.3.fa
Supplementary_files_format_and_content: tab-delimited text files include the mapped read counts for each Sample

organism: Aedes aegypti

source_name: KW_ab_ZK, whole animal

extract_protocol:
All samples (10 mosquitoes per pool) were homogenized with a plastic pestle in the 1 mL TRIzol reagent (Ambion, Life Technologies). Total RNAs were isolated using TRIzol reagent according to the manufacturer’s instruction and followed the standard protocol (Ambion, Life Technologies). To avoid genomic DNA contamination, the RNA samples were processed by DNase I (RNase-free) following the manufacturer’s instructions (Thermo Scientific, Wilmington, Delaware USA). The RNA samples were quantitated by NANODROP 2000 Spectrophotometer (Thermo Scientific, Wilmington, DE).
Preparation and sequencing libraries were carried out at the Interdisciplinary Center for Biotechnology Research (ICBR), at the University of Florida following the manufacturer’s protocol (Illumina, Inc., San Diego, CA). The TruSeq DNA Library Preparation Kit (Illumina, Inc., San Diego, CA) was used to prepare DNA libraries with insert sizes from 300–500 bp for high-throughput sequencing. For the Illumina NextSeq 500 run, the NCS v1.2 control software was used. The libraries were pooled at equimolar concentrations to yield a 4 nM stock solution, containing 0.33 nM of each library. The library pool was prepared for sequencing following the manufacturer protocol. The Illumina® NextSeq® 500 sequencing platform was used to create paired-end reads using Illumina’s sequencing-by-synthesis approach (Illumina®, San Diego, CA) using 2 X 150 cycles.

treatment_protocol: The parental collection of Ae. aegypti from the field was initially tested for permethrin resistance, then subjected to permethrin selection for 15 generations (see below) and again assayed for resistance (referred to as the resistant strain). The Orlando strain of Ae. aegypti was collected from Orlando (28.53°N, 81.37°W), Florida, USA and reared in the Mosquito and Fly Research Unit, Center for Medical, Agricultural and Veterinary Entomology, ARS-USDA in Gainesville, FL since 1952. The Orlando strain is recognized as a permethrin susceptible strain of Ae. Aegypti. Four-day-old female adults were fed defibrinated bovine blood containing either ZIKV (treatment) or blood lacking virus (control).

value: whole animal

tag: location

value: Key West (24.55°N, 81.78°W), Florida, USA

value: adult

tag: gender

value: female

tag: resistance

value: permethrin-resistant strain

tag: infection

value: ZIKV


title: OR_HI_cont rep3

source_name: OR_HI_cont, whole animal

tag: tissue

value: Orlando (28.53°N, 81.37°W), Florida, USA

tag: age

value: permethrin-susceptible strain

value: control


title: KW_ab_ZK rep2


title: KW_ab_ZK rep3


title: OR_HI_cont rep2


title: OR_HI_cont rep1


title: U87_shPRMT2_1_RNAseq


title: U87_scramble_RNAseq


title: OCI_Ly7.24h.ET.2

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing: The data were normalized using quantile method

source_name: OCI-Ly7 cell lines treated with Trabectedin for 24h

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: in vitro

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufacturer's recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyzer).

treatment_protocol: Treatment with Trabectedin as single agent in DLBCL cell lines

tag: cell line type

tag: treatment

value: Trabectedin

tag: time point

tag: replicate


title: KW_AB_cont rep3

source_name: KW_AB_cont, whole animal


title: KW_AB_cont rep1


title: liver_rep3

city: Brisbane

first: Amin

middle: Roushdy

last: Mohamed

state: Queensland

address: 306 Carmody Rd, University of Queensland

department: Agriculture and Food

country: Australia

institute: CSIRO

data_processing:
Data were mapped to Atlantic salmon genome (ICSASG_v2) using tophat2, fragments mapped to exon regions were counted using the Python package HTSeq-count. Differential gene expression was infered based on mapping counts using edgeR
Genome_build: http://www.ncbi.nlm.nih.gov/assembly/487001
Supplementary_files_format_and_content: matrix of counts

organism: Salmo salar

source_name: liver

extract_protocol:
Total RNA was isolated from each tissue using RNeasy Kit (QIAGEN), eluted in 40 uL RNase-Free Water
Messenger RNA (mRNA) was isolated from 500 ng total RNA and a total of 16 RNA-Seq libraries (4 biological replicates per tissue) prepared using the Illumina TruSeq stranded library Preparation Kit. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing platform

value: liver


title: liver_rep4


title: OR_MM_ZK rep3

source_name: OR_MM_ZK, whole animal


title: OCI_Ly7.8h.ET.2

source_name: OCI-Ly7 cell lines treated with Trabectedin for 8h


title: OCI_Ly7.24h.ET.1


title: KW_AB_cont rep2


title: OCI_Ly7.24h.DMSO.3

source_name: OCI-Ly7 cell lines treated with DMSO for 24h

value: DMSO


title: OCI_Ly7.8h.ET.1


title: OCI_Ly7.8h.DMSO.3

source_name: OCI-Ly7 cell lines treated with DMSO for 8h


title: genomic DNA from cardiac left ventricle G

type: genomic

description: Left Ventricle Endocardium

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

molecule: genomic DNA

source_name: cardiac left ventricle

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from Human Left Ventricle Pre-LVAD samples using Qiagen DNeasy Kit according to standard instructions

tag: Sex

value: Male

tag: race

value: CAU

tag: ischemia

value: NICM


title: genomic DNA from cardiac left ventricle I

description: Left Ventricle Endocardium

value: ISCH


title: OCI_Ly7.8h.ET.3


title: dnr164_non-stimulated_p2

city: Utrecht

first: Judith

middle: Anne

last: Vivié

state: Utrecht

address: Uppsalalaan 8

department: Single Cell Sequencing Facility

country: Netherlands

institute: Hubrecht Institute

data_processing:
Paired end reads were aligned to human transcriptome using bwa (version 0.7.10) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.  The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded.  The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases.
Genome_build: hg19
Supplementary_files_format_and_content: *.TranscriptCounts.tsv
Tab separated data file for each sequencing library, listing all genes in rows and the number of sequenced transcripts for all samples. Column name refers to well number in the used 384-well plates. First column lists official gene symbol followed by chromosome name after a double underscore separation

source_name: freshly isolated plasmacytoid dendritic cell

growth_protocol: dnr174: PDCs were freshly isolated from human blood and directly encapsulated in picoliter droplets containing X-Vivo 15 media (Lonza) supplemented with 2% pooled human serum; dnr162&dnr164: cells were freshly isolated from human blood and directly analyzed via scRNA-seq

extract_protocol:
Cells were sorted into mineral oil (Sigma Aldrich) and cells were lysed at 65 ℃ for 5 minutes
mRNA was processed using the previously described SORTseq method (Muraro et al, 2016). Resulting DNA libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing

treatment_protocol: Single pDCs were encapsulated in picoliter droplets and stimulated with 50 ug/mL CpG-C for 0h, 1h, or 2h

value: plasmacytoid dendritic cells

value: non-stimulated

tag: source

value: blood, dnr164

tag: isolation method

value: density gradient isolation, AKC buffer lysis, FACS isolation based on LIN1- and CD304+ selection


title: genomic DNA from cardiac left ventricle J

description: Left Ventricle Endocardium


title: genomic DNA from cardiac left ventricle K

description: Left Ventricle Endocardium


title: OCI_Ly7.24h.ET.3


title: OR_MM_ZK rep2

value: whole animal

value: adult

value: female


title: genomic DNA from cardiac left ventricle H

description: Left Ventricle Endocardium


title: dnr162_non-stimulated_p2

tag: cell type

value: blood, dnr162


title: OR_MM_ZK rep1

value: Orlando (28.53°N, 81.37°W), Florida, USA

value: permethrin-susceptible strain

value: ZIKV


title: OCI_Ly7.8h.DMSO.2


title: dnr162_non-stimulated_p1


title: liver_rep2

value: liver


title: genomic DNA from cardiac left ventricle A

description: Left Ventricle Endocardium

value: AA


title: dnr174_50cpgc_2h

value: CpG-C, 2h

value: blood, dnr174


title: OR_cont rep3

source_name: OR_cont, whole animal

value: control


title: OCI_Ly7.24h.DMSO.2

value: DMSO


title: ovary_rep4

source_name: ovary

value: ovary


title: liver_rep1


title: genomic DNA from cardiac left ventricle C

description: Left Ventricle Endocardium

value: Male

value: ISCH


title: genomic DNA from cardiac left ventricle F

description: Left Ventricle Endocardium

value: CAU

value: NICM


title: ovary_rep3


title: genomic DNA from cardiac left ventricle D

description: Left Ventricle Endocardium


title: OR_cont rep2

value: whole animal

value: adult


title: ovary_rep2


title: genomic DNA from cardiac left ventricle B

description: Left Ventricle Endocardium


title: OCI_Ly7.8h.DMSO.1


title: OR_cont rep1

value: female


title: dnr174_50cpgc_0h

value: plasmacytoid dendritic cells

value: CpG-C, 0h

value: density gradient isolation, AKC buffer lysis, FACS isolation based on LIN1- and CD304+ selection


title: dnr174_50cpgc_1h

value: CpG-C, 1h


title: OCI_Ly7.24h.DMSO.1


title: KW_ZK rep3

source_name: KW_ZK, whole animal

value: Key West (24.55°N, 81.78°W), Florida, USA

value: permethrin-resistant strain

value: ZIKV


title: genomic DNA from cardiac left ventricle E

description: Left Ventricle Endocardium


title: X4_3

city: Shanghai

first: Moyang

last: Liu

address: dongchuan road 800

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads containing poly-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008)
Genome_build: http://www.mbkbase.org/Pinku1/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values or raw counts for each Sample. A FASTA file with transcript sequence is included on the series record.

organism: Fagopyrum tataricum

source_name: seeds

growth_protocol: Seeds of Tartary buckwheat (XIQIAO NO.2) were collected in 2016 at the experimental field of College of Life Science, Sichuan Agricultural University (Lat. 29°97’ N, 102°97’ E, Alt. 580 m), China. It had been introduced to the field and grown in the same ecoenvironmental and cultivation conditions for five years. We observed the seed development process from anthesis till maturation in April-May, 2016. Seeds were hand-collected at intervals of two days, from the beginning of seed until full maturity,covering a total range of 30 d.

extract_protocol:
Buckwheat seeds were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the transcriptome sampling, seeds at three developing stages (13, 19, 25 dpa) were collected from the same individual, and seeds with the same developing stage from three plants comprised of three replicates. the collected samples were flash frozen in liquid nitrogen and stored at −80°c until further use.

