title: U23674: EP_U23674_panobinostat

city: Beaverton

first: Noah

last: Berlow

address: 12655 SW Beaverdam Rd

institute: CC-TDI

description: genetically engineered mouse model

data_processing:
raw reads were aligned to the GRCh38.87 human genome (RH30, CF1, RD, RH41, RH18, J099761) or mouse genome GRCm38.68 (U23674, U37125, U57810) using STAR aligner in paired end mode
aligned transcripts were quantified used RSEM-calculate-expression function in paired end mode
Genome_build: GRCh38.87
Genome_build: GRCm38.68
Supplementary_files_format_and_content: result files are In genes.results.txt file format. These files have quantified RPKM and TPM values

source_name: tumor

growth_protocol: cells were cultured in Dulbecco's Modified Eagle Medium + 10% fetal bovine serum + 1% penicillin streptomycin

extract_protocol:
RNA isolation from snap frozen  was performed at Beijing Genomics Institute (BGI)
library construction was performed at Beijing Genomics Institute (BGI)

treatment_protocol: cell lines were cultured in growth media, then treated with one of several histone deacetylase inhibitors (or with vehicle control) for up to 72 hours

value: alveolar rhabdomyosarcoma

tag: treatment

value: panobinostat

tag: tissue type

value: cell culture


title: U23674: EP_U23674_dmso

status: Public on Jun 13 2018

type: SRA

country: USA

description: genetically engineered mouse model

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

value: DMSO


title: U23674: EP_U23674_entinostat

description: genetically engineered mouse model

value: entinostat


title: Rh30: RH30_DMSO

description: genetically engineered mouse model

value: cell line


title: Rh30: RH30_ENT

description: genetically engineered mouse model


title: U23674: U23674_DMSO

description: genetically engineered mouse model


title: mdx heart IKK[beta]f/f (control) - rep1

type: RNA

city: Toledo

first: Jennifer

middle: M

last: Peterson

state: OH

address: 2801 W Bancroft St

department: SERS

institute: The University of Toledo

description: whole heart

hyb_protocol: Following fragmentation, 10 mg of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Gene summary expression estimates were retrieved using Robust multi-array average (RMA) method from probe level data after back ground correction and quantile normalization with Partek software (http://www.r-project.org/). RMA and gene expression data were also obtained using Expression Console software from Affymetrix.

label: Biotin

source_name: heart, mdx

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

extract_protocol: Total RNA was extracted using Trizol. Rneasy kit was used for further purification

tag: genotype/variation

value: IKK[beta]f/f

tag: age

value: 7 months


title: mdx heart Myh6-cre;IKK[beta][delta] (experimental) - rep4

description: whole heart

source_name: heart, mdx, cardiomyocyte IKKb-/-


title: mdx heart Myh6-cre;IKK[beta][delta] (experimental) - rep1

description: whole heart


title: U37125: RNA141231JA_37125B-DMSO

description: genetically engineered mouse model


title: U37125: RNA141231JA_37125-Ent

description: genetically engineered mouse model


title: U57810: RNA141231JA_57810-Ent

description: genetically engineered mouse model


title: mdx heart IKK[beta]f/f (control) - rep3

description: whole heart


title: U57810: RNA141231JA_57810-DMSO

description: genetically engineered mouse model


title: CD8 No2 IL27

status: Public on Jun 14 2018

city: Boston

first: Asaf

last: Madi

state: MA

address: 60 Fenwood Road, BTM 10016F

department: Neurology

institute: BWH

description: Naïve T cells stimulated with IL-27

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Individual .CEL files were RMA normalized and merged to an expression matrix using the ExpressionFileCreator of GenePattern with default parameters.

label: biotin

source_name: primary CD8 T cells

label_protocol: standard Affymetrix protocol

growth_protocol: Naïve CD4+ and CD8+ T cells were isolated from WT or IL27ra KO mice, and differentiated in vitro with or without IL-27. Cells were collected at 72 hours for CD8+ and 96 hours for CD4+.

extract_protocol: standard Affymetrix protocol

treatment_protocol: Affymetrix GeneChip Mouse Genome 430 2.0 Arrays were used to measure the resulting mRNA levels.

value: wild type


title: mdx heart IKK[beta]f/f (control) - rep2

description: whole heart


title: mdx heart Myh6-cre;IKK[beta][delta] (experimental) - rep3

description: whole heart


title: mdx heart Myh6-cre;IKK[beta][delta] (experimental) - rep2

description: whole heart


title: U23674: RNA141231JA_23674-DMSO

description: genetically engineered mouse model


title: U23674: U23674_ENT

description: genetically engineered mouse model


title: U23674: RNA141231JA_23674B-Ent

description: genetically engineered mouse model


title: obese 37

city: Xi’an

first: Yuesheng

last: Liu

state: Shaanxi

address: 157 Xiwu Road

country: China

institute: The Second Affiliated Hospital of Xi’an Jiaotong University

description: lncRNA and mRNA expression data from abdomen subcutaneous adipose tissue of obese children.

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

scan_protocol: GeneChips were scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

label: fluorescent

organism: Homo sapiens

source_name: adipose tissue of obese child

label_protocol: Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

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

treatment_protocol: Immediately after skin incision and subcutaneous tissue exposure during the operation, adipose tissue were separated bluntly, washed in cold PBS, and stored at liquid nitrogen for further use

value: Abdomen subcutaneous adipose tissue

value: 9 years

tag: Sex

value: Male


title: U23674: RNA141231JA_23674A-Ent

description: genetically engineered mouse model


title: [m-Th1]_[C2]_[2]

city: West Lafayette

first: Chang

last: Kim

state: IN

address: 725 Harrison St

department: Comparative Pathobiology

institute: Purdue

description: Mouse CD4+ T Cells were cultured in vitro to obtain RNA for the assay.

hyb_protocol: Gene Chips were scanned using GeneChip Scanner 3000 7G enabled for High-Resolution Scanning. The instruments were controlled using GCOS version 1.4 software.

data_processing: The data were condensed with MAS 5.0 using the GeneChip Operation Software.

source_name: Mouse Spleen, peripheral lymph nodes, mesenteric lymph nodes

label_protocol: Following fragmentation, 10 ug of cRNA were hybridized with a GeneChip Hybridization Oven 640 for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 400 with fludics protocol EukGE_WS2v5 and user prepared solutions, as per protocols provided by Affymetrix in the GeneChip Expression Analysis Technical Manual, 2004. This included Enzo Life Sciences' Bio Array Eukaryotic Hybridization Controls.

extract_protocol: Trizol Qiagen Total RNA Isolation Kit

treatment_protocol: hIL2(100U/ml), mIL-12(10ng/ml), and anti-mIL4(clone 11B11, 10ug/ml) and Acetone 10mM for 5 days

tag: sample type

value: m-Th1 C2

value: Spleen + Lymph Nodes

tag: cell type

value: CD4+ T cells


title: [m-Th1]_[control]_[2]

scan_protocol: Gene Chips were scanned using GeneChip Scanner 3000 7G enabled for High-Resolution Scanning. The instruments were controlled using GCOS version 1.4 software.

treatment_protocol: hIL2(100U/ml), mIL-12(10ng/ml), and anti-mIL4(clone 11B11, 10ug/ml) for 5 days

value: m-Th1 control


title: [m-Treg]_[control]_[2]

treatment_protocol: hIL2(100U/ml), and hTGF-b1(5ng/ml) for 5 days

value: m-Treg control


title: [m-Treg]_[C2]_[2]

treatment_protocol: hIL2(100U/ml), and hTGF-b1(5ng/ml), and Acetone 10mM for 5 days

value: m-Treg C2


title: [m-Treg]_[C2]_[1]


title: [m-Th1]_[C2]_[1]


title: H3K27ac mdx heart Myh6-cre;IKK[beta][delta]

library_source: genomic

data_processing:
A data analysis pipeline SCS v2.5 (Illumina) was employed to perform the initial bioinformatics analysis including base calling and converting the results into raw reads in FASTQ format.
ChIPseq reads were aligned to mm9 using bowtie2 software
Regions were called using peak caller algorithm in HOMER suite at default filters
Genome_build: mm9
Supplementary_files_format_and_content: Processed data is in txt format and contains sequenced regions that were found more numerous than would be expected by chance and as determined by background reads generated with input samples.

molecule: genomic DNA

extract_protocol:
Sonicated soluble chromatin was immunoprecipitated with 15 mg of H3K27ac antibody and pulled down by protein G sepharose beads equillibriated with yeast tRNA and BSA.
Purified DNA (10 ng) was end-repaired and A-nucleotide overhangs were added by incubation with the Taq Klenow fragment lacking exonuclease activity. After the attachment of anchor sequences, fragments were PCR-amplified using Illumina-supplied primers. The purified DNA library products were evaluated using Bioanalyzer (Agilent).

tag: antibody

value: H3K27ac (Millipore 17-683)

value: IKKb-/-


title: [m-Th1]_[control]_[1]


title: U37125: RNA141231JA_37125A-DMSO

description: genetically engineered mouse model

value: alveolar rhabdomyosarcoma

value: DMSO

value: cell culture


title: Input mdx heart Myh6-cre;IKK[beta][delta]


title: H3K27ac mdx heart IKK[beta]f/f

value: IKK[beta]f/f


title: [m-Treg]_[control]_[1]


title: SL Neural d7

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
RNA-seq reads were all trimmed to 40nt and then adapter- and quality-trimmed, and aligned with Tophat2 (Kim et al., 2013) against the mouse reference (GRCm38/mm10) genome. Read counts per ENSEMBL were obtained by featureCounts. Differential expression was evaluated with the DESeq2 package (Love et al., 2014).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Processed data files contain read counts per ENSEMBL transcript obtained by featureCounts

source_name: Differentiating embryonic stem cells into neural cells

growth_protocol: ESCs were cultured in 2iL or SL as indicated.

extract_protocol:
Total RNA was isolated from cells using the RNeasy mini kit (Qiagen).
RNA integrity was assessed on a Qubit Fluorometer (ThermoFisher Scientific) and Agilent Bioanalyzer Nano Chips (Agilent Technologies). Depletion of ribosomal RNA was performed on 2-5 μg of total RNA using the Ribo-Zero rRNA Removal Kit (Illumina) and libraries were produced from 10-100ng of ribosomal-depleted RNA using NextFlex Rapid Directional RNA-seq Kit (Bioo Scientific) with 12 cycles of PCR amplification. Libraries were pooled in equimolar quantities and sequenced on the HiSeq4000 platform (Illumina).

treatment_protocol: ESCs were differented into embryoid bodies (EB), EpiCSs, or neural cells.

