title: MIX-C3,MIX rep3

city: Shanghai

first: Xiaojun

last: Chen

address: No. 419, Fangxie Road

institute: Obstetrics and Gynecology Hospital of Fudan University

description: Gene expression data from ovariectomized mice endometrium(estrogen + high-fat diet)

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

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

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

source_name: endometrium isolated from subcutaneous implantation of the 17-β estradiol (E2) pellet and high-fat diet mice

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

growth_protocol: Mice were matained in above four treatment for 3 months

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

treatment_protocol: Mouse uterus was longitudinally dissected and scraped using the back of a scalpel into RNA Later on ice.

value: female

tag: strain

value: Endometrium


title: WT_WNV_24hr_3

status: Public on Jan 12 2018

type: RNA

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

country: USA

institute: University of Minnesota

description:
251486836592
WT BMDCs were WNV treated and harvested at 24 hours. Replicate number 3

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

molecule: total RNA

organism: Mus musculus

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: BMDCs were prepared from WT or Il-1r-/- mice. Cells from both genotypes were infected with WNV (MOI 2.5). Total RNA was harvested at 24 and 48 hours post-treatment from these and time-matched mock control cells from the appropriate genotype. Relative gene expression levels were determined by Agilent Whole-Genome mouse microarray (4x44K chip)

extract_protocol: Total RNA was extracted from BMDCs using 350 ml/sample buffer RLT in 350 ml of RNA extraction buffer (RLT, Qiagen), and total RNA was extracted using an RNeasy kit (Qiagen).

treatment_protocol: WT or IL-1R KO BMDCs were either mock-treated or pre-treated with 100 ng IL-1b for 24 hours. Cells were then either mock-infected or infected with WNV at an MOI of 2.5.

tag: genotype/variation

value: WT

tag: cell type

value: bone marrow-derived dendritic cells (BMDCs)

tag: treatment

value: WNV

tag: timepoint

tag: replicate


title: CON-B1,CON rep3

country: China

description: Gene expression data from ovariectomized mice endometrium(control group)

label: biotin

source_name: endometrium isolated from chow diet mice

tag: Sex

tag: tissue


title: WT_WNV_24hr_1

description:
251486836640
WT BMDCs were WNV treated and harvested at 24 hours. Replicate number 1


title: WT_WNV_48hr_1

description:
251486836644
WT BMDCs were WNV treated and harvested at 48 hours. Replicate number 1


title: WT_MK_48hr_2

description:
251486836591
WT BMDCs were Mock treated and harvested at 48 hours. Replicate number 2

value: Mock


title: E2C2,E2 rep4

description: Gene expression data from ovariectomized mice endometrium(estrogen)

source_name: endometrium isolated from subcutaneous implantation of the 17-β estradiol (E2) pellet mice


title: WT_MK_48hr_3

description:
251486836643
WT BMDCs were Mock treated and harvested at 48 hours. Replicate number 3


title: WT_MK_24hr_2

description:
251486836590
WT BMDCs were Mock treated and harvested at 24 hours. Replicate number 2


title: IRF5dbdmut_K96S_250nM

type: protein

city: Boston

first: Trevor

last: Siggers

state: MA

address: 24 Cummington Mall

department: Department of Biology

institute: Boston University

description: Each scan voltage is associated with an independent raw data file.

hyb_protocol: Double stranded microarrays were first pre-wetted in PBS containing 0.01% Triton X-100 for five minutes, rinsed in a PBS bath, and then blocked with 2% milk in PBS for 1 hour. Following the blocking step, arrays were washed in PBS containing 0.1% Tween-20 for 5 minutes, then in PBS containing 0.01% Triton X-100 for 2 minutes and finally briefly rinsed in a PBS bath. Arrays were then incubated with the protein sample(s) for one hour in a binding reaction containing: 2% milk with 10 mM Tris, pH 7.5; 50 mM NaCl; 2 mM DTT; 0.2 mg/mL BSA; 0.02% Triton X-100; and 0.4 mg/mL salmon testes DNA (Sigma D7656). After protein incubation, microarrays were washed with PBS containing 0.5% Tween-20 for 3 minutes, then in PBS containing 0.01% Triton X-100 for 2 minutes followed by a brief PBS rinse. Microarrays were then incubated with 20 μg/mL of Alexa Fluor-488 conjugated Anti-GST antibody (LifeTech, Cat# A-11131) in 2% milk in PBS for 20 minutes. Excess antibody was removed by washing with PBS containing 0.05% Tween-20 for 3 minutes, then PBS for 2 minutes.

scan_protocol: Microarrays were scanned with a GenePix 4400A scanner with 50% laser power at multiple PMT voltages. Bad spots were manually flagged and removed.

data_processing: Array scan data were normalized using the MicroArray LINEar Regression software and spatially detrended using the PBM analysis suite (Bulyk Lab)

molecule: protein

organism: Homo sapiens

source_name: Human IRF5

label_protocol: Protein was detected using Alexa Fluor-488 conjugated Anti-GST antibody (LifeTech, Cat# A-11131)

growth_protocol: Transformed bacteria were propagated on Terrific Broth (TB) + 1% glucose + antibiotic plates. Protein expression was carried out in TB + 1% glucose + antibiotic with an initial outgrowth at 37°C up to OD 0.6 followed by 0.5mM IPTG induction and expression at room temperature (~20°C) for 5 hours.

extract_protocol: Bacterial pellets were lysed using a french press homogenizer. Proteins were purified with Glutathione-S-Transferase (GST) affinity chromatography using GSTrapFF columns.

tag: protein sample

tag: sample volume

tag: protein concentration

tag: scan voltage


title: WT_MK_24hr_3

description:
251486836590
WT BMDCs were Mock treated and harvested at 24 hours. Replicate number 3


title: WT_WNV_24hr_2

description:
251486836593
WT BMDCs were WNV treated and harvested at 24 hours. Replicate number 2


title: 3-1,HD rep1

description: Gene expression data from ovariectomized mice endometrium(high-fat diet)

source_name: endometrium isolated from high-fat diet mice


title: WT_WNV_48hr_3

description:
251486836593
WT BMDCs were WNV treated and harvested at 48 hours. Replicate number 3


title: 3-3,HD rep2

source_name: endometrium isolated from high fat-diet mice


title: NHNE post of infection 8 hours

city: Seoul

first: Yung Jin

last: Jeon

address: 101, Daehak-ro

country: South Korea

institute: Seoul National University Hospital

description: PI 8h

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner.

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0).

label: Biotin

source_name: Human middle turbinate mucosa

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: Cultured normal human nasal epithelial (NHNE) cells at 14 days after the creation of the air–liquid interface were used and PAO1 strain of Pseudomonas aeruginosa was inoculated to the apical compartment of the cell culture at 0.25 multiplicity of infection.

extract_protocol: Total RNA was isolated from cell lysates of NHNE cells which were infected with PAO1 at post of infection (PI) 0h and 8h using TRIzol.

treatment_protocol: The cell lysates which were also harvested for microarray and total RNA was isolated from homogenized cell lysates infected with PAO1 at 8 hours using TRIzol® reagent (Invitrogen, Waltham, MA).

value: Cultured normal human nasal epithelial cells


title: WT_MK_48hr_1

description:
251486836591
WT BMDCs were Mock treated and harvested at 48 hours. Replicate number 1


title: NHNE post of infection 0 hour

description: PI 0h


title: MIX-A3,MIX rep2


title: 2-3,E2 rep3


title: HF-C3,HD rep3


title: IRF7_16uL

label: Alexa Fluor-488 conjugated Anti-GST antibody

source_name: Human IRF7

value: 16 uL


title: MIX-A2,MIX rep1


title: IRF5_50uL

value: 50 uL


title: IRF7dbdmut_S101K_250nM


title: IRF7_1.6uL


title: IRF7_0.16uL

value: 22 nM


title: IRF7_8uL

value: 8 uL


title: 2-2,E2 rep2


title: WT_IL1b_48hr_3

description:
251486836642
WT BMDCs were ILB treated and harvested at 48 hours. Replicate number 3

value: ILB


title: unstimulated [Donor C]

city: Oxford

first: Stephen

last: Taylor

address: Headington

country: United Kingdom

institute: CBRG

description:
Donor C
uns_2_C

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using  lumiT followed LumiN using R using the lumi package

source_name: MDMs

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

growth_protocol: We cultured CD14 enriched monocytes in RPMI supllemented with 10% FBS, 2 mM L-Glutamin, 1% penicillin streptomyci and with 100ng/ml hrM-CSF for 5 days.

extract_protocol: RNA was extracted using Rneasu Mini Kit (Qiagen). Quality and integrity of extracted RNA was measured by Nanodrop and Agilent 2100 Bioanalyzer

treatment_protocol: MDMs were pretreated with 10 µM ICG-001 or DMSO vehicle control for 30 min and then stimulated with 200 ng/ml L18-MDP for 2 h.

value: monocyte derived macrophages

tag: agent

value: unstimulated


title: 10 µM ICG-001/L18-MDP [Donor B]

description:
Donor B
mdp_2_icg_B

value: 10 microM ICG-001/L18-MDP


title: JS170307

type: SRA

city: West Haven

first: Matthew

middle: D

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

description: Input sample from TT-TimeLapse-seq with s4U treatment.

library_source: transcriptomic

data_processing:
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
Reads were aligned to the GRCm38 or GRCh38 genome (MEF or K562, respectively) using STAR aligned with default parameters and --mp 4,2 .
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C mutations were identified using Rsamtools and a custom R script (available upon request). Only mutations at positions with a base quality score of greater than 45 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph), and tracks were normalized using DESeq2 (estimateSizeFactors).
Tracks were converted to binary format using IGVtools (toTDF).
Genome_build: GRCm38
Genome_build: GRCh38

source_name: immortalized K562s

growth_protocol: MEF cells were grown in DMEM containing 1% penicillin/streptomycin, 10% FBS, at 37°C. K562 cells were grown in RPMI containing 1% penicillin/streptomycin, 10% FBS, at 37°C.

extract_protocol:
MEF RNA was harvested with Trizol reagent, followed by chloroform extraction and ethanol precipitation. K562 RNA was harvested with a modified RNeasy protocol as described in the methods section. Chemically treated RNAs were treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in the methods section. MTS-enriched RNAs for transient transcriptome studies were prepared using a modified protocol from Duffy et al. Mol Cell (2015), as described in the methods section.
Libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian (Takara Bio USA, cat. 635005).