tag: developmental stage

value: initial maturity stage

value: seeds

tag: cultivar

value: XIQIAO NO.2


title: X4_2


title: KW_ZK rep2

tag: location

tag: gender


title: U2932.24h.DMSO.3

source_name: U2932 cell lines treated with DMSO for 24h

value: DMSO


title: U2932.24h.DMSO.2


title: pituitary_rep3

source_name: pituitary gland

value: pituitary gland


title: KW_ZK rep1

tag: resistance

tag: infection


title: X4_1

tag: tissue


title: U2932.8h.DMSO.2

source_name: U2932 cell lines treated with DMSO for 8h

tag: cell line type


title: pituitary_rep2


title: X3_3

value: discoloration stage


title: ovary_rep1

value: ovary


title: KW_cont rep3

source_name: KW_cont, whole animal

value: whole animal

tag: age

value: control


title: KW_cont rep2

value: adult

value: female


title: X3_2


title: pituitary_rep4


title: brain_rep4

source_name: mid brain

value: mid brain


title: OR_ZK rep3

source_name: OR_ZK, whole animal

value: Orlando (28.53°N, 81.37°W), Florida, USA

value: permethrin-susceptible strain


title: brain_rep3


title: KW_cont rep1

value: Key West (24.55°N, 81.78°W), Florida, USA


title: X3_1


title: X2_3

value: green fruit stage


title: brain_rep2


title: X2_2


title: OR_ZK rep2

value: ZIKV


title: pituitary_rep1


title: OR_ZK rep1


title: U2932.8h.ET.3

source_name: U2932 cell lines treated with Trabectedin for 8h

tag: treatment

value: Trabectedin

tag: time point


title: U2932.24h.DMSO.1

tag: replicate


title: U2932.8h.DMSO.1


title: U2932.24h.ET.2

source_name: U2932 cell lines treated with Trabectedin for 24h


title: U2932.24h.ET.3


title: X2_1

value: seeds


title: U2932.8h.ET.2


title: U2932.24h.ET.1


title: U2932.8h.ET.1


title: brain_rep1


title: OE Riboseq rep3

status: Public on Aug 21 2018

city: La Jolla

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

data_processing:
library strategy: Ribo-seq
Adaptors in single-end sequencing reads were trimmed by using the cutadapt program with parameters ‘-m16 -e 0.2’ plus ‘-a AGATCGGAAGAGCACACGTCTGAACTC’ for eCLIP-seq and ‘-a ATCTCGTATGCCGTCTTCTGCTTGAAA’ for Ribo-seq data, respectively. Gene annotation from human refGene (hg19) was downloaded from UCSC genome browser for mapping. The ensemble of mRNA sequences named as hmg was constructed by joining mRNA sequences (with 1kb N) of coding genes, and the longest isoform was chosen as the representative isoform for each transcript. The first random 6nt of eCLIP-seq reads were used to remove PCR products, and only those equal to or longer than 16 nt were mapped to hmg by using Bowtie2 in the end-to-end model. The first 4nt barcode sequence from Ribo-seq and RNA-seq reads was removed before mapping to hmg by using STAR. For each group of mapped reads with same genomic position and same barcode, only one is retained to avoid PCR products. For each replicate group of eCLIP-seq libraries, peak calling was performed by using CLIPper on combined reads from WT and OE miR-17/20a samples. The Ago2 peaks were filtered on the relative enrichment of Ago2 CLIP reads counts over those in input control samples. The reads counts of peaks were computed by using featureCounts program and the enrichment was calculated with edgeR package. The peaks corresponding to miR17/20a were computed in a similar manner by comparing eCLIP under miR-17/20a OE over WT.
Genome_build: hg19. Gene annotation from human refGene (hg19) was downloaded from UCSC genome browser. The ensemble of mRNA sequences, named as hmg, was constructed by joining mRNA sequences (with 1kb N) of coding genes, and the longest isoform was chosen as the representative isoform for each transcript.
Supplementary_files_format_and_content: bigWig for normalized coverage signals in forward strand of hmg

source_name: OE Riboseq

growth_protocol: HeLa cells were grown in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS) plus 100 U penicillin/streptomycin (Gibico) at 37oC in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted by TRIZOL reagent.
For Aog2 CLIP-seq, HeLa cells grown on 15 cm plates were first UV irradiated at 400 mj and collected by scraping the cells. After IP, the 3’ RNA adapter was ligated to RNA fragments on beads, which was followed by reverse transcription and ligation of a 3’ single-stranded DNA adapter to the cDNA. Libraries were sequenced by Hi-Seq 2500. For Ribo-seq, transfected cells were collected and resuspended with ice-cold lysis buffer (10 mM Tris-Cl pH7.4, 5mM MgCl2, 100 mM KCl, 1% Triton X-100) and placed on ice for 20 min. The cell lysate were centrifuged at 12000g for 20 min, and then the supernatant was loaded on a 10%-50% linear sucrose gradient and centrifuged at 36400 rpm for 3 hrs in SW41Ti rotor (Beckman). After centrifugation, ribosome and polyribosome fractions were collected and monitored by UV254. The collected fractions were pelleted by ultracentrifuge at 50,000 rpm in SW60 rotor for 6 hrs and ribosomal bound RNAs were digested with RNase I (Ambion). The RNA fragments were size selected (~30 nt) and rRNA depleted by antisense oligo and RNase H strategy. Ribosome protected fragments(RPFs) were ligated with the 5’ and 3’ adaptor and sequenced on Hi-Seq 2500. For RNA-seq, A fraction of total RNA from the same cells was each isolated using TRIZOL Reagent (Ambion) and fragmented using reverse transcriptase buffer (Invitrogen) at 94oC for 10 min. RNA fragments were size selected (180-220 nt) and rRNA depleted by antisense oligo and RNase H strategy, and then ligated with 5′ and 3′ adaptor. The libraries were sequenced on Hi-Seq X10.

treatment_protocol: microRNA mimics were transfected into cells with  RNAi Max. Cells were harvested 48 hrs post-transfection for subsequent analysis.

tag: cell line

value: HeLa

value: cervical adenocarcinoma cells

tag: genotype/variation

value: miR17/20a OE


title: OE Riboseq rep1


title: Myo1c Knockdown 1

city: Charleston

first: Deepak

last: Nihalani

state: SC

address: 70 President St.

department: Medicine/Nephrology

institute: Medical University of South Carolina

description: Myo1c KD 1

data_processing:
Data processing step: Libraries are fed into HiSeq/MiSeq machines for sequencing after library quality up to standard. Raw image data file from high-throughput sequencing was transformed to Sequenced Reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling) (Casava 1.8).
Data analysis: Downstream analysis was performed using a combination of programs including Bowtie2, Tophat2, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/DEGseq. GO and KEGG enrichment were implemented by the GOseq R package and KOBAS. Gene fusion and difference of alternative splicing event were detected by MISO and TopHatfusion software.
Mapping to reference genome: Reference genome and gene model annotation files were obtained from genome website browser (NCBI/UCSC/Ensembl). Indexes of the reference genome were built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Quantification of gene expression level: HTSeq v0.6.1 was used to count the read numbers mapped of each gene. Then, RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene (Mortazavi et al., 2008).
Differential expression analysis: (For DESeq2 with biological replicates) Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression.
Genome_build: Not provided
Supplementary_files_format_and_content: *.DEG.txt: Tab-delimited text files include RPKM values for each Sample.

source_name: Immortalized Human Podocytes Cell Lines

growth_protocol: RPMI 1640-based medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen), 2 g/liter of sodium bicarbonate (NaHCO3), insulin-transferrin-selenium (ITS) supplement (Sigma-Aldrich), and 200 units/ml penicillin and streptomycin (Roche Applied Science).

extract_protocol:
RNA was isolated using the Qiagen RNeasy Mini Kit (Cat. No # 74104) and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Podocytes were incubated overnight in the RPMI medium supplemented with 0.1% FBS and stimulation was performed with 5ng/ml of TGF-β in the same medium for a period of 48 hours.

value: Podocytes (Glomerulus cells)

value: Myo1c knockdown

tag: differentiation

value: 14 days


title: Control Knockdown 2

description:
Control KD 2
Scramble Knockdown

value: Control knockdown


title: Control Knockdown 3+TGFβ

description:
Control TGF-3
Scramble Knockdown

value: TGFbeta


title: Control Knockdown 2+TGFβ

description:
Control TGF-2
Scramble Knockdown


title: Myo1c Knockdown 3

description: Myo1c KD 3


title: Myo1c Knockdown 1+TGFβ

description: Myo1c TGF-1


title: Control Knockdown 1+TGFβ

description:
Control TGF-1
Scramble Knockdown


title: Control Knockdown 1

description:
Control KD 1
Scramble Knockdown


title: WT Riboseq rep2

source_name: WT Riboseq

value: WT


title: Myo1c Knockdown 2+TGFβ

description: Myo1c TGF-2


title: Myo1c Knockdown 2

description: Myo1c KD 2


title: Control Knockdown 3

description:
Control KD 3
Scramble Knockdown


title: WT Riboseq rep1


title: OE Riboseq rep2


title: OE Ago2 eCLIP-seq input rep2

data_processing:
library strategy: eCLIP-seq
Adaptors in single-end sequencing reads were trimmed by using the cutadapt program with parameters ‘-m16 -e 0.2’ plus ‘-a AGATCGGAAGAGCACACGTCTGAACTC’ for eCLIP-seq and ‘-a ATCTCGTATGCCGTCTTCTGCTTGAAA’ for Ribo-seq data, respectively. Gene annotation from human refGene (hg19) was downloaded from UCSC genome browser for mapping. The ensemble of mRNA sequences named as hmg was constructed by joining mRNA sequences (with 1kb N) of coding genes, and the longest isoform was chosen as the representative isoform for each transcript. The first random 6nt of eCLIP-seq reads were used to remove PCR products, and only those equal to or longer than 16 nt were mapped to hmg by using Bowtie2 in the end-to-end model. The first 4nt barcode sequence from Ribo-seq and RNA-seq reads was removed before mapping to hmg by using STAR. For each group of mapped reads with same genomic position and same barcode, only one is retained to avoid PCR products. For each replicate group of eCLIP-seq libraries, peak calling was performed by using CLIPper on combined reads from WT and OE miR-17/20a samples. The Ago2 peaks were filtered on the relative enrichment of Ago2 CLIP reads counts over those in input control samples. The reads counts of peaks were computed by using featureCounts program and the enrichment was calculated with edgeR package. The peaks corresponding to miR17/20a were computed in a similar manner by comparing eCLIP under miR-17/20a OE over WT.
Genome_build: hg19. Gene annotation from human refGene (hg19) was downloaded from UCSC genome browser. The ensemble of mRNA sequences, named as hmg, was constructed by joining mRNA sequences (with 1kb N) of coding genes, and the longest isoform was chosen as the representative isoform for each transcript.
Supplementary_files_format_and_content: bigWig for normalized coverage signals in forward strand of hmg

source_name: OE Ago2 eCLIP-seq input


title: WT Riboseq rep3


title: OE Ago2 eCLIP-seq rep2

source_name: OE Ago2 eCLIP-seq

tag: antibody


title: OE Ago2 eCLIP-seq input rep1

tag: cell type


title: WT Ago2 eCLIP-seq input rep1

source_name: WT Ago2 eCLIP-seq input


title: WT Ago2 eCLIP-seq input rep2


title: OE Ago2 eCLIP-seq rep1


title: WT Ago2 eCLIP-seq rep2

source_name: WT Ago2 eCLIP-seq


title: WT Ago2 eCLIP-seq rep1


title: dnr164_non-stimulated_p1

source_name: freshly isolated plasmacytoid dendritic cell

value: plasmacytoid dendritic cells

value: non-stimulated

tag: source

value: blood, dnr164

tag: isolation method

value: density gradient isolation, AKC buffer lysis, FACS isolation based on LIN1- and CD304+ selection


title: WD-37323

city: Duarte

first: Xiwei

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
reads were aligned to hg19 genome assembly using Tophat2 with default  settings
gene expression levels of Refseq genes were counted with customized R scripts
The expression data were normalized using the trimmed mean of M values (TMM) method,  implemented in the Bioconductor package “edgeR” to obtain counts per million (CPM) and then   scaled by gene length in kb
the data was log2 transformed with offset of 1
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file

source_name: Skin Biopsy of normal tissue

extract_protocol:
Total RNA from formalin-fixed paraffin-embedded (FFPE) skin from healthy controls and CTCL  patients was extracted with miRNAeasy FFPE kit (Quiagen). Total RNA was rRNA-depleted with the Ribo-Zero low input kit for Human/Mouse/Rat (Illumina, San Diego, USA) using 300ng of starting material.
RNAseq libraries were prepared from Ribo-Zero mRNA-enriched material using KAPA Stranded RNA-Seq Library Preparation Kit (Illumina Platforms) (Kapa Biosystems, Wilmington, USA) and 10 cycles of PCR amplification.

