title: Limousin - differentiated bovine satellite cells (6th day)_rep 1

description: Biological replicate 1 of 8. Differentiated bovine satellite cells (6th day) from Limousin


title: Limousin - differentiated bovine satellite cells (6th day)_rep 2

status: Public on Jan 27 2018

type: RNA

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

description: Biological replicate 2 of 8. Differentiated bovine satellite cells (6th day) from Limousin

hyb_protocol: For hybridization, Microarray Hybridization Chamber (Agilent, USA) and Hyb-Buffer (Agilent, USA) were used according to manufacturer protocol.

scan_protocol: Microarray Scanner (model G2565CA) with SureScan High-Resolution Technology (Agilent, USA). Microarray data were extracted, the background subtracted and LOWESS normalisation performed using the standard procedures contained in the Agilent Feature Extraction (FE) Software Version 10.7.3.1.

data_processing: The statistical analysis was performed using Gene Spring 13 software default protocol (Agilent Technologies, USA). The statistical significance of the differences was evaluated using student test (p<0.05) and fold change FC>2.0. A multiple testing correction was performed using Benjamini and Hochberg False Discovery Rate (FDR) ≤0.05.

molecule: total RNA

organism: Bos taurus

source_name: musculus semitendinosus

label_protocol: MiRNA Complete Labeling and Hyb Kit (Version 2.3, December 2010) (Agilent) was used for labeling, according to manufacturer protocol.

growth_protocol: Bovine satellite cells (BSC) were isolated from semitendinosus muscle of bulls of different performance based on the protocol using pronase from Streptomyces griseus. Next, BSC were cultured in Primaria culture flask (BD, USA) using the growth medium (10%FBS//DMEM/AB), which was changed every two days. On the 10th day of proliferation cells were transferred to Collagen I Cellware 6-well plate (BD, USA). After obtaining 80% of confluence proliferation medium was replaced by differentiation medium (2%HS/DMEM/AB) and maintain through 6 days, changed every 48h. FBS - fetal bovine serum, HS - horse serum, DMEM - Dulbecco's Modified Eagle Medium, AB - antibiotics: 1% Penicillin-Streptomycin, 0.5% Amphotericin B.

extract_protocol: Total RNA was isolated according to the protocol supplied with the miRNeasy Mini Kit (Qiagen, USA). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9,5 were included into the analysis.

tag: cattle breed

value: LIM

tag: day of differentiation

value: 6th day of differentiation

tag: tissue

value: semitendinosus


title: BRK055

city: colombo

first: Aruna Dharshan

last: De Silva

address: Kandawala Road, Ratmalana

country: Sri Lanka

institute: Kotelawala Defense University

description: control

data_processing:
18srRNA was the house keeping gene used for normalization
The statistical significance of the Relative expression ratios are taken from a paired T-test. For each subject the value of the
expression ratio = log( Etarget )( Ctarget ) – log( Eref )( Cref) is computed. A paired t-test compares the mean of theses values between select subpopulations.
The resulting test is the parametric equivalent of randomization tests  implemented in the ‘REST’ PCR analysis software, where Relative expression ratio (R)= (E target) ΔCT target/(E ref) ΔCT ref
where ΔCT target = Average control samples – Average experimental samples of the relevant target gene
ΔCT ref = Average control samples – Average experimental samples of the reference house keeping gene
Analysis is carried out with SAS version 9.4, SAS PROC MIXED.

label: SYBR Green

organism: Homo sapiens

source_name: PBMC

label_protocol: Real Time qPCR was performed in a 25ml reaction mixture containing 12.5ml of RT2 SYBR green ROX qPCR master mix (catalog no: 330520), 1ml each of 10uM forward and reverse primers, 9.5ml of nuclease free water and 1ml of cDNA template, on the Qiagen Q5 plex thermal cycler. The PCR conditions were 94°C-2 min of initial denaturation followed by 35 cycles of 94°C-30 sec, 63°C-1 min, 72°C-1 min.

extract_protocol: Total RNA was extracted with Qiagen RNeasy Mini Kit

tag: disease state

value: Sepsis cases

tag: cell type

value: PBMC


title: BRK124

description: Test

value: Melioidosis cases


title: Limousin - differentiated bovine satellite cells (6th day)_rep 5

description: Biological replicate 5 of 8. Differentiated bovine satellite cells (6th day) from Limousin


title: Hereford - differentiated bovine satellite cells (6th day)_rep 4

description: Biological replicate 4 of 8. Differentiated bovine satellite cells (6th day) from Hereford

value: HER


title: Hereford - differentiated bovine satellite cells (6th day)_rep 7

description: Biological replicate 7 of 8. Differentiated bovine satellite cells (6th day) from Hereford


title: Limousin - differentiated bovine satellite cells (6th day)_rep 3

description: Biological replicate 3 of 8. Differentiated bovine satellite cells (6th day) from Limousin


title: BRK119

description: Test


title: Hereford - differentiated bovine satellite cells (6th day)_rep 3

description: Biological replicate 3 of 8. Differentiated bovine satellite cells (6th day) from Hereford


title: Hereford - differentiated bovine satellite cells (6th day)_rep 8

description: Biological replicate 8 of 8. Differentiated bovine satellite cells (6th day) from Hereford


title: Holstein-Friesian - differentiated bovine satellite cells (6th day)_rep 7

description: Biological replicate 7 of 8. Differentiated bovine satellite cells (6th day) from Holstein-Friesian

value: HF


title: Limousin - differentiated bovine satellite cells (6th day)_rep 4

description: Biological replicate 4 of 8. Differentiated bovine satellite cells (6th day) from Limousin


title: Holstein-Friesian - differentiated bovine satellite cells (6th day)_rep 8

description: Biological replicate 8 of 8. Differentiated bovine satellite cells (6th day) from Holstein-Friesian


title: BRK054

description: control


title: Limousin - differentiated bovine satellite cells (6th day)_rep 6

description: Biological replicate 6 of 8. Differentiated bovine satellite cells (6th day) from Limousin


title: Hereford - differentiated bovine satellite cells (6th day)_rep 1

description: Biological replicate 1 of 8. Differentiated bovine satellite cells (6th day) from Hereford


title: BRK049

description: control


title: BRK114

description: Test


title: BRK109

description: Test


title: BRK112

description: Test


title: Hereford - differentiated bovine satellite cells (6th day)_rep 6

description: Biological replicate 6 of 8. Differentiated bovine satellite cells (6th day) from Hereford


title: Holstein-Friesian - differentiated bovine satellite cells (6th day)_rep 2

description: Biological replicate 2 of 8. Differentiated bovine satellite cells (6th day) from Holstein-Friesian


title: Hereford - differentiated bovine satellite cells (6th day)_rep 2

description: Biological replicate 2 of 8. Differentiated bovine satellite cells (6th day) from Hereford


title: Holstein-Friesian - differentiated bovine satellite cells (6th day)_rep 1

description: Biological replicate 1 of 8. Differentiated bovine satellite cells (6th day) from Holstein-Friesian


title: Hereford - differentiated bovine satellite cells (6th day)_rep 5

description: Biological replicate 5 of 8. Differentiated bovine satellite cells (6th day) from Hereford


title: BRK108

description: Test


title: BRK116

description: Test


title: BRK106

description: Test


title: BRK024

description: Test


title: Holstein-Friesian - differentiated bovine satellite cells (6th day)_rep 6

description: Biological replicate 6 of 8. Differentiated bovine satellite cells (6th day) from Holstein-Friesian


title: Holstein-Friesian - differentiated bovine satellite cells (6th day)_rep 5

description: Biological replicate 5 of 8. Differentiated bovine satellite cells (6th day) from Holstein-Friesian


title: St2-/- => St2-/- biological replicate 3

type: SRA

city: Heidelberg

first: Moritz

middle: Falk

last: Eissmann

state: Victoria

address: 145 Studley Road

country: Australia

institute: Olivia Newotn-John Cancer Research Institute

description:
115_top
115_C81U4ANXX_GCCAAT_L001

library_source: transcriptomic

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Untrimmed reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the TopHat aligner with Bowtie2
Genewise counts were obtained using HTseqCount. Genes were discarded for further downstream analysis if they failed to achieve at least 0.5 counts per million in at least two samples.
Genome_build: GRCm38/mm10 build of the Mus musculus genome
Supplementary_files_format_and_content: Tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

organism: Mus musculus

growth_protocol: Mice were euthanised with Co2 prior to excision of the tumors from the colon that were then immediately snap-frozen in dry-ice.

extract_protocol:
Total RNA was extracted from snap-frozen tumors collected from the colon of  bone marrow chimeras using Trizol®Reagent (Life Technologies). Extracted RNA was then further purified using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.
Libraries were generated using the Illumina Truseq RNA sample preparation kit according to the manufacturer’s instructions. Three biological replicates were generated and sequenced for each group of BM chimeras by subjecting 1μg of RNA to single-end (50 pb) sequencing on an Illumina HiSeq 2500 instrument at the Australian Genome Research Facility.

treatment_protocol: The tumor was excised from the colon of bone marrow chimeras treated for 6 consecutive weeks with azoxymethane (AOM)  13 to 14 weeks after last AOM injection.

tag: strain background

value: Balb/c

tag: gender

value: Male

tag: origin

value: Colon tumor

tag: protocol

value: 6xAOM treated

tag: time last  after aom injection

value: 13 weeks


title: Holstein-Friesian - differentiated bovine satellite cells (6th day)_rep 4

description: Biological replicate 4 of 8. Differentiated bovine satellite cells (6th day) from Holstein-Friesian


title: St2-/- => St2-/- biological replicate 1

description:
108_top
108_C81U4ANXX_TGACCA_L001

value: 14 weeks


title: HM-1_control, biological rep2

city: kyoto

first: Mana

last: Taki

state: kyoto

address: 54, shogoinkawahara-cho, sakyo-ku

department: Gynecology and Obstetrics

country: Japan

institute: Kyoto University

hyb_protocol: Samples were hybridized with Affimetrix GeneChip Mouse Transcriptome Array 1.0.