tag: background strain

tag: genotype

value: Wild type


title: DGRP-551_1d_WholeBrainNuclei_Unstranded_Rep1_RNA-seq

city: LEUVEN

first: Stein

last: Aerts

address: Herestraat 49, bus 602

department: Center for Brain & Disease Research

country: Belgium

institute: KULeuven/VIB

description:
processed data file:
WholeBrain_Bulk_RNA-seq_Comparison_DGEM_DESeq_Normalized.tsv.gz

data_processing:
The 10X samples were each processed (alignment, barcode assignment and UMI counting) with Cell Ranger (version 2.0.0) count pipeline. All 10X samples were then merged with Cell Ranger (version 2.0.0) aggr pipeline.
The Drop-seq samples were each processed (alignment, barcode assignment and UMI counting) with the Drop-seq tools (version 1.12) developped by Jim Nemesh from McCarroll lab. Gene expression matrices where outer joined.
The reads from CEL-seq2 samples were first cleaned for adapters using fastq-mcf (Aronesty, 2011) and a list of sequencing primers. Multiplexed CEL-seq2 cells were demultiplexed with custom scripts utilizing pysam (Li et al., 2009). Cleaned reads were then mapped to the 3rd 2017 FlyBase release (D. melanogaster r6.16) genome using STAR with default parameters. Reads were counted per gene using featureCounts.
The reads from SMART-seq2 and Adapted SMART-seq2 samples were mapped using STAR (2.5.1) and the expression matrices were generated using featureCounts from Subread 1.5.1.
For the ATAC samples the raw reads were first filtered and scanned for adapters using fastq‐mcf from the ea‐utils r819 package. Read quality was then checked using FastQC 0.11.4. The reads were mapped to the Drosophila genome (dm6) using STAR 2.5.1. The outputted BAM file from STAR was then indexedand sorted using Samtools 1.2. Using genomeCoverageBed from Bedtools 2.23.0, the BAM file was converted to a BedGraph file. For fast, visualization in the IGV GenomeBrowser, the BedGraph file was further processed to a BigWig file using bedGraphtoBigWig.
Genome_build: dm6 (dmel_r6.16_FB2017_03)
Supplementary_files_format_and_content: 10X DGRP-551 + w1118 high quality dataset (57k) raw UMI count matrix stored in compressed Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively
10X DGRP-551 + w1118 large dataset (157k) raw UMI count matrix stored in compressed Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively
CEL-seq2 FAC-sorted R23E10 neurons raw count matrix
SMART-seq2 FAC-sorted R23E10 neurons raw count matrix
Adapted SMART-seq2 FAC-sorted R23E10 neurons raw count matrix
Drop-seq DGRP-551 dataset raw UMI matrix
ATAC-seq bigWig files

molecule: polyA RNA

organism: Drosophila melanogaster

extract_protocol:
Adult flies were anesthetised by placing them in ice cold glass dishes, heads were removed and brains were dissected removing any cuticle, retina and trachea. Dissected brains were placed in ice cold PBS. When 40 brains were collected, they were processed using the Nuclei EZ kit and RNA was isolated from collected nuclei using the Ambion RNAqueous-micro kit.
Tn5 Mediated RNA-seq

treatment_protocol: Flies were grown on molasses based flyfood at 25'C with a 12hour/12hour day night cycle

value: 1 Day

value: brain


title: SL Neural d2

value: Differentiating embryonic stem cells into neural cells


title: SL Neural d5


title: Input mdx heart IKK[beta]f/f

value: 7 months


title: [m-Th17]_[C2]_[2]

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with a GeneChip Hybridization Oven 640 for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 400 with fludics protocol EukGE_WS2v5 and user prepared solutions, as per protocols provided by Affymetrix in the GeneChip Expression Analysis Technical Manual, 2004. This included Enzo Life Sciences' Bio Array Eukaryotic Hybridization Controls.

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA according to the Single Round RNA Amplification and Biotin Labeling System(Enzo Life Sciences Intl. Plymouth Meeting, PA)

treatment_protocol: hIL-2(100U/ml), hTGF-b1(5ng/ml), mIL-6(20ng/ml), mIL-1b(10ng/ml), mIL-23(10ng/ml), mIL-21(10ng/ml), mTNF-a(20ng/ml), anti-mIL-4(clone 11B11, 10ng/ml) and anti-mIFN-gamma(clone XMG2.4, 10ug/ml) and acetate 10mM cultured for 5 days.

value: m-Th17 C2


title: [m-Th17]_[control]_[2]

treatment_protocol: hIL-2(100U/ml), hTGF-b1(5ng/ml), mIL-6(20ng/ml), mIL-1b(10ng/ml), mIL-23(10ng/ml), mIL-21(10ng/ml), mTNF-a(20ng/ml), anti-mIL-4(clone 11B11, 10ng/ml) and anti-mIFN-gamma(clone XMG2.4, 10ug/ml) cultured for 5 days.

value: m-Th17 control

value: Spleen + Lymph Nodes


title: DGRP-551_9d_r2_SDP

extract_protocol:
Adult flies were anesthetised by placing them in ice cold glass dishes, heads were removed and brains were dissected removing any cuticle, retina and trachea. Dissected brains were placed in ice cold PBS. When 40 brains were collected, brains were dissociated at 25'C for 15 hours in a mix of Collagenase (75µl @ 100mg/ml), Dispase (50µl @ 3mg/ml) and Trypsin 0.05% EDTA (125µl), the sample was pipette mixed every 5 minutes. Cells washed in PBS twice centrifuging at 800 xg) and resuspended in 400µl PBS. A single cell suspension was obtained by filtering with an 11µm cell strainer.
Drop-seq and 10x Genomics CHROMIUM Single Cell 3’ Solution V2 Chemistry

value: 9 Days


title: SL Neural d2.5


title: SL d0

source_name: Embryonic stem cells

value: Embryonic stem cells


title: [m-Th17]_[C2]_[3]

value: CD4+ T cells


title: [m-Th17]_[control]_[3]


title: SL Neural d3


title: DGRP-551_15d_r2_SDP

value: 15 Days


title: SL Neural d1


title: SL Neural d1.5


title: SL EpiSC d7

source_name: Differentiating embryonic stem cells into EpiSCs


title: SL EpiSC d5

value: Differentiating embryonic stem cells into EpiSCs


title: SL EpiSC d3


title: SL EpiSC d2


title: SL EpiSC d2.5


title: DGRP-551_1d_r2_SDP


title: SL EpiSC d1


title: SL EpiSC d1.5


title: SL EB d7

source_name: Differentiating embryonic stem cells into embryoid bodies


title: SL EB d5

value: Differentiating embryonic stem cells into embryoid bodies


title: SL EB d3


title: SL EB d2


title: [mCD4+ T-Cells]_[Progesterone]_[2]

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with a GeneChip Hybridization Oven 640 for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays.  GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 400 with fludics protocol EukGE_WS2v5 and user prepared solutions, as per protocols provided by Affymetrix in the GeneChip Expression Analysis Technical Manual, 2004.  This included Enzo Life Sciences' Bio Array Eukaryotic Hybridization Controls.

scan_protocol: Gene Chips were scanned using GeneChip Scanner 3000 7G enabled for High-Resolution Scanning.  The instruments were controlled using GCOS version 1.4 software.

growth_protocol: Naive CD4+ T cells were cultured for 7 days in RPMI 1640 medium supplemented with 10% FBS and concanavalin A (2.5 ug/ml).

extract_protocol: Trizol  Qiagen Total RNA Isolation Kit

treatment_protocol: Naive CD4+ T cells were treated with hTGFb1 (1 ng/ml). Progesterone was added to culture at 2000 ng/ml.

tag: agent

value: TGFb1 and progesterone


title: [mCD4+ T-Cells]_[Progesterone]_[1]


title: [mCD4+ T-Cells]_[TGFb]_[2]

treatment_protocol: Naive CD4+ T cells were treated with hTGFb1 (1 ng/ml).

value: TGFb


title: [m-Th17]_[C2]_[1]

treatment_protocol: hIL-2(100U/ml), hTGF-b1(5ng/ml), mIL-6(20ng/ml), mIL-1b(10ng/ml), mIL-23(10ng/ml), mIL-21(10ng/ml), mTNF-a(20ng/ml), anti-mIL-4(clone 11B11, 10ng/ml) and anti-mIFN-gamma(clone XMG2.4, 10ug/ml)  and Acetate 10mM cultured for 5 days.


title: SL EB d2.5


title: Knee synovial tissues of AIA_H5_NS, biological rep1

city: Beijing

first: Yanqiong

last: Zhang

address: No 16, Nanxiaojie, Dongzhimennei

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

organism: Rattus norvegicus

source_name: Lewis rats knee synovial tissues

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Male Lewis rats (n=78, 6-8 weeks old, 200+/-20g in weight) were kept under specific pathogen-free conditions, with a constant temperature of 24 +/- 1C in a 12-hour light/dark cycle room, and ad libitum water and food access.

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 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 RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)

treatment_protocol: Male Lewis rats were randomly divided into ten groups (six per group): (1) Normal control group; (2) AIA (Adjuvant induced arthritis) model group; (3) AIA-cold model group; (4) AIA-cold-WTD treatment group; (5) AIA-cold-BACs treatment group; (6) AIA-cold-MTX (methotrexate) treatment group; (7) AIA-hot model group; (8) AIA-hot-WTD treatment group; (9) AIA-hot-BACs treatment group; (10) AIA-hot-MTX treatment group.

tag: strain

value: Lewis rat

value: knee synovial tissue

tag: gender

value: Male

tag: group

value: AIA-hot rats


title: SL EB d1

value: Wild type


title: Knee synovial tissues of Mod2_NS, biological rep1

value: AIA model rats


title: SL EB d1.5


title: Knee synovial tissues of Con1_NS, biological rep1

value: normal control rats


title: Knee synovial tissues of Mod4_NS, biological rep1


title: Knee synovial tissues of Con3_NS, biological rep1


title: Knee synovial tissues of Con2_NS, biological rep1


title: Knee synovial tissues of Mod3_NS, biological rep1


title: Knee synovial tissues of AIA_H_Z2_NS, biological rep1

value: AIA-hot-WTD treatment rats


title: [mCD4+ T-Cells]_[TGFb]_[1]

value: Spleen + Lymph Nodes


title: 2iL Neural d7

value: Differentiating embryonic stem cells into neural cells


title: Knee synovial tissues of AIA_H_G2_NS, biological rep1


title: Knee synovial tissues of AIA_H4_NS, biological rep1


title: [m-Th17]_[control]_[1]

treatment_protocol: hIL-2(100U/ml), hTGF-b1(5ng/ml), mIL-6(20ng/ml), mIL-1b(10ng/ml), mIL-23(10ng/ml), mIL-21(10ng/ml), mTNF-a(20ng/ml), anti-mIL-4(clone 11B11, 10ng/ml) and anti-mIFN-gamma(clone XMG2.4, 10ug/ml)  cultured for 5 days.

value: m-Th17 control


title: Knee synovial tissues of AIA_H1_NS, biological rep1


title: Knee synovial tissues of AIA_C_G5_NS, biological rep1

value: AIA-cold-WTD treatment rats


title: Knee synovial tissues of AIA_H_D6_NS, biological rep1


title: Knee synovial tissues of AIA_C_Z6_NS, biological rep1


title: Knee synovial tissues of AIA_C_Z1_NS, biological rep1


title: Knee synovial tissues of AIA_C4_NS, biological rep1

value: AIA-cold rats


title: 2iL Neural d5


title: Rh30: EP_rh30_panobinostat

description: human-derived cell line

growth_protocol: cells were cultured in RPMI 1640 + 10% fetal bovine serum + 1% penicillin streptomycin

