title: 256449110010_b4 - 16_D20_F2 vs 14_D15_F2

hyb_protocol: 14_D15_F2 Cy5 / 16_D20_F2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 14_D15_F2:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: 16_D20_F2:100mg. (Qiagen_RNeasy.pdf)


title: Donor2_control

status: Public on Sep 12 2018

type: RNA

city: Isehara

first: Tomoko

last: Nakai

state: Kanagawa

department: Orthopaedic Surgery, Surgical Science

country: Japan

institute: Tokai University School of Medicine

hyb_protocol: Hybridized on a SurePrint G3 Human GE 860K v2 Microarray (Agilent Technology) using a Gene Expression Hybridization Kit (Agilent Technology).

scan_protocol: Analyzed using an Agilent DNA Microarray Scanner (G2600D SG13164306) with the AgilentG3_HiSen_GX_1Color protocol (Agilent Technology).

data_processing:
Probe level data were converted to expression values using the Agilent Feature Extraction 11.5.1.1 (Agilent Technology).
Gene Spring ver.13 (Agilent Technology) was used for 75-percentile normalization, detection of genes with an average two-fold or higher change in expression, and for graphing.

molecule: total RNA

organism: Homo sapiens

source_name: cultured 1week,control,replicate 2

label_protocol: Cy3-labeled cRNA was prepared from 100ng RNA using a Low Input Quick Amp Labeling Kit (Agilent Technology, Santa Clara CA).

growth_protocol: Nucleus pulposus (NP) cells were enzymatically isolated from lumber IVD herniation that were harvested from four donor patients. Cells were cultured in alpha MEM supplemented with 10% fetal bovine serum.

extract_protocol: RNA was prepared using SV Total RNA Isolation System (Promega, Madison, WI)  following the manufacturer's recommendations. The protocol includes an on-column DNase digestion.

treatment_protocol: The biological activity of NTP was expressed in NTP Units (NU).The cells were treated with 1.0 mNU/ml NTP with 0.17 mM ascorbic acid 2 phosphate every second day.

tag: treatment

value: control


title: Donor3_treatment

source_name: cultured 1week,NTP,replicate 3

value: NTP


title: Donor2_treatment

source_name: cultured 1week,NTP,replicate 2


title: 256449110010_b3 - 14_D15_F2 vs 16_D20_F2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Delineation of the metabolic pathways involved in maize endosperm vitreousness.

hyb_protocol: 16_D20_F2 Cy5 / 14_D15_F2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Zea mays

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: seed - outdoor

treatment_protocol: no treatment

tag: days after pollination

tag: tissue

value: floury endosperm

tag: line

value: dent maize

tag: harvest date


title: 256449110010_b1 - 6_D15_F1 vs 8_D20_F1

hyb_protocol: 8_D20_F1 Cy5 / 6_D15_F1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 8_D20_F1:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: 6_D15_F1:100mg. (Qiagen_RNeasy.pdf)


title: Donor1_treatment

source_name: cultured 1week,NTP,replicate 1


title: Donor1_control

source_name: cultured 1week,control,replicate 1


title: 256449110009_b1 - 5_D15_V1 vs 7_D20_V1

hyb_protocol: 7_D20_V1 Cy5 / 5_D15_V1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 7_D20_V1:100mg. (Qiagen_RNeasy.pdf)

value: vitreous endosperm

extract_protocol: 5_D15_V1:100mg. (Qiagen_RNeasy.pdf)


title: WT_a-_ChIP3

type: SRA

city: New York

first: Hajime

last: Murakami

state: NY

address: 1275 york ave

department: Molecular Biology

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
source of  scaled coverage
Mer2_ChIP_scaled.txt
Mer2_ChIP.txt

library_source: genomic

data_processing:
Base calls perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Reads trimmed with cutadapt
Mapped with BWA MEM
Sort by Queryname with PICARD
Compute coverage using a custom script of bedtools and custom python code
Coverage maps were scaled by qPCR as described (Murakami and Keeney 2014)
Genome_build: Reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary_files_format_and_content: (scaled Mer2 ChIP coverage map: Me2_ChIP_scaled.txt) tab delimited text files include each scaled ChIP efficiency (ChIP/input) for the each time point at each nucleotide position in the genome
Supplementary_files_format_and_content: (Me2 ChIP coverage map: Mer2_ChIP.txt) tab delimited text files include ChIP coverage for the each time point at each nucleotide position in the genome
Supplementary_files_format_and_content: (Me2 input coverage map: Mer2_input.txt) tab delimited text files include input coverage for the each time point at each nucleotide position in the genome

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: meiotic culture

growth_protocol: Synchronized meiotic cultures were prepared in 2% potassium acetate at 30°C by the SPS pre-growth method as described in Murakami et al. (2009) Methods Mol Biol 557: 117-142.

extract_protocol: ChIP was performed as described (Aparicio et al., 2004; Mendoza et al., 2009; Metivier et al., 2003; Panizza et al., 2011) with modifications. Mer2-Myc diploids were sporulated and 50 mL of meiotic culture (2 x 10^9 cells) was collected at different times and crosslinked with 1% formaldehyde for 30 min at room temperature. Crosslinking was terminated by 5 min incubation with 131 mM glycine. Cells were washed twice with ice-cold TBS, flash frozen with liquid nitrogen and stored at -80°C. Cells were suspended in 1 mL of Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1 mM PMSF, 7 μg/mL aprotinin, 1% protease inhibitor cocktail (Sigma), 1x Complete Protease Inhibitor Cocktail (Roche)) with ca. 900 μL of 0.5 mm zirconia/silica beads (BioSpec Products) in 2 mL screw-cap tubes. Cells were disrupted by vigorous shaking at 6.5 m/s for 1 min x 10 times in FastPrep24 (MP Biomedicals). 1 mL of Lysis buffer was added after cell disruption. Subsequently, chromatin in the whole cell extracts (WCE) was sheared by sonication with “M” intensity, 30 sec ON/ 30 sec OFF for 15 min x 3 times in Bioruptor Sonication System UCD200 (Diagenode) in 15 mL polystyrene conical tubes. Insoluble fraction (cell debris) was removed by centrifugation at 21,130 g, 5 min, 4°C. WCE was further sonicated with the same conditions 3–5 times to yield average DNA size less than 500 bp. WCE was flash frozen and stored at -80°C.

tag: developmental stage

value: meiotic prophase

tag: genotype

value: MER2-Myc ars_delta

tag: time in meiosis

value: time =1 hr  in meiosis

tag: chip antibody

value: anti-Myc antibody (9E10); BioXcell (catalog number:BE0238)


title: WGC022997_mRNA

city: Shenzhen

first: Yan

last: Zhang

state: Guangdong

address: No.3688，Nanhai Avenue

department: College of Life Sciences and Oceanography

country: China

institute: Shenzhen University

library_source: transcriptomic

data_processing:
The original reads were mapped to human genome (hg19, UCSC) using TopHat2 tool (version 2.0.
The raw counts of genes were obtained using htseq-count package (version 0.6.1) in Python (version 2.7) with default settings
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Normal

extract_protocol:
Fresh samples were collected after the surgery, frozen in RNAlater solution (Invitrogen, Carlsbad, CA) immediately, and then stored at -80°C. Total RNA was extracted with Trizol reagent (Invitrogen, Carlsbad, CA). The Illumina TruSeq Small RNA Sample Preparation protocol was used to prepare small RNA library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: normal pancreas

tag: subject id

tag: patient diagnosis

value: pancreatic cancer


title: 256449110008_b4 - 12_C20_F2 vs 10_C15_F2

hyb_protocol: 10_C15_F2 Cy5 / 12_C20_F2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 10_C15_F2:100mg. (Qiagen_RNeasy.pdf)

value: flint maize

extract_protocol: 12_C20_F2:100mg. (Qiagen_RNeasy.pdf)


title: WT_a-_ChIP2

value: time = 0.5 hr  in meiosis


title: 256449110009_b2 - 7_D20_V1 vs 5_D15_V1

hyb_protocol: 5_D15_V1 Cy5 / 7_D20_V1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: WT_a-_ChIP1

value: time = 0 hr  in meiosis


title: 256449110008_b2 - 4_C20_F1 vs 2_C15_F1

hyb_protocol: 2_C15_F1 Cy5 / 4_C20_F1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 2_C15_F1:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: 4_C20_F1:100mg. (Qiagen_RNeasy.pdf)


title: 256449110009_b3 - 13_D15_V2 vs 15_D20_V2

hyb_protocol: 15_D20_V2 Cy5 / 13_D15_V2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 15_D20_V2:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: 13_D15_V2:100mg. (Qiagen_RNeasy.pdf)


title: H3K9me2_ccp1Depe1D_2

city: Hangzhou

first: Min

last: Lu

state: Zhejiang

address: Yuhangtang road 866

institute: Zhejiang University, Life Sciences Institute

data_processing:
Quality control performed using FASTX-Toolkit.
ChIP-seq reads were trimmed to ensure uniformity using FASTX-Toolkit.
ChIP-seq reads were aligned to the S. pombe genome assembly ASM294v.2.22 using Burrows-Wheeler Aligner (BWA)’s default parameters, which randomly assigned the ChIP-seq reads to the repetitive DNA sequences.
Model-based Analysis of ChIP-seq (MACS) was used for peak calling. Briefly, the mapped reads were filtered to keep one tag at the same location (--keep-dup) and were normalized by "macs2 randsample". The mapped reads were extended to the size of 146 bp to define the nucleosome positions (--shift 73 --extsize 146). Others were set as the default parameters.
Genome_build: S. pombe genome ASM294v.2.22
Supplementary_files_format_and_content: bdg files were generated using MACS2.