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console)

data_processing: The data were processed with Affymetrix Expression Console.

label: biotin

source_name: mouse ovarian cancer cell line HM-1, control

label_protocol: Labeling was performed according to Affymetrix GeneChip MouseTranscriptome Array 1.0 protocol.

growth_protocol: Cells were cultured in Minimum Essential Mediumα (MEMα, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 g/mL streptomycin in an atmosphere containing 5% CO2 at 37˚C.

extract_protocol: Total RNA was extracted using the RNAeasy Kit (Qiagen).

treatment_protocol: HM-1-shSnail cells were generated by lentiviral transfection with short hairpin RNAs (shRNAs) targeting Snail using Mouse GIPZ Lentiviral shRNA viral particles (GE Healthcare UK, Buckinghamshire, England; sh1, clone ID V3LMM_523301, gene target sequence AGTTTATTGATATTCAATA; sh2, clone ID V3LMM_523299, gene target sequence TGGTTAATTTATATACTAA).

tag: cell line

value: ovarian cancer


title: HM-1_sh1, biological rep1

source_name: mouse ovarian cancer cell line HM-1, shSnail sh1


title: HM-1_sh1, biological rep2


title: WT => St2-/- biological replicate 3

description:
110_top
110_C81U4ANXX_ATCACG_L001

value: Female


title: HM-1_sh2, biological rep2

source_name: mouse ovarian cancer cell line HM-1, shSnail sh2


title: WT => St2-/- biological replicate 2

description:
114_top
114_C81U4ANXX_TTAGGC_L001


title: St2-/- => WT biological replicate 3

description:
10227_top
10227_C81U4ANXX_CTTGTA_L001


title: WT => St2-/- biological replicate 1

description:
107_top
107_C81U4ANXX_CGATGT_L001


title: BRK115

description: Test


title: HM-1_sh2, biological rep1


title: BRK083

description: Test


title: Holstein-Friesian - differentiated bovine satellite cells (6th day)_rep 3

description: Biological replicate 3 of 8. Differentiated bovine satellite cells (6th day) from Holstein-Friesian


title: BRK110

description: Test


title: St2-/- => St2-/- biological replicate 2

description:
109_top
109_C81U4ANXX_ACAGTG_L001


title: WT => WT biological replicate 2

description:
10223_top
10223_C81U4ANXX_ACTTGA_L001

source_name: WT => WT


title: BRK095

description: Test


title: BRK088

description: Test


title: BRK033

description: Test


title: HM-1_control, biological rep3


title: St2-/- => WT biological replicate 2

description:
10226_top
10226_C81U4ANXX_GGCTAC_L001


title: BRK028

description: Test


title: St2-/- => WT biological replicate 1

description:
10225_top
10225_C81U4ANXX_TAGCTT_L001


title: WT => WT biological replicate 3

description:
10224_top
10224_C81U4ANXX_GATCAG_L001


title: K2 vs W2

city: Beijing

first: Jiao

last: Fan

address: Fuxing road

country: China

institute: 301 hospital

hyb_protocol: samples were applied to microarrays enclosed in  hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on ancapitalbio luxscan scanner.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

source_name: ApoE-/-CKIP-1-/- mouse2

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

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

value: aorta

tag: genotype

value: ApoE-/-


title: BRK017

description: Test


title: BRK018

description: Test


title: WT => WT biological replicate 1

description:
10222_top
10222_C81U4ANXX_CAGATC_L001


title: BRK034

description: Test


title: BRK051

description: Test


title: Wild type macrophages, biological rep3

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

country: USA

institute: University of Minnesota

hyb_protocol: A ligation reaction was then performed to attach to the miRNA population a multiple-biotin molecule containing a 3DNA dendrimer. After hybridization for 16 h at 48C, the arrays were washed and stained in an Affymetrix Fluids station 450.

scan_protocol: All arrays were scanned in an Affymetrix 3000 7G scanner.

data_processing:
Partek Genomic Suite® was used to read the raw image files, and pre-process the data with the following settings: Pre-background Adjustement - GC and prob Sequence, Background correction: RMA, Normalization: Quantile, Log: 2, Probset level Summary: Median Polish. The cleaned data matrix was then exported to R and analyzed by limma package for differential expression of miRNAs.
The significantly differentially expressed miRNAs were those that showed at least 2-fild change in expression with an FDR corrected p values less than 0.05.

source_name: Bone marrow from naïve C57BL/6 mice

label_protocol: 1μg of total RNA was labeled using the Genisphere FlashTag Biotin HSR kit (Hatfield, PA) and incubated with ATP and Poly A polymerase to add a polyA tail.

growth_protocol: Bone marrow-derived macrophage cells lines generated from either C57BL/6  WT or A-FABP knockout mice were cultured in RPMI-1640 medium with 5% FBS.

extract_protocol: Total RNA was extracted from tumor-stimulated macrophages using miRNA isolation kit following the manufacturer's protocol.

treatment_protocol: 1 million of WT and A-FABP knockout macrophages were cocultured with 2 millions of E0771 mammary tumor cells in a transwell plate for 24h, respectively.

value: wild type


title: BRK032

description: Test


title: A-FABP knockout macrophages, biological rep2

source_name: Bone marrow from A-FABP -/- C57BL/6 mice

value: A-FABP knockout


title: HM-1_control, biological rep1


title: BRK020

description: Test


title: A-FABP knockout macrophages, biological rep1


title: DEG-T

city: Lanzhou

first: Ruiqing

last: Zhu

state: Gansu

address: DingxiSouth Road 197

department: Instituye of biology

institute: Gansu Academy of Sciences

data_processing:
Sequencing-received raw image data were transformed by base calling into sequence data. Prior to mapping reads to the reference database, all sequences were filtered to remove 3′ adaptor sequence, low quality sequences (tags with unknown sequences ‘N’), tags with a copy number of 1 (probably sequencing error), and tags which are too long or too short, leaving clean tags of 21 nt. For annotation, all clean tags were mapped to the reference sequences, and a mismatch of only 1 bp was considered. The clean reads mapped to reference database from multiple genes were filtered. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags
Supplementary_files_format_and_content: sequences and counts

organism: Reaumuria songarica

source_name: leaf

growth_protocol: the plants was under natural conditions in Lanzhou.

extract_protocol:
CTAB-method library construction, and sequencing were carried out at Beijing Genome Institute at Shenzhen, China.
An extract of 8 μg of total RNA was obtained and treated with oligo(dT) magnetic bead adsorption to purify mRNA; oligo(dT) was then used as a primer to synthesize the first- and second-strand cDNA. The 5′-ends of tags can be generated by two types of endonuclease: NlaIII or DpnII. Then, the bead-bound cDNA is subsequently digested with restriction enzyme NlaIII, which recognizes and severs the CATG sites. Fragments other than the 3′-cDNA fragments connected to oligo(dT) beads are washed away, and the Illumina adaptor 1 is ligated to the sticky 5′-end of the digested bead-bound cDNA fragments. The junction of the Illumina adaptor 1 and the CATG site constitutes the recognition site of MmeI, which is a type of endonuclease with separate recognition and digestion sites; it breaks 17 bp downstream of the CATG site, producing tags with adaptor 1. After removal of 3′ fragments with magnetic beads precipitation, the Illumina adaptor 2 is ligated to the 3′-ends of tags, acquiring tags with different adaptors of both ends to form a tag library.

treatment_protocol: the C gropup was under natural conditions in Lanzhou. The T group was treated with supplementary 0.2 W UV-B radiaton.

tag: treatment

value: UV-B


title: BRK007

description: Test

value: PBMC


title: BRK009

description: Test

value: Melioidosis cases


title: TIGR4 DFO treated cells. Treated 4

city: Cordoba

first: Antonio

middle: Rodriguez

last: Franco

state: CORDOBA

address: Rabanales. Ed Severo Ochoa

department: Bioquímica y Biología Molecular

country: Spain

institute: Universidad de Córdoba

description: Biological replicate 4 of 4. Iron chelated with DFO

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Microarrays were scanned using an Agilent DNA Microarray Scanner (Model G2505C) according to manufacturers' instructions

data_processing: Data extracted with Feature Extraction v.10.7 (Agilent), which marked non valid outliers. Data was processed with thr R package limma, background substracted with the "normexp" method, after that a normalizeWithinArray with the "lowess" method, and finally a normalizeBetweenArray with the "Aquantile" method was applied

organism: Streptococcus pneumoniae TIGR4

source_name: TIGR4 bacteria

label_protocol: RNA was labeled with Cy5 and Cy3

growth_protocol: Bacteria were grown at 37 ºC in Todd Hewitt Broth (THB) until mid-exponential phase (OD600 = 0.3 approximately)

extract_protocol: total RNA was extracted with Tri-Reagent (Sigma–Aldrich). RIN values ranged between 7.0 and 9.2

treatment_protocol: DFO (deferoxamine) was dissolved in water and added to the treatment samples at a final concentration of 100 micromolar

tag: virulence

value: Virulent strain

tag: agent

value: 100microM DFO

value: Control


title: K3 vs W3

source_name: ApoE-/-CKIP-1-/- mouse3


title: Wild type macrophages, biological rep1


title: TIGR4 DFO treated cells. Treated 3

description: Biological replicate 3 of 4. Iron chelated with DFO


title: TIGR4 strain Control 1

description: Biological replicate 1 of 4. Control, untreated bacteria


title: A-FABP knockout macrophages, biological rep3


title: BRK019

description: Test


title: VSMC-Alginate hydrogel-d6-rep3

status: Public on Jan 26 2018

city: Lincoln

first: Chi

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to rice genome using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each gene with  htseq-count
Genome_build: Human genome GRC37/Hg19
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is gene IDs and the second column is reads counts

source_name: Vascular smooth muscle cells

growth_protocol: H9s were maintained in E8 medium for routine culture. Then H9s were differentiated into ECs, NSCs and VSMCs in 2D, 3D PEG hydrogel and alginate hydrogel cell culture system according to their differentiation protocol. mRNAs were sequenced.

extract_protocol:
Cells were harvested after differentiation and total RNA was isolated with RNAeasy isolation kit (Qiagen) according to manufacturer’s instructions. On-column DNAse treatment was performed to remove genomic DNA contamination (Qiagen).
Libraries were prepared using TruSeq RNA v2 library preparation reagents. 15 samples including ECs and NSCs were sequenced one lane and the rest samples were sequenced another lane.

