title: TEC1A3 Flp-in rAIRE+ cell line repeat C

city: Sheffield

first: Thomas

middle: Richard

last: Lovewell

address: Beech Hill

department: Infection and Immunity

institute: University of Sheffield

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Human Genome 133 Plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: The GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

source_name: TEC1A3 Flp-in rAIRE+ cell line

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

growth_protocol: Three separate cultures of cells for each cell line variant were grown concurrently, starting from equal volumes of the same seed culture.

extract_protocol: SV Total RNA isolation kit (Promega) was used for RNA extraction according to manufacturers' instructions

tag: cell line

value: TEC 1A3

tag: genotype/variation

value: transgenic Flp-In rAIRE+ expression variant


title: TEC1A3 Flp-in rAIRE+ cell line repeat A

status: Public on Jun 01 2018

type: RNA

country: United Kingdom

label: biotin

molecule: total RNA

organism: Homo sapiens


title: LV5

type: SRA

city: Worcester

first: Ricardo

middle: Tostes

last: Gazzinelli

state: Massachusetts

address: 364 Plantation Street

department: Medicine

country: USA

institute: University of Massachusetts Medical School

description: Control 2  06 Hours

library_source: transcriptomic

data_processing:
Reads were trimmed with Trimmomatic and mapped to the Genome Reference Consortium Mouse Build 38 patch release 5 (GRCm38.p5) using STAR aligner
FPKM values were calculated with CUFFLINKS.
Data were then analyzed with the software Short Time-series Expression Miner (STEM, version 1.3.11) to identify genes with variable expression patterns along the period of 24h sampled at each 6 hours.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

organism: Mus musculus

source_name: Liver

growth_protocol: Mice were fed ad libitum and kept on a regular light cycle with lights on from 7:00 am (ZT 0) to 7:00 pm (ZT 12) and lights off from 7:00 pm (ZT 12) to 7:00 am (ZT 24)

extract_protocol:
Total RNA was harvested using Qiagen Rneasy mini kit following manufacturer's instructions.
Poly-A containing mRNA molecules were purified using poly-T oligo attached magnetic beads and fragmented using divalent cations. The RNA fragments were transcribed into cDNA using  II Reverse Transcriptase (Invitrogen), followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Finally, cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched by PCR using paired-end primers (Illumina) for 15 cycles to create the final cDNA library.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: Liver from C57BL/6 mice non-infected or after 8 days post infection with 10E5 P. chabaudi infected red blood

tag: strain

tag: tissue

value: Liver

tag: Sex

value: Female

tag: age

value: 10 weeks

tag: genotype

value: Wild Type

tag: agent

value: Control

tag: time point

value: 06 Hours


title: 3998998123_R06C01

type: genomic

city: Exeter

first: Therese

middle: M

last: Murphy

address: RILD building

department: University of Exeter Medical School

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization).   Probes containing a SNP with minor allele frequency (MAF) >5% within 10bp of the single base extension site based on   Illumina’s database and probes identified by Chen et al.* were removed. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.

label: Cy3, Cy5

molecule: genomic DNA

source_name: whole blood

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: Genomic DNA was isolated from whole blood  using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.

treatment_protocol: Individuals with a self-reported history of doctor's diagnosed depression & a self-reported history of an inflammatory disorder (code = 1); Individuals with a self-reported history of doctor's diagnosed depression (code = 2); Individuals with a self-reported history of an inflammatory disorder (code = 3); Healthy controls (code = 4 )

tag: groupid

tag: gender

value: F


title: LV2

description: Control 2  00 Hours

value: 00 Hours


title: dsc3 deletion, 0min 100% nitrogen gas (NH_82_1_2)

city: Glassboro

first: Mark

last: Hickman

state: NJ

address: 201 Mullica Hill Road

department: Biological Sciences

institute: Rowan University

data_processing:
Each raw file is a de-multiplexed fastq file
FASTQ Quality Trimmer, 5' and 3' ends, window size=1,step size=1,min score=10
Reads aligned to yeast genome using TopHat2
Number of reads per feature was calculated using HTSeq,mode=union
When a sample was sequenced two times (e.g., NH_101_1_1.fastqsanger.gz and NH_101_1_2.fastqsanger.gz), then the FASTQ files were processed separately resulting in two HTSEQ files (e.g., NH_101_1_1.tabular and NH_101_1_2.tabular). The counts were then added to obtain the total counts for that sample.
Genome_build: saccharomyces_cerevisiae_R64-1-1_20110208.fasta
Supplementary_files_format_and_content: tab-delimited text files, first column= feature, second column=number of reads that overlap feature

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: strain yMH949 (S288C background with repaired HAP1)

growth_protocol: A saturated culture was diluted and grown to mid-log phase (~1-2x10^7 cells/ml). Then the cells were diluted again and placed in 100% nitrogen gas for the indicated time, with the gas flowing through flasks.  Cells were collected in mid-log phase, filtered and frozen in liquid nitrogen.

extract_protocol:
The Qiagen RNeasy kit, using mechanical lysis with beads, to isolate total RNA. PolyA selection was done through oligo-dT capture
TruSeq RNA Sample Preparation Kit (Illumina).
Samples were multiplexed. Some of the libraries were sequenced in two different lanes (e.g., NH_91_8_1 and NH_91_8_2). These were processed separtely but then combined later at the HTSEQ step

tag: time in 100% n2

value: 0 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 dsc3d


title: TEC1A3 Flp-in host cell line repeat 3

source_name: TEC1A3 Flp-in host cell line

value: transgenic Flp-In host cell line variant


title: 3998998123_R01C01

value: M


title: LV1

description: Control 1  00 Hours


title: 3998998123_R02C01


title: TEC1A3 Flp-in host cell line repeat 2


title: dsc3 deletion, 0min 100% nitrogen gas (NH_82_1_1)


title: dsc2 deletion, 240min 100% nitrogen gas (NH_78_8_2)

source_name: strain yMH947 (S288C background with repaired HAP1)

value: 240 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 dsc2d


title: A318 3 hours post exposure

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

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

scan_protocol: BeadChips were imaged using HiScan with standard recommended Illumina scanner setting

data_processing: Raw intensities extracted using GenomeStudio v2010.1 and exported into R. Lumi colour correction and background subtraction, followed by quantile and peak-based probe type correction.

label: Cy5 and Cy3

source_name: Lymphocyte enriched PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: Within 1h of collection we layered blood, diluted 1:1 with McCoy’s 5A medium (Gibco, Burlington, Canada), onto Lymphoprep (Axis, Norway) for lymphocyte-enriched PBMC isolation.  Cells were homogenized using QiaShredder Columns (Qiagen, Germantown, MD), and DNA was isolated using the DNeasy kit (Qiagen).

treatment_protocol: 15 allergic participants and 8 non-allergic controls were exposed to 2000-3500 grains/m3 of rye grass pollen in the Environmental Exposure Unit (EEU) for 3h on two consecutive days.

tag: atopic

value: no


title: dsc2 deletion, 120min 100% nitrogen gas (NH_78_6_1)

value: 120 minutes


title: A691 3 hours post exposure

value: Male

value: yes


title: dsc2 deletion, 240min 100% nitrogen gas (NH_78_8_1)


title: TEC1A3 Flp-in host cell line repeat 1

value: TEC 1A3


title: TEC1A3 Flp-in rAIRE+ cell line repeat B

value: transgenic Flp-In rAIRE+ expression variant


title: dsc2 deletion, 60min 100% nitrogen gas (NH_78_5_2)

value: 60 minutes


title: dsc2 deletion, 180min 100% nitrogen gas (NH_78_7_2)

value: 180 minutes


title: A107 3 hours post exposure


title: dsc2 deletion, 60min 100% nitrogen gas (NH_78_5_1)


title: A470 Baseline


title: A107 Baseline


title: A633 3 hours post exposure

value: Female


title: dsc2 deletion, 120min 100% nitrogen gas (NH_78_6_2)


title: A470 3 hours post exposure


title: A064 3 hours post exposure


title: dsc3 deletion, 5min 100% nitrogen gas (NH_82_2_2)

value: 5 minutes


title: dsc2 deletion, 10min 100% nitrogen gas (NH_78_3_2)

value: 10 minutes


title: dsc2 deletion, 30min 100% nitrogen gas (NH_78_4_1)

value: 30 minutes


title: A633 Baseline


title: dsc2 deletion, 10min 100% nitrogen gas (NH_78_3_1)


title: dsc2 deletion, 5min 100% nitrogen gas (NH_78_2_2)


title: dsc2 deletion, 5min 100% nitrogen gas (NH_78_2_1)


title: dsc2 deletion, 30min 100% nitrogen gas (NH_78_4_2)


title: dsc2 deletion, 180min 100% nitrogen gas (NH_78_7_1)


title: dsc2 deletion, 0min 100% nitrogen gas (NH_78_1_2)

value: 0 minutes


title: dsc2 deletion, 0min 100% nitrogen gas (NH_78_1_1)


title: LCC2-LCC9 (P40-P25) dye-swap array CGH

city: Aarhus

first: Jian

last: Li

address: The Bartholin Building

department: Institute of Biomedicine

country: Denmark

institute: Aarhus University

description:
Analysis copy number variations between the LCC cell lines
[sample] LCC2 vs. [reference] LCC9
LCC2-LCC9_P40-P25_fused.txt_LOG2RATIO CH1/CH2

hyb_protocol: The mixture of the differentially labelled cell line DNA (22~24 ug) and reference DNA (22~24 ug), together with 230 ul (1 mg/ml) Cot-1 DNA (Invitrogen) for blocking hybridization to repetitive sequences was hybridized to the BAC DNA on the CytoChip array. The hybridization was performed with HS 4800 Pro hybridization station (TECAN).

scan_protocol: The array was imaged in a GenePix 4000 B laser scanner (Axon Instruments). After optimizing exposure time, the array was scanned in Cy3 and Cy5 channels, respectively.

data_processing:
Two single-channel 16-bit images were combined for analysis using the image-analysis software BlueFuse v3.5 (BlueGnome).
Bluefuse Multi software performed analysis of the both hybridizations (of a dyeswap pair) simultaneously and combined  both hybridization results in one output file. Thus, in our study, the two dye-swap hybridizations have one raw data file (i.e., *combined_output_fused.txt).  In *combined_output_fused.txt, CH1=sample and CH2=reference.
Normalized log2 ratio (sample/reference) was calcualted. The thresholds for deletion and amplification were by default. The breakpoints in the genome were determined by the flanking clones that located the boundaries of the aberration regions.