organism: Schizosaccharomyces pombe

source_name: fission yeast haploid cells

growth_protocol: Single colonies of each strains were struck and cultured in YES medium at 29 °C. The cell cultures were harvested when the optical density (OD) reached aound 1.

extract_protocol:
Cells were digested with Zymolase and lysed, the chromatin lysates were treated with micrococcal nuclease to digest chromatin into mononucleosomes. The histone-DNA complexes were isolated with antibody.
Libraries of DNA were prepared using KAPA library preparation kit following the accompanied instructions.

tag: cell growth stage

value: log phase

tag: temperature condition

value: 29 degrees C

value: H3K9me2 (Abcam 1220)


title: H3K9me2_brl1D_1


title: 256449110008_b1 - 2_C15_F1 vs 4_C20_F1

hyb_protocol: 4_C20_F1 Cy5 / 2_C15_F1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: H3K9me2_ccp1Depe1D_1


title: H3K9me2_h3.3D_1


title: Riboseq.recovery.lso2_1

city: New Haven

first: Yinuo

last: Wang

address: 333 Cedar St C129

department: Molecular Biophysics and Biochemistry

institute: Yale University

description:
lso2_1
Ribosome footprint profiling

data_processing:
Library strategy: Ribo-Seq
For eCLIP, adapters were trimmed using Cutadapt 1.11.
Trimmed reads were mapped using STAR 2.5.1b to a masked version of Sigma1278b MIT_2009_ACVY01000000 containing single copies of tRNA and rRNA genes on an artificial chromosome.
PCR duplicates were removed using a custom script (van Nostrand et al., 2016).
CLIPper 0.2.0 with default parameters was used to call peaks on IP samples. The fraction of reads within peaks was normalized to the fraction of reads in corresponding regions of the control samples (SMI and untagged) to identify IP-specific and reproducible clusters.
For high RNase samples, coverage vectors were calculated using fractional assignment of multi-mapping reads.
Mutation analysis of ribosomal RNA-mapping reads was performed as described in Sexton et al., 2017.
For ribosome profiling of recovery samples, FASTX-Toolkit 0.0.14 was used to collapse PCR duplicates.
Adapters and barcodes were trimmed using Cutadapt 1.9.1.
Trimmed reads were mapped using STAR 2.5.3 to a joint reference of GRCh38 (GENCODE release 20) and a masked version of Sigma1278b MIT_2009_ACVY01000000 containing single copies of tRNA and rRNA genes on an artificial chromosome.
Uniquely mapped yeast reads were used to determine read 5' ends and raw counts.
Yeast gene RPKMs were scaled using human gene RPKMs, which served as an internal standard in each library.
For ribosome profiling of replete and glucose-starved samples, adapters were trimmed using Cutadapt 1.10.
Trimmed reads were mapped using tophat2 2.0.8b to the Sigma1278b reference downloaded from Saccharomyces Genome Database on June 29, 2014.
Uniquely mapped reads were used to determine read 5′ ends and raw counts.Raw counts were transformed into RPKMs.
Genome_build: GRCh38, Sigma1278b MIT_2009_ACVY01000000, Sigma1278b from SGD on 6/29/2014.
Supplementary_files_format_and_content: fasta: Genome sequence of masked Sigma1278b MIT_2009_ACVY01000000 reference.   GFF3: Annotations of masked Sigma1278b MIT_2009_ACVY01000000 reference.   bed: eCLIP peaks called on IP samples using CLIPper 0.2.0. bedGraph: Read coverage (eCLIP) or read 5' ends (recovery ribosome profiling), no scaling to library size.   wig: Read 5′ ends per million reads (replete and glucose-starved ribosome profiling).  tab-delimited text: Yeast gene raw counts (all ribosome profiling); RPKMs (replete and glucose-starved ribosome profiling); and RPKMs rescaled to internal standard (recovery ribosome profiling).

source_name: Budding yeast cells

growth_protocol: Cells were grown for 96 hours to stationary phase, then shifted to rich medium for 30 minutes.

extract_protocol:
Cells were ground in lysis buffer (20 mM Tris-HCl pH 8.0, 140 mM KCl, 1.5 mM MgCl2, 1% Triton X-100, 0.1 mg/mL cycloheximide) using a cryogenic ball mill.
Lysate was digested with 15U/A260 RNase I. Footprinted HeLa lysate was doped in at a fixed fraction to ribosomal RNA per volume of yeast lysate. 80S footprints were isolated from a sucrose gradient, enriched for small RNAs, and size-selected from 15-34 nucleotides. A 3′ adapter was ligated and samples treated with RiboZero. The RNA was reverse transcribed, circularized, and PCR amplified.

treatment_protocol: Cells were collected by rapid filtration and freezing in the absence of translation inhibitors.

tag: background

value: Sigma1278b Strain F1950

value: MATa ura3 his3 leu2 trp1 lso2{delta}::kan

tag: antibody

tag: fraction

value: Ribosome-protected mRNA


title: Riboseq.recovery.lso2_2

description:
lso2_2
Ribosome footprint profiling


title: Riboseq.recovery.WT_2

description:
WT_2
Ribosome footprint profiling

value: MATa ura3 his3 leu2 trp1


title: iOL_IgG_ChIP-Seq

city: xiamen

first: Liu

last: Zhixiong

state: Fujian

address: Xiangan Nanlu 4221-120

department: School of Life Sciences

institute: Xiamen University

data_processing:
The image analysis and base calling were performed by using Illumina’s Genome Analysis pipeline.
The sequencing reads were aligned to the human genome UCSC build hg18 by using Bowtie2 alignment programs in two ways: only uniquely aligned reads were kept or both uniquely aligned reads and the sequencing reads that align to repetitive regions were kept for downstream analysis (if a read aligns to multiple genome locations, only one location is arbitrarily chosen).
The multiple reads were collapsed in order to reduce the PCR biases. The aligned reads were used for peak finding with HOMER
Peaks were identified by searching locations of high read density using a 200-bp sliding window. Regions of maximal density exceeding a given threshold were called as peaks, and we required adjacent peaks to be at least 500 bp away to avoid redundant detection
Peaks from separate experiments were considered equivalent/co-bound if their peak centers were located within 200 bp of each other. Read density heat maps were created by first using HOMER to generate read densities and then visualized using Java TreeView
Genome_build: Rat rn6

organism: Rattus norvegicus

source_name: oligodendrocyte

growth_protocol: OPCs were trypsinized and plated onto poly-D-lysine-coated plates. Cells were grown in DMEM/F-12 (GIBCO) with addition of 2% B-27 (GIBCO), 1% N2 (GIBCO), 20 ng/ml PDGF-AA (Peprotech, 100-13A), 10 ng/ml CNTF (Peprotech, 450-02), 20 ng/ml bFGF (Sino Biological, 10014-HNAE), and 1 ng/ml NT3 (Peprotech, 450-03). For OPCs differentiation, triiodothyronine (T3) (60 nM) added to the media and PDGF-AA, bFGF and NT3 were removed.