value: alveolar rhabdomyosarcoma

value: panobinostat

value: cell line


title: Rh30: EP_rh30_entinostat

description: human-derived cell line

value: entinostat


title: 2iL Neural d2


title: 2iL Neural d3


title: Rh30: EP_rh30_dmso

description: human-derived cell line

value: DMSO


title: Knee synovial tissues of AIA_C1_NS, biological rep1

value: Lewis rat

value: knee synovial tissue


title: 2iL Neural d2.5


title: J099761: J099761_DMSO

description: patient-derived xenograft culture

value: cell culture


title: 2iL Neural d1

value: Wild type


title: CF1: CF1_DMSO

description: patient-derived xenograft culture


title: J099761: J099761_ENT

description: patient-derived xenograft culture


title: 2iL Neural d1.5


title: CF1: CF1_ENT

description: patient-derived xenograft culture


title: 2iL Neural d0

value: Embryonic stem cells


title: Rh41: RNA141231JA_Rh41-Ent

description: human-derived cell line


title: Rh41: RNA141231JA_Rh41-DMSO

description: human-derived cell line


title: 2iL EpiSC d3

value: Differentiating embryonic stem cells into EpiSCs


title: 2iL EpiSC d2


title: 2iL EpiSC d7


title: Rh30: RNA141231JA_Rh30-Ent

description: human-derived cell line


title: Rh30: RNA141231JA_Rh30-DMSO

description: human-derived cell line


title: Knee synovial tissues of AIA_C3_NS, biological rep1

value: Male


title: 2iL EpiSC d1


title: Rh18: RNA141231JA_Rh18-DMSO

description: human-derived cell line


title: Rh18: RNA141231JA_Rh18-Ent

description: human-derived cell line


title: 2iL EpiSC d0


title: RD: RNA141231JA_RD-Ent

description: human-derived cell line


title: 2iL EpiSC d1.5


title: RD: RNA141231JA_RD-DMSO

description: human-derived cell line


title: 2iL EB d3

value: Differentiating embryonic stem cells into embryoid bodies


title: 2iL EB d5


title: 2iL EB d7


title: 2iL EB d2


title: 2iL EB d2.5


title: 2iL EpiSC d2.5


title: 2iL EB d1.5


title: 2iL EB d1


title: 2iL EB d0


title: HFF_c-Myc_2

city: Seoul

first: Jae whan

last: Song

address: Yonsei-ro 50

department: Department of Biochemistry

country: South Korea

institute: College of Life Science and Biotechnology

hyb_protocol: Following fragmentation, RNAs were hybridized for 16 hrs at 45°C on GeneChip™ Hybridization Oven 645.GeneChips were washed and stained in GeneChip™ Fluidics Station 450

scan_protocol: Genechip was scaned using Affymetrix GeneChip® Scanner 3000 7G

data_processing: The data was analyzed with Affymetrix GeneChip® Operating (GCOS) software, and normalized with RMA(Robust Multi-array Average)

label: TdT labeling

label_protocol: The targets were labeled using terminal deoxynucleotidyl transferase (TdT) for hybridization to the arrays

growth_protocol: HFF cells were grown in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: After c-Myc infection, cells were lysed by trizol, and RNAs were extracted from the lyaste.

treatment_protocol: HFF cells were infected with lentiviral c-Myc

tag: cell line

value: human fore skin fibroblast (HFFs) cell line

value: stably expressing c-Myc


title: HFF_c-Myc_3


title: PBMC of non-infected dogs_rep5

city: Araçatuba

first: Jaqueline

middle: Poleto

last: Bragato

state: SP

address: Clóvis Pestana, 793

department: Department of animal clinic, surgery and reproduction

country: Brazil

institute: Universidade Estadual Paulista Júlio de Mesquita Filho - UNESP

description: miRNA profile expression in PBMC of non-infected dogs

hyb_protocol: For hybridization of samples to the strips was carried on at 48ºC for 20h using the GeneAtlas® Hybridization,  Wash, and Stain Kit for miRNA Array Strips. Following this period, strips were processed and scanned using the GeneAtlas® System (Affymetrix).

scan_protocol: After the array strip are registered in the GeneAtlas Software and the target hybridization steps are complete, scanning processing on the GeneAtlas System was made. Transfer of the strip assembly into the imaging station's drawer starts the imaging process.

data_processing: Raw intensity values were background corrected, log2 transformed and then quantile normalized by the software Expression Console (Affymetrix) using the Robust Multi-array Average (RMA) algorithm.

organism: Canis lupus familiaris

source_name: PBMC of healthy and non-infected dogs

label_protocol: MicroRNA profiles were obtained from 250 ng/sample of total RNA (RNA Integrity Number over than 7) using the FlashTag™ Biotin HSR RNA Labeling Kit, and the Affymetrix® miRNA 4.1 Array strip (Affymetrix, Santa Clara, Califórnia, EUA), according to the manufacturer’s instructions. A recommended ELOSA quality control assay was run for all samples.

extract_protocol: PBMC were isolated by gradient Histopaque® 1077 (Sigma-Aldrich, St. Louis, MO, USA) following the manufacturer's instructions. Total RNA was extracted from 5x106 cells with a miRVana™ miRNA Isolation Kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions.  RNA samples were immediately stored at -80ºC. Quantification was performed using NanoDrop (ND-2000 spectrophotometer, Thermo Scientific, Wilmington, DE, USA) and quality of samples was assessed using a Capillary electrophoresis (Bioanalyzer 2100 Agilent, Santa Clara, CA, USA).

value: PBMC

tag: infected with


title: PBMC of non-infected dogs_rep2


title: HFF_control_2

value: control


title: PBMC of non-infected dogs_rep4


title: HFF_c-Myc_1


title: w1118_1d_WholeBrain_Unstranded_RNA-seq

extract_protocol:
Adult flies were anesthetised by placing them in ice cold glass dishes, heads were removed and brains were dissected removing any cuticle, retina and trachea. Dissected brains were placed in ice cold PBS. When 40 brains were collected, RNA was isolated using the Ambion RNAqueous-micro kit.
Tn5 Mediated RNA-seq

value: 1 Day

value: brain


title: w1118_1d_WholeBrain_Stranded_RNA-seq

extract_protocol:
Adult flies were anesthetised by placing them in ice cold glass dishes, heads were removed and brains were dissected removing any cuticle, retina and trachea. Dissected brains were placed in ice cold PBS. When 40 brains were collected, RNA was isolated using the Ambion RNAqueous-micro kit.
Illumina Stranded RNA-seq kit


title: PBMC of non-infected dogs_rep3


title: DGRP-551_1d_WholeBrain_Unstranded_RNA-seq


title: PBMC of infected dogs_rep8

description: miRNA profile expression in PBMC of dogs naturally infected with L. infantum

value: L. infantum


title: PBMC of non-infected dogs_rep1


title: PBMC of infected dogs_rep10

source_name: PBMC of dogs naturally infected with L. infantum


title: PBMC of infected dogs_rep7


title: PBMC of infected dogs_rep6


title: PBMC of infected dogs_rep2


title: HFF_control_3


title: PBMC of infected dogs_rep9


title: TFAP2AMO1/2, biological rep2

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Xenopus laevis Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Styation 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with GeneSpring GX (Agilent Technologies).

organism: Xenopus laevis

source_name: non-treated ACs injected with TFAP2A MO1/2

label_protocol: Biotinylated cRNA were prepared from 250 ng total RNA using the GeneChip 3’ IVT Express Kit (Affymetrix) according to the manufacturer’s instruction.

growth_protocol: Xenopus laevis embryos were obtained by in vitro fertilization and cultured in 0.1x MBS.

treatment_protocol: Control MO (80 ng), ERK3 MO1/2 (40 ng each of MO1 and MO2), or TFAP2A MO1/2 (40 ng each of MO1 and MO2) were injected into the animal regions of all blastomeres at the 4-cell stage. The animal caps were dissected from the injected embryos at stage 9, cultured alone, and harvested at stage 15.

value: animal cap

tag: developmental stage

tag: injected mo

value: TFAP2A MO1/2

tag: treatment


title: PBMC of infected dogs_rep1


title: DGRP-551_1d_WholeBrain_Stranded_RNA-seq

tag: genotype/variation

tag: tissue


title: PBMC of infected dogs_rep3


title: Adapted_SMART_seq2_R23E10_Cell_9

description:
processed data file:
R23E10_Adapted_SMART-seq2_DGEM.tsv.gz

extract_protocol:
Adult flies were anesthetised by placing them in ice cold glass dishes, heads were removed and brains were dissected removing any cuticle, retina and trachea. Dissected brains were placed in ice cold PBS. When 40 brains were collected, brains were dissociated at 25'C for 2 hours in a mix of Collagenase (75µl @ 100mg/ml) and Dispase (50µl @ 3mg/ml), the sample was pipette mixed every 15 minutes. Cells washed in PBS twice centrifuging at 800 xg) and resuspended in 400µl PBS. A single cell suspension was obtained by filtering with an 11µm cell strainer. Cells were sorted into single wells containing RTL buffer.
Adapted SMART-Seq

tag: age

value: 0-7 Days

value: R23E10-Gal4 x UAS-CD8::GFP


title: HFF_control_1


title: TFAP2AMO1/2, biological rep1

description: TFAP2A MO1/2 (40 ng each of MO1 and MO2) were injected into the animal regions of all blastomeres at the 4-cell stage. The animal caps were dissected from the injected embryos at stage 9, cultured alone, and harvested at stage 15.


title: Adapted_SMART_seq2_R23E10_Cell_6


title: Adapted_SMART_seq2_R23E10_Cell_7


title: ERK3 MO1/2, biological rep1

description: ERK3 MO1/2 (40 ng each of MO1 and MO2) were injected into the animal regions of all blastomeres at the 4-cell stage. The animal caps were dissected from the injected embryos at stage 9, cultured alone, and harvested at stage 15.

source_name: non-treated ACs injected with ERK3 MO1/2

value: ERK3 MO1/2


title: ERK3 MO1/2, biological rep2


title: PBMC of infected dogs_rep4


title: Control MO, biological rep1

description: Control MO (80 ng) was injected into the animal regions of all blastomeres at the 4-cell stage. The animal caps were dissected from the injected embryos at stage 9, cultured alone, and harvested at stage 15.

source_name: non-treated ACs injected with control MO

value: Control MO


title: Control MO, biological rep2


title: activin/RA-treated AC_ERK3 MO3

description:
Kidney_3rd_15
ERK3 MO3 (80 ng) was injected into the animal regions of all blastomeres at the 4-cell stage. The animal caps were dissected from the injected embryos at stage 9, cultured in the presence of activin plus retinoic acid (activin/RA), and harvested at stage 15.

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Xenopus laevis Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Styation 450.

source_name: activin/RA-treated ACs injected with ERK3 MO3, stage 15

treatment_protocol: Control MO (80 ng), ERK3 MO1/2 (40 ng each of MO1 and MO2), or ERK3 MO3 (80 ng) were injected into the animal regions of all blastomeres at the 4-cell stage. The animal caps were dissected from the injected embryos at stage 9, cultured alone or in the presence of activin plus retinoic acid (activin/RA), and harvested at stage 15.

value: ERK3 MO3

value: activin/RA


title: PBMC of infected dogs_rep5


title: non-treated AC_ERK3 MO1/2

description:
AC_AB_15
ERK3 MO1/2 (40 ng each of MO1 and MO2) were injected into the animal regions of all blastomeres at the 4-cell stage. The animal caps were dissected from the injected embryos at stage 9, cultured alone, and harvested at stage 15.

source_name: non-treated ACs injected with ERK3 MO1/2, stage 15


title: activin/RA-treated AC_ERK3 MO1/2

description:
Kidney_AB_15
ERK3 MO1/2 (40 ng each of MO1 and MO2) were injected into the animal regions of all blastomeres at the 4-cell stage. The animal caps were dissected from the injected embryos at stage 9, cultured in the presence of activin plus retinoic acid (activin/RA), and harvested at stage 15.

source_name: activin/RA-treated ACs injected with ERK3 MO1/2, stage 15


title: DGRP-551_1d_WholeBrainNuclei_Unstranded_Rep2_RNA-seq


title: Adapted_SMART_seq2_R23E10_Cell_4


title: Adapted_SMART_seq2_R23E10_Cell_5


title: activin/RA-treated AC_Control MO

description:
Kidney_CMO_15
Control MO (80 ng) was injected into the animal regions of all blastomeres at the 4-cell stage. The animal caps were dissected from the injected embryos at stage 9, cultured in the presence of activin plus retinoic acid (activin/RA), and harvested at stage 15.

source_name: activin/RA-treated ACs injected with control MO, stage 15


title: non-treated AC_ERK3 MO3

description:
AC_3rd_15
ERK3 MO3 (80 ng) was injected into the animal regions of all blastomeres at the 4-cell stage. The animal caps were dissected from the injected embryos at stage 9, cultured alone, and harvested at stage 15.