source_name: LCC2 (derived from LCC1 with increased small-dosage TAM  treatment, estrogen-independent, and TAM-resistant) vs. LCC9 (derived from LCC1 with increased small-dosage fluvestrant treatment, estrogen-independent, and cross-resistance to fluvestrant and TAM)

label_protocol: One cell line sample (for instance, LCC2) and reference (for instance, LCC1) DNA was labelled with Cy3-dCTP and Cy5-dCTP (Amersham Biosciences), respectively, using a random priming method with the labelling kit BioPrime® DNA labelling system (Invitrogen), and the reverse labelling for sample and reference DNA was performed as well.

growth_protocol: The LCC0 is derived from MCF-7 presenting estrogen-dependent and tamoxifen-responsive phenotype. LCC1 was established from the estrogen-dependent parent cell line MCF-7 through prolonged withdrawal from potent estrogenic stimuli both in vivo and in vitro. The above in vivo selected cell line was further passaged in ovary-comprised nude mice and re-established in vitro to generate a new cell line, MCF-7/LCC1, which is estrogen-independent, but tamoxifen-responsive as its parent cell line. Furthermore, a new cell hormone-independent, tamoxifen-resistant subline, LCC2 was developed through growth of LCC1 in incrementally increased dosages of tamoxifen in vitro. And a new cell hormone-independent, cross-resistance to tamoxifen and fluvestrant subline, LCC9 was developed through growth of LCC1 in incrementally increased dosage of fluvestrant.

extract_protocol: Genomic DNA was isolated from the LCC cell lines using DNeasy® Blood & Tissue Kit (QIAGEN) following manufacturer's protocol. The extracted genomic DNA was verified by agarose gel electrophoresis, and the concentration was estimated by NanoDrop (Thermo Scientific). Furthermore, BioAnalyzer 2100 DNA Chip was used to ensure the quality, quantity and integrity for the genomic DNA. Subsequently, the genomic DNA was subject to digestion of RNase A (Invitrogen), and then purified by ethanol precipitation for subsequent analyses.

treatment_protocol: The LCC cell lines were cultured in DMEM/F12 without phenol red, supplemented with 5% DCC and 1% penicillin/streptomycin. The cells were maintained at 37°C in a humidified atmosphere of 95% ambient air and 5% CO2.

source_name: LCC9 (derived from LCC1 with increased small-dosage fluvestrant treatment, estrogen-independent, and cross-resistance to fluvestrant and TAM) vs. LCC2 (derived from LCC1 with increased small-dosage TAM  treatment, estrogen-independent, and TAM-resistant)


title: LCC2-LCC1 (P40-P42) dye-swap array CGH

description:
Analysis copy number variations between the LCC cell lines
[sample] LCC2 vs. [reference] LCC1
LCC2-LCC1_P40-P42_fused.txt_LOG2RATIO CH1/CH2

source_name: LCC2 (derived from LCC1 with increased small-dosage TAM  treatment, estrogen-independent, and TAM-resistant) vs. LCC1 (estrogen-independent and TAM-sensitive)

source_name: LCC1 (estrogen-independent and TAM-sensitive) vs. LCC2 (derived from LCC1 with increased small-dosage TAM  treatment, estrogen-independent, and TAM-resistant)


title: LCC9-LCC1 (P25-P42) dye-swap array CGH

description:
Analysis copy number variations between the LCC cell lines
[sample] LCC9 vs. [reference] LCC1
LCC9-LCC1_P25-P42_fused.txt_LOG2RATIO CH1/CH2

source_name: LCC9 (derived from LCC1 with increased small-dosage fluvestrant treatment, estrogen-independent, and cross-resistance to fluvestrant and TAM) vs. LCC1 (estrogen-independent and TAM-sensitive)

source_name: LCC1 (estrogen-independent and TAM-sensitive) vs. LCC9 (derived from LCC1 with increased small-dosage fluvestrant treatment, estrogen-independent, and cross-resistance to fluvestrant and TAM)


title: LCC1-LCC0 (P42-P62) dye-swap array CGH

description:
Analysis copy number variations between the LCC cell lines
[sample] LCC1 vs. [reference] LCC0
LCC1-LCC0_P42-P62_fused.txt_LOG2RATIO CH1/CH2

source_name: LCC1 (estrogen-independent and TAM-sensitive) vs. LCC0 (estrogen-dependent and TAM-sensitive)

source_name: LCC0 (estrogen-dependent and TAM-sensitive) vs. LCC1 (estrogen-independent and TAM-sensitive)


title: A174 3 hours post exposure


title: A434 3 hours post exposure


title: A434 Baseline


title: A691 Baseline


title: dsc1 deletion, 240min 100% nitrogen gas (NH_76_8_1)

source_name: strain yMH945 (S288C background with repaired HAP1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 dsc1d


title: dsc1 deletion, 180min 100% nitrogen gas (NH_76_7_2)


title: M0021-E-rerun

city: Stanford

first: Andrew

last: Gentles

state: CA

address: 1201 Welch Road

institute: Stanford University

data_processing:
Expression levels of genes were quantified using Salmon (Patro et al., 2017) v 0.8.2, with Gencode v23 reference transcriptome  and hg38 as the reference human genome
TPMs were summed for gene-level quantification.
Genome_build: hg38
Supplementary_files_format_and_content: Transcripts per million (TPM)

source_name: Endothelial from Melanoma

extract_protocol:
After FACS sorting, cells were saved in RNA-later. After washing in PBS, cell pellets were used to prepare RNA with the RNAeasy + micro kit with column removal of genomic RNA
SMARTer Stranded Total RNA-seq v2 Pico input mammalian kit (Clontech)
500pg-5ng of total RNA input were usedm followed by pooling of 8-12 samples into Hiseq4000 lanes

value: Melanoma

tag: population

value: Endothelial

tag: batch


title: SCC7211B-L

source_name: Lymphocyte from HNSCC

value: HNSCC

value: Pan immune


title: SCC7211B-F

source_name: Fibroblast from HNSCC

value: Fibroblast


title: A882 3 hours post exposure


title: A208 3 hours post exposure


title: dsc1 deletion, 240min 100% nitrogen gas (NH_76_8_2)

value: 240 minutes


title: A855 3 hours post exposure

value: Male

value: yes


title: A318 Baseline

value: no


title: dsc1 deletion, 180min 100% nitrogen gas (NH_76_7_1)


title: A246 3 hours post exposure


title: SCC7211B-T

source_name: Malignant from HNSCC

value: Malignant


title: dsc1 deletion, 120min 100% nitrogen gas (NH_76_6_2)

value: 120 minutes


title: A855 Baseline


title: A473 3 hours post exposure

value: Female


title: dsc1 deletion, 120min 100% nitrogen gas (NH_76_6_1)


title: SCC7211-E

source_name: Endothelial from HNSCC


title: A246 Baseline


title: SCC7211-L


title: A882 Baseline


title: SCC7211-T


title: dsc1 deletion, 30min 100% nitrogen gas (NH_76_4_2)


title: dsc1 deletion, 60min 100% nitrogen gas (NH_76_5_2)

value: 60 minutes


title: A290 3 hours post exposure


title: dsc1 deletion, 60min 100% nitrogen gas (NH_76_5_1)


title: A064 Baseline


title: SCC7209-L


title: A174 Baseline


title: dsc1 deletion, 30min 100% nitrogen gas (NH_76_4_1)


title: SCC7209-T


title: A095 3 hours post exposure


title: S-MEL0027-T

source_name: Malignant from Melanoma


title: dsc1 deletion, 10min 100% nitrogen gas (NH_76_3_2)

value: 10 minutes


title: S-MEL0027-L

source_name: Lymphocyte from Melanoma


title: A851 3 hours post exposure

source_name: Lymphocyte enriched PBMC


title: dsc1 deletion, 5min 100% nitrogen gas (NH_76_2_2)

value: 5 minutes


title: dsc1 deletion, 10min 100% nitrogen gas (NH_76_3_1)


title: S-MEL0027-F

source_name: Fibroblast from Melanoma


title: A842 3 hours post exposure


title: A208 Baseline


title: dsc1 deletion, 5min 100% nitrogen gas (NH_76_2_1)


title: dsc1 deletion, 0min 100% nitrogen gas (NH_76_1_2)

value: 0 minutes


title: S-MEL0027-E


title: SCC7190-L-rerun


title: SCC7207-T-e


title: SCC7207-L-m


title: dsc1 deletion, 0min 100% nitrogen gas (NH_76_1_1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 dsc1d


title: 346 Tumor

city: Houston

first: Sharmistha

last: Sarkar

state: Texas

address: 1515 Holcombe Boulevard

department: Genomic Medicine

institute: The University of Texas MD Anderson Cancer Center

description: Gene expression data from tumors of doxycycline inducible GEMM

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Robust multi-array average (RMA) method was used with default options (with background correction, quantile normalization, and log transformation) to normalize raw data from batches using R/Bioconductor‘s affy package

source_name: Tumor 346

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

growth_protocol: Mice were bred following the IACUC protocol at MD Anderson Cancer Center mouse facility.