extract_protocol:
Briefly, for ChIP-Seq, approximately 5 x10^6 cells were cross-linked with 1% formaldehyde for 10 min at room temperature and then were quenched with 125 mM glycine for 5min. Sonicated chromatin was used for immunoprecipitation by incubation with appropriate antibodies (4 g) overnight at 4°C. Immunoprecipitated complexes were collected using protein 40l A/G plus agarose beads (Millipore). SubSequently, beads were washed Sequentially with low-salt buffer, high-salt buffer, LiCl buffer and twice with TE and elution in 500 l of elution buffer (1% SDS, 0.1M NaHCO3). The elutes were heated at 42°C for 2h and treatment with proteinaseK followed by 65°C 10 h to reverse the cross-linking and were treated  with RNaseA for 30 min before DNA was extracted and purified.
The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 7962347001)

tag: strain

value: Sprague Dawley

value: forebrain

value: IgG

tag: age

value: post natal day 1-2


title: Riboseq.recovery.WT_1

description:
WT_1
Ribosome footprint profiling


title: iOL_Seh1_ChIP-Seq


title: 256449110007_b2 - 3_C20_V1 vs 1_C15_V1

hyb_protocol: 1_C15_V1 Cy5 / 3_C20_V1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1_C15_V1:100mg. (Qiagen_RNeasy.pdf)

tag: days after pollination

value: vitreous endosperm

extract_protocol: 3_C20_V1:100mg. (Qiagen_RNeasy.pdf)


title: 256449110007_b4 - 11_C20_V2 vs 9_C15_V2

hyb_protocol: 9_C15_V2 Cy5 / 11_C20_V2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 9_C15_V2:100mg. (Qiagen_RNeasy.pdf)

tag: tissue

extract_protocol: 11_C20_V2:100mg. (Qiagen_RNeasy.pdf)


title: OPC_Seh1_ChIP-Seq


title: H3K9me2_h3.1D_1


title: 256449110007_b3 - 9_C15_V2 vs 11_C20_V2

hyb_protocol: 11_C20_V2 Cy5 / 9_C15_V2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: line


title: H3K9me2_brl2D_1


title: 256449110007_b1 - 1_C15_V1 vs 3_C20_V1

hyb_protocol: 3_C20_V1 Cy5 / 1_C15_V1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: harvest date


title: SHR

city: guangzhou

first: Kai

last: Chen

institute: TCM

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rat whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: myocardium

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

tag: disease state

value: spontaneously hypertensive rats

tag: agent

value: distilled water

tag: time

value: administration for 12 weeks

value: myocardium


title: KXH

value: KXH


title: H3K9me2_hip1D_1

tag: genotype

value: log phase

tag: chip antibody


title: H3K9me2_nap1D_1

value: 29 degrees C


title: RR587_m6A IP sample 12

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
small RNA
Mettl16_in_vitro_meth_table.csv.gz

data_processing:
The genotype of the mouse embryos giving rise to the individual samples was assessed based on the presence of the reads derived from WT Mettl16 allele (containing CACCAGGATTCGGACAAAACTA or TAGTTTTGTCCGAATCCTGGTG sequence) and from Mettl16 KO allele (containing TCACCAATGTAAATAGATGAGG or CCTCATCTATTTACATTGGTGA sequence). The paired-end reads were sorted into individual libraries based on the barcodes and aligned to NCBI RefSeq transcripts (build mm10) using Salmon v0.7.2 (Patro et al., 2017). The transcript estimates were imported into DESeq2 1.18.1  (Love et al., 2014) and summarized to gene levels using tximport 1.2.0 (Soneson et al., 2015). The DESeq2 was used to obtain lists of differentially expressed genes with statistical significance (adjusted p-value <=0.1). To compare the expression from individual exons and introns, the sequenced reads were aligned to reference mm10 genome using STAR (Dobin et al., 2013) and featureCounts (Liao et al., 2014) was used to obtain the read counts. DESeq2 was applied to search for differences in between genotypes.
For in vitro methylation experiments, the reads were sorted into individual libraries based on the barcodes and the 3′ adaptor sequences were removed using cutadapt 1.9.1 (https://doi.org/10.14806/ej.17.1.200). Only reads of final length of 30 nucleotides with correctly sequenced TACAGAGAA consensus motif at position 12-20 and without any Ns were kept for further analysis using R 3.4.3 (R Core Team, 2017) and Bioconductor (Huber et al., 2015).  For each sequence we obtained the minimum free energy (MFE) secondary structure using RNAfold (Lorenz et al., 2011). We used DESeq2 1.18.1 bioconductor package (Love et al., 2014) to obtain the lists of structures significantly enriched or depleted in m6A-IP libraries when compared to input libraries (adjusted p value < 0.1).
Genome_build: mm10
Supplementary_files_format_and_content: The file for in vitro methylation experiment contains the DESeq2 calculated log2fold changes between m6A IP and input samples for individual RNA structures represented in dot-bracket notation.  The files for mouse testicular samples contain the gene level comparisons obtained by Salmon followed by DESeq2 and comparisons of individual exons/introns obtained by STAR alignment followed by featureCounts and DESeq2 analysis.

organism: synthetic RNA

source_name: in vitro methylation_m6A_IP

growth_protocol: We targeted the endogenous Mettl16 locus in mouse embryos of the B6D2F1/J hybrid line (also called B6D2; The Jackson Laboratory, stock no. 100006). It is a cross between C57BL/6J (B6) and DBA/2J (D2), and heterozygous for all B6 and D2 alleles. Single-cell mouse embryos were injected with a guide RNA (gRNA) that directs the DNA endonuclease Cas9, and a 170 nt single-stranded DNA (ssDNA) repair template (IDT). The ssDNA carries a triple-stop codon flanked by a 81 nt 5ʹ homology arm and a 75 nt 3ʹ homology arm.  Founder mice were identified by genotyping and crossed with wildtype C57BL/6JRj (Janvier) partners to obtain germline transmission. We obtained two lines: line #2112 where the homology recombination template was inserted, resulting in insertion of a triple-stop codon cassette (sequence: ATGTAAATAGATGA) into exon 3, and line #2175 where a 7 bp deletion led to removal of a splicing donor site in intron 4. It is expected that creation of premature termination codons in both lines should result in removal of the transcripts via nonsense-mediated decay (NMD). Both the generated Mettl16 -/- (KO) lines showed the embryonic lethality phenotype. We used the line #2112 (with the triple-stop codon cassette) for sequence analysis of early embryos.

extract_protocol:
For single-embryo transcriptome sequencing, the isolated E2.5 and E3.5 embryos were visually examined for viability and cell number, and transferred separately into single tubes of 0.2 ml thin-walled 8-tube PCR strips (Thermo, AB-0451). The tubes contained 2 μl of the following mix: 0.4% Triton-X100 (vol/vol) in H2O + 2U/μl SUPERase• In™ RNase Inhibitor (20 U/μL; Thermo, AM2694). Embryos were stored at -80°C prior to processing for Smart-seq2 library preparation.   For in vitro methylation with METTL16 the libraries of randomized 30 nt RNA sequences were chemically synthesized. The sequences had a constant central 9-mer sequence flanked by randomized (represented by N) sequences (MM-RNA-14: N11-UACAGAGAA-N10). In vitro methylation with METTL16 protein was followed by m6A immunoprecipitation using rabbit polyclonal antibody (5 µg; Synaptic Systems, catalog no. 202003).
Polyadenylated transcripts from single embryos (E2.5 or E3.5) were amplified using the Smart-seq2 protocol. The protocol generates libraries that lack strand specificity. Multiple libraries with different barcodes were mixed in equimolar ratios and paired-end sequencing reads were obtained with the NextSeq 500 (EMBL GeneCore facility, Heidelberg). The maximum sequencing length was 80 nt.   Sequencing libraries  for in vitro methylation experiments were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Cat No:E7300) according to manufacturer instructions and sequenced on Illumina HiSeq 2000 platform (EMBL Heidelberg Gene core facility).


title: H3K9me2_rtt109D_1

value: H3K9me2 (Abcam 1220)


title: H3K9me2_h3.2D_1


title: RR586_m6A IP sample 11


title: RR583_Input sample 12

source_name: in vitro methylation_input


title: H3K9me2_chz1D_1


title: H3K9me2_slm9D_1


title: 256449110008_b3 - 10_C15_F2 vs 12_C20_F2

hyb_protocol: 12_C20_F2 Cy5 / 10_C15_F2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: floury endosperm

value: flint maize


title: RR582_Input sample 11


title: adipogenic-induced ADSCs, biological rep2

city: Chengdu

first: Yuanwei

address: No.14 South Renmin road

institute: Sichuan University

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

label: biotin

source_name: ADSCs from inguinal fat tissue of 2-week-old female Wistar rats with adipogenic induction for 7 days

label_protocol: Biotinylated cRNAwere prepared according to the standard Affymetrix protocaol from 6 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The ADSCs were cultured in alpha-modified eagle medium (α-MEM) with 10% fetal bovine serum (FBS) and incubated in a humidified atmosphere of 5% CO2 at 37°C

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

treatment_protocol: The adipogenic-induced ADSCs were cultured in adipogenic stimulation medium containing 0.5 mM 3-isobutyl-1-methylxanthine, 1 μM dexamethasone, and 5 μg/ml insulin (MDI) in α-MEM with 20% FBS.

tag: strain background

value: Wistar

tag: Sex

value: female

value: inguinal fat tissue

tag: cell type

value: Adipogenic-induced Adipose-derived stem cells (ADSCs)


title: WAT_KO_rep1

city: Chongqing

first: Min-Dian

last: Li

state: China

address: 30 Gaotanyan Main Street

department: Department of Cardiovascular Medicine

institute: Southwest Hospital, Army Medical University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

organism: Mus musculus

source_name: perigonadal white adipose tissue

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

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.