value: hESC-derived vascular smooth muscle cells

tag: initial cell type

tag: culture system

value: alginate hydrogel


title: VSMC-Alginate hydrogel-d6-rep2


title: BRK015

description: Test


title: BRK016

description: Test


title: TIGR4 DFO treated cells. Treated 1

description: Biological replicate 1 of 4. Iron chelated with DFO


title: TIGR4 DFO treated cells. Treated 2

description: Biological replicate 2 of 4. Iron chelated with DFO


title: TIGR4 strain Control 4

description: Biological replicate 4 of 4. Control, untreated bacteria


title: VSMC 3D PEG hydrogel rep2

value: 3D PEG hydrogel


title: VSMC-Alginate hydrogel-d1-rep1


title: K1 vs W1

source_name: ApoE-/-CKIP-1-/- mouse1


title: BRK010

description: Test


title: VSMC 3D PEG hydrogel rep1


title: VSMC 2D rep2


title: DEG-C


title: TIGR4 strain Control 3

description: Biological replicate 3 of 4. Control, untreated bacteria


title: NSC Alginate hydrogel rep1

source_name: Neural stem cells

value: hESC-derived neural stem cells


title: VSMC-Alginate hydrogel-d1-rep3


title: EC Alginate hydrogel rep3

source_name: Vascular endothelial cells

value: hESC-derived vascular endothelial cells


title: BRK006

description: Test


title: TIGR4 strain Control 2

description: Biological replicate 2 of 4. Control, untreated bacteria


title: VSMC-Alginate hydrogel-d1-rep2


title: EC 3D PEG hydrogel rep2


title: EC Alginate hydrogel rep2


title: EC Alginate hydrogel rep1


title: VSMC 3D PEG hydrogel rep3


title: EC 2D rep2


title: VSMC-Alginate hydrogel-d6-rep1


title: VSMC 2D rep3


title: NSC 2D rep2


title: KG1_Suz12

city: Marseille

first: Estelle

last: Duprez

address: 27 boulevard Lei Roure

department: Centre de Recherche en Cancérologie de Marseille

country: France

institute: INSERM

library_source: genomic

data_processing:
for shEZH2 dataset basecalling was performed using RTA v2, for other datasets we used Illumina CASAVA
Reads with Phred quality score less than 30 were filtered out
Replicate concurrency was verified by PCA plots, and sample replicates were merged into a single fastq file
Sequences were mapped to the human genome (hg19) using Bowtie2 alignment tool (ref: PMID 22388286) with default parameters
For each datasets, tag counts were normalized by the total number of mapped tags such that each file contains the same amount of reads.
Input normalized bigwig files were generated from bam files using either a customed script or Deeptools 2.0 suite (bamCompare)
High confidence binding sites were determined through peak calling using MACS2 (in sharp mode for transcription factors; in broad mode for histone marks) using inputs as controls
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

molecule: genomic DNA

source_name: KG1 cell line

growth_protocol: Human myeloblastic cell line KG1 were maintained at exponential growth in RPMI with 10% foetal calf serum and 1% sodium pyruvate

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA or proteins-DNA complexes were isolated with antibody. DNA was purified using the i-Pure kit (Diagenode)
Libraries were prepared according to Illumina's instructions accompanying the Illumina's TruSeq ChIP sample Prep Kit Protocol

treatment_protocol: for shRNA induction, cells were treated with 2mg/ml for 7 days

value: bone marrow

tag: culture properties

value: suspension

tag: antibody


title: H3K27me3_ChIPSeq_shEZH2

tag: tissue


title: PLZF_ChIPSeq_shEZH2

value: shPLZF

value: PLZF


title: NSC Alginate hydrogel rep2


title: Wild type macrophages, biological rep2

value: wild type


title: NSC Alginate hydrogel rep3


title: Lu2052-TC

city: Rochester

first: Michael

middle: K

last: Asiedu

address: 200 Fisrt ST SW

department: Surgery

institute: Mayo Foundation for Medical Education and Research

hyb_protocol: About 100-200 ng of total RNA were used for whole genome mRNA expression profiling which was performed using the Illumina Human WG-6_v2 BeadArray Chip in the Mayo Clinic Advanced Microarray Shared Resource.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 and performed by the Mayo Clinic Genomic Core

data_processing: Gene expression data were loaded into the Beadstudio v3 software (Illumina Inc., San Diego, CA) and data were normalized using the cubic spline method. Data were analyzed with Partek Genomics suite software.

source_name: Typical Carcinoid

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was purified with the RNeasy Mini-kit (Qiagen, CA).

value: Lung Frozen Tissue

tag: tissue type

value: Typical Carcinoid


title: Lu2082-TC


title: Lu677A-S

source_name: Small cell lung cancer

value: Small cell lung cancer


title: Lu670A-S


title: VSMC 2D rep1

tag: cell type


title: EC 3D PEG hydrogel rep1


title: Lu508A-S


title: Lu546A-S


title: NSC 2D rep1


title: Lu342A-S


title: Lu2350-TC


title: NSC 2D rep3


title: EC 3D PEG hydrogel rep3


title: EC 2D rep3


title: Lu2119-NL

source_name: adjacent Normal

value: adjacent Normal


title: Lu2378A-S


title: Lu28A-S


title: Lu2268-TC


title: Lu2093-NL


title: EC 2D rep1


title: Lu2046-NL


title: Lu2093-TC


title: Lu2200-NL


title: Lu2027-NL


title: Lu2091A-S


title: H3K4me3_ChIPSeq_shEZH2


title: Lu2201A-S


title: Lu2200-AC

source_name: Atypical Carcinoid

value: Atypical Carcinoid


title: Lu154A-S


title: Lu-1354-AC


title: Lu-1655-AC


title: Lu-876-AC


title: Lu-511-AC


title: Lu2004-AC


title: Lu2046-AC


title: Lu1342A-S


title: Lu2027-TC


title: Lu2119-TC


title: Lu-1315-TC


title: Lu-1466-TC


title: Lu-245B-N


title: Lu2004-NL


title: Lu-1420-TC


title: Lu-533B-N


title: Lu-993-TC


title: Lu-1299-AC


title: Lu1808-AC


title: Lu-820-TC


title: Lu-1655B-N


title: Lu-866-TC


title: Lu-558-TC


title: Lu-1615-TC


title: Lu-302-TC


title: Lu-938-TC


title: Lu-1184-AC


title: Lu-748-AC


title: Lu-383-TC


title: Lu-509-TC


title: Lu1808-NL


title: Lu-1567-TC


title: Lu-553A-TC


title: Lu-564-TC


title: Lu-1752-TC


title: Lu-1768-TC


title: Lu-278-TC


title: Lu-421-TC


title: Lu-349-TC


title: Lu-245A-TC


title: Lu-348-TC


title: Lu-1005-TC


title: patient7-periphery

city: Kumamoto

first: Takuichiro

last: Hide

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

department: Department of Neurosurgery

institute: Kumamoto University

description: SAMPLE 18

hyb_protocol: Hybridization was performed following the Agilent protocols v.2.4.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using miRNA setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters.The data were summarized by the GeneSpring GX software using 31181_v16_0 technology.

source_name: GBM patient_priphery

label_protocol: 100 ng of total RNA was Cy3 labeled using miRNA Complete Labeling and Hyb Kit (Agilent) following the manufacturer's protocols.

extract_protocol: Each piece of tissue was divided into two parts; half was used for pathological examination, and the other half was kept frozen. RNAs were purified from another half of frozen tissue using an miRNeasy Mini Kit (Qiagen, Hilden, Germany) after confirmation of pathological features.

tag: subject id #

tag: subject status

value: Glioblastoma (GBM) patient

tag: age

value: male

value: priphery


title: patient7-border

description: SAMPLE 17

source_name: GBM patient_border

tag: gender

value: border


title: patient8-periphery

description: SAMPLE 20


title: patient11-periphery

description: SAMPLE 27


title: Lu-710-TC


title: patient9-tumor

description: SAMPLE 21

source_name: GBM patient_tumor

value: tumor


title: patient11-border

description: SAMPLE 28


title: patient9-border

description: SAMPLE 22


title: patient9-periphery

description: SAMPLE 23


title: patient7-tumor

description: SAMPLE 16


title: patient11-tumor

description: SAMPLE 29


title: Lu2A-S


title: patient8-tumor

description: SAMPLE 19


title: patient12-tumor

description: SAMPLE 31

value: female


title: patient10-border

description: SAMPLE 25


title: patient6-border

description: SAMPLE 15


title: patient5-periphery

description: SAMPLE 13


title: patient10-tumor

description: SAMPLE 26


title: patient10-periphery

description: SAMPLE 24


title: patient6-tumor

description: SAMPLE 14


title: patient5-tumor

description: SAMPLE 11


title: patient5-border

description: SAMPLE 12


title: patient4-periphery

description: SAMPLE 10


title: SK-N-BE(2)_Normoxia

city: Chicago

first: Christopher

last: Mariani

state: IL

institute: University of Chicago

description: hMe-SEAL

data_processing:
DNA reads were aligned using BWA aligner.
Peaks were called using MACS1.4
Genome_build: hg19
Supplementary_files_format_and_content: peak file

growth_protocol: DMEM with 10% FBS

extract_protocol:
hMe-SEAL followed previously described methods (Song et al., Nature Biotechnology, 2011)
Standard Illumina protocols

treatment_protocol: 1% O2 (hypoxia) or 20% O2 (normoxia) for 48 hours

value: 48 hours Normoxia


title: SK-N-BE(2)_Normoxia_input

description: hMe-SEAL


title: NBL-WN_Normoxia_hMe-SEAL

description: hMe-SEAL

data_processing:
DNA reads were aligned using BWA aligner.
Peaks were called using MACS1.4
Genome_build: hg19
Supplementary_files_format_and_content: wig file

source_name: NBL-WN cells

value: NBL-WN


title: patient4-tumor

description: SAMPLE 8


title: patient4-border

description: SAMPLE 9


title: NBL-WN_Hypoxia_RNA-seq

description:
processed data file:
WN_RNA-seq_Normoxia_vs_Hypoxia.txt

data_processing:
RNA-Seq: Reads aligned with tophat2 and bowtie2
RNA-Seq: Cufflinks (cufflinks, cuffcompare, cuffdiff) for expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited output of FPKM for RNA

source_name: NBl-WN cells

extract_protocol:
RNA extracted with Trizol reagent.
Standard Illumina protocols

value: Treatment:48 hours Hypoxia


title: SK-N-BE(2)_Hypoxia

description: hMe-SEAL

value: 48 hours Hypoxia


title: SK-N-BE(2)_Hypoxia_input

description: hMe-SEAL


title: patient1-border

description: SAMPLE 2


title: NBL-WN_input

description:
input
Please note that the 'WCP_Peaks_control_afterfiting_all.wig.gz' and 'WHP_Peaks_control_afterfiting_all.wig.gz' files are the corresponding input files for the NBL-WN_Normoxia_hMe-SEAL (WCP_Peaks_treat_afterfiting_all.wig.gz) and NBL-WN_Hypoxia_hMe-SEAL (WHP_Peaks_treat_afterfiting_all.wig.gz) processed data, respectively.


title: patient3-tumor

description: SAMPLE 6


title: NBL-WN_Hypoxia_hMe-SEAL

description: hMe-SEAL


title: patient12-border

description: SAMPLE 30


title: patient3-periphery

description: SAMPLE 7


title: patient2-tumor

description: SAMPLE 4


title: patient1-periphery

description: SAMPLE 3


title: patient2-border

description: SAMPLE 5


title: patient1-tumor

description: SAMPLE 1


title: NBL-WN_Normoxia_RNA-seq

value: Treatment:48 hours Normoxia


title: E12/13_Pum2_1

city: Toronto

first: Freda

last: Miller

state: ON

address: 686 Bay Street

country: Canada

institute: Hospital For Sick Children

description:
RNA enriched from Pum2 immunoprecipitates from E12/E13 cortex
Pum2 IP, biological replicate 1

hyb_protocol: Samples were hybridized with Mouse Gene 2.0 ST Arrays (Thermo Fisher)

scan_protocol: The hybridized microarray image was scanned with the GeneChip Scanner 3000 7G (Thermo Fisher) at the HSC Microarray Facility

data_processing: Raw probe intensity values were background corrected, normalized with quantile normalization, transformed into the log2 scale, and summarized into probesets using the Robust Multichip Analysis (RMA) algorithm at the gene level with the Expression Console program (Thermo Fisher).