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

treatment_protocol: Tumors were generated by treatment of mice with doxycycline. Control mice were also treated with doxycycline before fallopian tube extraction.

value: Tumor from GEMM


title: 367 Tumor

source_name: Tumor 367


title: A067 3 hours post exposure


title: SCC7207-L-e


title: SCC7207-E-e

value: Endothelial


title: rox1 mot3 deletion, 240min 100% nitrogen gas (NH_75_8_2)

source_name: strain yMH926 (S288C background with repaired HAP1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 rox1d mot3d


title: 316 Tumor

source_name: Tumor 316


title: 333 Tumor

source_name: Tumor 333


title: SCC7206b-L

value: HNSCC

value: Pan immune


title: 291 Tumor

source_name: Tumor 291


title: rox1 mot3 deletion, 180min 100% nitrogen gas (NH_75_7_1)

value: 180 minutes


title: SCC7205-T


title: Z2_P53_NF1_glioma_4

city: Washington DC

first: Yuan

last: Zhu

state: DC

address: 111 Michigan Ave NW

institute: Children's National Medical Center

description: phenotype: malignant glioma

hyb_protocol: Hybridization was performed following a published protocol (Miller D et al, Curr. Protoc. Hum. Genet. 2012. PMID: 18633976)

scan_protocol: GeneChips were scanned according to manufacturer recommendation

data_processing: The CEL files were preprocessed and normalized by the aroma package using a custom CDF file from AffyProbeMiner (GPL9523)

source_name: malignant glioma

label_protocol: Complementary RNA synthesis and labeling/hybridization/scanning of Mouse Genome 430 2.0 microarrays using GeneChip products (Affymetrix) was done as described in the GeneChip manual (see below fields).

growth_protocol: Cell cultures were prepared based on a previously published protocol (Wang et al., Cell 150, 816-830, 2012), and chromosome metaphase assays were performed according to an established protocol.

extract_protocol: Total RNAs and genomic DNAs were extracted from wild-type control brain tissues, high-grade gliomas and MBs by using AllPrep DNA/RNA Mini Kit (Qiagen). cDNA synthesis was performed using QuantiTect Reverse Transcription Kit (Qiagen) and RT-PCR was performed using SYBR Select Master Mix (Applied Biosystems).

treatment_protocol: Mice carry various genotypic configurations as indicated for each case.

tag: phenotype

value: malignant glioma


title: rox1 mot3 deletion, 240min 100% nitrogen gas (NH_75_8_1)

value: 240 minutes


title: FT3 Control

description: Gene expression data from fallopian tube of wild type mice treated with doxycycline

value: Fallopian tube


title: A067 Baseline

value: Male

value: no


title: A473 Baseline

value: Female


title: rox1 mot3 deletion, 180min 100% nitrogen gas (NH_75_7_2)


title: SCC7205-T-Col

value: Malignant


title: A328 3 hours post exposure

value: yes


title: rox1 mot3 deletion, 120min 100% nitrogen gas (NH_75_6_2)

value: 120 minutes


title: A681 3 hours post exposure


title: Z2_P53_NF1_glioma_2

description: phenotype: malignant glioma


title: FT2 Control


title: A674 3 hours post exposure


title: Z2_P53_NF1_glioma_3

description: phenotype: malignant glioma


title: SCC7205-L


title: rox1 mot3 deletion, 120min 100% nitrogen gas (NH_75_6_1)


title: A851 Baseline


title: A328 Baseline


title: rox1 mot3 deletion, 60min 100% nitrogen gas (NH_75_5_2)

value: 60 minutes


title: A422 3 hours post exposure


title: SCC7205-L-Col


title: SCC7211-F

value: Fibroblast


title: A681 Baseline


title: SCC7205-F


title: A290 Baseline


title: A642 3 hours post exposure


title: rox1 mot3 deletion, 30min 100% nitrogen gas (NH_75_4_2)

value: 30 minutes


title: SCC7205-E

value: Endothelial


title: SCC7205b-L


title: rox1 mot3 deletion, 60min 100% nitrogen gas (NH_75_5_1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 rox1d mot3d


title: A674 Baseline


title: Z2_P53glioma_9

description: phenotype: malignant glioma


title: rox1 mot3 deletion, 10min 100% nitrogen gas (NH_75_3_2)

value: 10 minutes


title: rox1 mot3 deletion, 30min 100% nitrogen gas (NH_75_4_1)


title: (+)/(+)6

city: Shinjuku-ku, Tokyo

first: Koji

last: Nishihara

state: -- Please Select --

address: 35 Shinanomachi

department: physiology

country: Japan

institute: Keio University school of medicine

description: iPSCs reprogrammed with 3i, maintenanced with 3i

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: The data was analyzed by using the GeneSpring GX.

label_protocol: Biotinylated RNA was prepared

extract_protocol: Total RNA was isolated by TRIzol reagent according to the manufacturer's instructions.

tag: cell type

value: iPSCs


title: Z2_P53glioma_8

description: phenotype: malignant glioma


title: SCC7205b-E

value: HNSCC


title: Z2_P53glioma_7

description: phenotype: malignant glioma

value: malignant glioma


title: (+)/(+)5

source_name: iPSCs reprogrammed with 3i, maintenanced with 3i


title: Z2_P53glioma_6

description: phenotype: malignant glioma


title: A422 Baseline


title: (+)/(+)4


title: (-)/(+)3

description: iPSCs reprogrammed without 3i, maintenanced with 3i


title: A095 Baseline


title: SCC7204-T


title: rox1 mot3 deletion, 5min 100% nitrogen gas (NH_75_2_2)

value: 5 minutes


title: SCC7204b-L

value: Pan immune


title: rox1 mot3 deletion, 10min 100% nitrogen gas (NH_75_3_1)


title: SCC7204-L


title: rox1 mot3 deletion, 0min 100% nitrogen gas (NH_75_1_2)

value: 0 minutes


title: rox1 mot3 deletion, 5min 100% nitrogen gas (NH_75_2_1)


title: SCC7202b-L


title: SCC7202-T


title: Z2_P53glioma_5

description: phenotype: malignant glioma


title: hap1 rox1 mot3 deletion, 240min 100% nitrogen gas (NH_73_8_2)

source_name: strain yMH983 (S288C background with repaired HAP1)

value: 240 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 hap1d rox1d mot3d


title: SCC7202-L

source_name: Lymphocyte from HNSCC


title: Z2_P53glioma_4

description: phenotype: malignant glioma


title: hap1 rox1 mot3 deletion, 240min 100% nitrogen gas (NH_73_8_1)


title: (-)/(+)1

source_name: iPSCs reprogrammed without 3i, maintenanced with 3i


title: Z2_P53glioma_2

description: phenotype: malignant glioma


title: SCC7202c-T

source_name: Malignant from HNSCC

value: Malignant


title: hap1 rox1 mot3 deletion, 180min 100% nitrogen gas (NH_73_7_2)

value: 180 minutes


title: rox1 mot3 deletion, 0min 100% nitrogen gas (NH_75_1_1)


title: Z2_P53glioma_3

description: phenotype: malignant glioma


title: SCC7202c-L


title: Hippocampus_ kainate_24h_rep1

city: Chaidari

first: Despina

last: Sanoudou

address: Rimini 1

department: 4th Department of Internal Medicine

country: Greece

institute: National and Kapodistrian University of Athens

description: Gene expression data from pooled RNA from 3 kainate-injected hippocampi, treatment group at 24h post injection

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Mouse Genome Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing:
The data were analyzed with Affymetrix GeneChip Operating Software (GCOS)
The primary analysis was performed using the Affymetrix Microarray Suite 5.0 (MAS 5.0 algorithm). For correlation coefficient analysis, r-values for overall, un-normalized gene expression signatures were calculated for all 18 data set pairwise comparisons. All data sets were then normalized to a slope of 1 with a reference data set (Sal_6hr_1).

source_name: Hippocampus, kainate-injected, 24 hours post injection

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.

growth_protocol: Following surgery, mice were housed in individual cages with food and water ad libitum and kept in a 12-h light-dark cycle (room temperature = 22 ± 1°C).

extract_protocol: Total RNA was extracted from dissected hippocampi using the Trizol extraction protocol as previously described (Sanoudou et al, 2003;DOI:10.1073/pnas.0330960100)

treatment_protocol: Mice were stereotaxically injected with either 50 nL of a 20 mM solution of KA (Sigma-Aldrich Chimie, St Quentin Fallavier, France) in NaCl 0.9% (i.e., 1 nmol) or saline (50 nL of NaCl 0.9%) unilaterally in the dorsal hippocampus, while under chloral hydrate (400 mg/kg, i.p.) generalized anesthesia, [anteroposterior, -2; mediolateral, -1.5; dorsoventral, -2] with bregma as the reference. KA- or saline-injected mice were decapitated at either 6h, 12h or 24h . Their brain was rapidly removed from the skull at 4°C, the injected hippocampus was dissected, and the anterior part was snap frozen in liquid nitrogen.

value: dorsal hippocampus

value: male

value: 8-10 weeks


title: Z2_Normal_forebrain_4

description: phenotype: normal

source_name: normal forebrain

value: normal forebrain

value: normal


title: (-)/(+)2


title: Hippocampus_ kainate_24h_rep2


title: SCC7202c-F

source_name: Fibroblast from HNSCC

value: Fibroblast


title: hap1 rox1 mot3 deletion, 180min 100% nitrogen gas (NH_73_7_1)


title: Z2_Normal_forebrain_3

description: phenotype: normal


title: Z2_Normal_forebrain_2

description: phenotype: normal


title: Z2_P53glioma_1

description: phenotype: malignant glioma


title: Hippocampus_ saline_24h_rep1

description: Gene expression data from pooled RNA from 3 saline-injected hippocampi, control group at 24h post injection

source_name: Hippocampus, saline-injected, 24 hours post injection


title: A642 Baseline

source_name: Lymphocyte enriched PBMC

value: Male

value: no


title: Hippocampus_ saline_24h_rep3


title: Z2_Normal_forebrain_1

description: phenotype: normal


title: Hippocampus_ kainate_12h_rep3

description: Gene expression data from pooled RNA from 3 kainate-injected hippocampi, treatment group at 12h post injection

source_name: Hippocampus, kainate-injected, 12 hours post injection


title: Hippocampus_ kainate_12h_rep2


title: FT1 Control

value: Fallopian tube


title: SCC7202c-E

source_name: Endothelial from HNSCC

value: HNSCC

value: Endothelial


title: Z2_Normal_cerebellum_4

description: phenotype: normal

source_name: normal cerebellum

value: normal cerebellum


title: hap1 rox1 mot3 deletion, 120min 100% nitrogen gas (NH_73_6_2)

value: 120 minutes


title: Hippocampus_ saline_24h_rep2


title: hap1 rox1 mot3 deletion, 120min 100% nitrogen gas (NH_73_6_1)


title: SCC7202bc-T


title: SCC7202bc-L

value: Pan immune


title: A842 Baseline

value: Female

value: yes


title: SCC7202bc-F


title: hap1 rox1 mot3 deletion, 30min 100% nitrogen gas (NH_73_4_2)

value: 30 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 hap1d rox1d mot3d


title: SCC7202bc-E


title: hap1 rox1 mot3 deletion, 30min 100% nitrogen gas (NH_73_4_1)


title: hap1 rox1 mot3 deletion, 60min 100% nitrogen gas (NH_73_5_2)

value: 60 minutes


title: SCC7200-L


title: hap1 rox1 mot3 deletion, 10min 100% nitrogen gas (NH_73_3_2)

value: 10 minutes


title: Z2_Normal_cerebellum_1

description: phenotype: normal


title: hap1 rox1 mot3 deletion, 60min 100% nitrogen gas (NH_73_5_1)


title: Hippocampus_ kainate_12h_rep1

value: dorsal hippocampus

value: male

value: 8-10 weeks


title: Hippocampus_ saline_12h_rep3

description: Gene expression data from pooled RNA from 3 saline-injected hippocampi, control group at 12h post injection

