title: PPAB_25_4b-PPT_244k

description: PK-PB mouse


title: PPAB_17_2c-PPT_244k

status: Public on Jan 24 2018

type: genomic

city: Munich

first: Roland

last: Rad

state: Bavaria

address: Ismaninger Str. 22

country: Germany

institute: Center for Translational Cancer Research (TranslaTUM)

description: PK-PB 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.

molecule: genomic DNA

organism: Mus musculus

source_name: Primary pancreatic cancer cell culture

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: PK-PB

tag: originating tissue

value: pancreatic cancer

source_name: Corresponding tail

value: tail


title: PPAB_25_4g-PPT_244k

description: PK-PB mouse


title: 5320-Lu1_244k

description: PK mouse

source_name: Lung metastasis cancer cell culture

value: PK

value: lung metastasis


title: PPAB_24_1f-PPT_244k

description: PK-PB mouse


title: PPAB_3_10i-PPT_244k

description: PK-PB mouse


title: SAMPLE 7

type: RNA

city: Yangzhou

first: Dongsheng

last: Zhao

address: Wenhui east road

country: China

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).

molecule: total RNA

organism: Oryza sativa

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.

tag: tissue

value: seeds

tag: age

tag: rice strain

value: transgenic line 35S-15

tag: phenotype

value: high lysine level


title: SAMPLE 5

value: transgenic line GR14


title: 5320-Li3_244k

description: PK mouse

source_name: Liver metastasis cancer cell culture

value: liver metastasis


title: SAMPLE 9


title: SAMPLE 11

value: transgenic line HFL1


title: SAMPLE 1

value: wild-type Wuxiangjiang9

value: normal lysine level


title: SAMPLE 2


title: 3202-LN1_244k

description: PK mouse

source_name: Lymph node metastasis cancer cell culture

value: lymph node metastasis


title: SAMPLE 8


title: SAMPLE 4


title: Sample15_Hay

type: SRA

city: Piacenza

first: Marcello

last: Del Corvo

address: Via Emilia Parmense, 84

department: Institute of Zootechnics, Faculty of Agricultural, Food and Environmental Sciences

country: Italy

institute: Università Cattolica del S. Cuore

library_source: genomic

data_processing:
Illumina raw sequences were filtered with Trimmomatic software v. 0.33 to remove adapters, and a sliding window approach used to remove lower quality bases at the sequence end. Trimmed reads were subsequently aligned to the sheep reference genome Oar_v3.1 by the BWA-mem aligner v.0.7.15, and duplicates were marked and removed using Picard-tools v1.107.
Peak detection was then performed for each sample by the ChIPseeqer software using the following parameter: reads length = 101 bp, and length of the fragments whose extremities have been sequenced was 250 bp. The ChIPseeqer software constructs a read density map by counting the number of overlapping reads at each nucleotide position and then uses a Poisson distribution probability model to compare the observed read count to the expected read count and to compute a normalized peak score for each nucleotide position (based on probabilities).
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: Tab-delimited text files include peaks score/location for each sample

organism: Ovis aries

source_name: Longissimus dorsi muscle

extract_protocol:
Genomic DNA was extracted from longissimus dorsi muscle samples, following a salt-chloroform extraction protocol. DNA concentration and quality were estimated by PicoGreen® (Thermo Fisher, Waltham, MA, USA) and by agarose gel electrophoresis. One μg of genomic DNA was sonicated to produce DNA fragments of about 350 bp. Methyl-binding domain (MBD) enrichment was performed using the MethylMinerTM Methylated DNA Enrichment Kit (Invitrogen, Carlsbad, CA, USA), following the manufacturer’s instructions. Construction of the sequencing library was performed using the TruSeq® Nano Library Preparation Kit (Illumina, San Diego, CA, USA).
Libraries were quality checked, quantified on an Agilent 2200 TapeStation High Sensitivity D1000 and used for sequencing in two lanes of an Illumina Hi-Seq 2000 (San Diego, CA). 100-base paired-end reads were generated.

value: Fetal longissimus dorsi muscle tissues

tag: diet

value: Hay


title: SAMPLE 3


title: SAMPLE 6


title: S134-Li1_244k

description: PK mouse

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


title: S134-Li2_244k

description: PK mouse


title: WT 3 Mix

city: London

first: Tristan

last: Rodriguez

address: Du Cane Road, Hammersmith Hospital Campus

department: National Heart and Lung Institute

country: United Kingdom

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.

label: Biotin

source_name: Wild-type 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

value: wildtype

tag: gfp expression status

value: negative

tag: growth condition

value: mixed genotypes


title: Sample16_Hay


title: PPAB_9_3k-PPT_244k

description: PK-PB mouse

value: PK-PB

value: pancreatic cancer

value: tail


title: Sample10_Hay


title: 53704-Li3_244k

description: PK mouse

value: PK


title: 53631-Lu1_244k

description: PK mouse

value: lung metastasis


title: S134-Li3_244k

description: PK mouse

value: liver metastasis


title: Sample14_Corn

value: Corn


title: 53631-Li2_244k

description: PK mouse


title: 3202-Li1_244k

description: PK mouse


title: 5320-Li1_244k

description: PK mouse


title: Sample3_Hay


title: Sample5_Hay


title: Sample6_Corn


title: Sample12_Hay


title: Sample13_Corn


title: Sample9_Corn


title: Sample11_Hay


title: Sample7_Corn


title: Sample8_Hay


title: 8513-Li1_244k

description: PK mouse


title: Sample1_Corn


title: 53646-PPT_244k

description: PK mouse


title: 53704-Li2_244k

description: PK mouse


title: Sample2_Corn


title: S302-PPT_244k

description: PK mouse


title: Sample4_Corn


title: 53631-Lu2_244k

description: PK mouse


title: HepG2_TUC338-A

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

country: USA

institute: Mayo Clinic

data_processing:
Library strategy: ChIRP-Seq
Raw reads were mapped to reference human genome (hg19) using Bowtie.
The MACS algorithm was used to find true peaks, corresponding to high confidence using thresholds of average coverage >1.5 and a Pearson correlation of 1.
Binding motifs were identified using MEME-ChIP.
Alignments with known motifs were performed using TOMTOM and Jaspar and UniPROBE databases
The annotations of nearby genes were analyzed using GREAT version 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: Peak Sequences were generated into FASTA format

organism: Homo sapiens

source_name: HepG2 cells

extract_protocol:
HepG2 cells were collected, crosslinked, and lysed. Lysates was sonicated and hybridzed to biotinylated RNA probes, TUC338 set A and set B. DNA was extracted from these ChIRP samples and sequenced.
Libraries were prepared according to Illumina's instructions

value: HepG2 Hepatocellular Carcinoma cells


title: HepG2_TUC338-B


title: 9591-PPT_244k

description: PK mouse


title: 8305-PPT_244k

description: PK mouse


title: 53631-Li1_244k

description: PK mouse


title: 53704-PPT_244k

description: PK mouse


title: 8570-PPT_244k

description: PK mouse


title: 5123-Li1_244k

description: PK mouse


title: 9091-PPT_244k

description: PK mouse


title: 8513-PPT_244k

description: PK mouse


title: 8296-PPT_244k

description: PK mouse


title: S559-PPT_244k

description: PK mouse


title: 8248-PPT_244k

description: PK mouse


title: S821-PPT_244k

description: PK mouse


title: R1035-PPT_244k

description: PK mouse


title: 6075-PPT_244k

description: PK mouse


title: 8349-PPT_244k

description: PK mouse


title: 2259-PPT_244k

description: PK mouse


title: S914-PPT_244k

description: PK mouse


title: 8442-PPT_244k

description: PK mouse


title: 53631-PPT_244k

description: PK mouse


title: S134-PPT_244k

description: PK mouse


title: 8661-PPT_244k

description: PK mouse


title: 3250-PPT_244k

description: PK mouse


title: 4900-PPT_244k

description: PK mouse


title: 4706-PPT_244k

description: PK mouse


title: xrn3-8_time60_rep2

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description: xrn3-8 after cordycepin treatment