treatment_protocol: s4U plus and minus MEF cells had their media replaced with growth media supplemented with 1 mM s4U or left unsupplemented, respectively. HS and NHS cells were incubated during this 1h feed at 42°C and 37°C, respectively. For transcriptome-wide studies, s4U plus and minus K562 cells had their growth media supplemented with 100 µM s4U for 4h or left unsupplemented, respectively.  For transient transcriptome studies, s4U plus and minus K562 cells had their growth media supplemented with 1 mM s4U for 5min or left unsupplemented, respectively.

tag: heat shock

value: No

tag: s4u feed

value: Yes

tag: chemical treatment


title: 2-1,E2 rep1

value: female


title: 200 ng/ml L18-MDP [Donor C]

description:
Donor C
mdp_2_C

value: 200 ng/ml L18-MDP


title: 10 µM ICG-001/L18-MDP [Donor C]

description:
Donor C
mdp_2_icg_C


title: 1-3,CON rep1

value: Endometrium


title: 1-2,CON rep2


title: JS170308


title: 200 ng/ml L18-MDP [Donor B]

description:
Donor B
mdp_2_B


title: WT_IL1b_48hr_1

description:
251486836594
WT BMDCs were ILB treated and harvested at 48 hours. Replicate number 1

value: WT

value: bone marrow-derived dendritic cells (BMDCs)


title: WT_IL1b_24hr_3

description:
251486836642
WT BMDCs were ILB treated and harvested at 24 hours. Replicate number 3


title: JS170302

description:
MTS-enriched RNA
TT-TimeLapse-seq samples. For the processed data files, reads of combined replicates (JS170301 and JS170302) filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)
TTtimeLapse.0.min.bedGraph
TTtimeLapse.0.pos.bedGraph
TTtimeLapse.1.min.bedGraph
TTtimeLapse.1.pos.bedGraph
TTtimeLapse.2.min.bedGraph
TTtimeLapse.2.pos.bedGraph
TTtimeLapse.3.min.bedGraph
TTtimeLapse.3.pos.bedGraph
TTtimeLapse.4.min.bedGraph
TTtimeLapse.4.pos.bedGraph
TTtimeLapse.5.min.bedGraph
TTtimeLapse.5.pos.bedGraph


title: WT_IL1b_24hr_2

description:
251486836591
WT BMDCs were ILB treated and harvested at 24 hours. Replicate number 2


title: IRF5_25uL

value: 25 uL


title: WT_IL1b_48hr_2

description:
251486836644
WT BMDCs were ILB treated and harvested at 48 hours. Replicate number 2


title: WT_IL1b_24hr_1

description:
251486836590
WT BMDCs were ILB treated and harvested at 24 hours. Replicate number 1


title: 10 µM ICG-001/L18-MDP [Donor A]

description:
Donor A
mdp_2_icg_A


title: JS170301


title: IRF5_0.5uL


title: KO_WNV_48hr_3

description:
251486836591
IL-1R KO BMDCs were WNV treated and harvested at 48 hours. Replicate number 3

value: IL-1R KO

value: WNV


title: unstimulated [Donor B]

description:
Donor B
uns_2_B


title: IRF5_5uL

value: 5 uL

value: 94 nM


title: IRF3_5uL

source_name: Human IRF3


title: KO_WNV_48hr_2

description:
251486836643
IL-1R KO BMDCs were WNV treated and harvested at 48 hours. Replicate number 2


title: KO_WNV_48hr_1

description:
251486836590
IL-1R KO BMDCs were WNV treated and harvested at 48 hours. Replicate number 1


title: IRF3_10uL

description: Each scan voltage is associated with an independent raw data file.

value: 10 uL


title: KO_WNV_24hr_1

description:
251486836592
IL-1R KO BMDCs were WNV treated and harvested at 24 hours. Replicate number 1


title: 200 ng/ml L18-MDP [Donor A]

description:
Donor A
mdp_2_A


title: KO_WNV_24hr_3

description:
251486836592
IL-1R KO BMDCs were WNV treated and harvested at 24 hours. Replicate number 3


title: IRF3_1uL

value: 1 uL


title: cs142_NS_control_day7

city: St Louis

first: Audrey

last: McAlinden

state: MO

address: 660 South Euclid Avenue

department: Orthopaedic Surgery

institute: Washington University

description: cs142_ns-d7.GCAACGC.run_2243_s_*_withindex_sequence.txt_GCAACGC

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45
Genome_build: Ensembl GRCh38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text MS Excel format

growth_protocol: Human osteoarthritic articular chondrocytes were cultured up to passage 3-4 in DMEM/F12 medium containing 10% FBS to obtain de-differentiated chondrocytes (DDCs).

extract_protocol:
RNA was extracted from lentiviral transduced DDCs using the Total RNA Purification Kit (Norgen) 2 days or 7 days after osteogenic induction
Illumina oligo-DT standard protocol

treatment_protocol: DDCs were seeded in 12 well plates at a density of 2 x10^5 cells/well and transduced with lentivirus over-expressing either pre-miR-138, pre-miR-181ab1 or a non-silencing control RNA (NS). Osteogenic differentiation was then induced by addition of a standard induction α-MEM medium containing 10% FBS, β-glycerophosphate, ascorbate and dexamethsone. At Day 2 or 7 following induction, total RNA was harvested.

tag: clone id

value: Human osteoarthritic articular cartilage

value: De-differentiated chondrocytes (DDCs)

tag: passages

tag: transduced with

value: lentivirus expressing a non-silencing (NS) control precursor RNA

tag: number of reads


title: KO_WNV_24hr_2

description:
251486836642
IL-1R KO BMDCs were WNV treated and harvested at 24 hours. Replicate number 2

tag: genotype/variation

tag: cell type

tag: treatment


title: unstimulated [Donor A]

description:
Donor A
uns_2_A

value: monocyte derived macrophages

value: unstimulated


title: IRF3_0.1uL


title: cs142_mir181_day7

description: cs142_181-d7.TACAGAC.run_2243_s_*_withindex_sequence.txt_TACAGAC

value: lentivirus expressing precursor miR-181ab1


title: cs142_NS_control_day2

description: cs142_ns-d2.ATGACAG.run_2243_s_*_withindex_sequence.txt_ATGACAG


title: cs142_mir181_day2

description: cs142_181-d2.TACATGG.run_2243_s_*_withindex_sequence.txt_TACATGG


title: CAMA1_parental

city: Baltimore

first: Josh

last: Lauring

state: MD

address: 1650 Orleans Street, CRB1 Room 146

department: Oncology

institute: Dr.

hyb_protocol: 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55°C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed.

scan_protocol: Dried arrays were stored in a dark box until scanned with iScan System.

data_processing: Data were extracted with Gene Expression Module in GenomeStudio Software.

source_name: CAMA1 cell line

label_protocol: 500 ng total RNA from each sample was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) as described in the instruction manual.

growth_protocol: Cells were grown in DMEM/F12 medium with 0.5% charcoal dextran treated FBS

extract_protocol: Qiagen RNeasy mini kit with on-column DNAaseI digestion

tag: cell line

value: GATA3 wild type


title: KO_MK_48hr_1

description:
251486836594
IL-1R KO BMDCs were Mock treated and harvested at 48 hours. Replicate number 1

value: Mock

tag: timepoint

tag: replicate


title: KO_MK_48hr_3

description:
251486836644
IL-1R KO BMDCs were Mock treated and harvested at 48 hours. Replicate number 3


title: MCF-7_GATA3_WT_clone1_rep4

source_name: MCF-7-derived GATA3 wild type knock-in clone1 cell line


title: MCF-7_parental_rep4

source_name: MCF-7 cell line

value: GATA3 mutant


title: cs142_mir138_day7

description: cs142_138-d7.TCCCAGC.run_2243_s_*_withindex_sequence.txt_TCCCAGC

tag: tissue

value: lentivirus expressing precuror miR-138


title: CAMA1_GATA3_mutant_knock-in

source_name: CAMA1-derived GATA3 mutant knock-in cell line


title: MCF-7_GATA3_WT_clone1_rep5


title: KO_MK_24hr_2

description:
251486836641
IL-1R KO BMDCs were Mock treated and harvested at 24 hours. Replicate number 2

value: bone marrow-derived dendritic cells (BMDCs)


title: cs131_NS_control_day7

description: cs131_ns-d7.GCTTAGA.run_2243_s_*_withindex_sequence.txt_GCTTAGA


title: MCF-7_GATA3_WT_clone1_rep3


title: MCF-7_GATA3_WT_clone2_rep2

source_name: MCF-7-derived GATA3 wild type knock-in clone2 cell line


title: MCF-7_GATA3_WT_clone2_rep1


title: KO_MK_48hr_2

description:
251486836594
IL-1R KO BMDCs were Mock treated and harvested at 48 hours. Replicate number 2

value: IL-1R KO


title: MCF-7_parental_rep3


title: MCF-7_GATA3_WT_clone1_rep2


title: cs131_mir181_day7

description: cs131_181-d7.TGTTTGT.run_2243_s_*_withindex_sequence.txt_TGTTTGT


title: MCF-7_parental_rep2


title: MCF-7_GATA3_WT_clone1_rep1


title: KO_MK_24hr_3

description:
251486836592
IL-1R KO BMDCs were Mock treated and harvested at 24 hours. Replicate number 3


title: MCF-7_parental_rep1


title: cs142_mir138_day2

description: cs142_138-d2.CGGTGGC.run_2243_s_*_withindex_sequence.txt_CGGTGGC


title: cs131_NS_control_day2

description: cs131_ns-d2.CAATATC.run_2243_s_*_withindex_sequence.txt_CAATATC


title: cs128_mir138_day2

description: cs128_138-d2.GTCTGAT.run_2243_s_*_withindex_sequence.txt_GTCTGAT


title: cs131_mir138_day7

description: cs131_138-d7.GGTCCTC.run_2243_s_*_withindex_sequence.txt_GGTCCTC


title: cs128_mir181_day7

description: cs128_181-d7.TTTAACT.run_2243_s_*_withindex_sequence.txt_TTTAACT


title: cs131_mir138_day2

description: cs131_138-d2.GGGTCAA.run_2243_s_*_withindex_sequence.txt_GGGTCAA


title: mouseZFY(F7-F13).unbound

city: Palo Alto

first: Zheng

last: Zuo

state: CA

address: Stanford

department: Genetics

institute: Stanford university

library_source: genomic

data_processing:
Library strategy: Spec-seq
Binding site extraction: For each sequencing read, the binding site is embedded in the middle with prefixed flanking sequences. So I used unix command "sed -n 's/^.*TCAC.\(.................\)AGAT.*/\1/p' ZFY.bound.raw" to extract the binding site content.
Variant reads counting and sorting: For each randomized binding site, its number in Bound and Unbound portions were counted separately. The Bound/Unbound ratio was supposedly porportional to its relative binding affinity, and the negative logarithm of this ratio indicates the relative binding energy in kT unit.
Energy logo visualization: Based on the binding energy for particular reference and all its single variants, an energy logo can be generated to indicate the specificity of particular protein-DNA interactions.
Energy matrix regression: http://stormo.wustl.edu/cgi-bin/gsahota/sampling.pl
Energy logo visualization: http://stormo.wustl.edu/EnergyModel
Supplementary_files_format_and_content: All processed data were saved in excel files, including the sequence, bound reads, unbound reads, Bound/Unbound ratio, relative binding energy for each variant.