tag: gender

value: male

value: white adipose tissue

tag: developmental stage

value: 15 weeks

tag: genotype/variation

value: adipocyte OGT knockout


title: WAT_KO_rep3

description: replicate 3

tag: strain


title: WAT_WT_rep5

description: replicate 5

value: wildtype


title: Seh1cKO

data_processing:
RNA from control and Seh1cKO spinal cord or OPCs were subjected to 50-bp single-end sequencing with a BGISEQ-500 sequencer
At least 20 million clean reads of sequencing depth were obtained for each sample
ChIP was performed on rat oligodendrocyte progenitor cells and immature oligodendrocytes(T3 D1) using antibodies against seh1 or IgG. RNA-seq was performed on mouse control or Seh1cKO immature oligodendrocytes(T3 D2). Atac-seq was performed on mouse control or Seh1cKO oligodendrocyte progenitor cells and immature oligodendrocytes(T3 D1).
Raw counts for each gene were calculated by Htseq
StringTie was used to estimate the expression level of detected genes
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Oligodendrocyte

growth_protocol: Mouse OPCs were obtained from cortices of mouse brains as described7. Briefly, dissociated P4-P7 mouse cortices cells were sequentially immunopanned on anti-GalC, and then anti-O4 antibody coated plates to harvest OPCs. Purified OPCs were trypsinized and plated onto poly-D-lysine-coated plates. Cells were grown in DMEM/F-12 (GIBCO) with addition of 2% B-27 (GIBCO), 1% N2 (GIBCO), 20 ng/ml PDGF-AA (Peprotech, 100-13A), 10 ng/ml CNTF (Peprotech, 450-02), 20 ng/ml bFGF (Sino Biological, 10014-HNAE), and 1 ng/ml NT3 (Peprotech, 450-03). For OPCs differentiation, triiodothyronine (T3) (60 nM) added to the media and PDGF-AA, bFGF and NT3 were removed.

extract_protocol:
Total RNA fraction was extracted using Eastep®Super Total RNA Extraction Kit (Promega)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Forebrain tissue

tag: age

value: post natal day 4-7

value: mutant


title: WAT_KO_rep2

description: replicate 2


title: control

value: wild type


title: adipogenic-induced ADSCs, biological rep1


title: WAT_WT_rep1

description: replicate 1


title: WAT_WT_rep3

description: replicate 3


title: ADSCs, biological rep3

source_name: ADSCs from inguinal fat tissue of 2-week-old female Wistar rats

value: Adipose-derived stem cells (ADSCs)


title: WAT_WT_rep2

description: replicate 2


title: adipogenic-induced ADSCs, biological rep3


title: WAT_WT_rep4

description: replicate 4


title: ADSCs, biological rep2


title: SNAI2.MET.D20.R2

status: Public on Sep 11 2018

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

hyb_protocol: 1650 ng of the labeled cRNA were hybridised onto a custom Agilent oligo micrarray at 65⁰C for 17 hours.

scan_protocol: Arrays were scanned on an Agilent scanner (G2565CA) using the Agilent Scan Control Software (A.8.4.1) and feature extraction was performed using the Agilent Feature Extraction Software (10.7).

data_processing: A quantile between array normalization was applied and differential expression was determined using the Baysian adjusted t-statistic linear model of the ‘Linear Models for Microarray Data’ (LIMMA) package in R.

source_name: LNCaP prostate cancer cell line

label_protocol: 150 ng of total RNA was amplified and labelled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's protocol.

growth_protocol: LNCaP-iGFP, LNCaP-iSnail, and LNCaP-iSlug cells were cultured in phenol-red free RPMI-1640 medium + 5% fetal calf serum and maintained at 37°C in an atmosphere containing 5% CO2 for the duration of the experiment.

extract_protocol: Total cellular RNA was extracted using the Directzol kit including on-column DNAse-I treatment.

treatment_protocol: LNCaP-iGFP, LNCaP-iSnail, and LNCaP-iSlug cells were either left untreated, treated with doxycycline for 5 days to stimulate expression of either GFP or Snail expression, or treated with doxycycline for 5 days and subsequently removed for 3, 5, and 20 days to repress the expression of GFP or Snail.

tag: cell line

value: LNCaP prostate cancer cell line

tag: model

value: inducible SNAI2

tag: treatment

value: Treated with doxycycline for 5 days and then removed for 20 days

value: 20 days


title: ADSCs, biological rep1

value: Wistar

value: female

tag: tissue


title: SNAI2.MET.D20.R3

value: Treated with Doxycycline for 5 days and then removed for 20 days


title: SNAI2.MET.D5.R1

value: Treated with doxycycline for 5 days and then removed for 5 days

value: 5 days


title: SNAI2.MET.D5.R2


title: SNAI2.MET.D3.R2

value: Treated with doxycycline for 5 days and then removed for 3 days

value: 3 days


title: SNAI2.MET.D3.R1


title: SNAI2.EMT.D5.R1

value: Treated with doxycycline for 5 days


title: SNAI2.EMT.D5.R2


title: SNAI2.EMT.D5.R3


title: SNAI2.MET.D20.R1


title: SNAI2.MET.D3.R3


title: GFP.MET.D5.R3

value: inducible GFP


title: SNAI2.MET.D5.R3


title: SNAI2.D0.R1

value: Untreated

value: 0 days


title: SNAI1.MET.D20.R1

hyb_protocol: 1650 ng of the labeled cRNA were hybridised onto a custom Agilent oligo microarray at 65⁰C for 17 hours.

data_processing: A quantile between array normalization was applied and differential expression was determined using the Bayesian adjusted t-statistic linear model of the ‘Linear Models for Microarray Data’ (LIMMA) package in R.

source_name: LNCaP-iSnail, treated with doxycycline for 5 days and then removed for 20 days

growth_protocol: LNCaP-iGFP and LNCaP-iSnail cells were cultured in phenol-red free RPMI-1640 medium + 5% fetal calf serum and maintained at 37°C in an atmosphere containing 5% CO2 for the duration of the experiment.

extract_protocol: Total cellular RNA was extracted using the Directzol kit including on-column DNase-I treatment.

treatment_protocol: LNCaP-iGFP and LNCaP-iSnail cells were either left untreated, treated with doxycycline for 5 days to stimulate expression of either GFP or Snail expression, or treated with doxycycline for 5 days and subsequently removed for 3, 5, and 20 days to repress the expression of GFP or Snail.

value: LNCaP

value: prostate cancer cell line

value: inducible SNAI1


title: SNAI1.EMT.D5.R1

source_name: LNCaP-iSnail, treated with doxycycline for 5 days

value: treated with doxycycline for 5 days


title: SNAI1.MET.D3.R1

source_name: LNCaP-iSnail, treated with doxycycline for 5 days and then removed for 3 days


title: SNAI1.EMT.D5.R3


title: SNAI2.D0.R3

value: LNCaP prostate cancer cell line

value: inducible SNAI2


title: SNAI2.D0.R2


title: SNAI1.MET.D20.R3

value: treated with doxycycline for 5 days and then removed for 20 days

value: 20 days


title: SNAI1.MET.D5.R3

source_name: LNCaP-iSnail, treated with doxycycline for 5 days and then removed for 5 days


title: SNAI1.MET.D5.R1

value: treated with doxycycline for 5 days and then removed for 5 days


title: SNAI1.EMT.D5.R2


title: SNAI1.MET.D5.R2


title: SNAI1.MET.D3.R3

value: treated with doxycycline for 5 days and then removed for 3 days


title: SNAI1.MET.D20.R2


title: SNAI1.D0.R3

source_name: LNCaP-iSnail, untreated

value: untreated


title: GFP.MET.D3.R1

source_name: LNCaP-iGFP, treated with doxycycline for 5 days and then removed for 3 days


title: SNAI1.D0.R1


title: SNAI1.MET.D3.R2


title: GFP.MET.D3.R2


title: GFP.MET.D5.R2

source_name: LNCaP-iGFP, treated with doxycycline for 5 days and then removed for 5 days

value: 5 days


title: SNAI1.D0.R2


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (2M23_HEART_24HR)

city: Bethesda

first: Myrtle

last: Davis Millin

state: MD

address: 31 Center Drive

institute: The National Cancer Institute

description: The rat was administered a single bolus intravenous (iv) dose of gemcitabine or appropriate vehicle formulation.  Thirty (30) minutes after iv administration of gemcitabine or vehicle formulation, sorafenib, erlotinib, or vehicle formulation was administered po.  IV doses were administered in a dose volume of 5 mL/kg.  PO doses were administered in a dose volume of 10 mL/kg.  Dose volumes were based on the most recent individual body weights taken.  Dose formulations containing erlotinib were suspensions and these were stirred for at least 5 minutes prior to use for dosing and continuing throughout their period of use for dosing.