source_name: Hippocampus, saline-injected, 12 hours post injection


title: hap1 rox1 mot3 deletion, 10min 100% nitrogen gas (NH_73_3_1)


title: Z2_P53_NF1_glioma_1

description: phenotype: malignant glioma

value: malignant glioma


title: Z2_Normal_cerebellum_2

description: phenotype: normal

value: normal


title: Hippocampus_ saline_12h_rep2


title: Z1_Normal_forebrain_3

description: phenotype: normal

value: normal forebrain


title: Hippocampus_ saline_12h_rep1


title: Z1_Normal_forebrain_1

description: phenotype: normal


title: Hippocampus_ kainate_6h_rep2

description: Gene expression data from pooled RNA from 3 kainate-injected hippocampi, treatment group at 6h post injection

source_name: Hippocampus, kainate-injected, 6 hours post injection


title: Hippocampus_ kainate_6h_rep3


title: Z1_Astrocytoma_9

description: phenotype: malignant glioma


title: Hippocampus_ kainate_6h_rep1


title: Z1_Astrocytoma_8

description: phenotype: malignant glioma


title: Z1_Normal_forebrain_2

description: phenotype: normal


title: Hippocampus_ saline_6h_rep3

description: Gene expression data from pooled RNA from 3 saline-injected hippocampi, control group at 6h post injection

source_name: Hippocampus, saline-injected, 6 hours post injection


title: Z1_Astrocytoma_7

description: phenotype: malignant glioma

source_name: malignant glioma


title: SCC7197-L

value: HNSCC


title: hap1 rox1 mot3 deletion, 5min 100% nitrogen gas (NH_73_2_1)

value: 5 minutes


title: SCC7197-T

value: Malignant


title: hap1 rox1 mot3 deletion, 5min 100% nitrogen gas (NH_73_2_2)


title: SCC7200-E

value: Endothelial


title: SCC7197-E


title: SCC7197b-T


title: hap1 rox1 mot3 deletion, 0min 100% nitrogen gas (NH_73_1_1)

value: 0 minutes


title: rox1 deletion, 240min 100% nitrogen gas (NH_70_8_1)

source_name: strain yMH923 (S288C background with repaired HAP1)

value: 240 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 rox1d


title: rox1 deletion, 240min 100% nitrogen gas (NH_70_8_2)


title: SCC7197-F

value: Fibroblast


title: SCC7197b-E


title: hap1 rox1 mot3 deletion, 0min 100% nitrogen gas (NH_73_1_2)

source_name: strain yMH983 (S288C background with repaired HAP1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 hap1d rox1d mot3d


title: SCC-7195-T


title: SCC7197b-L

source_name: Lymphocyte from HNSCC

value: Pan immune


title: SCC-7195-L


title: rox1 deletion, 180min 100% nitrogen gas (NH_70_7_1)

value: 180 minutes


title: rox1 deletion, 180min 100% nitrogen gas (NH_70_7_2)


title: Hippocampus_ saline_6h_rep2

value: dorsal hippocampus


title: rox1 deletion, 120min 100% nitrogen gas (NH_70_6_2)

value: 120 minutes


title: SCC-7195-F


title: rox1 deletion, 120min 100% nitrogen gas (NH_70_6_1)


title: Sample_3 - RS1 ATRT D9 unsorted

city: Ramat-Gan

first: Tomer

last: Kalisky

address: Faculty of Engineering

department: Bioengineering

country: Israel

institute: Bar-Ilan University

data_processing:
Data from the high throughput sequencing was analyzed base on the protocol by Anders et al (Anders et al., 2013)
TopHat
DESeq
HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes normlized read counts for each gene and sample

source_name: Malignant Rhabdoid Tumor

extract_protocol:
Zymo Research's  RNA Isolation kit (the Direct-zol™-96 RNA) - purification of  RNA directly from samples in TRIZOL.
Illumina TruSeq RNA

tag: aldh level

value: Unsorted


title: rox1 deletion, 60min 100% nitrogen gas (NH_70_5_2)

value: 60 minutes


title: SCC-7195B-T

source_name: Malignant from HNSCC


title: Sample_2 - RS1 ATRT D9 ALDH-

value: Low


title: Z1_Astrocytoma_5

description: phenotype: malignant glioma

value: malignant glioma


title: Z1_Astrocytoma_6

description: phenotype: malignant glioma


title: SCC-7195B-L

value: HNSCC


title: SCC7195b-F


title: rox1 deletion, 60min 100% nitrogen gas (NH_70_5_1)


title: Hippocampus_ saline_6h_rep1

value: male

value: 8-10 weeks


title: SCC-7190-T

value: Malignant


title: Z1_Astrocytoma_3

description: phenotype: malignant glioma


title: Z1_Astrocytoma_2

description: phenotype: malignant glioma


title: Z1_Astrocytoma_1

description: phenotype: malignant glioma


title: SCC-7195B-E

value: Endothelial


title: MOLM13, sh-FIS1-#B, Rep 3

city: Aurora

first: Shanshan

last: Pei

state: CO

institute: University of Colorado

library_source: genomic

data_processing:
ChIP-seq reads were mapped to human genome using Bowtie2 v2.2.6.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file for each sample

source_name: Leukemic cell line MOLM-13 cells

extract_protocol:
QIAGEN RNeasy Plus
ThruPLEX DNA-seq Kit (Rubicon Genomics)
Samples were barcoded and pooled in equimolar amounts and sent out for next-generation sequencing

treatment_protocol: shRNA-mediated knock down

tag: cell line

tag: shRNA

tag: chip antibody

value: H3K27Ac (Active Motif Cat# 39133, RRID:AB_2561016)


title: MOLM13, CHIP input control Rep 2

value: sh-RNA Control

value: CHIP Input control


title: Z1_Astrocytoma_4

description: phenotype: malignant glioma


title: CD49fHi Lgr5Hi biological replicate 3

city: Brussels

first: Aline

last: Wuidart

address: Route de Lennik 808

country: Belgium

institute: ULB

hyb_protocol: Affymetrix MG-430 PM array strips were hybridized with 8 mg of labeled cDNA, washed, stained and scanned according to the protocol described in GeneAtlas 3’IVT express kit User Manual.

scan_protocol: Arrays were scanned with GeneAtlasImaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: All the results were normalized using the RMA normalization algorithm using R-bioconductor affy package with standard parameters. Cross experiment normalization was further performed to eliminate the batch effect using non-parametric empirical Bayes frameworks for adjusting data implemented in ComBat  function of the Surrogate Variable Analysis package (SVA) in R-bioconductor

label: Biotin

source_name: CD49fHi Lgr5Hi mammary cells from Lgr5-IRES-GFP female embryos isolated at E14

label_protocol: cDNA was labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Mice were maintained in a certified animal house according to European guidelines

extract_protocol: RNA isolation and cDNA amplification was performed as described by Gonzalez-Roca et al. (2010).In brief, 813 or 2000 cells were sorted into lysis buffer and RNA was purified using magnetic beads (RNAClean XP beads, Agencourt).RNA was reverse transcribed and cDNA was amplified using Whole Transcriptome Amplification chemistry (WTA2, Sigma Aldrich). For monitoring amplification, SYBR Green was added to the reaction; it was stopped after 25 cycles when SYBR Green signal reached a plateau. cDNA was purified using Genelute PCR Clean-Up kit (Sigma Aldrich).

treatment_protocol: Pregnant females bearing Lgr5-IRES-GFP embryos were sacrificed at 14 days of gestation and E14 embryos were collected and epidermis + mammary gland were digested in Collagenase+hyaluronidase. Single cells were stained with the appropriate antibodies and FACS sorted.

tag: tissue

value: Embryonic mouse mammary gland FACS purified cells


title: SCC-7195-E


title: MOLM13, CHIP input control Rep 1


title: rox1 deletion, 30min 100% nitrogen gas (NH_70_4_1)

value: 30 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 rox1d


title: rox1 deletion, 10min 100% nitrogen gas (NH_70_3_1)

value: 10 minutes


title: rox1 deletion, 10min 100% nitrogen gas (NH_70_3_2)


title: CD49fHi Lgr5Hi biological replicate 2


title: rox1 deletion, 30min 100% nitrogen gas (NH_70_4_2)


title: SCC-7190-L

value: Pan immune


title: rox1 deletion, 5min 100% nitrogen gas (NH_70_2_2)

value: 5 minutes


title: CD49fHi Lgr5Hi biological replicate 1


title: Sample_1 - RS1 ATRT D9 ALDH+

value: High


title: MOLM13, sh-FIS1-#B, Rep 1


title: rox1 deletion, 5min 100% nitrogen gas (NH_70_2_1)


title: SCC-7190-F

source_name: Fibroblast from HNSCC

value: Fibroblast


title: SCC7190-E


title: MOLM13, sh-RNA control, Rep 3


title: rox1 deletion, 0min 100% nitrogen gas (NH_70_1_2)

value: 0 minutes


title: SCC-7184-T

value: HNSCC


title: MOLM13, sh-RNA control, Rep 2


title: rox1 deletion, 0min 100% nitrogen gas (NH_70_1_1)


title: MOLM13, sh-FIS1-#B, Rep 2


title: MOLM13, sh-RNA control, Rep 1


title: SCC7184-L


title: mot3 deletion, 240min 100% nitrogen gas (NH_68_8_2)

source_name: strain yMH918 (S288C background with repaired HAP1)

value: 240 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 mot3d


title: SCC-7184-E


title: SA2Q+gRNA_rep1

city: STANFORD

first: Jin

middle: Billy

address: 300 Pasteur Dr.

department: Genetics

data_processing:
Raw reads were filtered using Trim Galore! to remove low quality and adaptor bases. Reads shorter than 16nt were discarded.
Filtered reads were mapped to hg19 reference genome sequences using STAR v2.4.2a with parameters: --outFilterMultimapNmax 20   --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.1   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000
RSeQC was used for quality checking and quantifying gene expression level in FPKM values.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited plain txt with header information. The FPKM value for gene expression is in the last column.

source_name: 293 Flip-In T-Rex_SNAP-ADAR2Q

extract_protocol:
RNA was isolated with the RNeasy MinElute Kit (Qiagen, Germany), treated with DNaseI and purified again with the RNeasy MinElute Kit. Purified RNA (1.2 µg) was delivered to CeGaT (Germany) for Poly(A)+ mRNA sequencing
The library was prepared from 100 ng RNA with the TruSeq Stranded mRNA Library Prep Kit (Illumina, USA)
RNA-Seq was performed with the HiSeq4000 (50 M reads, 2 × 100 bp paired end, Illumina, USA)

value: 293 Flip-In T-REx cells

tag: genotype/variation

value: SNAP-ADAR2Q gene


title: SA2Q+gRNA_rep2


title: SCC-7184-F


title: SA1Q+gRNA_rep2

source_name: 293 Flip-In T-Rex_SNAP-ADAR1Q

value: SNAP-ADAR1Q gene


title: mot3 deletion, 180min 100% nitrogen gas (NH_68_7_2)

value: 180 minutes

tag: genotype


title: TOSE PRKCI expression, rep 2

description:
TOSE.prkci2
Gene expression data from ovarian cell line with PRKCI expression.

