title: ID8-P0 (duplicate-2)

city: Indianapolis

first: Yan

last: Xu

state: Indiana

address: 1044 W. Walnut St

institute: Indiana University School of Medicine

data_processing:
Demultiplexing of sequenced data was performed using CASAVA v1.8.2 fastq files.
Trimmomatic (v0.22) was used to trimming with: -phred33 ILLUMINACLIP:adapter.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17; Additional trimming was done with fastx_clipper (v0.0.13.2) with parameters: -l 17 -v -M 1; Identical sequences within a particular sample were collapsed to make a pseudo-read with a known count
The collapsed read set was repeat masked using RepeatMasker (v open-3.2) with the following parameters: -e cross-match -species human -no_is -frag 300000 -small –xm. The abundance of the collapsed read set was then used to calculate the actual abundance of reads containing a particular class of repeat.
Read mapping was performed with tophat2 (v 2.0.6) using -b2-very-sensitive -read-edit-dist 2 -max-multihits 100 -keep-tmp -library-type fr-sencondstrand; The mapping relies on bowtie2 (v 2.0.2). The reads were mapped to hg19 from UCSC using Gencode annotation (v13). Reads also mapped to bacterial genomes (NCBI as of Nov 30th, 2012)
Mapped reads were associated with genes using custom perl scripts that allowed no more than 2 unmapped bases to make an association
Differential analysis was done using edgeR (v 3.20.8)
Genome_build: USCS hg19
Supplementary_files_format_and_content: Xlsx format containing raw counts and differential analysis

growth_protocol: Cells were cultured in suspension for 24 hrs. Cells (50,0000) were plated onto poly-HEMA-coated six-well plates (Corning, Tewksbury, MA, USA) in growth medium (Dulbecco's modified Eagle'smedium supplemented with 4% FBS) to prohibit attachment.

extract_protocol:
Cells (10^7) were lysed and RNA was extracted according to manufacturer’s protocol (Qiagen RNeasy Mini kit).
Total RNA was fractionated by size using ethanol concentration manipulations. The large RNA fraction (>200 nt) was fragmented prior to library construction. Ribosomal RNA was reduced by duplex specific nuclease (DSN) following limited hybridizations of both fractions and then amplified to add barcodes for multiplexing on the Illumina HiSeq2000 platform.

tag: strain background

value: In vitro transformed mouse ovarian surface epithelial cells from C57BL6 mice


title: ID8-P0 (duplicate-1)

status: Public on May 09 2018

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: genotype/variation

value: wild type


title: ID8-PW2 (duplicate-1)

value: In vivo passaged in C57BL6 tumor cells from paritoneal wall


title: mRNA_ctrl_16

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

description:
exp ID: 160512_0435_s05
sample name: S52

data_processing:
alignment: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1
RPKM calculation: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek6.6
Genome_build: hg19
Supplementary_files_format_and_content: excel for a RPKM file

organism: Homo sapiens

source_name: Human whole blood

extract_protocol:
Peripheral blood was collected by venipuncture in PAXgene Blood RNA Tubes (BD Diagnostics) and stored at -80C. RNA was isolated using Paxgene Blood RNA Kit (Qiagen, Inc.)
cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina). RNA seq data were generated on Illumina HiSeq 2500 or 3000 instruments according to the manufacturer's instructions

tag: tissue

value: whole blood

tag: diagnosis

value: Healthy Control

tag: vascular phenotype

value: Control


title: mRNA_ctrl_15

description:
exp ID: 160512_0435_s04
sample name: S51


title: mRNA_ctrl_17

description:
exp ID: 160512_0435_s06
sample name: S53


title: PD-1posP01

city: Rochester

first: Jie

state: MN

address: 200 First Street SW

institute: Mayo Clinic

description: non-responder

data_processing:
Basecalls performed using Illumina bcl2fastq2 versions bcl2fastq-1.8.4 (before therapy) and 2.17.1.14 after therapy)
Sequence reads were aligned to the hg38 genome assembly using TopHat2
Raw and normalized gene genecounts (RPKM) are generated by Featuregenecounts
Genome_build: hg38
Supplementary_files_format_and_content: counts

source_name: T cells from peripheral blood

extract_protocol:
CD8+ T cells were sorted by flow cytometer, and RNA was extracted with RNeasy Mini kit . A total of 1 ng RNA was used to generate double stranded cDNA using SMARTer Ultra Low RNA kit for Illumina. The libraries were sequenced using the 101 bases paired-end protocol on Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PD-1 antibody was given every 3 weeks for a total of 4 doses as one cycle. All these samples were collected after one cycle of treatment.

tag: marker

value: CD11a-high CD8+ T cells

tag: group

value: before PD-1 blockade therapy


title: PD-1posR01

description: responder


title: BXPC-3 scr-1

type: RNA

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

description:
SAMPLE10
Cell 10

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Genome Studio 5.0
rank invariant normalization

label: Biotin

source_name: BXPC-3 cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Pancreas cancer cell lines were cultured and subjected to various exosomes based treatments.

extract_protocol: RNA was extracted with Trizol reagent,Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: The cells were harvested (untreated control 'cont') for RNA extraction, or treated for 3 hours with various exosomes preparations. The exosomes were collected from BJ human foreskin fibroblast culture supernatant without further processing (control exosomes or 'CE'), or engineered to contain scrambled siRNA ('scr') or KRASG12D siRNA ('iExo). Two or three distinct wells of cells were evaluated per treatment condition and assigned a well number (well -1, -2 or 3).

tag: cell line

value: BXPC-3 cells

tag: treatment

value: scramble siRNA containing exosomes

tag: well


title: mRNA_lupus_LL_NCB_8

description:
exp ID: 160512_0435_s02
sample name: S49

value: Lupus

value: Normal NCB


title: mRNA_lupus_LL_NCB_9

description:
exp ID: 160512_0435_s03
sample name: S50


title: CytoplasmicRNA_DBP5-siRNA_3

city: Kyoto City

first: Masumi

last: Okamura

state: Kyoto Prefecture

address: Kitashirakawa Oiwakechou

country: Japan

institute: Kyoto University

hyb_protocol: Hybridization were performed using Agilent’s Low Input Quick Amp WT Labeling kit, one-color (Agilent Technology, USA), according to the manufacturer’s instructions.

scan_protocol: The microarrays were scaned in the Agilent G2505 DNA Microarray Scanner equipment (Agilent).

data_processing: The raw data of gene expression was normalized LOESS regression via R software

molecule: cytoplasmic RNA

source_name: Cytoplasmic RNA, DBP5-siRNA, replicate 3

label_protocol: Labeling  were performed using Agilent’s Low Input Quick Amp WT Labeling kit, one-color (Agilent Technology, USA), according to the manufacturer’s instructions.

growth_protocol: U2OS cells were grown in Dulbecco's modified Eagle medium containing 10% fatal bovine serum.

extract_protocol: Cytoplasmic RNA was extracted with Sepasol RNA I Super G solution according to manufacture's instruction following to the separation of cytosolic fraction by using lysis buffer (20 mM Tris-HCl pH, 8.0, 200 mM NaCl, 1 mM MgCl2, 1 % NP40).

treatment_protocol: 20nM of siRNA was transfected with Lipofectamine2000 according to manufacture's instruction.

tag: sirna

tag: rna fraction

value: cytoplasmic


title: mRNA_lupus_LH_NCB_9

description:
exp ID: 160512_0435_s01
sample name: S48

value: High NCB


title: Panc-1 cont-1

description:
SAMPLE8
Cell 8

source_name: Panc-1 cells

value: Panc-1 cells

value: untreated control


title: Panc-1 CE-3

description:
SAMPLE4
Cell 4

value: control exosomes


title: Panc-1 scr-1

description:
SAMPLE1
Cell 1


title: CytoplasmicRNA_Control-siRNA_1

source_name: Cytoplasmic RNA, control-siRNA, replicate 1

value: control


title: Panc-1 iExo-1

description:
SAMPLE5
Cell 5

value: KRASG12D siRNA containing exosomes


title: mRNA_ctrl_14

description:
exp ID: 160512_0434_s25
sample name: S47


title: CytoplasmicRNA_Control-siRNA_2

source_name: Cytoplasmic RNA, control-siRNA, replicate 2


title: Panc-1 scr-2

description:
SAMPLE2
Cell 2


title: CytoplasmicRNA_Control-siRNA_3

source_name: Cytoplasmic RNA, control-siRNA, replicate 3


title: ID8-PW2 (duplicate-2)

value: In vivo passaged in C57BL6 tumor cells from paritoneal wall

value: wild type


title: Panc-1 CE-1

description:
SAMPLE3
Cell 3


title: Panc-1 iExo-2

description:
SAMPLE6
Cell 6


title: Acox1Lampe1 HFHCD 2

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Liver from Acox1Lampe1  Male Mus musculus fed Chow for 8 weeks, followed by high-fat, high-carb for 4 weeks

data_processing:
Illumina HiSeq2000 was used for base calling
Following adapter and barcode trimming, high-quality raw reads were aligned (mm8 mouse genome using Ensembl annotations) and quantified using the TopHap Cufflinks pipeline.
Computed RPKM were normalized using a 75th percentil shift and baselined to the median of all samples.
Genome_build: mm8
Supplementary_files_format_and_content: Tab-delimited with gene symbol and RPKM.

source_name: Liver

extract_protocol:
Ilumina TruSeq. RNA was isolated using Trizol and cleaned using Quiagen Cleanup kit
Standard Illumina protocols

treatment_protocol: Wildtype and Acox1Lampe1 mice were fed either regular chow (fat 13.5%kcal, carbohydrate 59%kcal, protein 27.5 kcal) for 12 weeks, or regular chow for 8 weeks followed by 4 weeks on high-fat high-carbohydrate (fat 58% kcal, carbohydrate 25.5% kcal, protein 16.4 kcal).