hyb_protocol: 11 μg of purified cRNA was applied to Affymetrix GeneChip Rat Genome 230 2.0 Arrays, and incubated at 45°C for 16 hours. Following hybridization, arrays were washed and stained using standard Affymetrix procedures.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 using factory PMT settings. Data extraction was completed with Expression Console software using a target scaling of 500.

data_processing: Data analysis was performed using the Bioconductor R package using the affyQCReport, simpleaffy and arrayQualityMetrics packages. The raw data was normalized using the robust multichip average (RMA) algorithm (Irizarry et. al. Biostatistics, 2003) with log2 transformation.

label: Biotin

label_protocol: Total RNA samples were converted into labeled target antisense RNA (cRNA) using the Single-Round RNA Amplification and Biotin Labeling System (Enzo Life Sciences, Farmingdale, NY).

growth_protocol: Rats used in this study were procured with an indwelling femoral vein cannula.  Prior to dosing on day 1, the catheter of each rat was checked for patency. Rats with patent catheters were randomly assigned to one of 8 treatment groups. On the day of randomization, the hair was clipped from the inguinal area of each animal to facilitate skin collection at necropsy. Re-clipping was accomplished prior to necropsy, as required.  On day 1, the rats weighed between 256.6–307.3 grams. Teklad Certified Rodent Diet 2016C (Harlan; Madison, WI) and tap water (Birmingham public water supply) were provided ad libitum to the rats prior to and throughout the study. The animals were individually housed in solid-bottom polycarbonate cages on stainless steel racks in a room maintained at a temperature of 70-79°F and a relative humidity of 44-66%. Room lights were controlled by an automatic timer set to provide a 12/12 light:dark cycle

extract_protocol: RNA isolation from individual tissues was accomplished using an RNeasy microarray kit (QIAGEN Inc.). After extraction, the RNA concentration of each sample was determined using a RiboGreen assay. The RNA Integrity Number (RIN) of each sample was determined using an Agilent 2100 Bioanalyzer with 2100 Expert Software. Only samples with a RIN of 7.5 or higher were deemed acceptable for gene expression analysis.

treatment_protocol: At 1, 6, or 24 hours after the completion of dosing, rats were euthanized by CO2 asphyxiation. Immediately after euthanasia, tissues of interest were collected for RNA isolation.  Skin (inguinal area), heart (apex, with left and right ventricles), liver (left lateral and median lobes).   Samples collected for RNA isolation were cut into sections ≤ 2 mm in thickness and immediately placed into pre-filled tubes containing RNAlater® (Applied Biosystems; Foster City, CA).  After collection into RNAlater®, tissues were maintained refrigerated (approximately 4-5 °C) for at least 24 hours and then stored at or below -20 °C.

value: Sprague-Dawley

value: Male

value: 8-9 weeks

value: Heart

tag: compound given 1st

tag: dose (mg/kg) compound given 1st

tag: compound given 2nd

tag: dose (mg/kg) compound 2nd

value: 24 hr


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Liver for 1 hr(s) (1M2_LIVER_1HR)

value: Liver

tag: time

value: 1 hr


title: GFP.MET.D20.R1

source_name: LNCaP-iGFP, treated with doxycycline for 5 days and then removed for 20 days

value: LNCaP

value: prostate cancer cell line

value: inducible GFP


title: GFP.MET.D5.R1


title: GFP.D0.R2

source_name: LNCaP-iGFP, untreated

value: 0 days


title: 0.9%saline followed by Sorafenib (po) in Liver for 1 hr(s) (8M85_LIVER_1HR)

source_name: 0.9%saline followed by Sorafenib (po)

value: Sorafenib


title: Gemcitabine (iv) followed by Sorafenib (po) in Liver for 6 hr(s) (6M69_LIVER_6HR)

value: Gemcitabine

value: 6 hr


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (2M18_LIVER_24HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Skin for 6 hr(s) (6M63_SKIN_6HR)

value: Skin


title: GFP.EMT.D5.R2

source_name: LNCaP-iGFP, treated with doxycycline for 5 days

value: treated with doxycycline for 5 days


title: GFP.D0.R3

value: untreated


title: Gemcitabine (iv) followed by Erlotinib (po) in Heart for 6 hr(s) (5M57_HEART_6HR)

value: Sprague-Dawley

value: Erlotinib


title: GFP.EMT.D5.R1

value: 5 days


title: GFP.D0.R1


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (2M15_LIVER_6HR)

value: Male

value: 8-9 weeks


title: GFP.MET.D20.R3

value: treated with doxycycline for 5 days and then removed for 20 days

value: 20 days


title: GFP.MET.D3.R3

value: LNCaP

value: treated with doxycycline for 5 days and then removed for 3 days

value: 3 days


title: 0.9%saline (iv) followed by Erlotinib (po) in Heart for 1 hr(s) (7M73_HEART_1HR)

value: Heart

value: 1 hr


title: Gemcitabine (iv) followed by Erlotinib (po) in Liver for 24 hr(s) (5M53_LIVER_24HR)

value: Liver

value: Gemcitabine

value: 24 hr


title: 0.9%saline (iv) followed by Erlotinib (po) in Heart for 6 hr(s) (7M97_HEART_6HR)

value: 6 hr


title: Gemcitabine (iv) followed by Erlotinib (po) in Skin for 24 hr(s) (5M59_SKIN_24HR)

value: Skin


title: Gemcitabine (iv) followed by Erlotinib (po) in Liver for 6 hr(s) (5M52_LIVER_6HR)

value: Sprague-Dawley


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Skin for 24 hr(s) (4M42_SKIN_24HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Liver for 1 hr(s) (1M7_LIVER_1HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (2M19_HEART_1HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Skin for 6 hr(s) (6M70_SKIN_6HR)

value: Sorafenib


title: 0.9%saline followed by Sorafenib (po) in Skin for 1 hr(s) (8M86_SKIN_1HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Skin for 24 hr(s) (6M65_SKIN_24HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Liver for 1 hr(s) (6M68_LIVER_1HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Skin for 1 hr(s) (7M79_SKIN_1HR)

value: Erlotinib


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Heart for 6 hr(s) (1M3_HEART_6HR)

value: Male


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Heart for 6 hr(s) (1M9_HEART_6HR)

value: 8-9 weeks


title: 0.9%saline followed by Sorafenib (po) in Skin for 1 hr(s) (8M92_SKIN_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Heart for 6 hr(s) (3M33_HEART_6HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Skin for 1 hr(s) (4M38_SKIN_1HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Heart for 1 hr(s) (5M56_HEART_1HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Liver for 1 hr(s) (6M61_LIVER_1HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (4M48_HEART_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Skin for 1 hr(s) (7M73_SKIN_1HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (2M22_LIVER_6HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (4M45_LIVER_6HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (4M41_HEART_24HR)


title: 0.9%saline followed by Sorafenib (po) in Heart for 6 hr(s) (8M93_HEART_6HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Skin for 6 hr(s) (2M22_SKIN_6HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Skin for 6 hr(s) (2M16_SKIN_6HR)


title: 0.9%saline followed by Sorafenib (po) in Heart for 24 hr(s) (8M95_HEART_24HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Heart for 24 hr(s) (6M66_HEART_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Heart for 24 hr(s) (7M83_HEART_24HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Liver for 24 hr(s) (6M72_LIVER_24HR)


title: 0.9%saline followed by Sorafenib (po) in Skin for 24 hr(s) (8M95_SKIN_24HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Skin for 1 hr(s) (3M25_SKIN_1HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Skin for 1 hr(s) technical replicate (2M14_SKIN_1HR.N2)


title: 0.9%saline followed by Sorafenib (po) in Skin for 6 hr(s) (8M88_SKIN_6HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Liver for 6 hr(s) (7M81_LIVER_6HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (4M44_LIVER_1HR)


title: 0.9%saline followed by Sorafenib (po) in Heart for 6 hr(s) (8M88_HEART_6HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) technical replicate (2M13_LIVER_1HR.N2)


title: 0.9%saline followed by Sorafenib (po) in Liver for 1 hr(s) (8M91_LIVER_1HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Skin for 1 hr(s) (7M80_SKIN_1HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Skin for 24 hr(s) (1M11_SKIN_24HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (2M16_LIVER_6HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (2M20_LIVER_1HR)


title: 0.9%saline followed by Sorafenib (po) in Liver for 1 hr(s) (8M86_LIVER_1HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Skin for 1 hr(s) (2M19_SKIN_1HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Liver for 1 hr(s) (7M80_LIVER_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Heart for 24 hr(s) (3M35_HEART_24HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Liver for 24 hr(s) (1M12_LIVER_24HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Heart for 24 hr(s) (1M5_HEART_24HR)