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with R/Bioconductor workflow (www.bioconductor.org/help/workflows/arrays/) using packages affy (v1.48.0) and limma (v3.26.9).

label: biotin

organism: Arabidopsis thaliana

source_name: xrn3-8, time60

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA.

growth_protocol: MS plates, long day conditions, harvested on 14 day after stratification.

extract_protocol: Qiagen RNeasy Plant Mini Kit

treatment_protocol: Seedlings were treated with 150 mg/l cordycepin to inhibit transcription and collected after 60 min.

tag: agent

value: cordycepin

tag: time

value: 60 min

value: 14 day old

value: seedling


title: xrn3-8_time60_rep3

description: xrn3-8 after cordycepin treatment


title: xrn3-8_time0_rep3

description: xrn3-8 before cordycepin treatment

source_name: xrn3-8, time0

value: control

value: 0 min


title: 5748-PPT_244k

description: PK mouse

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


title: xrn3-8_time60_rep1

description: xrn3-8 after cordycepin treatment


title: Col0_time60_rep2

description: wild type after cordycepin treatment

source_name: Col0, time60

value: wild type


title: Col0_time0_rep1

description: wild type before cordycepin treatment

source_name: Col0, time0


title: S411-PPT_244k

description: PK mouse


title: Col0_time60_rep3

description: wild type after cordycepin treatment


title: Col0_time0_rep3

description: wild type before cordycepin treatment


title: xrn3-8_time0_rep2

description: xrn3-8 before cordycepin treatment


title: 3202-PPT_244k

description: PK mouse


title: 5123-PPT_244k

description: PK mouse


title: Col0_time60_rep1

description: wild type after cordycepin treatment


title: 16992-PPT_244k

description: PK mouse


title: 53578-PPT_244k

description: PK mouse


title: Col0_time0_rep2

description: wild type before cordycepin treatment


title: xrn3-8_time0_rep1

description: xrn3-8 before cordycepin treatment


title: Sirt1WT_TSC_Diff.d7_605_2443_1_1

city: La Jolla

first: Mana

last: Parast

state: California

address: 9500 Gilman drive #0695

department: Pathology

institute: University of California San Diego

description: SAMPLE 22

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were filtered for detection pValue > 0.01 and normalized using Robust Spline Normalization with lumi in R

source_name: Sirt1WT_TSC_day 7

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

growth_protocol: TS cells were cultured in RPMI 1640 media supplemented with 20% fetal bovine serum, 1 mM sodium pyruvate (Invitrogen), 1X penicillin/streptomycin, 55nM β-mercaptoethanol (Invitrogen), 25 ng/mL  fibroblast growth factor 4 (FGF4; Sigma), 1 μg/mL heparin (Sigma) and 10ng/mL Activin A (Stemgent).

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion). Total RNA was quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina MouseRef-8 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

treatment_protocol: TS cells were differentiated in growth media in which 25 ng/mL  fibroblast growth factor 4(FGF4; Sigma), 1 μg/mL heparin (Sigma) and 10ng/mL Activin A (Stemgent) were removed.

tag: pipeline

tag: origin

value: Trophoblast

value: Wild-type

tag: day of differentiation

value: day 7


title: Sirt1WT_TSC_Diff.d0_605_2440_3_1

description: SAMPLE 15

source_name: Sirt1WT_TSC_day 0

value: day 0


title: B590-PPT_244k

description: PK mouse

tag: strain/background

value: PK

value: pancreatic cancer

value: tail


title: Sirt1WT_TSC_Diff.d7_605_2443_2_1

description: SAMPLE 23


title: Sirt1NULL_TSC_Diff.d7_709_2447_3_1

description: SAMPLE 12

source_name: Sirt1NULL_TSC_day 7


title: Sirt1WT_TSC_Diff.d5_605_2442_3_1

description: SAMPLE 21

source_name: Sirt1WT_TSC_day 5

value: day 5


title: Sirt1WT_TSC_Diff.d0_605_2440_2_1

description: SAMPLE 14


title: 9203-PPT_244k

description: PK mouse

source_name: Primary pancreatic cancer cell culture

tag: genotype/variation


title: Sirt1WT_TSC_Diff.d1_605_2441_3_1

description: SAMPLE 18

source_name: Sirt1WT_TSC_day 1

value: day 1


title: Sirt1NULL_TSC_Diff.d5_709_2446_3_1

description: SAMPLE 9

source_name: Sirt1NULL_TSC_day 5


title: 8182-PPT_244k

description: PK mouse

tag: originating tissue

source_name: Corresponding tail


title: Sirt1WT_TSC_Diff.d5_605_2442_1_1

description: SAMPLE 19


title: Sirt1NULL_TSC_Diff.d5_709_2446_2_1

description: SAMPLE 8


title: Sirt1WT_TSC_Diff.d5_605_2442_2_1

description: SAMPLE 20


title: Sirt1WT_TSC_Diff.d0_605_2440_1_1

description: SAMPLE 13


title: Sirt1NULL_TSC_Diff.d7_709_2447_1_1

description: SAMPLE 10


title: Sirt1WT_TSC_Diff.d7_605_2443_3_1

description: SAMPLE 24


title: Sirt1WT_TSC_Diff.d1_605_2441_1_1

description: SAMPLE 16


title: Sirt1NULL_TSC_Diff.d5_709_2446_1_1

description: SAMPLE 7


title: Sirt1NULL_TSC_Diff.d1_709_2445_2_1

description: SAMPLE 5

source_name: Sirt1NULL_TSC_day 1


title: Sirt1WT_TSC_Diff.d1_605_2441_2_1

description: SAMPLE 17


title: Sirt1NULL_TSC_Diff.d7_709_2447_2_1

description: SAMPLE 11


title: Sirt1NULL_TSC_Diff.d1_709_2445_3_1

description: SAMPLE 6


title: 5671-PPT_244k

description: PK mouse


title: 4072-PPT_244k

description: PK mouse


title: 8028-PPT_244k

description: PK mouse


title: NCI-H1299

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

library_source: transcriptomic

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 Hisat
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using ribosome minus standed RNAseq protocols

tag: tissue


title: HEK-293T


title: RNA-seq Both siZFX and siZNF711 rep2 in MCF7 for siZNF711,siZFX, siBoth experiment

city: Los Angeles

first: Suhn

middle: K

last: Rhie

state: CA

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: cell line

tag: chip antibody

tag: sirna

value: Both siZFX and siZNF711


title: 16990-PPT_244k

description: PK mouse


title: Sirt1NULL_TSC_Diff.d1_709_2445_1_1

description: SAMPLE 4


title: 5320-PPT_244k

description: PK mouse


title: HuH-7


title: ZFX ChIP-seq in PrEC

data_processing:
ChIP-seq reads were aligned to hg19 genome assembly using bwa.
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 ChIP-seq, tab-delimited text files include location of peaks

source_name: Human normal prostate epithelial cell PrEC

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 human normal prostate epithelial cells (PrEC) were obtained from Lonza (Cat# CC-2555, Lonza, Walkersville, MD, 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. PrEC cells were grown with PrEGM Bullet Kit (Prostate Epithelial Cell Growth Medium with supplements), which were obtained from Lonza (Cat# CC-3166, Walkersville, MD, USA).