tag: acox1 genotype

tag: background

tag: diet

tag: age at sacrifice

value: 12 weeks

tag: Sex

value: Male


title: Acox1Lampe1 HFHCD 1

value: Chow for 8 weeks, followed by high-fat, high-carb for 4 weeks


title: Acox1Lampe1 HFHCD 3


title: mRNA_lupus_LL_NCB_7

description:
exp ID: 160512_0434_s23
sample name: S45

value: whole blood


title: Acox1Lampe1 Ctrl2

description: Liver from Acox1Lampe1  Male Mus musculus fed Chow for 12 weeks

value: Chow for 12 weeks


title: mRNA_lupus_LL_NCB_6

description:
exp ID: 160512_0434_s22
sample name: S44


title: mRNA_lupus_LL_NCB_5

description:
exp ID: 160512_0434_s21
sample name: S43


title: Acox1Lampe1 Ctrl1


title: WT HFHCD 3

description: Liver from Wildtype Male Mus musculus fed Chow for 8 weeks, followed by high-fat, high-carb for 4 weeks

value: Wildtype


title: Acox1Lampe1 Ctrl3


title: WT HFHCD 2


title: WT HFHCD 1


title: mRNA_ctrl_13

description:
exp ID: 160512_0434_s24
sample name: S46

value: Healthy Control

value: Control


title: WT Ctrl 3

description: Liver from Wildtype Male Mus musculus fed Chow for 12 weeks


title: WT Ctrl 2


title: mRNA_lupus_LH_NCB_8

description:
exp ID: 160512_0434_s19
sample name: S41

value: Lupus


title: WT Ctrl 1


title: mRNA_lupus_LH_NCB_7

description:
exp ID: 160512_0434_s18
sample name: S40

value: High NCB


title: mRNA_lupus_LH_NCB_5

description:
exp ID: 160512_0434_s16
sample name: S38


title: mRNA_lupus_LN_TBR_8

description:
exp ID: 161220_0011_s39
sample name: S23

value: Normal TBR


title: mRNA_lupus_LN_TBR_9

description:
exp ID: 161220_0011_s40
sample name: S24


title: mRNA_lupus_LH__TBR_8

description:
exp ID: 161220_0011_s41
sample name: S25

value: High TBR


title: mRNA_lupus_LH_7

description:
exp ID: 161220_0011_s38
sample name: S22


title: mRNA_ctrl_11

description:
exp ID: 160512_0434_s10
sample name: S36


title: mRNA_lupus_LH_TBR_9

description:
exp ID: 161220_0011_s42
sample name: S26


title: mRNA_ctrl_12

description:
exp ID: 160512_0434_s11
sample name: S37


title: mRNA_lupus_LN_TBR_7

description:
exp ID: 161220_0011_s36
sample name: S20


title: mRNA_ctrl_8

description:
exp ID: 161220_0011_s37
sample name: S21


title: mRNA_ctrl_9

description:
exp ID: 160512_0434_s08
sample name: S34


title: mRNA_lupus_LL_NCB_4

description:
exp ID: 160512_0434_s20
sample name: S42

value: Normal NCB


title: mRNA_lupus_LH_TBR_6

description:
exp ID: 161220_0011_s34
sample name: S18


title: mRNA_lupus_LL_NCB_3

description:
exp ID: 160512_0434_s07
sample name: S33


title: mRNA_lupus_LH_NCB_4

description:
exp ID: 160512_0434_s04
sample name: S30


title: mRNA_ctrl_5

description:
exp ID: 161220_0011_s16
sample name: S16


title: mRNA_lupus_LL_NCB_2

description:
exp ID: 160512_0434_s06
sample name: S32


title: mRNA_ctrl_10

description:
exp ID: 160512_0434_s09
sample name: S35


title: mNA_lupus_LL_NCB_1

description:
exp ID: 160512_0434_s05
sample name: S31


title: mRNA_ctrl_6

description:
exp ID: 161220_0011_s33
sample name: S17


title: mRNA_ctrl_4

description:
exp ID: 161220_0011_s15
sample name: S15


title: mRNA_lupus_LH_NCB_6

description:
exp ID: 160512_0434_s17
sample name: S39


title: AMPKa2WT2 (dataset 2)

city: Pullman

first: Zhihua

last: Jiang

state: WA

address: Veterinary and Biomedical Research Building, Room 151

department: Animal Science

institute: Washington State University

data_processing:
Raw reads were trimmed of adaptor sequence,  masked for low-complexity or low-quality sequence, and  mapped to the mouse genome using the TMAP aligner. The transcriptional start sites were clustered using a 20-bp window.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: counts

source_name: skeletal muscle

extract_protocol:
Total RNA was harvested using Trizol reagent.
WTSS-seq libraries were constructed based on our protocols. The WTSS-seq method includes: rRNA depletion, 1st strand cDNA synthesis, size selection and PCR amplification.

value: muscle

tag: developmental stage

value: Adult


title: mRNA_lupus_LH_NCB_2

description:
exp ID: 160512_0434_s02
sample name: S28


title: mRNA_lupus_LN_TBR_6

description:
exp ID: 161220_0011_s13
sample name: S13


title: mRNA_ctrl_3

description:
exp ID: 161220_0011_s14
sample name: S14


title: mRNA_lupus_LH_NCB_1

description:
exp ID: 160512_0434_s01
sample name: S27


title: AMPKa2WT1 (dataset 2)


title: mRNA_lupus_LH_TBR_5

description:
exp ID: 161220_0011_s12
sample name: S12


title: mRNA_lupus_LN_TBR_5

description:
exp ID: 161220_0011_s11
sample name: S11


title: AMPKa2KO2 (dataset 2)


title: AMPKa2KO1 (dataset 2)


title: mRNA_ctrl_7

description:
exp ID: 161220_0011_s35
sample name: S19


title: ras_atm_a

city: Stockholm

first: Erik

last: Fasterius

address: AlbaNova University Center

department: Proteomics and nanotechnology

country: Sweden

institute: KTH Royal Institute of Technology

description: average insert size of library: 325.2

data_processing:
Kallisto, v0.42.1, default parameters
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited file containing ENSTIDs and transcript abundances for each sample, condition and replicate.

source_name: Human fibroblast cell line

growth_protocol: All four cell lines in the model were cultivated in Dulbecco’s modified Eagle’s Medium (Sigma-Aldrich) supplemented with 10% Fetal Bovine Serum (Sigma-Aldrich) for six passages at 37 °C.

extract_protocol:
The cells were grown up to 80% confluence and counted with a Scepter 2.0 Cell Counter (Merck Millipore, Billerica, MA, USA). Cells were cultivated in duplicate plates in parallel for each cell line and oxygen condition. RNA was extracted from the cells using the RNeasy kit (Qiagen), generating high quality total RNA (i.e. RIN>8).
Illumina TruSeq Stranded mRNA according to the manufacturer's instructions.

treatment_protocol: Cultivation was performed in a humidified atmosphere containing 5% CO2 and both under atmospheric oxygen pressure (files labelled "_atm") and under what is considered moderate hypoxia (3% oxygen, files labelled "_3") for six passages.

value: Human fibroblast cell line

tag: cell type

value: BJ hTERT+ SV40+ Ras-G12V cell line

value: Atmospheric oxygen


title: ras_atm_b

description: average insert size of library: 313.57

tag: tissue


title: mRNA_lupus_LN_TBR_4

description:
exp ID: 161220_0011_s10
sample name: S10

tag: diagnosis


title: ras_3_a

description: average insert size of library: 343

value: 3% oxygen


title: mRNA_lupus_LH_NCB_3

description:
exp ID: 160512_0434_s03
sample name: S29

tag: vascular phenotype


title: ras_3_b

description: average insert size of library: 306


title: mRNA_lupus_LH__TBR_4

description:
exp ID: 161220_0011_s09
sample name: S09


title: mRNA_lupus_LN_TBR_3

description:
exp ID: 161220_0011_s08
sample name: S08


title: sv_atm_b

description: average insert size of library: 263.74

value: BJ hTERT+ SV40+ cell line


title: sv_atm_a

description: average insert size of library: 315.62


title: htert_atm_b

description: average insert size of library: 311.97

value: BJ hTERT+ cell line


title: mRNA_lupus_LH__TBR_3

description:
exp ID: 161220_0011_s07
sample name: S07

value: whole blood


title: sv_3_b

description: average insert size of library: 324.61


title: mRNA_lupus_LN__TBR_2

description:
exp ID: 161220_0011_s06
sample name: S06


title: mRNA_lupus_LH__TBR_2

description:
exp ID: 161220_0011_s05
sample name: S05


title: htert_3_b

description: average insert size of library: 364


title: mRNA_lupus_LH_TBR_1

description:
exp ID: 161220_0011_s04
sample name: S04


title: mRNA_lupus_LN_TBR_1

description:
exp ID: 161220_0011_s02
sample name: S02


title: mRNA_ctrl_2

description:
exp ID: 161220_0011_s03
sample name: S03


title: htert_3_a

description: average insert size of library: 327


title: htert_atm_a

description: average insert size of library: 307


title: bj_atm_b

description: average insert size of library: 306.38

value: Primary BJ cell line


title: bj_atm_a

description: average insert size of library: 314.37


title: sv_3_a

description: average insert size of library: 312


title: bj_3_b

description: average insert size of library: 310


title: bj_3_a

description: average insert size of library: 328.15


title: mRNA_ctrl_1

description:
exp ID: 161220_0011_s01
sample name: S01

value: Healthy Control


title: IFN-γ-stimulated human pericytes_1

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The first 6 nucleotides and the last nucleotides at the point where the Phred score of an examined base fell below 20 were trimmed using in-house scripts.  If, after trimming, the read was shorter than 45-bp, the whole read was discarded.
Trimmed reads were mapped to the human reference genome (hg19) with a known transcriptome index (UCSC Known Gene annotation) with Tophat v2.1.1 using the very-sensitive preset, first strand library type, and providing the corresponding gene model annotation. Only the reads that mapped to a single unique location within the genome, with a maximum of two mismatches in the anchor region of the spliced alignment, were reported in these results.
Tophat alignments were then processed by Cuffdiff to obtain differential gene expression using first strand library type, providing gene model annotation and the genome sequence file for detection and correction of sequence-specific bias that random hexamer can cause during library preparation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKMs, fold changes, and p-values for each condition. Cuffdiff output format.

source_name: human placenta

growth_protocol: HUVECs: ECs, isolated from de-identified umbilical cords following enzymatic digestion by collagenase, were  serially cultured on 0.1% gelatin-coated tissue culture plates in M199 medium (Gibco) containing 20% fetal bovine serum, 2 mM L-glutamine, penicillin (100U/mL), streptomycin (100 µg/mL) supplemented with endothelial cell growth supplement (BD Bioscience) and porcine intestinal heparin (100 µg/mL, Sigma-Aldrich). Cells were used between 1st and 4th passage at which time they uniformly express CD31 and are free of contaminating CD45+ leukocytes assessed by flow cytometry.  Human placental PCs: Samples of de-identified human placenta (approximately 10 cm x 10 cm x 3 cm), taken from the region near the insertion of the umbilical cord, were manually minced and then subjected to collagenase digestion on shaker for 3 hours at 37C°. Microvessel segments were collected by sieving and PCs, obtained by explant outgrowth, were serially cultured in M199 medium (Gibco) containing 20% fetal bovine serum, 2 mM  L-glutamine, penicillin (100U/mL), and streptomycin (100 µg/mL). Cells were used between 2nd and 6th passage at which time they expressed NG2, Thy-1 (CD90) and PDGFR-beta assessed by flow cytometry. Where indicated, ECs and PCs were isolated form the same donor.

extract_protocol:
Total RNA was extracted using the TRIZOL-chloroform extraction method. RNA was cleaned using the QIAGEN Rneasy Cleanup kit.
Poly-A, strand-specific RNA library construction was performed by the Yale Center for Genomic Analysis utilizing the TruSeq Library Prep Kit 2.0 per the manufacturers specifications. . Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries.