source_name: non-treated ACs injected with ERK3 MO3, stage 15


title: Adapted_SMART_seq2_R23E10_Cell_8


title: Adapted_SMART_seq2_R23E10_Cell_34


title: Adapted_SMART_seq2_R23E10_Cell_35


title: Adapted_SMART_seq2_R23E10_Cell_33


title: Adapted_SMART_seq2_R23E10_Cell_31


title: Adapted_SMART_seq2_R23E10_Cell_30


title: non-treated AC_Control MO

description:
AC_CMO_15
Control MO (80 ng) was injected into the animal regions of all blastomeres at the 4-cell stage. The animal caps were dissected from the injected embryos at stage 9, cultured alone, and harvested at stage 15.

source_name: non-treated ACs injected with control MO, stage 15


title: Adapted_SMART_seq2_R23E10_Cell_28


title: Adapted_SMART_seq2_R23E10_Cell_25


title: Adapted_SMART_seq2_R23E10_Cell_26


title: IDLE_PJC_8S33_FAT_V2

city: Melbourne

first: Marta

last: Brozynska

state: VIC

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

hyb_protocol: The labelled samples were hybridised to the Human HT-12 v4.0 Expression BeadChip as per the manufacturer’s protocol (47,231 probes; Illumina, Scoresby, Vic, Australia).

scan_protocol: The BeadChips were scanned using the iScan microarray BeadStudio platform (Illumina).

data_processing: Quality standards for hybridization, labelling, staining, background signal, and basal level of housekeeping gene expression for each chip were verified. After scanning on the Illumina iScan, the resulting images were background subtracted, quantile normalised and processed using the GenomeStudio software (Illumina).

source_name: abdominal subcutaneous adipose tissue

label_protocol: The amplification and labelling of RNA was performed using the TotalPrep amplification kit according to manufacturer’s instructions (Ambion; ThermoFisher Scientific).

extract_protocol: RNA isolation from 100 mg of adipose tissue was performed using TRIzol Reagent as per manufacturer’s instructions (ThermoFisher Scientific, Scoresby, Vic, Australia). The RNA phase (the clear upper aqueous layer) was transferred to a new tube without disturbing the interphase. Then 1.5 volumes of 100% ethanol was added to the samples and loaded onto the RNeasy mini spin column (Qiagen, Chadstone, Vic, Australia). RNA was extracted according to the manufacturer’s protocol. The RNA was quantified using a Nanodrop spectrophotometer (ThermoFisher Scientific) and Qubit fluorometer (Life Technologies; ThermoFisher Scientific). The integrity of the RNA was assessed using a MultiNA Microchip Electrophoresis System (Shimadzu).

tag: Sex

value: male

tag: bmi

value: subcutaneous adipose


title: Adapted_SMART_seq2_R23E10_Cell_22


title: IDLE_BJC_389C_FAT_V3

value: female


title: IDLE_PJC_8S33_FAT_V3


title: IDLE_PJC_8S33_FAT_V1


title: IDLE_BJC_389C_FAT_V1


title: Adapted_SMART_seq2_R23E10_Cell_21


title: IDLE_BJC_389C_FAT_V2


title: IDLE_ATY_35T7_FAT_V2


title: Adapted_SMART_seq2_R23E10_Cell_24


title: Adapted_SMART_seq2_R23E10_Cell_27


title: IDLE_ATY_35T7_FAT_V3


title: Adapted_SMART_seq2_R23E10_Cell_20


title: Adapted_SMART_seq2_R23E10_Cell_3


title: Adapted_SMART_seq2_R23E10_Cell_29


title: Adapted_SMART_seq2_R23E10_Cell_23


title: Adapted_SMART_seq2_R23E10_Cell_2


title: IDLE_BMD_C4EH_FAT_V3


title: Adapted_SMART_seq2_R23E10_Cell_19


title: IDLE_RPH_71XM_FAT_V3


title: IDLE_CJP_V108_FAT_V2


title: IDLE_ATY_35T7_FAT_V1


title: Adapted_SMART_seq2_R23E10_Cell_17


title: IDLE_CJP_V108_FAT_V1


title: Adapted_SMART_seq2_R23E10_Cell_14


title: IDLE_CJP_V108_FAT_V3


title: IDLE_RPH_71XM_FAT_V1


title: Adapted_SMART_seq2_R23E10_Cell_15


title: IDLE_BMD_C4EH_FAT_V2


title: IDLE_RPH_71XM_FAT_V2


title: MACMock-26-2

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

data_processing:
Illumina Casava1.8.2 software was used for basecalling
Reads were processed using fastx toolkit to trim for adapter and low quality bases and filter for low quality reads.
Processed reads were mapped to the Mus musculus and murine norovirus genomes using Tophat v2.0.14
Reads mapping to genes were counted using htseq-count
Gene normalization and differential expression analysis were performed using Deseq2
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab delimited text file containing deseq2 normalized values in a single matrix format.

source_name: BMDM cells

extract_protocol:
RNA was extracted using Qiagen AllPrep DNA/RNA kit with an additional on-column Dnase I treatment
Total RNA libraries were prepared using the TruSeq Stranded Total RNA kit with Ribo-Zero Gold rRNA depletion (Illumina Inc., San Diego, CA)

tag: infection

value: Mock

tag: time point


title: MACMock-26-1


title: IDLE_BMD_C4EH_FAT_V1


title: IDLE_PJR_9WEZ_FAT_V2


title: IDLE_PJR_9WEZ_FAT_V3


title: Adapted_SMART_seq2_R23E10_Cell_13


title: Adapted_SMART_seq2_R23E10_Cell_12


title: Adapted_SMART_seq2_R23E10_Cell_16


title: MACMNV-26-2

value: MNV


title: Adapted_SMART_seq2_R23E10_Cell_11


title: Adapted_SMART_seq2_R23E10_Cell_18


title: MACMNV-26-3


title: MACMNV-26-1


title: Adapted_SMART_seq2_R23E10_Cell_10


title: IDLE_PAB_TPCW_FAT_V1


title: MACMNV-20-2


title: MACMNV-20-1


title: SMART_seq2_R23E10_Cell_8

description:
processed data file:
R23E10_SMART-seq2_DGEM.tsv.gz

extract_protocol:
Adult flies were anesthetised by placing them in ice cold glass dishes, heads were removed and brains were dissected removing any cuticle, retina and trachea. Dissected brains were placed in ice cold PBS. When 40 brains were collected, brains were dissociated at 25'C for 2 hours in a mix of Collagenase (75µl @ 100mg/ml) and Dispase (50µl @ 3mg/ml), the sample was pipette mixed every 15 minutes. Cells washed in PBS twice centrifuging at 800 xg) and resuspended in 400µl PBS. A single cell suspension was obtained by filtering with an 11µm cell strainer. Cells were sorted into single wells containing SMART-seq lysis buffer.
SMART-Seq


title: Adapted_SMART_seq2_R23E10_Cell_1


title: MACMNV-20-3


title: IDLE_PAB_TPCW_FAT_V3


title: SMART_seq2_R23E10_Cell_9


title: Mature Luminal population isolated from ErbB2, stromal PTEN deletion mice-Experiment#2

city: Columbus

first: Gina

last: Sizemore

address: 460 W. 12th Avenue

institute: Ohio State University

description: Gene expression data from Lin-CD24+CD29loCD61- mature luminal epithelial subpopulation collected by pooling pre-neoplastic mammary tissue from 6-8 virgin ErbB2;Ptenfl/fl (8-9 weeks of age) mice

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Eukaryotic Hybridization Controls (Affymetrix) •Heat 65oC for 5 minutes, 99oC for 5 minutes, 45oC for 5 minutes centrifuge top speed for 5 minutes  •Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G using AGCC

data_processing: The resulting array data was assessed for statistical quality control and normalized in Expression Console (Affymetrix) using an SST RMA algorithm. Heat maps for each independent sample were then created using dChip software using fold change and p-value parameters of 1.5 and < 0.05, respectively. GSEA v2.0 was used to determine the enrichment of the C5 category within the Molecular Signatures Database (MSigDB) in our gene expression data. Statistical significance (q<0.05) was determined through generation of a normalized enrichment score (NES) and a false discovery rate (FDR).

source_name: Mature Luminal population isolated by FACS (Lin-CD24+CD29loCD61-)

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

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and treated with DNAse I (DNA-free, Ambion). RNA quality was assessed using a NanoDrop TM2000 Spectrophotometer (Thermo Scientific). Sample quality was further ensured by characterizing size distribution via fluorescent capillary electrophoresis using the Bioanalyzer 2100 RNA 6000 Pico-Chip and Degradometer software (Agilent Technologies, Santa Clara, California, USA).

value: mature luminal cell population


title: Mature Luminal population isolated from ErbB2, stromal PTEN deletion mice-Experiment#3


title: SMART_seq2_R23E10_Cell_7


title: MACMNV-14-2


title: Mature Luminal population isolated from control ErbB2 mice-Experiment#3


title: MACMNV-14-3


title: SMART_seq2_R23E10_Cell_6


title: MACMNV-8-3


title: SMART_seq2_R23E10_Cell_5


title: rtg3_rep3

city: Buffalo

first: Paul

middle: J

last: Cullen

state: NY

address: 341 Cooke Hall

department: Biology

institute: SUNY-Buffalo

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4 (http://support.illumina.com/downloads /bcl2fastq_conversion_software_184.html).
Reads of low quality were filtered out prior to alignment to the R64-1-1 reference genome  using TopHat v2.0.19  Counts were generated from TopHat oBalignments using the Python package HTSeq v0.6.1 ( http://www-huber.embl.de/users/anders/ HTSeq/doc/overview.html).
Genome_build: S. cerevisiae R64-1-1
Supplementary_files_format_and_content: tab delimted text files including read counts for each gene

organism: Saccharomyces cerevisiae

source_name: rtg3, biofilm

growth_protocol: Cells were grown at 30C for 16h in YEPD liquid media with agitation. Cells were concentrated to OD600=20 and spotted in 10ul aliquots onto YEPGal agar media for 24h. Gross biofilm morphology was confirmed before harvesting.

extract_protocol:
Hot acid phenol chloroform extraction
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep Kit (Illumina, Inc.) and a Sciclone  NGSx Workstation (PerkinElmer).  Library size distributions were validated using an Agilent 4200 TapeStation (Agilent Technologies).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technology's Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen).
RNA-Seq on polyA selected mRNA

value: 24h on YEPGal 2% agar media

tag: genotype

value: rtg3 mutant

tag: phenotype

value: hypofilamentous biofilm


title: rtg3_rep1

tag: strain


title: ras2_rep3

source_name: ras2, biofilm

value: ras2 mutant


title: MACMNV-14-1


title: ras2_rep2


title: SMART_seq2_R23E10_Cell_49

value: brain


title: rtg3_rep2


title: IDLE_PAB_TPCW_FAT_V2


title: MACMNV-8-2


title: ras2_rep1


title: SMART_seq2_R23E10_Cell_47

value: 0-7 Days


title: SMART_seq2_R23E10_Cell_46

value: R23E10-Gal4 x UAS-CD8::GFP


title: MACMNV-4-3


title: Mature Luminal population isolated from ErbB2, stromal PTEN deletion mice-Experiment#1