tag: disease state

value: normal

value: skin

tag: tumor stage

value: Normal


title: WD-37322


title: WD-37320


title: S15.13213.A2

source_name: Skin Biopsy of tumor/Plaque/Patch

value: Cutaneous T-cell lymphoma


title: S15.11353.A2

value: IB


title: S15.6546.A1

value: IA


title: S15.8957.A1


title: S15.8104.C


title: S15.13213.B1


title: S15.5029.B

value: IIB


title: S16.1596.A1


title: S15.1874.A


title: S15.12439.


title: S15.5743.B


title: S16.1854.A2


title: S15.11600.A1


title: S15.12438.B1


title: S15.9737.B1


title: S15.11076.B1


title: S15.11580.A1


title: S15.9737.A1


title: S15.7535.B


title: S15.5741.A6


title: S15.5743.A


title: S15.4787.A1


title: S15.4786.A1


title: S15.11353.B1


title: S15.4306.A1


title: S15.4629.A1


title: S15.11601.A2


title: S15.10296.


title: S15.7247.B1


title: S15.6746.B


title: S15.4554.A1


title: S15.9248.A1

value: IIA


title: S15.3475.A1


title: S15.11356.A1


title: S15.5029.A


title: S15.6993.A1


title: S15.5506.A


title: S15.4303.A1


title: S15.5509.


title: S15.5295.B1


title: S15.6955.A


title: S15.7535.A


title: S15.6736.A1


title: S15.10848.A


title: S15.8147.A1


title: S15.11632.A2


title: U2932.8h.DMSO.3

value: DMSO


title: R1881 rep4

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve Uni

data_processing:
Sequences were mapped back to human genome using TopHat (v2.0.9) (Trapnell et al., 2012 Nat Protoc 2012;7:562-578).
Aligned reads were then processed by Cufflinks (v2.1.1) to assemble expressed genes and transcripts against the UCSC hg19 gene structure annotation and to estimate expression levels for each transcript.
Assembly files for each of the samples were then merged to create a single transcriptome annotation and differentially expressed genes identified by Cuffdiff. Samples were then normalized and expressed as FPKM and both a test statistic (P-value) and an adjusted P-value (q-value) were calculated.
FPKM values were subject to principle component analysis.
Biological processes associated with differentially expressed genes were identified using DAVID.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample ...

source_name: Epididymis

growth_protocol: Human epididymis tissue was obtained with Institutional Review Board approval from patients undergoing inguinal radical orchiectomy for a clinical diagnosis of testicular cancer.  None of the epididymides had extension of the testicular cancer. Adult human epididymis epithelial (HEE) cells (caput) were established as described previously, and grown in CMRL 1066 medium (containing 15% fetal calf serum. 2 mM L-glutamine, 1 μg/mL hydrocortisone, 0.2 U/mL insulin, and 10-10 M cholera toxin (CT)).

extract_protocol:
Confluent adult Caput HEE cells were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -80oC under ethanol. 1ug RNA was used for RNA-seq library preparation.
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 (Low-Throughput protocol, Illumina).

treatment_protocol: For experiments on androgen receptor (AR)-mediated pathways, cultures were grown in phenol red-free CMRL 1066 medium containing 15% charcoal stripped FCS without the other supplements described above for at least three days prior to treatment with 1 nM methyltrienolone (R1881; PerkinElmer NLP0050) for 12-16 hrs.

value: Primary human epididymis cells


title: Nalm6_Runx1_rep1

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

country: France

institute: University Rennes 1

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the reference human genome version GRCh37 (hg19)
The .sam files were converted to .bam files using SAMtools
The .bam files were then processed to yield .wig files using MACS
Genome_build: hg19
Supplementary_files_format_and_content: wig files

source_name: Pre-B lymphoblast cells

growth_protocol: Nalm6 cells were maintained in RPMI 1640 medium (Gibco, Thermo Fisher Scientific) containing 10% heat-inactivated fetal calf serum (FCS) (Eurobio) supplemented with antibiotics (100 U/mL penicillin-G and 100 U/mL streptomycin, Gibco).For pre-B acute lymphoblastic leukemia (BCP-ALL) patient cells, vital mononuclear cells were isolated from bone marrow by successive centrifugations through lymphocytes separation medium (Eurobio).

extract_protocol:
Cells were fixed in 1% formaldehyde (648336, Polysciences) at room temperature for 10 min and then quenched in 100 mM glycine for 1 min.  Cells were washed twice in PBS and lysed 15 min in 50 mM Tris-HCl ph8.1/10 mM EDTA/0.5% Empigen BB/1% SDS. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were generated using TruSeq® ChIP Library Preparation Kit (Illumina) according to the manufacturer’s protocol.

value: Pre-B lymphoblast cells

value: Peripheral blood

tag: chip antibody

value: RUNX1 (ab23980, Abcam)


title: Nalm6_input_rep1


title: R1881 rep3


title: S15.11632.B2


title: R1881 rep2


title: R1881 rep1


title: S15.5295.A1


title: S15.6746.A


title: RUNX1_R1881_rep2

data_processing:
Fastq files were aligned to the hg19 version of the human genome using Bowtie (v 1.0.0) with a seed length of 40 and a maximum number of 3 mismatches allowed in the seed. Only unique reads were used.
Using Homer (v 1.2) software, tag directories were created using the makeTagDirectory command with default settings.
Using Homer (v 1.2) peaks were called using the findPeaks command with an FDR of .1%, factor style, input tag directory as the control library, and all other settings as default.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files

extract_protocol:
Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protese Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with the AR antibody.
DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPsureXP beads. Sequencing was preformed on an Illumina Hi-Seq.

value: RUNX1 (Abcam  ab23980)


title: AR_R1881_rep2

value: AR (Santa Cruz Biotechnology sc-815x)


title: VC rep1


title: VC rep3


title: VC rep2


title: CEBPB_R1881_rep1

value: CEBPB (Santa Cruz Biotechnology sc-150x)


title: CEBPB_VC_rep2


title: RUNX1_VC_rep2


title: RUNX1_R1881_rep1


title: AR_VC_rep1


title: CEBPB_R1881_rep2


title: CEBPB_VC_rep1


title: AR_VC_rep2


title: AR_R1881_rep1


title: input_DNA


title: RUNX1_VC_rep1


title: VC rep4


title: MWK3

city: Pittsburgh

first: Andrew

middle: Scott

last: Clugston

state: PA

address: 872 Mirror Street

department: Integrative Systems Biology

institute: University of Pittsburgh

data_processing:
Adapter and read quality trimming was performed with BBDuk from the BBMap software package version 35.59; read quality scores below 30 and all Illumina adapters were trimmed.
Reads were aligned to the mm10 genome using Bowtie2 version 2.2.3, with the parameters -q --sensitive-local.
Bowtie2 alignment SAM files were formatted for use with miRDeep2 using miRDeep2's bwa_sam_converter.pl script.
Known miRNA mature strand, hairpin, and star strand sequences were retrieved from miRBase version 21.
Known miRNA and potential novel miRNA were identified, quantified, and normalized for library depth using miRDeep2 version 2.0.0.8.
Differential expression of miRNA expression between NP and WK samples was measured using DESeq2, version 1.18.1, adjusted p-value threshold 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files containing known and novel normalized read counts, BED files contain potential novel miRNA precursor locations.

source_name: Mouse whole kidney replicate 03

extract_protocol:
Nephron progenitors were isolated from intact whole embryonic kidney samples through limited digestion, followed by magnetic-activated cell sorting negative depletion of CD140a, CD105, Epcam and Ter119 in accordance to a published protocol (PMID: 26190145). Total RNA was extracted and purified using the Qiagen miRNeasy Micro Kit.
Libraries were barcoded and prepared using the NEBNext Multiplex Small RNA Library Prep Kit according to the manufacturer's protocol.

value: Whole kidney

tag: embryonic day

tag: strain

value: Kidney


title: MWK2

source_name: Mouse whole kidney replicate 02

tag: tissue


title: MWK1

source_name: Mouse whole kidney replicate 01


title: MNP3

source_name: Mouse nephron progenitor replicate 03

value: Nephron progenitor


title: MNP2

source_name: Mouse nephron progenitor replicate 02


title: MNP1

source_name: Mouse nephron progenitor replicate 01


title: Mid gestation placenta 4

city: Newcastle

first: Kirsty

middle: G

last: Pringle

state: NSW

address: 1 Kookaburra Circuit

department: HMRI

institute: University of Newcastle

hyb_protocol: Samples were hybridised to arrays for 20 hours at 55C rotating at 20 rpm.

scan_protocol: Slides were scanned using the AgilentG3_miRNA  scanner protocol for G3 format.

data_processing: Data was extracted using Feature Extraction Software – FE protocol miRNA_QCMT_Jan09

source_name: Greater than 12 weeks

label_protocol: 100 ng RNA  was labelled using the miRNA Microarray System with miRNA Complete Labeling and Hyb kit Protocol Version 3.0.

extract_protocol: Placental tissue was collected from each placenta from four random sampling sites on the villous aspect. Placentas were then snap frozen in liquid nitrogen, homogenized and pooled to provide a sample of the entire placenta. Placentae obtained prior to 18 weeks gestation were identified based on their villous structure. The entire placenta was frozen and subsequently homogenized for total RNA extraction with a miRNeasy kit.

tag: gender

value: female

value: Mid gestation placenta


title: Preeclamptic placenta 3

source_name: PE

value: Preeclamptic placenta


title: Early gestation placenta 4

source_name: less than 12 weeks

value: Early gestation placenta


title: Term placenta 4

source_name: Term

value: Term placenta


title: Term placenta 3


title: Mid gestation placenta 3


title: Preterm placenta 3

source_name: Preterm

value: Preterm placenta


title: Preterm placenta 4


title: Early gestation placenta 3


title: Mid gestation placenta 2


title: Eutopic_siCII, biological rep1

city: Tainan

first: Shaw-Jenq

last: Tsai

address: 1 , University Road

department: Department of Physiology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

hyb_protocol: cRNA were hybridized for 16hrs on Affymetrix human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics protocol FS450_0001.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol by GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method by the Affymetrix GeneChip Operating Software(GCOS).

source_name: eutopic stromal cell_siRNA oligo against COUP-TFII

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: primary eutopic stromal cells from endometriosis patients  grown on DMEM/F12 with 10%FBS medium