treatment_protocol: IFN-γ for 48 hours (50ng/mL)

tag: passage

value: pericytes

value: placenta


title: 3wpf meis2b+/- hearts

city: Bad Nauheim

first: Almary

middle: Victoria

last: Guerra Rodríguez

state: Hessen

address: Ludwigstrasse 43

department: Dept. III Developmental Genetics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

hyb_protocol: cRNA is hybridised on ArrayXS Zebrafish 8x60K at 65°C for 17 h

scan_protocol: Fluorescence signals on microarrays are detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron for SurePrint G3 Gene Expression Microarrays and 5 micron for HD Microarray formats

data_processing: Agilent's Feature Extraction software version 11 is used to read and process the TIFF files.

organism: Danio rerio

source_name: 48 hpf meis2b+/- hearts n=9

label_protocol: For 1st strand synthesis, either oligo-dT primer or a random primer / oligo-dT primer mixture (WT primer) is used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP is performed.

growth_protocol: Zebrafish were grown under standard conditions.  Animal housing was approved by the UCSF and MPG animal committee and concordant with the American and European regulations

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

value: whole heart

tag: age

value: 3 wpf

tag: genotype


title: 3wpf meis2bs988/s988 hearts

source_name: 48 hpf meis2bs988/s988 hearts n=9


title: abcg-C.KNO3-Rep4

city: Montpellier

first: Sandrine

last: Ruffel

address: 2 Place Viala

department: Montpellier University

country: France

institute: INRA

description: Gene expression data in shoots from abcg14 plants having roots treated in homogeneous nitrate media (C.KNO3)

hyb_protocol: Following fragmentation, 5.5 μg of ss-cDNA were hybridized for 16 hr at 48C on GeneChip® Arabidopsis Gene 1.1 ST Array Strip. GeneChips were washed and stained in the GeneAtlas Fluidics Station.

scan_protocol: GeneChips were washed and stained in the GeneAtlas Imaging station.

data_processing: The data were normalized using the Affymetrix software Expression Console using the GC-RMA method.

organism: Arabidopsis thaliana

source_name: Shoots from abcg14 plants having roots treated in homogeneous nitrate media (C.KNO3)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip WT PLUS Reagent kit, Affymetrix).

growth_protocol: Plants were grown in Short Day conditions (8hrs/16hrs) at 23°C day / 21°C night. Plants were grown on basal MS medium (no nitrogen) supplemented 0.5mM Ammonium succinate and 0.1mM Potassium nitrate as the nitrogen sources and 3mM sucrose. After 14 days, plants were transferred for 4 more days on basal MS medium (no nitrogen) supplemented 0.5mM Ammonium succinate and 3mM sucrose.

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

treatment_protocol: Plants were transferred on basal MS supplemented with 1mM Potassium nitrate 1mM for C.KNO3 samples or 1mM Potassium nitrate on one side and 1mM Potassium chloride on the other side for Split samples. Plants were treated for 24 hours before collection.

tag: root treatment


title: abcg-Split-Rep4

description: Gene expression data in shoots from abcg14 plants having roots treated in heterogeneous nitrate media (Split)

source_name: Shoots from abcg14 plants having roots treated in heterogeneous nitrate media (Split)

value: Split


title: IFN-γ-stimulated human pericytes_2


title: 3mpf WT Ventricle

source_name: 3 mpf WT ventricle n=10

value: Ventricle

value: 3 mpf

value: WT


title: 3mpf WT Atrium

source_name: 3 mpf WT atria n=10

value: atria


title: Col-C.KNO3-Rep4

description: Gene expression data in shoots from wild-type plants having roots treated in homogeneous nitrate media (C.KNO3)

source_name: Shoots from wild-type plants having roots treated in homogeneous nitrate media (C.KNO3)


title: IFN-γ-stimulated human pericytes_3


title: 3mpf meis2bs988/s988 atria

source_name: 3 mpf meis2bs988/s988 atria n=10


title: ipt-Split-Rep3

description: Gene expression data in shoots from ipt3,5,7 plants having roots treated in heterogeneous nitrate media (Split)

source_name: Shoots from ipt3,5,7 plants having roots treated in heterogeneous nitrate media (Split)


title: A549_mock_48h_rep1

city: Beijing

first: Sen

last: Zhang

address: East Street of Fengtai

country: China

institute: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

description: replicate 1

hyb_protocol: Array hybridization was performed according to the MicroRNA Assay Laboratory Workflow for BeadChips.

data_processing: The data were normalised using average normalisation with IlluminaGUI in R

label: biotin

source_name: A549 cells, mock-infected, 48h, replicate 1

label_protocol: Sample labeling was performed according to the MicroRNA Assay Laboratory Workflow for BeadChips.

growth_protocol: A549 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and maintained at 37℃ in a 5% CO2 incubator.

extract_protocol: Total RNA was extracted from cells using a mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific) in accordance with the prescribed protocol provided with the kit. And the RNA samples were quantitated with the RiboGreen RNA quantitation kit (Thermo Fisher Scientific).

treatment_protocol: Cells were infected with H5N1 virus at a multiplicity of infection (MOI) of 2 in DMEM medium supplemented with 2% FBS for 48h. And cells were infected with H1N1 virus at a MOI=5 in serum-free medium supplemented with 1% bovine serum albumin and 2 ug/ml TPCK-treated trypsin. Mock groups were treated with PBS in DMEM medium supplemented with 2% FBS for 48h.

value: wild-type A549 cells

tag: infection

value: mock


title: 48 hpf meis2b+/+ embryos

source_name: 48 hpf meis2b+/+ embryos n=20

value: whole embryo

value: 48 hpf


title: A549_H5N1_48h_rep1

description: replicate 1

source_name: A549 cells, infected with H5N1 (MOI=2), 48h, replicate 1


title: A549_mock_24h_rep1

description: replicate 1

source_name: A549 cells, mock-infected, 24h, replicate 1


title: Col-Split-Rep4

description: Gene expression data in shoots from wild-type plants having roots treated in heterogeneous nitrate media (Split)

source_name: Shoots from wild-type plants having roots treated in heterogeneous nitrate media (Split)


title: A549_H5N1_24h_rep1

description: replicate 1

source_name: A549 cells, infected with H5N1 (MOI=2), 24h, replicate 1


title: ipt-Split-Rep4


title: ipt-C.KNO3-Rep4

description: Gene expression data in shoots from ipt3,5,7 plants having roots treated in homogeneous nitrate media (C.KNO3)

source_name: Shoots from ipt3,5,7 plants having roots treated in homogeneous nitrate media (C.KNO3)


title: 48hpf meis2bs988/s988 embryos replicate

source_name: 48 hpf meis2b-/- embryos n=20


title: 3mpf meis2bs988/+ atria

source_name: 3 mpf meis2b+/- atria n=10


title: abcg-Split-Rep3


title: 48 hpf meis2b+/+ embryos replicate


title: ipt-C.KNO3-Rep3


title: Col-C.KNO3-Rep3


title: Col-Split-Rep3


title: abcg-C.KNO3-Rep3


title: Panc-1 iExo-3

description:
SAMPLE7
Cell 7

source_name: Panc-1 cells

tag: cell line

value: Panc-1 cells

tag: treatment

value: KRASG12D siRNA containing exosomes

tag: well


title: IFN-γ-stimulated human endothelial cells_3

source_name: human umbilical vein

value: endothelial cells

value: umbilical vein


title: 48hpf meis2bs988/s988 embryos


title: IFN-γ-stimulated human endothelial cells_1


title: unstimulated human endothelial cells_3


title: unstimulated human endothelial cells_1


title: unstimulated human endothelial cells_2


title: A549_H1N1_48h_rep1

description: replicate 1

source_name: A549 cells, infected with H1N1 (MOI=5), 48h, replicate 1


title: IFN-γ-stimulated human endothelial cells_2


title: A549_H1N1_24h_rep1

description: replicate 1

source_name: A549 cells, infected with H1N1 (MOI=5), 24h, replicate 1


title: 2.0 to 4.0 cm panicles [pare]

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: PARE (uncapped mRNA)

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 34 nucleotides. Small RNA reads were mapped to the rice genome (MSU7).
PARE: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths of 20 nucleotides. Small RNA reads were mapped to the rice genome (MSU7).
Genome_build: MSU7

organism: Oryza sativa Japonica Group

source_name: panicles

extract_protocol: Small RNA libraries were constructed using TruSeq Small RNA Sample Prep kits (Illumina, San Diego, CA). PARE libraries were constructed as previously described (Zhai et al., 2014). All libraries were sequenced on an Illumina HiSeq 2000 instrument at the Delaware Biotechnology Institute (Newark, DE).

value: panicles

tag: Stage


title: Col-C.KNO3-Rep2

source_name: Shoots from wild-type plants having roots treated in homogeneous nitrate media (C.KNO3)


title: abcg-Split-Rep2

source_name: Shoots from abcg14 plants having roots treated in heterogeneous nitrate media (Split)


title: Virus Infected cells_2

city: Bareilly

first: Deepak

last: Kumar

state: UP

address: IVRI Road

department: Division of Veterinary Biotechnology

country: India

institute: Indian Veterinary Research Institute

description:
Embryonated egg
Gene expression of virus infected cells after 48hr.
Replicate2

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 25x Agilent fragmentation buffer and 10x Gene expression blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55μl of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Chicken (V2) Gene Expression Microarray, 4x44K (G2519F-026441) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 4 x 44K array slides. Dye channel is set to Green and Green PMT is set to 100%.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Gallus gallus

source_name: Chicken Embryo Fibroblast collected at 48hr from virus infected group

label_protocol: One-colour microarray gene expression analysis was performed using the Chicken microarray slide (4X44K: Agilent - 026441). Total RNA (200 ng) was labelled with Low Input Quick Amp Labelling Kit as per manufacturer's instructions. RNA samples were proceeded (run as technical duplicates) for labelling. The quality check of the labelled cRNA was performed using NanoDrop and the yield and specific activity were estimated.

extract_protocol: RNA isolation from the tissues was performed using QIAGEN RNeasy® Mini Kit as per standard protocol. The purity and concentration of total RNA extracted was checked using NanoDrop spectrophotometer by using 1 µl of total RNA against nuclease-free water as blank to determine the absorbance ratio 260/280 nm. The quality check of the isolated RNA was performed in Agilent 2100 Bioanalyzer as per standard protocol using the Agilent RNA 6000 Nano Kit. The extracted RNA was found to be of good quality, having RNA integrity number (RIN) greater than 7.

treatment_protocol: Four groups of chicken embryo fibroblast cells, including one control, one transfected control, one virus infected and one σB-transfected, were used in the study. Group 2 and Group 4 were transfected with 3μg of plasmid and collected at 48hr seeing expression in cell by qPCR. Group 1, kept as control, was collected after 48 hr. Group 3 was infected with 15 MOI of Avian Reovirus and collected after 48hr. The cells were collected in RNase-free 1.5 ml centrifuge tube and proceeded further of total RNA isolation.