label: Biotin

source_name: WT Mouse E12/13 cortex, Pum2 immunoprecipitation

label_protocol: cDNA was generated and amplified with the GeneChip Pico Kit (Thermo Fisher) and then labeled with the WT Terminal Labeling Kit (Thermo Fisher).

growth_protocol: Timed CD1 pregnant mice were purchased from Charles River

extract_protocol: IgG or Pum2-bound RNA was purified with the Magna RIP RNA-Binding Protein Immunoprecipitation Kit as per manufacturer's instructions (Millipore). Total RNA was isolated, extracted with phenol/chloroform, and quality checked on a BioAnalyzer (Agilent).

treatment_protocol: E12/13 mouse embryonic cortices were freshly dissected and lysed RNA purification and extraction.

value: WT

tag: strain

tag: developmental stage

value: Embryonic cortex

tag: rip antibody

value: rabbit anti-Pumilio2 (MBL, Cat# RN027P)


title: E12/13_Input_3

description:
Total RNA from E12/13 cortex
Input, biological replicate 3

source_name: WT Mouse E12/13 cortex, total input RNA

tag: genotype


title: E12/13_IgG_3

description:
RNA enriched from IgG immunoprecipitates from E12/E13 cortex
IgG IP, biological replicate 3

source_name: WT Mouse E12/13 cortex, IgG immunoprecipitation

value: normal rabbit IgG (Millipore, Cat# 12-370)


title: E12/13_IgG_1

description:
RNA enriched from IgG immunoprecipitates from E12/E13 cortex
IgG IP, biological replicate 1


title: E12/13_Pum2_2

description:
RNA enriched from Pum2 immunoprecipitates from E12/E13 cortex
Pum2 IP, biological replicate 2


title: E12/13_Pum2_3

description:
RNA enriched from Pum2 immunoprecipitates from E12/E13 cortex
Pum2 IP, biological replicate 3


title: Panc1 IRAK1+4 Inhibiton 16585.txt

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background-subtracted and quantile-normalized using  Illumina GenomeStudio software (V2011)

source_name: Panc1 IRAK1+4 Inhibiton

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

growth_protocol: All cells were cultured in RPMI + 10% FBS + 1% Pen/Strep, and incubated in 37C TC incubator at 5% CO2.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: For drug treatment, cells were incubated with DMSO or 10uM IRAK1/4 inhibitor for 24 hours before harvest. For shRNA experiments, cells were first infected with pSuperRetroPuro retroviruses encoding a scramble sequence, shIRAK1 or shIRAK4 and then selected with 1ug/mL or puromycin for 48 hours. Resultant cells were then infected with pSuperRetroNeoGFP viruses encoding scramble sequence (for scram, shIRAK1, shIRAK4 cells) or shIRAK4 (for shIRAK1 cells) and selected with geneticin 500ug/mL for 4 days. Cells were then harvested for RNA extraction.

tag: cell line

value: Panc1 pancreatic cancer cell line


title: Panc1 IRAK1+4 Inhibiton 16586.txt

description: replicate 2


title: E12/13_IgG_2

description:
RNA enriched from IgG immunoprecipitates from E12/E13 cortex
IgG IP, biological replicate 2


title: Panc1 shIRAK1+4 16602.txt

description: replicate 2

source_name: Panc1 shIRAK1+4


title: Panc1 Scram 16595.txt

description: replicate 1

source_name: Panc1 Scram


title: Panc1 shIRAK1+4 16601.txt

description: replicate 1


title: Panc1 shIRAK1 16597.txt

description: replicate 1

source_name: Panc1 shIRAK1


title: Panc1 shIRAK4 16599.txt

description: replicate 1

source_name: Panc1 shIRAK4


title: E12/13_Input_1

description:
Total RNA from E12/13 cortex
Input, biological replicate 1


title: Capan1 shIRAK1+4 16594.txt

description: replicate 2

source_name: Capan1 shIRAK1+4

value: Capan1 pancreatic cancer cell line


title: Panc1 shIRAK1 16598.txt

description: replicate 2


title: E12/13_Input_2

description:
Total RNA from E12/13 cortex
Input, biological replicate 2


title: Panc1 DMSO control 16584.txt

description: replicate 2

source_name: Panc1 DMSO control


title: Panc1 Scram 16596.txt

description: replicate 2


title: CTX0E16_siRNA_B_3

city: Lodon

first: Deepak

middle: P

last: Srivastava

address: 5 Cutcombe Road

department: Department of Basic & Clinical Neuroscience

country: United Kingdom

institute: King's College London

data_processing: Data were backgroundcorrected, transformed (log2) and normalised (quantile) in Lumi (R package)

source_name: CTX0E16 NPCs

label_protocol: Standard Illumina TotalPrep kit amplification and labeling protocol

growth_protocol: The conditionally-immortalised neural stem cell line CTX0E16 was used to investigate global gene expression changes caused by the knockdown of the schizophrenia susceptibility gene NT5C2. This cell line was kindly provided by ReNeuron (www.reneuron.com) as part of a Material Transfer Agreement. This cell line was derived from the brain of a 12-week male foetus as detailed elsewhere (Pollock et al., 2006). Cells were routinely maintained at the proliferative state as described elsewhere (Pollock et al., 2006). Cells were routinely maintained at the proliferative stage as described elsewhere (Anderson et al., 2015; Deans et al., 2016). Cultures were kept at 37oC, with 5% CO2, and split using Accutase when necessary. The proliferative state was maintained by culturing cells in DMEM:F12 (Sigma) supplemented with 0.03% human serum albumin (PAA), 100 μg.ml-1 apo-transferrin (Scipac), 16.2 µg.ml-1 putrescine (Sigma), 5 µg.ml-1 human insulin (Sigma), 60 ng.ml-1 progesterone (Sigma), 2 mM L-glutamine (Sigma) and 40 ng.ml-1 sodium selenite (Sigma), 10 ng.ml-1 human FGF2, 20 ng.ml-1 human EGF (PeproTech) and 100 nM 4-hydroxy-tamoxifen (4-OHT) (Sigma).

extract_protocol: Tri-Reagent (Sigma) following the standard protocol, with an additional ethanol precipitation step

treatment_protocol: The Trilencer 27-mer NT5C2 siRNA kit (SR307908, Origene, Rockville, MD, USA) was used to knockdown full length NT5C2 RefSeq transcripts NM_012229 and NM_001134373, using the siRNA sequences A (UGAGAAGUAUGUAGUCAAAGAUGGA, n=3) and B (ACAACUGUAAUAGCUAUUGGUCUTC, n=4), in parallel with a negative scramble control sequence (SR30004). A million cells of CTX0E16 neural progenitors were plated in T75 flasks 24 hours before transfection, and incubated with transfection media containing 10 nM siRNAs and N-TER Nanoparticle siRNA Transfection System (Sigma) for 72 hrs. RNA and protein were extracted as described in the manuscript attached.

value: human neural progenitor cells

tag: biological replicate


title: CTX0E16_siRNA_scramble_3


title: CTX0E16_siRNA_A _3


title: Panc1 DMSO control 16583.txt

description: replicate 1


title: Capan1 shIRAK4 16592.txt

description: replicate 2

source_name: Capan1 shIRAK4


title: CTX0E16_siRNA_scramble_4


title: CTX0E16_siRNA_scramble_2


title: CTX0E16_siRNA_B_4


title: Capan1 shIRAK1+4 16593.txt

description: replicate 1


title: Panc1 shIRAK4 16600.txt

description: replicate 2


title: CTX0E16_siRNA_B_1


title: Capan1 shIRAK4 16591.txt

description: replicate 1


title: CTX0E16_siRNA_A _1


title: CTX0E16_siRNA_scramble_1


title: CTX0E16_siRNA_A _2


title: Capan1 shIRAK1 16589.txt

description: replicate 1

source_name: Capan1 shIRAK1


title: Capan1 shIRAK1 16590.txt

description: replicate 2


title: Capan1 Scram 16587.txt

description: replicate 1

source_name: Capan1 Scram


title: Input shPLZF

source_name: KG1 cell line

value: bone marrow

value: suspension

value: shPLZF


title: Capan1 IRAK1+4 Inhibiton 16606.txt

description: replicate 2

source_name: Capan1 IRAK1+4 Inhibiton


title: RD-pBabe-PAX3-FOXO1

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description:
MEH032
Gene expression data from Human FN-RMS cell line with forced PAX3-FOXO1 expression.

hyb_protocol: Microarray hybridization was performed at 55°C for 20 hours in Agilent's microarray hybridization chambers, followed by wash procedures according to the manufacturer’s recommended protocols.

scan_protocol: Microarray was scanned in an Agilent scanner at 5μm resolution, and the array data was extracted with Agilent feature extraction software using the miRNA_105_Jan09 protocol.

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used, followed by a log transformation, percentile normalization across probes, and scaling through the samples, prior to actual analysis.

source_name: Human RD cells transduced with pBabe-PAX3-FOXO1-Puro

label_protocol: 100ng of total RNA were labeled with Cy3 according to Agilent's labeling protocol.

growth_protocol: Cells grown in 10% FBS, DMEM at 37°C.

extract_protocol: miRNeasy extraction of total RNA according to manufacturer's instructions.

treatment_protocol: shRNA cells treated with 50ng/mL doxycycline.

value: RD

value: RN-RMS cell line

tag: expression


title: RD-pBabe-Empty

description:
MEH031
Gene expression data from Human FN-RMS cell line Control.

source_name: Human RD cells transduced with pBabe-Empty-Puro

value: pBabe-Empty-Puro


title: Rh41-shP3F, biological rep3

description:
MEH030
Gene expression data from Human FP-RMS cell line with shP3F.

source_name: Human Rh41 cells transduced with shP3F, treated with doxycycline

value: FP-RMS cell line

tag: shRNA


title: CTX0E16_siRNA_B_2


title: Capan1 Scram 16588.txt

description: replicate 2


title: Rh41-shP3F, biological rep2

description:
MEH028
Gene expression data from Human FP-RMS cell line with shP3F.


title: DFO-untreated cells

city: Setagayaku

first: horofumi

last: INOUE

address: 1-1-1 Sakuragaoka

institute: Tokyo University of Agriculture

description:
CTL
Gene expression after cells were exposed to 0 μM DFO (DW) for 24hour.
US10443845_252827910598_S01_GE1_107_Sep09_2_1.txt

hyb_protocol: Cy3-labeled cRNA (1.65 μg) was fragmented to an average size of about 50–100 nucleotides and then hybridized for 17 h at 65°C to a rat liver, kidney and FAO cells oligonucleotide microarray slide. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned in Cy3 channel with the Agilent DNA Microarray Scanner (Agilent).