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: transient siCOUP-TFII knock down or control  for 48 hours in eutopic stroma cell

tag: donor status

value: human endometriosis patient

value: primary eutopic stromal cells

tag: transfected with

value: siRNA oligo against COUP-TFII


title: Eutopic_siCON, biological rep2

source_name: eutopic stromal cell_control siRNA

value: control siRNA oligo


title: Eutopic_siCII, biological rep2


title: Eutopic_siCON, biological rep3


title: 03_a2-T6: CD4 Tcells cultured with TGFb and IL-6

city: Kyoto

first: Hiroyuki

last: Yoshitomi

address: 53, Kawahara-Cho, Shogoin,

country: Japan

institute: Institute for Frontier Life and Medical Sciences, Kyoto University

description: Gene expression data from TGFb and IL-6 treated cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip Scanner 3000 7G

data_processing: The data were analyzed with AGCC using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Peripheral blood CD4 T cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT PLUS Reagent Kit. P/N 703210 Rev. 1).

growth_protocol: Human blood CD4 T cells labeled with CellTrace™ Violet were differentiated in the presence of the indicated cytokines and neutralizing anti-IL-2 antibody for 5 days.

extract_protocol: Total RNA extraction was performed according to the manufacturer's instructions of RNeasy mini plus.

treatment_protocol: Cells with more than one division were sorted.

value: Peripheral blood CD4 T cells

value: lymphyocytes


title: Eutopic_siCII, biological rep3


title: 02_a2-T1: CD4 Tcells cultured with TGFb and IL-1b

description: Gene expression data from TGFb and IL-1b treated cells


title: Early gestation placenta 2


title: Preterm placenta 2


title: Preterm preeclamptic placenta 2

source_name: PrePE

value: Preterm preeclamptic placenta


title: Preterm preeclamptic placenta 4


title: 01_a2-12: CD4 Tcells cultured with IL-12

description: Gene expression data from IL-12 treated cells


title: Preeclamptic placenta 4


title: Preeclamptic placenta 2


title: Term placenta 2


title: Preterm preeclamptic placenta 3


title: Preterm placenta 1


title: Preterm preeclamptic placenta 1


title: Preeclamptic placenta 1


title: Term placenta 1


title: Myo1c Knockdown 3+TGFβ

description: Myo1c TGF-3

source_name: Immortalized Human Podocytes Cell Lines

value: Podocytes (Glomerulus cells)

value: Myo1c knockdown

value: 14 days

tag: treatment

value: TGFbeta


title: Eutopic_siCON, biological rep1


title: Early gestation placenta 1

value: female


title: Rag_cKit-_012317_C71_1

city: Worcester

first: Nicholas

last: Spidale

state: MA

address: 368 Plantation St.

department: Pathology

institute: University of Massachusetts Medical School

data_processing: Cq values (matrix non-normalized data) are automatically calculated by the Fluidigm Realtime PCR analysis software using the Auto(Detectors) setting, which sets independent baseline and threshold values for each target gene.  Cycle 24 is considered the limit of detection, and any amplification at cycle 24 or later is recorded as 24.  Any target for which the melt curve falls outside of the set optimal paramaters for the target is also recorded as 24.  Matrix normalized data (called Log2Exp by Fluidigm) is calculted as follows:  Log2Exp = 24-Cq.  No fold change analysis is performed.

label: Eva Green

source_name: Thymus

label_protocol: RT was performed using the following reagent mix:  1.94 microliters Stop Solution (Life Technologies) + 5.84 microliters Single Cell VILO RT Mix (Life Technologies) + 3.62 microliters Single Cell SuperScript RT (Life Technologies) + 0.6 microliters Loading Reagent (Fluidigm).  RT thermal cycling protocol:  25 C, 600 s; 42 C, 3600 s; 85 C, 300 s.  Preamplification was performed using the following reagent mix:  12 microliters Single Cell PreAmp Mix (Life Technologies) + 42 microliters C1 PreAmp Dilution Reagent + 6 microliters Pooled qPCR Primers (500 nM).  PreAmp thermal cycling protocol:  95 C, 600 s; [18 cycles of:  95 C, 15 s; 60 C, 240 s]; 4 C, hold.  qPCR was performed using SsoFast EvaGreen Supermix (Bio-Rad) and assay-specific primer pairs.  qPCR thermal cycling protocol:  95 C, 60 s; [30 cycles of:  96 C, 5 s; 60 C, 20 s (read)]; 60-95 C, ramp 1 C/3 s (melt curve analysis).

extract_protocol: Cells are lysed using the following mixture as advised by the manufacturer:  12.75 microliters Single Cell Lysis Solution (Life Technologies Single Cell-to-CT Kit) + 4.35 microliters C1 Lysis Plus Reagent (Fluidigm) + 0.9 microliters C1 DNA Dilution Reagent (Fluidigm)