molecule: genomic DNA

organism: synthetic construct

extract_protocol:
After EMSA, DNA fragments were cut and extracted by gel extraction buffer at 50C for 30mins.
For each portion of DNA fragment, PE1-Genetics and indexed PE2 PCR primers were used to PCR amplify extracted DNA by at least 8 cycles (95C 15s, 52C 15s, 72C 30s)
For each particular sample, there are two raw data files, i.e., bound reads and unbound reads with different Illumina Index. The processed data file was based on analysis of Bound and Unbound data together.

treatment_protocol: All EMSA reactions were done in 12% Tris-glycine gel, 200V, 30mins

tag: experimental condition

value: In vitro protein-DNA binding reactions

tag: dna library composition

tag: recombinant protein

value: mouse ZFY DNA binding domain (F7-F13)


title: mouseZFY(F7-F13).bound


title: cs131_mir181_day2

description: cs131_181-d2.AGATACT.run_2243_s_*_withindex_sequence.txt_AGATACT


title: cs128_NS_control_day2

description: cs128_ns-d2.TTTTGTC.run_2243_s_*_withindex_sequence.txt_TTTTGTC


title: cs128_mir138_day7

description: cs128_138-d7.TGAGGTT.run_2243_s_*_withindex_sequence.txt_TGAGGTT


title: humanZFY(F7-F13).unbound

value: human ZFY DNA binding domain (F7-F13)


title: humanZFY(F7-F13).bound


title: humanZFY(F1-F11).bound

value: human ZFY DNA binding domain (F1-F11)


title: cs128_mir181_day2

description: cs128_181-d2.CAAGCCG.run_2243_s_*_withindex_sequence.txt_CAAGCCG


title: cs128_NS_control_day7

description: cs128_ns-d7.ACGTCTG.run_2243_s_*_withindex_sequence.txt_ACGTCTG


title: humanZFY(F1-F11).unbound


title: PC9E1_rep1

status: Public on Jan 11 2018

first: Wen Cai

last: Zhang

state: MASSACHUSETTS

address: 330 BROOKLINE AVENUE, CLS417

department: Pathology

institute: Beth Israel Deaconess Medical Center

description: replicate 1

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

growth_protocol: Human lung cancer cell line PC9 was cultured in DMEM (high glucose) with 10% FBS, 2 MM L-Glutamine and and 1% penicillin-streptomycin.

extract_protocol: RNA was extracted with mirVana miRNA isolation Kit in accordance with the prescribed protocol. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The single cell-derived clones were treated with 0.4 uM- 2 uM gefitinib for 14 days.

value: lung cancer

tag: response to gefitinib

value: tolerant


title: PC9D6_rep1

description: replicate 1


title: PC9E6_rep2

description: replicate 2


title: PC9E3_rep1

description: replicate 1


title: PC9E6_rep1

description: replicate 1


title: PC9E3_rep2

description: replicate 2


title: PC9E2_rep2

description: replicate 2


title: PC9E2_rep1

description: replicate 1


title: PC9B7_rep2

description: replicate 2

value: sensitive


title: PC9D6_rep2

description: replicate 2


title: PC9B7_rep1

description: replicate 1


title: Short period afer parturition cow_010

city: Aichi-gun

first: Shuichi

last: Matsuyama

address: 94 Hatajiri, Morowa

country: Japan

institute: Nagoya University

hyb_protocol: For microarray hybridization, 1650 ng of Cy3-labeled cRNA was fragmented and hybridized on a slide of bovine 4 × 44K microarray (Agilent Technologies; 023647) at 65°C for 17 hours.

scan_protocol: Slides were scanned on the Agilent G2505C DNA microarray scanner.

data_processing: Background correction of the Cy3 raw signals was performed using the Agilent Feature Extraction software (version 10.5.1.1). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Bos taurus

source_name: Endometrial tissue in cow_010

label_protocol: One-color spike-mix was added to the total RNA prior to the labeling reaction. Labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from the endometrial samples using RNeasy Plus Universal Mini kit (Qiagen) according to the manufacturer’s instructions. Total RNA quality and quantity were confirmed using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and a NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA), respectively.

tag: Sex

value: female

tag: animal no.

tag: days after parturition


title: Short period afer parturition cow_008

source_name: Endometrial tissue in cow_008


title: Long period afer parturition cow_005

source_name: Endometrial tissue in cow_015


title: Long period afer parturition cow_006

source_name: Endometrial tissue in cow_016


title: Long period afer parturition cow_008

source_name: Endometrial tissue in cow_018


title: Long period afer parturition cow_009

source_name: Endometrial tissue in cow_019


title: Long period afer parturition cow_004

source_name: Endometrial tissue in cow_014


title: Short period afer parturition cow_005

source_name: Endometrial tissue in cow_005


title: Short period afer parturition cow_007

source_name: Endometrial tissue in cow_007


title: PC9E1_rep2

description: replicate 2


title: Long period afer parturition cow_002

source_name: Endometrial tissue in cow_012


title: Long period afer parturition cow_007

source_name: Endometrial tissue in cow_017


title: Short period afer parturition cow_004

source_name: Endometrial tissue in cow_004


title: Short period afer parturition cow_009

source_name: Endometrial tissue in cow_009


title: Long period afer parturition cow_010

source_name: Endometrial tissue in cow_020


title: Long period afer parturition cow_003

source_name: Endometrial tissue in cow_013


title: Long period afer parturition cow_001

source_name: Endometrial tissue in cow_011


title: Short period afer parturition cow_006

source_name: Endometrial tissue in cow_006


title: CE71

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software v3.8

source_name: primary desmoid tumor

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Illumina WG-DASL Expression Profiling Assay Guide).

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: ctnnb1 mutational status

value: primary desmoid tumor


title: Subfertile cow_003

source_name: Endometrial tissue in subfertile cow_003


title: CE69


title: Subfertile cow_005

source_name: Endometrial tissue in subfertile cow_005


title: CE70


title: Subfertile cow_004

source_name: Endometrial tissue in subfertile cow_004


title: Short period afer parturition cow_002

source_name: Endometrial tissue in cow_002


title: Short period afer parturition cow_001

source_name: Endometrial tissue in cow_001


title: Subfertile cow_001

source_name: Endometrial tissue in subfertile cow_001


title: Subfertile cow_002

source_name: Endometrial tissue in subfertile cow_002


title: CE63


title: Fertile cow_004

source_name: Endometrial tissue in fertile cow_004


title: Fertile cow_006

source_name: Endometrial tissue in fertile cow_006


title: CE68


title: CE62


title: CE61


title: Fertile cow_005

source_name: Endometrial tissue in fertile cow_005


title: Fertile cow_003

source_name: Endometrial tissue in fertile cow_003


title: 6670 N4sc

city: Pittsburgh

first: Eric

middle: Smith

last: Weiss

state: PA

address: RKMFI, 4401 Penn Ave

department: Pediatrics

institute: University of Pittsburgh

data_processing:
Sequenced using Illumina HiSeq 2000, mapped to mm9 using Tophat v2.1
It was quantified using Partek GSv6.6 software
Reads were converted to TPM and a .5 TPM offset was added to all transcripts
Genome_build: mm9
Supplementary_files_format_and_content: an excel file includes RPKM for all samples

source_name: duodenal epithelium

extract_protocol:
Duodenums were removed, cut open to reveal lumen, irrigated gently with PBS, and the lumens were scraped with an Rnase-treated slide, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: duodenum

tag: age

value: 6 weeks

tag: genotype


title: 6668 N4sc


title: 6695 WTsc

value: wild type


title: 6696 WTsc


title: 6667 N4sc


title: 6693 WTsc


title: CE56


title: CE53


title: CE55


title: CE57

value: WT


title: CE60


title: 6669 N4sc


title: CE58


title: Fertile cow_002

source_name: Endometrial tissue in fertile cow_002


title: CE59


title: CE50


title: Fertile cow_001

source_name: Endometrial tissue in fertile cow_001


title: CE52


title: CE51


title: CE45


title: ixr1-1 isoxaben rep2

city: Trondheim

first: Thorsten

last: Hamann

address: Høgskoleringen 5

country: Norway

institute: NTNU

data_processing:
Base-calling was performed on the NS500 instrument by Illumina RTA v2.4.6. FASTQ files were generated using bcl2fastq2 Conversion Software v1.8.4
Each FASTQ file was subjected to quality control trough fastQC v11.1
The reads were aligned to the A. thaliana genome (Ensembl v82) with STAR v2.4.1 in two-pass mode
The reads that aligned uniquely to the genome were aggregated into gene counts with FeatureCounts v1.4.6 using the genome annotations defined in Ensembl v82
Genome_build: A. thaliana genome (Ensembl v82)
Supplementary_files_format_and_content: Tab-separated values files including AGI code, chromosomes, start, end, length and read count values for each sample

organism: Arabidopsis thaliana

source_name: ixr1-1 isoxaben_seedlings

growth_protocol: 30 mg of seeds were sterilized by sequential incubation with 70 % ethanol and 50 % bleach on a rotating mixer for 10 min each and washed 3 times with sterile water. Seeds were then transferred into 250 ml erlenmayer flasks containing 125 ml half-strength Murashige and Skoog growth medium (2.1 g/L Murashige and Skoog Basal Medium, 0.5 g/L MES salt and 1 % sucrose at pH 5.7). Seedlings were grown in long-day conditions (16 h light, 22°C / 8 h dark, 18°C) at 150 μmol m-2 s-1 photon flux density on a IKA KS501 flask shaker at a constant speed of 130 rotations per minute. Seedlings were grown for 6 days prior to treatment.

extract_protocol:
Total RNA was extracted using a Spectrum Plant Total RNA Kit (Sigma-Aldrich). RNA concentration was measured using a Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and integrity assessed using a Agilent RNA 6000 Pico Kit.
RNA Seq libraries were prepared using a TruSeq Stranded mRNA Kit (Illumina) according to the manufacturer's instructions. 500 ng total RNA was used as starting material.