extract_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.
ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes) (Bio Scientific, Austin, TX).

value: PrEC

value: ZFX


title: POLR2A ChIP-seq in C42B

data_processing:
ChIP-seq reads were aligned to hg19 genome assembly using bwa.
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 this ChIP-seq sample,a bedGraph file is provided.

source_name: Human prostate cancer cell line C42B

value: Human prostate cancer cell line C42B


title: ChIP-seq Input in MCF7 rep3


title: Sirt1NULL_TSC_Diff.d0_709_2444_3_1

description: SAMPLE 3

source_name: Sirt1NULL_TSC_day 0


title: H3K4me3 ChIP-seq in C42B


title: RNA-seq Both siZFX and siZNF711 rep3 in MCF7 for siZNF711,siZFX, siBoth experiment


title: Sirt1NULL_TSC_Diff.d0_709_2444_2_1

description: SAMPLE 2


title: RNA-seq siZFX rep2 in MCF7 for siZNF711,siZFX, siBoth experiment

value: siZFX


title: RNA-seq Both siZFX and siZNF711 rep1 in MCF7 for siZNF711,siZFX, siBoth experiment


title: RNA-seq siZFX rep3 in MCF7 for siZNF711,siZFX, siBoth experiment


title: RNA-seq siZNF711 rep3 in MCF7 for siZNF711,siZFX, siBoth experiment


title: RNA-seq siRNA control rep3 in MCF7 for siZNF711,siZFX, siBoth experiment

value: siCtrl


title: RNA-seq siZNF711 rep1 in MCF7 for siZNF711,siZFX, siBoth experiment


title: RNA-seq siZFX rep1 in MCF7 for siZNF711,siZFX, siBoth experiment


title: Sirt1NULL_TSC_Diff.d0_709_2444_1_1

description: SAMPLE 1


title: Control_7d_male_rep2

city: Maastricht

first: Héloïse

last: Proquin

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

hyb_protocol: Hybridization was performed according to the manufacturer’s protocol on SurePrint G3 mouse Gene exp 60kv2 microarrays slides

scan_protocol: After hybridization, the microarray slides were scanned using an Agilent DNA Microarray Scanner with Surescan High-resolution Technology (Agilent Technologies, The Netherlands) with scanner settings to Dye Channel: G, Profile: AgilentG3_GX_1Color, Scan region: Agilent HD (61 x 21.3 mm), Scan resolution 3 µm, Tiff file dynamic range: 20 bit, Red PMT gain: 100%, Green PMT gain: 100%.

data_processing: First the quality of the microarrays was checked by the quality control pipeline provided by Agilent (Feature extraction software (FES) version 10.7.3.1). All samples met the quality criteria of the FES. In order to have a thorough quality check and normalize the data, an in-house QC pipeline was developed and is publically available (github.com/BiGCAT-UM/arrayQC_Module). All samples met the in-house quality check. Raw data with expression values and genes were selected for data analysis based on flags and missing values. Height groups were defined: E171 2 days, 7 days, 14 days, 21 days for the exposed samples and control 2 days, 7 days, 14 days, 21 days for the controls. Within each group, at least four out of six or five out of seven samples had to have a pass for the spot. Also, within each group, unique identifiers passed when there were less than three missing values out of six or seven values. The unique identifiers with an average expression less than four in all of the groups were omitted. The missing values were pre-processed using the GenePattern ImputeMissingValues.KNN module v13, with standard settings. Unique identifiers were removed and identical Agilent probe identifiers were merged with Babelomics 5, using the median method for pre-processing data. Next, the data was re-annotated from Agilent probe identifiers to EntrezGene identifiers (EntrezGene IDs). The expression data for all genes with an identical EntrezGeneIDs were subsequently merged with Babelomics 5, using the median method for pre-processing data. Using an R-script, a Linear Mixed Model Analysis for Microarrays (LIMMA) (version 1.0) was performed to extract differentially expressed genes (DEG). The data of each control time point (control) was subtracted from the time-matched exposed mice to E171. The standard cut-off values of a fold-change (FC) of 1.5 and a p-value of 0.05 were used in LIMMA. The DEG for each time point were subsequently used in Consensus Pathway Database (CPDB) for an over-expression gene set analysis. All the available databases from CPDB were used (release 31, 1 sept. 2015) with a p<0.01.

source_name: distal colon, vehicle, 7 days, male

label_protocol: Total RNA was synthesized into cRNA and labelled according to the One-Color Microarray-Based Gene Expression Analysis protocol version 6.6

extract_protocol: Isolation of RNA was performed using the miRNeasy Mini Kit (Qiagen, The Netherlands) including a DNase treatment, according to the manufacturer’s protocols for “Animal Cells and Animal Tissues”

treatment_protocol: Gavage of vehicle (water)