tag: markers

tag: strain/genotype

value: Thymus

tag: developmental stage


title: Rag_cKit-_012317_C72_1


title: Rag_cKit-_012317_C73_1


title: Rag_cKit-_012317_C77_1


title: Rag_cKit-_012317_C82_1


title: Rag_cKit-_012317_C81_1


title: Rag_cKit-_012317_C80_1


title: Rag_cKit-_012317_C83_1


title: Rag_cKit-_012317_C74_1


title: Rag_cKit-_012317_C76_1


title: Rag_cKit-_012317_C84_1


title: Mid gestation placenta 1

value: Mid gestation placenta


title: Rag_cKit-_012317_C70_1


title: Rag_cKit-_012317_C60_1


title: Rag_cKit-_012317_C61_1


title: Rag_cKit-_012317_C68_1


title: Rag_cKit-_012317_C58_1


title: Rag_cKit-_012317_C62_1


title: Rag_cKit-_012317_C63_1


title: Rag_cKit-_012317_C67_1


title: Rag_cKit-_012317_C57_1


title: Rag_cKit-_012317_C65_1


title: Rag_cKit-_012317_C64_1


title: Rag_cKit-_012317_C79_1


title: Rag_cKit-_012317_C55_1


title: Rag_cKit-_012317_C54_1


title: Rag_cKit-_012317_C53_1


title: Rag_cKit-_012317_C52_1


title: Rag_cKit-_012317_C56_1


title: Rag_cKit-_012317_C50_1


title: Rag_cKit-_012317_C51_1


title: Rag_cKit-_012317_C44_1


title: Rag_cKit-_012317_C38_1


title: Rag_cKit-_012317_C43_1


title: Rag_cKit-_012317_C41_1


title: Rag_cKit-_012317_C47_1


title: Rag_cKit-_012317_C36_1


title: Rag_cKit-_012317_C46_1


title: Rag_cKit-_012317_C37_1


title: Rag_cKit-_012317_C45_1


title: Rag_cKit-_012317_C35_1


title: Rag_cKit-_012317_C42_1


title: Rag_cKit-_012317_C49_1


title: Rag_cKit-_012317_C40_1


title: Rag_cKit-_012317_C39_1


title: Rag_cKit-_012317_C48_1


title: Rag_cKit-_012317_C34_1


title: Rag_cKit-_012317_C33_1


title: Rag_cKit-_012317_C32_1


title: Rag_cKit-_012317_C27_1


title: Rag_cKit-_012317_C30_1


title: Rag_cKit-_012317_C28_1


title: Rag_cKit-_012317_C31_1


title: Rag_cKit-_012317_C29_1


title: Rag_cKit-_012317_C25_1


title: Rag_cKit-_012317_C26_1


title: Rag_cKit-_012317_C24_1


title: Rag_cKit-_012317_C23_1


title: Rag_cKit-_012317_C22_1


title: Rag_cKit-_012317_C21_1


title: Rag_cKit-_012317_C19_1


title: Rag_cKit-_012317_C18_1


title: Rag_cKit-_012317_C05_1


title: Rag_cKit-_012317_C06_1


title: Rag_cKit-_012317_C03_1


title: Rag_cKit-_012317_C09_1


title: Rag_cKit-_012317_C11_1


title: Rag_cKit-_012317_C01_1


title: Rag_cKit-_012317_C04_1


title: Rag_cKit-_012317_C08_1


title: Rag_cKit-_012317_C15_1


title: Rag_cKit-_012317_C02_1


title: Rag_cKit-_012317_C13_1


title: B6_DN2_092216_C94_1


title: Rag_cKit-_012317_C10_1


title: B6_DN2_092216_C96_1


title: B6_DN2_092216_C95_1


title: B6_DN2_092216_C92_1


title: B6_DN2_092216_C93_1


title: B6_DN2_092216_C89_1


title: B6_DN2_092216_C91_1


title: Rag_cKit-_012317_C16_1


title: Rag_cKit-_012317_C17_1


title: B6_DN2_092216_C88_1


title: Rag_cKit-_012317_C07_1


title: Rag_cKit-_012317_C12_1


title: B6_DN2_092216_C87_1


title: B6_DN2_092216_C86_1


title: B6_DN2_092216_C84_1


title: B6_DN2_092216_C90_1


title: B6_DN2_092216_C71_1


title: B6_DN2_092216_C72_1


title: B6_DN2_092216_C85_1


title: B6_DN2_092216_C70_1


title: B6_DN2_092216_C76_1


title: B6_DN2_092216_C78_1


title: B6_DN2_092216_C75_1


title: B6_DN2_092216_C68_1


title: B6_DN2_092216_C81_1


title: B6_DN2_092216_C80_1


title: B6_DN2_092216_C69_1


title: B6_DN2_092216_C79_1


title: B6_DN2_092216_C67_1


title: B6_DN2_092216_C73_1


title: B6_DN2_092216_C63_1


title: B6_DN2_092216_C66_1


title: B6_DN2_092216_C65_1


title: B6_DN2_092216_C62_1


title: B6_DN2_092216_C61_1


title: B6_DN2_092216_C59_1


title: B6_DN2_092216_C60_1


title: B6_DN2_092216_C57_1


title: B6_DN2_092216_C56_1


title: B6_DN2_092216_C55_1


title: B6_DN2_092216_C53_1


title: B6_DN2_092216_C52_1


title: B6_DN2_092216_C49_1


title: B6_DN2_092216_C50_1


title: B6_DN2_092216_C48_1


title: B6_DN2_092216_C44_1


title: B6_DN2_092216_C37_1


title: B6_DN2_092216_C47_1


title: B6_DN2_092216_C45_1


title: B6_DN2_092216_C38_1


title: B6_DN2_092216_C41_1


title: B6_DN2_092216_C42_1


title: B6_DN2_092216_C33_1


title: B6_DN2_092216_C32_1


title: B6_DN2_092216_C43_1


title: B6_DN2_092216_C35_1


title: B6_DN2_092216_C46_1


title: B6_DN2_092216_C34_1


title: B6_DN2_092216_C29_1


title: B6_DN2_092216_C27_1


title: B6_DN2_092216_C22_1


title: B6_DN2_092216_C23_1


title: B6_DN2_092216_C24_1


title: B6_DN2_092216_C25_1


title: B6_DN2_092216_C21_1


title: Rag_cKit-_012317_C78_1


title: B6_DN2_092216_C20_1


title: B6_DN2_092216_C19_1


title: B6_DN2_092216_C17_1


title: B6_DN2_092216_C18_1


title: B6_DN2_092216_C16_1


title: B6_DN2_092216_C28_1


title: B6_DN2_092216_C30_1


title: B6_DN2_092216_C26_1


title: B6_DN2_092216_C15_1


title: B6_DN2_092216_C14_1


title: B6_DN2_092216_C13_1


title: B6_DN2_092216_C09_1


title: B6_DN2_092216_C11_1


title: B6_DN2_092216_C01_1


title: B6_DN1d_082316_C92_1


title: B6_DN1d_082316_C90_1


title: B6_DN1d_082316_C87_1


title: B6_DN1d_082316_C91_1


title: B6_DN2_092216_C08_1


title: B6_DN1d_082316_C86_1


title: B6_DN2_092216_C05_1


title: B6_DN2_092216_C04_1


title: B6_DN1d_082316_C85_1


title: B6_DN1d_082316_C83_1


title: B6_DN1d_082316_C79_1


title: B6_DN1d_082316_C82_1


title: B6_DN1d_082316_C77_1


title: B6_DN1d_082316_C81_1


title: B6_DN1d_082316_C74_1


title: B6_DN1d_082316_C96_1


title: B6_DN1d_082316_C95_1


title: B6_DN1d_082316_C73_1


title: B6_DN1d_082316_C70_1


title: B6_DN1d_082316_C71_1


title: B6_DN1d_082316_C69_1


title: B6_DN1d_082316_C72_1


title: B6_DN1d_082316_C67_1


title: B6_DN1d_082316_C65_1


title: B6_DN1d_082316_C63_1


title: B6_DN1d_082316_C62_1


title: B6_DN1d_082316_C64_1


title: B6_DN1d_082316_C84_1


title: B6_DN1d_082316_C61_1


title: B6_DN1d_082316_C60_1


title: B6_DN1d_082316_C58_1


title: B6_DN1d_082316_C59_1


title: B6_DN1d_082316_C57_1


title: B6_DN1d_082316_C52_1


title: B6_DN1d_082316_C53_1


title: B6_DN1d_082316_C55_1


title: B6_DN1d_082316_C54_1


title: B6_DN1d_082316_C51_1


title: B6_DN1d_082316_C49_1


title: B6_DN1d_082316_C50_1


title: B6_DN1d_082316_C48_1


title: B6_DN1d_082316_C47_1


title: B6_DN1d_082316_C46_1


title: B6_DN1d_082316_C45_1


title: B6_DN1d_082316_C37_1


title: B6_DN1d_082316_C44_1


title: B6_DN1d_082316_C42_1


title: B6_DN1d_082316_C43_1


title: B6_DN1d_082316_C40_1


title: B6_DN1d_082316_C35_1


title: B6_DN1d_082316_C41_1


title: B6_DN1d_082316_C38_1


title: B6_DN1d_082316_C31_1


title: B6_DN1d_082316_C34_1


title: B6_DN1d_082316_C56_1


title: B6_DN1d_082316_C30_1


title: B6_DN1d_082316_C29_1


title: B6_DN1d_082316_C33_1


title: B6_DN1d_082316_C32_1


title: B6_DN1d_082316_C26_1


title: B6_DN1d_082316_C28_1


title: B6_DN1d_082316_C18_1


title: B6_DN1d_082316_C20_1


title: B6_DN1d_082316_C21_1


title: B6_DN1d_082316_C22_1


title: B6_DN1d_082316_C19_1


title: B6_DN1d_082316_C16_1


title: B6_DN1d_082316_C17_1


title: B6_DN1d_082316_C23_1


title: B6_DN1d_082316_C13_1


title: B6_DN1d_082316_C14_1


title: B6_DN1d_082316_C09_1


title: B6_DN1d_082316_C08_1


title: B6_DN1d_082316_C11_1


title: B6_DN1d_082316_C10_1


title: B6_DN1d_082316_C07_1


title: B6_DN1d_082316_C04_1


title: B6_DN1d_082316_C25_1


title: B6_DN1d_082316_C27_1


title: B6_DN1d_082316_C05_1


title: B6_DN1d_082316_C24_1


title: B6_DN1d_082316_C01_1


title: B6_DN1d_082316_C02_1


title: B6_DN1d_092916_C95_1


title: B6_DN1d_092916_C96_1


title: B6_DN1d_092916_C93_1


title: B6_DN1d_092916_C91_1


title: B6_DN1d_092916_C88_1


title: B6_DN1d_092916_C89_1


title: B6_DN1d_092916_C86_1


title: B6_DN1d_092916_C85_1


title: B6_DN1d_092916_C84_1


title: B6_DN1d_082316_C12_1


title: B6_DN1d_092916_C82_1


title: B6_DN1d_092916_C83_1


title: B6_DN1d_092916_C79_1


title: B6_DN1d_092916_C94_1


title: B6_DN1d_092916_C80_1


title: B6_DN1d_092916_C73_1


title: B6_DN1d_092916_C77_1


title: B6_DN1d_092916_C67_1


title: B6_DN1d_092916_C74_1


title: B6_DN1d_092916_C70_1


title: B6_DN1d_092916_C66_1


title: B6_DN1d_092916_C90_1


title: B6_DN1d_092916_C92_1


title: B6_DN1d_092916_C60_1


title: B6_DN1d_092916_C64_1


title: B6_DN1d_092916_C62_1


title: B6_DN1d_092916_C58_1


title: B6_DN1d_092916_C59_1


title: B6_DN1d_092916_C65_1


title: B6_DN1d_092916_C71_1


title: B6_DN1d_092916_C81_1


title: B6_DN1d_092916_C55_1


title: B6_DN1d_092916_C54_1


title: B6_DN1d_092916_C52_1


title: B6_DN1d_092916_C53_1


title: B6_DN1d_092916_C50_1


title: B6_DN1d_092916_C49_1


title: B6_DN1d_092916_C48_1


title: B6_DN1d_092916_C45_1


title: B6_DN1d_092916_C76_1


title: B6_DN1d_092916_C47_1


title: B6_DN1d_092916_C41_1


title: B6_DN1d_092916_C43_1


title: B6_DN1d_092916_C44_1


title: B6_DN1d_092916_C57_1


title: B6_DN1d_092916_C37_1


title: B6_DN1d_092916_C36_1


title: B6_DN1d_092916_C28_1


title: B6_DN1d_092916_C27_1


title: B6_DN1d_092916_C33_1


title: B6_DN1d_092916_C34_1


title: B6_DN1d_092916_C24_1


title: B6_DN1d_092916_C21_1


title: B6_DN1d_092916_C23_1


title: B6_DN1d_092916_C30_1


title: B6_DN1d_092916_C25_1


title: B6_DN1d_092916_C18_1


title: B6_DN1d_092916_C20_1


title: B6_DN1d_092916_C16_1


title: B6_DN1d_092916_C15_1


title: B6_DN1d_092916_C14_1


title: B6_DN1d_092916_C12_1


title: B6_DN1d_092916_C09_1


title: B6_DN1d_092916_C11_1


title: B6_DN1d_092916_C08_1


title: B6_DN1d_092916_C07_1


title: B6_DN1d_092916_C40_1


title: B6_DN1d_092916_C06_1


title: B6_DN1d_092916_C26_1


title: B6_DN1d_092116_C95_1


title: B6_DN1d_092116_C93_1


title: B6_DN1d_092116_C89_1


title: B6_DN1d_092116_C90_1


title: B6_DN1d_092116_C88_1


title: B6_DN1d_092116_C86_1


title: B6_DN1d_092916_C13_1


title: B6_DN1d_092116_C84_1


title: B6_DN1d_092116_C85_1


title: B6_DN1d_092116_C79_1


title: B6_DN1d_092116_C78_1


title: B6_DN1d_092116_C74_1


title: B6_DN1d_092116_C81_1


title: B6_DN1d_092116_C80_1


title: B6_DN1d_092116_C75_1


title: B6_DN1d_092116_C77_1


title: B6_DN1d_092116_C76_1


title: B6_DN1d_092116_C72_1


title: B6_DN1d_092116_C73_1


title: B6_DN1d_092916_C02_1


title: B6_DN1d_092116_C70_1


title: B6_DN1d_092116_C69_1


title: B6_DN1d_092116_C68_1


title: B6_DN1d_092116_C65_1


title: B6_DN1d_092116_C66_1


title: B6_DN1d_092116_C62_1


title: B6_DN1d_092116_C60_1


title: B6_DN1d_092116_C63_1


title: B6_DN1d_092116_C59_1


title: B6_DN1d_092116_C57_1


title: B6_DN1d_092116_C55_1


title: B6_DN1d_092116_C71_1


title: B6_DN1d_092116_C49_1


title: B6_DN1d_092116_C46_1


title: B6_DN1d_092116_C47_1


title: B6_DN1d_092116_C67_1


title: B6_DN1d_092116_C45_1


title: B6_DN1d_092116_C43_1


title: B6_DN1d_092116_C44_1


title: B6_DN1d_092116_C42_1


title: B6_DN1d_092116_C39_1


title: B6_DN1d_092116_C36_1


title: B6_DN1d_092116_C37_1


title: B6_DN1d_092116_C40_1


title: B6_DN1d_092116_C38_1


title: B6_DN1d_092116_C30_1


title: B6_DN1d_092116_C34_1


title: B6_DN1d_092116_C33_1


title: B6_DN1d_092116_C41_1


title: B6_DN1d_092116_C31_1


title: B6_DN1d_092116_C26_1


title: B6_DN1d_092116_C27_1


title: B6_DN1d_092116_C54_1


title: B6_DN1d_092116_C29_1


title: B6_DN1d_092116_C28_1


title: B6_DN1d_092116_C23_1


title: B6_DN1d_092116_C24_1


title: B6_DN1d_092116_C25_1


title: B6_DN1d_092116_C22_1


title: B6_DN1d_092116_C21_1


title: B6_DN1d_092116_C18_1


title: B6_DN1d_092116_C16_1


title: B6_DN1d_092116_C14_1


title: B6_DN1d_092116_C13_1


title: B6_DN1d_092116_C10_1


title: B6_DN1d_092116_C08_1


title: B6_DN1d_092116_C07_1


title: B6_DN1d_092116_C12_1


title: B6_DN1d_092116_C03_1


title: B6_DN1d_092116_C04_1


title: B6_DN1d_092116_C02_1


title: B6_DN1d_092116_C06_1


title: B6_DN1d_092116_C01_1


title: B6_DN1d_092116_C05_1


title: CIT

city: Zhenjiang

first: Xiangfeng

last: Zheng

state: Jiangsu

address: 301, Xuefu Road

department: Food school

institute: Jiangsu university

data_processing:
Trinity was used for de novo transcriptome assembly.
Cufflinks was used for expression quantification.
Genome_build: The file Unigenes.cds_pep.stat.txt is available on the series record and contains transcript and peptide sequence.
Supplementary_files_format_and_content: text file with log2 CIT(FPKM)/CK(FPKM), FDR and gene annotation information.

organism: Saitozyma podzolica

source_name: Yeast cell

growth_protocol: Cryptococcus podzolicus Y3  was inoculated in NYDB medium, an was incubated at 28℃， 180 rpm. For 24 h.