value: Chicken embryo fibroblasts

value: 10 days

value: Avian Reovirus infected


title: 6.0 to 8.0 cm panicles, rep 2 [pare]

description: PARE (uncapped mRNA)


title: pDs-Red-σB transfected cells_2

description:
Embryonated egg
Gene expression of pDs-Red-σB transfected cells after 48hr.
Replicate2

source_name: Chicken Embryo Fibroblast collected at 48hr from pDs-Red-σB transfected group

value: pDs-Red-sigmaB transfected


title: Anthers - microspore stage [pare]

description: PARE (uncapped mRNA)

source_name: anther

value: anther

value: microspore stage


title: abcg-Split-Rep1

value: Split


title: Virus Infected cells_1

description:
Embryonated egg
Gene expression of virus infected cells after 48hr.
Replicate1


title: 6.0 to 8.0 cm panicles, rep 1 [pare]

description: PARE (uncapped mRNA)


title: Col-Split-Rep2


title: pDs-Red-σB transfected cells_1

description:
Embryonated egg
Gene expression of pDs-Red-σB transfected cells after 48hr.
Replicate1


title: Anthers - pollen stage, rep 3

description: small RNA

value: pollen stage


title: ipt-C.KNO3-Rep2


title: Col-Split-Rep1


title: abcg-C.KNO3-Rep1

source_name: Shoots from abcg14 plants having roots treated in homogeneous nitrate media (C.KNO3)


title: ipt-C.KNO3-Rep1


title: ipt-Split-Rep2

source_name: Shoots from ipt3,5,7 plants having roots treated in heterogeneous nitrate media (Split)


title: ipt-Split-Rep1


title: pDs-Red transfected cells_2

description:
Embryonated egg
Gene expression of pDs-Red transfected cells after 48hr.
Replicate2

source_name: Chicken Embryo Fibroblast collected at 48hr from pDs-Red transfected group

value: pDs-Red transfected


title: Anthers - pollen stage, rep 2

description: small RNA


title: pDs-Red transfected cells_1

description:
Embryonated egg
Gene expression of pDs-Red transfected cells after 48hr.
Replicate1


title: abcg-C.KNO3-Rep2


title: Control Cell_2

description:
Embryonated egg
Gene expression of control cells after 48hr.
Replicate2

source_name: Chicken Embryo Fibroblast collected at 48hr from control group

value: Control


title: Control Cell_1

description:
Embryonated egg
Gene expression of control cells after 48hr.
Replicate1


title: Anthers - pollen stage, rep 1

description: small RNA


title: Anthers - mitosis stage, rep 3

description: small RNA

value: mitosis stage


title: Anthers - microspore stage, rep 2

description: small RNA


title: Anthers - microspore stage, rep 3

description: small RNA


title: ATAC-seq from A549 (ENCLB804WMR)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR288YMH/
***************
biological replicate number: 3
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR288YMH
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB804WMR
size range: >200

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 4 hours

extract_protocol: not provided

tag: line

value: cell line

tag: biosample encode accession

value: male

tag: dev stage

value: adult

value: 58 year

tag: lab

value: Tim Reddy, Duke

tag: treatments

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

tag: link

value: ENCBS006KFZ at ENCODE; https://www.encodeproject.org/ENCBS006KFZ/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ATAC-seq from A549 (ENCLB846KGA)

description:
https://www.encodeproject.org/experiments/ENCSR288YMH/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR288YMH
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB846KGA
size range: >200

tag: Sex

value: ENCBS402NSI at ENCODE; https://www.encodeproject.org/ENCBS402NSI/


title: Anthers - microspore stage, rep 1

description: small RNA

tag: tissue


title: Col-C.KNO3-Rep1


title: Ky-72 and salt stress rep. 3

city: Lubbock

first: chien

middle: Van

last: ha

address: 1006 Carton Avenue, Box 43135

department: IGCAST

institute: texas tech university

hyb_protocol: 600 ng of cRNAs  were hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2505B and raw data was extracted using Feature Extraction program ver 9.1.

data_processing: RMA normalization was performed for signals of microarray probes using limma package (Ritchie et al., 2015) on R 2.12.1 program.

label_protocol: Fluorescent-labeled (Cy3) cRNAs were prepared from 400 ng total RNA from each sample using a Quick Amp labeling kit (Agilent Technologies)

growth_protocol: The seeds of Arabidopsis thaliana (ecotype Columbia-0) were sterilized and sown in half-strength Murashige and Skoog (MS) liquid medium (1% sucrose, 0.1% agar) and the plants were grown at 22°C under 16-h-light/8-h-dark for 4 days.

extract_protocol: RNA was extracted from three biological replicates with the RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer’s instructions

treatment_protocol: 5-day-old seedlings that were treated with or without 100 mM NaCl for 2 h after 24 h treatment with 1 μM Ky-9 or Ky-72 or DMSO

tag: agent

tag: group

value: salt stress

tag: ecotype


title: Hair follicle_cyclosporine A treated_6 hours_rep2

city: Manchester

first: Nathan

middle: John

last: Hawkshaw

address: Oxford Road

department: Dermatology

country: United Kingdom

institute: University of Manchester

hyb_protocol: Following fragmentation, 0.05ug/ul of aRNA were hybridized for 16 hours at 45°C on Affymetrix U133 plus 2.0 genechip. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000.

data_processing: Technical quality control and outlier analysis was performed with dChip (V2005) using the default settings. Background correction, quantile normalization, and gene expression analysis were performed using RMA in Bioconductor. To establish relationships and compare variability between samples, principal components analysis (PCA) was used since this method is able to reduce the effective dimensionality of complex gene-expression space without significant loss of information. Differential expression analysis was performed using Limma using a paired-test and functions lmFit and eBayes. Gene lists of differentially expressed genes were controlled for false discovery rate (fdr) errors using the method of QVALUE.

source_name: Male human hair follicles, cyclosporine A, 6 hours.

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from  200ng total RNA (GeneChip 3' IVT Express Kit User Manual, Affymetrix).

growth_protocol: Human hair follicles were incubated in either vehicle control or cyclosporine A for 6 hours.

extract_protocol: Total RNA was extracted from 5 full length HFs for each condition using the RNAeasy mini kit (Qiagen, Manchester, UK) according to manufacturer’s protocol and guidelines.

treatment_protocol: Human hair follicles were cultured with 500μl of CsA at 10-7M (Cat no. #9973S, Cell signalling; Technology, Beverly, MA) or vehicle control. CsA solutions (both stock (10-3M) and working (10-7M)) and vehicle controls were made as previously described (Taylor et al.1993;Journal of investigative dermatology)

value: cyclosporine A, 6 hours.

value: Full length anagen hair follicles

tag: gender

value: Male

tag: age

value: Adult


title: ATAC-seq from A549 (ENCLB622FZX)

description:
https://www.encodeproject.org/experiments/ENCSR265ZXX/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR265ZXX
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB622FZX
size range: >200

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 12 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS533ZLP at ENCODE; https://www.encodeproject.org/ENCBS533ZLP/


title: Ky-72 and salt stress rep. 1


title: Hair follicle_vehicle control_6 hours_rep3

source_name: Male human hair follicles, vehicle control, 6 hours.

value: vehicle control, 6 hours.


title: Anthers - mitosis stage, rep 2

description: small RNA

value: anther

value: mitosis stage


title: Ventricles vs. Atria

hyb_protocol: cRNA is hybridised on 4x44K microarrays at 65°C for 17 h

source_name: 6mpf zebrafish atria, pool of 12

value: Atria

value: 6 mpf

tag: strain

value: AB

source_name: 6mpf zebrafish ventricles, pool of 12

value: Ventricles


title: Ky-9 and salt stress rep. 1

source_name: Ky-9 2h


title: Hair follicle_cyclosporine A treated_6 hours_rep1

tag: treatment


title: Hair follicle_cyclosporine A treated_6 hours_rep3


title: Anthers - mitosis stage, rep 1

description: small RNA


title: Paracancerous tissue 3-2

city: Ningbo

first: Junming

last: Guo

address: 818 Fenghua Road

department: Department of Biochemistry and Molecular Biology, and Zhejiang Provincial Key Laboratory of Pathophysiology

institute: Ningbo University

description: This sample is paired paracancerous tissue from a patient with gastric cancer

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Axon GenePix 4000B microarray scanner.

data_processing: Scanned images were imported into GenePix Pro 6.0 software (Axon) for grid alignment and raw data extraction.Quantile normalization of raw data and subsequent data processing were performed using the R limma software package. The LncRNAs that at least 3 out of 6 samples have flag expressed (greater than 2 times background standard deviation) were retained for further differential analyses.

source_name: Paracancerous tissue,surgery

label_protocol: Samples were amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: LncRNAs/mRNAs were purified from total RNA after removal of rRNA (Arraystar rRNA removal kit).

value: male

value: Paracancerous tissue


title: salt stress rep. 2

source_name: DMSO 2h

value: DMSO


title: 6.0 to 8.0 cm panicles, rep 2

description: small RNA

source_name: panicles

value: panicles


title: Ky-72 and salt stress rep. 2

value: salt stress


title: Hair follicle_vehicle control_6 hours_rep2

value: Full length anagen hair follicles


title: salt stress rep. 3


title: Hair follicle_vehicle control_6 hours_rep1

value: Male


title: Paracancerous tissue 2-2

value: female


title: 6.0 to 8.0 cm panicles, rep 3

description: small RNA


title: Ky-9 and salt stress rep. 3

source_name: ky-9 2h


title: ATAC-seq from A549 (ENCLB330STL)

description:
https://www.encodeproject.org/experiments/ENCSR288YMH/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR288YMH
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB330STL
size range: >200

value: cell line

value: adult

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS360YMB at ENCODE; https://www.encodeproject.org/ENCBS360YMB/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: salt stress rep. 1


title: 6.0 to 8.0 cm panicles, rep 1

description: small RNA


title: Paracancerous tissue 1-2


title: ATAC-seq from A549 (ENCLB969KTX)

description:
https://www.encodeproject.org/experiments/ENCSR265ZXX/
***************
biological replicate number: 3
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR265ZXX
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB969KTX
size range: >200

