title: Participant # WH97

city: Bethesda

first: Wendy

middle: A.

last: Henderson

state: MD

address: 10 Center Drive, 2-1341

department: Intramural Research Program

institute: National Institutes of Health, NINR, DHHS

hyb_protocol: Biotinylated cDNA (4.4 μg) from each sample was mixed with the control buffer and hybridized on each Human Genome U133 plus 2.0 array (Affymetrix, Santa Clara, CA) at 45°C for 16 hours in a GeneChip hybridization oven at 60 rpm.

scan_protocol: GeneChip arrays were washed on Fluidics Station 450 using manufacturer’s recommended scripts and scanned on GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). GeneChip Command Console (AGCC 3.0, Affymetrix) was used to scan the images and for data acquisition.

data_processing: Expression data within each batch were generated by the RMA approach, available in the Bioconductor “Affy” package. Then, microarray expression data from the two batches were merged and normalized using quantile normalization.Next, Then, the Combat software was implemented to remove the batch effects in the microarray expression data.

source_name: Human whole blood PAXgene RNA

label_protocol: Double-stranded cDNA, was synthesized from 10 ng total RNA followed by a linear isothermal amplification to produce single-strand cDNA, which was direct labeled by biotin using Ovation Whole Blood Solution kit (NuGEN technologies, Inc., San Carlos, CA) following manufacturer’s protocol.

extract_protocol: Whole blood peripheral human samples in PAXgeneTM RNA (Qiagen, Valencia, CA) tubes and frozen at -80ºC. Total RNA was extracted and purified with RNA PAXgene kit (Qiagen, Valencia, CA)  and stored at -80oC.  RNA quantity, purity, and integrity were assessed via spectrometry and by RNA 6000 Nano LabChip kit on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Total RNA passed quality control criteria prior to microarray analysis.

tag: batch

value: Whole blood

tag: bmi


title: ME1_24h_-As_rep.2

status: Public on Jan 25 2018

type: RNA

city: Hanover

first: Thomas

middle: H.

last: Hampton

state: NH

address: Dewey Field Road, HB 7550

department: Microbiology and Immunology

country: USA

institute: Geisel School of Medicine at Dartmouth

description:
D6_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 24h that were not exposed to arsenic, replicate 2

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

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

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

molecule: total RNA

organism: Fundulus heteroclitus

source_name: ME1 SFW 24h

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

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

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

tag: population

tag: arsenic exposure

tag: hours exposed to fresh water

tag: tissue

value: gill

tag: slide number


title: ME1_1h_+As_rep.1

description:
D1_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 1h that were exposed to 100ug/l arsenic, replicate 1

source_name: ME1 SFW As 1h


title: Participant # WH95

label: biotin

organism: Homo sapiens


title: Participant # WH99


title: Participant # WH98


title: VA_1h_+As_rep.2

description:
B2_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 1h that were exposed to 100ug/l arsenic, replicate 2

source_name: VA SFW As 1h

value: VA


title: ME1_0h_+As_rep.2

description:
C6_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish not exposed to freshwater that were exposed to 100ug/l arsenic, replicate 2

source_name: ME1 SW As


title: Participant # WH94


title: VA_0h_+As_rep.2

description:
A6_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish not exposed to freshwater that were exposed to 100ug/l arsenic, replicate 2

source_name: VA SW As


title: ME1_24h_+As_rep.2

description:
D10_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 24h that were exposed to 100ug/l arsenic, replicate 2

source_name: ME1 SFW As 24h


title: Participant # WH92


title: ME1_1h_-As_rep.2

description:
C10_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish exposed to freshwater for 1h that were not exposed to arsenic, replicate 2

source_name: ME1 SFW 1h


title: Participant # WH96


title: ME1_0h_-As_rep.2

description:
C2_2
This sample is of gill tissue from saltwater acclimated Northeast Creek killifish not exposed to freshwater that were not exposed to arsenic, replicate 2

source_name: ME1 SW


title: VA_24h_+As_rep.2

description:
B10_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 24h that were exposed to 100ug/l arsenic, replicate 2

source_name: VA SFW As 24h


title: VA_24h_-As_rep.2

description:
B6_2
This sample is of gill tissue from saltwater acclimated Kings Creek killifish exposed to freshwater for 24h that were not exposed to arsenic, replicate 2

source_name: VA SFW 24h


title: Participant # WH90


title: Participant # WH89


title: Participant # WH86


title: Participant # WH84


title: Participant # WH87


title: Participant # WH79


title: Participant # WH81


title: Participant # WH85


title: Participant # WH76


title: Participant # WH82


title: Participant # WH74


title: Participant # WH75


title: Participant # WH83


title: Participant # WH88


title: Participant # WH78


title: Participant # WH69


title: Participant # WH77


title: Participant # WH71


title: Participant # WH80


title: Participant # WH70


title: Participant # WH68


title: Participant # WH67


title: 61_94_S53_R1_001

type: SRA

city: Lyon

first: Guillaume

last: Marcy

address: 8 avenue Rockefeller

country: France

institute: Universite Lyon 1

library_source: transcriptomic

data_processing:
Image analysis, intensity/extraction and correction, base calling and QC were done with NCS V1.4.1.2 and RTA v2.4.6.0 softwares.
Demultiplexing was done with Bcl2fastq v2.15.0.4 and trimming was done with Cutadapt v1.9.1
Sequenced reads were aligned on the latest mouse reference genome assembly (GRCm38) using STAR (Spliced Transcripts Alignment to a Reference) (Dobin et al., 2013).
The number of reads per transcript was calculated with FeatureCounts (Anders, et al., 2015). For each cell, Reads per Million (RPM) are divided by the length of the gene to obtain normalized Reads Per Kilobase Million (RPKM)
Genome_build: GRCm38p4
Supplementary_files_format_and_content: text file with rpkm.

organism: Mus musculus

source_name: E15 tdTom+ cells

extract_protocol:
Brains were removed and region of interest (i.e. pallium or dorsal SVZ at E15 and P2, respectively) were microdissected. tdTom+ cells were FAC-sorted on a BD FACS Aria. Single cells were isolated with the C1 Single-Cell Auto Prep System, and validated by a visual check on an inverted microscope. Reverse-transcription and preamplification of the single-cell cDNAs were done within the IFC chip using the SMARTer Ultra low RNA kit for Illumina (Clontech) according to the C1 protocol. Upon termination of the run, amplified cDNA was harvested and the concentration of cDNA assessed on a SpectraMax Gemini Fluorimeter (Molecular Devices).
RNA-sequencing libraries of the harvested cDNA were prepared using the Illumina Nextera XT DNA Sample Preparation kit.

treatment_protocol: Tamoxifen injection 12 hrs prior tissue harvesting and cells isolation

tag: strain

value: Brain

tag: cell type

value: glutamatergic progenitors

tag: age

value: embryonic day 15

tag: genotype

value: Neurog2CreERT x Ai14+/+


title: 58_72_S51_R1_001


title: 55_95_S48_R1_001


title: 59_76_S52_R1_001


title: 47_90_S42_R1_001


title: 56_54_S49_R1_001


title: 45_78_S41_R1_001


title: 51_71_S44_R1_001


title: 67_8_S59_R1_001


title: Participant # WH65


title: Participant # WH66


title: 57_66_S50_R1_001


title: 53_83_S46_R1_001


title: 43_64_S39_R1_001


title: 54_89_S47_R1_001


title: 49_53_S43_R1_001


title: 52_77_S45_R1_001


title: Participant # WH54


title: Participant # WH57


title: Participant # WH64


title: Participant # WH58


title: 40_48_S36_R1_001


title: Participant # WH51


title: Participant # WH31


title: Participant # WH42


title: Participant # WH34


title: Participant # WH26


title: Participant # WH63


title: 38_22_S34_R1_001


title: Participant # WH61


title: 37_4_S33_R1_001


title: 35_35_S31_R1_001


title: 39_36_S35_R1_001


title: 42_58_S38_R1_001


title: 33_28_S29_R1_001


title: 36_41_S32_R1_001


title: 41_52_S37_R1_001


title: 34_46_S30_R1_001


title: Participant # WH18


title: Participant # WH09


title: 32_24_S28_R1_001


title: 69_32_S61_R1_001


title: Participant # WH20


title: Participant # WH15


title: Participant # WH07


title: Participant # WH14


title: 31_18_S27_R1_001


title: 65_31_S57_R1_001


title: Participant # WH19


title: Participant # WH04


title: Participant # WH21


title: Participant # WH72


title: Participant # WH05


title: 66_2_S58_R1_001


title: 30_12_S26_R1_001


title: 28_91_S24_R1_001


title: Participant # WH01


title: Participant # WH02


title: Participant # WH56


title: 27_79_S23_R1_001


title: Participant # WH55


title: 68_26_S60_R1_001


title: 26_73_S22_R1_001


title: Participant # WH52


title: 29_6_S25_R1_001


title: 25_69_S21_R1_001


title: Participant # WH49


title: 64_25_S56_R1_001


title: Participant # WH46


title: Participant # WH45


title: 21_62_S17_R1_001


title: 22_68_S18_R1_001


title: 63_21_S55_R1_001


title: 20_56_S16_R1_001


title: 19_50_S15_R1_001


title: 18_61_S14_R1_001


title: Participant # WH44


title: 23_80_S19_R1_001


title: Participant # WH47


title: Participant # WH39


title: Participant # WH41


title: Participant # WH40


title: Participant # WH37


title: 24_86_S20_R1_001


title: Participant # WH38


title: 16_39_S12_R1_001


title: Participant # WH35


title: 62_15_S54_R1_001


title: 17_45_S13_R1_001


title: Participant # WH29


title: Participant # WH28


title: Participant # WH36


title: Participant # WH32


title: Participant # WH25


title: Participant # WH24


title: Participant # WH27


title: 13_19_S9_R1_001


title: 14_27_S10_R1_001


title: 15_33_S11_R1_001


title: 08_26_S6_R1_001


title: 06_2_S5_R1_001


title: 04_31_S4_R1_001


title: Participant # WH16


title: 03_15_S3_R1_001


title: 10_44_S7_R1_001


title: 11_7_S8_R1_001


title: 94_S60_R1_001


title: 96_S49_R1_001


title: 01_3_S1_R1_001


title: Participant # WH06


title: Participant # WH11


title: Participant # WH22


title: 90_S48_R1_001


title: Participant # WH13


title: 02_9_S2_R1_001


title: 88_S59_R1_001


title: 44_70_S40_R1_001


title: 93_S17_R1_001


title: 91_S27_R1_001


title: Participant # WH08


title: 95_S54_R1_001


title: Participant # WH33


title: 82_S58_R1_001


title: Participant # WH12


title: 79_S26_R1_001


title: 78_S47_R1_001


title: 80_S21_R1_001


title: 2/v testis, biological rep2

city: Iowa City

first: Pamela

last: Geyer

state: Iowa

address: 375 Newton Rd

department: Biochemistry

institute: University of Iowa

description: Gene expression data from dissected 3-day old testis of su(Hw) Null , replicate 2

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix GeneChip Drosophila Genome 2.0 arrays (Part No. 900531), and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven.  Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing: Data were analyzed with Partek Genomics Suite 6.5 Gene Expression pipeline, normalized with Robust Multi-array Average (RMA). Differentially expressed genes were determined using one-way Anova, as genes that showed a twofold change with 1% false discovery rate (FDR) as cutoff.