treatment_protocol: Seedlings from a single flask were divided into to two new flasks with fresh growth medium. One of the flasks contained 600 nM isoxaben added from a 1000x stock dissolved in DMSO. The other flask contained equal amount of DMSO without isoxaben. Treatment was started at 9 am and the samples were collected at 10 am.

tag: ecotype

value: Isoxaben-resistant mutant ixr1-1

tag: developmental stage

value: 6 days old seedlings

value: isoxaben


title: ixr1-1 isoxaben rep1

tag: treatment


title: ixr1-1 DMSO rep3

description: mock treatment

source_name: ixr1-1 DMSO_seedlings

value: DMSO


title: ixr1-1 DMSO rep1

description: mock treatment


title: CE41

source_name: primary desmoid tumor


title: nonstim_mock_gene_expression

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

description: MCF7 cells treated with mock siRNA (48h)

hyb_protocol: Samples were hybridised as per Affymetrix standard protocols

scan_protocol: Samples were scanned as per Affymetrix standard protocols

data_processing: Arrays were RMA normalized using Affymetrix Powertools and only ‘main’ and ‘rescue’ probesets were used for analysis. The 'main' and 'rescue' probe sets are defined in the HuGene-2_0-st-v1.na35.hg19.transcript.csv file in the 'category' column (Available from www.affymetrix.com).  Differences of Log2 0.5  (1.4-fold) were used as cut-off for expression changes.

source_name: MCF7, mock siRNA

label_protocol: Samples were labelled as per Affymetrix standard protocols

growth_protocol: Cells were cultured at 37C in low glucose DMEM (Gibco) and supplemented with 10% FCS, 2mM L-glutamine, and 0.1% PSN antibiotics.

extract_protocol: Trizol was used to extract RNA as per manufacturers instructions.

treatment_protocol: Cells were treated with mock or LSD1 siRNA (20nM) for 48h and then left or stimulated with PMA (1.29ng/ml) with a recombinant TGF-beta1 (5 ng/ml) for 60h.

tag: cell line

tag: genotype/variation

value: mock siRNA


title: PMATGF_LSDsiRNA_gene_expression

description: MCF7 cells treated with LSD siRNA (48h) and PMA/TGF (60h)

source_name: MCF7, LSD1 siRNA, PMA TGF

value: LSD1 siRNA

value: PMA and TGF


title: CE42

tag: tissue


title: ixr1-1 isoxaben rep3


title: PMATGF_mock_RNA_gene_expression

description: MCF7 cells treated with mock siRNA (48h) and PMA and TGF (60h)

source_name: MCF7, mock siRNA, PMA and TGF


title: CE43


title: CE48


title: CE44


title: Col-0 isoxaben rep2

source_name: Col-0 isoxaben_seedlings


title: Col-0 isoxaben rep1


title: Col-0 DMSO rep3

description: mock treatment

source_name: Col-0 DMSO_seedlings


title: nonstim_LSD1siRNA_gene_expression

description: MCF7 cells treated with LSD siRNA (48h)

source_name: MCF7, LSD1 siRNA


title: ixr1-1 DMSO rep2

description: mock treatment


title: Col-0 DMSO rep2

description: mock treatment


title: Col-0 isoxaben rep3


title: Col-0 DMSO rep1

description: mock treatment


title: CE40


title: CE38


title: CE37


title: CE35


title: Fig 6b siRNA-5-GNA replicate 3

city: Cambridge

first: Joseph

last: Barry

address: 300 Third Street #3

institute: Alnylam Pharmaceuticals

description:
siRNA-5-GNA_3
group_siRNA-5-GNA.vsMock.DESeq2.txt

data_processing:
Raw RNAseq reads were filtered with minimal mean quality scores of 25 and minimal remaining length of 36, using fastq-mcf. Filtered reads were aligned to the Rattus norvegicus genome (Rnor_6.0) using STAR (ultrafast universal RNA-seq aligner) with default parameters. Uniquely aligned reads were counted by featureCounts. Differential gene expression analysis was performed by the R package DESeq2.The open source DESeq2 R package was used for the RNAseq data analysis.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: DESeq2 output tables, tab separated fields, log2FoldChange and padj (adjusted p-value) fields used to create volcano plots in paper

organism: Rattus norvegicus

source_name: siRNA-5-GNA, hepatocytes

extract_protocol: RNA extracted with the miRNeasy kit (Qiagen) was used for cDNA library preparation with the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced on the HiSeq or NextSeq500 sequencers (Illumina), all according to manufacturer's instructions.

treatment_protocol: Rat livers were collected 24 h post-50 mg/kg single dose of GalNAc-siRNAs and snap-frozen. Rat hepatocytes (BioreclamationIVT) were transfected with 10 nM GalNAc-siRNAs using Lipofectamine RNAiMAX (Thermo Fisher Scientific) according to manufacturer?s instructions, and harvested 24 h post-transfection. Rat hepatocytes were not tested for mycoplasma contamination.

value: Sprague-Dawley

tag: gender

value: male

tag: cell type

value: hepatocytes (BioreclamationIVT, lot QDZ)


title: 4817_cRNA_4

city: Liverpool

first: Philipp

last: Antczak

state: Merseyside

address: Crown Street

institute: University of Liverpool

description: Myofibre cultures were isolated from male mice and cultured

hyb_protocol: Sample labelling and microarray hybridisations were carried out according to Agilent’s One-Colour Microarray-Based Gene Expression Analysis Protocol, Version 6.6 (Manual Part Number G4140-90040)

data_processing: Raw Agilent text files were read using the read.Agilent function in the marray R package (Yang, Paquet and Dudoit. Exploratory analysis for two-color spotted microarray data. R package version 1.50.0. http://www.maths.usyd.edu.au/u/jeany/). Data was background corrected and loess normalized against their respective 48h data point to allow for a direct comparison between the two culture systems at both time points. Loess normalization was performed using the normalizeWithinArrays function within the Limma package followed by a quantile normalization using the normalizeBetweenArrays function. Data was then summarized on the gene level by first averaging identical probes and then selecting a representative probe per gene name that showed the highest average intensity across the dataset. Lowly expressed genes were removed by selecting those with a median intensity level < 5 across all arrays. Differentially expressed genes were identified using the Samr package for each of the three comparisons: (1) 72h vs. 48h myofibre-associated myoblasts, (2) 72h vs. 48h dispersed myoblasts, and (3) 72h/48h dispersed vs. 72h/48h myofibre-associated myoblasts. Genes significant at 1% FDR in each comparison were extracted and used for further analysis.

source_name: myofibres

growth_protocol: Male C57Bl/6J mice were purchased from Charles River and housed until used in a pathogen-free facility at the University of Liverpool, UK, in accordance with the Animals (Scientific Procedures) Act 1986 and the EU Directive 2010/63/EU and after local ethical review and approval by Liverpool University's Animal Welfare and Ethical Review Body (AWERB). All cell preparations were obtained from mice aged 11-13 weeks. Single myofibres were isolated and cultured.

extract_protocol: RNA was extracted from myoblast preparations using the RNeasy kit from Qiagen according to manufacturer instructions. The quality and concentration of the RNA was assessed using a Bioanalyzer (Agilent 2100, Agilent). The RIN values for all samples were ≥ 7.5. Only for one of the 4 replicates of myofibre-associated myoblasts at 48 h, two distinct preparations were pooled to produce one biological replicate. In all other cases each biological replicate corresponded to one independent preparation. Two mice for each biological replicate were used for the myofibre-associated myoblast preparations, while one mouse for each biological replicate was used for dispersed myoblast preparations.

treatment_protocol: Forty-eight and 72 h after isolation myofibres were collected, washed twice with phosphate buffered saline (PBS) always collecting the supernatant which contained loosely attached myoblasts, then treated with 0.5% trypsin for 10 minutes at 37°C. The action of trypsin was then stopped by the addition of two volumes of primary SC growth medium and the myofibres separated from stripped myoblasts by centrifugation (3’ at 100 x g): the supernatant containing myoblasts was collected and combined with the two previous PBS washes, while the pellet containing stripped myofibres was discarded. Myoblasts were then collected by centrifuging at 500 xg, the pellet washed once in PBS and then immediately lysed with RLT buffer (RNeasy kit, Qiagen). This method yielded highly pure preparations of myofibre-associated myoblasts and high quality RNA. Prep quality control experiments revealed that no contaminant RNA from the myofibre was contained

tag: time

tag: grow type

value: dispersed


title: 4817_cRNA_3

scan_protocol: Sample labelling and microarray hybridisations were carried out according to Agilent’s One-Colour Microarray-Based Gene Expression Analysis Protocol, Version 6.6 (Manual Part Number G4140-90040)


title: Fig 6b siRNA-5-GNA replicate 2

description:
siRNA-5-GNA_2
group_siRNA-5-GNA.vsMock.DESeq2.txt


title: 4817_cRNA_8

label_protocol: Sample labelling and microarray hybridisations were carried out according to Agilent’s One-Colour Microarray-Based Gene Expression Analysis Protocol, Version 6.6 (Manual Part Number G4140-90040)