title: GFP.EMT.D5.R3

value: prostate cancer cell line

value: inducible GFP

value: treated with doxycycline for 5 days

value: 5 days


title: Gemcitabine (iv) followed by Sorafenib (po) in Skin for 24 hr(s) (6M71_SKIN_24HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (4M47_HEART_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Skin for 6 hr(s) (7M82_SKIN_6HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (2M24_LIVER_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Liver for 6 hr(s) (7M76_LIVER_6HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Skin for 1 hr(s) (1M8_SKIN_1HR)


title: 0.9%saline followed by Sorafenib (po) in Skin for 1 hr(s) (8M85_SKIN_1HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (4M47_LIVER_24HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (2M14_HEART_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Liver for 1 hr(s) (3M26_LIVER_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Heart for 6 hr(s) (3M34_HEART_6HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Liver for 24 hr(s) (5M59_LIVER_24HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Skin for 6 hr(s) (3M34_SKIN_6HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Skin for 6 hr(s) (3M28_SKIN_6HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Skin for 24 hr(s) (1M5_SKIN_24HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (4M46_LIVER_6HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Liver for 6 hr(s) (1M3_LIVER_6HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (4M38_HEART_1HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Skin for 24 hr(s) (6M66_SKIN_24HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Skin for 6 hr(s) (1M9_SKIN_6HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Skin for 6 hr(s) (2M15_SKIN_6HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (4M40_HEART_6HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Heart for 1 hr(s) (5M50_HEART_1HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Liver for 1 hr(s) (6M62_LIVER_1HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Liver for 6 hr(s) (1M9_LIVER_6HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Heart for 1 hr(s) (1M1_HEART_1HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Skin for 1 hr(s) (2M20_SKIN_1HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (2M18_HEART_24HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Liver for 1 hr(s) (5M55_LIVER_1HR)


title: 0.9%saline followed by Sorafenib (po) in Liver for 1 hr(s) (8M92_LIVER_1HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Heart for 6 hr(s) (6M70_HEART_6HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Skin for 1 hr(s) (4M37_SKIN_1HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Heart for 24 hr(s) (5M53_HEART_24HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Liver for 24 hr(s) (6M65_LIVER_24HR)


title: 0.9%saline followed by Sorafenib (po) in Liver for 24 hr(s) (8M96_LIVER_24HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Skin for 24 hr(s) (1M12_SKIN_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Liver for 6 hr(s) (7M82_LIVER_6HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Heart for 6 hr(s) (1M10_HEART_6HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Liver for 24 hr(s) (3M30_LIVER_24HR)


title: 0.9%saline followed by Sorafenib (po) in Skin for 6 hr(s) (8M87_SKIN_6HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Skin for 24 hr(s) (3M35_SKIN_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Liver for 24 hr(s) (7M84_LIVER_24HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Heart for 1 hr(s) (1M8_HEART_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Heart for 1 hr(s) (3M32_HEART_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Liver for 6 hr(s) (3M27_LIVER_6HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Skin for 6 hr(s) (2M21_SKIN_6HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (2M15_HEART_6HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Heart for 6 hr(s) (3M28_HEART_6HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (4M37_LIVER_1HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Skin for 6 hr(s) (1M3_SKIN_6HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Skin for 24 hr(s) (6M72_SKIN_24HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Heart for 6 hr(s) (5M58_HEART_6HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Skin for 6 hr(s) (7M81_SKIN_6HR)


title: 0.9%saline followed by Sorafenib (po) in Liver for 24 hr(s) (8M90_LIVER_24HR)


title: 0.9%saline followed by Sorafenib (po) in Skin for 6 hr(s) (8M94_SKIN_6HR)


title: 0.9%saline followed by Sorafenib (po) in Skin for 24 hr(s) (8M96_SKIN_24HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (2M17_LIVER_24HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Skin for 1 hr(s) (1M1_SKIN_1HR)


title: 0.9%saline followed by Sorafenib (po) in Liver for 6 hr(s) (8M87_LIVER_6HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Liver for 6 hr(s) (5M57_LIVER_6HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Liver for 6 hr(s) (7M97_LIVER_6HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Heart for 1 hr(s) (7M74_HEART_1HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Liver for 24 hr(s) (1M11_LIVER_24HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Heart for 24 hr(s) (6M72_HEART_24HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Skin for 24 hr(s) (2M17_SKIN_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Skin for 24 hr(s) (7M77_SKIN_24HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Heart for 6 hr(s) (6M64_HEART_6HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Heart for 1 hr(s) (6M61_HEART_1HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (4M45_HEART_6HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Liver for 24 hr(s) (3M36_LIVER_24HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Heart for 1 hr(s) (3M25_HEART_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Skin for 1 hr(s) (3M32_SKIN_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Skin for 6 hr(s) (3M33_SKIN_6HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Liver for 1 hr(s) (7M73_LIVER_1HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Liver for 1 hr(s) (7M79_LIVER_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Skin for 6 hr(s) (3M27_SKIN_6HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Liver for 6 hr(s) (6M63_LIVER_6HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (2M19_LIVER_1HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Skin for 6 hr(s) (4M46_SKIN_6HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Heart for 6 hr(s) (5M51_HEART_6HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Skin for 24 hr(s) (5M53_SKIN_24HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Liver for 1 hr(s) (5M56_LIVER_1HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Heart for 1 hr(s) (6M67_HEART_1HR)


title: 0.9%saline followed by Sorafenib (po) in Heart for 6 hr(s) (8M94_HEART_6HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Liver for 1 hr(s) (1M1_LIVER_1HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Heart for 24 hr(s) (1M12_HEART_24HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (2M24_HEART_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Liver for 24 hr(s) (7M77_LIVER_24HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (2M21_HEART_6HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Skin for 24 hr(s) (3M36_SKIN_24HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Skin for 1 hr(s) (5M49_SKIN_1HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (4M43_HEART_1HR)


title: 0.9%saline followed by Sorafenib (po) in Liver for 24 hr(s) (8M89_LIVER_24HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (4M39_HEART_6HR)


title: 0.9%saline followed by Sorafenib (po) in Skin for 1 hr(s) (8M91_SKIN_1HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Heart for 1 hr(s) (5M49_HEART_1HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (4M38_LIVER_1HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Liver for 1 hr(s) (1M8_LIVER_1HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Skin for 6 hr(s) (7M97_SKIN_6HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Skin for 24 hr(s) (2M18_SKIN_24HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Skin for 1 hr(s) (5M56_SKIN_1HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Heart for 24 hr(s) (7M77_HEART_24HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Heart for 24 hr(s) (5M59_HEART_24HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Liver for 24 hr(s) (1M6_LIVER_24HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Skin for 6 hr(s) (5M58_SKIN_6HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (4M42_LIVER_24HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Heart for 6 hr(s) (6M69_HEART_6HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Heart for 24 hr(s) (6M65_HEART_24HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Liver for 6 hr(s) (3M33_LIVER_6HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Liver for 24 hr(s) (6M71_LIVER_24HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Heart for 6 hr(s) (1M4_HEART_6HR)


title: 0.9%saline followed by Sorafenib (po) in Liver for 6 hr(s) (8M88_LIVER_6HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Skin for 1 hr(s) (5M50_SKIN_1HR)


title: 0.9%saline followed by Sorafenib (po) in Skin for 6 hr(s) (8M93_SKIN_6HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Liver for 1 hr(s) (3M31_LIVER_1HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Liver for 24 hr(s) (5M54_LIVER_24HR)


title: 0.9%saline followed by Sorafenib (po) in Heart for 1 hr(s) (8M85_HEART_1HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Heart for 24 hr(s) (7M78_HEART_24HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Skin for 6 hr(s) (4M45_SKIN_6HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Skin for 1 hr(s) (4M44_SKIN_1HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (2M14_LIVER_1HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Heart for 24 hr(s) (5M60_HEART_24HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Skin for 6 hr(s) (4M39_SKIN_6HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Liver for 6 hr(s) (6M64_LIVER_6HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Skin for 24 hr(s) (5M54_SKIN_24HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (4M40_LIVER_6HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Heart for 1 hr(s) (6M68_HEART_1HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Skin for 6 hr(s) (5M52_SKIN_6HR)


title: 0.9%saline followed by Sorafenib (po) in Heart for 24 hr(s) (8M96_HEART_24HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (2M23_LIVER_24HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (2M13_LIVER_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Liver for 6 hr(s) (3M34_LIVER_6HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Heart for 24 hr(s) (3M30_HEART_24HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Skin for 1 hr(s) (3M31_SKIN_1HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Skin for 24 hr(s) (4M47_SKIN_24HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Heart for 6 hr(s) (5M52_HEART_6HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Liver for 1 hr(s) (5M50_LIVER_1HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (4M44_HEART_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Skin for 24 hr(s) (3M29_SKIN_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Heart for 24 hr(s) (7M84_HEART_24HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Skin for 6 hr(s) (4M40_SKIN_6HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (2M22_HEART_6HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Skin for 1 hr(s) (6M62_SKIN_1HR)