organism: Drosophila melanogaster

source_name: Drosophila testes from 3-day 2/v males

label_protocol: 50 ng total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v2 (NuGEN Technologies, San Carlos, CA, Cat. #3302) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN QIAquick PCR Purification column (QIAGEN Cat #28104) according to modifications from NuGEN.  5 μg of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

growth_protocol: Flies were raised on standard cornmeal/agar medium at 25°C, 70% humidity.

extract_protocol: RNA from ~100 pairs of testes was extracted using TRIzol (Invitrogen) followed by purification on RNeasy spin columns (Qiagen).

treatment_protocol: Testes were dissected in ice-cold PBS and stored at -80C until RNA isolation.

value: testis

value: 3 days


title: A2663/2 testis, biological rep3

description: Gene expression data from dissected 3-day old testis of su(Hw) Null , replicate 3

source_name: Drosophila testes from 3-day A2663/2 males


title: 76_S57_R1_001


title: 71_S53_R1_001


title: BL15598 testis, biological rep1

description: Gene expression data from dissected 3-day old testis of su(Hw) WT , replicate 1

source_name: Drosophila testes from 3-day BL15598 males


title: A2663/2 testis, biological rep2


title: 2/v testis, biological rep3


title: CS testis, biological rep3

description: Gene expression data from dissected 3-day old testis of su(Hw) WT , replicate 3

source_name: Drosophila testes from 3-day CS males

value: Canton S


title: BL15598 testis, biological rep3


title: 81_S16_R1_001


title: 67_S15_R1_001


title: 60_S56_R1_001


title: A2663/2 testis, biological rep1

description: Gene expression data from dissected 3-day old testis of su(Hw) Null , replicate 1


title: 61_S14_R1_001


title: 2/v testis, biological rep1


title: 59_S51_R1_001


title: 73_S25_R1_001


title: 69_S24_R1_001


title: CS testis, biological rep2

description: Gene expression data from dissected 3-day old testis of su(Hw) WT , replicate 2


title: CS testis, biological rep1


title: 62_S19_R1_001


title: 55_S13_R1_001


title: 64_S46_R1_001


title: 54_S55_R1_001


title: 57_S22_R1_001


title: SO4_Treated Tamoxifen rat spermatozoa chromatin

city: Mumbai

first: N

middle: H

last: Balasinor

state: Maharashtra

address: J. M.  Street,parel

department: Neuroendocrinology

country: India

institute: NIRRH

description:
Micrococcal nuclease digested sperm chromatin of ~150 bp
SO4
SO_4897_Sample_4_R1

library_source: genomic

data_processing:
Raw data fastq files were quality checked using FASTX toolkit with standard parameters.
Alignment to reference genome was done using Bowtie2 with standard parameters and preset option of --fast-local mode. Alignment was done on individual chromosome files instead of the whole genome
SAM files were selected for mapping quality (MAPQ>=10) using the awk command $>awk '{if($5==42) print}'|<filename>
SAM files were converted to BAM files using SAMTOOLS v1.4
Peak calling and differentials were analyzed using the DANPOS algorithm (DANPOS2). The tools used to calculate occupancy, position change and fuzziness is ‘dpos’. SO1 and SO2 were used as control replicates and compared with either SO3 or SO4, as instructed in the danpos2 manual.  Profile command was used to calculate nucleosome around transcription start site. The parameters used is as follows:  python danpos.py profile controlfilename_danpos.pois_diff.wig, treatedfilename_danpos.pois_diff.wig --genomic_sites TSS,region,gene --heatmap 1 --genefile_paths /home/mandar/Downloads/tb_refgene_danpos_curated.xls --name profile_diff__Tam_CPA --wigfile_aliases Tam,CPA --plot_colors red,green
Data were analyzed on a chromosome-level. All the autosomes are showing similar pattern, except the sex chromosomes. I have included processed data for only one of the chromosomes as representative (1 for autosomes and 1 sex chromosome). I have also made a mention of the same in my publication.
Genome_build: rn6
Supplementary_files_format_and_content: The ‘integrative.xls’ files contain position, occupancy and fuzziness changes of nucleosomes in treatment versus control (or between two files. The ‘wig’ file contains wig data of peak co-ordinates and can be used for heatmaps, transcription start site nucleosome profile plotting etc. DANPOS2 google site will have more information on the potential applications of file formats (https://sites.google.com/site/danposdoc/)

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Caudal spermatozoa

growth_protocol: Randomly bred adult male rats of the Holtzman strain (75 days old) weighing ~ 300 grams were used for the  study. All animals were kept under controlled temperature (22 ± 1°C) and humidity (55 ± 5%) with 12 hour  day and 12 hour night cycle. Food and water was provided ad libitum. Prior approval was taken from the  Institutional Animal Ethics Committee for the use of animals.

extract_protocol:
Following treatment, animals were sacrificed and the caudal portion of the epididymis was harvested. The  cauda was given 3-4 clean cuts and kept at 37°C in PBS for 30 mins. The supernatant was carefully aspirated  without disturbing the debris, to collect the spermatozoa. To ensure pure sperm population, the  supernatant was treated with 50 μl of 1M DTT/ml for 2 hours at RT. The resultant solution was scanned  under phase contrast microscope for 3-4 fields for presence of any round cells. Absence of round cells was  ensured and the solution was assumed to be pure sperm population.
The pure spermatozoa population was then subjected to the protocol as described by Hisano et al. 2013.  Briefly, the amount of spermatozoa for digestion, amount of MNase enzyme, time and temperature of  digestion was determined for optimal MNase digestion. The final protocol was carried out with 10 million  spermatozoa, 4 units of MNase enzyme, digestion carried out at 37°C for 2 mins on a heating block. The  final digestion products were run on a 2% agarose gel and band showing around 150 bp were excised.
Micrococcal nuclease digests only nucleosome bearing chromatin into approximately 150 bp fragments (single nucleosomes). After digesting the associated histones, we are left with a uniform nucleosomal library of 150 bp which is purified using agarose gel electrophoresis
Briefly,Library preparationwas performed at Genotypic Technology's Genomics facility following NEXTFlex ChIP-Seqlibrary protocol outlined in  NEXTFlex ChIP-Seqkit guide (Cat # 5143-01) using 10 ng of DNA. ChIP DNA was subjected to end-repairing, A-tailing, and ligation of the Illumina multiplexing adaptors. The resulting ligated DNA was cleaned up using Agencourt AMPURE XP beads (Beckman Coulter #A63881). These adapter ligated fragments were subjected to 5 rounds of PCR (denaturation at 98   C for 2 min, cycling (98   C for 30S, 65   C for 30S and 72   C for 1 min) and final extension at 72   C for 1 min) using primers provided in the NEXTFlex ChIP-Seq kit. Amplified library was size selected (200   400bp) by running on 2% low melting agarose gel and cleaned using MinElute column (QIAGEN, India). These size selected adapter ligated fragments were subjected to 13 rounds of PCR (denaturation at 98   C for 2 min, cycling (98   C for 30S, 65   C for 30S and 72   C for 1 min) and final extension at 72   C for 4 min) using primers provided in the NEXTFlex ChIP-Seq kit. The PCR products were purified using Agencourt AMPURE XP beads. Quantification and size distribution of the prepared library was determined using the Agilent High Sensitivity DNA Kit (Agilent Technologies) according to the manufacturers instructions and Qubit flourometer. Sequencing was performed at Genotypic Technology's Genomics facility following certified protocols from Illumina.

treatment_protocol: Tamoxifen (group 1: dose - 0.4 mg/kg/day)  and CPA (group 2: dose - 20 mg/kg/day) were administered orally to adult male rats for 60 days. The drugs  were dissolved in sterile MilliQ water. The dose and the duration of the treatment were followed as  described by Aleem et al. 2005 and Kedia-Mokashi et al. 2013. The controls (group 3) were maintained only  on sterile MilliQ water. A total of 6 animals were allocated in each group.

value: epididymis

value: spermatozoa

value: Holtzman

value: 75 days


title: Met/PIK3CA Shp2ΔH(7d)-3

city: La Jolla

first: Jijun

last: Liu

state: CA

address: Rm1220 Bay-C, Biomedical Research Facility II, 9500 Gilman Drive

department: Pathology

institute: UC San Diego

data_processing:
Sequenced reads were de-multiplexed
Sequenced reads were mapped to GRCm38 genome using STAR with parameters --runThreadN 16 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Mapped SAM files were then compressed and sorted using samtools view, sort and index
Find significant changes in gene expression using Cuffdiff
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample as well as fold changes and q value between two groups.

molecule: polyA RNA

source_name: Liver

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Library Prep Kit V2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Oncogene and sleeping beauty plasmids dissolved in PBS solution (GFP: 15μg/10g Body weight; Met/β-Catenin: 5μg/10g Body Weight each oncogene; Met/PIK3CA: 10ug/10g BW each oncogene) were hydrodynamically injected into Shp2F/F and Shp2∆H (Shp2F/F:Alb-cre) mice. Liver tissue collected 7 days after hydrodynamic injection.

value: Liver

value: Shp2 KO in hepatocytes


title: 50_S18_R1_001


title: 68_S20_R1_001


title: Met/PIK3CA Shp2ΔH(7d)-1


title: Met/PIK3CA Shp2ΔH(7d)-2


title: SO1_Control replicate 1 of rat spermatozoa chromatin

description:
Micrococcal nuclease digested sperm chromatin of ~150 bp
SO1
SO_4897_Sample_1_R1


title: SO2_Control replicate 2 of rat spermatozoa chromatin

description:
Micrococcal nuclease digested sperm chromatin of ~150 bp
SO2
SO_4897_Sample_2_R1


title: 53_S50_R1_001


title: 47_S39_R1_001


title: nia1/2 isoxaben_rep1

city: Trondheim

first: Thorsten

last: Hamann

address: Høgskoleringen 5

department: Department of Biology

country: Norway

institute: NTNU

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

organism: Arabidopsis thaliana

source_name: seedlings

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

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

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

tag: ecotype

tag: developmental stage

value: 6 days old seedlings

tag: treatment

value: isoxaben

value: seedlings


title: nia1/2 isoxaben_rep2


title: nia1/2 DMSO_rep1

value: DMSO


title: nia1/2 DMSO_rep2


title: Met/PIK3CA Shp2F/F(7d)-2


title: SO3_Treated Cyperoterone acetate rat spermatozoa chromatin

description:
Micrococcal nuclease digested sperm chromatin of ~150 bp
SO3
SO_4897_Sample_3_R1


title: Col-0 isoxaben_rep3

description: Sample same as GSM2918408

value: wild type


title: Met/PIK3CA Shp2F/F(7d)-1


title: Met/β-Catenin Shp2ΔH(7d)-3


title: Col-0 isoxaben_rep2

description: Sample same as GSM2918407


title: Col-0 DMSO_rep3

description: Sample same as GSM2918405


title: 43_S2_R1_001

value: Brain

value: glutamatergic progenitors


title: Met/β-Catenin Shp2F/F(7d)-3


title: Met/PIK3CA Shp2F/F(7d)-3


title: 46_S31_R1_001

value: embryonic day 15

value: Neurog2CreERT x Ai14+/+


title: Col-0 isoxaben_rep1

description: Sample same as GSM2918406


title: Met/β-Catenin Shp2F/F(7d)-2


title: 49_S12_R1_001


title: Met/β-Catenin Shp2ΔH(7d)-2


title: 45_S11_R1_001


title: Met/β-Catenin Shp2F/F(7d)-1


title: 35_S37_R1_001


title: 38_S5_R1_001


title: 41_S38_R1_001


title: GFP injection control Shp2ΔH-2


title: GFP injection control Shp2F/F-3


title: 36_S44_R1_001


title: 34_S30_R1_001


title: GFP injection control Shp2F/F-1


title: GFP injection control Shp2ΔH-1


title: 28_S29_R1_001


title: GFP injection control Shp2ΔH-3


title: Col-0 DMSO_rep2

description: Sample same as GSM2918404


title: Met/β-Catenin Shp2ΔH(7d)-1


title: 29_S36_R1_001


title: BL15598 testis, biological rep2

value: testis

value: 3 days


title: 44_S6_R1_001


title: 30_S43_R1_001


title: OV-MO-VC_2

city: London

first: Daniela

last: Loessner

address: Mile End Rd

country: United Kingdom

institute: Queen Mary University of London

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

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

data_processing: A quantile between array normalization was applied and differential expression was determined using the Baysian adjusted t-statistic linear model of the ‘Linear Models for Microarray Data’ (LIMMA) package in R. Annotation based on Ensembl 77 (GRCh38).