title: Fig 6b siRNA-5-GNA replicate 1

description:
siRNA-5-GNA_1
group_siRNA-5-GNA.vsMock.DESeq2.txt


title: 4817_cRNA_7


title: Fig 5b siRNA-5-iB replicate 2

description:
siRNA-5-iB_2
group_siRNA-5-iB.vsMock.DESeq2.txt

source_name: siRNA-5-iB, hepatocytes


title: Fig 5b siRNA-5-iB replicate 3

description:
siRNA-5-iB_3
group_siRNA-5-iB.vsMock.DESeq2.txt


title: Fig 5b siRNA-5-iB replicate 1

description:
siRNA-5-iB_1
group_siRNA-5-iB.vsMock.DESeq2.txt


title: Fig 5b siRNA-1-iB replicate 1

description:
siRNA-1-iB_1
group_siRNA-1-iB.vsMock.DESeq2.txt

source_name: siRNA-1-iB, hepatocytes


title: Fig 5b siRNA-1-iB replicate 3

description:
siRNA-1-iB_3
group_siRNA-1-iB.vsMock.DESeq2.txt


title: 4817_cRNA_1


title: Fig 5b mock control iB replicate 3

source_name: mock control iB, hepatocytes

value: mock control iB


title: Fig 5b mock control iB replicate 1


title: Fig 5b mock control iB replicate 2


title: CE32

value: primary desmoid tumor


title: CE34


title: Fig 5a siRNA-6 replicate 3

description:
siRNA-6_3
group_siRNA-6.vsMock.DESeq2.txt

source_name: siRNA-6, hepatocytes


title: CE30


title: CE22


title: Fig 5a siRNA-6 replicate 2

description:
siRNA-6_2
group_siRNA-6.vsMock.DESeq2.txt


title: 4817_cRNA_2


title: Fig 5b siRNA-1-iB replicate 2

description:
siRNA-1-iB_2
group_siRNA-1-iB.vsMock.DESeq2.txt


title: 4817_cRNA_6


title: Fig 5a siRNA-6 replicate 1

description:
siRNA-6_1
group_siRNA-6.vsMock.DESeq2.txt


title: 4816_cRNA_10+11

value: myofibre-associated


title: CE26


title: Fig 5a, Fig 6b siRNA-5 replicate 3

description:
siRNA-5_3
group_siRNA-5.vsMock.DESeq2.txt

source_name: siRNA-5, hepatocytes


title: Fig 5a, Fig 6b siRNA-5 replicate 1

description:
siRNA-5_1
group_siRNA-5.vsMock.DESeq2.txt


title: 4817_cRNA_5


title: Fig 5a siRNA-4 replicate 3

description:
siRNA-4_3
group_siRNA-4.vsMock.DESeq2.txt

source_name: siRNA-4, hepatocytes


title: CE29


title: 4816_cRNA_8


title: Fig 5a siRNA-2 replicate 2

description:
siRNA-2_2
group_siRNA-2.vsMock.DESeq2.txt

source_name: siRNA-2, hepatocytes


title: Fig 5a siRNA-4 replicate 2

description:
siRNA-4_2
group_siRNA-4.vsMock.DESeq2.txt


title: 4816_cRNA_9

description: Myofibre cultures were isolated from male mice and cultured


title: Fig 5a siRNA-2 replicate 1

description:
siRNA-2_1
group_siRNA-2.vsMock.DESeq2.txt


title: Fig 5a siRNA-2 replicate 3

description:
siRNA-2_3
group_siRNA-2.vsMock.DESeq2.txt


title: 4816_cRNA_4


title: Fig 5a, Fig 6b siRNA-5 replicate 2

description:
siRNA-5_2
group_siRNA-5.vsMock.DESeq2.txt


title: Fig 5a siRNA-4 replicate 1

description:
siRNA-4_1
group_siRNA-4.vsMock.DESeq2.txt


title: 4816_cRNA_7


title: Fig 5a, Fig 6b mock control replicate 2

source_name: mock control, hepatocytes

value: mock control


title: Fig 5a, Fig 6b mock control replicate 1


title: 4816_cRNA_2


title: 4816_cRNA_3


title: 4816_cRNA_1


title: Fig 5a, Fig 6b mock control replicate 3


title: REV infected CEF2

city: Tai'an

first: Defang

last: Zhou

address: Daizong street NO.61

institute: Shandong Agricultural University

data_processing:
Raw Data was processed with Python scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows: 1) Removed reads without 3’adapter; 2) Removed reads without insert fragment; 3) Removed reads with too much poly A/T; 4) Removed reads with length out of certain range; 5) Removed the low quality reads; 6) Removed the reads which contained N base more than 5% for total bases;
Reference gene and genome annotation files downloaded from the Ensemble (http://www.ensembl.org/index.html) or other reference genome, using Bowtie1.0.1 to build the reference genome library, and then the clean data were mapped to the reference genome by Bowtie1.0.1. The software bowtie1 was better used to align short reads (mostly shorter than 50bp) to huge genome accurately and fast
The basic idea of known miRNA identification is to get overlap (100%) between genome location of mapping reads and the genome location of reference miRNA. If genome annotation data can be found in miRBase (Release 21), we just need to get overlap by software Bedtools, otherwise,we will firstly map the reference miRNA to the reference genome to obtain location information, then get overlap
For every sample, count and RPM of miRNAs will be collected. RPM (reads per million total reads) value can be considered as normalized count of sample, and can be directly used in  inter-library comparison.
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: excel files include read counts and RPM values for each Sample ...

organism: Gallus gallus

source_name: CEF cells

extract_protocol:
Total RNA was separated by 15% agarose gels to extract the small RNA (18-30 nt).After precipitated by ethanol and centrifugal enrichment of small RNA sample, the library was prepared according to the method and process of Small RNA Sample  Preparation Kit (Illumina, RS-200-0048).
Illumina small RNA deep sequencing

value: chicken embryo fibroblast

value: 10-day of embryonic age


title: ALV-J and REV co-infected CEF2


title: WT CEF2


title: ALV-J infected CEF2


title: Fig  5b siRNA-5 replicate 2

description:
siRNA-5_2
group_siRNA-5_Fig5b.vsMock.DESeq2.txt


title: ALV-J and REV co-infected CEF1


title: ALV-J infected CEF1


title: REV infected CEF1


title: cortical astrocytes cocultured with Oli-neu cells_I4

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
raw data file:
I3-4_US83300186_252665513680_S01_GE2_1105_Oct12_1_1.txt

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two biological replicas were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) mouse (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction vs.11 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas, Biological Theory, 11(3):123-137, 2016..
normalized ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because it is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Preparation of primary astrocyte cultures: At E19 stage of pregnancy, cesarean sections were performed on a C57Bl/6j mouse mother and brains from 4 pups were separately minced in 500μl of 0.05% trypsin-EDTA, transferred to 1 ml Eppendorf tubes containing 500μl Dulbecco’s Modified Eagle medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin and spun down at 2000 RPM for 10 min. Pellets were then re-suspended in culture medium and the cells were plated in 100 mm culture dishes and maintained in a humidified 5% CO2 incubator at 37°C. After 2 weeks in culture, primary confluent cell cultures were trypsinized (0.05% trypsin) and replated. About 90% of the cells were immunopositive for glial acidic fibrillary protein (GFAP). The mouse oligodendrocyte precursor cell line Oli-neu was a kind gift from Dr. J. Trotter (University of Mainz, Germany). This cell line was generated by retroviral transduction of oligodendrocyte precursors with the t-neu oncogene (Jung et al., 1995). Cells were grown on poly-L-lysine-coated culture dishes maintained at 37°C in 5% CO2 in a humidified incubator. Immature Oli-neu cells were seeded in culture flasks coated with 0.01% poly-L-lysine, cultured in DMEM medium + 1% B27, N2, PSG, SP and horse serum (GIBCO®), and passaged following dissociation with Trypsin-EDTA.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a Thermo Scientific NanoDrop ND-2000 and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Control Oli neu cells were co-cultured with mouse cortical astrocytes in FalconTM cell culture 6 well insert system, with astrocytes in the insert and Oli-neu cells on the bottom of the system. The insert had pores of 0.4µm allowing the two types of cells to exchange neurotransmitters and other signaling molecules; contact and formation of gap junction channels between the cell types was precluded by small size of the filter pores and location of Oli-neu cells at the bottom of the chamber (about 2 mm below the filter insert).


title: cortical astrocytes cocultured with Oli-neu cells_I1

description:
raw data file:
I1-2_US83300186_252665513680_S01_GE2_1105_Oct12_1_2.txt


title: cortical astrocytes cultured alone_C3

description:
raw data file:
C3-4_US83300186_252665513680_S01_GE2_1105_Oct12_1_3.txt

source_name: cortical astrocytes cultured alone

value: cortical astrocytes cultured alone


title: NonV50-OKS-SW480(Exp.2)

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

institute: Kobe University

description: OKS

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: The data were analyzed using the Gene Spring GX 13.1.1 software program (Agilent Technologies).The data processing was performed as follows; (i) Threshold raw signals were set to 1.0, (ii) Log base 2 transformation was performed, (iii) 75th percentile normalization was chosen as the normalized algorithm.

source_name: colorectal cancer cell

label_protocol: Agilent standard protocol

extract_protocol: Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacturer's instruction.

tag: agent

value: Retrovirus


title: Fig  5b siRNA-5 replicate 1

description:
siRNA-5_1
group_siRNA-5_Fig5b.vsMock.DESeq2.txt


title: 2ndV50-OKS-SW480(Exp.2)

description: OKS


title: cortical astrocytes cultured alone_C1

description:
raw data file:
C1-2_US83300186_252665513680_S01_GE2_1105_Oct12_1_4.txt


title: cortical astrocytes cocultured with Oli-neu cells_I2


title: NonV50-OKS-SW480(Exp.1)

description: OKS


title: cortical astrocytes cultured alone_C4


title: WT CEF1


title: NonV50-OKS-SW480(Exp.3)

description: OKS


title: cortical astrocytes cocultured with Oli-neu cells_I3


title: Fig  5b siRNA-5 replicate 3

description:
siRNA-5_3
group_siRNA-5_Fig5b.vsMock.DESeq2.txt


title: Mock-SW480(Exp.3)


title: 2ndV50-OKS-SW480(Exp.3)

description: OKS


title: 2ndV50-OKS-SW480(Exp.1)

description: OKS


title: Fig  5b siRNA-1 replicate 1

description:
siRNA-1_1
group_siRNA-1.vsMock.DESeq2.txt

source_name: siRNA-1, hepatocytes


title: Mock-SW480(Exp.1)


title: Short period afer parturition cow_003

source_name: Endometrial tissue in cow_003

tag: Sex

value: female

tag: animal no.


title: cortical astrocytes cultured alone_C2


title: Fig  5b siRNA-1 replicate 2

description:
siRNA-1_2
group_siRNA-1.vsMock.DESeq2.txt


title: Fig  5b siRNA-1 replicate 3

description:
siRNA-1_3
group_siRNA-1.vsMock.DESeq2.txt


title: Fig 5b mock control replicate 3


title: Fig 5b mock control replicate 2


title: Fig 5b mock control replicate 1


title: 137_developing human neocortex: GZ

city: Chapel Hill

first: Jason

middle: L

last: Stein

state: NC

address: Neuroscience Research Building 8109C, 115 Mason Farm Rd

institute: UNC Chapel Hill

description:
processed data file:
readswithinpeaks.csv
cqnnormalizationfactors.csv

data_processing:
Sequencing files from each sequencing lane were de-multiplexed and poor quality reads were excluded (PF=1 reads were retained). Reads were then mapped to the human genome including decoy sequences (hg19; 1000 Genomes Project Phase 2 reference assembly) using bwa mem (v0.7.12). Optical and PCR duplicates were then removed using PicardTools (v1.128). De-duplicated BAM files from the same sample were merged from separate lanes and PicardTools was again used to remove duplicate reads. Only uniquely mapped reads mapping to chr 1-22 and X were kept (mitochondrial genome, Y chromosome, and unmapped contigs were removed). Peaks were called for each sample using MACS2 (v2.1.0.20140616). Peaks that overlapped with ENCODE blacklisted regions (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz) were removed.
The DiffBind package (v1.10.2) within R version 3.1.1 (2014-07-10) was used to find high confidence peaks present in at least 40% of samples. The union across samples of those remaining peaks (called peaksets in DiffBind, but hereafter simply referred to as peaks) was used for subsequent analyses. The number of reads within each peak was counted and then normalization factors for each peak across samples were calculated accounting for GC content, peak width, and total number of unique non-mitochondrial fragments sequenced using conditional quantile normalization from the cqn package (v1.10.0).
Genome_build: hg19