data_processing: Signal intensity per spot was generated from the scanned image with Agilent scan control 8.0 software according to Agilent Technologies standard operation procedures. The scanned images were analyzed using commercial software (GeneSpring GX11.5) as follows: (i) threshold raw signals were set at unify, and (ii) submitted to 75th percentile normalization.

organism: Rattus norvegicus

source_name: DFO non-treatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice in the CTL (n=6) and ID groups (n=6) were fed AIN-93G diet with or without iron for 4 weeks. FAO cells incubated DMEM medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the TRIzol following the manufacturer's recommendations. And then, we collected three (FAO cells) or six (rat liver or kidney) extraction of total RNA all together and mixed it, respectively. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The cultures were exposed by 100 μM DFO (n=3) and vesicle solution (n=3) for 24 hours at 37 ºC in a humidified incubator with 5% CO2. Mice in the CTL and ID groups were fed AIN-93G diet with or without iron for 4 weeks.

value: FAO

value: liver cell line

tag: treatment

value: no deferoxamine (DFO)


title: DFO-treated cells

description:
DFO
Gene expression after cells were exposed to 100μM DFO for 24hour.
US10443845_252827910598_S01_GE1_107_Sep09_2_2.txt

source_name: DFO treatment

value: deferoxamine (DFO)


title: AIN-93G normal diets kidney

description:
CTL kidney
Mice in the CTL group was fed AIN-93G diet for 4 weeks.
US10443845_252827910598_S01_GE1_107_Sep09_1_3.txt

source_name: Fed AIN-93G diet

tag: strain/background

value: Wistar

value: kidney

value: AIN-93G diet


title: Rh41-shP3F, biological rep1

description:
MEH026
Gene expression data from Human FP-RMS cell line with shP3F.


title: AIN-93G diet without iron liver

description:
ID Liver
Mice in the ID group was fed AIN-93G diet without iron for 4 weeks.
US10443845_252827910598_S01_GE1_107_Sep09_1_2.txt

source_name: Fed AIN-93G diet without iron

tag: tissue

value: liver

value: AIN-93G diet without iron


title: Capan1 DMSO control 16580.txt

description: replicate 2

source_name: Capan1 DMSO control

value: Capan1 pancreatic cancer cell line


title: Capan1 IRAK1+4 Inhibiton 16605.txt

description: replicate 1


title: AIN-93G normal diets liver

description:
CTL Liver
Mice in the CTL group was fed AIN-93G diet for 4 weeks.
US10443845_252827910598_S01_GE1_107_Sep09_1_1.txt


title: AIN-93G diet without iron kidney

description:
ID kidney
Mice in the ID group was fed AIN-93G diet without iron for 4 weeks.
US10443845_252827910598_S01_GE1_107_Sep09_1_4.txt


title: Rh41-shSCR, biological rep3

description:
MEH029
Gene expression data from Human FP-RMS cell line with shScr.

source_name: Human Rh41 cells transduced with shSCR, treated with doxycycline

value: shSCR


title: PolII_ChIPSeq_shCtrl

value: bone marrow

tag: culture properties

value: suspension

value: wild type

tag: antibody

value: PolII


title: Rh41

description:
MEH019
Gene expression data from Human RMS cell line.

source_name: Human Rh41 cells

tag: cell type


title: PLZF_ChIPSeq_shCtrl

value: PLZF


title: Rh41-shSCR, biological rep1

description:
MEH025
Gene expression data from Human FP-RMS cell line with shScr.

value: FP-RMS cell line


title: Capan1 DMSO control 16579.txt

description: replicate 1


title: Rh41-shSCR, biological rep2

description:
MEH027
Gene expression data from Human FP-RMS cell line with shScr.


title: Rh2

description:
MEH012
Gene expression data from Human RMS cell line.

source_name: Human Rh2 cells

value: FN-RMS cell line


title: Rh28

description:
MEH017
Gene expression data from Human RMS cell line.


title: Input shCtrl


title: RD

description:
MEH010
Gene expression data from Human RMS cell line.

source_name: Human RD cells

value: RD


title: EZH2_ChIPSeq_shCtrl


title: Rh4

description:
MEH016
Gene expression data from Human RMS cell line.

source_name: Human Rh4 cells


title: H3K36me3_ChIPSeq_shCtrl


title: Rh30

description:
MEH018
Gene expression data from Human RMS cell line.

source_name: Human Rh30 cells


title: Rh3

description:
MEH015
Gene expression data from Human RMS cell line.

source_name: Human Rh3 cells


title: EZH2_ChIPSeq_shPLZF

source_name: KG1 cell line

value: shPLZF


title: SJRHB_TB-12_6400

description:
MEH009
Gene expression data from Patient-derived xenograft.

source_name: Human FP-RMS PDX sample

value: FP-RMS xenograft


title: H3K4me3_ChIPSeq_shCtrl


title: H3K4me3_ChIPSeq_shPLZF


title: SJRHB012_X

description:
MEH003
Gene expression data from Patient-derived xenograft.

source_name: Human FN-RMS PDX sample

value: FN-RMS xenograft


title: H3K27me3_ChIPSeq_shPLZF


title: H3K27me3_ChIPSeq_shCtrl


title: SJRHB012_Z

description:
MEH005
Gene expression data from Patient-derived xenograft.


title: SJRHB_TB-12_0493

description:
MEH008
Gene expression data from Patient-derived xenograft.


title: SJRHB026_X

description:
MEH007
Gene expression data from Patient-derived xenograft.


title: SJRHB011_X

description:
MEH002
Gene expression data from Patient-derived xenograft.


title: SJRHB013_X

description:
MEH006
Gene expression data from Patient-derived xenograft.


title: SJRHB012_Y

description:
MEH004
Gene expression data from Patient-derived xenograft.


title: Aero Spleen

city: Tokyo

first: Masayuki

last: Tsukasaki

address: 7-3-1 Hongo Bukyo-ku

department: Department of Immunology  Graduate School of Medicine and Faculty of Medicine

institute: The University of Tokyo

description:
Bacteria
Total bacterial DNA extracted from aerobic culture of the spleen cells of periodontitis-induced mice.
processed data file: Processed_data.txt

data_processing:
Sequenced paired-end reads were imported into CLC Genomics Workbench v.9.0 (CLC). Paired-end reads were merged, trimmed and clustered into operational taxonomic units (OTUs) (97%) by reference-based OTU clustering using Greengenes v13_5.
Supplementary_files_format_and_content: Processed_data.txt: Tab-delimited text file includes the read number of each bacterium in each sample (Aero Liver: aerobic culture of liver cells, Anero Liver: anaerobic culture of liver cells, Aero Spleen: aerobic culture of spleen cells, Anero Spleen: anaerobic culture of spleen cells, Oral: periodontitis-inducing ligatures, Gut: fecal samples). Listed in a decreasing order of the read number of bacterium in Aero Liver.

organism: mouse metagenome

source_name: aerobic culture of mouse spleen cells

growth_protocol: The liver and spleen were sterilely collected and mechanically homogenized using Tissue homogenizing CKMix (Bertin Technologies) in sterile saline, and cultured on Trypticase Soy Agar with 5% Sheep Blood (BD Bioscience) under an aerobic condition or CDC Anaerobe blood agar (BD Bioscience) under an anaerobic condition for two days at 37°C.

extract_protocol:
Extraction of bacterial DNA was performed according to the manufacturer's instructions (NucleoSpin® Tissue Kit (Takara)).
The V4 region of 16S rRNA genes was PCR amplified (25 cycles, primer pair F515/R806), followed by barcoding (8 cycles) using a Nextera XT Index Kit v2 (Illumina) in triplicate. Barcoded amplicons were sequenced (150-bp paired-end sequencing) on an Illumina MiSeq (Illumina).

tag: mouse strain

value: Female

value: 9-10 weeks

tag: disease status

value: Periodontitis

value: Spleen

tag: culture type

value: Aerobic


title: Anero Spleen

description:
Bacteria
Total bacterial DNA extracted from anaerobic culture of the spleen cells of periodontitis-induced mice.
processed data file: Processed_data.txt

source_name: anaerobic culture of mouse spleen cells

tag: gender

tag: age

value: Anaerobic


title: SJRHB011_Y

description:
MEH001
Gene expression data from Patient-derived xenograft.


title: Anero Liver

description:
Bacteria
Total bacterial DNA extracted from anaerobic culture of the liver cells of periodontitis-induced mice.
processed data file: Processed_data.txt

source_name: anaerobic culture of mouse liver cells

value: Liver


title: Fecal

description:
Bacteria
Total bacterial DNA extracted from fecal sample of periodontitis-induced mice.
processed data file: Processed_data.txt

source_name: mouse fecal sample

value: Fecal sample


title: Oral

description:
Bacteria
Total bacterial DNA extracted from periodontitis-inducing ligature.
processed data file: Processed_data.txt

source_name: mouse oral cavity

value: Oral cavity


title: Aero Liver

description:
Bacteria
Total bacterial DNA extracted from aerobic culture of the liver cells of periodontitis-induced mice.
processed data file: Processed_data.txt

source_name: aerobic culture of mouse liver cells


title: STL_Rat_Liver_8

city: Jefferson

first: Aline

last: de Conti

state: Arkansas

address: 3900 NCTR Road

department: Biochmical Toxicology

institute: FDA-NCTR

description:
Gene expression in  rat livers treated with butyrate containing structured lipid.
STL_1.4

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity > 9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Unrestricted Gene Expression 8x60K Microarray (Agilent), for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent Technologies G2600D SG14324425) using one color scan setting for G3 Microarray format 8x60k (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data were normalized using ArrayTrack software (USFDA National Center for Toxicological Research, Jefferson, AR).