source_name: Ovarian Cancer Cells, empty vector expressing, Monoculture

label_protocol: 100 ng of total RNA was amplified and labelled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's protocol.

growth_protocol: 3D mono and coculture system: Mesothelial cells (Met-5A) were grown on melt electrospun written polycaprolactone scaffolds. Ovarian cancer cell (OV-MZ-6) spheroids were grown within RGD-functionalized hydrogels.

extract_protocol: Total cellular RNA was extracted using the Qiagen RNeasy Micro Kit including on-column DNAse-I treatment.

treatment_protocol: 3D co-cultures were constructed by assembling ovarian cancer cell-laden hydrogels with mesothelial cell-layered scaffolds. Ovarian cancer cells were either overexpressing KLK4-7 or the empty vector. 3 biological repeats of each condition were processed for microarray analysis.

tag: cell line

value: OV-MZ-6 ovarian cancer

tag: modification

value: vector control

tag: culture model

value: monoculture


title: GFP injection control Shp2F/F-2


title: OV-MO-VC_3


title: 20_S4_R1_001


title: Col-0 DMSO_rep1

description: Sample same as GSM2918403


title: OV-MO-KLK4-7_3

source_name: Ovarian Cancer Cells, KLK4-7 overexpressing, Monoculture

value: KLK4-7 overexpressing


title: 22_S42_R1_001


title: 39_S10_R1_001


title: OV-MO-VC_1


title: 19_S8_R1_001


title: OV-MO-KLK4-7_1


title: OV-CO-VC_3

source_name: Ovarian Cancer Cells, empty vector expressing, Coculture (with mesothelial cells)

value: coculture


title: OV-CO-VC_2


title: OV-CO-KLK4-7_3

source_name: Ovarian Cancer Cells, KLK4-7 overexpressing, Coculture (with mesothelial cells)


title: 18_S28_R1_001


title: 13_S7_R1_001


title: A549 cells treated with TCDD-CH223191 for 6h_rep3

city: Brno

first: Jirina

last: Prochazkova

address: Kralovopolska 135

department: Cytokinetics

country: Czech Republic

institute: Institute of Biophysics CAS

description: TCDD+CH223191 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation

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

growth_protocol: A549 cells were cultivated in plastic cell culture dishes (TPP, Transadigen, Switzerland) at 37 °C in an atmosphere of 5% CO2.

extract_protocol: Total RNA was isolated with NucleoSpin RNA II Purification Kit (Macherey Nagel, Düren, Germany) kit in accordance with the prescribed protocol provided with the kit. Quality control was performed.

treatment_protocol: A549 cells were treated with DMSO (0.01%), TCDD 10 nM, CH223191 10 microM or with TCDD+CH223191 for 6 h

value: lung carcinoma cell line

tag: treated with

value: TCDD-CH223191 for 6h


title: 17_S34_R1_001


title: OV-CO-VC_1


title: OV-CO-KLK4-7_2


title: 14_S3_R1_001


title: 16_S41_R1_001


title: 65_S52_R1_001


title: A549 cells treated with TCDD-CH223191 for 6h_rep2

description: TCDD+CH223191 2


title: 58_S45_R1_001


title: A549 cells treated with CH223191 for 6h_rep2

description: CH223191 2


title: OV-CO-KLK4-7_1


title: A549 cells treated with CH223191 for 6h_rep3

description: CH223191 3


title: 10_S40_R1_001


title: A549 cells treated with TCDD-CH223191 for 6h_rep1

description: TCDD+CH223191 1


title: A549 cells treated with CH223191 for 6h_rep1

description: CH223191 1


title: 11_S33_R1_001


title: HPC7_ChIPseq_Input

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

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

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

data_processing:
All reads were mapped to the mouse genome (mm9) using the BWA alignment software. Unique reads were kept.
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute) and  the Integrative Genomics Browser (IGB, Affymetrix).
The MACS software was used for peak identification with data from input as controls and default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: wig files; enrichment values in 25bp windows

source_name: HPC7 murine HSPC-mimicking line

growth_protocol: HPC-7 cells, a cell line mimicking HSPCs, were cultured, maintained and validated by FACS before use as previously described (Dahl et al., 2008; Wilson et al., 2010).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina 2000 sequencer following the manufacturer's protocols.

tag: chip antibody

value: input


title: Bptf-cKO_LSK_ATAC-seq replicate 3

data_processing:
ATAC-seq reads were aligned to the mouse genome (mm9) using the software BWA (version “0.7.15-r1140”) and default parameters (Li and Durbin, 2010). The software MACS2 (Feng et al., 2012) was used for calling peaks from the individual replicates, with the “--nomodel --extsize 150 –q 0.1” option.
Genome_build: mm9

source_name: LSK cells sorted from bone marrow

extract_protocol:
Total bone marrow cells were isolated from long bones (femur and tibia; 5 mice per experimental replicate) following by treatment with the ACK lysis buffer (0.15 M NH4Cl, 10 mM KHCO3, 0.1 mM EDTA [pH 7.2]) to remove red blood cells. An sorting of FACS-based analysis of lineage-/Sca1+/c-Kit+ (LSK) cells was carried out using a FACSAria II machine (UNC flow core) using the already defined protocol.
ATAC-seq was carried out utilizing the Epicentre Tn5 transposome and Illuminia kit according to standard manufacturer’s manuals.

value: LSK cells

value: bone marrow

value: ~3 month old

value: Bptf -/-


title: 63_S23_R1_001

value: Brain

value: glutamatergic progenitors


title: OV-MO-KLK4-7_2


title: 5_S32_R1_001

value: embryonic day 15

value: Neurog2CreERT x Ai14+/+


title: 23_S35_R1_001


title: A549 cells treated with TCDD for 6h_rep2

description: TCDD 2

source_name: A549_TCDD for 6h

value: TCDD for 6h


title: 3_S1_R1_001


title: A549 cells treated with DMSO for 6h_rep2

description: DMSO 2

source_name: A549_DMSO for 6h

value: DMSO for 6h


title: A549 cells treated with DMSO for 6h_rep1

description: DMSO 1


title: control_LSK_ATAC-seq replicate 2

value: control


title: A549 cells treated with TCDD for 6h_rep3

description: TCDD 3


title: A549 cells treated with TCDD for 6h_rep1

description: TCDD 1


title: 94_plaque2_S53_R1_001

source_name: P2 tdTom+ cells

value: post natal day 2


title: 88_plaque2_S52_R1_001


title: control_LSK_ATAC-seq replicate 3


title: A549 cells treated with DMSO for 6h_rep3

description: DMSO 3


title: 27_S9_R1_001

source_name: E15 tdTom+ cells


title: Bptf-cKO_LSK_ATAC-seq replicate 2


title: 86_plaque2_S19_R1_001


title: 84_plaque2_S44_R1_001


title: 95_plaque2_S50_R1_001


title: 9_plaque2_S2_R1_001


title: control_LSK_RNA-seq replicate 1

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

source_name: LSK cells sorted from control mice

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


title: HPC7_ChIPseq_H3K4me3


title: 79_plaque2_S23_R1_001


title: 70_plaque2_S43_R1_001


title: 89_plaque2_S49_R1_001


title: 60_plaque2_S51_R1_001


title: 43_plaque2_S6_R1_001


title: Bptf-cKO_LSK_ATAC-seq replicate 1


title: 93_plaque2_S18_R1_001


title: 85_plaque2_S24_R1_001


title: 77_plaque2_S48_R1_001


title: 51_plaque2_S20_R1_001


title: 59_plaque2_S47_R1_001


title: 90_plaque2_S45_R1_001


title: Bptf-cKO_LSK_RNA-seq replicate 1

source_name: LSK cells sorted from bptf_cKO mice


title: 48_plaque2_S42_R1_001


title: control_LSK_ATAC-seq replicate 1


title: 47_plaque2_S38_R1_001


title: 3_plaque2_S1_R1_001


title: 6_plaque2_S26_R1_001


title: 73_plaque2_S22_R1_001


title: 69_plaque2_S21_R1_001


title: 87_plaque2_S17_R1_001


title: 75_plaque2_S16_R1_001


title: 41_plaque2_S37_R1_001


title: 91_plaque2_S25_R1_001


title: 46_plaque2_S32_R1_001


title: 40_plaque2_S31_R1_001


title: 34_plaque2_S30_R1_001


title: 5_plaque2_S33_R1_001


title: 53_plaque2_S46_R1_001


title: 27_plaque2_S14_R1_001


title: 26_plaque2_S10_R1_001


title: 25_plaque2_S4_R1_001


title: 2_plaque2_S7_R1_001


title: 42_plaque2_S41_R1_001


title: 39_plaque2_S15_R1_001


title: 32_plaque2_S11_R1_001


title: 38_plaque2_S12_R1_001


title: 23_plaque2_S35_R1_001


title: 35_plaque2_S36_R1_001


title: 18_plaque2_S28_R1_001


title: 96_plaque1_S42_R1_001


title: 11_plaque2_S34_R1_001


title: 1_plaque2_S13_R1_001


title: 20_plaque2_S9_R1_001


title: 36_plaque2_S40_R1_001


title: 14_plaque2_S8_R1_001


title: 15_plaque2_S3_R1_001


title: 46_plaque1_S28_R1_001


title: 15_plaque1_S50_R1_001


title: 22_plaque2_S39_R1_001


title: 95_plaque1_S49_R1_001


title: 24_plaque2_S29_R1_001


title: 94_plaque1_S56_R1_001


title: input DNA

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

country: China

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Bowtie2
peaks were called using MACS.
Genome_build: hg38
Supplementary_files_format_and_content: Peaks bed files were genetated by MACS

source_name: HuH-7 cells

growth_protocol: HuH-7 cells were cultured in DMEM (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (Gibco), 100 IU/mL penicillin-streptomycin (Gibco) in a 37°C incubator with 5% CO2 and a humidified atmosphere.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

value: Liver cancer cells


title: RNApol II_ChIPSeq

value: RNApol II (Active Motif, 61667)


title: 92_plaque1_S14_R1_001


title: 12_plaque2_S27_R1_001


title: H3K27Ac_ChIPSeq

value: H3K27Ac (Active Motif, 39133)


title: 90_plaque1_S27_R1_001


title: 89_plaque1_S34_R1_001


title: HDF_r3

city: Koto-ku

first: Yutaka

last: Saito

state: Tokyo

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Gene expression of control human dermal fibroblasts (HDFs) replicate 3

hyb_protocol: The cRNA was fragmented and subsequently hybridized to the SurePrint G3 Human Gene Expression 8×60K v2 chip (Agilent Technologies) according to the manufacturer’s protocol, with 3 technical replicates used for each cell type.

scan_protocol: Microarray chips were scanned using a DNA Microarray Scanner (Agilent Technologies). Microarray data were feature-extracted using Agilent Feature Extraction software version 11.5.1.1.