title: MACMNV-8-1


title: rim101-531_rep3

source_name: rim101-531, biofilm

value: rim101-531 mutant


title: Mature Luminal population isolated from control ErbB2 mice-Experiment#2


title: Mature Luminal population isolated from control ErbB2 mice-Experiment#1


title: rim101-531_rep2


title: SMART_seq2_R23E10_Cell_45


title: MACMNV-4-2


title: SMART_seq2_R23E10_Cell_44


title: IDLE_PJR_9WEZ_FAT_V1


title: MACMNV-4-1


title: SMART_seq2_R23E10_Cell_42


title: SMART_seq2_R23E10_Cell_43


title: MACMock-0-2


title: MACMock-0-1


title: dig1_rep3

source_name: dig1, biofilm

value: dig1 mutant

value: hyperfilamentous biofilm


title: MACMNV-0-3


title: spt8_rep_2

source_name: spt8, biofilm

value: spt8 mutant


title: SMART_seq2_R23E10_Cell_41


title: SMART_seq2_R23E10_Cell_40


title: spt8_rep_3


title: rim101-531_rep1


title: dig1_rep2


title: SMART_seq2_R23E10_Cell_4


title: MACMNV-0-2


title: dig1_rep1


title: MACMNV-0-1


title: ste12_rep3

source_name: ste12, biofilm

value: ste12 mutant


title: ste12_rep2


title: spt8_rep_1


title: ste12_rep1


title: SMART_seq2_R23E10_Cell_35


title: SMART_seq2_R23E10_Cell_39


title: SMART_seq2_R23E10_Cell_34


title: WT_rep3

source_name: WT, biofilm

value: WT

value: wild-type biofilm


title: SMART_seq2_R23E10_Cell_36


title: SMART_seq2_R23E10_Cell_33


title: WT_rep1


title: WT_rep2


title: SMART_seq2_R23E10_Cell_3


title: SMART_seq2_R23E10_Cell_32


title: SMART_seq2_R23E10_Cell_24


title: SMART_seq2_R23E10_Cell_21


title: SMART_seq2_R23E10_Cell_26


title: SMART_seq2_R23E10_Cell_25


title: SMART_seq2_R23E10_Cell_27


title: SMART_seq2_R23E10_Cell_22


title: SMART_seq2_R23E10_Cell_23


title: SMART_seq2_R23E10_Cell_28


title: SMART_seq2_R23E10_Cell_20


title: SMART_seq2_R23E10_Cell_38


title: SMART_seq2_R23E10_Cell_18


title: SMART_seq2_R23E10_Cell_19


title: SMART_seq2_R23E10_Cell_17


title: SMART_seq2_R23E10_Cell_16


title: SMART_seq2_R23E10_Cell_13


title: SMART_seq2_R23E10_Cell_14


title: SMART_seq2_R23E10_Cell_12


title: SMART_seq2_R23E10_Cell_15


title: SMART_seq2_R23E10_Cell_30


title: SMART_seq2_R23E10_Cell_1


title: SMART_seq2_R23E10_Cell_10


title: CEL-seq2_R23E10

description:
processed data file:
R23E10_CEL-seq2_DGEM.tsv.gz

extract_protocol:
Adult flies were anesthetised by placing them in ice cold glass dishes, heads were removed and brains were dissected removing any cuticle, retina and trachea. Dissected brains were placed in ice cold PBS. When 40 brains were collected, brains were dissociated at 25'C for 2 hours in a mix of Collagenase (75µl @ 100mg/ml) and Dispase (50µl @ 3mg/ml), the sample was pipette mixed every 15 minutes. Cells washed in PBS twice centrifuging at 800 xg) and resuspended in 400µl PBS. A single cell suspension was obtained by filtering with an 11µm cell strainer. Cells were sorted into single wells containing barcoded CEL-seq2 primers.
CEL-seq2


title: Infected_48

city: Copenhagen

first: Khairul

last: Syahputra

address: Stigbøjlen 7

department: Veterinary and Animal Science

country: Denmark

institute: University of Copenhagen

description:
Sample_48
none

data_processing:
Illumina Casava software used for basecalling: SCS2.7/RTA1.7
Reads were aligned to the Rainbow trout reference genome (http://www.genoscope.cns.fr/trout/data/) using TopHat (version 2.0.5)
The resulting files were filtered using SAMtools (version 0.1.18) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.5.3p9)
To make comparisons across samples possible, these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scalling factor, we employed library size estimates determined using the R/Bioconductor (release 2.11) package DESeq85. Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Correction for false positives is included in the statistical analysis of gene expression through DESeq.
Genome_build: Oncorhynchus_mykiss_chr_annot.gff
Supplementary_files_format_and_content: ZFG-17-10_All_mapped_reads.xlsx; Scores represent …

organism: Oncorhynchus mykiss

source_name: Gill

extract_protocol:
Gill samples placed in 1.5 mL tubes containing Lysis Solution and 2-mercaptoethanol were homogenized by TissueLyser II (Qiagen, USA). Total RNA was extracted using RTN350 (Sigma-Aldrich), according to the manufacturer’s instruction and subsequently, DNase treated with DNase I (Thermo Scientific, USA)
Quality and integrity of the total RNA were checked on an Agilent Bioanalyzer 2100 total RNA Nano series II chip (Agilent, Amstelveen, Netherlands). Illumina RNAseq libraries were prepared from 500 ng total RNA using the Illumina TruSeqTM Stranded mRNA LT Sample Prep Kit according to the manufacturer’s instructions (Illumina Inc. San Diego, CA, USA).

value: Gill

value: infected by I. multifiliis


title: Infected_49

description:
Sample_49
none


title: Infected_44

description:
Sample_44
none


title: Infected_47

description:
Sample_47
none


title: SMART_seq2_R23E10_Cell_11


title: Infected_50

description:
Sample_50
none


title: Infected_46

description:
Sample_46
none


title: Infected_43

description:
Sample_43
none


title: SMART_seq2_R23E10_Cell_2


title: Normal colon sample 2

city: L'Hospitalet de Llobregat

first: Manuel

last: Castro

state: Barcelona

address: Av. Gran Vía de l'Hospitalet 199

department: PEBC

country: Spain

institute: IDIBELL

description:
Commercial total RNA from normal colon sample
NormalcolonAM7986

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

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction.  Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that have flags in “P” or “M” (“All Targets Value”) for enough samples were retained for further analyses.  Differentially expressed circRNA with statistical significance between the two groups were identified through P-value and FDR filtering. Differentially expressed circRNA between the two samples were identified through Fold Change filtering.

source_name: normal colon

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, circRNA were treated with Rnase R (Epicentre, Inc.) to remove linear RNAs. Then, each sample was amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Cell lines were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% FBS, penicillin and streptomycin, at 37ºC in a humidified atmosphere of 5% (v/v) carbon dioxide.

extract_protocol: Total RNA was purified from samples by using Trizol reagent according to the manufacturer's protocol. The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1000 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel.

treatment_protocol: not applicable

value: colon


title: Normal colon sample 3

description:
Commercial total RNA from normal colon sample
NormalcolonB302060


title: HCT116 sample replicate 2

source_name: Cell line


title: Control_40

description:
Sample_40
none

value: control


title: CD30 B GC_C

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.

scan_protocol: Scanning was performed according to the Affymetrix protocol with Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization (together with all samples from GSE records 12453, 14879 and 40160) was conducted using the variance stabilization method (vsn) from Huber et al..
probe group file: Unsupported Human Genome U133 Plus 2.0 Array CDF Files
meta-probeset file: Human Genome U133 Plus 2.0  Probeset Annotations, CSV Format, Release 33

source_name: CD20+CD30+CD38+ B cells isolated by cell sorting from a tonsil

label_protocol: Samples were labelled, washed and stained using the Labeling and HWS Kit from Affymetrix.

extract_protocol: RNA was isolated with the Purescript RNA isolation kit from Gentra, according to the protocol of the supplier, reducing all volumes to one tenth of the volume recommended for a standard isolation

value: tonsil

tag: cell type

value: B cells

tag: cell subtype

value: CD20+CD30+CD38+ B cells


title: HCT116 sample replicate 3

tag: cell line


title: Infected_41

description:
Sample_41
none


title: Normal colon sample 1

description:
Commercial total RNA from normal colon sample
NormalcolonA601602


title: CD30 B GC_H


title: CD30 B GC_A


title: CD30 B GC_B


title: CD30 B non-GC_J

source_name: CD20+CD30+CD38low/- B cells isolated by cell sorting from a tonsil

value: CD20+CD30+CD38low/- B cells


title: Infected_42

description:
Sample_42
none


title: Infected_45

description:
Sample_45
none


title: Control_37

description:
Sample_37
none


title: CD30 B GC_G


title: Control_35

description:
Sample_35
none


title: CD30 B non-GC_K


title: CD30 B non-GC_F


title: CD30 B non-GC_D


title: Control_38

description:
Sample_38
none


title: Control_36

description:
Sample_36
none


title: Control_39

description:
Sample_39
none


title: CD30 B non-GC_L


title: DKO sample replicate 2

value: DKO


title: DKO sample replicate 3


title: Control_34

description:
Sample_34
none


title: DKO sample replicate 1


title: Control_33

description:
Sample_33
none


title: Control_32

description:
Sample_32
none


title: HCT116 sample replicate 1


title: Control_31

description:
Sample_31
none


title: FHV-1,Raltegravir-3

city: Ithaca

first: Jennifer

middle: K

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description:
MockFHVvsRaltFHV_gene_exp.diff: C4_2
MockFHVvsRaltFHV_genes.read_group_tracking: C4_2

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--library-type fr-firststrand) was used to map reads to the Felis catus 6.2 reference genome+transcriptome (Ensembl).
cufflinks and cuffmerge were used to generate a project-specific transcriptome guided by the Felis catus 6.2 reference genome+transcriptome (Ensembl).
cuffquant (--library-type fr-firststrand) was used to quantify transcripts guided by the Felis catus 6.2 reference genome+transcriptome (Ensembl).
cuffdiff v2.2.1 was used to call differentially expressed genes based on the Felis catus 6.2 reference genome+transcriptome (Ensembl).
Genome_build: Felis_catus_6.2 (Ensembl)
Supplementary_files_format_and_content: Tab delimited text files are standard cuffdiff2 output files for gene-level analysis, including counts, FPKM values, and q-values for differential expression testing (corrected for multiple hypothesis testing). The 'gene_exp.diff' file contains average FPKM values for each pair of replicates as well as results for statistical testing for differential expression. The 'genes.read_group_tracking' file contains raw mapped read counts and FPKM values for individual samples.

organism: Felis catus

source_name: Corneal epithelial cells

growth_protocol: Primary corneal epithelial cells were isolated from a healthy SPF free cat and maintained in DMEM/F12 supplemented with 10% FBS, 100 U/ml penicillin, 100 ug/ml stretomycin, 2 mM L-glutamine, 0.1 ug/ml cholera toxin, 10 ng/ml human recombinant epithelial growth factor, 1 ug/ml hydrocortisone, and 5 ug/ml recombinant human insulin

extract_protocol:
Cells were lysed using trizol, lysates were frozen, and total RNA was isolated using the manufacturer's protocol.
Diretional RNA-seq libraries were prepared from 1 ug total RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: For analysis of infected samples- 300,000 cells were plated in T25s and grown 2 days. Cells were serum starved in 2% FBS media for 6 hours, infected with FHV-1 MOI=10, grown 2 hours, rinsed with PBS to remove virus, and then treated with 500 uM Raltegravir or DMSO. Cells were collected 2 h later (4 hpi). For analysis of uninfected samples- 300,000 cells were plated in T25s and grown 2 days. Cells were serum starved in 2% FBS media for 6 hours, treated with 500 uM raltegravir or DMSO, grown for 2 h, and then collected

tag: cell source

value: Liberty Research cat primary isolation

tag: virus status

value: 500 uM Raltegravir


title: FHV-1,Raltegravir-1

description:
MockFHVvsRaltFHV_gene_exp.diff: C4_0
MockFHVvsRaltFHV_genes.read_group_tracking: C4_0


title: FHV-1,DMSO-3

description:
MockFHVvsRaltFHV_gene_exp.diff: C2_2
MockFHVvsRaltFHV_genes.read_group_tracking: C2_2

value: DMSO


title: FHV-1,DMSO-2

description:
MockFHVvsRaltFHV_gene_exp.diff: C2_1
MockFHVvsRaltFHV_genes.read_group_tracking: C2_1


title: MEF A485 replicate 4

first: Brian

middle: Tate

last: Weinert

address: Blegdamsvej 3, 6b

description: Gene expression data from MEF's treated for 16h, 3uM compound A-485, PMID: 28953875

hyb_protocol: Samples were then hybridized to the G4852A SurePrint G3 Mouse GE 8x60K Microarray slides (60000 probes, Agilent Technologies).