data_processing: Robust multi-array average (RMA) method was used with default options (with background correction, quantile normalization, and log transformation) to normalize raw data from batches using R/Bioconductor's affy package (12925520). For genes, which are represented by multiple probes on the array, maximum expression value was retained for further analyses. A gene is called as differentially expressed if FDR corrected p-value is less than 0.05, which is calculated with empirical Bayes method by eBayes function in Bioconductor's limma package.

source_name: TOSE, PRKCI expression

growth_protocol: Cells were grown in RPMI 1640 media with 10% FBS in humidified incubator at 37C and 5% CO2.

treatment_protocol: Cells were infected with Lentiviral vector expressing constructs and checked for expression 48hrs post infection.

value: TOSE

value: ovarian cell line

tag: expression construct

value: PRKCI


title: mot3 deletion, 240min 100% nitrogen gas (NH_68_8_1)


title: mot3 deletion, 180min 100% nitrogen gas (NH_68_7_1)


title: SA1Q+gRNA_rep1


title: TOSE GFP control, rep 3

description:
TOSE.gfp3
Gene expression data from ovarian cell line with GFP expression.

source_name: TOSE, GFP control

value: GFP


title: mot3 deletion, 120min 100% nitrogen gas (NH_68_6_2)

value: 120 minutes


title: TOSE PRKCI expression, rep 3

description:
TOSE.prkci3
Gene expression data from ovarian cell line with PRKCI expression.


title: TOSE GFP control, rep 2

description:
TOSE.gfp2
Gene expression data from ovarian cell line with GFP expression.


title: TOSE PRKCI expression, rep 1

description:
TOSE.prkci1
Gene expression data from ovarian cell line with PRKCI expression.


title: SA2Q_rep2


title: mot3 deletion, 120min 100% nitrogen gas (NH_68_6_1)


title: SCC-7183B-E

source_name: Endothelial from HNSCC

value: Endothelial


title: SCC7183B-F


title: TOSE GFP control, rep 1

description:
TOSE.gfp1
Gene expression data from ovarian cell line with GFP expression.


title: SA2Q_rep1


title: mot3 deletion, 60min 100% nitrogen gas (NH_68_5_1)

value: 60 minutes


title: SA1Q_rep2


title: mot3 deletion, 60min 100% nitrogen gas (NH_68_5_2)


title: SCC-7183B-T

value: Malignant


title: OVCAR8 PRKCI expression, rep 3

description:
OVCAR8.prkci3
Gene expression data from ovarian cancer cell line with PRKCI expression.

source_name: OVCAR8, PRKCI expression

value: ovarian cancer cell line


title: OVCAR8 PRKCI expression, rep 2

description:
OVCAR8.prkci2
Gene expression data from ovarian cancer cell line with PRKCI expression.


title: SCC-7174-L

value: Pan immune


title: SA1Q_rep1


title: OVCAR8 PRKCI expression, rep 1

description:
OVCAR8.prkci1
Gene expression data from ovarian cancer cell line with PRKCI expression.


title: mot3 deletion, 30min 100% nitrogen gas (NH_68_4_2)

value: 30 minutes


title: SCC-7183B-L

value: HNSCC


title: SCC-7174-F

value: Fibroblast


title: SA2+gRNA_rep2

source_name: 293 Flip-In T-Rex_SNAP-ADAR2

value: 293 Flip-In T-REx cells

value: SNAP-ADAR2 gene


title: mot3 deletion, 30min 100% nitrogen gas (NH_68_4_1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 mot3d


title: SCC-7174-E


title: SA2+gRNA_rep1


title: M0026-F

source_name: Fibroblast from Melanoma

value: Melanoma


title: SA1+gRNA_rep2

source_name: 293 Flip-In T-Rex_SNAP-ADAR1

value: SNAP-ADAR1 gene


title: M0026-T

source_name: Malignant from Melanoma


title: OVCAR8 GFP control, rep 2

description:
OVCAR8.gfp2
Gene expression data from ovarian cancer cell line with GFP expression.

source_name: OVCAR8, GFP control


title: SCC7174-T


title: OVCAR8 GFP control, rep 1

description:
OVCAR8.gfp1
Gene expression data from ovarian cancer cell line with GFP expression.


title: SA1+gRNA_rep1


title: mot3 deletion, 10min 100% nitrogen gas (NH_68_3_2)

value: 10 minutes


title: M-0026L

source_name: Lymphocyte from Melanoma


title: MEL0024-E

source_name: Endothelial from Melanoma


title: ctrl_rep1

source_name: 293 Flip-In T-Rex_empty vector

value: empty vector


title: mot3 deletion, 5min 100% nitrogen gas (NH_68_2_2)

value: 5 minutes


title: ctrl_rep2


title: mot3 deletion, 0min 100% nitrogen gas (NH_68_1_2)

value: 0 minutes


title: mot3 deletion, 0min 100% nitrogen gas (NH_68_1_1)


title: mot3 deletion, 5min 100% nitrogen gas (NH_68_2_1)


title: M-0024-T


title: M-0024-L


title: mot3 deletion, 10min 100% nitrogen gas (NH_68_3_1)


title: M0024F


title: MEL0021-L


title: hap2 hap3 hap4 hap5 deletion, 240min 100% nitrogen gas (NH_66_8_1)

source_name: strain yMH1029 (S288C background with repaired HAP1)

value: 240 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 hap2d hap3d hap4d hap5d


title: hap2 hap3 hap4 hap5 deletion, 180min 100% nitrogen gas (NH_66_7_2)

value: 180 minutes


title: M-0021-T

value: Malignant


title: OVCAR8 GFP control, rep 3

description:
OVCAR8.gfp3
Gene expression data from ovarian cancer cell line with GFP expression.

value: ovarian cancer cell line

value: GFP


title: M14-VSV-B2_Rep3

city: Ottawa

first: Adrian

last: Pelin

state: Ontario

address: 501 Smyth Rd.

institute: Ottawa Hospital Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: M14 cells infected by a Nodamura B2 gene expressing VSV virus

growth_protocol: Cell grown in 10% FBS, virus grown in Vero cells

extract_protocol: RNA was extracted using the RNeasy RNA extraction kit (Qiagen).

treatment_protocol: Treatment done at MOI 0.1

value: M14 melanoma cell line

tag: growth condition

value: in-vitro cells

tag: infection

value: Nodamura B2 gene expressing VSV virus


title: M-0021-F

value: Fibroblast


title: M14-VSV-B2_Rep1


title: hap2 hap3 hap4 hap5 deletion, 120min 100% nitrogen gas (NH_66_6_2)

value: 120 minutes


title: M14-VSV-eGFP_Rep3

source_name: M14 cells infected by a eGFP expressing VSV virus

value: eGFP expressing VSV virus


title: hap2 hap3 hap4 hap5 deletion, 120min 100% nitrogen gas (NH_66_6_1)


title: hap2 hap3 hap4 hap5 deletion, 180min 100% nitrogen gas (NH_66_7_1)


title: SSCC-7151-Primary-HNSCC-TIL

source_name: Lymphocyte from HNSCC

value: HNSCC

value: Pan immune


title: M-0021-E

value: Melanoma

value: Endothelial


title: M14-Mock_Rep3

source_name: M14 cells

value: control


title: hap2 hap3 hap4 hap5 deletion, 240min 100% nitrogen gas (NH_66_8_2)

value: 240 minutes


title: M14-VSV-eGFP_Rep1


title: hap2 hap3 hap4 hap5 deletion, 60min 100% nitrogen gas (NH_66_5_2)

value: 60 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 hap2d hap3d hap4d hap5d


title: M14-VSV-eGFP_Rep2


title: M14-Mock_Rep2


title: hap2 hap3 hap4 hap5 deletion, 60min 100% nitrogen gas (NH_66_5_1)


title: SCC-7177-T

source_name: Malignant from HNSCC

value: Malignant


title: SCC-7177-L


title: hap2 hap3 hap4 hap5 deletion, 30min 100% nitrogen gas (NH_66_4_2)

value: 30 minutes


title: M14-VSV-B2_Rep2


title: hBMSCs_X_rep3

city: Dalian

first: Zhou

last: Zhang

state: Liaoning

address: Linggong Road 2

department: Environmental Science and Technology

country: China

institute: Dalian University of Technology

description: Gene expression data of human mesenchymal stem cells exposed to organic extracts of surface water from site X for 48 hours

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit in Hybridization Oven 645 and Fluidics Station 450 followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 and Command Console Software 4.0 with default settings.

data_processing: Raw data were normalized by RMA algorithm, Affy packages in R.

source_name: human mesenchymal stem cells

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The human mesenchymal stem cells were seeded into 25 cm2 flasks with approximately 4000 cells/cm2 for 24 h incubation.

extract_protocol: Total RNA was extracted using TRIZOL Reagent following the manufacturer’s instructions.

treatment_protocol: Then the culture medium was replaced by fresh MSCM containing extracts or 0.1% DMSO. Three independent cultures were used for control group and each treatment. After 48 h exposure, cells were washed twice with PBS and were immediately subjected to RNA extraction.