data_processing: Microarray intensities were intra- and inter-array normalized using Limma package version 3.14.4 in the R statistical computing environment. Signal intensities for non-unique probe names were averaged.

source_name: Control human dermal fibroblasts (HDFs) replicate 3

label_protocol: To generate Cy3-labeled cRNA, total RNA (150 ng) was reverse-transcribed using a Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: HDFs purchased from Cell Applications were used within 3 passages from culturing of a new vial. HDFs were maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: We used the TRIzol reagent (Thermo Fisher Scientific) with 1.0-mm glass beads (WAKENBTECH), a KONTES Homogenizer pestle (Kimble Chase), and a ReliaPrep RNA Cell Miniprep System (Promega) for purification. RNA quality was assessed using a Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were collected using conventional trypsin digestion. The obtained cell suspensions were adjusted to approximately 2.5 × 105 cells/mL in PluriSTEM Human ES/iPS Medium (Merck) and then applied 2 ml to 6-well plate (Thermo Fisher Scientific) containing 20 µl of ribosome solution (1 µg /µl) that is extracted from Lactobacillus acidophillus. The plated cells were cultured for 14 days, with half the medium replaced every 3 or 4 days.

value: dermal fibroblast


title: HDF_r1

description: Gene expression of control human dermal fibroblasts (HDFs) replicate 1

source_name: Control human dermal fibroblasts (HDFs) replicate 1


title: 88_plaque1_S41_R1_001


title: RIC_r3

description: Gene expression of ribosome-induced cell clusters (RICs) replicate 3

source_name: Ribosome-induced cell clusters (RICs) replicate 3


title: HDF_r2

description: Gene expression of control human dermal fibroblasts (HDFs) replicate 2

source_name: Control human dermal fibroblasts (HDFs) replicate 2


title: 87_plaque1_S40_R1_001


title: RIC_r2

description: Gene expression of ribosome-induced cell clusters (RICs) replicate 2

source_name: Ribosome-induced cell clusters (RICs) replicate 2


title: 91_plaque1_S21_R1_001


title: 84_plaque1_S19_R1_001


title: 85_plaque1_S54_R1_001


title: 93_plaque1_S7_R1_001


title: 83_plaque1_S26_R1_001


title: 86_plaque1_S47_R1_001


title: 82_plaque1_S33_R1_001


title: 81_plaque1_S39_R1_001


title: NLS8_JA_rep3

city: Beijing

first: Fei

middle: fei

state: Beijing

address: No 19 Xin Jie Kou Wai Da Jie

department: Beijing Normal University

institute: College of Life Sciences,

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on GeneChip ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000

data_processing: Our .cel files were read into R, and normalized using the RMA procedures.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Arabidopsis thaliana plants used in this study were grown on 16 h light (120 μmol m-2 s-1)/8 h dark at 22℃ and 60% relative humidity.

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

treatment_protocol: After stratification at 4°C in the dark for 3 days, the seeds of different geneotype were transferred to the growth chamber under 16 h light (120 μmol m-2 s-1)/8 h dark at 22°C for another 3 days. Then the seedlings were moved to the 1/2 x MS plates with 10 μM ABA, 50 μM MeJA, 1 μM ACC separately or without hormones under the same culture condition for five days.

value: NLS transgenic

value: 50 µM MeJA

value: seedling


title: RIC_r1

description: Gene expression of ribosome-induced cell clusters (RICs) replicate 1

source_name: Ribosome-induced cell clusters (RICs) replicate 1


title: 80_plaque1_S46_R1_001


title: WTACC

source_name: WTACC

value: Wild type

value: 1 µM ACC


title: WTABA

source_name: WTABA

value: 10 µM ABA


title: NLS8_ACC_rep3


title: WTJA

source_name: WTJA


title: NLS5_JA_rep2


title: NLS8_ABA_rep3


title: NLS5_ACC_rep2


title: 74_plaque1_S4_R1_001

value: Brain

value: glutamatergic progenitors


title: NLS5_ABA_rep2


title: 72_plaque1_S31_R1_001

value: Neurog2CreERT x Ai14+/+


title: NES11_JA_rep3

value: NES transgenic


title: 79_plaque1_S53_R1_001


title: NLS4_JA_rep1


title: 37_plaque2_S5_R1_001


title: NLS4_ABA_rep1


title: 73_plaque1_S11_R1_001


title: 75_plaque1_S52_R1_001


title: 66_plaque1_S44_R1_001


title: 67_plaque1_S3_R1_001


title: 65_plaque1_S37_R1_001


title: NES11_ACC_rep3


title: NLS4_ACC_rep1


title: 60_plaque1_S43_R1_001


title: 71_plaque1_S24_R1_001


title: NES7_ABA_rep2


title: NES1_JA_rep1


title: NES7_ACC_rep2


title: NES7_JA_rep2


title: NES11_ABA_rep3


title: NLS5_control_rep2

value: Control


title: C065-PPT_60k

type: genomic

city: Munich

first: Roland

last: Rad

state: Bavaria

address: Ismaninger Str. 22

country: Germany

institute: Center for Translational Cancer Research (TranslaTUM)

description: PKT∆HOM mouse

hyb_protocol: The labelled DNA was hybridised onto the array slides in a 24h incubation at 65°C according to the manufacturer's (Agilent) protocol.

scan_protocol: The slides were washed and scanned and the data extracted as tab-delimited text files according to the manufacturer's protocol.

data_processing: Agilent Genomic Workbench software v7.0.4.0 was used for aCGH data preprocessing. Legacy centralization option was used for re-centralization of raw log ratios to the most common ploidy state. ADM-2 algorithm was applied for aberration calling. Normalized and curated data was imported into R.

source_name: Corresponding tail

label_protocol: 250ng of genomic DNA were fluorescence labelled (Cy3 sample and Cy5 reference) by random primed labelling using the Enzo Oligo Array CGH Labelling kit according to the manufacturer's protocol. The labelling activity was determined using a NanoDrop spectrophotometer.

growth_protocol: For all primary culture experiments, culturing medium (DMEM supplemented with 10% FCS and 1x P/S) and cultures with less than 10 passages were used.

extract_protocol: gDNA from murine primary cell culture pellets was isolated using the DNeasy Blood & Tissue Kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: No treatment was applied.

tag: strain/background

value: mixed (C57Bl/6;129S6/SvEv)

tag: genotype/variation

value: PKT<delta>HOM

tag: originating tissue

value: tail

source_name: Primary pancreatic cancer cell culture

value: pancreatic cancer


title: 5_plaque1_S8_R1_001

tag: tissue

value: post natal day 2


title: 59_plaque1_S36_R1_001


title: NES1_ABA_rep1


title: 56_plaque1_S22_R1_001


title: NLS4_control_rep1


title: wild type_control_rep2

source_name: wild type_control


title: 47_plaque1_S35_R1_001

source_name: P2 tdTom+ cells


title: C3356-PPT_60k

description: PKT∆HOM mouse


title: NLS8_control_rep3


title: NES7_control_rep2


title: 45_plaque1_S55_R1_001


title: C2532-PPT_60k

description: PKT∆HOM mouse


title: wild type_control_rep1


title: 42_plaque1_S20_R1_001


title: C3443-PPT_60k

description: PKT∆HOM mouse


title: C2810-PPT_60k

description: PKT∆HOM mouse


title: KG526-PPT_60k

description: PKT∆HET mouse

value: PKT<delta>HET


title: NES1_ACC_rep1


title: 53_plaque1_S15_R1_001


title: C4468-PPT_60k

description: PKT∆HET mouse


title: 44_plaque1_S48_R1_001


title: NES1_control_rep1


title: 51_plaque1_S1_R1_001


title: KG471-PPT_60k

description: PKT∆HET mouse


title: NES11_control_rep3


title: C5081-PPT_60k

description: PKT∆HET mouse


title: 34_plaque1_S5_R1_001


title: C2922-PPT_60k

description: PKT∆HET mouse


title: 41_plaque1_S13_R1_001


title: 40_plaque1_S6_R1_001


title: 35_plaque1_S12_R1_001


title: C4604-PPT_60k

description: PKT∆HET mouse


title: 24_plaque1_S10_R1_001


title: 33_plaque1_S32_R1_001


title: 27_plaque1_S45_R1_001


title: 22_plaque1_S17_R1_001


title: 18_plaque1_S16_R1_001


title: 26_plaque1_S38_R1_001


title: C5040-PPT_60k

description: PKP∆HOM mouse

value: PKP<delta>HOM


title: 29_plaque1_S18_R1_001


title: W22-PPT_60k

description: PKP∆HOM mouse


title: R254-PPT_60k

description: PKP∆HOM mouse


title: C4692-PPT_60k

description: PKP∆HOM mouse


title: 30_plaque1_S25_R1_001


title: KG537-PPT_60k

description: PKP∆HOM mouse


title: 21_plaque1_S51_R1_001


title: C5315-PPT_60k

description: PKP∆HOM mouse


title: 17_plaque1_S23_R1_001


title: AA966-PPT_60k

description: PKP∆HOM mouse


title: C4466-PPT_60k

description: PKT∆HET mouse


title: 6554-PPT_60k

description: PKP∆HOM mouse


title: 13_plaque1_S9_R1_001


title: 14_plaque1_S2_R1_001


title: 16_plaque1_S30_R1_001


title: smyd4

first: deyong

last: xiao

address: Room 308, Mingdao building, Research Center For Birth Defects, School of Basic Medical Sciences,  Fudan University, 130 Dongan Road, Shanghai , China

institute: Fudan university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008)
Genome_build: ftp://ftp.ensembl.org/pub/release-89/fasta/danio_rerio/dna/
Supplementary_files_format_and_content: text file with RPKM

organism: Danio rerio

source_name: heart

extract_protocol:
zebrafish heart were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

value: Tu

value: homozygous smyd4 L544Efs*1


title: KG564-PPT_60k

description: PKP∆HOM mouse


title: 14390-PPT_60k

description: PKP∆HOM mouse


title: 10_plaque1_S29_R1_001


title: wt

value: wt


title: JG_35

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

data_processing:
The raw sequence data generated was converted into FASTQ files using Illumina CASSAVA 1.8.2, which were then imported into CLC Genomics Workbench 7.5.1. Low quality base pairs were trimmed from the ends and the sequence reads were mapped to the C. japonicus reference genome with RPKM values calculated for genes. Log2 transformation and quantile normalization was performed for the RPKM values and a Student’s T-test conducted to compare gene expression between various groups of samples. Additional analysis and visualization of the data was performed using ArrayStar.
Genome_build: GCA_000019225.1
Supplementary_files_format_and_content: Tab-delimited text files includes comparative analysis for glucose vs xylan (exponential) samples, RPKM replicates, and RPKM means
Supplementary_files_format_and_content: Glu_vs_XyG_EXP.txt Comparative analysis (fold change)
Supplementary_files_format_and_content: Glu_vs_XyG_RPKM_Means.txt Normalized RPKM means for glucose (GSE90955) and xyloglucan growth conditions
Supplementary_files_format_and_content: Glu_vs_XyG_RPKM_Replicates.txt Normalized individual RPKM measurements for glucose (GSE90955) and xyloglucan grown samples

organism: Cellvibrio japonicus

source_name: bacterial cell pellet

growth_protocol: MOPS defined medium

extract_protocol:
Standard extraction protocols
Sstandard Illumina protocols

treatment_protocol: 95%EtOH:5%Phenol to stop cellular metabolism

value: WT

value: xyloglucan - stationary


title: JG_36


title: JG_34


title: KG513-PPT_60k

description: PKP∆HOM mouse


title: NS490-PPT_60k

description: PKP∆HOM mouse


title: JG_33

value: xyloglucan - exponential


title: C4340-PPT_60k

description: PKP∆HOM mouse


title: C4617-PPT_60k

description: PKP∆HOM mouse


title: NS418-PPT_60k

description: PKP∆HOM mouse


title: Mutu_3_EBVloss

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

description: Gene expression data from EBV loss cell line

hyb_protocol: 10ug of fragmented cRNA was hybridized to HG-U133 Plus 2.0 microarrays

scan_protocol: Affymetrix Standard protocol  Affymetrix Standard protocol

data_processing:
Probe level quantile normalisation  and robust multi-array analysis on the raw CEL files were performed using the affy package of the Bioconductor project and HGU133Plus2_Hs_ENTREZG v21.0.0
log2 gene expression obtained by RMA method of the affy package in Bioconductor using default parameters

source_name: Mutu_EBV loss

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 25 ug total RNA

growth_protocol: Cells were maintained in exponential growth in RPMI1640 medium containing 10% foetal calf serum and 2mM glutamine.          Cells were maintained in exponential growth in RPMI1640 medium containing 10% foetal calf serum and 2mM glutamine.          Cells were maintained in exponential growth in RPMI1640 medium containing 10% foetal calf serum and 2mM glutamine.