value: distal colon

tag: strain

value: Balb/c

tag: treatment

value: vehicle

tag: gender

value: male

tag: time point

value: 7 days


title: RNA-seq siZNF711 rep2 in MCF7 for siZNF711,siZFX, siBoth experiment


title: ZNF711 ChIP-seq in MCF7 rep2


title: RNA-seq siRNA control rep1 in MCF7 for siZNF711,siZFX, siBoth experiment


title: E171_21d_female_rep2

source_name: distal colon, 5 mg/kg bw/day of E171, 21 days, female

value: 5 mg/kg bw/day of E171

value: female

value: 21 days


title: RNA-seq siRNA control rep2 in MCF7 for siZNF711,siZFX, siBoth experiment


title: Control_7d_female_rep2

source_name: distal colon, vehicle, 7 days, female


title: E171_2d_male_rep2

source_name: distal colon, 5 mg/kg bw/day of E171, 2 days, male

value: 2 days


title: ZNF711 ChIP-seq in MCF7 rep1


title: E171_21d_male_rep2

source_name: distal colon, 5 mg/kg bw/day of E171, 21 days, male


title: Control_14d_female_rep2

source_name: distal colon, vehicle, 14 days, female

value: 14 days


title: E171_7d_male_rep2

source_name: distal colon, 5 mg/kg bw/day of E171, 7 days, male


title: Control_21d_female_rep2

source_name: distal colon, vehicle, 21 days, female


title: E171_7d_female_rep2

source_name: distal colon, 5 mg/kg bw/day of E171, 7 days, female


title: E171_2d_female_rep2

source_name: distal colon, 5 mg/kg bw/day of E171, 2 days, female


title: E171_14d_female_rep2

source_name: distal colon, 5 mg/kg bw/day of E171, 14 days, female


title: Control_14d_male_rep2

source_name: distal colon, vehicle, 14 days, male


title: Control_2d_female_rep2

source_name: distal colon, vehicle, 2 days, female


title: E171_14d_male_rep2

source_name: distal colon, 5 mg/kg bw/day of E171, 14 days, male


title: E171_21d_female_rep1


title: Control_21d_male_rep2

source_name: distal colon, vehicle, 21 days, male


title: Control_7d_female_rep1


title: Control_14d_male_rep1


title: E171_21d_male_rep1


title: Control_7d_male_rep1


title: Control_14d_female_rep1


title: Control_2d_male_rep2

source_name: distal colon, vehicle, 2 days, male


title: Control_21d_female_rep1


title: E171_2d_male_rep1


title: Control_2d_female_rep1


title: E171_14d_female_rep1


title: E171_14d_male_rep1


title: E171_7d_male_rep1


title: E171_2d_female_rep1


title: E171_7d_female_rep1


title: Control_21d_male_rep1


title: Control_2d_male_rep1


title: KO-Input 1

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were quality assessed using FastQC v0.11.5 and then quality trimmed using Trimmomatic (parameters used were “trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36”)
Surviving reads were then aligned against the mouse reference genome (GRCm38.p4) using Bowtie2
Resulting BAM alignments were then processed through PICARD tools (http://broadinstitute.github.io/picard), to clean, sort and deduplicate (PCR and Optical duplicates).
Processed alignments were normalized using Deeptools2, bamcoverage function in RPKM. Bigwig coverage file was generated the number of reads per bin of 10 bases.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: bigwig

source_name: connective tissue, mouse embryonic fibroblast

growth_protocol: Dulbecco’s modified Eagle medium (DMEM) with high glucose (Sigma), 10% fetal bovine serum (Sigma) and 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma), in a humidified incubator with 5% CO2 at 37 Deg.

extract_protocol:
50 ug total fragmented chromatin were mixed with 7 ug antibody overnight at 4 degree with rotation. The chromatin-antibody complex were then precipitated with protein A/G magnetic beads (Thermo Fisher Scientific). After washes with low salt wash buffer (20mM Tris, 2mM EDTA, 50mM NaCl, 0.01% SDS and 1% SDS), high salt wash buffer (same composition, 250 mM NaCl) and LiCL-wash buffer (10mM Tris, 1mM EDTA, 250 mM LiCl, 1% NP40 and 1% sodium deoxycholate), precipitated chromatin was eluted in 200µl of elution buffer (10µl 20% SDS, 20µl 1M NaHCO3 and 170µl dH2O). Reverse cross linking was done by adding 8 ul 5M NaCl and incubate at 65 deg overnight. 1 ul 10 mg/ml RNase A was added to the tube for 30 mins incubation at 37°C. Then 4µl 0.5M EDTA, 8µl 1M Tris-HCl and 1µl 20 mg/ml Proteinase K was added for 2h incubation at 42°C. The released DNA was purified using QIAquick PCR purification kit (Qiagen).
Two biological replicates were prepared for library preparation using TruSeq Nano DNA Library Prep Kit (Illumina) according to the manufacturer's instructions

tag: cell type

value: mouse embryonic fibroblast

value: BALB/c

tag: age

value: 10.5 day old embryos

tag: genotype

value: Actb -/-

tag: antibody


title: KO-Input 2


title: 9769100094_R06C02

city: Amsterdam

first: Peter

last: Henneman

state: Noord Holland

address: Meibergdreef 9

department: Clinical Genetics

institute: Academic Medical Center Amsterdam

hyb_protocol: Bisulfite converted DNA was hybridized to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Minfi (v1.16.0) for reading the data; MethylAid (v1.14.0) for quality control - Due to failing the QC, samples Crohn100, Crohn32 and Crohn75 were removed from the processed data

label: CY3 and CY5

source_name: genomic DNA whole blood 51

label_protocol: Standard Illumina protocol

extract_protocol: Peripheral blood was drawn and stored in EDTA to prevent coagulation. Erythrocytes were lysed before proteins were aggregated out of the sample. Genomic DNA was extracted through ethanol precipitation, after which the DNA was dissolved in tris-ethylenediaminetetraacetic buffer (Tris-EDTA) and stored at 4°C.

tag: group

value: PTSD

value: whole blood


title: 9769100105_R04C02

source_name: genomic DNA whole blood 55

value: Control


title: 9769100105_R05C01

source_name: genomic DNA whole blood 56


title: 9769100113_R02C02

source_name: genomic DNA whole blood 57


title: 9769100113_R04C02

source_name: genomic DNA whole blood 59


title: 9769100105_R03C02

source_name: genomic DNA whole blood 54


title: 9769100113_R06C02

source_name: genomic DNA whole blood 61


title: 9769100113_R03C02

source_name: genomic DNA whole blood 58


title: KO-TFAM ChIP 1

value: Anti-TFAM antibody, ABE483, Millipore


title: 9769100132_R06C02

source_name: genomic DNA whole blood 67


title: 9769100132_R03C02

source_name: genomic DNA whole blood 65


title: 9769100085_R06C01

source_name: genomic DNA whole blood 44


title: 9769100085_R05C01

source_name: genomic DNA whole blood 43


title: 9769100113_R05C01

source_name: genomic DNA whole blood 60


title: WT-Input 2

value: Actb +/+


title: 9769100130_R02C01

source_name: genomic DNA whole blood 62


title: 9769100130_R03C01

source_name: genomic DNA whole blood 64


title: 9769100085_R04C01

source_name: genomic DNA whole blood 41


title: KO-TFAM ChIP 2

source_name: connective tissue, mouse embryonic fibroblast


title: 9769100094_R04C02

source_name: genomic DNA whole blood 48


title: 9769100085_R04C02

source_name: genomic DNA whole blood 42


title: 9769100085_R03C02

source_name: genomic DNA whole blood 40


title: 9769100105_R01C01

source_name: genomic DNA whole blood 52


title: 9769100105_R02C01

source_name: genomic DNA whole blood 53


title: WT-TFAM ChIP 1


title: 9769100094_R01C01

source_name: genomic DNA whole blood 46


title: 9769100130_R02C02

source_name: genomic DNA whole blood 63


title: 9769100094_R06C01

source_name: genomic DNA whole blood 50


title: 4WeekSevere_rep3_10311

city: Philadelphia

first: Amber

last: Wang

state: Pennsylvania

address: 3400 Civic Center Blvd, SCTR 12-164

department: Genetics

institute: University of Pennsylvania

description:
#10311
TrapSeqCompare.xls

data_processing:
Library strategy: TRAP-Seq
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.

molecule: polyA RNA

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.