Supplementary_files_format_and_content:
peakfile: MACS2 locations of peaks called within each sample
readquantification: The number of reads mapping to each peakset across samples
normalizationfactors: The conditional quantile normalization factors which normalize for GC content, peak width, and total number of unique non-mitochondrial reads.

source_name: developing human neocortex: GZ

extract_protocol:
Tissue was enzymatically dissociated followed by inactivation with ovomucoid. 50,000 cells were aliquotted for each tissue. Nuclei were isolated  using an IGEPAL solution following the protocol outlined in Buenrostro et al., Nat Methods, 2013.
Library construction followed the protocol outlined in Buenrostro et al., Nat Methods, 2013. Tn5 transposase (Illumina Nextera kit) was added to the isolated nuclei, DNA was isolated, barcoded and amplified for (8-11 cycles). Quality control was assessed via gel electrophoresis and quantification was assessed via Kapa Library Quantification Kit.  Massively parallel 50 bp paired end (PE) sequencing was completed on an Illumina HiSeq2000 to acquire ~25M fragments per sample. For each donor, GZ and CP samples were dissected, library prepped, and sequenced within the same batch to prevent batch effects correlated with the biological condition of interest.

tag: donor id

value: developing human neocortex

tag: lamina

value: GZ

tag: post conception weeks (pcw)

tag: total read pairs sequenced

tag: unique non-mitochondrial reads sequenced

tag: added pcr amplification cycles

tag: kapa library concentration (300bp segment in nm)


title: 128_developing human neocortex: CP

source_name: developing human neocortex: CP

value: CP


title: 139_developing human neocortex: CP


title: 135_developing human neocortex: GZ


title: 140_developing human neocortex: CP


title: 138_developing human neocortex: CP


title: 136_developing human neocortex: GZ


title: 124_developing human neocortex: GZ


title: 126_developing human neocortex: CP


title: 125_developing human neocortex: GZ


title: 123_developing human neocortex: GZ


title: 127_developing human neocortex: CP


title: Mock-SW480(Exp.2)


title: 18_developing human neocortex: CP


title: 14_developing human neocortex: GZ


title: 19_developing human neocortex: CP


title: 13_developing human neocortex: GZ


title: 17_developing human neocortex: CP


title: 15_developing human neocortex: GZ


title: 16_developing human neocortex: GZ


title: tumor_endometrial [GL4590E], Dataset B

status: Public on Jan 10 2018

city: New York

first: Li-Xuan

last: Qin

state: New York

address: 485 Lexington Ave

department: Epidemiology and Biostatistics

institute: Memorial Sloan Kettering Cancer Center

description:
GL4590E
microRNA expression of tumor tissue.
Total RNA or miRNA

hyb_protocol: Human miRNA v16.0 microarrays (Agilent Technologies), containing 3,523 markers that represent 1,205 human and 142 human viral miRNAs, were used for miRNA expression profiling according to the manufacturer’s protocol.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner G2505C US83903565 using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters. Raw data were preprocessed with log2 transformation and median probe-set summarization using R-3.3.0 software.

source_name: endometrial tumor sample

label_protocol: For samples meeting the quality control standards, 200 ng of total RNA was labeled using the miRNA Complete Labeling and Hybridization Kit (Agilent). The manufacturer's instructions were followed.

extract_protocol: Sample preparation used strict quality control on the specimens. Freshly harvested tissue was snap frozen for eventual cryomold embedding and RNA extraction or microarray analysis. Before RNA extraction, a 5-um hematoxylin and eosin histologic section was cut from the top of the cryomold to assess for tumor content and percentage of necrosis. For any specimens with less than 60% tumor cell nuclei, we used macrodissection to obtain enriched areas so as to make the specimen usable for RNA extraction and as uniform as possible. All specimens had less than 20% necrosis. All pathology specimens used for molecular study were diagnosed by dedicated gynecologic pathologists to establish histologic cell type, grade of malignancy, and site of origin. RNA was extracted from 30 to 100 mg of macrodissected cryomold tissue using the Ambion mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol. Total RNA yield and quality were assessed using a NanoDrop spectrophotometer and an Agilent Bioanalyzer.

tag: disease state

value: endometrioid endometrial cancer

value: tumor

tag: batch


title: tumor_endometrial [GL4666E], Dataset B

description:
GL4666E
microRNA expression of tumor tissue.
Total RNA or miRNA

tag: tissue


title: tumor_endometrial [GL4660E], Dataset B

description:
GL4660E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL4627E], Dataset B

description:
GL4627E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [GL4490V], Dataset B

description:
GL4490V
microRNA expression of tumor tissue.
Total RNA or miRNA

source_name: ovarian tumor sample

value: advanced serous ovarian cancer


title: tumor_endometrial [GL4440E], Dataset B

description:
GL4440E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL4472E], Dataset B

description:
GL4472E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4952V], Dataset B

description:
JB4952V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL4530E], Dataset B

description:
GL4530E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL4300E], Dataset B

description:
GL4300E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL4415E], Dataset B

description:
GL4415E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [GL4487V], Dataset B

description:
GL4487V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [GL5113V], Dataset B

description:
GL5113V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL4366E], Dataset B

description:
GL4366E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL4431E], Dataset B

description:
GL4431E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL4668E], Dataset B

description:
GL4668E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL4254E], Dataset B

description:
GL4254E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB4933E], Dataset B

description:
JB4933E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: S96 normal cells grown in YPD, not treated with MCHM, replicate 2

city: Morgantown

first: Xiaoqing

last: Rong-Mullins

state: West Virginia

address: 53 Campus Dr

institute: West Virginia University

description:
mchm_fC1_count_table_clean.tsv
mchm_fC1_DESeq_c2.tsv

data_processing:
Base-calling was performed via Illumina CASAVA version 1.7.
Tophat v2.0.12 (Kim et al. 2013; Trapnell et al. 2009) was used to map the RNA-Seq reads to the S288c genome and to generate .bam files for mapped reads. The reads were first mapped to ribosomal RNA and transfer RNA genes, then unmatched reads were mapped to the whole gene pool of S288c. The reads matched to rRNA and tRNA were excluded because these RNAs tend to be extracted at high and/or variable abundances across replicates, thus may bias the calculation of FPKM (fragments per kb gene per million mapped fragments).
Gene expression was quantified from the mapped reads in .bam files. R-package Rsubread v1.18.0 (Liao et al. 2013) was used to generate count tables based on the annotations of S288c genome release R64-1-1, and then DESeq2 v1.8.1 (Anders and Huber. 2010) was used for differential expression.
Genome_build: sacCer3
Supplementary_files_format_and_content: mchm_fC1_count_table_clean.tsv' is tab-delimited read count data. 'mchm_fC1_DESeq_c2.tsv' is tab-delimited differential expression data. In each comparison for differential expression in the format of ‘condition_A…condition_B’, condition_A is the denominator and condition_B is the numerator when calculating fold change.

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Two types of cells, normal and petite, were grown as two replicated cultures in liquid YM or YPD medium to mid-log phase. Each culture was diluted to early-log phase and divided into two subcultures. One subculture was incubated in liquid medium with 0.055% (v:v) MCHM and the other subculture without MCHM. Both subcultures for each replicate were further grown for 2.5 h.

extract_protocol:
Total RNA was extracted from each sample and multiplexed unstranded paired-end cDNA libraries were prepared using Illumina TruSeq RNA Sample Prep Kit v2.
RNA libraries were prepared for sequencing on Illumina MiSeq using standard Illumina protocols

value: normal

value: YPD

tag: mchm

value: no


title: S96 normal cells grown in YM, treated with MCHM, replicate 2

value: YM

value: yes


title: S96 normal cells grown in YM, not treated with MCHM, replicate 2


title: S96 normal cells grown in YPD, treated with MCHM, replicate 1


title: S96 normal cells grown in YPD, treated with MCHM, replicate 2


title: S96 normal cells grown in YPD, not treated with MCHM, replicate 1


title: tumor_ovarian [GL4200V], Dataset B

description:
GL4200V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: S96 normal cells grown in YM, treated with MCHM, replicate 1


title: tumor_ovarian [GL4371V], Dataset B

description:
GL4371V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL4080E], Dataset B

description:
GL4080E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL4064E], Dataset B

description:
GL4064E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [GL4226V], Dataset B

description:
GL4226V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: S96 normal cells grown in YM, not treated with MCHM, replicate 1


title: S96 petite cells grown in YPD, treated with MCHM, replicate 2

value: petite


title: S96 petite cells grown in YPD, not treated with MCHM, replicate 1


title: tumor_endometrial [GL4282E], Dataset B

description:
GL4282E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: S96 petite cells grown in YPD, not treated with MCHM, replicate 2


title: S96 petite cells grown in YM, not treated with MCHM, replicate 2


title: tumor_endometrial [GL3736E], Dataset B

description:
GL3736E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL3934E], Dataset B

description:
GL3934E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL3907E], Dataset B

description:
GL3907E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: SiYAP

city: Shanghai

first: Shi

last: Jiao

address: 320 Yue Yang Road

institute: Shanghai Institutes of Biological Sciences

data_processing:
Before read mapping, clean reads were obtained from the raw reads by rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
Clean reads after filtering were aligned to human genome (hg38) by Tophat v2.0.9(1).
The differentially expressed genes were achieved by EBSeq algorithms.
Genes were considered significantly differentially expressed under the following criteria: (1) fold change > 1.5 or < 0.667; (2) FDR < 0.05 (2).
Genome_build: hg38
Supplementary_files_format_and_content: xls file includes RPKM values for each Sample.

source_name: HGC-27 cells

growth_protocol: HGC-27 cells were maintained in culture supplemented with 10% heat-inactivated fetal calf serum (FCS), 100 µg ml-1 of penicillin, and 100 µg ml-1 of streptomycin at 37°C with 5% CO2 in a humidified incubator (Thermo, MA, USA). The cells were passaged for ≤ 3 months from the frozen early-passage stocks that had been received from the indicated sources.