title: 0.9%saline followed by Sorafenib (po) in Heart for 24 hr(s) (8M90_HEART_24HR)


title: 0.9%saline followed by Sorafenib (po) in Skin for 24 hr(s) (8M90_SKIN_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Heart for 6 hr(s) (7M81_HEART_6HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Heart for 24 hr(s) (1M11_HEART_24HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Liver for 6 hr(s) (6M70_LIVER_6HR)


title: 0.9%saline followed by Sorafenib (po) in Liver for 6 hr(s) (8M93_LIVER_6HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Skin for 24 hr(s) (1M6_SKIN_24HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Skin for 1 hr(s) (5M55_SKIN_1HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Skin for 1 hr(s) (6M68_SKIN_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Liver for 24 hr(s) (3M29_LIVER_24HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (2M17_HEART_24HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Liver for 6 hr(s) (1M10_LIVER_6HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Skin for 1 hr(s) (2M14_SKIN_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Heart for 24 hr(s) (3M36_HEART_24HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Skin for 24 hr(s) (2M23_SKIN_24HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Liver for 6 hr(s) (1M4_LIVER_6HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Skin for 1 hr(s) (1M2_SKIN_1HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (4M48_LIVER_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Skin for 24 hr(s) (7M83_SKIN_24HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Liver for 1 hr(s) (3M32_LIVER_1HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Skin for 24 hr(s) (5M60_SKIN_24HR)


title: 0.9%saline followed by Sorafenib (po) in Heart for 1 hr(s) (8M86_HEART_1HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (2M20_HEART_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Liver for 1 hr(s) (3M25_LIVER_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Heart for 24 hr(s) (3M29_HEART_24HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Liver for 6 hr(s) (3M28_LIVER_6HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (4M41_LIVER_24HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Heart for 1 hr(s) (3M26_HEART_1HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (2M16_HEART_6HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Heart for 6 hr(s) (6M63_HEART_6HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Skin for 6 hr(s) (5M57_SKIN_6HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (2M13_HEART_1HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Skin for 24 hr(s) (3M30_SKIN_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Heart for 1 hr(s) (7M80_HEART_1HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Heart for 1 hr(s) (7M79_HEART_1HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Skin for 6 hr(s) (6M64_SKIN_6HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Skin for 24 hr(s) (7M78_SKIN_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Liver for 24 hr(s) (7M83_LIVER_24HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Liver for 24 hr(s) (6M66_LIVER_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Heart for 6 hr(s) (7M76_HEART_6HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Skin for 6 hr(s) (5M51_SKIN_6HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Liver for 6 hr(s) (5M58_LIVER_6HR)


title: 0.9%saline followed by Sorafenib (po) in Liver for 24 hr(s) (8M95_LIVER_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Liver for 1 hr(s) (7M74_LIVER_1HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Liver for 24 hr(s) (5M60_LIVER_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Skin for 6 hr(s) (7M76_SKIN_6HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Heart for 1 hr(s) (1M7_HEART_1HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Skin for 6 hr(s) (1M4_SKIN_6HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Skin for 1 hr(s) (7M74_SKIN_1HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Liver for 24 hr(s) (7M78_LIVER_24HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Heart for 24 hr(s) (6M71_HEART_24HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (4M42_HEART_24HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Skin for 1 hr(s) (1M7_SKIN_1HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Skin for 24 hr(s) (4M48_SKIN_24HR)


title: 0.9%saline followed by Sorafenib (po) in Heart for 24 hr(s) (8M89_HEART_24HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Skin for 24 hr(s) (4M41_SKIN_24HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Skin for 1 hr(s) (4M43_SKIN_1HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Heart for 1 hr(s) (6M62_HEART_1HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Liver for 6 hr(s) (5M51_LIVER_6HR)


title: 0.9%saline followed by Sorafenib (po) in Liver for 6 hr(s) (8M94_LIVER_6HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Liver for 1 hr(s) (6M67_LIVER_1HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Heart for 1 hr(s) (1M2_HEART_1HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (4M46_HEART_6HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Liver for 24 hr(s) (3M35_LIVER_24HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Heart for 24 hr(s) (5M54_HEART_24HR)


title: 0.9%saline (iv) followed by Erlotinib (po) in Heart for 6 hr(s) (7M82_HEART_6HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Heart for 24 hr(s) (1M6_HEART_24HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Heart for 1 hr(s) (5M55_HEART_1HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Skin for 6 hr(s) (1M10_SKIN_6HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Skin for 24 hr(s) (2M24_SKIN_24HR)


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Heart for 6 hr(s) (3M27_HEART_6HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (4M39_LIVER_6HR)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (A905GDKN_03A)

description: The rat was administered an intravenous (iv) infusion dose, given over a 30-minute interval, of oxaliplatin or corresponding vehicle formulation (D5W).  Thirty (30) minutes after iv administration of oxaliplatin or corresponding vehicle formulation, sorafenib, sunitinib, or the respective vehicle formulation was administered po.  IV infusion doses were administered at a flow rate of approximately 4 mL/kg/30 minute infusion.  The actual infusion rates were based on the mean body weight of animals dosed on each day of dosing.  PO doses were administered in a dose volume of 10 mL/kg.

source_name: D5W (30 minute infusion) followed by F68/PG/PEG400 (po)

growth_protocol: Rats used in this study were procured with an indwelling femoral vein cannula.  Prior to dosing on day 1, the catheter of each rat was checked for patency. Rats with patent catheters were randomly assigned to one of 8 treatment groups. On day 1, the rats weighed between 251.5–336.2 grams. Teklad Certified Rodent Diet 2016C (Harlan; Madison, WI) and tap water (Birmingham public water supply) were provided ad libitum to the rats prior to and throughout the study. The animals were individually housed in solid-bottom polycarbonate cages on stainless steel racks in a room maintained at a temperature of 70-79°F and a relative humidity of 44-66%. Room lights were controlled by an automatic timer set to provide a 12/12 light:dark cycle

treatment_protocol: At 1, 6, or 24 hours after the completion of dosing, rats were euthanized by CO2 asphyxiation. Immediately after euthanasia, tissues of interest were collected for RNA isolation.  Kidney (left), heart (apex, with left and right ventricles), liver (left lateral and median lobes).   Samples collected for RNA isolation were cut into sections ≤ 2 mm in thickness and immediately placed into pre-filled tubes containing RNAlater® (Applied Biosystems; Foster City, CA).  After collection into RNAlater®, tissues were maintained refrigerated (approximately 4-5 °C) for at least 24 hours and then stored at or below -20 °C.

value: 8 weeks


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Skin for 1 hr(s) (3M26_SKIN_1HR)


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Skin for 1 hr(s) (2M13_SKIN_1HR)


title: Gemcitabine (iv) followed by Sorafenib (po) in Skin for 1 hr(s) (6M61_SKIN_1HR)


title: 0.9%saline followed by Sorafenib (po) in Heart for 6 hr(s) (8M87_HEART_6HR)

value: Heart


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Liver for 6 hr(s) (A905GDKN_05F)

source_name: Oxaliplatin (30 minute infusion) followed by sterile water (po)

value: Oxaliplatin

value: sterile water


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Kidney for 24 hr(s) (A905GDKO_02C)

source_name: Oxaliplatin (30 minute infusion) followed by Sunitinib (po)

value: Kidney

value: Sunitinib


title: 0.9%saline followed by Sorafenib (po) in Heart for 1 hr(s) (8M91_HEART_1HR)

value: 1 hr


title: 0.9%saline (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (2M21_LIVER_6HR)

value: Liver

value: 6 hr


title: Gemcitabine (iv) followed by Sorafenib (po) in Skin for 6 hr(s) (6M69_SKIN_6HR)

value: Sprague-Dawley

value: Skin

value: Gemcitabine

value: Sorafenib


title: 0.9%saline followed by Sorafenib (po) in Heart for 1 hr(s) (8M92_HEART_1HR)

value: Male

value: 8-9 weeks


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Kidney for 6 hr(s) (A905GDKP_08A)

source_name: Oxaliplatin (30 minute infusion) followed by Sorafenib (po)


title: 0.9%saline (iv) followed by Erlotinib (po) in Skin for 24 hr(s) (7M84_SKIN_24HR)

value: Erlotinib

value: 24 hr


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Kidney for 6 hr(s) (A905GDKP_05E)

value: 8 weeks


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (4M37_HEART_1HR)