value: Fah-/-

tag: cell state

value: 4-week regenerating after severe injury

value: Hepatocytes


title: 4WeekSevere_rep1_7414

description:
#7414
TrapSeqCompare.xls


title: WT-TFAM ChIP 2


title: 9769100085_R06C02

source_name: genomic DNA whole blood 45

value: male


title: WT-Input 1


title: 9769100085_R02C02

source_name: genomic DNA whole blood 39


title: 4WeekSevere_rep2_7578

description:
#7578
TrapSeqCompare.xls


title: 9769100132_R05C02

source_name: genomic DNA whole blood 66


title: 9769100094_R04C01

source_name: genomic DNA whole blood 47

value: female


title: 4Week_rep5_10127

description:
#10127
TrapSeqCompare.xls

value: 4-week regenerating


title: 4Week_rep6_10290

description:
#10290
TrapSeqCompare.xls


title: 4Week_rep4_10123

description:
#10123
TrapSeqCompare.xls


title: 4Week_rep3_7579

description:
#7579
TrapSeqCompare.xls


title: 9769100094_R05C01

source_name: genomic DNA whole blood 49


title: 4Week_rep2_7577

description:
#7577
TrapSeqCompare.xls


title: 4Week_rep1_7413

description:
#7413
TrapSeqCompare.xls


title: 1Week_rep2_7569

description:
#7569
TrapSeqCompare.xls

value: 1-week regenerating


title: Quiescent_rep4_GL5_2

description:
#GL5-A
Samples with the same 'GL#' are the same mouse but prepared by different investigators at separate batches. For instance, #GL5-K and #GL5-A are from the same mouse.
TrapSeqCompare.xls

value: Quiescent


title: 1Week_rep3_7573

description:
#7573
TrapSeqCompare.xls


title: 1Week_rep1_7568

description:
#7568
TrapSeqCompare.xls


title: 9769100084_R06C02

source_name: genomic DNA whole blood 37


title: 9769100084_R05C02

source_name: genomic DNA whole blood 36


title: Quiescent_rep4_GL5_1

description:
#GL5-K
Samples with the same 'GL#' are the same mouse but prepared by different investigators at separate batches. For instance, #GL5-K and #GL5-A are from the same mouse.
TrapSeqCompare.xls


title: Quiescent_rep2_GL2_2

description:
#GL2-A
Samples with the same 'GL#' are the same mouse but prepared by different investigators at separate batches. For instance, #GL2-K, #GL2-A, and #GL2-A_n are from the same mouse.
TrapSeqCompare.xls


title: Quiescent_rep2_GL2_1

description:
#GL2-K
Samples with the same 'GL#' are the same mouse but prepared by different investigators at separate batches. For instance, #GL2-K, #GL2-A, and #GL2-A_n are from the same mouse.
TrapSeqCompare.xls


title: Quiescent_rep3_GL3

description:
#GL3-K
TrapSeqCompare.xls


title: Quiescent_rep1_GL1_2

description:
#GL1-A
Samples with the same 'GL#' are the same mouse but prepared by different investigators at separate batches. For instance, #GL1-K and #GL1-A are from the same mouse.
TrapSeqCompare.xls


title: Quiescent_rep2_GL2_3

description:
#GL2-A_n
Samples with the same 'GL#' are the same mouse but prepared by different investigators at separate batches. For instance, #GL2-K, #GL2-A, and #GL2-A_n are from the same mouse.
TrapSeqCompare.xls


title: 9769100084_R04C02

source_name: genomic DNA whole blood 35


title: 9769100085_R01C02

source_name: genomic DNA whole blood 38


title: Quiescent_rep1_GL1_1

description:
#GL1-K
Samples with the same 'GL#' are the same mouse but prepared by different investigators at separate batches. For instance, #GL1-K and #GL1-A are from the same mouse.
TrapSeqCompare.xls


title: 9769100084_R04C01

source_name: genomic DNA whole blood 34


title: 9769100084_R03C02

source_name: genomic DNA whole blood 33


title: 9769100084_R02C01

source_name: genomic DNA whole blood 32


title: 9769100081_R05C01

source_name: genomic DNA whole blood 30


title: 9721365150_R06C01

source_name: genomic DNA whole blood 26


title: 9721365150_R03C02

source_name: genomic DNA whole blood 24


title: 9769100081_R06C02

source_name: genomic DNA whole blood 31


title: 9721365012_R06C01

source_name: genomic DNA whole blood 15


title: 9721365015_R03C01

source_name: genomic DNA whole blood 18


title: 9721365015_R06C01

source_name: genomic DNA whole blood 21


title: 9721365150_R01C01

source_name: genomic DNA whole blood 22


title: 9721365150_R02C01

source_name: genomic DNA whole blood 23


title: 9721365150_R06C02

source_name: genomic DNA whole blood 27


title: 9721365015_R04C02

source_name: genomic DNA whole blood 19


title: 9721365150_R04C02

source_name: genomic DNA whole blood 25


title: 9721365015_R05C01

source_name: genomic DNA whole blood 20


title: 20uM SMIFH2 wt liquid medium repeat 2

city: Praha 2

first: Fatima

last: Cvrckova

address: Vinicna 5

department: Experimental Plant Biology

country: Czech Republic

institute: Charles University, Faculty of Science

description: This is a backrossed wt sister of the fh1-1 line described in Rosero et al. 2013 PMID: 23202131.

hyb_protocol: Labelling, hybridization and scanning performed by NASC. Standard Affymetrix hybridization protocol was used - see Affymetrix manuals .

scan_protocol: Labelling, hybridization and scanning performed by NASC. Standard Affymetrix scanning protocol was used - see Affymetrix manuals.

data_processing: The data were analyzed using Affymetrix Expression Console 1.4 software. RMA analysis with default settings for gene-level analysis was used to generate CHP files that were further analysed using Affymetrix Transcriptome Analysis Console 3.1.

source_name: 7 days old in vitro grown seedlings

label_protocol: Labelling, hybridization and scanning performed by NASC. Standard NASC Labelling protocol (NASCLabelProtocol:1) was used - see https://www.ebi.ac.uk/arrayexpress/protocols/90396/

growth_protocol: Surface-sterilized seeds were germinated and seedlings subsequently grown for 6 days on solid vertical MS plates (see Rosero et al. 2013 PMID: 23202131) under long-day conditions (16 h light/8 h dark). Approximately 120 seedlings were used per biological replicate.

extract_protocol: Qiagen RNAeasy kit extraction of total RNA according to manufacturer´s instructions, yielding approx., 100 mg RNA per sample.

treatment_protocol: Samples were treated for 1 day prior to RNA extraction as specified for each sample, i.e. either cultured on solid MS under long day conditions (no treatment), or transferred to liquid MS with or without addition of 20 uM SMIFH2 under continuous light conditions.

tag: cultlivar

value: Columbia

value: FH1 wt

value: 7 days

tag: treatment protocol

value: 1 day liquid MS medium, 20 uM SMIFH2, with shaking, continuous light

value: whole seedlings


title: 20uM SMIFH2 wt liquid medium repeat 1


title: 9721365012_R01C01

source_name: genomic DNA whole blood 11

value: whole blood


title: 9769100081_R01C02

source_name: genomic DNA whole blood 28

value: Control


title: 9721365012_R04C02

source_name: genomic DNA whole blood 13

value: PTSD


title: 9721365012_R05C01

source_name: genomic DNA whole blood 14


title: NOMe-seq in C42B

data_processing:
Library strategy: NOMe-seq
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 prostate cancer cell line C42B

value: Human prostate cancer cell line C42B


title: ZFX ChIP-seq in HEK293T rep2

source_name: Human kidney cancer cell line HEK293T

value: Human kidney cancer cell line HEK293T

value: ZFX


title: 9721365015_R02C01

source_name: genomic DNA whole blood 17


title: 9704031158_R05C02

source_name: genomic DNA whole blood 10


title: ChIP-seq Input in HEK293T rep1


title: wt solid medium repeat 2

value: 1 day solid MS medium, long day (i.e. no treatment)


title: ZFX ChIP-seq in HEK293T rep1


title: control wt liquid medium repeat 1

value: 1 day liquid MS medium with shaking, continuous light


title: 9704031158_R04C02

source_name: genomic DNA whole blood 9

value: male


title: control wt liquid medium repeat 2


title: fh1-1 solid medium_repeat 1

description: This is the fh1-1 line described in Rosero et al. 2013 PMID: 23202131.