extract_protocol: Total RNA was prepared using Trizol according to the manufacturer's instructions. RNA quality was confirmed with an Agilent 2100 BioAnalyser and all samples had RIN values >9.8.

value: Mutu

tag: cell line clone id

tag: ebv status

value: EBV loss


title: Eli_c5_EBVpos

description: Gene expression data from EBV positive cell line

source_name: Elijah_EBV positive

value: Elijah

value: EBV positive


title: Awia_5e10_EBVloss

source_name: Awia_EBV loss

value: Awia


title: AA1377-PPT_60k

description: PKC∆HOM mouse

value: mixed (C57Bl/6;129S6/SvEv)

value: PKC<delta>HOM

value: tail


title: AA168-PPT_60k

description: PKC∆HOM mouse

value: pancreatic cancer


title: AA456-PPT_60k

description: PKC∆HOM mouse


title: AA852-PPT_60k

description: PKC∆HOM mouse


title: AA172-PPT_60k

description: PKC∆HOM mouse


title: Awia_9_EBVpos

source_name: Awia_EBV positive


title: Mutu_59_EBVpos

source_name: Mutu_EBV positive


title: Awia_gl2_a11_EBVloss


title: AA169-PPT_60k

description: PKC∆HOM mouse


title: JG_31


title: JG_32


title: Eli_1f2_EBVloss

source_name: Elijah_EBV loss


title: AA1261-PPT_60k

description: PKC∆HOM mouse


title: Mutu_1_EBVloss


title: AA1370-PPT_60k

description: PKC∆HOM mouse


title: 13886-PPT_60k

description: PKP∆HOM mouse

value: PKP<delta>HOM


title: AA728-PPT_60k

description: PKC∆HOM mouse


title: AA821-PPT_60k

description: PKC∆HOM mouse


title: Akata_e1_EBVpos

source_name: Akata_EBV positive

value: Akata


title: AA267-PPT_60k

description: PKC∆HOM mouse


title: AA348-PPT_60k

description: PKC∆HOM mouse


title: AA1165-PPT_60k

description: PKC∆HOM mouse


title: AA1467-PPT_60k

description: PKC∆HOM mouse


title: Akata_d3_EBVloss

source_name: Akata_EBV loss


title: Akata_a3_EBVloss


title: 1Week_rep3_3604

status: Public on Jan 24 2018

city: Philadelphia

first: Amber

state: Pennsylvania

address: 3400 Civic Center Blvd, SCTR 12-164

department: Genetics

institute: University of Pennsylvania

description:
#3604
AtacSeqW1.pval.signal.bigwig

data_processing:
For RNA-seq, poor quality sequences was trimmed from FASTQ files and then aligned to mouse genome mm9 using RUM (Grant et al. 2011). Differential gene expression was identified with EdgeR.
For ATAC-seq, individual FASTQ files were processed with the pipeline developed by the Kundaje lab (https://github.com/kundajelab/atac_dnase_pipelines) first and aligned bam files were obtained. Bam files from the same biological replicate were then merged and analyzed with the same pipeline as described above.
Genome_build: mm9
Supplementary_files_format_and_content: xls file contains the differential gene expression for the TRAP-seq data in the 'Compare' tab. The 'QuantileNormReads' and the 'RawReads' tabs contain the quantile-normalized reads and the raw read counts for the TRAP-seq data, respectively. The BigWig files contain the peak calling results for the pooled control and 1-week regeneration samples, respectively. Peaks were called based on a cut-off of p-value < 0.05.

source_name: Hepatocytes

extract_protocol:
For TRAP-seq, livers were prepared as previously described (Heiman et al. 2014). Briefly, liver homogenates were incubated with GFP-conjugated magnetic beads to affinity purify GFP-tagged ribosomal subunit L10A along with the attached translating mRNAs. RNAs were then isolated with the Absolutely RNA Nanoprep Kit (#400753, Agilent). For ATAC-seq, hepatocyte nuclei were prepared as previously described (Fang et al. 2014) and GFP-positive nuclei were labeled with Alexa Fluor 647 anti-GFP antibody (#338006, clone FM264G, 1:25, BioLegend) and sorted using BD AriaII.
For TRAP-seq, mRNAs were isolated with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (#E7490, NEB) followed by cDNA library construction with the NEBNext® Ultra RNA Library Prep Kit for Illumina® (#E7530S, NEB). For ATAC-seq, nueclei were tagmented and PCR amplified according to previously published ATAC-seq protocol (Ackermann et al. 2016).

treatment_protocol: Fah-/- mice were hydrodynamically injected with plasmids coexpressing the Fah transgene and either GFP-L10A (for TRAP-seq) or SUN1-GFP (for ATAC-seq) fusion proteins. Liver injury was then induced and the mice were repopulated for one or four weeks prior to extracting repopulating hepatocytes. All quiescent control mice were injected with AAV8.TBG.Cre to induce hepatocyte-specific expression of GFP-L10A (for TRAP-seq) or SUN1-GFP (for ATAC-seq) and livers were harvested one week after virus injection.

tag: strain

value: Fah-/-

tag: cell state

value: 1-week regenerating

tag: cell type

value: Hepatocytes


title: 1Week_rep1_2301

description:
#2301
AtacSeqW1.pval.signal.bigwig

tag: genotype


title: Quiescent_rep1_SUN1GFP

description:
#SUN1GFP1
AtacSeqCtl.pval.signal.bigwig

value: Quiescent


title: Akata_d1_EBVpos


title: AA199-PPT_60k

description: PKC∆HOM mouse


title: Wild Type

city: College Station

first: Cole

middle: M

last: McQueeen

address: 4467 VMRB

institute: Texas A&M University

data_processing:
FASTQ reads were de-multiplexed and assessed for quality using FastQC.
Sample reads were then aligned to mouse reference genome assembly (mm10, ENSEMBL 74) using HISAT2
Differential gene expression was identified using cuffdiff
Genome_build: mm10, ENSEMBL 74

source_name: Mammary gland

extract_protocol:
Mouse mammary glands were harvested from virgin WT (n=3) and Per2ldc (n=4) mice followed by a primary mammary epithelial cell isolation.  Glands were homogenized on a 10cm plate using scalpels and digested in DMEM/F12 containing 10% FBS and 2mg/ml collagenase A for 30 min at 37°C.  Samples were then treated with DNAseI and pulse spins performed to remove red blood cells. RNA was isolated from MECs using the High Pure RNA Isolation Kit (Roche, Mannheim, Germany).
Illumina true seq

value: Wild Type

value: Mammary gland

value: mammary epithleial cells


title: 1Week_rep3_3603

description:
#3603
AtacSeqW1.pval.signal.bigwig


title: Per2ldc

value: mammary epithelial cells


title: AA1116-PPT_60k

description: PKC∆HOM mouse


title: Mutu_148_EBVpos

value: Mutu


title: Awia_20_EBVpos

value: EBV positive


title: 54_15_hMSC-hTERT_GFP

city: Columbus

first: Nilay

last: Shah

state: Ohio

address: 700 Children’s Dr.

department: Center for Childhood Cancer and Blood Diseases

institute: The Research Institute at Nationwide Children’s Hospital

description:
processed data file: 160509_RNAseq_de.xlsx
54_15_hMSC-hTERT_GFP

data_processing:
Each sample was aligned to the reference using version 2.5.2b of STAR (https://www.ncbi.nlm.nih.gov/pubmed/23104886)
Transcript features were identified from the GFF file provided with the GRCh38.p5 assembly from NCBI and raw coverage counts were calculated using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html)
The raw RNA-Seq gene expression data was normalized and post-alignment statistical analyses were performed using DESeq2 (http://genomebiology.com/2014/15/12/550) and custom analysis scripts written in R
Transcripts were considered significantly differentially expressed using a 10% false discovery rate (DESeq2 adjusted p value <= 0.1)
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: Excel spreadsheet containing normalized read counts for each sample and differential expression data for each feature

source_name: hTERT-hMSC_GFP overexpression

growth_protocol: cells grown in DMEM+10% FBS

extract_protocol:
RNA was extracted with the Nucleospin RNA Isolation kit (Takara Bio). 1 mcg of total RNA was used for library construction.
RNA libraries prepared for sequencing using standard Illumina protocols.

treatment_protocol: GapmeR treated cells transfected with GapmeR (10 nM) by use of Lipofectamine 3000, per Exiqon protocol. 48 hours after transfection, cells harvested by scraping. For hTERT-hMSCs, stable pools of cells generated by successive lentiviral infection expressing either GFP or GFP and HOTAIR, then with GFP or GFP and EWS-FLI1. Cells were selected with puromycin and expression confirmed by RT-qPCR (HOTAIR and EWS-FLI1) and western blot (for EWS-FLI1). Cells then expanded and harvested for RNA extraction by scraping.