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

treatment_protocol: The sample  of CK is the control which no treatment with citrinin, sample CIT was treated with 20mg/mL citrinin

value: C. podzolicus Y3 (CK) in  NYDB containing 20 mg/L citrinin (CIT)

tag: treatment duration


title: Tcrd_DN1d_020617_C94_1


title: Tcrd_DN1d_020617_C95_1


title: Tcrd_DN1d_020617_C90_1


title: Tcrd_DN1d_020617_C91_1


title: Tcrd_DN1d_020617_C93_1


title: Tcrd_DN1d_020617_C87_1


title: Tcrd_DN1d_020617_C83_1


title: Tcrd_DN1d_020617_C82_1


title: Tcrd_DN1d_020617_C79_1


title: Tcrd_DN1d_020617_C81_1


title: Tcrd_DN1d_020617_C78_1


title: CRC26_E

city: Hamburg

first: Simon

middle: A

last: Joosse

address: Martinistrasse 52

department: Institute of Tumor Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: hybridized to Illumina Human 610-quad bead-chip, containing 610,000 probes covering the whole genome

scan_protocol: Spot intensities were measured using the Illumina Bead Array Reader

data_processing:
Log transformed intensity measurements were processed by circular binary segmentation (CBS) algorithm (Matlab R2015a, The MathWorks) to identify chromosomal aberrations
Calling of copy number levels was performed as described in Joosse et al (2009, 2012)

label: C-Bio and A-DNP

source_name: Colorectal cancer

label_protocol: processed according to manufacturer's protocol (Infinium Assay, Illumina)

extract_protocol: 10 tissue sections of 10 μm were cut, scraped, and processed according to manufacturers’ protocol (DNA mini kit, QIAgen cat.no. 51304).

tag: group

value: colorectal cancer

value: E

tag: tnm

tag: metastasis

value: Liver, Lung, Bone


title: CRC36_E

value: Liver, Lung


title: CK

value: Cryptococcus podzolicus Y3 cell cultured  in NYDB medium


title: CRC08_E

value: Lung


title: Tcrd_DN1d_020617_C77_1


title: CRC69_D

value: D


title: Tcrd_DN1d_020617_C86_1


title: Tcrd_DN1d_020617_C89_1


title: CRC62_D


title: Tcrd_DN1d_020617_C85_1


title: CRC63_D

value: Liver


title: CRC70_D


title: Tcrd_DN1d_020617_C75_1


title: CRC61_D


title: Tcrd_DN1d_020617_C74_1


title: Tcrd_DN1d_020617_C76_1


title: Tcrd_DN1d_020617_C73_1


title: Tcrd_DN1d_020617_C80_1


title: Tcrd_DN1d_020617_C70_1


title: CRC60_D


title: CRC58_D


title: Tcrd_DN1d_020617_C72_1


title: CRC57_D


title: Tcrd_DN1d_020617_C69_1


title: CRC52_D


title: CRC50_D


title: CRC48_D


title: Tcrd_DN1d_020617_C68_1


title: Tcrd_DN1d_020617_C67_1


title: Tcrd_DN1d_020617_C65_1


title: CRC72_D


title: Tcrd_DN1d_020617_C64_1


title: Tcrd_DN1d_020617_C63_1


title: CRC45_D


title: CRC42_D


title: Tcrd_DN1d_020617_C62_1


title: CRC37_D


title: CRC35_D


title: CRC41_D


title: CRC32_D


title: CRC28_D


title: CRC20_D


title: CRC18_D


title: Tcrd_DN1d_020617_C60_1


title: CRC27_D


title: Tcrd_DN1d_020617_C61_1


title: Tcrd_DN1d_020617_C57_1


title: Tcrd_DN1d_020617_C58_1


title: CRC29_D


title: CRC04_D


title: Tcrd_DN1d_020617_C59_1


title: CRC44_C

value: C


title: CRC01_D


title: Tcrd_DN1d_020617_C56_1


title: Tcrd_DN1d_020617_C54_1


title: Tcrd_DN1d_020617_C55_1


title: Tcrd_DN1d_020617_C53_1


title: CRC19_C


title: Tcrd_DN1d_020617_C50_1


title: Tcrd_DN1d_020617_C49_1


title: Tcrd_DN1d_020617_C51_1


title: CRC65_B

value: B


title: CRC54_B


title: CRC51_B


title: Tcrd_DN1d_020617_C48_1


title: SB2b xenograft

first: Brett

middle: William

last: Stringer

address: 300 Herston Road

institute: QIMR Berghofer Medical Research Institute

description: single sample

hyb_protocol: Microarray hybridisation and Cy3-streptavidin labelling was performed using standard Illumina protocols.

scan_protocol: Standard Illumina scanning protocol for iScan.

data_processing: Quantile normalisation with background subtraction using GenomeStudio software (illumina).

source_name: Human glioblastoma

label_protocol: Biotinylated cRNA was prepared with TotalPrep RNA amplification kits (Ambion).

growth_protocol: Cell lines were grown as adherent cultures in matrigel-coated flasks in RHB-A stem cell culture medium (StemCells Inc) supplemented with 20 ng/ml EGF (Gibco) and 10 ng/ml FGFb (Gibco) and containing 100 U/ml penicillin and 100 mg/ml streptomycin. Cells were cultured in 5 % CO2 / 95 % humidified air at 37°C. All cell lines were routinely tested for mycoplasma and confirmed to be mycoplasma-free. Xenografts were initiated with 150,000 cells injected incranially (3 mm below the brain surface, 1.6 mm rostral of the bregma and 0.8 mm right of the midline) into 5 week old NOD/SCID mice housed in pathogen-free conditions.

extract_protocol: RNA was extracted using RNeasy kits. DNA was removed by on-column DNase I digestion. Standard Qiagen protocols were followed.

treatment_protocol: RNA was extracted from fresh or snap frozen tissue.

tag: tumour

value: Recurrent GBM

tag: patient age (years)

tag: patient gender

value: Male

tag: tumour site

value: Right parietal


title: WK1 xenograft

description: single sample

value: Primary GBM

value: Right parietal occipital


title: Tcrd_DN1d_020617_C47_1

tag: strain

value: Thymus


title: CRC38_B


title: SJH1 xenograft

description: single sample

value: Left temporal


title: CRC25_B

value: colorectal cancer


title: RKI1 xenograft

description: single sample

value: Female


title: RN1 xenograft

description: single sample


title: CRC16_B


title: Tcrd_DN1d_020617_C45_1

tag: tissue


title: CRC14_B


title: Tcrd_DN1d_020617_C44_1


title: Tcrd_DN1d_020617_C46_1


title: Tcrd_DN1d_020617_C42_1


title: CRC09_B


title: CRC15_C


title: Tcrd_DN1d_020617_C41_1


title: PB1 xenograft

description: single sample

value: Left frontal


title: MN1 xenograft

description: single sample


title: HW1 xenograft

description: single sample

value: Right frontal parietal


title: JK2 xenograft

description: single sample

value: Right frontal


title: Tcrd_DN1d_020617_C43_1


title: WK1 tumour tissue

description: single sample


title: FPW1 xenograft

description: single sample

value: Right temporal


title: CRC43_A

value: A


title: MMK1 xenograft

description: single sample


title: CRC39_A


title: CRC59_A


title: CRC34_A


title: Tcrd_DN1d_020617_C38_1


title: Tcrd_DN1d_020617_C37_1


title: CRC31_A


title: CRC23_A


title: CRC24_A


title: Tcrd_DN1d_020617_C35_1


title: Tcrd_DN1d_020617_C36_1


title: Tcrd_DN1d_020617_C34_1


title: Tcrd_DN1d_020617_C39_1


title: Tcrd_DN1d_020617_C33_1


title: Tcrd_DN1d_020617_C32_1


title: Tcrd_DN1d_020617_C31_1


title: BAH1 xenograft

description: single sample


title: CRC21_A


title: CRC22_A


title: RN1 tumour tissue

description: single sample


title: CRC13_A


title: Tcrd_DN1d_020617_C30_1


title: PB1 tumour tissue

description: single sample


title: MN1 tumour tissue

description: single sample


title: Tcrd_DN1d_020617_C29_1


title: CRC11_A


title: SJH1 tumour tissue

description: single sample


title: Tcrd_DN1d_020617_C28_1


title: JK2 tumour tissue

description: single sample


title: CRC03_A


title: SB2b tumour tissue

description: single sample


title: HW1 tumour tissue

description: single sample


title: MMK1 tumour tissue

description: single sample


title: Tcrd_DN1d_020617_C27_1


title: RKI1 tumour tissue

description: single sample


title: Tcrd_DN1d_020617_C25_1


title: FPW1 tumour tissue

description: single sample


title: Tcrd_DN1d_020617_C24_1


title: CRC06_A


title: Tcrd_DN1d_020617_C23_1


title: Tcrd_DN1d_020617_C22_1


title: Tcrd_DN1d_020617_C20_1


title: Tcrd_DN1d_020617_C21_1


title: SJH1 cell line

description: single sample

growth_protocol: Cell lines were grown as adherent cultures in matrigel-coated flasks in RHB-A stem cell culture medium (StemCells Inc) supplemented with 20 ng/ml EGF (Gibco) and 10 ng/ml FGFb (Gibco) and containing 100 U/ml penicillin and 100 mg/ml streptomycin. Cells were cultured in 5 % CO2 / 95 % humidified air at 37°C. All cell lines were routinely tested for mycoplasma and confirmed to be mycoplasma-free.

treatment_protocol: RNA was extracted from fresh cells lysed in situ in culture once growth medium was removed.

tag: cell line


title: BAH1 tumour tissue

description: single sample


title: BS161 FFPE sample

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: BS161 FFPE sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. After eliminating  samples with poor quality data, the raw data were normalized using the cubic spline.  algorithm using the IlluminaDASL pipeline within GenePattern.

source_name: Formalin-fixed paraffin-embedded (FFPE)

extract_protocol: Based on hematoxylin/eosin staining, tumor tissue was macro-dissected from non-tumor liver parenchyma by an expert liver pathologist. Total RNA was isolated from freshly cut FFPE sections using the miRNeasy FFPE kit (Qiagen). The Qiacube system (Qiagen) was used to automatize the extraction process.

value: hepatocellular carcinoma

value: Sor

tag: outcome

value: non-responder


title: BS195 FFPE sample

description: BS195 FFPE sample

value: responder


title: Tcrd_DN1d_020617_C19_1


title: SB2b cell line

description: single sample

value: Recurrent GBM

value: Male


title: WK1 cell line

description: single sample

value: Primary GBM


title: BS149 FFPE sample

description: BS149 FFPE sample


title: BS171 FFPE sample

description: BS171 FFPE sample

value: Plac


title: MN1 cell line

description: single sample


title: RKI1 cell line

description: single sample


title: Tcrd_DN1d_020617_C17_1

value: Thymus


title: MMK1 cell line

description: single sample


title: Tcrd_DN1d_020617_C16_1


title: PB1 cell line

description: single sample


title: BS151 FFPE sample

description: BS151 FFPE sample


title: Tcrd_DN1d_020617_C15_1


title: Tcrd_DN1d_020617_C14_1


title: JK2 cell line

description: single sample


title: BS193 FFPE sample

description: BS193 FFPE sample


title: BS117 FFPE sample

description: BS117 FFPE sample


title: BS123 FFPE sample

description: BS123 FFPE sample


title: HW1 cell line

description: single sample


title: Tcrd_DN1d_020617_C13_1


title: BS107 FFPE sample

description: BS107 FFPE sample


title: BS429 FFPE sample

description: BS429 FFPE sample


title: BAH1 cell line

description: single sample


title: Tcrd_DN1d_020617_C12_1


title: 27m_100

city: Cambrdige

first: Yunyu

last: Zhang

address: 22 Windsor Ave

institute: Novartis Institute for Biomedical Research

description: Gene expression data from gastrocnemius muscle of 27m old rat

hyb_protocol: RNA sample were subjected to microarray analysis using the GeneChip Rat Genome 230 2.0 Array (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChip Scanner 3000

data_processing: The raw intensity file from CEL files are normalized and summarized into probe set level expression index using the PLIER (probe logarithm intensity error) method.