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from liver tissue using miRNeasy Mini kits (Qiagen, Valencia, CA) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male Wistar rats were obtained from a colony from the Faculty of Pharmaceutical Sciences (Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil). They were housed in a temperature-controlled room (24ºC) with a 12-h light-dark cycle and given ad libitum access to water and commercial chow diet (Nuvital, Colombo, PR, Brazil). After 1 week of adaptation, the rats (n = 4/group) were allocated randomly to a control group and to experimental group. Rats in the control group were treated with 3.0 g/kg body weight (bw) of maltodextrin (Nestle, Brazil; control group). Rats in the experimental group were treated with 1.65 g/kg bw of STLs daily by gavage. The doses of maltodextrin were isocaloric to doses of STLs. Two weeks after treatment initiation, rats from control and experimental group were subjected to a “resistant hepatocyte” model of hepatocarcinogenesis. Rats from the control and experimental group were euthanized 8 weeks after treatment initiation. All experimental procedures were carried out in accordance with the animal study protocol approved by the Faculty of Pharmaceutical Sciences of the University of Sao Paulo Ethics Committee for Animal Research (protocol CEUA/FCF/77/2012).

value: male

tag: strain

value: Wistar

tag: agent

value: STL

value: liver


title: Control_Rat_Liver _4

description:
Gene expression in controls age matched rat livers
Control_2.4

source_name: Control_Rat_Liver _4

value: Control


title: STL_Rat_Liver_7

description:
Gene expression in  rat livers treated with butyrate containing structured lipid.
STL_ 2.3


title: MUC1 Vaccine + Indomethacin 1

city: Charlotte

first: Timothy

last: Erick

state: North Carolina

address: 9201 University City Blvd, Woodward Hall 461

department: Biological Sciences

institute: University of North Carolina at Charlotte

description: Gene expression data from the tumor RNA of mice that were treated with the MUC1 peptide vaccine + indomethacin

hyb_protocol: The cRNA samples together with probe array controls were hybridized onto Affymetrix HT MG-430 PM array strips, which cover 39,000 mouse transcripts and variants selected from GenBank, dbEST, and RefSeq. Hybridization controls were spiked into the cRNA samples in order to monitor and troubleshoot hte hybridization process. Probes for housekeeping genes were used to assess ample integrity.

scan_protocol: Hybridization, washing, staining, and scanning were performed using Affymetrix GeneAtlas personal microarray system instruments. Affymetrix GeneAtlas instrument control software version 1/0/5/267 was used to analyze microarray image data and to compute intensity values.

data_processing: Affymetrix.CEL files containing raw, probe-level signal intensities were analyzed using Partek Genomics Suite version 6.6.12.0713 (Partek). Robust multichip averaging (RMA) was used for background correction, quantile normalization, and probe set summarization with median polish.

source_name: Mtag.MUC1 tumors removed from indomethacin + vaccine-treated mice at Day 27/28 post-tumor cell injection

label_protocol: RNA samples were reverse transcribed, amplified, and labeled using 3' IVT Express Kit (Affymetrix, Inc.). The resulting labeled cRNA was purified and fragmented as per the vendor's instructions.

growth_protocol: 1 x 10^6 Mtag.MUC1 breast cancer cells were injected into the mammary fat pad of 8-12 week old female MUC1.Tg mice

extract_protocol: The mice were sacrificed, tumors were resected, and total RNA was extracted from the tumors.

treatment_protocol: Once tumors of at least 3 mm x 3 mm were detected by calipers, two mice per group were left untreated, or treated with the MUC1 peptide vaccine, indomethacin, or the MUC1 peptide vaccine + indomethacin. Treatment continued until Day 27/28 post-tumor cell injection.

value: Orthotopic mammary tumor

tag: genotype

value: MUC1.Tg mice

value: 8-12 weeks

value: the MUC1 peptide vaccine + indomethacin


title: STL_Rat_Liver_6

description:
Gene expression in  rat livers treated with butyrate containing structured lipid.
STL_1.2


title: STL_Rat_Liver_5

description:
Gene expression in  rat livers treated with butyrate containing structured lipid.
STL_2.1


title: Control_Rat_Liver _3

description:
Gene expression in controls age matched rat livers
Control_1.3

source_name: Control_Rat_Liver _3


title: MUC1 Vaccine + Indomethacin 2


title: MUC1 Vaccine 1

description: Gene expression data from the tumor RNA of mice that were treated with the MUC1 peptide vaccine

source_name: Mtag.MUC1 tumors removed from MUC1 vaccine-treated mice at Day 27/28 post-tumor cell injection

value: the MUC1 peptide vaccine


title: Untreated 2

description: Gene expression data from the tumor RNA of mice that were left untreated

source_name: Mtag.MUC1 tumors removed from untreated mice at Day 27/28 post-tumor cell injection

value: untreated


title: MUC1 Vaccine 2


title: Control_Rat_Liver _2

description:
Gene expression in controls age matched rat livers
Control_2.2

source_name: Control_Rat_Liver _2


title: Indomethacin 1

description: Gene expression data from the tumor RNA of mice that were treated with indomethacin

source_name: Mtag.MUC1 tumors removed from indomethacin-treated mice at Day 27/28 post-tumor cell injection

value: indomethacin


title: Untreated 1


title: E-selectinWT PM

status: Public on Jan 25 2018

city: Beijing

first: xiaoqing

last: xu

address: No.5 Dongdan Santiao, Dongcheng District

department: Immunology

institute: Chinese Academy of Medical Sciences

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: Peritoneal macrophages from E-selectin+/+ mouse infected with Listeria Monocytogenes in vivo on day3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: peritoneal macrophages were collected from E-selectin+/+ and E-selectin-/- mouse infected with Listeria Monocytogenes in vivo on day3

extract_protocol: Total RNA of mouse PM was extracted with Trizol  according to the manufacturer's instructions.

treatment_protocol: the collected peritoneal macrophages were washed by PBS and centrifuged at 4 degree, and then the cells was put into 1.0ml Trizol (Sigmma)

value: Peritoneal macrophages

value: E-selectin+/+


title: Indomethacin 2


title: WT peritoneal macrophage

city: Los Angeles

first: Tamer

last: Sallam

state: CA

address: 675 Charles E Young

institute: UCLA

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: standard Agilent protocol

source_name: macrophages

label_protocol: standard Agilent protocol

growth_protocol: DMEM with 10% FBS and 1%P/S

extract_protocol: Trizol and column purification

value: bl6 mice


title: MeXis null peritoneal macrophage


title: Tom+/Pecam1+ Cells, biological repeat3

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: Gene expression data of Tomato +/Pecam1+ population collected by FACS

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Affymetrix Titan scanner

data_processing: RMA summarization via Partek Genomics 6.6 (St Louis, MO USA) in two series: MEH 45-56   and  MEH101-120 which was batch corrected within this series CD31 series.  Provided data is a merged file of the two processing steps.

source_name: mouse tumor

label_protocol: cDNA was prepared using NuGen ovation pico v2 assay according to manufacturer's instructions

growth_protocol: not applicable

extract_protocol: Rneasy  microkit extraction of total RNA according to manufacturer's instructions including DNAse I treatment

treatment_protocol: tissues were digested by collagenase B/Dispase II for 1 hour prior to isolation by Flow Cytometry

tag: tissue type

value: tumor


title: Tom+/Pecam1- Cells, biological repeat2

description: Gene expression data of Tomato +/Pecam1- population collected by FACS


title: Tom+/Pecam1+ Cells, biological repeat4


title: Control_Rat_Liver _1

description:
Gene expression in controls age matched rat livers
Control_1.1

source_name: Control_Rat_Liver _1


title: Tom+/Pecam1- Cells, biological repeat3


title: Tom+/Pecam1+ Cells, biological repeat2


title: Tom-/Pecam1- Cells, biological repeat4

description: Gene expression data of Tomato -/Pecam1- population collected by FACS


title: Tom+/Pecam1- Cells, biological repeat4


title: E-selectinKO PM

source_name: Peritoneal macrophages from E-selectin-/- mouse infected with Listeria Monocytogenes in vivo on day3

value: E-selectin-/-


title: Tom-/Pecam1- Cells, biological repeat3


title: Tom-/Pecam1- Cells, biological repeat2


title: Tom+/Pecam1+ Cells, biological repeat1


title: Tom+/Pecam1- Cells, biological repeat1


title: Tom-/Pecam1- Cells, biological repeat1


title: Isolated Tom + Cells, biological repeat 2

description: Gene expression data of Tomato + population collected by FACS

source_name: normal muscle

value: sternocleidomastoid muscle


title: Isolated Tom - Cells, biological repeat 3

description: Gene expression data of Tomato - population collected by FACS


title: ser_sal_ub_210

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

description:
mRNA
processed data file: sert_trap_processed.csv

data_processing:
Library strategy: TRAP-seq
Reads were mapped to the mm10 mouse genome using STAR v 2.4.1c with default settings.
Reads per gene was computed using rpkmforgenes.py with default settings and NCBI RefSeq annotation with addition of the mCherry cDNA sequence.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: sert_trap_processed.csv: Comma-separated text file containing mapped reads per gene for 16 libraries.

source_name: Adult hindbrain

extract_protocol:
TRAP-seq. Midbrains of Tamoxifen-treated SERT-cre-Rpl10a-mCherry mice subjected to saline or methamphetamine administration were dissected in ice cold PBS and snap frozen on dry ice for later use. Then translating ribosomes from mDA were captured from the tissue as previously described. Briefly, frozen tissue was thawed in a pre-chilled 1 mL tissue homogenizer on ice and homogenized with 20 dounces in a lysis buffer containing 20 mM HEPES KOH (pH 7.3), 150 mM KCl, 10 mM MgCl2, 1% (vol/vol) NP-40. EDTA-free complete proteinase inhibitor cocktail (Roche, 011873580001), 0.5 mM DTT (Invitrogen, P2325), 100 ug/mL cycloheximide (Sigma, C4859) and 10 uL/mL rRNasin Ribonuclease Inhibitor (Promega, N2511) and Superase-In (Applied Biosystems, AM2694) was added before use. A post-nuclear supernatant was obtained by centrifugation at 4°C for 10 min at 2,000 g and mixed with NP-40 to a final concentration of 1% and incubated for 5 min with DHPC (1,2-diheptanoyl-sn-glycero-3-phosphocholine) (Avanti Polar Lipids, 850306P) to final concentration of 30 mM. Then, a post-mitochondrial supernatant was prepared by centrifugation at 4 °C for 10 min at 20,000 g and subsequently incubated with pre-washed anti-RFP Magnetic Beads (MBL, M165-9) at 4 °C for 18 h on a rotator. After incubation, the beads were collected with a magnet and washed 4x in a buffer containing the same components as the lysis buffer but with the KCl concentration increased to 350 mM and without the addition of RNase inhibitors. To elute immunoprecipitated RNA, the washed beads were incubated with buffer RLT from a Qiagen RNeasy kit (Qiagen, 74004), supplemented with beta-mercaptoethanol and purified on an RNeasy Micro column from the same kit. RNA quality was assessed on a 2100 Bioanalyzer using a RNA 6000 Pico kit (Agilent 5067-1513). Sequencing libraries were generated using the smart-seq2 protocol in a similar way as for bulk RNA-seq described earlier and sequenced to 50 bp single-end reads on a Illumina HiSeq2500 sequencer. Mapping of reads and differential gene expression analysis was performed as for bulk RNA-seq, except that no lfcThreshold cutoff was used in DESeq2.
Smart-seq2

treatment_protocol: Mice were injected intraperitoneally in a volume of 10 ml per kilogram of body weight with either saline or 30 mg/kg (+)-Methamphetamine hydrochloride (Sigma, M8750) dissolved in saline, and were sacrificed by CO2 2h after injections.

value: SER

tag: mouse-id

tag: fraction

value: Unbound

value: saline treated


title: ser_sal_ub_211

tag: treatment


title: Isolated Tom + Cells, biological repeat 3


title: Isolated Tom + Cells, biological repeat 1


title: Isolated Tom - Cells, biological repeat 1


title: Rh18

description:
MEH014
Gene expression data from Human RMS cell line.

source_name: Human Rh18 cells

tag: cell line

value: FN-RMS cell line


title: ME2_1h_-As_rep.3

city: Hanover

first: Thomas

middle: H.