title: fh1-1 solid medium_repeat 2


title: 9721365015_R01C01

source_name: genomic DNA whole blood 16

value: female


title: 9704031097_R04C01

source_name: genomic DNA whole blood 2


title: wt solid medium repeat 1


title: ZFX ChIP-seq in HCT116 rep1

source_name: Human colon cancer cell line HCT116

value: Human colon cancer cell line HCT116


title: ChIP-seq Input in HCT116 rep1


title: ChIP-seq Input in MCF7 rep2

source_name: Human breast cancer cell line MCF7

value: Human breast cancer cell line MCF7


title: 9769100081_R02C02

source_name: genomic DNA whole blood 29


title: ChIP-seq Input in MCF7 rep1


title: 9704031158_R03C02

source_name: genomic DNA whole blood 8


title: ChIP-seq Input in HEK293T rep2


title: ZFX ChIP-seq in HCT116 rep2


title: ChIP-seq Input in HCT116 rep2


title: 9704031097_R01C02

source_name: genomic DNA whole blood 1


title: blood case indiv 6

status: Public on Jan 23 2018

first: Harry

middle: Taegyun

last: Yang

address: Engineering VI 286

department: Computer Science

institute: University of California, Los Angeles

data_processing:
We mapped reads onto the human transcriptome (Ensembl GRCh37) and genome reference (Ensembl hg19) using TopHat2 (v 2.0.13) with the default parameters. TopHat2 was supplied with a set of known transcripts (as a GTF formatted file, Ensembl GRCh37) using –G option.
The mapped reads of each sample are stored in a binary format (.bam). ROP (gprofile.py) categorizes the reads into genomic categories (junction read, CDS, intron, UTR3, UTR5, introns, inter-genic read, deep a deep inter-genic read, mitochondrial read, and multi-mapped read) based on their compatibility with the features defined by Ensembl (GRCh37) gene annotations.
ROP (rprofile.py) categorizes reads into repeat elements (classes and families) based on their compatibility with repeat instances defined by RepeatMasker annotation (RepeatMasker v3.3, Repeat Library 20120124).
We count the number of reads overlapping variable(V), diversity (D), joining (J), and constant (C) gene segments of B cell receptor (BCR) and T cell receptor (TCR) loci using htseq-count (HTSeq v0.6.1).
We remapped the remaining unmapped reads to the human reference genome (hg19) and transcriptome (known transcripts, Ensembl GRCh37) using Megablast (BLAST+ 2.2.30).
The remaining unmapped reads were mapped to the reference repeat sequences using Megablast (BLAST+ 2.2.30). The reference repeat sequences were downloaded from Repbase v20.07 (http://www.girinst.org/repbase/). Human repeat elements (humrep.ref and humsub.ref) were merged into a single reference.
. We used IgBlast (v. 1.4.0) with a stringent e-value threshold (e-value < 10-20) to map the remaining unmapped reads onto the V(D)J gene segments of the of the B cell receptor (BCR) and T cell receptor (TCR) loci. Gene segments of B cell receptors (BCR) and T cell receptors (TCR) were imported from IMGT version: 3.1.17 (International ImMunoGeneTics information system). The IMGT database contains: variable (V) gene segments; diversity (D) gene segments; and joining (J) gene segments.
We used Megablast (BLAST+ 2.2.30) to align remaining unmapped reads onto the collection of bacterial, viral, and eukaryotic reference genomes. Bacterial and viral genomes were downloaded from NCBI (ftp://ftp.ncbi.nih.gov/). Genomes of eukaryotic pathogens were downloaded from EuPathDB (http://eupathdb.org/eupathdb/). We used MetaPhlAn2 (Metagenomic Phylogenetic Analysis, v 2.0) to obtain the taxonomic profile of microbial communities present in the sample.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: BLAST Tabular Output (more details provided in the readme.txt)

source_name: Ashmatic_peripheral blood

extract_protocol:
Nasal epithelial cells were collected from behind the inferior turbinate with a cytology brush using a nasal illuminator. Whole blood was collected using PAXgene RNA blood tubes. RNA was isolated using PAXgene RNA blood extraction kits.
Poly(A) selected RNA-seq libraries (n=38) were constructed using 500 ng of blood and nasal airway epithelial total RNA from 9 atopic asthmatics and 10 non-atopic controls. Libraries were constructed and barcoded with the Illumina TruSeq RNA Sample Preparation v2 protocol. Barcoded nasal airway RNA-seq libraries from each of the 19 subjects were pooled and sequenced as 2 x 100bp paired-end reads across two flow cells of an Illumina HiSeq 2000. Barcoded blood RNA-seq libraries from each of the 19 subjects were pooled and sequenced as 2 x 100bp paired end reads across 4 lanes of an Illumina Hiseq 2000 flow cell.

tag: disease status

value: Ashmatic

value: peripheral blood


title: blood case indiv 5

tag: tissue


title: blood case indiv 4


title: 9704031158_R02C01

source_name: genomic DNA whole blood 6


title: blood case indiv 8


title: 9704031158_R01C02

source_name: genomic DNA whole blood 5


title: blood control indiv 8

source_name: Normal_peripheral blood

value: Normal


title: 9704031158_R03C01

source_name: genomic DNA whole blood 7


title: blood case indiv 7


title: blood control indiv 9


title: ZFX ChIP-seq in MCF7 rep2

tag: cell line


title: blood control indiv 5


title: 9704031097_R05C02

source_name: genomic DNA whole blood 3


title: blood control indiv 4


title: blood control indiv 7


title: blood case indiv 9


title: blood control indiv 6


title: blood case indiv 2


title: blood case indiv 3


title: ZFX ChIP-seq in MCF7 rep1

tag: chip antibody


title: 9721365012_R02C02

source_name: genomic DNA whole blood 12


title: blood control indiv 3


title: blood control indiv 2


title: blood case indiv 1


title: nasal control indiv 9

source_name: Normal_nasal epitheilium

value: nasal epitheilium


title: 9704031097_R06C01

source_name: genomic DNA whole blood 4


title: nasal control indiv 8


title: nasal control indiv 7


title: nasal control indiv 5


title: nasal control indiv 2


title: nasal control indiv 10


title: nasal control indiv 1


title: nasal control indiv 3


title: blood control indiv 1


title: nasal case indiv 4

source_name: Ashmatic_nasal epitheilium


title: nasal case indiv 7


title: nasal case indiv 9


title: nasal control indiv 4


title: nasal case indiv 8


title: nasal case indiv 1


title: nasal case indiv 2


title: nasal case indiv 3


title: nasal case indiv 5


title: CSF1Ri rep3

city: Seattle

first: Robert

middle: Anthony

last: Amezquita

state: WA

address: 1100 Fairview Ave. N.

department: Integrated Immunotherapy Research Center

institute: Fred Hutchinson Cancer Research Institute

data_processing:
Alignment with STAR
Quantification with HTSeq
Differential expression with DESeq2 in R
Genome_build: mm10
Supplementary_files_format_and_content: Count tables

source_name: melanoma

growth_protocol: BrafCA; Tyr::CreER; Ptenlox4-5  mice have been previously described(Dankort et al., 2009b). Local tumor induction was performed as previously described(Ho et al., 2014). Age-matched mice that were housed in the same room of the same facility were used for each experiment. Mice were randomized to mouse size and litter, and treated mice were co-housed with controls whenever possible. The investigators were not blinded to mouse allocation. Group size was chosen based on constraints of age-matched litters.