scan_protocol: Images were scanned using the high sensitivity protocol (AgilentG3_HiSen_GX_1color) on a SureScan microarray scanner (Agilent Technologies) and probe intensities were obtained by taking the gProcessedSignal from the output of Agilent feature extraction software using default settings.

data_processing: Probe intensities were quantile normalized and significance analysis was performed using the samr R package (https://cran.r-project.org/web/packages/samr/samr.pdf).

source_name: Cultured MEFs

label_protocol: RNA was amplified into cRNA and 100ng of total RNA was labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies- 5190-2305).

extract_protocol: Total RNA was collected using  the RNeasy Mini Kit (Qiagen). Genomic DNA was eliminated by DNAse treatment (Qiagen).

treatment_protocol: see description above, inhibitors were applied 16 hours before harvest, gene KO by 4-hydroxy-tamoxifen (4x 2uM over 48h, harvest at 84h)

value: MEF

value: 16h, 3uM compound A-485


title: Mock,Raltegravir-3

description:
MockVsRalt_gene_exp.diff: C3_2
MockVsRalt_genes.read_group_tracking: C3_2

value: Non-infected


title: FHV-1,DMSO-1

description:
MockFHVvsRaltFHV_gene_exp.diff: C2_0
MockFHVvsRaltFHV_genes.read_group_tracking: C2_0


title: MEF A485 replicate 3


title: Mock,Raltegravir-2

description:
MockVsRalt_gene_exp.diff: C3_1
MockVsRalt_genes.read_group_tracking: C3_1


title: Mock,Raltegravir-1

description:
MockVsRalt_gene_exp.diff: C3_0
MockVsRalt_genes.read_group_tracking: C3_0


title: MEF Cmpd-R replicate 4

description: Gene expression data from MEF's treated for 16h, 3uM compound "R", US Patent 20,160,235,716 filed 17 Sept. 2015, and issued 18 Aug. 2016

value: 16h, 3uM compound R


title: MEF Cmpd-R replicate 3


title: MEF A485 replicate 1


title: MEF Cmpd-R replicate 5


title: MEF Cmpd-R replicate 1


title: Mock,DMSO-3

description:
MockVsRalt_gene_exp.diff: C1_2
MockVsRalt_genes.read_group_tracking: C1_2


title: FHV-1,Raltegravir-2

description:
MockFHVvsRaltFHV_gene_exp.diff: C4_1
MockFHVvsRaltFHV_genes.read_group_tracking: C4_1


title: MEF A485 replicate 2


title: Mock,DMSO-1

description:
MockVsRalt_gene_exp.diff: C1_0
MockVsRalt_genes.read_group_tracking: C1_0


title: Control MEF for samples 16-25, replicate 3

description: Gene expression data from MEF's untreated

value: untreated


title: Control MEF for samples 16-25, replicate 2


title: MEF Cmpd-R replicate 6


title: Juvenile coho May creek #13

city: Tacoma

first: Andrew

middle: Ronald

last: Spanjer

state: WA

address: 934 Broadway STE 300

department: Department of the Interior

institute: US Geological Survey

hyb_protocol: nCounter Gene Expression Assay

scan_protocol: nCounter Gene Expression Assay

data_processing: nSolver software, house keeping gene normalization

label: color-coded digital barcodes

organism: Oncorhynchus kisutch

source_name: Coho liver

label_protocol: nCounter Gene Expression Assay

growth_protocol: NA; captured wild fish

extract_protocol: RNAzol RT/Turbo DNAfree

treatment_protocol: No applied treatment

tag: location

value: May creek

value: Liver


title: Juvenile coho May creek #12


title: Control MEF for samples 16-25, replicate 5

tag: treatment


title: Control MEF for samples 16-25, replicate 4


title: Mock,DMSO-2

description:
MockVsRalt_gene_exp.diff: C1_1
MockVsRalt_genes.read_group_tracking: C1_1


title: Juvenile coho May creek #11


title: Control MEF for samples 16-25, replicate 1


title: MEF Cmpd-R replicate 2


title: MEF CBP/p300 KO replicate 3

description: Gene expression data from MEFs 2uM 4-hyroxy-tamoxifen, 4x in total every 12h for 48h, cell harvested at ~84h


title: MEF CBP112 replicate 3

description: Gene expression data from MEFs treated with5uM CBP112, 16h


title: MEF CBP112 replicate 1


title: MEF CBP112 replicate 2


title: MEF CBP/p300 KO replicate 1

value: 2uM 4-hyroxy-tamoxifen, 4x in total every 12h for 48h, cell harvested at ~84h


title: MEF CBP/p300 KO replicate 2


title: Juvenile coho Woodland creek #5

value: Woodland creek


title: Juvenile coho Woodland creek #8


title: Control MEF for samples 5-10, replicate 4

description: Gene expression data from MEFs Utreated


title: Juvenile coho Woodland creek #3


title: Juvenile coho Woodland creek #2


title: Juvenile coho Harris creek #10

value: Harris creek


title: Control MEF for samples 5-10, replicate 2

description: Gene expression data from MEFs Utreated


title: Juvenile coho Harris creek #8


title: Juvenile coho Harris creek #6


title: Control MEF for samples 5-10, replicate 1

description: Gene expression data from MEFs Utreated


title: Juvenile coho Harris creek #5


title: Juvenile coho Harris creek #2


title: Juvenile coho Longfellow creek #3

value: Longfellow creek


title: Juvenile coho Longfellow creek #8


title: Juvenile coho Longfellow creek #5


title: Juvenile coho E. Fork Dairy creek #19

value: E. Fork Dairy creek


title: Juvenile coho Longfellow creek #2


title: Juvenile coho Longfellow creek #1


title: Juvenile coho Woodland creek #7


title: Control MEF for samples 5-10, replicate 3

description: Gene expression data from MEFs Utreated


title: Juvenile coho Harris creek #7


title: WT3b

city: Ames

first: Maura

last: McGrail

state: IA

address: 2310 Pammel Dr

department: GDCB

institute: Iowa State University

description:
processed data file: Mutant raw count.txt
processed data file: Mutant FPKM.txt
processed data file: Mutant DGE.txt

data_processing:
Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “-N 1 -t 8 -B 4 -m 5 -A sam --split-output”.
Count data was generated from HT-Seq.
Differential gene expression analysis was conducted using DESeq2.
(FPKM) was calculated using the following equation: FPKM = (10^9 x Number of mapped reads to a gene)/(Gene exonic length x Total mapped reads in the experiment).
Genome_build: GRCz10 using GMAP.
Supplementary_files_format_and_content: Mutant raw count.txt: Tab-delimited text file includes raw expression values.
Supplementary_files_format_and_content: Mutant FPKM.txt: Tab-delimited text file includes normalized expression values.
Supplementary_files_format_and_content: Mutant DGE.txt: Tab-delimited text file includes differential gene expression statistics.

organism: Danio rerio

source_name: Wildtype head

extract_protocol:
Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent.
Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.

tag: strain/background

value: WIK

tag: genotype/variation

value: wildtype +/+

value: 5 days post fertilization larva

value: 5 pooled dissected heads


title: WT3a

tag: age

tag: tissue


title: Juvenile coho E. Fork Dairy creek #14


title: WT2a


title: Juvenile coho Longfellow creek #10


title: WT2b


title: WT1b


title: Mut3b

source_name: rb1 homozygous mutant head


title: Mut3a


title: Juvenile coho E. Fork Dairy creek #9


title: WT1a


title: Juvenile coho Church creek #18

value: Church creek


title: Juvenile coho E. Fork Dairy creek #7


title: Juvenile coho E. Fork Dairy creek #6


title: Juvenile coho E. Fork Dairy creek #8


title: 7_GTGAAA_L008_R1_001

city: Urbana

first: Alison

last: Bell

state: Illinois

address: Justin Smith Morrill Hall, 505 S Goodwin Ave #393

department: Animal Biology

institute: University of Illinois at Urbana Champaign

data_processing:
Fastq files were generated with the software Casava 1.8.2 (Illumina)
read alignment: Tophat 2.0.8, default parameters
read quantification: Reads inside of exon features were counted in union mode using htseq version 0.6.1.
differential expression: Done in R using the Bioconductor package limmavoom.
Genome_build: Gacu Ensembl release 75
Supplementary_files_format_and_content: mm_mrsb_allcounts_for_GEO_2016-04-12.txt: Tab delimited text file of the matrix of raw read counts mapped to the mouse genome (Ensembl annotation of the NCBIM37 version of the mouse genome) as created by the edgeR function readDGE. TopHat2 version 2.0.8 (Kim et al. 2013) was used to align reads.  Reads inside of exon features were counted in union mode using htseq version 0.6.1 (Anders et al. 2015). Note that the counts include meta tags that are prefixed by "__" that were removed from counts before further processing.

organism: Gasterosteus aculeatus

source_name: exposed to predation risk_unexposed (NoPred)_whole brain

extract_protocol:
Individuals for brain gene expression profiling were gently netted directly from their home tanks and rapidly decapitated with sharp scissors. Heads were flash frozen and stored at -80°C until dissection. We first scraped the skull with rongeurs to expose brain tissue. Heads were placed in RNALater for 24 hours at 4°C. We then dissected whole brains in RNAlater (Thermo Fisher Scientific) on dry ice and extracted RNA using the PicoPure RNA Isolation Kit with optional DNase treatment (Thermo Fisher Scientific).
Poly-A RNA was enriched from 1–2 μg of total RNA by using Dynabeads Oligo(dT)25 (Life Technologies), following the manufacturer’s protocol. Two rounds of poly(A) enrichment were performed with a final elution in 14μL of water. The poly-A–enriched RNA was used to prepare RNAseq libraries, using the Illumina TruSeq kit (Illumina). Manufacturer’s instructions were followed and 13–15 cycles of PCR amplification were performed depending on the starting input of total RNA. All samples were barcoded, libraries were quantified on a Qubit fluorometer using the dsDNA High Sensitivity Assay Kit (Life Technologies), and library size was assessed on a Bioanalyzer High Sensitivity DNA chip (Agilent). Libraries were pooled and diluted to a final concentration of 10 nM. Final library pools were quantified using real-time PCR, using the Illumina compatible kit and standards (KAPA) by the W. M. Keck Centre for Comparative and Functional Genomics at the Roy J. Carver Biotechnology Centre (University of Illinois). Single-end sequencing was performed on an Illumina HiSeq 2500 instrument by the W. M. Keck Centre for Comparative and Functional Genomics at the Roy J. Carver Biotechnology Centre (University of Illinois). Not all individuals yielded enough RNA, therefore the final sample sizes for RNA-seq informatics were no paternal cue/no personal cue: N = 5, paternal only: N = 9, personal only: N = 9, both: N = 7.