last: Hampton

state: NH

address: Dewey Field Road, HB 7550

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

description:
G3
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 1h that were not exposed to arsenic, replicate 3

hyb_protocol: Labelled samples were randomly hybridized using the Hybridization Kit (Roche NimbleGen) to a custom NimbleGen array whose design and annotation has been previously described (Shaw et al. 2014). Briefly, this platform interrogates 135,000 probes that map to 34,713 gene models and 16,104 unique Fundulus heteroclitus genes from a high-quality killifish reference genome (Reid et al., 2017)

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. Raw data were extracted using NimbleScan v2.4 software (Roche NimbleGen)

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Fundulus heteroclitus

source_name: ME2 SFW 1h

label_protocol: RNA was amplified using MessageAmp II kits (Ambion) and aRNA labeled using a single channel design with Cy3 dye using NimbleGen Labeling Kit (Roche NimbleGen)

growth_protocol:
Fish were pre-acclimated to common garden conditions, housed, maintained, and exposed to arsenic as  described in Shaw, J. R., Hampton, T. H., et al. (2014). Natural selection canalizes expression variation of environmentally induced plasticity-enabling genes. Molecular Biology and Evolution, 31(11), 3002–3015.
72 killifish were acclimated to seawater for two weeks. Of these, 36 fish (12 from each of the three populations) were exposed to freshwater for  0 h, 1 h, or 24 h, and an additional 36 fish were exposed to the same time course in the presence of 100 micrograms per liter of arsenic.

extract_protocol: RNAeasy kits were used for RNA extraction (Qiagen, Valencia, CA). Tissue samples were removed from RNA-later and rinsed before being homogenized using a Tissue-Tearor (Biospec Products, Barlesville, OK). The homogenized tissue was then processed using RNeasy kits with DNase treatment (Qiagen, Valencia, CA) to extract RNA. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

tag: population

tag: arsenic exposure

tag: hours exposed to fresh water

tag: tissue

value: gill

tag: slide number


title: control_LSK_RNA-seq replicate 2

city: Durham

first: Greg

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

data_processing:
Sequencing data were trimmed for Illumina adapter sequences using a custom script (UNC’s HTSF/Genomics core) and mapped to the mouse reference genome (GRCm38) using the HISAT2 with default parameters (Kim et al., 2015).
Gene expression levels were quantified with featureCounts (Liao et al., 2014) using default parameters that discarded multi-mapping reads.
Raw gene counts were normalized and differential expression was calculated using DESeq2 with “betaPrior” turned on (Love et al., 2014).
Genome_build: GRCm38/mm10

source_name: LSK cells sorted from control mice

extract_protocol:
Total bone marrow cells were isolated from long bones (femur and tibia; 5 mice per experimental replicate) following by treatment with the ACK lysis buffer (0.15 M NH4Cl, 10 mM KHCO3, 0.1 mM EDTA [pH 7.2]) to remove red blood cells. An sorting of FACS-based analysis of lineage-/Sca1+/c-Kit+ (LSK) cells was carried out using a FACSAria II machine (UNC flow core) using the already defined protocol.
Total RNA was extracted from the sorted LSK cell population by using the picoRNA Kit (Applied Biosystems). RNA-seq libraries were prepared with Illumina kits according to manufacturer’s manuals.

tag: cell type

value: LSK cells

value: bone marrow

value: ~3 month old

value: control


title: Bptf-cKO_LSK_RNA-seq replicate 2

source_name: LSK cells sorted from bptf_cKO mice

value: Bptf -/-


title: ME2_0h_+As_rep.4

description:
H12
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish not exposed to freshwater that were exposed to 100ug/l arsenic, replicate 4

source_name: ME2 SW As


title: ME2_1h_-As_rep.4

description:
G4
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 1h that were not exposed to arsenic, replicate 4


title: Isolated Tom - Cells, biological repeat 2


title: ME2_24h_-As_rep.4

description:
G8
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 24h that were not exposed to arsenic, replicate 4

source_name: ME2 SFW 24h


title: ME2_24h_-As_rep.3

description:
G7
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 24h that were not exposed to arsenic, replicate 3


title: ser_sal_ub_208


title: ser_sal_trap_211

value: TRAP


title: ME2_0h_-As_rep.3

description:
H7
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish not exposed to freshwater that were not exposed to arsenic, replicate 3

source_name: ME2 SW


title: ser_sal_trap_209


title: ser_sal_trap_210


title: ME2_24h_+As_rep.3

description:
H3
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 24h that were exposed to 100ug/l arsenic, replicate 3

source_name: ME2 SFW As 24h


title: ME2_24h_+As_rep.4

description:
H4
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 24h that were exposed to 100ug/l arsenic, replicate 4


title: ME2_1h_+As_rep.4

description:
G12
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 1h that were exposed to 100ug/l arsenic, replicate 4

source_name: ME2 SFW As 1h


title: ME2_1h_+As_rep.3

description:
G11
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 1h that were exposed to 100ug/l arsenic, replicate 3


title: ser_sal_ub_209


title: ser_meth_ub_206

value: methamphetamine treated


title: ME2_0h_-As_rep.4

description:
H8
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish not exposed to freshwater that were not exposed to arsenic, replicate 4


title: ME2_1h_+As_rep.2

description:
G10
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 1h that were exposed to 100ug/l arsenic, replicate 2


title: ser_sal_trap_208


title: ser_meth_ub_204


title: ser_meth_ub_205


title: ME2_24h_-As_rep.2

description:
G6
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 24h that were not exposed to arsenic, replicate 2


title: ser_meth_ub_196


title: ME2_0h_+As_rep.3

description:
H11
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish not exposed to freshwater that were exposed to 100ug/l arsenic, replicate 3


title: ME2_1h_-As_rep.2

description:
G2
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 1h that were not exposed to arsenic, replicate 2


title: ME2_24h_+As_rep.2

description:
H2
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 24h that were exposed to 100ug/l arsenic, replicate 2


title: ser_meth_trap_204

description:
mRNA
processed data file: sert_trap_processed.csv


title: ser_meth_trap_205


title: ser_meth_trap_206


title: ME2_1h_-As_rep.1

description:
G1
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 1h that were not exposed to arsenic, replicate 1


title: ME2_0h_-As_rep.2

description:
H6
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish not exposed to freshwater that were not exposed to arsenic, replicate 2


title: mDA_sal_trap_270

description:
mRNA
processed data file: mDA_meth_trap_processed.csv

data_processing:
Library strategy: TRAP-seq
Reads were mapped to the mm10 mouse genome using STAR v 2.4.1c with default settings.
Reads per gene was computed using rpkmforgenes.py with default settings and NCBI RefSeq annotation with addition of the mCherry cDNA sequence.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: mDA_meth_trap_processed.csv: Comma-separated text file containing mapped reads per gene for 16 libraries.

source_name: Adult midbrain

extract_protocol:
TRAP-seq. Midbrains of Tamoxifen-treated DatCreERT2-Rpl10a-mCherry mice subjected to saline or methamphetamine administration were dissected in ice cold PBS and snap frozen on dry ice for later use. Then translating ribosomes from mDA were captured from the tissue as previously described. Briefly, frozen tissue was thawed in a pre-chilled 1 mL tissue homogenizer on ice and homogenized with 20 dounces in a lysis buffer containing 20 mM HEPES KOH (pH 7.3), 150 mM KCl, 10 mM MgCl2, 1% (vol/vol) NP-40. EDTA-free complete proteinase inhibitor cocktail (Roche, 011873580001), 0.5 mM DTT (Invitrogen, P2325), 100 ug/mL cycloheximide (Sigma, C4859) and 10 uL/mL rRNasin Ribonuclease Inhibitor (Promega, N2511) and Superase-In (Applied Biosystems, AM2694) was added before use. A post-nuclear supernatant was obtained by centrifugation at 4°C for 10 min at 2,000 g and mixed with NP-40 to a final concentration of 1% and incubated for 5 min with DHPC (1,2-diheptanoyl-sn-glycero-3-phosphocholine) (Avanti Polar Lipids, 850306P) to final concentration of 30 mM. Then, a post-mitochondrial supernatant was prepared by centrifugation at 4 °C for 10 min at 20,000 g and subsequently incubated with pre-washed anti-RFP Magnetic Beads (MBL, M165-9) at 4 °C for 18 h on a rotator. After incubation, the beads were collected with a magnet and washed 4x in a buffer containing the same components as the lysis buffer but with the KCl concentration increased to 350 mM and without the addition of RNase inhibitors. To elute immunoprecipitated RNA, the washed beads were incubated with buffer RLT from a Qiagen RNeasy kit (Qiagen, 74004), supplemented with beta-mercaptoethanol and purified on an RNeasy Micro column from the same kit. RNA quality was assessed on a 2100 Bioanalyzer using a RNA 6000 Pico kit (Agilent 5067-1513). Sequencing libraries were generated using the smart-seq2 protocol in a similar way as for bulk RNA-seq described earlier and sequenced to 50 bp single-end reads on a Illumina HiSeq2500 sequencer. Mapping of reads and differential gene expression analysis was performed as for bulk RNA-seq, except that no lfcThreshold cutoff was used in DESeq2.
Smart-seq2

value: mDA


title: ME2_24h_-As_rep.1

description:
G5
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 24h that were not exposed to arsenic, replicate 1


title: ME2_0h_+As_rep.2

description:
H10
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish not exposed to freshwater that were exposed to 100ug/l arsenic, replicate 2


title: ME2_0h_+As_rep.1

description:
H9
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish not exposed to freshwater that were exposed to 100ug/l arsenic, replicate 1


title: mDA_sal_ub_214


title: ME2_0h_-As_rep.1

description:
H5
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish not exposed to freshwater that were not exposed to arsenic, replicate 1


title: mDA_sal_ub_270


title: mDA_sal_trap_214


title: mDA_sal_ub_197


title: ser_meth_trap_196


title: mDA_sal_ub_213


title: ME2_1h_+As_rep.1

description:
G9
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 1h that were exposed to 100ug/l arsenic, replicate 1


title: VA_0h_+As_rep.4

description:
A8_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish not exposed to freshwater that were exposed to 100ug/l arsenic, replicate 4

source_name: VA SW As

value: VA


title: VA_1h_-As_rep.4

description:
A12_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 1h that were not exposed to arsenic, replicate 4

source_name: VA SFW 1h


title: ME2_24h_+As_rep.1

description:
H1
This sample is of gill tissue from saltwater acclimated Horseshoe Cove killifish exposed to freshwater for 24h that were exposed to 100ug/l arsenic, replicate 1


title: mDA_sal_trap_213


title: mDA_meth_ub_269


title: mDA_meth_ub_195


title: mDA_meth_trap_269


title: mDA_sal_trap_197


title: VA_0h_-As_rep.4

description:
A4_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish not exposed to freshwater that were not exposed to arsenic, replicate 4

source_name: VA SW


title: VA_1h_+As_rep.4

description:
B4_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 1h that were exposed to 100ug/l arsenic, replicate 4

source_name: VA SFW As 1h


title: mDA_meth_trap_195


title: mDA_meth_ub_192


title: VA_24h_+As_rep.4

description:
B12_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 24h that were exposed to 100ug/l arsenic, replicate 4

source_name: VA SFW As 24h


title: ME1_0h_+As_rep.4

description:
C8_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish not exposed to freshwater that were exposed to 100ug/l arsenic, replicate 4

source_name: ME1 SW As


title: ME1_24h_+As_rep.4

description:
D12_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 24h that were exposed to 100ug/l arsenic, replicate 4

source_name: ME1 SFW As 24h


title: ME1_0h_-As_rep.4

description:
C4_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish not exposed to freshwater that were not exposed to arsenic, replicate 4

source_name: ME1 SW


title: mDA_meth_trap_192


title: mDA_meth_ub_186


title: mDA_meth_trap_186


title: mDA_6ohda_ub_268R

description:
mRNA
processed data file: 6ohda_trap_processed.csv

data_processing:
Library strategy: TRAP-seq
Reads were mapped to the mm10 mouse genome using STAR v 2.4.1c with default settings.
Reads per gene was computed using rpkmforgenes.py with default settings and NCBI RefSeq annotation with addition of the mCherry cDNA sequence.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: 6ohda_trap_processed.csv: Comma-separated text file containing mapped reads per gene for 20 libraries.