tag: cell line background

value: hTERT-hMSC

value: hTERT-immortalized mesenchymal stem cell

value: GFP overexpression


title: 62_17_hMSC-hTERTHOTAIR_EWS-Fli-1

description:
processed data file: 160509_RNAseq_de.xlsx
62_17_hMSC-hTERTHOTAIR_EWS-Fli-1

source_name: hTERT-hMSC_GFP, HOTAIR, and EWS-FLI1 overexpression


title: 63_17_hMSC-hTERTHOTAIR_EWS-Fli-1

description:
processed data file: 160509_RNAseq_de.xlsx
63_17_hMSC-hTERTHOTAIR_EWS-Fli-1

value: GFP, HOTAIR, and EWS-FLI1 overexpression


title: 61_17_hMSC-hTERTHOTAIR_EWS-Fli-1

description:
processed data file: 160509_RNAseq_de.xlsx
61_17_hMSC-hTERTHOTAIR_EWS-Fli-1


title: 55_15_hMSC-hTERT_GFP

description:
processed data file: 160509_RNAseq_de.xlsx
55_15_hMSC-hTERT_GFP


title: 56_15_hMSC-hTERT_GFP

description:
processed data file: 160509_RNAseq_de.xlsx
56_15_hMSC-hTERT_GFP


title: 51_14_hMSC-hTERTParental

description:
processed data file: 160509_RNAseq_de.xlsx
51_14_hMSC-hTERTParental


title: 60_16_hMSC-hTERT_HOTAIR

description:
processed data file: 160509_RNAseq_de.xlsx
60_16_hMSC-hTERT_HOTAIR

source_name: hTERT-hMSC_GFP and HOTAIR overexpression

value: GFP and HOTAIR overexpression


title: 57_16_hMSC-hTERTHOTAIR

description:
processed data file: 160509_RNAseq_de.xlsx
57_16_hMSC-hTERTHOTAIR


title: Quiescent_rep2_SUN1GFP

description:
#SUN1GFP2
AtacSeqCtl.pval.signal.bigwig


title: 1Week_rep2_2302

description:
#2302
AtacSeqW1.pval.signal.bigwig


title: 17-0116_SK-ES_CTL_B_4

description:
processed data file: 170425_RNASeq_de.xlsx
17-0116_SK-ES_CTL_B_4

source_name: SK-ES_control GapmeR

value: SK-ES

value: Ewing sarcoma cell line

value: control GapmeR


title: 52_14_hMSC-hTERTParental

description:
processed data file: 160509_RNAseq_de.xlsx
52_14_hMSC-hTERTParental


title: 50_14_hMSC-hTERTParental

description:
processed data file: 160509_RNAseq_de.xlsx
50_14_hMSC-hTERTParental


title: 59_16_hMSC-hTERT_HOTAIR

description:
processed data file: 160509_RNAseq_de.xlsx
59_16_hMSC-hTERT_HOTAIR


title: 53_15_hMSC-hTERTGFP

description:
processed data file: 160509_RNAseq_de.xlsx
53_15_hMSC-hTERTGFP


title: 58_16_hMSC-hTERT_HOTAIR

description:
processed data file: 160509_RNAseq_de.xlsx
58_16_hMSC-hTERT_HOTAIR


title: 17-0117_SK-ES_HOT_GapmeR_1

description:
processed data file: 170425_RNASeq_de.xlsx
17-0117_SK-ES_HOT_GapmeR_1

source_name: SK-ES_HOTAIR-repressing GapmeR

value: HOTAIR-repressing GapmeR


title: 17-0120_SK-ES_HOT_GapmeR_4

description:
processed data file: 170425_RNASeq_de.xlsx
17-0120_SK-ES_HOT_GapmeR_4


title: 48_12_A673HOTAIRGapmer

description:
processed data file: 160205_RNASeq_de.xlsx
48_12_A673HOTAIRGapmer

source_name: A673_HOTAIR-repressing GapmeR


title: 17-0113_SK-ES_CTL_B_1

description:
processed data file: 170425_RNASeq_de.xlsx
17-0113_SK-ES_CTL_B_1


title: 64_17_hMSC-hTERTHOTAIR_EWS-Fli-1

description:
processed data file: 160509_RNAseq_de.xlsx
64_17_hMSC-hTERTHOTAIR_EWS-Fli-1


title: 17-0115_SK-ES_CTL_B_3

description:
processed data file: 170425_RNASeq_de.xlsx
17-0115_SK-ES_CTL_B_3


title: 49_14_hMSC-hTERTParental

description:
processed data file: 160509_RNAseq_de.xlsx
49_14_hMSC-hTERTParental


title: 47_12_A673HOTAIRGapmer

description:
processed data file: 160205_RNASeq_de.xlsx
47_12_A673HOTAIRGapmer


title: 46_12_A673HOTAIRGapmer

description:
processed data file: 160205_RNASeq_de.xlsx
46_12_A673HOTAIRGapmer


title: 17-0119_SK-ES_HOT_GapmeR_3

description:
processed data file: 170425_RNASeq_de.xlsx
17-0119_SK-ES_HOT_GapmeR_3


title: 44_11_A673Control

description:
processed data file: 160205_RNASeq_de.xlsx
44_11_A673Control

source_name: A673_control GapmeR


title: 23_6_ES2HOTAIRGapmer

description:
processed data file: 160205_RNASeq_de.xlsx
23_6_ES2HOTAIRGapmer

source_name: ES2_HOTAIR-repressing GapmeR


title: 20_5_ES2Control

description:
processed data file: 160205_RNASeq_de.xlsx
20_5_ES2Control

source_name: ES2_control GapmeR


title: 19_5_ES2Control

description:
processed data file: 160205_RNASeq_de.xlsx
19_5_ES2Control


title: 17-0118_SK-ES_HOT_GapmeR_2

description:
processed data file: 170425_RNASeq_de.xlsx
17-0118_SK-ES_HOT_GapmeR_2


title: 17-0114_SK-ES_CTL_B_2

description:
processed data file: 170425_RNASeq_de.xlsx
17-0114_SK-ES_CTL_B_2


title: 41_11_A673Control

description:
processed data file: 160205_RNASeq_de.xlsx
41_11_A673Control


title: 43_11_A673Control

description:
processed data file: 160205_RNASeq_de.xlsx
43_11_A673Control


title: 17_5_ES2Control

description:
processed data file: 160205_RNASeq_de.xlsx
17_5_ES2Control


title: 45_12_A673HOTAIRGapmer

description:
processed data file: 160205_RNASeq_de.xlsx
45_12_A673HOTAIRGapmer


title: 21_6_ES2HOTAIRGapmer

description:
processed data file: 160205_RNASeq_de.xlsx
21_6_ES2HOTAIRGapmer


title: 22_6_ES2HOTAIRGapmer

description:
processed data file: 160205_RNASeq_de.xlsx
22_6_ES2HOTAIRGapmer


title: 24_6_ES2HOTAIRGapmer

description:
processed data file: 160205_RNASeq_de.xlsx
24_6_ES2HOTAIRGapmer


title: RNA-seq siZFX in MCF7 rep3

city: Los Angeles

first: Suhn

middle: K

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
RNA-seq reads were aligned to hg19 genome assembly using STAR and processed with the Partek® Flow® software.
ChIP-seq reads were aligned to hg19 genome assembly using bwa.
For RNA-seq, GENCODE v19 was used to quantify to transcriptome.
For RNA-seq, differentially expressed genes analyzed by using the Gene Specific Algorithm (Upper Quartile normalization) from Partek Flow version 3.
For NOMe-seq, the fastq files were aligned to a bisulfite-converted genome using the BSMAP, and the Bis-SNP was used to call methylation sites. NDR was called using the findNDRs function from the aaRon R package (https://github.com/astatham/aaRon)
For ChIP-seq, MACS2 (Zhang et al. 2008) was used to call peaks with the IDR tool (https://github.com/nboley/idr) according to the ENCODE3 ChIP-seq piepeline (https://www.encodeproject.org/chip-seq/).
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include normalized Upper Quartile for each gene.
Supplementary_files_format_and_content: For ChIP-seq, tab-delimited text files include location of peaks
Supplementary_files_format_and_content: For NOMe-seq, tab-delimited text files include location of nucleosome depleted regions

source_name: Human breast cancer cell line MCF7

growth_protocol: The human kidney HEK293T (ATCC# CRL-3216), colon HCT116 (ATCC# CCL-247), and breast cancer MCF7 (ATCC# HTB-22) cells were obtained from ATCC (https://www.atcc.org/). The human prostate cancer C42B cells were obtained from ViroMed Laboratories (Minneapolis, MN, USA). The corresponding medium of each cell lines (DMEM for HEK293T, McCoy’s 5A for HCT116, RPMI 1640 for C42B, DMEM for MCF7) was supplemented 10% fetal bovine serum (Gibco by Thermo Fisher Scientific, Waltham, MA, USA) and 1% penicillin and streptomycin at 37ºC with 5% CO2. All cell stocks were authenticated at the USC Norris Cancer Center cell culture facility by comparison to the ATCC and/or published genomic criteria for that specific cell line; all cells are documented to be free of mycoplasma.

extract_protocol:
For RNA-seq, RNA was extracted using Trizol reagent (15596-026) (Life technologies, Carlsbad, CA) following its protocol.
For ChIP-seq, cells were crosslinked using 1% formaldehyde andl lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
For NOMe-seq, after isolating nuclei from the cells, M.CviPI was treated to methylate accessible GpCs. After purifying M.CvPI-treated DNA, sonication was performed. Bisulfite treatment of M.CviPI-methylated DNA resulted to convert all unmethylated Cs to Ts.
RNA-seq libraries were made using KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (KK8420) (Kapa Biosystems, Woburn, MA).
ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes) (Bio Scientific, Austin, TX).
NOMe-seq: Libraries were generated using the Accel-NGS Methyl-Seq DNA Library Kit for Illumina Platforms.

treatment_protocol: For transient knockdown, cells were transfected in triplicate with 100nM of siRNA oligonucleotides targeting human ZFX (Cat# L006572000005), ZNF711 (Cat# L008444020005) or control oligonucleotides (Cat# D0018101005) using SMART pool Dharmafect transfection reagent 3 (Cat# T200301) for C42B and reagent 1 (Cat# T200101) for MCF7 (Dharmacon, Lafayette, CO, USA). Cells were incubated for 24 hours and transfected again with the same concentration of siRNAs and the incubation was continued for an additional 24 hours.

value: Human breast cancer cell line MCF7

tag: sirna

value: siZFX


title: RNA-seq siRNA control in MCF7 rep1

tag: cell line

value: siCtrl


title: RNA-seq siZFX in MCF7 rep1


title: 18_5_ES2Control

description:
processed data file: 160205_RNASeq_de.xlsx
18_5_ES2Control


title: RNA-seq siRNA control in MCF7 rep2


title: RNA-seq siZFX in MCF7 rep2


title: R4/imdca larvae, biological rep3

city: Edmonton

first: Saeideh

last: Davoodi

state: Alberta

address: 116 st and 85 ave

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

description: Gene expression data from R4-GAL4/imdca third instar larvae

hyb_protocol: 12 ug of cRNA was used for fragmentation, fragmented cRNA was hybridized on GeneChip®Drosophila Genome 2.0 Array, washed and stained according to the Affymetrix protocol (User Guide GeneChip® 3' IVT PLUS Reagent Kit, 2013-2015, Affymetrix).

scan_protocol: Affymetrix GeneChip 3000 7G Scanner

data_processing: The data were analyzed with Expression Console (Affymetrix) using default analysis settings.

source_name: Drosophila third instar larvae,with imd activation in the fat body, R4-GAL4/imdca

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix GeneChip 3' IVT plus protocol from 100 ng total RNA (User Guide GeneChip® 3' IVT PLUS Reagent Kit, 2013-2015, Affymetrix).

growth_protocol: To induce innate immune responses, we generated a transgenic Drosophila line that allows cell-restricted activation of Imd and crossed it with a fat body specific driver (R4-GAL4). Larvae from  R4-GAL4/imdca group  and control genotypes (CA/+ and R4-GAL4/+) were raised on standard food at 25°C until they reached third instar stage and then collected for RNA extraction.