value: human mesenchymal stem cells

tag: cell passage


title: SCC-7177-F

source_name: Fibroblast from HNSCC


title: hap2 hap3 hap4 hap5 deletion, 30min 100% nitrogen gas (NH_66_4_1)

tag: time in 100% n2


title: SSCC-7151-Primary-HNSCC-CancerCells


title: hBMSCs_X_rep2


title: M14-Mock_Rep1

value: M14 melanoma cell line


title: hBMSCs_H6_rep3

description: Gene expression data of human mesenchymal stem cells exposed to organic extracts of surface water from site H6 for 48 hours


title: hBMSCs_X_rep1


title: SCC-7177-E

source_name: Endothelial from HNSCC


title: SCC-7176-T


title: hap2 hap3 hap4 hap5 deletion, 10min 100% nitrogen gas (NH_66_3_2)

value: 10 minutes


title: SCC-7176-F


title: hap2 hap3 hap4 hap5 deletion, 5min 100% nitrogen gas (NH_66_2_1)

value: 5 minutes


title: hBMSCs_H5_rep3

description: Gene expression data of human mesenchymal stem cells exposed to organic extracts of surface water from site H5 for 48 hours


title: hap2 hap3 hap4 hap5 deletion, 5min 100% nitrogen gas (NH_66_2_2)


title: SCC-7176-L


title: hap2 hap3 hap4 hap5 deletion, 10min 100% nitrogen gas (NH_66_3_1)


title: hap2 hap3 hap4 hap5 deletion, 0min 100% nitrogen gas (NH_66_1_2)

value: 0 minutes


title: SCC-7175-T


title: hap2 hap3 hap4 hap5 deletion, 0min 100% nitrogen gas (NH_66_1_1)


title: SCC-7176-E


title: hBMSCs_H6_rep2


title: hap5 deletion, 240min 100% nitrogen gas (NH_64_8_2)

source_name: strain yMH991 (S288C background with repaired HAP1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 hap5d


title: hBMSCs_H5_rep2


title: hBMSCs_H5_rep1


title: SCC-7175-L


title: hBMSCs_H6_rep1


title: hap5 deletion, 240min 100% nitrogen gas (NH_64_8_1)


title: hBMSCs_H2_rep2

description: Gene expression data of human mesenchymal stem cells exposed to organic extracts of surface water from site H2 for 48 hours


title: hBMSCs_H2_rep3


title: SCC-7175-F

value: Fibroblast


title: SCC-7175-E

value: HNSCC


title: hap5 deletion, 180min 100% nitrogen gas (NH_64_7_2)

value: 180 minutes


title: hap5 deletion, 180min 100% nitrogen gas (NH_64_7_1)


title: MELB-0018B-LN-Melanoma-TIL

value: Melanoma

value: Pan immune


title: hBMSCs_H1_rep3

description: Gene expression data of human mesenchymal stem cells exposed to organic extracts of surface water from site H1 for 48 hours


title: hBMSCs_H1_rep2


title: hBMSCs_H2_rep1


title: hBMSCs_H1_rep1


title: MEL-0018B-LN-Melanoma-CAF

source_name: Fibroblast from Melanoma


title: MELB-0018B-LN-Melanoma-CancerCells


title: hap5 deletion, 120min 100% nitrogen gas (NH_64_6_1)

value: 120 minutes


title: hap5 deletion, 60min 100% nitrogen gas (NH_64_5_2)


title: hap5 deletion, 120min 100% nitrogen gas (NH_64_6_2)


title: MEL-0018-Primary-Melanoma-TIL


title: MEL-0018-Primary-Melanoma-CancerCells


title: MEL-0018-Primary-Melanoma-CAF


title: hap5 deletion, 60min 100% nitrogen gas (NH_64_5_1)


title: hap5 deletion, 30min 100% nitrogen gas (NH_64_4_2)


title: hBMSCs_D_rep1

description: Gene expression data of human mesenchymal stem cells exposed to organic extracts of surface water from site D for 48 hours


title: MZ3

city: Nanjing

first: You-Qiang

last: Su

state: Jiangsu

address: 140 Hanzhong Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

data_processing:
All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the mm10 reference genome using tophat2 (v2.0.13)
Reads aligned to genes are counted by cufflinks (v2.2.1). The FPKMs are normalized usingcuffnorm. Differentially expressed genes are calculated using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: ovary

extract_protocol:
The cell was lysised and the RNA was amplificated according to Smart-seq2 procedures.
The mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment.

treatment_protocol: Mice used for the experiment were initially primed with PMSG at the dose of 5 IU/mouse. Forty-six  hours later,   they were euthanized, and the FGOs were collected.

tag: strain

tag: age

value: 6 months

value: MZ


title: MZ2


title: hBMSCs_Control_rep3

description: Gene expression data of human mesenchymal stem cells exposed to 0.1% DMSO as negative control for 48 hours


title: hBMSCs_D_rep2


title: hap5 deletion, 30min 100% nitrogen gas (NH_64_4_1)


title: hBMSCs_D_rep3


title: hBMSCs_Control_rep1


title: hBMSCs_Control_rep2


title: hap5 deletion, 10min 100% nitrogen gas (NH_64_3_2)


title: 300_120L_20W_C4_H3K27ac

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

description: LIFE-ChIP-seq data. Name format: Cell Number_Loading Volume_Washing Time_Chamber Number_Device Number(If applicable)

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed reads were aligned using bowtie 1.1.2
Reads were extended to 250bp
Sample was normalized and input subtracted
Sample was converted to BigWig format
Genome_build: hg19
Supplementary_files_format_and_content: Normalized ChIP-seq signal in BigWig format

source_name: GM12878 cell line

growth_protocol: GM12878 cells were cultured in RPMI 1640 medium (11875-093, Gibco) plus 15% fetal bovine serum (26140-079, Gibco) and 100 U/ml penicillin-streptomycin (15140-122, Gibco) at 37 ℃ in a humidified incubator with 5% CO2. Cells were sub-cultured every 2-3 days to maintain them in exponential growth phase.

extract_protocol:
Sample containing 10^6 cells was used as the starting material and centrifuged at 1,600 g for 5 min and washed twice with 1 ml cold PBS. Cells were crosslinked by adding 1 ml freshly made 1% formaldehyde and incubating at room temperature for 5 min on a shaker. Crosslinking was promptly terminated by adding 50 µl of 2.5 M glycine and shaking for 5 min. The pellet was resuspended in 130 μl Covaris buffer (10 mM Tris-HCl, pH 8.1, 1 mM EDTA, 0.1% SDS and 1× protease inhibitor cocktail) and sonicated using the following conditions. Using Covaris M 220 (Covaris), the sample was sheared at 4 oC with 75 W peak incident power, 5% duty factor, and 200 cycles per burst for 12 min. The sheared sample was centrifuged in a 4 oC centrifuge at 14,000g for 10 min, and the supernatant was transferred to a new tube. Sheared chromatin was diluted with IP buffer (20 mM Tris-HCl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100, with 1% freshly added PMSF and PIC) and aliquoted into 25 μl samples containing 250, 500, 1500, and 5,000 cell samples and stored at -80 oC.
Library preparation was performed using the Swift Bio S2 library preparation kit (Swift Biosciences) using 40 μl of purified DNA. 2.5 μl of the low EDTA TE buffer in the 50 μl amplification cycle reaction mix was replaced with 2.5 μl of 20x EvaGreen, and amplification was terminated after samples saw an >3000 RFU increase (BioRad CFX Connect). Amplified DNA was then eluted into 7 μl low EDTA TE buffer where 2 μl could be used for qPCR analysis for preliminary quality control analysis, Kappa DNA quantification, and Tapestation fragment size analysis and the other 5 μl for library pooling. Libraries were pooled at 10 nM for sequencing by Illumina HiSeq 4000 with single-end 50 nt read.
LIFE-ChIP-seq (Low-Input Fluidized-bed Enabled Chromatin Immunoprecipitation combined with sequencing), procedures are detailed in our paper

tag: cell number

value: H3K27ac (Abcam, Cat# ab4729 lot GR286678-2)


title: 300_120L_20W_C3_H3K27ac


title: MG3

value: MG


title: 300_120L_20W_C2_H3K4me3


title: MG2


title: hap5 deletion, 5min 100% nitrogen gas (NH_64_2_2)

data_processing:
Each raw file is a de-multiplexed fastq file
FASTQ Quality Trimmer, 5' and 3' ends, window size=1,step size=1,min score=10
Reads aligned to yeast genome using TopHat2
Number of reads per feature was calculated using HTSeq,mode=union
When a sample was sequenced two times (e.g., NH_101_1_1.fastqsanger.gz and NH_101_1_2.fastqsanger.gz), then the FASTQ files were processed separately resulting in two HTSEQ files (e.g., NH_101_1_1.tabular and NH_101_1_2.tabular). The counts were then added to obtain the total counts for that sample.
Genome_build: saccharomyces_cerevisiae_R64-1-1_20110208.fasta
Supplementary_files_format_and_content: tab-delimited text files, first column= feature, second column=number of reads that overlap feature


title: 300_120L_20W_C1_H3K4me3


title: MZ1


title: WT-3

value: WT


title: hap5 deletion, 5min 100% nitrogen gas (NH_64_2_1)


title: MG1


title: hap5 deletion, 10min 100% nitrogen gas (NH_64_3_1)


title: hap5 deletion, 0min 100% nitrogen gas (NH_64_1_1)


title: WT-1


title: hap3 deletion, 240min 100% nitrogen gas (NH_62_8_1)

source_name: strain yMH1011 (S288C background with repaired HAP1)

value: 240 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 hap3d


title: hap3 deletion, 180min 100% nitrogen gas (NH_62_7_2)


title: hap5 deletion, 0min 100% nitrogen gas (NH_64_1_2)


title: hap3 deletion, 120min 100% nitrogen gas (NH_62_6_2)


title: hap3 deletion, 120min 100% nitrogen gas (NH_62_6_1)


title: hap3 deletion, 180min 100% nitrogen gas (NH_62_7_1)


title: hap3 deletion, 60min 100% nitrogen gas (NH_62_5_1)

value: 60 minutes


title: hap3 deletion, 60min 100% nitrogen gas (NH_62_5_2)


title: hap3 deletion, 30min 100% nitrogen gas (NH_62_4_2)

value: 30 minutes


title: hap3 deletion, 30min 100% nitrogen gas (NH_62_4_1)


title: hap3 deletion, 10min 100% nitrogen gas (NH_62_3_1)

value: 10 minutes


title: hap3 deletion, 10min 100% nitrogen gas (NH_62_3_2)


title: hap3 deletion, 5min 100% nitrogen gas (NH_62_2_1)

value: 5 minutes


title: hap4 deletion, 240min 100% nitrogen gas (NH_62_16_2)

source_name: strain yMH989 (S288C background with repaired HAP1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 hap4d


title: WT-2


title: hap4 deletion, 240min 100% nitrogen gas (NH_62_16_1)


title: hap4 deletion, 120min 100% nitrogen gas (NH_62_14_2)


title: hap4 deletion, 180min 100% nitrogen gas (NH_62_15_2)


title: hap4 deletion, 180min 100% nitrogen gas (NH_62_15_1)


title: hap4 deletion, 60min 100% nitrogen gas (NH_62_13_2)


title: hap4 deletion, 60min 100% nitrogen gas (NH_62_13_1)


title: hap4 deletion, 30min 100% nitrogen gas (NH_62_12_2)


title: hap3 deletion, 5min 100% nitrogen gas (NH_62_2_2)


title: hap4 deletion, 10min 100% nitrogen gas (NH_62_11_2)


title: hap4 deletion, 10min 100% nitrogen gas (NH_62_11_1)


title: hap4 deletion, 5min 100% nitrogen gas (NH_62_10_2)


title: hap4 deletion, 5min 100% nitrogen gas (NH_62_10_1)


title: hap3 deletion, 0min 100% nitrogen gas (NH_62_1_2)

value: 0 minutes


title: hap4 deletion, 120min 100% nitrogen gas (NH_62_14_1)


title: hap3 deletion, 0min 100% nitrogen gas (NH_62_1_1)


title: 257.14_D20_P

first: Stephen

last: Popper

department: Division of Infectious Diseases, Dept. of Medicine

description: 257.14_D20_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

hyb_protocol: reference URL : http://dx.doi.org/10.1371/journal.pntd.0001966 Hybridization method : 8 ug of Cy5-labeled amplified RNA and 5 ug of Cy3-labeled Universal Human Reference aRNA (Stratagene) were hybridized to Human Exonic Evidence Based Oligonucleotide (HEEBO) microarrays at 65C using the HYBEX hybridization system (SciGene) for 14 hours. Following hybridization, microarrays were washed in a series of four solutions containing 2_ SSC with 0.05% SDS, 2x SSC, 1x SSC, and 0.2x SSC, respectively. The first wash was performed for 5 min at 60C; subsequent washes were performed at room temperature for 2 min each.