tag: dad

tag: paternal experience

value: exposed to predation risk

tag: personal experience

value: unexposed (NoPred)

tag: Sex

value: M

value: whole brain


title: 8_GCCAAT_L008_R1_001

source_name: exposed to predation risk_predation risk as juveniles_whole brain

value: predation risk as juveniles


title: Juvenile coho Church creek #9


title: Mut2a


title: Mut2b


title: 5_CCGTCC_L007_R1_001


title: Mut1b


title: Juvenile coho Church creek #5


title: Juvenile coho Church creek #3


title: Mut1a


title: Juvenile coho Church creek #2


title: 36_CAGATC_L005_R1_001

source_name: unexposed (NoPred)_predation risk as juveniles_whole brain

value: F


title: Control2a

description:
processed data file: Tumor raw count.txt
processed data file: Tumor FPKM.txt
processed data file: Tumor DGE.txt

data_processing:
Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “-N 1 -t 8 -B 4 -m 5 -A sam --split-output”.
Count data was generated from HT-Seq.
Differential gene expression analysis was conducted using DESeq2.
(FPKM) was calculated using the following equation: FPKM = (10^9 x Number of mapped reads to a gene)/(Gene exonic length x Total mapped reads in the experiment).
Genome_build: GRCz10 using GMAP.
Supplementary_files_format_and_content: Tumor raw count.txt: Tab-delimited text file includes raw expression values.
Supplementary_files_format_and_content: Tumor FPKM.txt: Tab-delimited text file includes normalized expression values.
Supplementary_files_format_and_content: Tumor DGE.txt: Tab-delimited text file includes differential gene expression statistics.

source_name: Normal Adult Brain

extract_protocol:
Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent.
Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.

tag: genotype

value: wild type

value: 6.5-10 months

value: midbrain-hindbrain


title: Control2b


title: Control1b


title: 33_GCCAAT_L006_R1_001


title: 34_AGTTCC_L008_R1_001


title: Juvenile coho Swamp creek #17

value: Swamp creek

value: Liver


title: Control1a


title: Juvenile coho Swamp creek #15


title: Tumor10b

source_name: Brain tumor tissue

value: rb1- TALEN somatic targeted

value: rb1-brain tumor


title: 6_TGACCA_L006_R1_001


title: 30_GTCCGC_L005_R1_001


title: Tumor10a

value: WIK


title: 3_AGTCAA_L005_R1_001


title: Juvenile coho Swamp creek #7


title: 29_ACAGTG_L006_R1_001


title: 35_CTTGTA_L007_R1_001


title: Juvenile coho Swamp creek #5


title: Juvenile coho Swamp creek #4


title: 28_ATGTCA_L004_R1_001


title: Tumor9a


title: Tumor8b


title: Juvenile coho Jenkins creek #11

value: Jenkins creek


title: 27_CTTGTA_L008_R1_001


title: Juvenile coho Church creek #1


title: 25_CAGATC_L007_R1_001


title: Juvenile coho Jenkins creek #9


title: Tumor8a


title: 32_AGTCAA_L007_R1_001


title: 23_CGATGT_L006_R1_001


title: Juvenile coho Jenkins creek #6


title: 22_CTTGTA_L006_R1_001

source_name: unexposed (NoPred)_unexposed (NoPred)_whole brain


title: Tumor6b


title: Tumor6a


title: Juvenile coho Jenkins creek #3


title: Tumor9b


title: 21_CGATGT_L005_R1_001


title: Juvenile coho Swamp creek #3


title: Tumor5b


title: Tumor7a


title: Juvenile coho Issaquah creek #16

value: Issaquah creek


title: Juvenile coho Jenkins creek #1


title: 19_CCGTCC_L005_R1_001


title: Tumor4b


title: Tumor5a


title: Tumor7b


title: Juvenile coho Jenkins creek #4


title: 16_ACAGTG_L004_R1_001


title: 15_TGACCA_L005_R1_001


title: 17_GTGAAA_L004_R1_001


title: 14_ACAGTG_L008_R1_001


title: Juvenile coho Issaquah creek #7


title: Tumor4a


title: Juvenile coho Issaquah creek #4


title: Tumor3b


title: 2_GTGAAA_L006_R1_001


title: 13_GCCAAT_L004_R1_001


title: 12_GCCAAT_L007_R1_001


title: Tumor2b


title: Juvenile coho Issaquah creek #8


title: Juvenile coho Issaquah creek #1


title: Juvenile coho Coulter creek #13

value: Coulter creek


title: Tumor1b


title: Tumor2a


title: 11_TGACCA_L004_R1_001


title: Juvenile coho Coulter creek #12


title: 1_AGTTCC_L004_R1_001

value: exposed to predation risk


title: 10_CGATGT_L007_R1_001

value: unexposed (NoPred)


title: Tumor1a


title: Juvenile coho Coulter creek #10


title: Juvenile coho Coulter creek #11


title: Juvenile coho Coulter creek #8


title: Juvenile coho Coulter creek #3


title: Tumor3a


title: Abdominal Aorta (Injured) 03HR Experimental Batch 1 MouseID C1B

status: Public on Jun 12 2018

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Alignment: HISAT 2.0.3 default parameters per Galaxy server 16.10, excepting: (use ENSEMBL GTF file with known splice sites for spliced alignment)
Generation of Raw Counts: Htseq-count 0.6.1galaxy3, default parameters per Galaxy server 16.10
Count normalization and testing for differential expression: DESeq2 1.14.1, default parameters
Genome_build: Mus_musculus GRCm38.84 (from ENSEMBL - http://www.ensembl.org/Mus_musculus/Info/Annotation)
Supplementary_files_format_and_content: Excel file containing: 1) Regularized log values of transcripts counts for each sample 2) Normalized counts for each sample and 3) Pairwise comparisons between each set of samples

source_name: Mouse Aorta

extract_protocol:
RLT buffer (Qiagen RNEasy kit) flush through lumen of vessel; for "tissue" fraction, RNA was extracted from homogenized post-flush vessel. See Briot et al, Dev Cell, 2014 (PMID: 25535917) for details.
Library construction was performed using the NuGEN Oviation Ultralow Library V2 kit according to manufacturer's recommended protocol.

treatment_protocol: Aortae were wounded using mechanical pressure. See Shirali et al, JOvE, 2016 (PMID: 27911412)  for details.

value: Abdominal Aorta

tag: segment

value: Injured Segment

tag: time point

value: 03HR post-injury

tag: strain


title: Thoracic Aorta (Uninjured) 48HR Experimental Batch 3 MouseID E3B

value: Thoracic Aorta

value: Uninjured Segment

value: 48HR post-injury


title: Thoracic Aorta (Uninjured) 48HR Experimental Batch 3 MouseID E3C


title: Abdominal Aorta (Injured) 03HR Experimental Batch 2 MouseID C2A


title: Abdominal aorta post-flush aorta tissue 48HR Experimental Batch 1 MouseID E1A


title: Abdominal Aorta (Injured) 03HR Experimental Batch 2 MouseID C2C


title: Abdominal Aorta (Injured) 03HR Experimental Batch 3 MouseID C3B


title: Abdominal aorta post-flush aorta tissue 48HR Experimental Batch 3 MouseID E3A


title: Abdominal Aorta (Injured) 03HR Experimental Batch 1 MouseID C1A


title: Abdominal aorta post-flush aorta tissue 48HR Experimental Batch 2 MouseID E2A


title: Thoracic Aorta (Uninjured) 48HR Experimental Batch 2 MouseID E2C


title: Thoracic Aorta (Uninjured) 48HR Experimental Batch 2 MouseID E2B


title: Thoracic Aorta (Uninjured) 48HR Experimental Batch 2 MouseID E2A


title: Juvenile coho Woodland creek #17

value: Woodland creek


title: Thoracic Aorta (Uninjured) 48HR Experimental Batch 1 MouseID E1B


title: Thoracic Aorta (Uninjured) 48HR Experimental Batch 1 MouseID E1A


title: Abdominal Aorta (Injured) 48HR Experimental Batch 3 MouseID E3B


title: Abdominal Aorta (Injured) 48HR Experimental Batch 3 MouseID E3A


title: Abdominal Aorta (Injured) 48HR Experimental Batch 3 MouseID E3C


title: Abdominal Aorta (Injured) 48HR Experimental Batch 2 MouseID E2C


title: Abdominal Aorta (Injured) 48HR Experimental Batch 2 MouseID E2A


title: Abdominal Aorta (Injured) 48HR Experimental Batch 2 MouseID E2B


title: Abdominal Aorta (Injured) 48HR Experimental Batch 1 MouseID E1C


title: Abdominal Aorta (Injured) 48HR Experimental Batch 1 MouseID E1B


title: Abdominal Aorta (Injured) 48HR Experimental Batch 1 MouseID E1A


title: Thoracic Aorta (Uninjured) 48HR Experimental Batch 3 MouseID E3A


title: Thoracic Aorta (Uninjured) 48HR Experimental Batch 1 MouseID E1C


title: S78.H2

city: San Francisco

first: Alex

middle: Aaron

last: Pollen

state: California

address: 35 Medical Center Way

institute: UCSF

data_processing:
Trim Galore 3.7
HISAT2
subread-1.5.0 function featureCounts
GRCh38.79.gtf
Genome_build: GRCh38.p2/Clint_PTRv2; UCSC: panTro6; GCF_002880755.1
Supplementary_files_format_and_content: log(CPM+1)

organism: Pan troglodytes

source_name: chimp_iPS-derived cerebral organoid

growth_protocol: Cerebral organoids from Kadoshima et al., 2013

extract_protocol:
Fluidigm C1 small IFC (100-5759; 100-6201);  SMARTer® Ultra™ Low RNA Kit (634832)
Nextera XT tagmentation kit (FC-131-096)

tag: donor id

tag: clone id

tag: age (weeks)

tag: date captured

value: Male

tag: cell type

value: iPS-derived cerebral organoid

tag: organoid id

tag: capture plate

tag: capture chamber


title: S5.H10


title: S77.H1


title: S77.B3


title: S5.F7


title: S12.B3


title: S5.A9


title: retina-normal-P0-rep1

city: Guangzhou

first: YISHEN

last: WANG

address: No.54 Xianlie South Road, Yuexiu District

institute: State Key Laboratory of Ophthalmology, Image Reading Center, Zhongshan Ophthalmic Center, Sun Yat-Sen University

description: Total RNA from mouse retina was isolated and purified.

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

source_name: normal retinal tissue

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:  a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling   reaction was incubated for 1 h at 16°C. c, Terminated by incubation for 15 min at 65°C.

growth_protocol: Mouse were reared under normal conditions.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen ,  Carlsbad, CA) and purified with the RNeasy Mini Kit (QIAGEN, Hilden, Germany.), according to the manufacturer’s instructions. RNA quality and quantity were measured using a nanodrop spectrophotometer (ND-1000, Nanodrop Technologies, Wilmington, Delaware USA), and RNA integrity was determined by gel electrophoresis.

treatment_protocol: None.

tag: age

value: Postnatal day 0

tag: tissue

value: normal retinal tissue


title: retina-normal-P14-rep1

value: Postnatal day 14


title: retina-normal-P3-rep1

value: Postnatal day 3


title: Juvenile coho Issaquah creek #5

tag: location

value: Issaquah creek

value: Liver


title: retina-normal-P10-rep1

value: Postnatal day 10


title: retina-normal-P7-rep1

value: Postnatal day 7


title: retina-normal-P8-rep1

value: Postnatal day 8


title: retina-normal-P21-rep1

value: Postnatal day 21


title: retina-normal-P4-rep1

value: Postnatal day 4


title: SCC9 ShRNA1

first: Guokai

last: Pan

address: 107 Yanjiang West Road

department: Department of Oral and Maxillofacial Surgery

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description:
Human tongue squamous cell carcinoma (TSCC) cell line
Gene expression data

hyb_protocol: miRNA Complete Labeling and Hyb Kit (Agilent p/n 5190-0456) was applied for hybridization as described by the manufacturer. Slides were hybridized at 55°C for 20h in Agilent's SureHyb Hybridization Chambers.

scan_protocol: Slides were scanned at 3 μm/pixel resolution using an Agilent Microarray Scanner (Agilent p/n G2505C) , then the data were extracted using Agilent Feature Extraction Software

data_processing: Data was extracted using Agilent Feature Extraction software. Results were provided in the Raw Data Files. Normalization was performed using the Agilent GeneSpring GX v12.0 software. Differentially expressed genes were identified through Fold Change filtering.