extract_protocol:
TRAP-seq. Midbrains of Tamoxifen-treated DatCreERT2-Rpl10a-mCherry mice subjected to unilateral 6-OHDA lesions were dissected in ice cold PBS and snap frozen on dry ice for later use. Then translating ribosomes from mDA were captured from the tissue as previously described. Briefly, frozen tissue was thawed in a pre-chilled 1 mL tissue homogenizer on ice and homogenized with 20 dounces in a lysis buffer containing 20 mM HEPES KOH (pH 7.3), 150 mM KCl, 10 mM MgCl2, 1% (vol/vol) NP-40. EDTA-free complete proteinase inhibitor cocktail (Roche, 011873580001), 0.5 mM DTT (Invitrogen, P2325), 100 ug/mL cycloheximide (Sigma, C4859) and 10 uL/mL rRNasin Ribonuclease Inhibitor (Promega, N2511) and Superase-In (Applied Biosystems, AM2694) was added before use. A post-nuclear supernatant was obtained by centrifugation at 4°C for 10 min at 2,000 g and mixed with NP-40 to a final concentration of 1% and incubated for 5 min with DHPC (1,2-diheptanoyl-sn-glycero-3-phosphocholine) (Avanti Polar Lipids, 850306P) to final concentration of 30 mM. Then, a post-mitochondrial supernatant was prepared by centrifugation at 4 °C for 10 min at 20,000 g and subsequently incubated with pre-washed anti-RFP Magnetic Beads (MBL, M165-9) at 4 °C for 18 h on a rotator. After incubation, the beads were collected with a magnet and washed 4x in a buffer containing the same components as the lysis buffer but with the KCl concentration increased to 350 mM and without the addition of RNase inhibitors. To elute immunoprecipitated RNA, the washed beads were incubated with buffer RLT from a Qiagen RNeasy kit (Qiagen, 74004), supplemented with beta-mercaptoethanol and purified on an RNeasy Micro column from the same kit. RNA quality was assessed on a 2100 Bioanalyzer using a RNA 6000 Pico kit (Agilent 5067-1513). Sequencing libraries were generated using the smart-seq2 protocol in a similar way as for bulk RNA-seq described earlier and sequenced to 50 bp single-end reads on a Illumina HiSeq2500 sequencer. Mapping of reads and differential gene expression analysis was performed as for bulk RNA-seq, except that no lfcThreshold cutoff was used in DESeq2.
Smart-seq2

treatment_protocol: Mice were anesthetized in a separate cage with air supplemented with 4 mg/mL isoflurane and mounted in a stereotaxic frame (David Kopf Instruments, Tujunga, CA) equipped with a mouse adaptor. Mice were kept anesthetized throughout the procedure by inhalational administration of 2 mg/mL isoflurane. 6-OHDA-HCl (Sigma-Aldrich Sweden AB) was dissolved in 0.02% ascorbic acid in saline at a concentration of 3 µg of free-base 6-OHDA per microliter. Each mouse received one unilateral (right hemisphere) injection of 6-OHDA of 1 µl (0.5 µl/min) into the medial forebrain bundle according to the following coordinates (mm): anteroposterior (AP), −1.2; mediolateral (ML), −1.2; dorsoventral (DV), −4.8 (all millimeters relative to bregma). Animals were sacrificed two weeks post surgery by CO2.

value: 6-OHDA lesioned hemisphere


title: ME1_24h_-As_rep.4

description:
D8_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 24h that were not exposed to arsenic, replicate 4

source_name: ME1 SFW 24h


title: VA_24h_-As_rep.4

description:
B8_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 24h that were not exposed to arsenic, replicate 4

source_name: VA SFW 24h


title: mDA_6ohda_trap_259R


title: mDA_6ohda_trap_268R


title: mDA_6ohda_ub_259R


title: ME1_1h_-As_rep.4

description:
C12_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 1h that were not exposed to arsenic, replicate 4

source_name: ME1 SFW 1h


title: mDA_6ohda_trap_258R


title: VA_24h_-As_rep.3

description:
B7_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 24h that were not exposed to arsenic, replicate 3


title: ME1_24h_+As_rep.3

description:
D11_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 24h that were exposed to 100ug/l arsenic, replicate 3


title: ME1_1h_+As_rep.4

description:
D4_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 1h that were exposed to 100ug/l arsenic, replicate 4

source_name: ME1 SFW As 1h


title: mDA_6ohda_ub_219R


title: mDA_6ohda_ub_258R


title: ME1_1h_+As_rep.3

description:
D3_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 1h that were exposed to 100ug/l arsenic, replicate 3


title: VA_0h_-As_rep.3

description:
A3_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish not exposed to freshwater that were not exposed to arsenic, replicate 3


title: VA_0h_+As_rep.3

description:
A7_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish not exposed to freshwater that were exposed to 100ug/l arsenic, replicate 3


title: ME1_1h_-As_rep.3

description:
C11_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 1h that were not exposed to arsenic, replicate 3


title: mDA_6ohda_ub_257R


title: mDA_6ohda_ub_268L

value: control hemisphere


title: mDA_6ohda_trap_268L


title: ME1_24h_-As_rep.3

description:
D7_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 24h that were not exposed to arsenic, replicate 3


title: VA_0h_+As_rep.1

description:
A5_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish not exposed to freshwater that were exposed to 100ug/l arsenic, replicate 1


title: ME1_24h_+As_rep.1

description:
D9_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 24h that were exposed to 100ug/l arsenic, replicate 1


title: mDA_6ohda_trap_259L


title: ME1_0h_+As_rep.3

description:
C7_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish not exposed to freshwater that were exposed to 100ug/l arsenic, replicate 3


title: ME1_0h_-As_rep.3

description:
C3_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish not exposed to freshwater that were not exposed to arsenic, replicate 3


title: mDA_6ohda_ub_259L


title: mDA_6ohda_trap_258L


title: VA_24h_+As_rep.1

description:
B9_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 24h that were exposed to 100ug/l arsenic, replicate 1


title: VA_24h_+As_rep.3

description:
B11_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 24h that were exposed to 100ug/l arsenic, replicate 3


title: VA_1h_+As_rep.3

description:
B3_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 1h that were exposed to 100ug/l arsenic, replicate 3


title: mDA_6ohda_trap_219R

description:
mRNA
processed data file: 6ohda_trap_processed.csv


title: VA_1h_-As_rep.3

description:
A11_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 1h that were not exposed to arsenic, replicate 3


title: mDA_6ohda_ub_258L


title: mDA_6ohda_ub_257L


title: mDA_6ohda_trap_257R


title: mDA_6ohda_trap_257L


title: mDA_6ohda_ub_219L


title: mDA_6ohda_trap_219L


title: ME1_0h_-As_rep.1

description:
C1_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish not exposed to freshwater that were not exposed to arsenic, replicate 1


title: VA_1h_+As_rep.1

description:
B1_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 1h that were exposed to 100ug/l arsenic, replicate 1


title: VA_0h_-As_rep.1

description:
A1_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish not exposed to freshwater that were not exposed to arsenic, replicate 1


title: VA_24h_-As_rep.1

description:
B5_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 24h that were not exposed to arsenic, replicate 1


title: VA_1h_-As_rep.1

description:
A9_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 1h that were not exposed to arsenic, replicate 1


title: ME1_0h_+As_rep.1

description:
C5_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish not exposed to freshwater that were exposed to 100ug/l arsenic, replicate 1


title: ME1_1h_+As_rep.2

description:
D2_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 1h that were exposed to 100ug/l arsenic, replicate 2


title: ME1_1h_-As_rep.1

description:
C9_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 1h that were not exposed to arsenic, replicate 1


title: Test

city: Zunyi

first: Tao

last: Ding

state: Guizhou Province

address: Xuefu Road, Honghuagang District

institute: Zunyi medical college

description: tumor tissue from xenograft model treated with the 100μg plasmid of p-miR-21-ASOs was given locally by direct injection into the tumor tissues of nude mice at four times every three days.

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

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

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

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

treatment_protocol: Athymic nude mice (BALB/C, 4-6 weeks old, female) were purchased from the Shanghai Laboratory Animal Research Center (Shanghai, China). Animals were in line with the   Guidelines for the Care and Use of Laboratory Animals (Ministry of Health, People’s Republic of China, 1998), and all the experimental procedures were approved by the ethical guidelines of Shanghai Medical Laboratory Animal Care and Use Committee (permit number: 2013018). For preparation of subcutaneous xenograft model, cells were subcutaneously implanted into the right flanks of nude mice at 3.5×10e6 SW620 cells density (n=20). Then 7 days after tumor cells inoculation with confirmation of successful maturation of tumors, 20 mice were divided randomly into two groups (10 mice per group). The 100μg plasmid of p-miR-21-ASOs or p-Cont was given locally by direct injection into the tumor tissues of nude mice at four times every three days.

value: tumor tissue from xenograft model

tag: treatement


title: Control

description: tumor tissue from xenograft model treated with the 100μg plasmid of p-Cont was given locally by direct injection into the tumor tissues of nude mice at four times every three days.

source_name: p-Cont

value: p-Cont


title: ME1_24h_-As_rep.1

description:
D5_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 24h that were not exposed to arsenic, replicate 1


title: VA_0h_-As_rep.2

description:
A2_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish not exposed to freshwater that were not exposed to arsenic, replicate 2


title: VA_1h_-As_rep.2

description:
A10_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 1h that were not exposed to arsenic, replicate 2