scan_protocol: Scan Power : 100 PMT Volts : 507 Pixel Size : 10 Laser on time : 184134 Laser Power : 3.09 Scan Date : 2012-07-11 Scan Temperature : 34.11 Scan Time : 13:48:09 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 840, 6130
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.

source_name: Strat UHR and v4 MJ doping control aa-aRNA

extract_protocol: Extraction method : Human Universal Reference RNA (Stratagene)

tag: sample name

label_protocol:
Type of label : Cy5
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-1

extract_protocol:
Extraction method : PreAnalytiX PAXgene Blood RNA Kit
Amplification method : Epicentre TargetAmp Aminoallyl aRNA Amp Kit

treatment_protocol:
Treatment : Placebo
Day : 20

tag: tissue type

value: Whole Bood


title: 257.14_D6_P

description: 257.14_D6_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 482 Pixel Size : 10 Laser on time : 184043 Laser Power : 3.09 Scan Date : 2012-07-11 Scan Temperature : 33.62 Scan Time : 12:18:28 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 840, 5670
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.

value: Human Universal Reference RNA (Stratagene)

treatment_protocol:
Treatment : Placebo
Day : 6


title: 257.14_D180_P

description: 257.14_D180_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 493 Pixel Size : 10 Laser on time : 184167 Laser Power : 3.09 Scan Date : 2012-07-11 Scan Temperature : 34.29 Scan Time : 14:21:15 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 180


title: hap3 deletion, 240min 100% nitrogen gas (NH_62_8_2)

first: Mark

extract_protocol:
The Qiagen RNeasy kit, using mechanical lysis with beads, to isolate total RNA. PolyA selection was done through oligo-dT capture
TruSeq RNA Sample Preparation Kit (Illumina).
Samples were multiplexed. Some of the libraries were sequenced in two different lanes (e.g., NH_91_8_1 and NH_91_8_2). These were processed separtely but then combined later at the HTSEQ step


title: 257.14_D28_P

description: 257.14_D28_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 500 Pixel Size : 10 Laser on time : 184184 Laser Power : 3.08 Scan Date : 2012-07-11 Scan Temperature : 34.38 Scan Time : 14:37:47 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 28


title: 257.14_D12_P

description: 257.14_D12_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 482 Pixel Size : 10 Laser on time : 184100 Laser Power : 3.08 Scan Date : 2012-07-11 Scan Temperature : 33.96 Scan Time : 13:13:40 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 12


title: 257.14_D0_P

description: 257.14_D0_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 486 Pixel Size : 10 Laser on time : 183909 Laser Power : 3.12 Scan Date : 2012-07-11 Scan Temperature : 33.19 Scan Time : 10:04:09 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol: Treatment : Placebo


title: 257.14_D42_P

description: 257.14_D42_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 495 Pixel Size : 10 Laser on time : 184151 Laser Power : 3.09 Scan Date : 2012-07-11 Scan Temperature : 34.20 Scan Time : 14:05:43 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 42


title: 257.14_D8_P

description: 257.14_D8_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 481 Pixel Size : 10 Laser on time : 184062 Laser Power : 3.10 Scan Date : 2012-07-11 Scan Temperature : 33.77 Scan Time : 12:35:32 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 8


title: 257.14_D2_P

description: 257.14_D2_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 493 Pixel Size : 10 Laser on time : 183997 Laser Power : 3.10 Scan Date : 2012-07-11 Scan Temperature : 33.47 Scan Time : 11:32:42 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 2


title: hap4 deletion, 0min 100% nitrogen gas (NH_62_9_2)


title: hap4 deletion, 0min 100% nitrogen gas (NH_62_9_1)


title: hap4 deletion, 30min 100% nitrogen gas (NH_62_12_1)


title: 257.14_D5_P

description: 257.14_D5_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 485 Pixel Size : 10 Laser on time : 184025 Laser Power : 3.09 Scan Date : 2012-07-11 Scan Temperature : 33.53 Scan Time : 12:00:14 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 5


title: hap2 deletion, 240min 100% nitrogen gas (NH_55_8_2)

source_name: strain yMH917 (S288C background with repaired HAP1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 hap2d


title: 257.14_D9_P

description: 257.14_D9_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 494 Pixel Size : 10 Laser on time : 184074 Laser Power : 3.08 Scan Date : 2012-07-11 Scan Temperature : 33.86 Scan Time : 12:48:34 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 9


title: 257.14_D14_P

description: 257.14_D14_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 497 Pixel Size : 10 Laser on time : 187066 Laser Power : 3.08 Scan Date : 2012-07-19 Scan Temperature : 34.29 Scan Time : 13:59:53 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 970, 5730
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.

treatment_protocol:
Treatment : Placebo
Day : 14


title: hap2 deletion, 240min 100% nitrogen gas (NH_55_8_1)


title: 257.14_D0_Pamp2

description: 257.14_D0_Pamp2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 484 Pixel Size : 10 Laser on time : 183925 Laser Power : 3.12 Scan Date : 2012-07-11 Scan Temperature : 33.35 Scan Time : 10:20:04 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.12_D42_P

description: 257.12_D42_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 496 Pixel Size : 10 Laser on time : 165569 Laser Power : 3.12 Scan Date : 2011-11-15 Scan Temperature : 29.56 Scan Time : 17:53:16 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 520, 6040
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.


title: hap2 deletion, 180min 100% nitrogen gas (NH_55_7_2)

value: 180 minutes


title: 257.12_D14_P

description: 257.12_D14_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 504 Pixel Size : 10 Laser on time : 165519 Laser Power : 3.13 Scan Date : 2011-11-15 Scan Temperature : 29.23 Scan Time : 17:02:43 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.12_D20_P

description: 257.12_D20_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 502 Pixel Size : 10 Laser on time : 165538 Laser Power : 3.13 Scan Date : 2011-11-15 Scan Temperature : 29.38 Scan Time : 17:21:44 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: hap2 deletion, 120min 100% nitrogen gas (NH_55_6_2)

value: 120 minutes


title: 257.12_D29_P

description: 257.12_D29_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 503 Pixel Size : 10 Laser on time : 165557 Laser Power : 3.13 Scan Date : 2011-11-15 Scan Temperature : 29.47 Scan Time : 17:40:00 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 29


title: hap2 deletion, 120min 100% nitrogen gas (NH_55_6_1)


title: hap2 deletion, 30min 100% nitrogen gas (NH_55_4_2)


title: hap2 deletion, 30min 100% nitrogen gas (NH_55_4_1)


title: hap2 deletion, 60min 100% nitrogen gas (NH_55_5_2)


title: hap2 deletion, 10min 100% nitrogen gas (NH_55_3_2)


title: hap2 deletion, 180min 100% nitrogen gas (NH_55_7_1)


title: 257.12_D9_P

description: 257.12_D9_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 506 Pixel Size : 10 Laser on time : 165486 Laser Power : 3.14 Scan Date : 2011-11-15 Scan Temperature : 28.98 Scan Time : 16:30:03 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.12_D6_P

description: 257.12_D6_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 497 Pixel Size : 10 Laser on time : 165452 Laser Power : 3.11 Scan Date : 2011-11-15 Scan Temperature : 28.68 Scan Time : 15:55:06 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.12_D8_P

description: 257.12_D8_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 507 Pixel Size : 10 Laser on time : 165468 Laser Power : 3.12 Scan Date : 2011-11-15 Scan Temperature : 28.83 Scan Time : 16:11:54 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: hap2 deletion, 10min 100% nitrogen gas (NH_55_3_1)


title: 257.12_D12_P

description: 257.12_D12_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 504 Pixel Size : 10 Laser on time : 165503 Laser Power : 3.13 Scan Date : 2011-11-15 Scan Temperature : 29.10 Scan Time : 16:46:18 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: hap2 deletion, 5min 100% nitrogen gas (NH_55_2_1)


title: 257.12_D5_P

description: 257.12_D5_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 496 Pixel Size : 10 Laser on time : 165438 Laser Power : 3.09 Scan Date : 2011-11-15 Scan Temperature : 28.46 Scan Time : 15:41:14 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: hap2 deletion, 5min 100% nitrogen gas (NH_55_2_2)


title: 257.12_D180_P

description: 257.12_D180_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 508 Pixel Size : 10 Laser on time : 165583 Laser Power : 3.12 Scan Date : 2011-11-15 Scan Temperature : 29.62 Scan Time : 18:06:54 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: hap2 deletion, 60min 100% nitrogen gas (NH_55_5_1)


title: 257.12_D0_P

description: 257.12_D0_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 519 Pixel Size : 10 Laser on time : 165385 Laser Power : 3.13 Scan Date : 2011-11-15 Scan Temperature : 27.85 Scan Time : 14:47:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: hap2 deletion, 0min 100% nitrogen gas (NH_55_1_2)


title: hap1 deletion, 180min 100% nitrogen gas (NH_54_7_2)

source_name: strain yMH939 (S288C background with repaired HAP1)