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HGC-27 cells were transfected with siRNAs (n.c. siYAP or siIRF3) for 48 h

tag: cell type

value: gastric cancer cells

tag: passages

tag: transfection

value: YAP siRNA (siYAP)


title: tumor_ovarian [GL3793V], Dataset B

description:
GL3793V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL3709E], Dataset B

description:
GL3709E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: S96 petite cells grown in YPD, treated with MCHM, replicate 1


title: tumor_endometrial [GL3694E], Dataset B

description:
GL3694E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL3898E], Dataset B

description:
GL3898E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 2% Input DNA

city: Kolkata

first: Amitava

last: Sengupta

state: West Bengal

address: CN 6, Sector V, Salt Lake

department: Cancer Biology & Inflammatory Disorder Division

country: India

institute: CSIR - Indian Institute of Chemical Biology (Translational Research Unit of Excellence)

data_processing:
Quality control analysis has been done using NGSQC v2.3.3
Bowtie has been used for read alignment
MACS1.4 has been used for peak calling
Peak analyzer has been used for peak annotation
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using MACS1.4 tool

source_name: Normal peripheral blood nuclear cells

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were precipitated with antibody.
ChIP-seq library preparation was performed using TruSeqChIP Sample Prep Kit (Illumina) according to the manufacturer’s instructions.10ng of input ChIP-enriched DNA was used for ChIP-seq library preparation. Final libraries were checked using High Sensitivity chips in 2100 Bioanalyzer (Agilent). Average fragment size of final libraries was found to be 280 ± 8bp. Paired-end sequencing (2 x 100 bp) of these libraries were performed in HiSeq-2500 (Illumina) according to the manufacturer's protocols.

value: Peripheral blood

tag: chip antibody


title: NC

value: control siRNA (n.c.)


title: SMARCC1_ChIPSeq

value: BAF155 (R-18) (Santa Cruz Biotechnology, Cat. sc-9746, Lot B1513)


title: AML patient 3 SMARCC1_ChIPSeq

source_name: AML patient 3 bone marrow nuclear cells

value: Bone marrow


title: H3K27ac_ChIPSeq


title: H3K27me3_ChIPSeq


title: AML patient 3 H3K27ac_ChIPSeq


title: SiIRF3

value: IRF3 siRNA (siIRF3)


title: S96 petite cells grown in YM, not treated with MCHM, replicate 1


title: S96 petite cells grown in YM, treated with MCHM, replicate 2


title: AML patient 3 H3K27me3_ChIPSeq


title: AML patient 2 SMARCC1_ChIPSeq

source_name: AML patient 2 bone marrow nuclear cells


title: AML patient 3 2% Input DNA


title: tumor_endometrial [GL3686E], Dataset B

description:
GL3686E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: S96 petite cells grown in YM, treated with MCHM, replicate 1


title: AML patient 2 2% Input DNA


title: tumor_endometrial [GL3816E], Dataset B

description:
GL3816E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: AML patient 2 H3K27ac_ChIPSeq


title: AML patient 1 SMARCC1_ChIPSeq

source_name: AML patient 1 bone marrow nuclear cells


title: AHEP

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

institute: Yokohama City University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) 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 by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner using one color scan setting for micro array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
The raw signal intensities of samples were log2-transformed and normalised by the quantile algorithm.

source_name: Adult hepatocyte

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Purification kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Adult hepatocyte


title: AML patient 1 H3K27me3_ChIPSeq


title: tumor_ovarian [GL3597V], Dataset B

description:
GL3597V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: ALT_30yrs_b

source_name: Adult liver tissue

value: Adult liver tissue


title: tumor_ovarian [GL3632V], Dataset B

description:
GL3632V
microRNA expression of tumor tissue.
Total RNA or miRNA

value: tumor


title: ALT_30yrs_a


title: tumor_ovarian [GL3537V], Dataset B

description:
GL3537V
microRNA expression of tumor tissue.
Total RNA or miRNA

value: advanced serous ovarian cancer


title: tumor_ovarian [GL3520V], Dataset B

description:
GL3520V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: AML patient 1 H3K27ac_ChIPSeq


title: tumor_ovarian [GL3623V], Dataset B

description:
GL3623V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL3542E], Dataset B

description:
GL3542E
microRNA expression of tumor tissue.
Total RNA or miRNA

value: endometrioid endometrial cancer


title: tumor_ovarian [GL3599V], Dataset B

description:
GL3599V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: AML patient 1 2% Input DNA


title: AML patient 2 H3K27me3_ChIPSeq


title: tumor_ovarian [JB5242V], Dataset B

description:
JB5242V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [GL3500V], Dataset B

description:
GL3500V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB5294E], Dataset B

description:
JB5294E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB5307E], Dataset B

description:
JB5307E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [GL3529E], Dataset B

description:
GL3529E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB5273E], Dataset B

description:
JB5273E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [GL3576V], Dataset B

description:
GL3576V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: Reconstructed epidermis_2D_normal medium_rep4

city: SAINT-VIANCE

first: VINCENT

last: BARRUCHE

state: If applicable (USA / Canada)

address: ZI de la Nau

department: R&D

country: France

institute: SILAB

description: Gene expression after exposure to normal medium

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutesusing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays (G4851B) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for AgilentG3 GX array slides (Scan Area 61x21.6 mm, Scan resolution 3um, 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 (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Reconstructed epidermis, 2 days with normal medium, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp labeling  kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

growth_protocol: Normal human keratinocytes (NHK) were isolated from human foreskin, collected from donors undergoing medical surgery and were cultured in a monolayer with the CnT 57 medium (CELLnTEC) supplemented with 2% penicillin/streptomycin (Invitrogen) until 80% confluent. REs were obtained by seeding 0.2x106 NHK into culture inserts (Millipore). Cells were cultured submerged in complete CnT 57 medium (CELLnTEC) for 3 days and in CnT-02-3D Prime medium (CELLnTEC) for 1 day. The cultures were then raised to the air-liquid interface and grown for additional 10 days.

extract_protocol: Total RNA was extracted using the RNeasy Kit (Qiagen). Quantification and quality assessment of the isolated RNA samples were performed and verified using a NanoDrop 2000c spectrophotometer (ThermoFisher) and an Agilent Bioanalyzer2100 (Agilent Technologies) according to the manufacturer's instructions.

treatment_protocol: Culture medium was added for additional 2 days, either alone (normal RE) or supplemented with the following inflammatory cocktail (compromised RE): Poly I:C (10 µg/ml), TNF-α (10 ng/ml), IL-4 and IL-13 (50 ng/ml each)

value: reconstructed epidermis

tag: cells

value: human foreskin keratinocytes


title: Reconstructed epidermis_2D_inflammatory cocktail_rep3

description: Gene expression after exposure to inflammatory cocktail

source_name: Reconstructed epidermis, 2 days with inflammatory cocktail, replicate 3


title: Reconstructed epidermis_2D_inflammatory cocktail_rep4

source_name: Reconstructed epidermis, 2 days with inflammatory cocktail, replicate 4


title: Reconstructed epidermis_2D_inflammatory cocktail_rep1

source_name: Reconstructed epidermis, 2 days with inflammatory cocktail, replicate 1


title: tumor_ovarian [JB5153V], Dataset B

description:
JB5153V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB5240E], Dataset B

description:
JB5240E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: Reconstructed epidermis_2D_normal medium_rep1

source_name: Reconstructed epidermis, 2 days with normal medium, replicate 1


title: tumor_endometrial [JB5221E], Dataset B

description:
JB5221E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB5223V], Dataset B

description:
JB5223V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB5227E], Dataset B

description:
JB5227E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB5234V], Dataset B

description:
JB5234V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: Reconstructed epidermis_2D_normal medium_rep2

source_name: Reconstructed epidermis, 2 days with normal medium, replicate 2


title: tumor_ovarian [JB5150V], Dataset B

description:
JB5150V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB5143V], Dataset B

description:
JB5143V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB5142E], Dataset B

description:
JB5142E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: Reconstructed epidermis_2D_normal medium_rep3

source_name: Reconstructed epidermis, 2 days with normal medium, replicate 3


title: Reconstructed epidermis_2D_inflammatory cocktail_rep2

source_name: Reconstructed epidermis, 2 days with inflammatory cocktail, replicate 2


title: tumor_ovarian [JB5141V], Dataset B

description:
JB5141V
microRNA expression of tumor tissue.
Total RNA or miRNA

source_name: ovarian tumor sample


title: tumor_ovarian [JB5068V], Dataset B

description:
JB5068V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB5043E], Dataset B

description:
JB5043E
microRNA expression of tumor tissue.
Total RNA or miRNA

source_name: endometrial tumor sample


title: tumor_endometrial [JB5096E], Dataset B

description:
JB5096E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB5051V], Dataset B

description:
JB5051V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB5019V], Dataset B

description:
JB5019V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536146_R02C02

type: genomic

first: Elisabeth

middle: B.

last: Binder

state: DEUTSCHLAND

address: Kraepelinstraße 2-10

department: Dept. Translational Research in Psychiatry

country: Germany

institute: Max Planck Institute of Psychiatry

description: blood sample

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

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

data_processing: minfi Bioconductor R package version 1.18.2; Functional Normalization

label: Cy5 and Cy166

source_name: Blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from whole blood using the Gentra Puregene Blood Kit (QIAGEN)

value: blood

tag: gender

value: M

tag: diagnosis

value: PD


title: tumor_endometrial [JB5049E], Dataset B

description:
JB5049E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB5017E], Dataset B

description:
JB5017E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536134_R02C01

description: blood sample

label: Cy5 and Cy158

value: Control


title: 9989536137_R03C02

description: blood sample

label: Cy5 and Cy162


title: 9989536137_R04C01

description: blood sample

label: Cy5 and Cy163


title: tumor_ovarian [JB5014V], Dataset B

description:
JB5014V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536134_R03C02

description: blood sample

label: Cy5 and Cy160

value: F


title: 9989536134_R03C01

description: blood sample

label: Cy5 and Cy159


title: 9989536146_R01C01

description: blood sample

label: Cy5 and Cy165


title: tumor_endometrial [JB5000E], Dataset B

description:
JB5000E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536146_R06C01

description: blood sample

label: Cy5 and Cy168


title: tumor_ovarian [JB5011V], Dataset B

description:
JB5011V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536146_R03C02

description: blood sample

label: Cy5 and Cy167


title: 9989536134_R06C01

description: blood sample

label: Cy5 and Cy161


title: tumor_ovarian [JB4960V], Dataset B

description:
JB4960V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4998V], Dataset B

description:
JB4998V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4962V], Dataset B

description:
JB4962V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB4916E], Dataset B

description:
JB4916E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536128_R02C01