value: Heart


title: Gemcitabine (iv) followed by 0.5% CMC (po) in Heart for 1 hr(s) (3M31_HEART_1HR)


title: Gemcitabine (iv) followed by Erlotinib (po) in Liver for 1 hr(s) (5M49_LIVER_1HR)


title: 0.9%saline (iv) followed by 0.5% CMC (po) in Liver for 24 hr(s) (1M5_LIVER_24HR)


title: Gemcitabine (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (4M43_LIVER_1HR)


title: 0.9%saline followed by Sorafenib (po) in Skin for 24 hr(s) (8M89_SKIN_24HR)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Heart for 6 hr(s) (A905GDKS_08D)

value: Oxaliplatin


title: D5W  (30 min infusion) followed by Sunitinib (po) in Heart for 24 hr(s) (A905GDKR_02F)

source_name: D5W  (30 minute infusion) followed by Sunitinib (po)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (A905GDKL_03D)


title: Gemcitabine (iv) followed by Sorafenib (po) in Skin for 1 hr(s) (6M67_SKIN_1HR)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Liver for 6 hr(s) (A905GDKN_08B)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Heart for 1 hr(s) (A905GDKS_01H)

value: sterile water


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Heart for 1 hr(s) (A905GDKS_04D)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Kidney for 24 hr(s) (A905GDKO_04H)

source_name: D5W  (30 minute infusion) followed by Sorafenib (po)

value: Kidney


title: D5W (30 min infusion) followed by sterile water (po) in Heart for 24 hr(s) (A905GDKR_01B)

source_name: D5W (30 minute infusion) followed by sterile water (po)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Heart for 6 hr(s) (A905GDKS_05E)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Heart for 24 hr(s) (A905GDKR_02C)

value: Sunitinib


title: D5W  (30 min infusion) followed by Sunitinib (po) in Kidney for 1 hr(s) (A905GDKP_02F)

value: 1 hr


title: D5W  (30 min infusion) followed by Sunitinib (po) in Liver for 6 hr(s) (A905GDKN_06G)

value: Liver


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 24 hr(s) (A905GDKO_03D)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Heart for 1 hr(s) (A905GDKS_01E)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Kidney for 1 hr(s) (A905GDKP_01E)


title: D5W (30 min infusion) followed by sterile water (po) in Liver for 6 hr(s) (A905GDKN_05C)

value: 6 hr


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Liver for 1 hr(s) (A905GDKN_01F)

value: Sprague-Dawley


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Liver for 1 hr(s) (A905GDKN_04B)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 6 hr(s) (A905GDKP_07G)

source_name: Oxaliplatin (30 minute infusion) followed by F68/PG/PEG400 (po)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Liver for 24 hr(s) (A905GDKL_04E)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Heart for 24 hr(s) (A905GDKR_04H)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Liver for 1 hr(s) (A905GDKN_02G)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (A905GDKR_03G)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Heart for 6 hr(s) (A905GDKS_08A)


title: D5W (30 min infusion) followed by sterile water (po) in Kidney for 6 hr(s) (A905GDKP_05B)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Heart for 6 hr(s) (A905GDKS_06F)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (A905GDKL_03A)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Heart for 1 hr(s) (A905GDKS_04A)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (A905GDKN_07H)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Kidney for 24 hr(s) (A905GDKO_04E)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Kidney for 1 hr(s) (A905GDKP_04A)


title: D5W (30 min infusion) followed by sterile water (po) in Kidney for 1 hr(s) (A905GDKP_01B)


title: D5W (30 min infusion) followed by sterile water (po) in Liver for 1 hr(s) (A905GDKN_01C)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Kidney for 6 hr(s) (A905GDKP_06F)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (A905GDKR_03D)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (A905GDKS_07G)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Liver for 24 hr(s) (A905GDKL_01F)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Heart for 6 hr(s) (A905GDKS_08H)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (A905GDKS_03G)


title: D5W (30 min infusion) followed by sterile water (po) in Heart for 6 hr(s) (A905GDKS_05B)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 24 hr(s) (A905GDKO_03A)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Heart for 1 hr(s) (A905GDKS_02F)


title: D5W (30 min infusion) followed by sterile water (po) in Heart for 1 hr(s) (A905GDKS_01B)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Kidney for 6 hr(s) (A905GDKP_06C)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (A905GDKN_03E)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Liver for 24 hr(s) (A905GDKL_02G)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Liver for 24 hr(s) (A905GDKL_04B)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 1 hr(s) (A905GDKP_03G)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Liver for 1 hr(s) (A905GDKN_02D)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 6 hr(s) (A905GDKP_07D)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (A905GDKN_07E)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Kidney for 24 hr(s) (A905GDKO_01F)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Liver for 6 hr(s) (A905GDKN_06D)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (A905GDKN_03H)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Heart for 6 hr(s) (A905GDKS_06C)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Kidney for 24 hr(s) (A905GDKO_04B)


title: D5W (30 min infusion) followed by sterile water (po) in Liver for 24 hr(s) (A905GDKL_01C)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (A905GDKR_03A)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Kidney for 1 hr(s) (A905GDKP_04H)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Kidney for 6 hr(s) (A905GDKP_08H)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Kidney for 1 hr(s) (A905GDKP_02C)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Liver for 6 hr(s) (A905GDKN_06A)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Heart for 24 hr(s) (A905GDKR_04E)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 1 hr(s) (A905GDKP_03D)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Kidney for 6 hr(s) (A905GDKP_08E)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Liver for 1 hr(s) (A905GDKN_02A)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Liver for 6 hr(s) (A905GDKN_08F)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Kidney for 24 hr(s) (A905GDKO_02G)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Liver for 1 hr(s) (A905GDKN_04F)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Heart for 1 hr(s) (A905GDKS_04H)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (A905GDKN_07B)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Heart for 24 hr(s) (A905GDKR_01F)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Liver for 24 hr(s) (A905GDKL_02D)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Heart for 1 hr(s) (A905GDKS_02C)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (A905GDKS_07D)


title: D5W (30 min infusion) followed by sterile water (po) in Kidney for 24 hr(s) (A905GDKO_01C)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (A905GDKS_03D)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Kidney for 1 hr(s) (A905GDKP_04E)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Heart for 6 hr(s) (A905GDKS_08E)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Heart for 24 hr(s) (A905GDKR_04B)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Heart for 24 hr(s) (A905GDKR_02G)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Kidney for 6 hr(s) (A905GDKP_05F)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Liver for 6 hr(s) (A905GDKN_05G)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (A905GDKN_03B)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (A905GDKL_03E)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 24 hr(s) (A905GDKO_03H)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Kidney for 24 hr(s) (A905GDKO_02D)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Liver for 6 hr(s) (A905GDKN_08C)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 1 hr(s) (A905GDKP_03A)


title: D5W (30 min infusion) followed by sterile water (po) in Heart for 24 hr(s) (A905GDKR_01C)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Kidney for 6 hr(s) (A905GDKP_08B)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Heart for 1 hr(s) (A905GDKS_04E)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (A905GDKS_07A)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (A905GDKR_03H)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Kidney for 1 hr(s) (A905GDKP_01F)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Liver for 6 hr(s) (A905GDKN_06H)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Heart for 24 hr(s) (A905GDKR_02D)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Heart for 6 hr(s) (A905GDKS_08B)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Kidney for 6 hr(s) (A905GDKP_06G)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Liver for 1 hr(s) (A905GDKN_02H)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Heart for 6 hr(s) (A905GDKS_05F)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Kidney for 1 hr(s) (A905GDKP_02G)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Kidney for 24 hr(s) (A905GDKO_02A)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Liver for 1 hr(s) (A905GDKN_01G)


title: D5W (30 min infusion) followed by sterile water (po) in Kidney for 6 hr(s) (A905GDKP_05C)


title: D5W (30 min infusion) followed by sterile water (po) in Liver for 1 hr(s) (A905GDKN_01D)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Kidney for 1 hr(s) (A905GDKP_04B)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 24 hr(s) (A905GDKO_03E)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Kidney for 24 hr(s) (A905GDKO_04F)


title: D5W (30 min infusion) followed by sterile water (po) in Kidney for 1 hr(s) (A905GDKP_01C)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Heart for 1 hr(s) (A905GDKS_01F)


title: D5W (30 min infusion) followed by sterile water (po) in Liver for 6 hr(s) (A905GDKN_05D)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Heart for 1 hr(s) (A905GDKS_04B)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (A905GDKR_03E)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Heart for 6 hr(s) (A905GDKS_06G)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Liver for 1 hr(s) (A905GDKN_04C)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Liver for 24 hr(s) (A905GDKL_02A)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Liver for 24 hr(s) (A905GDKL_04F)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (A905GDKL_03B)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 6 hr(s) (A905GDKP_07H)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (A905GDKS_03A)