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS404OUV at ENCODE; https://www.encodeproject.org/ENCBS404OUV/


title: ATAC-seq from A549 (ENCLB170KFO)

description:
https://www.encodeproject.org/experiments/ENCSR265ZXX/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR265ZXX
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB170KFO
size range: >200

value: male

value: ENCBS301SWX at ENCODE; https://www.encodeproject.org/ENCBS301SWX/


title: 2.0 to 4.0 cm panicles, rep 3

description: small RNA


title: ATAC-seq from A549 (ENCLB514OGC)

description:
https://www.encodeproject.org/experiments/ENCSR220ASC/
***************
biological replicate number: 3
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR220ASC
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB514OGC
size range: >200

source_name: Homo sapiens A549 cell line

value: ENCBS565TIR at ENCODE; https://www.encodeproject.org/ENCBS565TIR/


title: 2.0 to 4.0 cm panicles, rep 2

description: small RNA

value: panicles


title: ATAC-seq from A549 (ENCLB768JUJ)

description:
https://www.encodeproject.org/experiments/ENCSR220ASC/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR220ASC
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB768JUJ
size range: >200

value: ENCBS586UFT at ENCODE; https://www.encodeproject.org/ENCBS586UFT/


title: 2.0 to 4.0 cm panicles, rep 1

description: small RNA


title: Gastric cancer tissue 3-1

description: This sample is cancer tissue from a patient with gastric cancer

source_name: Gastric cancer tissue,surgery

value: Gastric cancer tissue


title: ATAC-seq from A549 (ENCLB522HCS)

description:
https://www.encodeproject.org/experiments/ENCSR220ASC/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR220ASC
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB522HCS
size range: >200

value: ENCBS213TPT at ENCODE; https://www.encodeproject.org/ENCBS213TPT/


title: 0.5 to 1.0 cm panicles, rep 3

description: small RNA


title: Gastric cancer tissue 2-1

value: female


title: Mated queen 3

city: College Station

first: Cecilia

last: Tamborindeguy

address: Heep Center

institute: Texas A&M University

data_processing:
Libraries were sequenced using the Illumina HiSeq 2500. Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.68 and RTA 1.18.66.3 software with default parameter settings. Sequencer .bcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2.17.1.14 script configureBclToFastq.pl.
The RNA-seq reads that passed the quality filters were mapped to the fire ant reference genome (Si_gnG, official gene set v.2.2.3)  using the Tuxedo RNA-seq pipeline (Trapnell et al., 2013, Trapnell et al., 2009, Trapnell et al., 2010) in cyverse.org
Genome_build: GCA_000188075.1
Supplementary_files_format_and_content: .gtf file reports Cufflinks output

organism: Solenopsis invicta

source_name: Mated queen, brain

extract_protocol:
Brains were disssected in ice-cold PBS , flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq   Stranded Total RNA library Prep Kit was used with 1 ug of total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols with the Illumina TruSeq  Stranded Total RNA library Prep Kit  with 1 ug of total RNA

value: brain

tag: developmental stage

value: de-alate mated

tag: social form

value: polygyne


title: Mated queen 2


title: Mated queen 1


title: ATAC-seq from A549 (ENCLB371TNS)

description:
https://www.encodeproject.org/experiments/ENCSR139OYS/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR139OYS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB371TNS
size range: >200

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 1 hour

tag: line

value: cell line

value: adult

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

value: ENCBS211HEU at ENCODE; https://www.encodeproject.org/ENCBS211HEU/


title: ATAC-seq from A549 (ENCLB287TUS)

description:
https://www.encodeproject.org/experiments/ENCSR139OYS/
***************
biological replicate number: 3
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR139OYS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB287TUS
size range: >200

tag: biosample encode accession

value: male

value: ENCBS542BDV at ENCODE; https://www.encodeproject.org/ENCBS542BDV/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ATAC-seq from A549 (ENCLB072IUX)

description:
https://www.encodeproject.org/experiments/ENCSR139OYS/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR139OYS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB072IUX
size range: >200

tag: dev stage

value: ENCBS017CJM at ENCODE; https://www.encodeproject.org/ENCBS017CJM/


title: Mated queen 4


title: 0.5 to 1.0 cm panicles, rep 1

description: small RNA

value: panicles

tag: Stage


title: 0.5 to 1.0 cm panicles, rep 2

description: small RNA


title: Ky-9 and salt stress rep. 2

value: salt stress


title: 0.1 to 0.2 cm panicles, rep 3

description: small RNA


title: ATAC-seq from A549 (ENCLB870IBA)

description:
https://www.encodeproject.org/experiments/ENCSR074AHH/
***************
biological replicate number: 3
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.
experiment encode accession: ENCSR074AHH
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB870IBA
size range: >200

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 8 hours

tag: lab

tag: treatments

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:8; duration_units:hour;

value: ENCBS353ZPN at ENCODE; https://www.encodeproject.org/ENCBS353ZPN/


title: 0.1 to 0.2 cm panicles, rep 2

description: small RNA


title: Gastric cancer tissue 1-1

value: Gastric cancer tissue


title: Ky-72 rep. 2

value: non-stress


title: Ky-72 rep. 3


title: Virgin queen 3

source_name: Virgin queen, brain

value: brain

value: alate virgin

value: polygyne

tag: Sex

value: female


title: Virgin queen 4

tag: tissue


title: Ky-72 rep. 1

tag: agent


title: Ky-9 rep. 2

source_name: Ky-9 0h

tag: group


title: Ky-9 rep. 3

tag: ecotype


title: Ky-9 rep. 1


title: DMSO control rep. 1

source_name: DMSO 0h

value: DMSO


title: DMSO control rep. 2


title: DMSO control rep. 3


title: ATAC-seq from A549 (ENCLB541HCS)

description:
https://www.encodeproject.org/experiments/ENCSR074AHH/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.
experiment encode accession: ENCSR074AHH
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB541HCS
size range: >200

value: cell line

value: adult

value: 58 year

value: Tim Reddy, Duke

tag: link

value: ENCBS998NWZ at ENCODE; https://www.encodeproject.org/ENCBS998NWZ/


title: 0.1 to 0.2 cm panicles, rep 1

description: small RNA


title: Virgin queen 2


title: HYP

city: Rochester

first: Jie

last: Sun

institute: Mayo Clinic

description: non-responder

data_processing:
Basecalls performed using Illumina bcl2fastq2 versions bcl2fastq-1.8.4 (before therapy) and 2.17.1.14 after therapy)
Sequence reads were aligned to the hg38 genome assembly using TopHat2
Raw and normalized gene genecounts (RPKM) are generated by Featuregenecounts
Genome_build: hg38
Supplementary_files_format_and_content: counts

source_name: T cells from peripheral blood

extract_protocol:
CD8+ T cells were sorted by flow cytometer, and RNA was extracted with RNeasy Mini kit . A total of 1 ng RNA was used to generate double stranded cDNA using SMARTer Ultra Low RNA kit for Illumina. The libraries were sequenced using the 101 bases paired-end protocol on Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: marker

value: CD11a-high CD8+ T cells

value: after PD-1 blockade therapy


title: Virgin queen 1


title: ATAC-seq from A549 (ENCLB501QMW)

description:
https://www.encodeproject.org/experiments/ENCSR074AHH/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.
experiment encode accession: ENCSR074AHH
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2018-04-23
lab: Tim Reddy, Duke
library encode accession: ENCLB501QMW
size range: >200

value: male

tag: age

value: ENCBS435CFB at ENCODE; https://www.encodeproject.org/ENCBS435CFB/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: COM

description: responder


title: THP-1_Cgyps(1-11)(delta)_6h_rep2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description: Gene expression after 6 h in Cgyps(1-11)Δ infected THP-1 cells

hyb_protocol: 600 ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Agilent designed Human Gene expression Microarray 8x60K (AMADID No: G4858A_39494) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using the Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the quantile normalization method .

source_name: THP-1-Cgyps(1-11)(delta), 6h, replicate 2

label_protocol: Samples for Gene expression were labeled using the Agilent Quick-Amp labeling Kit (p/n5190-0442). 500 ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasyMini kit columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: THP-1 monocytes were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum at 37°C in a humified incubator with 5% CO2. For THP-1 cells differentiation, cells were treated with 16 nM PMA for 12 h and then replenished with fresh RPMI medium. Yeast cells were grown in YPD medium at 30°C for 14-16 h.

extract_protocol: RNA extraction was performed using the Trizol method. as per manufacturer’s protocol. The concentration and purity of the RNA extracted were evaluated using the Nanodrop Spectrophotometer (Thermo Scientific; 1000).

treatment_protocol: PMA-differentiated THP-1 cells were infected with Candida glabrata strains

tag: cell line

value: THP-1 macrophages

tag: timepoint

value: 6 h

tag: infection

value: Cgyps(1-11)(delta) infected


title: uninduced ∆letS+pletS (OFF), Fraquil OD600 = 1 for 2h at 42oC, biological rep 2

type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

description:
Legionella pneumophila uninduced ∆letS+pletS (OFF) exposed to Fraquil OD600 = 1 for 2h at 42oC, biological replicate 2
OFF_rep_2

hyb_protocol: Hybridization protocol was performed as previously described (Hovel-Miner, G. 2009. JB, 191: 2461)

scan_protocol: Scanning and image acquisition was performed on a InnoScan 710 using the mapix software. Spot intensity an local background was measured.

data_processing: Data were processed with the mapix software. Values from each channel were background subtracted and the % contribution of each spots to the total fluorsecence in each channel was calculated. Then the ratio Ch2/Ch1 was calculated. We used gDNA for data normalization accross slides, as described in Talaat, 2002, NAR.

label: Alexa Fluor 546

organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

source_name: Reference

label_protocol: RNA: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 647 as previously described (Hovel-Miner, G 2009. JB, 191:2461). Genomic DNA: 5 ug of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Porwollik, S. 2001. Mutat Res 483:1). Subsequently, the resulting DNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 546.

growth_protocol: Each strain was grown at 37oC for 3 days from a -80oC frozen stock by streaking on CYE agar.

extract_protocol: RNA: TRIzol reagent (Invitrogen). Genomic DNA: QIAamp kit (QIAgen).

treatment_protocol: Each strain was suspended at an OD600 of 1 in Fraquil and washed 3 times, before incubating at 42oC for 2 hours.

tag: strain

value: KS79 (WT)

tag: condition

value: AYE broth, 37oC shaking

label: Alexa Fluor 647

source_name: uninduced ∆letS+pletS (OFF)

value: uninduced ∆letS+pletS (OFF)

value: Fraquil, 42oC, 2h


title: uninduced ∆letS+pletS (OFF), Fraquil OD600 = 1 for 2h at 42oC, biological rep 3

description:
Legionella pneumophila uninduced ∆letS+pletS (OFF) exposed to Fraquil OD600 = 1 for 2h at 42oC, biological replicate 3
OFF_rep_3


title: THP-1_Cgvps34(delta)_6h_rep2

description: Gene expression after 6 h in Cgvps34Δ infected THP-1 cells

source_name: THP-1-Cgvps34(delta), 6h, replicate 2

value: Cgvps34(delta) infected


title: induced ∆letS+pletS (ON), Fraquil OD600 = 1 for 2h at 42oC, biological rep 1

description:
Legionella pneumophila induced ∆letS+pletS (ON) exposed to Fraquil OD600 = 1 for 2h at 42oC, biological replicate 1
ON_rep_1

source_name: induced ∆letS+pletS (ON)

value: induced ∆letS+pletS (ON)


title: induced ∆letS+pletS (ON), Fraquil OD600 = 1 for 2h at 42oC, biological rep 2

description:
Legionella pneumophila induced ∆letS+pletS (ON) exposed to Fraquil OD600 = 1 for 2h at 42oC, biological replicate 2
ON_rep_2


title: stroma_cultured with leukemic cells_rep4

city: Milan

first: Linda

last: Pattini

address: piazza Leonardo da Vinci, 32

department: Department of Electronics, Information and Bioengineering

country: Italy

institute: Politecnico di Milano

description:
replicate 4
9969472034_H

data_processing: Variance was stabilized and data were normalised using quantile normalisation with lumi in R

source_name: murine spleen stromal cell line (mSSC-YFP) cultured for 48 hrs with  Eμ-TCL1 leukemia cells

label_protocol: Biotin

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum and antibiotics.