organism: Rattus norvegicus

source_name: 27m, gastrocnemius muscle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: The muscle was pulverized under liquid nitrogen and total RNA extracted from a portion using the RNeasy fibrous tissue midi kit according to the manufacturer's protocol (Qiagen).

value: Sprague Dawley

tag: gender

value: male

tag: age

value: 27 months

value: gastrocnemius muscle


title: 27m_101


title: FPW1 cell line

city: Brisbane

description: single sample


title: BS155 FFPE sample

description: BS155 FFPE sample

tag: treatment


title: Tcrd_DN1d_020617_C10_1

tag: markers

tag: strain/genotype


title: 27m_99


title: Tcrd_DN1d_020617_C11_1

tag: developmental stage


title: RN1 cell line

description: single sample

value: Left temporal


title: Tcrd_DN1d_020617_C09_1


title: BS127 FFPE sample

description: BS127 FFPE sample


title: BS247 FFPE sample

description: BS247 FFPE sample


title: Tcrd_DN1d_020617_C08_1


title: BS439 FFPE sample

description: BS439 FFPE sample


title: 27m_97


title: 27m_98


title: 27m_96


title: Tcrd_DN1d_020617_C07_1


title: 27m_94


title: CRC02_A

tag: group

value: colorectal cancer


title: BS415 FFPE sample

description: BS415 FFPE sample


title: Tcrd_DN1d_020617_C05_1


title: Tcrd_DN1d_020617_C03_1


title: Tcrd_DN1d_020617_C06_1


title: Tcrd_DN1d_020617_C04_1


title: BS273 FFPE sample

description: BS273 FFPE sample


title: BS309 FFPE sample

description: BS309 FFPE sample


title: Tcrd_DN1d_020617_C02_1


title: 24m_76

description: Gene expression data from gastrocnemius muscle of 24m old rat

source_name: 24m, gastrocnemius muscle

value: 24 months


title: BS293 FFPE sample

description: BS293 FFPE sample


title: 24m_78


title: BS411 FFPE sample

description: BS411 FFPE sample


title: 24m_77


title: BS129 FFPE sample

description: BS129 FFPE sample


title: 24m_79


title: 24m_75


title: 24m_80


title: Tcrd_DN1d_020617_C01_1


title: BS167 FFPE sample

description: BS167 FFPE sample


title: BS281 FFPE sample

description: BS281 FFPE sample


title: Rag_cKit-_022417_C95_1


title: 24m_74


title: Rag_cKit-_022417_C96_1


title: Rag_cKit-_022417_C92_1


title: Rag_cKit-_022417_C93_1


title: Rag_cKit-_022417_C91_1


title: BS205 FFPE sample

description: BS205 FFPE sample


title: Rag_cKit-_022417_C94_1


title: BS197 FFPE sample

description: BS197 FFPE sample


title: BS409 FFPE sample

description: BS409 FFPE sample


title: 21m_64

description: Gene expression data from gastrocnemius muscle of 21m old rat

source_name: 21m, gastrocnemius muscle

value: 21 months


title: 24m_72


title: 21m_65


title: BS159 FFPE sample

description: BS159 FFPE sample

value: hepatocellular carcinoma


title: Rag_cKit-_022417_C90_1


title: BS373 FFPE sample

description: BS373 FFPE sample


title: Rag_cKit-_022417_C89_1


title: Rag_cKit-_022417_C88_1


title: BS255 FFPE sample

description: BS255 FFPE sample


title: 21m_61


title: BS283 FFPE sample

description: BS283 FFPE sample

value: Sor


title: BS341 FFPE sample

description: BS341 FFPE sample

value: non-responder


title: 24m_73


title: Rag_cKit-_022417_C87_1


title: BS405 FFPE sample

description: BS405 FFPE sample

value: responder


title: 21m_58


title: 21m_63


title: Rag_cKit-_022417_C86_1


title: BS169 FFPE sample

description: BS169 FFPE sample


title: 21m_56


title: Rag_cKit-_022417_C85_1


title: BS183 FFPE sample

description: BS183 FFPE sample


title: 21m_57


title: M231R_U2_3

city: Houston

first: James

middle: Michael

last: Arnold

state: Texas

address: 1 Baylor Plaza

department: Biochemistry and Molecular Biology

institute: Baylor College of Medicine

description:
shUGDH_2-3
combined_samples_deseq_counts.txt
NT_vs_U2.deseq.res.csv

data_processing:
Raw data was uploaded to BaseSpace (www.basespace.illumina.com)
Control (shNT) and comparison (shU1 or shU2) were analyzed using the RNA Express (v1.1.0) pipeline
Alignment was performed using STAR aligner
Differential gene expression was performed using DESeq2
Genome_build: USCS hg19
Supplementary_files_format_and_content: Output includes read counts (combined_samples_deseq_counts.txt)  and DESeq2 results (respective deseq.res files)

source_name: cell line

growth_protocol: Cells grown as biological replicates at 37˚C, 5% CO2, in DMEM media supplemented with 5% FBS

extract_protocol:
Cells were trypsinized, pelleted, and immediately processed according to QIAgen RNeasy kit (QIAgen, Cat # 74104). RNA underwent QC using RNA Pico 600 chip on Bioanalyzer 2100 (Agilent) and quantified with Qubit Fluorometer (Thermo).
The RNA libraries were prepared and sequenced at University of Houston Seq-N-Edit Core per protocols. Total libraries were prepared with Ovation® Universal Plus mRNA-Seq (NuGen) using 200 ng input RNA. The size selection for libraries were performed using SPRIselect beads (Beckman Coulter) and purity of the libraries were analyzed using the High Sensitivity DNA chip on Bioanalyzer 2100 (Agilent). The prepared libraries pooled and sequenced using NextSeq 500 (Illumina), generating ~15 million 2×76 bp paired-end reads per samples.

treatment_protocol: Cells were transduced with lentiviral particles carrying respective pGIPZ vector

tag: shRNA

value: shNT shUGDH-2

tag: pgipz cat#

tag: hairpin seq

value: ATATACTTCAGATCTGCTG


title: 18m_71

description: Gene expression data from gastrocnemius muscle of 18m old rat

source_name: 18m, gastrocnemius muscle

value: 18 months


title: 21m_59


title: Rag_cKit-_022417_C84_1


title: Rag_cKit-_022417_C83_1


title: Rag_cKit-_022417_C82_1


title: BS241 FFPE sample

description: BS241 FFPE sample


title: M231R_U2_2

description:
shUGDH_2-2
combined_samples_deseq_counts.txt
NT_vs_U2.deseq.res.csv


title: 18m_54


title: BS275 FFPE sample

description: BS275 FFPE sample

value: Plac


title: 18m_67


title: 18m_52


title: 18m_55


title: M231R_U1_3

description:
shUGDH_1-3
combined_samples_deseq_counts.txt
NT_vs_U1.deseq.res.csv

value: shNT shUGDH-1

value: TTGCATCAAATATGCGACG


title: BS441 FFPE sample

description: BS441 FFPE sample


title: BS279 FFPE sample

description: BS279 FFPE sample


title: Rag_cKit-_022417_C78_1

value: Thymus


title: BS311 FFPE sample

description: BS311 FFPE sample


title: BS265 FFPE sample

description: BS265 FFPE sample


title: 18m_49

value: Sprague Dawley

value: male


title: 18m_51

value: gastrocnemius muscle


title: BS369 FFPE sample

description: BS369 FFPE sample


title: M231R_NT_3

description:
shNT-3
combined_samples_deseq_counts.txt

value: shNT shNT

value: ATCTCGCTTGGGCGAGAGTAAG


title: Rag_cKit-_022417_C76_1


title: Rag_cKit-_022417_C77_1


title: Rag_cKit-_022417_C75_1


title: M231R_NT_2

description:
shNT-2
combined_samples_deseq_counts.txt


title: BS295 FFPE sample

description: BS295 FFPE sample


title: Rag_cKit-_022417_C80_1


title: M231R_U1_2

description:
shUGDH_1-2
combined_samples_deseq_counts.txt
NT_vs_U1.deseq.res.csv


title: M231R_NT_1

description:
shNT-1
combined_samples_deseq_counts.txt


title: 18m_48


title: BS173 FFPE sample

description: BS173 FFPE sample


title: M231R_U1_1

description:
shUGDH_1-1
combined_samples_deseq_counts.txt
NT_vs_U1.deseq.res.csv


title: Rag_cKit-_022417_C74_1


title: 18m_47


title: 18m_46


title: 6h CHX+ T3 rep4

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

institute: CNIC

data_processing:
Bcl2fastq was used for demultiplexing process with standard parameters and 1 mismatches allowed for the index identification.
Sequenced reads quality was evaluated from FastQC.
Reference Genome was indexed from Bowtie (Langmead B et al. 2009) and sequence reads were aligned using TopHat (Trapnell C et al. 2009). Mapping data quality was evaluated from Qualimap (Garcia-Alcalde F et al. 2012).
We quantified reads to specific genes and transcripts using the Python module HT-SEQ (Anders S et al. 2015).
RNA-Seq data were normalized using Trimmed Mean of M values (Robinson MD and A Oshlack 2010) from EdgeR.
Genome_build: Mouse sequenced genome GRCm38
Supplementary_files_format_and_content: *txt: Tab-delimited text files include TMM values for each sample.

source_name: Cerebral cortex

growth_protocol: Primary astrocytes cultures (ASTRO culture) were established from the whole neocortex of P3 mice. Protocols for animal handling were approved by the local institutional Animal Care Committee, according to European Union rules. Mice of a hybrid genetic background of 129/OLa+129/Sv+ and BALB/c+C57BL/6 were used. The pups were euthanized by decapitation; the brains were placed on a Petri dish in PBS and dissected under a stereomicroscope. A midline cut was made to separate each hemi brain, the meninges and blood vessels were carefully removed with forceps, and the cerebral cortices isolated from other structures. The tissue was disaggregated in culture medium (DMEM containing 10% TH-deprived FCS, glutamax 1%, fungizone 1% and antibiotics 1%) by passing up and down through a 1 mL and 0.2 mL Pipette. After 5 min centrifugation at 1200 rpm, the pellet was suspended in culture medium. The cells were established at low density in poly-L-ornithine-coated 12-well plates (130,000 cells per well) and incubated for 7 days, with medium changes every 72 hours. Astrocyte enrichment was above 95%.