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 hap1D


title: hap1 deletion, 240min 100% nitrogen gas (NH_54_8_1)


title: hap2 deletion, 0min 100% nitrogen gas (NH_55_1_1)


title: hap1 deletion, 240min 100% nitrogen gas (NH_54_8_2)


title: 257.11_D14_P

description: 257.11_D14_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 508 Pixel Size : 10 Laser on time : 183818 Laser Power : 3.07 Scan Date : 2012-07-11 Scan Temperature : 31.85 Scan Time : 08:33:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 640, 5400
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.


title: 257.12_D0_Phyb2

description: 257.12_D0_Phyb2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 508 Pixel Size : 10 Laser on time : 165401 Laser Power : 3.12 Scan Date : 2011-11-15 Scan Temperature : 27.97 Scan Time : 15:03:47 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.11_D9_P

description: 257.11_D9_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 487 Pixel Size : 10 Laser on time : 183439 Laser Power : 3.08 Scan Date : 2012-07-10 Scan Temperature : 34.54 Scan Time : 16:33:51 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 680, 4920
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.


title: 257.11_D42_P

description: 257.11_D42_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 505 Pixel Size : 10 Laser on time : 183873 Laser Power : 3.10 Scan Date : 2012-07-11 Scan Temperature : 32.74 Scan Time : 09:27:54 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.11_D180_P

description: 257.11_D180_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 485 Pixel Size : 10 Laser on time : 183892 Laser Power : 3.11 Scan Date : 2012-07-11 Scan Temperature : 33.01 Scan Time : 09:47:44 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.11_D8_P

description: 257.11_D8_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 485 Pixel Size : 10 Laser on time : 183427 Laser Power : 3.08 Scan Date : 2012-07-10 Scan Temperature : 34.38 Scan Time : 16:20:55 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.11_D12_P

description: 257.11_D12_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 505 Pixel Size : 10 Laser on time : 183805 Laser Power : 3.08 Scan Date : 2012-07-11 Scan Temperature : 31.58 Scan Time : 08:20:28 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.11_D20_P

description: 257.11_D20_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 510 Pixel Size : 10 Laser on time : 183840 Laser Power : 3.10 Scan Date : 2012-07-11 Scan Temperature : 32.22 Scan Time : 08:55:00 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.12_D2_P

description: 257.12_D2_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 497 Pixel Size : 10 Laser on time : 165421 Laser Power : 3.08 Scan Date : 2011-11-15 Scan Temperature : 28.25 Scan Time : 15:23:39 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.11_D28_P

description: 257.11_D28_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 497 Pixel Size : 10 Laser on time : 183858 Laser Power : 3.11 Scan Date : 2012-07-11 Scan Temperature : 32.49 Scan Time : 09:12:22 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: hap1 deletion, 180min 100% nitrogen gas (NH_54_7_1)


title: hap1 deletion, 120min 100% nitrogen gas (NH_54_6_2)


title: hap1 deletion, 120min 100% nitrogen gas (NH_54_6_1)


title: hap1 deletion, 60min 100% nitrogen gas (NH_54_5_2)


title: hap1 deletion, 60min 100% nitrogen gas (NH_54_5_1)


title: hap1 deletion, 30min 100% nitrogen gas (NH_54_4_1)


title: hap1 deletion, 30min 100% nitrogen gas (NH_54_4_2)


title: hap1 deletion, 10min 100% nitrogen gas (NH_54_3_2)


title: 257.11_D5_P

description: 257.11_D5_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 476 Pixel Size : 10 Laser on time : 183393 Laser Power : 3.09 Scan Date : 2012-07-10 Scan Temperature : 33.99 Scan Time : 15:47:21 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: hap1 deletion, 10min 100% nitrogen gas (NH_54_3_1)


title: 257.11_D0_Pamp2

description: 257.11_D0_Pamp2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 496 Pixel Size : 10 Laser on time : 183356 Laser Power : 3.12 Scan Date : 2012-07-10 Scan Temperature : 33.38 Scan Time : 15:11:02 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.11_D6_P

description: 257.11_D6_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 476 Pixel Size : 10 Laser on time : 183410 Laser Power : 3.09 Scan Date : 2012-07-10 Scan Temperature : 34.20 Scan Time : 16:04:08 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.11_D2_P

description: 257.11_D2_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 485 Pixel Size : 10 Laser on time : 183374 Laser Power : 3.09 Scan Date : 2012-07-10 Scan Temperature : 33.71 Scan Time : 15:28:43 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: hap1 deletion, 5min 100% nitrogen gas (NH_54_2_2)


title: 257.11_D180_V

description: 257.11_D180_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 488 Pixel Size : 10 Laser on time : 187052 Laser Power : 3.09 Scan Date : 2012-07-19 Scan Temperature : 34.23 Scan Time : 13:46:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 180


title: 257.11_D12_V

description: 257.11_D12_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 497 Pixel Size : 10 Laser on time : 186971 Laser Power : 3.09 Scan Date : 2012-07-19 Scan Temperature : 33.83 Scan Time : 12:25:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 12


title: 257.11_D20_V

description: 257.11_D20_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 500 Pixel Size : 10 Laser on time : 187003 Laser Power : 3.09 Scan Date : 2012-07-19 Scan Temperature : 33.96 Scan Time : 12:57:05 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 20


title: 257.11_D0_P

description: 257.11_D0_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 508 Pixel Size : 10 Laser on time : 183324 Laser Power : 3.09 Scan Date : 2012-07-10 Scan Temperature : 32.80 Scan Time : 14:38:42 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 720, 5240
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.


title: 257.11_D29_V

description: 257.11_D29_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 493 Pixel Size : 10 Laser on time : 187021 Laser Power : 3.08 Scan Date : 2012-07-19 Scan Temperature : 34.08 Scan Time : 13:14:48 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 29


title: 257.11_D42_V

description: 257.11_D42_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 494 Pixel Size : 10 Laser on time : 187037 Laser Power : 3.08 Scan Date : 2012-07-19 Scan Temperature : 34.17 Scan Time : 13:30:27 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 42


title: hap1 deletion, 0min 100% nitrogen gas (NH_54_1_2)


title: hap1 deletion, 5min 100% nitrogen gas (NH_54_2_1)


title: hap1 deletion, 0min 100% nitrogen gas (NH_54_1_1)


title: BE(2C).miR204 (+ dox) #2

city: Randwick

first: Daniel

last: Carter

address: Lowy Cancer Research Centre

country: Australia

institute: Children's Cancer Institute

hyb_protocol: Performed by Ramaciotti Centre of Genomics, UNSW

data_processing: Microarrays and data were summarized and normalized with the vsn method in the R statistical programming language using the ‘limma’ package.

growth_protocol: BE(2)C.miR204 cells subcultured every 3 days. Grown in DMEM 10%FCS

extract_protocol: Total RNA was extracted using the Purelink RNA kit (Life Technologies)

treatment_protocol: Doxcycline (1mg/ml) was added to media to induce miR204 overexpression and was compared to a vehicle control (DMSO). RNA was isolated 48 hours after doxycycline was added to cells

value: neuroblastoma

value: BE(2)C neuroblastoma cells with stably incorporated miR.204

tag: treatment

value: +dox

value: miR204 overexpression


title: 257.11_D14_V

description: 257.11_D14_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 505 Pixel Size : 10 Laser on time : 186986 Laser Power : 3.08 Scan Date : 2012-07-19 Scan Temperature : 33.86 Scan Time : 12:41:03 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 14


title: 257.11_D8_V

description: 257.11_D8_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 475 Pixel Size : 10 Laser on time : 186924 Laser Power : 3.08 Scan Date : 2012-07-19 Scan Temperature : 33.62 Scan Time : 11:37:54 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 8


title: tpa1 ett1 deletion, 240min 100% nitrogen gas (NH_101_8_1)

city: Glassboro

last: Hickman

source_name: strain yMH1079 (S288C background with repaired HAP1)

value: 240 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 tpa1d ett1d


title: tpa1 ett1 deletion, 180min 100% nitrogen gas (NH_101_7_2)


title: tpa1 ett1 deletion, 180min 100% nitrogen gas (NH_101_7_1)


title: 257.13_D180_P

description: 257.13_D180_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 527 Pixel Size : 10 Laser on time : 190351 Laser Power : 3.09 Scan Date : 2012-10-18 Scan Temperature : 32.22 Scan Time : 08:23:56 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 520, 3520
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.

treatment_protocol:
Treatment : Placebo
Day : 180


title: tpa1 ett1 deletion, 240min 100% nitrogen gas (NH_101_8_2)


title: BE(2C).miR204 (no dox) #2

scan_protocol: Performed by Ramaciotti Centre of Genomics, UNSW

source_name: BE(2C).miR204 (no dox)

tag: cell line

value: no dox

value: control


title: tpa1 ett1 deletion, 120min 100% nitrogen gas (NH_101_6_2)


title: 257.11_D9_V

description: 257.11_D9_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 486 Pixel Size : 10 Laser on time : 186937 Laser Power : 3.09 Scan Date : 2012-07-19 Scan Temperature : 33.74 Scan Time : 11:51:48 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 9


title: 257.11_D2_V

description: 257.11_D2_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 486 Pixel Size : 10 Laser on time : 186874 Laser Power : 3.10 Scan Date : 2012-07-19 Scan Temperature : 33.04 Scan Time : 10:47:08 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 700, 5540
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.

treatment_protocol:
Treatment : Vaccine
Day : 2


title: BE(2C).miR204 (no dox) #1

label_protocol: Performed by Ramaciotti Centre of Genomics, UNSW


title: 257.13_D28_P

description: 257.13_D28_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 554 Pixel Size : 10 Laser on time : 190138 Laser Power : 3.11 Scan Date : 2012-10-17 Scan Temperature : 33.44 Scan Time : 18:44:59 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 28


title: 257.13_D42_P

description: 257.13_D42_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 537 Pixel Size : 10 Laser on time : 190332 Laser Power : 3.05 Scan Date : 2012-10-18 Scan Temperature : 31.88 Scan Time : 08:05:21 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 42


title: BE(2C).miR204 (+ dox) #1


title: 257.11_D0_V

description: 257.11_D0_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 475 Pixel Size : 10 Laser on time : 186825 Laser Power : 3.06 Scan Date : 2012-07-19 Scan Temperature : 32.03 Scan Time : 09:54:54 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol: Treatment : Vaccine


title: 257.13_D20_P

description: 257.13_D20_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 589 Pixel Size : 10 Laser on time : 191535 Laser Power : 3.08 Scan Date : 2012-10-20 Scan Temperature : 32.28 Scan Time : 17:05:33 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 20


title: tpa1 ett1 deletion, 120min 100% nitrogen gas (NH_101_6_1)