extract_protocol: Total RNA was extracted from sorted stroma, using the RNeasy minikit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Stroma was co-cultured with control or leukemic splenic B cells in a ratio 1:20, for 40-48hrs. After, stroma was separated from the B-lymphocytes using MoFlo™ XDP (Beckman Coulter) cell sorter.

value: Stroma spleen-derived; Eu-TCL1 leukemia B cells spleen derived

tag: developmental stage

value: Stroma immortalized from E18.5 embryonic spleen; leukemia B cells spleen derived B cells from adult Eu-TCL1 mouse higly leukemic

tag: passage

value: Stroma from 2 to 6 passage;

tag: cell type

value: leukemic Bcells:primary


title: induced ∆letS+pletS (ON), Fraquil OD600 = 1 for 2h at 42oC, biological rep 3

description:
Legionella pneumophila induced ∆letS+pletS (ON) exposed to Fraquil OD600 = 1 for 2h at 42oC, biological replicate 3
ON_rep_3


title: uninduced ∆letS+pletS (OFF), Fraquil OD600 = 1 for 2h at 42oC, biological rep 1

description:
Legionella pneumophila uninduced ∆letS+pletS (OFF) exposed to Fraquil OD600 = 1 for 2h at 42oC, biological replicate 1
OFF_rep_1


title: THP-1_Cgyps(1-11)(delta)_6h_rep1

source_name: THP-1-Cgyps(1-11)(delta), 6h, replicate 1


title: stroma_cultured with control splenic B cells_rep3

description:
replicate 3
9969472034_E

source_name: murine spleen stromal cell line (mSSC-YFP) cultured for 48 hrs with control splenic B cells

value: Stroma spleen-derived; control B cells spleen derived

value: Stroma immortalized from E18.5 embryonic spleen; control B cells from adult mouse aged match with Eu-TCL1 mouse

value: Stroma from 2 to 6 passage

value: control Bcells:primary


title: stroma_cultured with control splenic B cells_rep4

description:
replicate 4
9969472034_G


title: THP-1_wt_6h_rep2

description: Gene expression after 6 h in Candida glabrata wt infected THP-1 cells

source_name: THP-1-wt, 6h, replicate 2

value: THP-1 macrophages

value: Candida glabrata wt infected


title: THP-1_PBS_6h_rep2

description: Gene expression after 6 h in uninfected THP-1 cells

source_name: THP-1-PBS, 6h, replicate 2

value: 6 h

value: uninfected


title: stroma_cultured with leukemic cells_rep3

description:
replicate 3
9969472034_F


title: ∆letS, Fraquil OD600 = 1 for 2h at 42oC, biological rep 3

description:
Legionella pneumophila ∆letS exposed to Fraquil OD600 = 1 for 2h at 42oC, biological replicate 3
letS_rep_3

value: KS79 (WT)

value: AYE broth, 37oC shaking

source_name: ∆letS

value: ∆letS


title: stroma_cultured with control splenic B cells_rep1

description:
replicate 1
9969472034_A


title: stroma_cultured with control splenic B cells_rep2

description:
replicate 2
9969472034_C


title: ∆letS, Fraquil OD600 = 1 for 2h at 42oC, biological rep 2

description:
Legionella pneumophila ∆letS exposed to Fraquil OD600 = 1 for 2h at 42oC, biological replicate 2
letS_rep_2

value: Fraquil, 42oC, 2h


title: stroma_cultured with leukemic cells_rep2

description:
replicate 2
9969472034_D


title: THP-1_wt_6h_rep1

source_name: THP-1-wt, 6h, replicate 1


title: stroma_cultured with leukemic cells_rep1

description:
replicate 1
9969472034_B


title: THP-1_Cgvps34(delta)_6h_rep1

source_name: THP-1-Cgvps34(delta), 6h, replicate 1

value: Cgvps34(delta) infected


title: cholesteatoma-3

first: Hua

last: Yang

address: Department of Otolaryngology, Peking Union Medical College Hospital, Beijing, 100730, China

institute: Peking Union Medical College Hospital

description: 11815 lncRNAs and 7692 mRNAs were detected

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).
After quantile normalization of the raw data, LncRNAs and mRNAs that 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: cholesteatoma

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: Total RNA was extracted from cholesteatoma and post-auricular skin tissues using TRIzol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis or Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: All specimens were stored at -80°C immediately after collection for later RNA extraction.

value: cholesteatoma

tag: gender

value: Female


title: ∆letS, Fraquil OD600 = 1 for 2h at 42oC, biological rep 1

description:
Legionella pneumophila ∆letS exposed to Fraquil OD600 = 1 for 2h at 42oC, biological replicate 1
letS_rep_1


title: KS79, Fraquil OD600 = 1 for 2h at 42oC, biological rep 1

description:
Legionella pneumophila KS79 exposed to Fraquil OD600 = 1 for 2h at 42oC, biological replicate 1
KS_rep_1


title: THP-1_PBS_6h_rep1

source_name: THP-1-PBS, 6h, replicate 1


title: normal skin-4

source_name: normal skin

value: normal skin

value: Male


title: cholesteatoma-4


title: normal skin-3


title: KS79, Fraquil OD600 = 1 for 2h at 42oC, biological rep 2

description:
Legionella pneumophila KS79 exposed to Fraquil OD600 = 1 for 2h at 42oC, biological replicate 2
KS_rep_2


title: drug (3853-EA_3207)

city: East Lansing

first: Jing-Ru

last: Jhan

state: MI

address: 567 Wilson Rd BPS 2120

department: Physiology

institute: Michigan State University

description: Gene expression data after drug treatment

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

scan_protocol: Affymetrix genechip scan system

data_processing: CHP data was generated using expression console.

source_name: mouse mammary tumors, drug

label_protocol: biotin

extract_protocol: Total RNA was isolated using Qiagen Rneasy midi prep kit.

value: mammary tumors

tag: treatment

value: combination of VX680, miltefosine, WP1066


title: drug (3854-EA_3208)

tag: tissue


title: Green receptacle R1

city: CÓRDOBA

first: Francisco

middle: Javier

last: Molina-Hidalgo

state: Cordoba

address: Edif. Severo Ochoa (C6.) Planta Baja-Ala Norte Campus de Rabanales

department: Biochemistry and molecular biology

country: Spain

institute: University of Cordoba

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Data analysis of the microarray expression studies was performed with the software for gene expression analysis Array Star (DNASTAR). The moderated t-test and FDR (Benjamini and Hochberg, 1995) for multiple testing corrections were used, with a confidence p-value < 0.05 in order to statistically identify significant differences.

organism: Fragaria x ananassa

source_name: Strawberry green unripen receptacle replicate 1

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Strawberry plants (F. x ananassa) were grown in plant chamber at 25 ºC, 10.000 lux and 80% humidity and afterwards maintained in a greenhouse.

extract_protocol: Total RNA was isolated from independent strawberry fruits as stated by Asif et al. (2000). The total RNA obtained was treated with DNase I (RNase free) (Invitrogen), in accordance with the manufacturer's instructions, to remove genomic DNA contamination, after which it was purified by using the RNeasy Mini kit (Qiagen).

treatment_protocol: Fruits were harvested in green and red stages.

value: green unripen receptacle replicate 1

value: Inmature fruits


title: KS79, Fraquil OD600 = 1 for 2h at 42oC, biological rep 3

description:
Legionella pneumophila KS79 exposed to Fraquil OD600 = 1 for 2h at 42oC, biological replicate 3
KS_rep_3

source_name: Reference


title: Green receptacle R2

source_name: Strawberry green unripen receptacle replicate 2

value: green unripen receptacle replicate 2


title: Red receptacle R3

source_name: Strawberry red ripen receptacle replicate 3

value: red ripen receptacle replicate 3

value: Mature fruits


title: vehicle (3850-EA_3204)

description: Gene expression data after vehicle treatment

source_name: mammary tumors, vehicle

value: vehicle


title: cholesteatoma-2


title: vehicle (3849-EA_3203)


title: Red receptacle R1

source_name: Strawberry red ripen receptacle replicate 1

value: red ripen receptacle replicate 1


title: cholesteatoma-1


title: Red receptacle R2

source_name: Strawberry red ripen receptacle replicate 2

value: red ripen receptacle replicate 2


title: Green receptacle R3

source_name: Strawberry green unripen receptacle replicate 3

value: green unripen receptacle replicate 3


title: drug (3852-EA_3206)


title: vehicle (3851-EA_3205)


title: normal skin-2


title: normal skin-1


title: 3159Cit-80

status: Public on May 08 2018

type: genomic

city: Lebanon

first: Lucas

middle: A.