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro Kit (Qiagen) and was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Two hundred ng of total RNA were used with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEW ENGLAND BIOLABS) (Ipswich, MA) to construct index-tagged cDNA libraries. Libraries were quantified using a Quant-iT™ dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and sequence-by-synthesis single reads of 50 base length using the TruSeq SBS Kit v5 (Illumina) (Illumina, San Diego, CA) were generated on the HiSeq 2500 following the standard RNA sequencing protocol. For demultiplexing process, we used bcl2fastq with standard parameters and 1 mismatch allowed for the index identification. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

treatment_protocol: The cells were incubated in DMEM containing 0.1% TH-deprived serum 24 hours before adding T3 (Sigma). CHX was added to the cells at a final concentration of 8 µg/ml 30 minutes before adding T3 (10 nM). The cells were incubated for 6 hours after T3 addition before harvesting.

tag: strain/background

value: hybrid (129/OLa+129/Sv+ and BALB/c+C57BL/6)

tag: cell type

value: cerebrocortical astrocytes

value: postnatal day 3

value: CHX + T3 10nM


title: Rag_cKit-_022417_C71_1


title: 6h CHX+ T3 rep3


title: 12m_31

description: Gene expression data from gastrocnemius muscle of 12m old rat

source_name: 12m, gastrocnemius muscle

value: 12 months


title: Rag_cKit-_022417_C72_1


title: 12m_43


title: Rag_cKit-_022417_C69_1


title: BS431 FFPE sample

description: BS431 FFPE sample

value: hepatocellular carcinoma

value: responder


title: Rag_cKit-_022417_C68_1


title: 12m_30


title: 6h CHX+ T3 rep1


title: 6h CHX+ T3 rep2


title: 6h Control CHX rep4

description: CHXD

value: CHX not T3


title: Rag_cKit-_022417_C67_1


title: BS323 FFPE sample

description: BS323 FFPE sample

value: Plac

value: non-responder


title: BS143 FFPE sample

description: BS143 FFPE sample


title: BS393 FFPE sample

description: BS393 FFPE sample


title: 6h Control CHX rep3

description: CHXC


title: 12m_28


title: Rag_cKit-_022417_C66_1


title: 12m_29


title: 12m_26


title: 12m_27


title: Rag_cKit-_022417_C65_1


title: BS287 FFPE sample

description: BS287 FFPE sample


title: 6h Control CHX rep2

description: CHXB


title: 12m_24


title: Rag_cKit-_022417_C64_1


title: Rag_cKit-_022417_C62_1


title: 6h + T3 rep4

value: T3 10nM


title: 6h Control CHX rep1

description: CHXA


title: 6h + T3 rep3


title: BS231 FFPE sample

description: BS231 FFPE sample


title: BS153 FFPE sample

description: BS153 FFPE sample


title: Rag_cKit-_022417_C60_1

value: Thymus


title: BS483 FFPE sample

description: BS483 FFPE sample


title: 12m_22

value: Sprague Dawley


title: BS329 FFPE sample

description: BS329 FFPE sample


title: 6h + T3 rep1


title: 6h + T3 rep2


title: Rag_cKit-_022417_C59_1


title: BS219 FFPE sample

description: BS219 FFPE sample

value: Sor


title: Rag_cKit-_022417_C58_1


title: 6h Control rep4

description: CD

value: not T3


title: 12m_23

value: male

value: gastrocnemius muscle


title: Rag_cKit-_022417_C57_1


title: 6m_17

description: Gene expression data from gastrocnemius muscle of 6m old rat

source_name: 6m, gastrocnemius muscle

value: 6 months


title: BS227 FFPE sample

description: BS227 FFPE sample


title: BS381 FFPE sample

description: BS381 FFPE sample


title: BS211 FFPE sample

description: BS211 FFPE sample


title: Rag_cKit-_022417_C61_1


title: 6h Control rep3

description: CC

value: hybrid (129/OLa+129/Sv+ and BALB/c+C57BL/6)

value: cerebrocortical astrocytes


title: 6m_11


title: BS325 FFPE sample

description: BS325 FFPE sample


title: Rag_cKit-_022417_C56_1


title: BS157 FFPE sample

description: BS157 FFPE sample


title: BS465 FFPE sample

description: BS465 FFPE sample


title: 6h Control rep2

description: CB

value: postnatal day 3


title: 6h Control rep1

description: CA


title: Rag_cKit-_022417_C55_1


title: 24h + T3 rep3

treatment_protocol: The cells were incubated in DMEM with 0.1% TH-deprived serum 24 hours before adding T3 (Sigma) at a final concentration of 10 nM. Cells were harvested 24 hours later.


title: Rag_cKit-_022417_C54_1


title: 24h + T3 rep2


title: 24h + T3 rep1


title: 6m_6


title: Rag_cKit-_022417_C52_1


title: Rag_cKit-_022417_C51_1


title: Rag_cKit-_022417_C53_1


title: 24h Control rep4


title: 24h Control rep3


title: Rag_cKit-_022417_C49_1


title: 6m_5


title: BS413 FFPE sample

description: BS413 FFPE sample


title: 6m_2


title: 6m_10


title: BS101 FFPE sample

description: BS101 FFPE sample


title: BS115 FFPE sample

description: BS115 FFPE sample


title: 6m_4


title: BS473 FFPE sample

description: BS473 FFPE sample


title: 6m_9


title: 6m_8


title: Rag_cKit-_022417_C48_1


title: 24h Control rep2


title: M231R_U2_1

description:
shUGDH_2-1
combined_samples_deseq_counts.txt
NT_vs_U2.deseq.res.csv

value: shNT shUGDH-2

value: ATATACTTCAGATCTGCTG


title: BS417 FFPE sample

description: BS417 FFPE sample

value: hepatocellular carcinoma


title: 6m_1


title: BS277 FFPE sample

description: BS277 FFPE sample


title: Rag_cKit-_022417_C47_1


title: 24h Control rep1


title: COMP group,  biological rep 12, 13, 14

city: ChongQing

first: Gang

last: Wu

address: 30 Gaotanyan, Shapingba, Chongqing

institute: Army Medical University

description:
Gene expression data from the cells of rat bronchoalveolar lavage fluid
8-week-old male Sprague-Dawley (SD) rats, weighing 200 ± 20 g, lung

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed withRMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: COMB group, with combined exposures of acute hypobaric hypoxia and LPS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: rats were housed in microisolator cages with specific pathogen-free (SPF) condition and free access to water and food. Before experimentation, rats were housed for 3 days to adapt them to the environment. All animals were fasted and banned water during the experiment.

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

treatment_protocol: For exposure of hypobaric hypoxia, the animals were subjected to stay in the decompression chamber for 6 hours with an ambient air pressure of 405.35 mmHg (approx. 0.53atm, or equivalent of 5000 m altitude, or the equivalent of 11.2% O2). The animals in COMB groups who received double-stimulus were first subjected to LPS administration, then stay in the decompression chamber, the time used about twenty minutes when it achieved the ambient air pressure of 5000 m altitude from the plains. The rats in CTL group were subjected to a tail vein injection of 0.2 ± 0.02 mL of saline (0.9% NaCl water).

value: Sprague-Dawley (SD)

value: lung


title: COMP group,  biological rep 2, 3

value: the cells of rat bronchoalveolar lavage fluid


title: Rag_cKit-_022417_C46_1


title: BS489 FFPE sample

description: BS489 FFPE sample

value: Plac

value: non-responder


title: COMP group,  biological rep 10, 11


title: HPO group,  biological rep 3, 5, 12

source_name: HPO group, with exposure of acute hypobaric hypoxia


title: Rag_cKit-_022417_C44_1

value: Thymus


title: Rag_cKit-_022417_C42_1


title: Rag_cKit-_022417_C45_1


title: BS137 FFPE sample

description: BS137 FFPE sample


title: Rag_cKit-_022417_C40_1


title: BS367 FFPE sample

description: BS367 FFPE sample

value: Sor


title: Rag_cKit-_022417_C41_1


title: HPO group,  biological rep 2, 4, 11


title: Rag_cKit-_022417_C39_1


title: HPO group,  biological rep 7, 8, 9


title: BS343 FFPE sample

description: BS343 FFPE sample


title: BS407 FFPE sample

description: BS407 FFPE sample

value: responder


title: BS321 FFPE sample

description: BS321 FFPE sample


title: BS111 FFPE sample

description: BS111 FFPE sample


title: LPS group,  biological rep 5, 7, 11

source_name: LPS group, with LPS treatment with normoxia


title: BS453 FFPE sample

description: BS453 FFPE sample


title: Rag_cKit-_022417_C38_1


title: LPS group,  biological rep 8, 9, 10


title: Rag_cKit-_022417_C37_1


title: LPS group,  biological rep 2, 3, 6


title: BS395 FFPE sample

description: BS395 FFPE sample


title: CTL group, biological rep 5, 6, 7

source_name: CTL group, naïve control rats with normoxia


title: CTL group, biological rep 8, 9, 10


title: CTL group, biological rep 1, 3, 4


title: Rag_cKit-_022417_C35_1

source_name: Thymus


title: BS313 FFPE sample

description: BS313 FFPE sample


title: Rag_cKit-_022417_C34_1


title: Rag_cKit-_022417_C33_1


title: BS113 FFPE sample

description: BS113 FFPE sample


title: Rag_cKit-_022417_C32_1


title: Rag_cKit-_022417_C30_1


title: Rag_cKit-_022417_C28_1


title: Rag_cKit-_022417_C26_1


title: Rag_cKit-_022417_C25_1


title: TW03-negative control-rep1

city: Stockholm

first: Ingemar

last: Ernberg

address: Solnavagen 9 C8

department: Department of Microbiology, Tumor and Cell Biology

institute: Karolinska Institutet

description:
TW03
Gene expression data from TW03 parental cells.

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 1.0 in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: TW03 parental cells

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit.

growth_protocol: All cells were incubated at 37℃ in a humidified atmosphere containing 5% CO2 and cultured in Modified Eagles Medium/High glucose (DMEM) medium supplemented with 10% fetal bovine serum (FBS) in the presence of streptomycin and penicillin.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free DNase Set.

treatment_protocol: Cell lines CNE1 and TW03 were originally established as derived from human nasopharyngeal carcinoma (NPC) cells. LMP2A positive cell lines were established by retroviral transduction. Briefly, a retroviral stock was prepared from PA317 cells carrying an amphotropic retroviral envelope protein. The LMP2A gene in a retroviral construct was from the pLNPOX vector, which was described in detail previously. After four days of selection in 4 μg/ml of puromycin, resistant cell clones were grown up and the transfection efficiency was validated for LMP2A expression by RT-qPCR.

value: nasopharyngeal carcinoma cell line

value: Male


title: BS451 FFPE sample

description: BS451 FFPE sample


title: BS317 FFPE sample

description: BS317 FFPE sample


title: Rag_cKit-_022417_C24_1


title: TW03-LMP2A-rep1

description:
TW03-LMP2A
Gene expression data from TW03 cells transfected by LMP2A.

source_name: TW03 cells transfected by LMP2A

tag: transfection


title: CNE1-LMP2A-rep1

description:
CNE1-LMP2A
Gene expression data from CNE1 cells transfected by LMP2A.

source_name: CNE1 cells transfected by LMP2A

value: Female


title: BS377 FFPE sample

description: BS377 FFPE sample

source_name: Formalin-fixed paraffin-embedded (FFPE)


title: BS223 FFPE sample

description: BS223 FFPE sample


title: CNE1-negative control-rep1

description:
CNE1
Gene expression data from CNE1 parental cells.

source_name: CNE1 parental cells


title: Rag_cKit-_022417_C31_1

tag: strain