extract_protocol:
Tumors for flow cytometry and RNAseq were minced in Hank’s Balanced Salt Solution with 0.5mg/ml collagenase IV and 200 mg/L DNase, digested in a 37C incubator for 30 minutes and filtered to remove debris. Tumors for Single Cell Barcode Chip or intracellular cytokine stain were minced in complete RPMI with 5% serum, 0.5mg/ml collagenase IV and 200 mg/L DNase, digested in a 37C incubator for 30 minutes and filtered to remove debris. The filtrate was incubated with ACK lysis buffer (Invitrogen) for 4 minutes, washed and re-suspended in complete RPMI. For RNAseq, single-cell suspension was purified of dead cells with Lymphoprep (Stem Cell) per protocol. For RNAseq, at least three tumors were pooled for each sample collected in triplicate, with further characterization of phenotype by flow cytometry of each independent tumor. Total RNA was purified with the use of QIAzol and RNeasy Mini kit (QIAGEN), in which an on-column DNase treatment was included. Purified RNA was submitted to the Yale Center for Genomic Analysis where it was subjected to mRNA isolation and library preparation.
Non-strand specific libraries were generated from 50ng total RNA using the SMARTer Ultra Low Input RNA for Illumina Sequencing kit.  Libraries were pooled, six samples per lane, and sequenced on an Illumina HiSeq 2500 (75-bp paired end reads), and aligned using STAR to the GRCm38 (mm10) reference genome. A count-based differential expression protocol was adapted for this analysis(Anders et al., 2013); mappable data were counted using HTSeq, and imported into R for differential expression analysis using the DESeq2.To find differentially regulated sets of genes for signature generation, a 1.5-Log2 fold-change difference between samples and p-adjusted (Holm-Sidak) ≤ 0.01 was used.
RNA-Seq, paired-end 75bp

treatment_protocol: 30 days after tumor induction, when tumors were measurable but total volume less than 100 mm3, BrafCA; Tyr::CreER; Ptenlox4-5  mice received normal or CSF1Ri PLX6134 chow (600mg PLX6134/kg, generously provided by Plexxikon) for 30 days or until tumors reached endpoint ( 2 cm3 as pre-specified in each experiment). In various experiments, mice also received either control vehicle (PBS) or CD40 agonistic antibody (FGK4.5 10mg/kg every three days i.p.)  for a total of ten treatments or until pre-specified tumor endpoint,

tag: transgene

value: BrafCA; Tyr::CreER; Ptenlox4-5

value: tumor associated macrophages

value: wild type


title: CD40 agonist+ CSF1Ri rept1


title: CD40 agonist+ CSF1Ri rept3


title: CD40 agonist+ CSF1Ri rept2


title: CSF1Ri rep2


title: CD40 agonist rept3


title: CD40 agonist rept2


title: CSF1Ri rep1


title: nasal control indiv 6


title: nasal case indiv 6


title: CD40 agonist rept1


title: Control rep3

description: Control


title: Control rep1

description: Control


title: Control rep2

description: Control


title: 4T1-nSMase2-control-exosome

city: Tokyo

first: Nobuyoshi

last: Kosaka

address: 5-1-1, Tsukiji, Chuo-ku

department: Research of Molecular Functions and Targets

country: Japan

institute: National Cancer Center

description: Exosomal total RNA from 4T1 cells. No modified expression of nSMase2.

hyb_protocol: Labeled RNA was hybridized to the mouse miRNA microarray, Release 18.0 (G4872A#38112 Agilent Technologies) with the miRNA Complete Labeling Reagent and Hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: Images were quantified using Agilent Feature Extraction software version 10.7.3.1 (Agilent) using default parameters (Grid:038112_D_F_20120106) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 4T1-nSMase2-control cells

label_protocol: 100 ng of each RNA sample was labeled with the miRNA Complete Labeling Reagent and Hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: Culture in RPMI1640 medium with 10% FCS and Antibiotic-Antimycotic

extract_protocol: Isolation of exosomal and cellular RNAs was performed using the miRNeasy Mini Kit according to the manufacture instruction.

treatment_protocol: These cells were genetically modified by shRNA or expression vector against nSMase2

tag: source of rna

value: exosome


title: FA-13-015_healthy

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description:
13-0017-H
Poly A mRNA

hyb_protocol: cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Microarray Processing batch were controlled for using the R package Combat. Differential gene expression between the control and mutant mice was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates.

source_name: lung, healthy

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

extract_protocol: Fresh lung samples were obtained directly from the Operating Room, and were placed into RNALater and stored at 4C. Within 12 hours of collection, RNA was extracted using Trizol per manufacturer's protocol. RNA quality was assessed using Agilent Bioanalyzer, and RNA quantity was measured with a Qubit Fluorimeter.

value: lung

value: healthy

tag: age (days)

value: Male


title: FA-14-018_Hybrid_BPS

description:
13-0035-D
Poly A mRNA

source_name: lung, hybrid_BPS

tag: gender

value: Female


title: FA-14-028_healthy

description:
14-0196-H
Poly A mRNA


title: FA-15-042_Microcystic

description:
14-0297-D
Poly A mRNA

source_name: lung, microcystic

value: Microcystic


title: 4T1-nSMase2-OE-exosome

description: Exosomal total RNA from 4T1 cells whose expression of nSMase2 was over-expressed.

source_name: 4T1-nSMase2-OE cells


title: FA-13-006_healthy

description:
13-0009-H
Poly A mRNA


title: 4T1-nSMase2-OE-cellular

description: Cellular total RNA from 4T1 cells whose expression of nSMase2 was over-expressed.

value: cellular


title: FA-14-032_Microcystic

description:
14-0289-D
Poly A mRNA


title: 4T1-nSMase2-control-cellular

description: Cellular total RNA from 4T1 cells. No modified expression of nSMase2.


title: FA-14-024_healthy

description:
14-0164-H
Poly A mRNA


title: FA-15-042_healthy

description:
14-0193-H
Poly A mRNA


title: FA-14-028_Hybrid_BPS

description:
14-0284-D
Poly A mRNA


title: 4T1-nSMase2-KD-cellular

description: Cellular total RNA from 4T1 cells whose expression of nSMase2 was knocked-down.

source_name: 4T1-nSMase2-KD cells

value: nSMase2 KD


title: FA-14-032_healthy

description:
14-0185-H
Poly A mRNA


title: FA-14-018_healthy

description:
13-0015-H
Poly A mRNA


title: FA-13-007_healthy

description:
13-0012-H
Poly A mRNA


title: FA-14-016_healthy

description:
13-0016-H
Poly A mRNA


title: FA-13-007_Hybrid_BPS

description:
13-0032-D
Poly A mRNA


title: FA-13-005_Microcystic

description:
13-0031-D
Poly A mRNA


title: FA-14-016_Microcystic

description:
13-0037-D
Poly A mRNA


title: FA-13-006_Hybrid_BPS

description:
13-0029-D
Poly A mRNA


title: FA-13-013_healthy

description:
13-0013-H
Poly A mRNA


title: FA-14-024_Hybrid_BPS

description:
14-0244-D
Poly A mRNA


title: FA-13-015_Microcystic

description:
13-0039-D
Poly A mRNA


title: FA-13-013_Microcystic

description:
13-0034-D
Poly A mRNA


title: FA-13-012_healthy

description:
13-0002-H
Poly A mRNA


title: FA-13-012_Hybrid_BPS

description:
13-0021-D
Poly A mRNA


title: 4T1-nSMase2-KD-exosome

description: Exosomal total RNA from 4T1 cells whose expression of nSMase2 was knocked-down.