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

treatment_protocol: Third instar larvae were collected for each genotype and a total of 50 larvae for each replicate were used to proceed with Trizol RNA extraction.

value: larvae

tag: age

value: third instar


title: R4-GAL4/+ larvae, biological rep3

description: Gene expression data from R4-GAL4/+ third instar larvae

source_name: Drosophila third instar larvae,no imd activation,served as control genotype, R4-GAL4/+


title: CA/+ larvae, biological rep2

description: Gene expression data from CA/+ third instar larvae

source_name: Drosophila third instar larvae,no imd activation,served as control genotype, CA/+

value: w;+/+;UASImdCA/+


title: 42_11_A673Control

description:
processed data file: 160205_RNASeq_de.xlsx
42_11_A673Control


title: CA/+ larvae, biological rep3


title: RNA-seq siRNA control in MCF7 rep3


title: siCtl n3

city: Frankfurt am Main

first: Philipp

last: Neumann

state: Hessen

address: Theodor-Stern-Kai 7

institute: Institute for Cardiovascular Regeneration

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: none provided by the submitter

source_name: Primary human umbilical vein endothelial cells

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

growth_protocol: HUVECs were transfected at a confluency of 70% and harvested 48h after transfection.

extract_protocol: All samples were prepared using miRNeasy Kit (Qiagen) including DNase treatment. cDNA synthesis and amplification was performed using the Ambion WT Expression Kit (Affymetrix).

treatment_protocol: not applicable

tag: passage


title: siLOXL2 n3


title: siCtl n1


title: siCtl n2


title: siLOXL2 n2


title: siCtl n4


title: LNA GATA6-AS n1


title: CA/+ larvae, biological rep1


title: R4-GAL4/+ larvae, biological rep1


title: R4-GAL4/+ larvae, biological rep2


title: R4/imdca larvae, biological rep1


title: LNA Ctl n2


title: R4/imdca larvae, biological rep2


title: siLOXL2 n1


title: LNA GATA6-AS n2


title: Prochloraz_20uM_+R1881_0.33nM_2

city: Research Triangle Park

first: Christopher

last: Corton

address: 109 TW Alexander Dr.

institute: US-EPA

description: replicate 2

hyb_protocol: After randomization, samples were hybridized in a blinded manner onto Human HT-12 v4 Expression BeadChip arrays (Illumina, San Diego, CA) in the EPA NHEERL Genomics Research Core Laboratory using standard Illumina protocols.

scan_protocol: Arrays were scanned, and raw data (.idat files) were obtained using Illumina iScan software (v3.3.28)

data_processing: The data were normalised using log2 transofrmation and quantile normalisation with limma in R

label_protocol: Standard Illumina scanning protocol

growth_protocol: LAPC4 cells were cultured in IMDM media (GIBCO) supplemented with 5% FBS (Omega Scientific) and 1x penicillin/streptomycin/glutamine (GIBCO). Cells were plated at 7.5x10^5 cells per well in 1mL media in 24-well plates.

extract_protocol: Total RNA was isolated and purified with the RNeasy MinElute column protocol (Qiagen GmbH, Hilden, Germany)

treatment_protocol: After 48 hours, media was replaced with dosing solutions containing DMSO (0.05%), R-1881 (0.33nM) alone or with one of 28 chemicals at the indicated doses. After 6 hours of exposure, media was removed, cells were rinsed with PBS and frozen

value: prostate cancer cell line

tag: treatment chemical

value: Prochloraz


title: MethylTestosterone_0.5uM_+R1881_0.33nM_3

description: replicate 3

value: MethylTestosterone


title: Fenitrothion_20uM_+R1881_0.33nM_3

description: replicate 3

value: Fenitrothion


title: Iprodione_20uM_+R1881_0.33nM_3

description: replicate 3

value: Iprodione


title: Prochloraz_20uM_+R1881_0.33nM_3

description: replicate 3


title: Flutamide_20uM_+R1881_0.33nM_3

description: replicate 3

value: Flutamide


title: Hydroxyflutamide_20uM_+R1881_0.33nM_3

description: replicate 3

value: Hydroxyflutamide


title: Fenitrothion_20uM_+R1881_0.33nM_1

description: replicate 1


title: Flutamide_20uM_+R1881_0.33nM_2

description: replicate 2


title: Prochloraz_20uM_+R1881_0.33nM_1

description: replicate 1


title: Hydroxyflutamide_20uM_+R1881_0.33nM_2

description: replicate 2


title: LNA Ctl n1


title: MethylTestosterone_0.5uM_+R1881_0.33nM_1

description: replicate 1


title: Fenitrothion_20uM_+R1881_0.33nM_2

description: replicate 2


title: Dexamethasone_10uM_+R1881_0.33nM_3

description: replicate 3

value: Dexamethasone


title: MethylTestosterone_0.5uM_+R1881_0.33nM_2

description: replicate 2


title: Hydroxyflutamide_20uM_+R1881_0.33nM_1

description: replicate 1


title: BisphenolA_20uM_+R1881_0.33nM_2

description: replicate 2

value: BisphenolA


title: Flutamide_20uM_+R1881_0.33nM_1

description: replicate 1


title: Progesterone_10uM_+R1881_0.33nM_2

description: replicate 2

value: Progesterone


title: Dexamethasone_10uM_+R1881_0.33nM_2

description: replicate 2


title: Progesterone_10uM_+R1881_0.33nM_3

description: replicate 3


title: Tebuconazole_20uM_+R1881_0.33nM_1

description: replicate 1

value: Tebuconazole


title: BisphenolA_20uM_+R1881_0.33nM_1

description: replicate 1


title: Dexamethasone_10uM_+R1881_0.33nM_1

description: replicate 1


title: BisphenolA_20uM_+R1881_0.33nM_3

description: replicate 3


title: Tebuconazole_20uM_+R1881_0.33nM_3

description: replicate 3


title: Iprodione_20uM_+R1881_0.33nM_2

description: replicate 2


title: Procymidone_20uM_+R1881_0.33nM_3

description: replicate 3

value: Procymidone


title: Cyproterone_acetate_20uM_+R1881_0.33nM_1

description: replicate 1


title: Tebuconazole_20uM_+R1881_0.33nM_2

description: replicate 2


title: Iprodione_20uM_+R1881_0.33nM_1

description: replicate 1


title: Progesterone_10uM_+R1881_0.33nM_1

description: replicate 1


title: Mifepristone_10um_+R1881_0.33nM_3

description: replicate 3

value: Mifepristone


title: Dihydrotestosterone_0.5uM_+R1881_0.33nM_2

description: replicate 2

value: Dihydrotestosterone


title: Dihydrotestosterone_0.5uM_+R1881_0.33nM_1

description: replicate 1


title: Dihydrotestosterone_0.5uM_+R1881_0.33nM_3

description: replicate 3


title: Cyproterone_acetate_20uM_+R1881_0.33nM_2

description: replicate 2


title: Bicalutamide_20uM_+R1881_0.33nM_1

description: replicate 1

value: Bicalutamide


title: Dehydroepiandrosterone_20uM_+R1881_0.33nM_2

description: replicate 2

value: Dehydroepiandrosterone


title: Testosterone_propionate_0.5uM_+R1881_0.33nM_1

description: replicate 1


title: Testosterone_propionate_0.5uM_+R1881_0.33nM_3

description: replicate 3


title: Procymidone_20uM_+R1881_0.33nM_1

description: replicate 1


title: Mifepristone_10um_+R1881_0.33nM_2

description: replicate 2


title: Dehydroepiandrosterone_20uM_+R1881_0.33nM_1

description: replicate 1


title: DDE_20uM_+R1881_0.33nM_2

description: replicate 2

value: DDE


title: Dehydroepiandrosterone_20uM_+R1881_0.33nM_3

description: replicate 3

value: prostate cancer cell line


title: Cyproterone_acetate_20uM_+R1881_0.33nM_3

description: replicate 3


title: Procymidone_20uM_+R1881_0.33nM_2

description: replicate 2


title: Bicalutamide_20uM_+R1881_0.33nM_2

description: replicate 2


title: Testosterone_propionate_0.5uM_+R1881_0.33nM_2

description: replicate 2


title: DDE_20uM_+R1881_0.33nM_3

description: replicate 3


title: Linuron_20uM_+R1881_0.33nM_2

description: replicate 2

value: Linuron


title: DDE_20uM_+R1881_0.33nM_1

description: replicate 1


title: Atrazine_20uM_+R1881_0.33nM_2

description: replicate 2

value: Atrazin


title: Atrazine_20uM_+R1881_0.33nM_1

description: replicate 1


title: Triticonazole_10uM_+R1881_0.33nM_1

description: replicate 1

value: Triticonazole


title: DMSO_2b

description: replicate 5

value: DMSO


title: DMSO_1

description: replicate 1


title: Linuron_20uM_+R1881_0.33nM_3

description: replicate 3


title: Atrazine_20uM_+R1881_0.33nM_3

description: replicate 3


title: DMSO_3b

description: replicate 6


title: DMSO_1b

description: replicate 4


title: Mifepristone_10um_+R1881_0.33nM_1

description: replicate 1


title: Linuron_20uM_+R1881_0.33nM_1

description: replicate 1


title: DMSO_3

description: replicate 3


title: Triticonazole_10uM_+R1881_0.33nM_3

description: replicate 3


title: Triticonazole_10uM_+R1881_0.33nM_2

description: replicate 2


title: Apigenin_20uM_+R1881_0.33nM_3

description: replicate 3

value: Apigenin


title: Androstenedione_10uM_+R1881_0.33nM_2

description: replicate 2

value: Androstenedione


title: Spironolactone_20uM_+R1881_0.33nM_1

description: replicate 1

value: Spironolactone


title: Vinclozolin_20uM_+R1881_0.33nM_3

description: replicate 3

value: Vinclozolin


title: Spironolactone_20uM_+R1881_0.33nM_3

description: replicate 3


title: Androstenedione_10uM_+R1881_0.33nM_3

description: replicate 3


title: Vinclozolin_20uM_+R1881_0.33nM_2

description: replicate 2


title: Finasteride_20uM_+R1881_0.33nM_3

description: replicate 3

value: Finasteride


title: Vinclozolin_20uM_+R1881_0.33nM_1

description: replicate 1


title: Norethindrone_0.5uM_+R1881_0.33nM_2

description: replicate 2

value: Norethindrone


title: DMSO_2

description: replicate 2


title: Bicalutamide_20uM_+R1881_0.33nM_3

description: replicate 3


title: Finasteride_20uM_+R1881_0.33nM_2

description: replicate 2


title: Spironolactone_20uM_+R1881_0.33nM_2

description: replicate 2


title: Norethindrone_0.5uM_+R1881_0.33nM_1

description: replicate 1


title: Trenbolone_0.5uM_+R1881_0.33nM_2

description: replicate 2

value: Trenbolone


title: Finasteride_20uM_+R1881_0.33nM_1

description: replicate 1


title: Apigenin_20uM_+R1881_0.33nM_2

description: replicate 2


title: Trenbolone_0.5uM_+R1881_0.33nM_1

description: replicate 1


title: Androstenedione_10uM_+R1881_0.33nM_1

description: replicate 1


title: Norethindrone_0.5uM_+R1881_0.33nM_3

description: replicate 3


title: R1881_0.33nM_2b

description: replicate 5


title: R1881_0.33nM_2

description: replicate 2


title: R1881_0.33nM_1b

description: replicate 4


title: Liver, AIN 93W (control) diet, age 28 months (G152_F09_098_A4_1)

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: Gender: male, Age: 28 months, Diet: Control (AIN-93W)

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1).

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Mice arrived at the age of 7 weeks and received AIN-93G for 2 weeks acclimatization period. At the age of 9 weeks, dietary intervention was started and the diets (Control, CR and MF) were maintained until sacrifice time points at the age of 28 months. At the age of 24 months, a subset of mice of the CR group was transferred to ad libitum MF feeding (CR-MF).