description: blood sample

label: Cy5 and Cy156


title: 9989536129_R01C01

description: blood sample

label: Cy5 and Cy157


title: 9989536119_R04C01

description: blood sample

label: Cy5 and Cy149


title: 9989536119_R05C01

description: blood sample

label: Cy5 and Cy150


title: DbGP33-specific CD8+ T cell, unvaccinated, isotype control #3

city: Boston

first: MALIKA

last: AID

state: MA

address: 3 blackfan street

institute: BIDMC

hyb_protocol: Samples were hybridized to the Affymetrix Mouse Genome 430 v2.0 chip at the Molecular Biology Core Facility at the Dana-Farber Cancer Institute

scan_protocol: Affymetrix protocol (performed at Molecular Biology Core Facility at the Dana-Farber Cancer Institute)

data_processing: Analysis of gene array output data was conducted using the R statistical language (http://www.r-project.org/) and the Linear Models for Microarray Data (LIMMA) statistical package from Bioconductor. Briefly, scanned array images were inspected for artifacts and unusual signal distribution within chips and arrays with low overall intensity or variability were removed from analysis. Raw data were processed using RMA method in R Affy package. The raw intensity values were background corrected, log2 transformed and then quantile normalized. Next a linear model was fit to the normalized data to obtain an expression measure for each probe set on each array. Differentially expressed gene analysis was performed using LIMMA. The moderated t-test implemented in the LIMMA package was used to assess the statistical significance (p< 0.05) of differential expression of genes

label: biotin

source_name: GP33-specific CD8+ T cell from spleen day 8 post LCMV Cl-13 challenge

label_protocol: Biotin (Affymetrix 3’ IVT Pico kit, performed at the Molecular Biology Core Facility at the Dana-Farber Cancer Institute)

growth_protocol: Mice were either vaccinated with 10^10 vp of Ad5-GP, or were unvaccinated. They were then given anti-NK1.1 or isotype-control antibody. Then they were challenged with 2x10^6 PFU of LCMV Cl-13, and CD8+ T cells were isolated on day 8 post-infection.

extract_protocol: RNA from GP33-specific CD8 T cells was obtained by phenol/chloroform extraction, followed by the RNAdvance Tissue Isolation protocol (Agencourt)

treatment_protocol: At day 8 post-LCMV Cl-13 infection, splenic CD8+ T cells were enriched via negative selection (MACS), stained (CD8, CD44, DbGP33, vital dye), and underwent FACS sorting on a BD Biosciences Aria II into Qiazol

value: DbGP33-specific CD8+ T cells

tag: protocol

value: unvaccinated, isotype control antibody treated, challenged with LCMV Cl-13

tag: strain

tag: Sex

value: female


title: tumor_ovarian [JB4912V], Dataset B

description:
JB4912V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536120_R05C01

description: blood sample

label: Cy5 and Cy153


title: DbGP33-specific CD8+ T cell, unvaccinated, isotype control #4


title: tumor_ovarian [JB4899V], Dataset B

description:
JB4899V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4889V], Dataset B

description:
JB4889V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536118_R06C01

description: blood sample

label: Cy5 and Cy148


title: DbGP33-specific CD8+ T cell, unvaccinated, isotype control #1


title: 9989536118_R05C02

description: blood sample

label: Cy5 and Cy147


title: DbGP33-specific CD8+ T cell, unvaccinated, isotype control #2


title: DbGP33-specific CD8+ T cell, unvaccinated, anti-NK1.1 #4

value: unvaccinated, anti-NK1.1 treated, challenged with LCMV Cl-13


title: tumor_endometrial [JB4870E], Dataset B

description:
JB4870E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536137_R06C01

description: blood sample

label: Cy5 and Cy164


title: tumor_ovarian [JB4878V], Dataset B

description:
JB4878V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536118_R03C01

description: blood sample

label: Cy5 and Cy146


title: 9989536117_R02C01

description: blood sample

label: Cy5 and Cy142


title: 9989536117_R05C02

description: blood sample

label: Cy5 and Cy144


title: tumor_ovarian [JB4860V], Dataset B

description:
JB4860V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536126_R01C01

description: blood sample

label: Cy5 and Cy155


title: tumor_ovarian [JB4833V], Dataset B

description:
JB4833V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536125_R02C01

description: blood sample

label: Cy5 and Cy154


title: 9989536117_R04C02

description: blood sample

label: Cy5 and Cy143


title: DbGP33-specific CD8+ T cell, unvaccinated, anti-NK1.1 #1


title: DbGP33-specific CD8+ T cell, unvaccinated, anti-NK1.1 #2


title: 9989536117_R06C01

description: blood sample

label: Cy5 and Cy145


title: tumor_ovarian [JB4900V], Dataset B

description:
JB4900V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: DbGP33-specific CD8+ T cell, vaccinated, isotype control #4

value: Ad5-GP vaccinated, isotype control antibody treated, challenged with LCMV Cl-13


title: tumor_ovarian [JB4757V], Dataset B

description:
JB4757V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4752V], Dataset B

description:
JB4752V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536120_R03C02

description: blood sample

label: Cy5 and Cy152


title: 9989536116_R03C02

description: blood sample

label: Cy5 and Cy139


title: tumor_ovarian [JB4744V], Dataset B

description:
JB4744V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: DbGP33-specific CD8+ T cell, vaccinated, isotype control #3


title: 9989536116_R05C02

description: blood sample

label: Cy5 and Cy140


title: 9989536119_R05C02

description: blood sample

label: Cy5 and Cy151


title: 9989536116_R03C01

description: blood sample

label: Cy5 and Cy138


title: DbGP33-specific CD8+ T cell, vaccinated, isotype control #2

label: biotin


title: tumor_ovarian [JB4743V], Dataset B

description:
JB4743V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536116_R06C01

description: blood sample

label: Cy5 and Cy141


title: DbGP33-specific CD8+ T cell, vaccinated, isotype control #1


title: tumor_ovarian [JB4715V], Dataset B

description:
JB4715V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: DbGP33-specific CD8+ T cell, vaccinated, anti-NK1.1 #4

value: Ad5-GP vaccinated, anti-NK1.1 treated, challenged with LCMV Cl-13


title: tumor_ovarian [JB4696V], Dataset B

description:
JB4696V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536114_R06C01

description: blood sample

label: Cy5 and Cy136


title: DbGP33-specific CD8+ T cell, vaccinated, anti-NK1.1 #3


title: tumor_ovarian [JB4650V], Dataset B

description:
JB4650V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536116_R02C02

description: blood sample

label: Cy5 and Cy137


title: 9989536114_R03C01

description: blood sample

label: Cy5 and Cy133


title: 9989536114_R05C01

description: blood sample

label: Cy5 and Cy135


title: DbGP33-specific CD8+ T cell, vaccinated, anti-NK1.1 #1


title: DbGP33-specific CD8+ T cell, vaccinated, anti-NK1.1 #2


title: tumor_ovarian [JB4676V], Dataset B

description:
JB4676V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4674V], Dataset B

description:
JB4674V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: Lung Urethane

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

description: FVB mouse lung cells after urethane injection

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
The data were processed and analyzed using GeneSpring 12.5 GX (Agilent) software.
RMA-16 normalized expression values by Genespring 12.5 GX (Agilent) software.

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: FULA1 mouse lung adenocarcinoma cells were cultured using Dulbecco's Modified Eagle's Medium (DMEM) from Sigma Lot D6429. To make the complete growth medium, we added fetal bovine serum to a final concentration of 10%. Cells incubated at 37°C with 5% CO2.

extract_protocol: Trizol followed by RNAeasy spin columns

value: FVB

tag: treatment

value: urethane

value: lung


title: tumor_ovarian [JB4684V], Dataset B

description:
JB4684V
microRNA expression of tumor tissue.
Total RNA or miRNA

value: advanced serous ovarian cancer

value: tumor


title: 9989536114_R01C02

description: blood sample

label: Cy5 and Cy132


title: DbGP33-specific CD8+ T cell, unvaccinated, anti-NK1.1 #3


title: MC38 sh IKKA (9_MC38-IKKA)

description: MC38 sh IKKA, mouse colon adenocarcinoma sh IKKA

source_name: MC38 shIKKA

growth_protocol: Cancer cells were cultured using Dulbecco's Modified Eagle's Medium (DMEM) from Sigma Lot D6429. To make the complete growth medium, we added fetal bovine serum to a final concentration of 10%. Cells incubated at 37°C with 5% CO2.

tag: cell line

value: sh IKKA


title: LLC sh Kras

description: LLC sh Kras Lewis lung carcinoma sh Kras mouse lung cancer

source_name: LLC shKras

value: LLC

value: sh Kras


title: FULA 1

description: FULA 1, mouse lung adenocarcinoma

source_name: FULA 1, mouse lung adenocarcinoma

value: FULA 1


title: Lung Saline

description: FVB mouse lung cells after saline injection

value: saline


title: tumor_ovarian [JB4649V], Dataset B

description:
JB4649V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536112_R03C01

description: blood sample

label: Cy5 and Cy130

value: blood

value: F

value: Control


title: 9989536114_R01C01

description: blood sample

label: Cy5 and Cy131

value: M

value: PD


title: 9989536112_R01C02

description: blood sample

label: Cy5 and Cy129


title: tumor_endometrial [JB4618E], Dataset B

description:
JB4618E
microRNA expression of tumor tissue.
Total RNA or miRNA

value: endometrioid endometrial cancer


title: 9989536110_R05C01

description: blood sample

label: Cy5 and Cy128


title: tumor_ovarian [JB4589V], Dataset B

description:
JB4589V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4561V], Dataset B

description:
JB4561V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: LLC Il-1b (2_LLC-IL1b)

description: LLC Il-1b, Lewis lung carcinoma treated with Il-1b mouse protein mouse lung cancer

source_name: LLC Il-1b


title: MC38 sh Ctrl (16_MC38wt)

description: MC38 sh Ctrl mouse colon adenocarcinoma sh Ctrl

source_name: MC38 sh Ctrl

value: sh Ctrl


title: LLC sh IKKB (05_LLCshIKKB)

description: LLC sh IKKB, Lewis lung carcinoma sh IKKB, mouse lung cancer

source_name: LLC sh IKKB

value: sh IKKB


title: MC38 sh IKKB (10_MC38-IKKB)

description: MC38 sh IKKB, mouse colon adenocarcinoma sh IKKB

source_name: MC38 sh IKKB


title: MC38 Il-1b (19_MC38wtIL1B)

description: MC38 Il-1b mouse colon adenocarcinoma treated with Il-1b mouse protein

source_name: MC38 Il-1b


title: 9989536110_R04C01

description: blood sample

label: Cy5 and Cy127