last: Salas

state: NH

address: 1 Medical Center Dr, DHMC

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

description: whole blood from a healthy male time 1

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

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

data_processing: BeadStudio software

label: Cy5 and Cy3

source_name: whole blood

label_protocol: Standard Illumina Protocol

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

tag: ChIP

tag: Sex

tag: array

tag: slide

tag: cd4t proportion

tag: cd8t proportion

tag: nk proportion

tag: bcell proportion

tag: monocytes proportion

tag: granulocytes proportion

tag: neutrophils proportion


title: 3045Cit-80

description: whole blood from a healthy male time 1

tag: age


title: 3082Cit-80

description: whole blood from a healthy male time 1


title: 3021Cit-80

description: whole blood from a healthy male time 1


title: 3177Cit-80

description: whole blood from a healthy male time 1


title: Mono1775

description:
Cell Pellet Mono
201870610056_R08C01

source_name: MACS purified blood cells

value: ChristensenLab

value: Mono

tag: bcell

tag: nk

tag: mono

tag: neu

tag: purity

value: M

tag: bmi

value: Overweight

value: Mixed

value: Mexican

tag: smoker

value: No


title: Th2546

description:
Cell Pellet CD4T
201870610111_R04C01

tag: ChIP

tag: cell type

tag: Sex

value: African-American

tag: array


title: B1 mix

description:
Reconstructed DNA mixture method B
201869680030_R07C01

value: B1 mix

value: MIX

tag: slide


title: Neut2270

description:
Cell Pellet Neu
201870610111_R05C01

value: Neu

value: Normal

value: Indo-European

value: Caucasian


title: A3 mix

description:
Reconstructed DNA mixture method A
201869680008_R06C01

value: A3 mix


title: A6 mix

description:
Reconstructed DNA mixture method A
201870610056_R03C01

value: A6 mix


title: Th2611

description:
Cell Pellet CD4T
201870610111_R06C01

value: East-Asian

value: Japanese


title: 3093Cit-80

description: whole blood from a healthy male time 1

value: Male

tag: cd4t proportion

tag: cd8t proportion

tag: nk proportion

tag: bcell proportion


title: B4 mix

description:
Reconstructed DNA mixture method B
201869680008_R03C01

value: B4 mix

value: ChristensenLab

tag: age


title: ST2007

description:
Cell Pellet CD8T
201869680009_R08C01

tag: bcell

value: M

value: Obese


title: NKpan2503

description:
Cell Pellet NK
201870610056_R07C01

value: NK

tag: nk

value: Portuguese

value: No


title: B0104

description:
Cell Pellet Bcell
201869680030_R02C01

value: Bcell

tag: mono

value: Yes


title: Th2535-2

description:
Cell Pellet CD4T
201869680030_R06C01

tag: replicate

tag: neu


title: B2005

description:
Cell Pellet Bcell
201870610111_R02C01

tag: purity

tag: bmi


title: A1 mix

description:
Reconstructed DNA mixture method A
201870610111_R03C01

value: A1 mix

tag: ChIP

value: MIX

tag: smoker


title: A4 mix

description:
Reconstructed DNA mixture method A
201869680008_R01C01

value: A4 mix

tag: cell type

tag: Sex


title: NKpan1879

description:
Cell Pellet NK
201870610111_R07C01

value: Normal

value: African-American

value: Irish/AA

tag: array

tag: slide


title: A5 mix

description:
Reconstructed DNA mixture method A
201870610056_R01C01

value: A5 mix


title: Th2535-1

description:
Cell Pellet CD4T
201869680030_R01C01

value: Indo-European

value: Caucasian


title: B1877

description:
Cell Pellet Bcell
201869680009_R06C01

value: ChristensenLab

value: F

value: Overweight


title: B5 mix

description:
Reconstructed DNA mixture method B
201869680030_R03C01

value: B5 mix


title: WB1145

description:
Cell Pellet Neu
201870610056_R02C01

value: Neu

value: M


title: B1681

description:
Cell Pellet Bcell
201870610056_R04C01

value: Bcell

value: No


title: NKpan2241

description:
Cell Pellet NK
201870610111_R01C01

value: NK


title: Mono1993

description:
Cell Pellet Mono
201868590267_R07C01

value: Mono

value: Yes


title: Mono2639

description:
Cell Pellet Mono
201869680009_R07C01

value: Normal

value: East-Asian

value: Chinese


title: Tc2637

description:
Cell Pellet CD8T
201868590267_R08C01


title: Tc2615

description:
Cell Pellet CD8T
201868590267_R06C01

value: Mixed

value: Caucasian/Hispanic


title: B3 mix

description:
Reconstructed DNA mixture method B
201868590267_R01C01

value: B3 mix

value: MIX


title: WB1147

description:
Cell Pellet Neu
201868590243_R07C01

value: ChristensenLab

value: F

value: Cauc/Mex/AA


title: PCA1547

description:
Cell Pellet CD8T
201868590243_R06C01

value: Obese

value: Hispanic


title: Mono0933

description:
Cell Pellet Mono
201868590243_R08C01

value: Indo-European

value: Caucasian


title: Tc2636

description:
Cell Pellet CD8T
201868590206_R04C01

value: M

value: No


title: B6 mix

description:
Reconstructed DNA mixture method B
201868590243_R02C01

value: B6 mix


title: Tc0123

description:
Cell Pellet CD8T
201868590206_R05C01

value: Overweight

value: African-American


title: Th1831

description:
Cell Pellet CD4T
201868590206_R08C01

value: Mex/Dutch

value: Yes


title: Neut16936

description:
Cell Pellet Neu
201868590206_R02C01

value: Neu

value: Normal

value: non-hispanic white


title: Th0093

description:
Cell Pellet CD4T
201868590243_R03C01

value: ChristensenLab


title: Mono1972

description:
Cell Pellet Mono
201868590206_R06C01

value: Mono


title: PCA0612

description:
Cell Pellet Neu
201868500150_R01C01

value: Mixed


title: B2 mix

description:
Reconstructed DNA mixture method B
201868590267_R05C01

value: B2 mix

value: MIX


title: Mono0689

description:
Cell Pellet Mono
201868590243_R04C01

value: Obese

value: Indo-European


title: NKpan2510

description:
Cell Pellet NK
201868500150_R03C01

value: NK

value: M

value: Caucasian


title: A2 mix

description:
Reconstructed DNA mixture method A
201868590193_R01C01

value: A2 mix


title: Th1702

description:
Cell Pellet CD4T
201868590193_R03C01

value: Cauc/Brazilian


title: Sample HDAC1/2 -null CM cells Pool 4

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: LA

address: 1430 Tulane Ave

department: Pediatrics

institute: Tulane University School of Medicine

description: MUT4 vs. WT1

hyb_protocol: Manufacturer's protocol (Agilent)

scan_protocol: Scan Protocol: GE2_107_Sep09 Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: Mut Pool 4: FACS-sorted Six2+ cells at embryonic day 15.5

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 μg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3‐ or 5‐labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent V1 Mouse Whole Genome Oligonucleotide Microarray.

extract_protocol: Total RNA was isolated from EGFP+ nephron progenitor cells FACS-sorted from embryonic day 15.5 Six2CreEGFP+; HDAC1&2f/f and Six2CreEGFP+; HDAC1&2+/+ kidneys using RNAqueous‐96 Automated Kit (Ambion) and purified by the RNeasy Mini Kit (Qiagen, Valencia, CA). The quality of RNA samples was assessed by capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: strain

value: embryonic day 15.5

value: FACS-sorted Six2+ nephron progenitor cells (EGFP+)

tag: genotype/variation

value: Mut

source_name: WT Pool 1: FACS-sorted Six2+ cells at embryonic day 15.5

value: WT


title: L12

tag: tissue

value: whole blood

value: Male

tag: time point (days)

tag: date of blood collection

tag: included in the analysis

value: Yes

tag: lymphocytes proportion

tag: monocytes proportion

tag: granulocytes proportion

tag: cd4t proportion

tag: cd8t proportion

tag: nontcells (b +nk) proportion


title: Sample HDAC1/2 -null CM cells Pool 2

description: MUT2 vs. WT1

source_name: Mut Pool 2: FACS-sorted Six2+ cells at embryonic day 15.5

tag: age


title: NKpan1850

description:
Cell Pellet NK
201868590193_R02C01

value: ChristensenLab

tag: ChIP

tag: cell type

tag: bcell

tag: nk

tag: mono

tag: neu

tag: purity

value: F

tag: bmi

value: Mixed

value: Finnish/Creole

tag: smoker

value: No


title: B0044

description:
Cell Pellet Bcell
201868500150_R07C01

value: Bcell

tag: Sex

value: Overweight

value: Indo-European

tag: array

tag: slide


title: Spleen_GR-C3 knockin_LPS_24hr_rep3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

hyb_protocol: Hybridization was done according to the manufacturer's instructions.

scan_protocol: Gene expression was quantified on the nCounter Digital AnalyzerTM.

data_processing: Data were normalized utilizing the manufacturer’s positive and negative experimental control probes, as well as all 4 housekeeping genes (G6pdx, Ppia, Oaz1, and Rpl19)

source_name: spleen, GR-C3 knockin, LPS-treated, 24hour

label_protocol: 100 ng of each total RNA sample was labeled according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from WT and rescued GR-C3 knockin spleens using TRIzol reagent according to the manufacturer's instructions.

tag: gender

value: male

tag: genetic background

value: GR-C3 knockin

tag: agent

value: LPS

tag: time

tag: tissue

value: spleen


title: Spleen_GR-C3 knockin_LPS_24hr_rep2


title: Spleen_GR-C3 knockin_LPS_24hr_rep1


title: NKpan1869

description:
Cell Pellet NK
201868500150_R08C01

tag: ChIP

value: NK

tag: age

value: Caucasian


title: Sample HDAC1/2 -null CM cells Pool 3

description: MUT3 vs. WT1

source_name: Mut Pool 3: FACS-sorted Six2+ cells at embryonic day 15.5

tag: strain

value: embryonic day 15.5

tag: cell type

value: FACS-sorted Six2+ nephron progenitor cells (EGFP+)

tag: genotype/variation

value: Mut

value: WT


title: Control wildtype CM cells Pool 4

description: WT4 vs. WT1

source_name: WT Pool 4: FACS-sorted Six2+ cells at embryonic day 15.5


title: L08

value: whole blood

value: Male

tag: time point (days)

tag: date of blood collection

tag: included in the analysis

value: Yes

tag: lymphocytes proportion

tag: monocytes proportion

tag: granulocytes proportion

tag: cd4t proportion

tag: cd8t proportion

tag: nontcells (b +nk) proportion


title: Control wildtype CM cells Pool 3

description: WT3 vs. WT1

source_name: WT Pool 3: FACS-sorted Six2+ cells at embryonic day 15.5


title: L11

tag: Sex

tag: array

tag: slide

value: No


title: Sample HDAC1/2 -null CM cells Pool 1

description: MUT1 vs. WT1

source_name: Mut Pool 1: FACS-sorted Six2+ cells at embryonic day 15.5


title: Control wildtype CM cells Pool 2

description: WT2 vs. WT1

source_name: WT Pool 2: FACS-sorted Six2+ cells at embryonic day 15.5


title: B1690

description:
Cell Pellet Bcell
201868590193_R06C01

value: ChristensenLab

tag: ChIP

value: Bcell

tag: bcell

tag: nk

tag: mono

tag: neu

tag: purity

value: M

tag: bmi

value: Normal

tag: smoker


title: L06

tag: tissue

tag: time point (days)

tag: date of blood collection

tag: included in the analysis

tag: lymphocytes proportion


title: L09

tag: monocytes proportion

tag: granulocytes proportion

tag: cd4t proportion

tag: cd8t proportion

tag: nontcells (b +nk) proportion


title: Spleen_GR-C3 knockin_LPS_3hr_rep2

source_name: spleen, GR-C3 knockin, LPS-treated, 3hour

tag: gender

value: male

tag: genetic background

value: GR-C3 knockin

tag: agent

tag: time


title: Spleen_GR-C3 knockin_LPS_3hr_rep3

value: LPS

value: spleen


title: Spleen_GR-C3 knockin_LPS_3hr_rep4


title: Sox2/Klf4/Oct4/cMyc and shMsx2 infected MEF at day4

city: Guangzhou

first: lilong

last: Lin

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health，Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: mm10
Supplementary_files_format_and_content: TPM