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Prior to sacrifice each mouse was first fasted for 4 hours after which they received an intragastric gavage of 400ul of 0.5% carboxymethyl cellulose, then fasted again for another 6 hours. The animals in CR diet group were fed with half of the portion they normally received 15 min before the first fasting. During the sacrifice, after sedation with a mixture of isoflurane (1.5%), nitrous oxide (70%) and oxygen (30%), liver tissue was snap-frozen and stored at -80C until further analysis.

tag: Sex

value: male

tag: age at sampling

value: 28 months

tag: diet group

value: AIN-93W (control)

tag: mouseid


title: Trenbolone_0.5uM_+R1881_0.33nM_3

description: replicate 3


title: Liver, calorie restriction (30%), age 28 months (G152_G05_107_B4_3)

description: Gender: male, Age: 28 months, Diet: CR (AIN-93W-CR in portions containing 70E% of Control group's)

value: caloric restriction, 30% (CR)


title: R1881_0.33nM_3

description: replicate 3


title: Liver, medium fat diet (25% energy), age 28 months (G152_G07_114_C4_5)

description: Gender: male, Age: 28 months, Diet: medium-fat (MF; AIN-93W-MF)

value: medium fat (25energy%) (MF)


title: Liver, AIN 93W (control) diet, age 28 months (G151_F09_101_A4_9_2)


title: Liver, medium fat diet (25% energy), age 28 months (G151_G07_119_C4_15)


title: Liver, calorie restriction (30%) to medium fat diet switch at 24 months, age 28 months (G150_H02_129_BC4_5)

description: Gender: male, Age: 28 months, Diet: CR diet till 24 month-old, then diet switch to a medium-fat (MF) diet for 4 months till 28 months

value: CR diet until 24 months of age, then diet switch to a medium-fat (MF) diet for (the last) 4 months until 28 months of age (when killed)


title: Liver, calorie restriction (30%) to medium fat diet switch at 24 months, age 28 months (G150_H05_133_BC4_15)


title: Liver, calorie restriction (30%) to medium fat diet switch at 24 months, age 28 months (G150_H01_127_BC4_1)


title: Liver, medium fat diet (25% energy), age 28 months (G150_G04_115_C4_7)


title: Liver, medium fat diet (25% energy), age 28 months (G150_G05_116_C4_9)


title: Liver, calorie restriction (30%) to medium fat diet switch at 24 months, age 28 months (G150_H04_132_BC4_13)


title: Liver, calorie restriction (30%) to medium fat diet switch at 24 months, age 28 months (G151_H05_128_BC4_3)


title: Liver, calorie restriction (30%), age 28 months (G151_G05_110_B4_13)


title: Liver, medium fat diet (25% energy), age 28 months (G150_G07_118_C4_13)


title: Liver, medium fat diet (25% energy), age 28 months (G150_G06_117_C4_11)


title: R1881_0.33nM_1

description: replicate 1

value: prostate cancer cell line


title: Liver, calorie restriction (30%) to medium fat diet switch at 24 months, age 28 months (G150_H03_130_BC4_9)


title: Liver, calorie restriction (30%), age 28 months (G150_F10_106_B4_1)


title: Liver, calorie restriction (30%), age 28 months (G150_F11_108_B4_5)


title: Liver, AIN 93W (control) diet, age 28 months (G150_F08_104_A4_19)


title: Liver, medium fat diet (25% energy), age 28 months (G150_G02_112_C4_1)


title: Liver, calorie restriction (30%), age 28 months (G150_F12_109_B4_7)


title: Liver, AIN 93W (control) diet, age 28 months (G150_F07_103_A4_17)


title: Liver, AIN 93W (control) diet, age 28 months (G150_F05_100_A4_5)


title: Liver, AIN 93W (control) diet, age 28 months (G150_F09_105_A4_21)


title: Apigenin_20uM_+R1881_0.33nM_1

description: replicate 1


title: RiceRoots_10days_1mM_rep4

city: Tsukuba

first: Mitsuhiro

last: Obara

state: Ibaraki

address: Ohwashi 1-1

institute: JIRCAS

description: Gene expression of 10-days-old seedling roots grown in 1 mM ammonium chloride

hyb_protocol: Cy-labeled cRNA (0.00165 mg) was fragmented for 30 min at 60 degree and the hybridized for 17 hrs at 65 degree with gentle shaking (10 rpm) using Gene Expression Hybridization Kit (Agilent Technologies). Following, the arrays were washed using Gene Expression Wash Buffers Pack (Agilent Technologies).

scan_protocol: Slides were scanned using a scanner, Agilent DNA Microarray Scanner (G2565CA).

data_processing: The scanned images were analyzed with Feature Extraction Software 10. 10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Oryza sativa

source_name: Rice Roots, 10days, 1mM, replicate4

label_protocol: Total RNA (100ng) was labeled with Cy3 using Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies).

extract_protocol: RNA was extracted from roots of Koshihikari grown for 10 days in 0.005 and 1 mM NH4Cl with RNeasy Plant Kit (QIAGEN).

tag: tissue

value: Whole roots

tag: treatment

value: ammonium


title: RiceRoots_10days_1mM_rep3

source_name: Rice Roots, 10days, 1mM, replicate3


title: RiceRoots_10days_0.005mM_rep2

description: Gene expression of 10-days-old seedling roots grown in 0.005 mM ammonium chloride

source_name: Rice Roots, 10days, 0.005mM, replicate2


title: RiceRoots_10days_1mM_rep2

source_name: Rice Roots, 10days, 1mM, replicate2


title: Liver, calorie restriction (30%) to medium fat diet switch at 24 months, age 28 months (G152_H05_131_BC4_11)


title: RiceRoots_10days_0.005mM_rep4

source_name: Rice Roots, 10days, 0.005mM, replicate4


title: R1881_0.33nM_3b

description: replicate 6


title: PPAB_25_4g

description:
SAMPLE 16
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.

hyb_protocol: RNA was hybridized using Illumina standard protocols.

scan_protocol: Slides were scanned using Illumina standard protocols.

data_processing: Raw data was VST-transformed followed by quantile normalization as implemented in lumiR. Detection p-value cutoff was set to 0.05.

label: Biotin

source_name: Primary pancreatic cancer cell culture

label_protocol: Biotinylated cRNA was hybridized to Illumina Sentrix Bead Chips and next labeled with streptavidin-conjugated Cy3 (Amersham) according to manufacturer’s protocol.

growth_protocol: Low passage murine pancreatic cancer cells were cultured at 37°C with 5% CO2 in DMEM medium supplemented with 10% fetal calf serum and 1% [vol/vol] P/S.

extract_protocol: Extraction of total RNA was performed using QIAGEN QIAshredder and the RNeasy Mini kit according to the manufacturer's instructions.

treatment_protocol: No special treatment was applied.

tag: strain/background

value: mixed (C57Bl/6;129S6/SvEv)

tag: genotype/variation

value: PK-PB

tag: originating tissue

value: pancreatic cancer


title: PPAB_3_10i

description:
SAMPLE 4
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: Liver, AIN 93W (control) diet, age 28 months (G150_F06_102_A4_13)

tag: strain


title: PPAB_4_5c

description:
SAMPLE 7
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: PPAB_3_5c

description:
SAMPLE 6
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: PPAB_9_4h

description:
SAMPLE 11
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: PPAB_3_5b

description:
SAMPLE 5
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: PPAB_4_9a

description:
SAMPLE 8
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: PPAB_25_4b

description:
SAMPLE 2
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: PPAA_4_1h

description:
SAMPLE 3
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: RiceRoots_10days_0.005mM_rep1

source_name: Rice Roots, 10days, 0.005mM, replicate1


title: PPAB_24_1h

description:
SAMPLE 15
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: PPAB_9_3k

description:
SAMPLE 10
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: PPAB_11_5c

description:
SAMPLE 12
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: RiceRoots_10days_1mM_rep1

source_name: Rice Roots, 10days, 1mM, replicate1


title: PPAB_26_2i

description:
SAMPLE 17
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: Liver, AIN 93W (control) diet, age 28 months (G150_F04_099_A4_3)

description: Gender: male, Age: 28 months, Diet: Control (AIN-93W)


title: PPAB_17_2c

description:
SAMPLE 13
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: RiceRoots_10days_0.005mM_rep3

source_name: Rice Roots, 10days, 0.005mM, replicate3


title: PPAB_24_1f

description:
SAMPLE 14
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: PPAB_4_9i-PPT_244k

description: PK-PB mouse

source_name: Corresponding tail

value: tail


title: PPAB_4_9i

description:
SAMPLE 9
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: Bmpr1a-/- 3 Separate

city: London

first: Tristan

last: Rodriguez

address: Du Cane Road, Hammersmith Hospital Campus

department: National Heart and Lung Institute

institute: NHLI Imperial College London

description: GPL6246 [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]

hyb_protocol: The hybridisation protocols were performed on GeneChip Fluidics Station 450.

scan_protocol: Samples were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data was normalised using the RMA normalisation algorithm in Expression Console 1.2. The array QC was performed using Expression Console first and then Bioconductor.  RMA was used as the standard method for probe summarization (i.e. calculating a transcript signal value from multiple independent probes as on Affy arrays) and normalisation of Affymetrix expression array data. Quality control of Affymetrix expression microarrays involves identifying outlier arrays, rather than setting defined cut-offs for the various quality control metrics that are generated from the various controls and the probe summarization/normalisation. Note that the signal values are all log base 2; this is standard practice for RMA analyzed data. The data was first QC'ed using the Affymetrix Expression console.

source_name: Bmpr1a-/- ESCs

label_protocol: Biotinylated cRNA were prepared using the Affymetrix GeneChip® WT Terminal Labeling Kit (Ambion, Invitrogen).

growth_protocol: Embryonic stem cells (ESCs) were grown in for 3 days in N2B27 media

extract_protocol: Cells were pelleted and total RNA was extracted using the Quiagen RNAeasy Kit and then prepared for analysis with the Ambion WT expression kit (Invitrogen)

treatment_protocol: Wild type ES cells and Bmpr1a-/- cell lines were grown in N2B27l culture conditions for 3 days and cells collected.

tag: cell type

value: Embryonic Stem Cell

tag: genotype

tag: gfp expression status

value: positive

tag: growth condition


title: PPAB_4_9a-PPT_244k

description: PK-PB mouse


title: PPAB_3_3g

description:
SAMPLE 1
Gene expression data from KrasG12D-driven murine pancreatic cancer cell cultures.


title: Bmpr1a-/- 2 Separate


title: Bmpr1a-/- 2 Mix

value: mixed genotypes


title: PPAB_9_4h-PPT_244k

description: PK-PB mouse


title: Bmpr1a-/- 3 Mix


title: Bmpr1a-/- 1 Separate


title: PPAB_4_5c-PPT_244k

description: PK-PB mouse


title: PPAA_4_1h-PPT_244k

description: PK-PB mouse


title: WT 2 Separate

source_name: Wild-type ESCs

value: wildtype

value: negative

value: wildtype alone


title: Bmpr1a-/- 1 Mix


title: WT 1 Separate


title: PPAB_3_5b-PPT_244k

description: PK-PB mouse


title: WT 3 Separate


title: WT 1 Mix


title: PPAB_3_3g-PPT_244k

description: PK-PB mouse


title: SAMPLE 12

city: Yangzhou

first: Dongsheng

last: Zhao

address: Wenhui east road

institute: Yangzhou university

description: Gene expression data from developing seeds in 10 days after flowering.

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0).

source_name: Rice 10DAF developing seeds

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: Rice plants were grown in natural field under normal condition.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and checked by an Agilent Bioanalyzer 2100.

value: seeds

tag: age

tag: rice strain

value: transgenic line HFL1

tag: phenotype

value: high lysine level


title: WT 2 Mix


title: PPAB_3_5c-PPT_244k

description: PK-PB mouse


title: PPAB_24_1h-PPT_244k

description: PK-PB mouse


title: PPAB_11_5c-PPT_244k

description: PK-PB mouse


title: SAMPLE 10


title: PPAB_26_2i-PPT_244k

description: PK-PB mouse