source_name: SCC9 shRNA1 group

label_protocol: miRNA Complete Labeling and Hyb Kit (Agilent p/n 5190-0456) was used for sample labeling.

growth_protocol: Two human tongue squamous cell carcinoma cell lines Cal-27 and Scc-9 were obtained from the American Type Culture Collection. Cal-27 cells were cultivated in Dulbecco’s modified Eagle’s medium (Gibco, Rockville, MD, USA) supplemented with 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA). Scc-9 cells were cultivated in Dulbecco’s modifed Eagle’s medium-F12 (Gibco) supplemented with 10% fetal bovine serum. Cells were cultured at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: CAL-27 and SCC-9 cells, with stably transduced with shRNA targeted NR_034085, were treated with the IC50 of cisplatin (Sigma, USA) for 24 hours for a miRNA microarray assay. Sample labeling and array hybridization were performed by Agilent_Human_miRNA_8x60k_70156_v21 (Agilent Technologies)  according to the Agilent miRNA Microarray protocol. After quantile normalization of the raw data, the miRNAs detected were chosen for further data analysis. Differentially expressed miRNAs with statistical significance between the two groups were identified through P value/FDR filtering.

tag: cell line

value: SCC-9 cells


title: retina-normal-P1-rep1

value: Postnatal day 1


title: SCC9 Ctl

source_name: SCC9 control group


title: CAL27 ShRNA1

source_name: CAL27 shRNA1 group

value: CAL-27 cells


title: CAL 27 Ctl

source_name: CAL27 control group


title: CAL27 ShRNA3

source_name: CAL27 shRNA3 group


title: S79.C1

department: Neurology

tag: Sex


title: SCC9 ShRNA3

source_name: SCC9 shRNA3 group


title: S77.D1


title: S77.G1


title: SCC-9

description: Gene expression data

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) was applied for hybridization as described by the manufacturer. Slides were hybridized at 65°C for 17h in Agilent's SureHyb Hybridization Chambers.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Agilent Microarray Scanner (Agilent p/n G2565BA) , then the data were extracted using Agilent Feature Extraction Software

label_protocol: Quick Amp Labeling Kit (Agilent p/n 5190-0442) was used for sample labeling.

treatment_protocol: CAL-27 and SCC-9 cells were treated with the IC50(25912308, 25843291) of cisplatin (Sigma, USA) for 24 hours for a LncRNA microarray assay. Sample labeling and array hybridization were performed by Arraystar Human lncRNA Microarray V3.0 according to the Arraystar microarray-based gene expression analysis protocol (Arraystar, Inc., Rockville, MD, USA). After quantile normalization of the raw data, the lncRNAs detected were chosen for further data analysis. Differentially expressed lncRNAs with statistical significance between the two groups were identified through P value/FDR filtering.

tag: treatment


title: Cryptococcus neoformans H99 treated with eltrombopag

city: Taipei

first: HAO TAI

last: KO

address: No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan(R.O.C)

country: Taiwan

institute: National Taiwan University

data_processing:
"Trinity v2.3.2" is a well-known transcriptome de-novo assembly tool. As the raw reads were sequenced by Illumina HiSeq platform, we are using "Trimmomatic v0.36" for low quality and adapter trimming to get the clean reads. We are using "MultiQC v1.2" for evaluating read quality.
In the read count quantification, we are using Cryptococcus neoformans var. grubii H99 (GCA_000149245.3) as reference. All of the sample are going to be alligned for calculating the abundance of read count.
The alignment tool we used is "bowtie2 v2.3.2", and the read count quantification tool we used is "RSEM v1.2.31". The alignment QC report we are using ''Qualimap v2'' for evaluation.
Basically, we are using "RSEM. Isoform.results" for the downstream jobs.
Supplementary_files_format_and_content: Count up the total reads in a sample and divide that number by 1,000,000 - this is our "per million" scaling factor. Divide the read counts by the "per million" scaling factor. This normalizes for sequencing depth, giving you reads per million. Divide the RPM values by the length of the gene, in kilobases. This gives you RPKM. FPKM is very similar to RPKM. RPKM was made for single-end RNA-seq, where every read corresponded to a single fragment that was sequenced. FPKM was made for paired-end RNA-seq. With paired-end RNA-seq, two reads can correspond to a single fragment, or, if one read in the pair did not map, one read can correspond to a single fragment. The only difference between RPKM and FPKM is that FPKM takes into account that two reads can map to one fragment (and so it doesn't count this fragment twice).

organism: Cryptococcus neoformans H99

growth_protocol: C. neoformans H99 cells were grown overnight in liquid YPD at 30°C, washed twice with ddH2O, diluted 1:100 in liquid YPD and grown at 30°C with agitation for 3 h to reach a density of 3 × 107 CFU/mL.

extract_protocol:
After this treatment, cultures were centrifuged and total RNA was extracted using Trizol reagent and treated with DNase I (Ambion, Thermo Fisher Scientific) to degrade contaminating DNA.
mRNAs were enriched with oligo (dT) magnetic beads. Fragmentation buffer allowed the mRNA to be shortened into ~200-base fragments. Then, the first strand of cDNA was synthesized using random hexamer, buffer, dNTPs, and RNase H, and the second strand of cDNA was synthesized by DNA polymerase I. The double-stranded cDNAs were purified with magnetic beads. End preparation and 3' end single nucleotide adenine addition was performed, and sequencing adaptors were ligated to the fragments, which were enriched by PCR amplification. During the quality control step, the Agilent 2100 Bioanaylzer and ABI StepOnePlus RealTime PCR system were used to qualify and quantify the sample library. The library products were sequenced via Illumina NextSeq 500.

treatment_protocol: At this point cultures were equally divided into two aliquots to which either 0.06 μg/mL eltrombopag or same amount of DMSO was added, followed by incubation at 30°C for 90 min.

value: treated with eltrombopag


title: Cryptococcus neoformans H99 untreated

value: untreated


title: S76.G3

value: Male

value: iPS-derived cerebral organoid


title: SM2_40_A8H_3_S15

city: Manchester

first: Adam

last: Stevens

address: Oxford Road

department: Medicine

country: United Kingdom

institute: University of Manchester

description:
PolyA RNA
processed data file: Full_normalised_data.csv

data_processing:
Ordered BAM files were generated against the human genome feature file Homo_sapiens.GRCh38.90.gtf downloaded from Ensembl (ftp://ftp.ensembl.org/pub/current_gtf).
Data analysis was performed using Qlucore Omics Explorer 3.3 (Qlucore, Lund, Sweden) with a FPKM (Fragments Per Kilobase Million) cut-off of 10.
To identify significant differentially regulated transcripts, RNAseq expression data analysis was carried out by applying a group ANOVA with p<0.01 to the entire dataset. For illustration of the comparisons between the effect on transcription with EVI1-WT and EVI1-AQA in relation to untransfected cells and empty vector-transfected control cells with and without DNA damage, values were normalized to the mean of 0 and a variance of one. In addition, differences between expression levels at individual conditions were assessed by two group comparison (t-test).
Genome_build: Homo_sapiens.GRCh38.90.gtf
Supplementary_files_format_and_content: Full_normalised_data.csv: Comma-separated text file of FPKM normalised (mean centered) for batch.

source_name: Transfected HEK293

growth_protocol: Cells were plated in 6-well plates and co-transfected with pCMV-EVI1-flag effector plasmids (EVI1-WT or EVI1-AQA), PLZF-luciferase or FOS-luciferase and TK-renilla luciferase reporter plasmid. Comparable expression of EVI1-WT and EVI1-AQA in HEK293 cells was monitored by RT-PCR. After 48 hours, cells were lysed and firefly and renilla luciferase activities were assayed using the Dual-luciferase reporter assay (Promega) measured on a Victor plate reader (Perkin Elmer).

extract_protocol:
PolyA RNA
Libraries were prepared with the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina (FWD) using an input of 200 ng and performing 14 cycles of amplification.
Indexed libraries were then quantified using the Kapa Illumina Library quantification kit (Cat 07960336001) and pooled. 1 x 75bp sequence reads were generated by clustering 2.0pM of the library pool on a NextSeq500 High throughput run.

treatment_protocol: Transfection experiments were exposed to 150 uM H2O2 or left untreated for 8 h.

tag: transfected plasmid

value: EVI1 AQA

tag: batch


title: SCMC P3F

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

description: DNA (ChIP-enriched)

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq and DNase-seq peaks were called by MACS2 version 2.1.0.  DNase was run in paired-end mode
The enhancers were identified using ROSE2 pipeline in bamliquidator 1.3
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
Chromatin states were learned using ChromeHMM version 1.10
Genome_build: Hg19
Supplementary_files_format_and_content: peak files are tab delimited text files for each sample.

source_name: RMS cell line with PAX3-FOXO1

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.

extract_protocol:
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.  DNase DNA purification was performed by column (MiniElute PCR purification kit, Qiagen).
Standard Illumina barcodes were introduced during library preparation

treatment_protocol: ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.  DNase samples were treated with DNaseI (fresh growing cells, without fixation). DNaseI (Roche 04-716-728-001) was added to the cells (0.25 to 0.5 units) and incubated for 5 minutes at 37 ˚C.  The digestion was halted with 50 µL of stop buffer (9.5 mL H2O + 100 µL 1M TrisHCl pH 7.4 + 20µL 5M NaCl + 200µL 0.5 M EDTA, with 150 µL 10% SDS and 125 µL proteinase K added just before use).  Proteinase K activation at 55 ˚C for 1 hour was followed by DNA purification by column (MiniElute PCR purification kit, Qiagen).

value: SCMC

value: rhabdomyosarcoma

tag: antibody

value: in house PAX3-FOXO1 antibody

tag: enrichment target

tag: target function

value: Oncogenic Transcription Factor


title: SM2_39_W8H_3_S17

value: EVI1 WT


title: SCC-9+ci24h

description: Gene expression data

source_name: SCC9 treated with cisplatin group


title: S76.G12

tag: donor id

tag: clone id

tag: age (weeks)


title: CAL-27+ci24h

description: Gene expression data

source_name: CAL27 treated with cisplatin group


title: CAL-27

description: Gene expression data


title: S76.F7

tag: date captured

tag: cell type

tag: organoid id


title: S76.D11

tag: capture plate

tag: capture chamber


title: RH3 P3F

description: DNA (ChIP-enriched)


title: SM2_35_W8_3_S21

value: Untreated


title: SM2_36_A8_3_S20


title: SM2_37_U8H_3_S19

value: Untransfected


title: SM2_38_E8H_3_S18

value: Empty Vector


title: SM2_34_E8_3_S22


title: S76.C5


title: SM2_24_A8H_2_S33


title: S76.B12


title: S76.A4


title: S76.B8


title: SM2_33_U8_3_S23


title: SM2_23_W8H_2_S34


title: SM2_22_E8H_2_S35


title: SM2_21_U8H_2_S36


title: SM2_20_A8_2_S37


title: S71.F1


title: S71.G6


title: S71.F11


title: S75.C3.repeat


title: S71.E6


title: SM2_19_W8_2_S39


title: SM2_18_E8_2_S40


title: S71.D5


title: S76.F4


title: S71.D2


title: SM2_17_U8_2_S41


title: SM2_8_A8H_1_S2


title: S71.C3


title: SM2_6_E8H_1_S4


title: S71.A8


title: S59.C1


title: SM2_5_U8H_1_S5


title: SM2_7_W8H_1_S3


title: SM2_4_A8_1_S6


title: S59.B7


title: SM2_2_E8_1_S27


title: S59.A2


title: S59.A9


title: S58.H3


title: S58.D4


title: S58.A7


title: S58.B6


title: S5.H3