source_name: Mouse embryonic fibroblast

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

tag: strain

tag: cell type

value: Mouse embryonic fibroblast

tag: passages


title: Sox2/Klf4/Oct4/cMyc and shMsx2 infected MEF at day8


title: Spleen_GR-C3 knockin_LPS_3hr_rep1

tag: tissue


title: Sox2/Klf4/Oct4/cMyc and Msx2 infected MEF at day8


title: Control wildtype CM cells Pool 1

description: WT1 vs. WT1

tag: age

value: embryonic day 15.5

tag: genotype/variation


title: Sox2/Klf4/Oct4/cMyc and Msx2 infected MEF at day4


title: Spleen_GR-C3 knockin_PBS_3hr_rep4

source_name: spleen, GR-C3 knockin, PBS-treated, 3hour

value: PBS


title: L07

tag: ChIP

tag: Sex

tag: time point (days)

tag: date of blood collection

tag: array

tag: slide

tag: included in the analysis


title: Spleen_GR-C3 knockin_LPS_24hr_rep4

tag: gender


title: Sox2/Klf4/Oct4/cMyc and Flag infected MEF at day8


title: L10

tag: lymphocytes proportion

tag: monocytes proportion

tag: granulocytes proportion

tag: cd4t proportion

tag: cd8t proportion

tag: nontcells (b +nk) proportion


title: Mouse embryonic stem cell

source_name: Mouse embryonic stem cell

tag: strain

tag: cell type

value: Mouse embryonic stem cell

tag: passages


title: Spleen_GR-C3 knockin_PBS_3hr_rep3

tag: genetic background

tag: agent

tag: time

tag: tissue


title: Sox2/Klf4/Oct4/cMyc and Flag infected MEF at day4


title: WB1148

description:
Cell Pellet Neu
201868500150_R05C01

tag: ChIP

value: Neu

tag: bcell

tag: nk

tag: mono

tag: neu

tag: purity

tag: Sex

tag: age

tag: bmi

value: Overweight

value: Indo-European

value: Persian

tag: smoker

tag: array


title: Mouse embryonic fibroblast

tag: strain

tag: cell type


title: Spleen_GR-C3 knockin_PBS_3hr_rep2

tag: gender

tag: genetic background


title: Spleen_GR-C3 knockin_PBS_3hr_rep1

tag: agent

tag: time


title: Spleen_WT_LPS_24hr_rep3

source_name: spleen, WT, LPS-treated, 24hour

value: WT

tag: tissue


title: L02

value: whole blood

tag: ChIP

value: Male

tag: time point (days)

tag: date of blood collection

tag: slide

tag: included in the analysis

value: Yes

tag: lymphocytes proportion

tag: monocytes proportion

tag: granulocytes proportion

tag: cd4t proportion

tag: cd8t proportion

tag: nontcells (b +nk) proportion


title: Spleen_WT_LPS_24hr_rep2


title: Spleen_WT_LPS_24hr_rep4


title: JM11_ChIA-PET-2_ZT06

first: Jerome

last: Menet

state: Texas

address: Texas A&M University Biology Department 3258 TAMU College Station, TX 77843

department: Biology

data_processing:
Reads from the orginal fastq files were processed to extract the tag 1 and 2 (i.e., read 1 and 2) along with their accompanying half-linker code and generate two fastq files (R1 and R2 file) containing the sequence identifier, the raw sequence, and the sequence quality values for each tag.
The R1 and R2 fastq files were aligned to the mouse genome (mm10 version) as paired-end reads using bowtie2 and the options -X 5 and --fast
Paired-end tags with both reads mapping uniquely to the mouse genome were filtered in and all other paired tags removed from the analysis.
Paired-end tags (PETs) were parsed based on the half-linker barcodes into non-chimeric PETs (specific products) or chimeric PETs (non-specific products).
Duplicated PETs were removed for both chimeric and non-chimeric products.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimitated text file containing all paired-end tags for the 3 biological replicates with the following data columns;
Supplementary_files_format_and_content: Experiment   Read1   Tag1   chr   start   Read2   Tag2   chr   start   Distance_Read1_Read2

growth_protocol: C57BL/6 mice (3-6 month-old) were entrained to a 12 hours light 12 hours dark cycle with food and water provided ad libitum

extract_protocol:
Mouse liver were collected at ZT06 (middle of the day) or ZT18 (middle of the night), rinsed in ice-cold 1X PBS and flash-frozen. Frozen livers were crushed to a fine powder in liquid nitrogen using a mortar, and crosslinked with 1% formaldehyde (JM11) or with 1. 5mM EGS and 1% formaldehyde (JM08 and JM12). Nuclei were purified, sonciated, and sonicated. Sonicated chromatin was then used to isolate Pol II -DNA complexes with an antibody.
Nuclei were sonicated in 10 mM Tris pH 7.5, 150 mM NaCl, 2 mM EDTA, 0.5% SDS, 0.2% Triton, 1X protease inhibitor cocktail. Chromatin samples from 3-7 livers were pulled together, diluted 5-fold to obtain a final concentration of ChIP buffer of 10mM Tris-Cl pH 7.5, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1X protease inhibitor cocktail. Pol II ChIP were performed in 50 ml canonical tube with 65 µg of anti-RNA Polymerase II 8WG16 monoclonal antibody (# MMS-126R, Covance). Immunoprecipitated chromatin was washed once with TSE I buffer (10mM Tris pH 7.5, 0.1%SDS, 1% Triton X-100, 2mM EDTA, 150mM NaCl, 1mM DTT, 1 mM PMSF), once with TSE II buffer (10mM Tris pH 7.5, 0.1%SDS, 1% Triton X-100, 2mM EDTA, 500mM NaCl, 1mM DTT, 1mM PMSF), once with LiCl Buffer III (10mM Tris pH 7.5, 0.25M LiCl, 1% NP-40, 1% Na Deoxycholate, 1mM EDTA, 1mM DTT, 1mM PMSF), and once with TET buffer (10mM Tris pH 7.5, 1mM EDTA, 0.1% Triton). Beads were finally resuspended in 2 ml of 1X TE buffer supplemented with 1X TE. Immunoprecipitated chromatin was end-repaired, processed for ligation with biotinylated half-linkers, and 5’ phosphorylated while still complexed with Pol II antibodies on magnetic beads following published protocols. Chromatin was then eluted, diluted to a final volume of 10 ml, and used for the proximity ligation step (performed for a minimum of 16 hours at 4ºC under extremely diluted conditions, i.e., < 0.2 ng DNA/μL, to favor ligation events within individual crosslinked chromatin complexes). Following the proximity ligation step, chromatin was treated with proteinase K, reverse crosslinked, and the DNA purified. ChIA-PET DNA was then digested with MmeI, immobilized on streptavidin beads, and ligated to the ChIA-PET adapters. The DNA samples were finally proceeded through nick translation and a PCR amplification step to generate the library. Libraries were ran on an agarose gel, and fragment of ~229 bp were gel-extracted, purified, and quantified.

tag: strain background

tag: genotype/variation

value: wild type

tag: age

value: 3-6 months

value: Liver

tag: time point

value: ZT06 (middle of the day)

tag: chip antibody

value: RNA Polymerase II, clone 8WG16  (Covance, MMS-126R)


title: JM11_ChIA-PET-2_ZT18

tag: tissue

value: ZT18 (middle of the night)


title: Spleen_WT_LPS_3hr_rep3

source_name: spleen, WT, LPS-treated, 3hour

tag: gender

value: male

tag: genetic background

tag: agent

value: LPS

tag: time

value: spleen


title: Spleen_WT_LPS_3hr_rep4


title: Spleen_WT_LPS_24hr_rep1


title: Spleen_WT_LPS_3hr_rep1


title: Spleen_WT_PBS_3hr_rep4

source_name: spleen, WT, PBS-treated, 3hour

value: PBS


title: Spleen_WT_PBS_3hr_rep3


title: Spleen_WT_PBS_3hr_rep2


title: L04

source_name: whole blood

tag: ChIP

tag: Sex

tag: time point (days)

tag: date of blood collection

tag: array

tag: slide

tag: included in the analysis


title: mRNA_Tg_Wh_17mo_rep3

city: Obu

first: SAYURI

last: HIGAKI

state: Aichi

address: 7-430 Morioka-cho

department: Medical Genome Center

institute: National Center for Geriatrics and Gerotology

description:
Transgenic mouse, whole brain, 17-month, replicate3
Gene expression in the whole brain from 17-month-old Tg2576 mouse

hyb_protocol: Cy3-labelled cRNA was hybridized to a Mouse miRNA Release 16.0 8x60 K array (Agilent) or a SurePrint G3 Mouse GE 8x60 K array (Agilent), according to manufacturer’s protocol.

scan_protocol: Slides were scanned using one color scan setting for 8 x 60K array slides with a G2505C Agilent DNA microarray scanner.

data_processing: Images were extracted with Feature Extraction Software 10.7.3.1 (Agilent). For per-chip normalization, miRNA expression data and gene expression data were normalized to the 90th percentiles and median of all values on that chip using GeneSpring GX  (Agilent).

source_name: Transgenic mouse, whole brain, 17-month

label_protocol: For miRNA array, the total RNA was labeled using a miRNA Complete Labeling and Hyb kit. For gene expression array, total RNA was labeled by a Low Input Quick Amp Labeling Kit (Agilent). All procedures were performed according to the manufacturer’s instructions.

extract_protocol: Total RNA including both large and small RNA was extracted from mouse cortices or whole brains using the mirVana PARIS (Ambion, Austin, TX) according to the manufacturer’s instructions. The purity and the quality of RNA samples evaluated by using Nanodrop (Thermo scientific, Hudson, NH) and bioanalyzer (Agilent, Santa Clara, CA) were the required levels for microarray analysis.

tag: genotype

tag: strain

value: Whole brain


title: mRNA_Tg_Wh_17mo_rep2

description:
Transgenic mouse, whole brain, 17-month, replicate2
Gene expression in the whole brain from 17-month-old Tg2576 mouse

tag: age


title: mRNA_Tg_Wh_17mo_rep1

description:
Transgenic mouse, whole brain, 17-month, replicate1
Gene expression in the whole brain from 17-month-old Tg2576 mouse


title: mRNA_Tg_Wh_10mo_rep2

description:
Transgenic mouse, whole brain, 10-month, replicate2
Gene expression in the whole brain from 10-month-old Tg2576 mouse

source_name: Transgenic mouse, whole brain, 10-month


title: mRNA_Wt_Wh_17mo_rep1

description:
Wild type mouse, whole brain, 17-month, replicate1
Gene expression in the whole brain from 17-month-old wild type mouse

source_name: Wild type mouse, whole brain, 17-month

value: Wild type


title: mRNA_Wt_Wh_17mo_rep2

description:
Wild type mouse, whole brain, 17-month, replicate2
Gene expression in the whole brain from 17-month-old wild type mouse


title: L03

tag: lymphocytes proportion

tag: monocytes proportion

tag: granulocytes proportion

tag: cd4t proportion

tag: cd8t proportion

tag: nontcells (b +nk) proportion


title: mRNA_Wt_Wh_10mo_rep2

description:
Wild type mouse, whole brain, 10-month, replicate2
Gene expression in the whole brain from 10-month-old wild type mouse

source_name: Wild type mouse, whole brain, 10-month

tag: tissue