title: FA-13-005_healthy

description:
13-0011-H
Poly A mRNA


title: WT

city: Davis

first: Sergi

last: Simo

address: One Shields Avenue, 3402 Tupper Hall

department: Cell Biology and Human Anatomy

institute: University of California Davis

description: WT_Control (CPM)

data_processing:
Base-calling software HCS 1.5/RTA 1.13
The fastq files were processed with expHTS (see https://dl.acm.org/citation.cfm?id=2811442) to remove PCR duplicates, and to trim low quality sequences and adapter contamination, keeping reads of minimum length 30 bases.
Trimmed reads were aligned to the GrCm38 primary assembly using the gencode vM10 annotation with STAR v.2.5.1b (parameters as recommended for ENCODE in STAR manual).  STAR also generated the read counts per gene.
Raw counts per gene were normalized using the cpm command in edgeR
Genome_build: GrCm38
Supplementary_files_format_and_content: Processed data file format: excel; Content: Counts per milion (CPM)

source_name: Retinal mRNA profiles of pooled 15-day-old wild-type

extract_protocol:
Retinas were removed and stored in RNAlater (Qiagen). RNA was purified with Total RNA purification Plus Micro kit (Norgen Biotek Corp.) following manufacter instructions. Poly-A enrichment using the Kapa Stranded mRNA-seq kit (KapaBiosystems) was done and sequenced on 1 high output flowcell of an Illumina NextSeq 500 (Illumina) with paired-end 40bp reads
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: C57BL/6J and 129 (mixed background)

value: post natal day 15

value: Retina


title: hsa.poly.TUBB_light

city: Baltimore

first: Manolis

last: Maragkakis

state: MD

address: 251 Bayview Blvd

institute: National Institute on Aging

description:
RNA isolated from light polysome fraction
processed data file available on GSM2881398.

data_processing:
Adaptor trimming: The adapter sequences were trimmed from the paired-end reads using the cutadapt software in paired-end mode. The adapter GTGTCAGTCACTTCCAGCGG was trimmed from the 3’ end of read1 whereas CCGCATCGTCCTCCCT was trimmed from the 3’ end of read2. A constant adapter sequence of 16 nt was removed from the 5’ end of read1. Only reads longer than 25 nt after adapter trimming were retained.
First alignment: The reads were aligned to the human genome (hg19) using the STAR aligner (v2.5.2a). Reads were aligned in paired-end mode.
Collapsing: To exclude potential PCR artifacts, reads with the same 5’ end (defined from read1) and the same 3’ end (defined from read2) were collapsed.
Alignment: Akron5: The retained reads were re-aligned in single end mode using read1 only and the following parameters --outFilterMultimapScoreRange 0 --alignIntronMax 50000 --outFilterMatchNmin 8 --outFilterMatchNminOverLread 0.7 --sjdbOverhang 80 --alignSJDBoverhangMin 1 --seedSearchStartLmax 15. Akron3: Only read2 were aligned after they were reverse complemented to facilitate downstream analysis. The STAR parameters were selected to permit the alignment of reads with poly(A) tails. Specifically the following parameters were used --alignIntronMax 50000 --outFilterMultimapScoreRange 0 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --outFilterScoreMin 30 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 30 --outFilterMatchNminOverLread 0 --sjdbOverhang 100 --alignSJDBoverhangMin 1.
Aligned reads were loaded into a SQLite3 database for further processing with CLIPSeqTools (v0.1.7).
The read 5' and 3' ends for Akron5 and Akron3, respectivelly were extracted in bedgraph format. For Akron-SMRT the whole reads were extracted in bedgraph format.
Bedgraph files were converted to BigWig with UCSCtools bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files correspond to the fragments 5’ and 3’ ends for Akron5 and Akron3, respectively and to the whole reads for Akron-SMRT.

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in DMEM (Gibco) supplemented with 10% FBS (Sigma), at 37 °C, in 5% CO2. Cells were harvested at ~80% confluence.

extract_protocol:
Total RNA was extracted with Trizol (Ambion)
For Akron-SMRT, total RNA was extracted by Trizol from HeLa total cells and sucrose gradient polysome fractions. RNA was treated with 5’-phosphate specific Terminator exonuclease to remove non-capped mRNA. The 3’ ends of mRNA molecules were marked by ligation to an adapter that contains a biotin group at the 3’ end, allowing for further purification. We generated cDNA in conditions that favor full-length molecule amplification using primers designed to specifically amplify mRNAs encoded by CDK4 and TUBB genes. To avoid capturing 5’ OH mRNAs we used two PCR amplification steps for each gene using forward primers that started at the 5’ UTR and at the start codon. We then size-selected by gel purification to enrich for larger mRNAs and performed SMRT sequencing.    For Akron3,  abundant small RNAs was first substracted by dynabeads size-selection, and ribosomal RNAs and small-capped RNAs (i.e U snRNAs) were depleted using synthesized biotinylated oligonucleotides.  Capped mRNAs were then  selected by Terminator exonuclease treatment followed by biotinylated adapter ligation at the 3’ end and streptavidin capture. Similarly, for Akron5, polyadenylated mRNAs were enriched using Oligo(dT) followed by biotinylated adapter ligation at the 5’ end and streptavidin capture. While capped mRNAs are carried over, only poly(A) mRNAs with 5’ monophosphate are captured. The native ends of RNAs in Akron3 and Akron5 are marked by adapter ligation. In Akron3 and Akron5, RNA was chemically fragmented before the second adapter ligation. After fragmentation, RNA in Akron3 was size selected (>400 bp) on denaturing polyacrylamide. In Akron3 and Akron 5, a second adatpter was ligated and cDNA was generated by Superscript III with specific primers that recognize the adapter sequence. PCR amplification was performed with primers compatible with Illumina sequencer. PCR products were purified (~500-800 bp) on Metaphore agarose gels and were identified by paired-end, sequence-by-synthesis

treatment_protocol: Cells were pretreated with 100 µg/ml cycloheximide (Sigma) for 10 min at 37 °C, only for sucrose gradient fractionation.

value: HeLa

tag: protocol

value: Akron-SMRT

tag: rna fraction

value: light polysomes

tag: amplified mrna

value: TUBB


title: hsa.poly.CDK4_light

description:
RNA isolated from light polysome fraction
processed data file available on GSM2881397.


title: PNT2-exosome

description: Exosomal total RNA from PNT2 cells

hyb_protocol: Labeled RNA was hybridized to the Human miRNA Microarray 3.0 8x15K (G4470C Agilent Technologies) with the miRNA Complete Labeling Reagent and Hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.

data_processing: Images were quantified using Agilent Feature Extraction software version 10.7.3.1 (Agilent) using default parameters (Grid: 021827_D_20081121) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: exosome from PNT2_normal_cells

growth_protocol: Cultured in RPMI containing 10% heat-inactivated FBS and an antibiotic-antimycotic.

extract_protocol: Isolation of exosomal RNA and cellular RNAs was performed using the miRNeasy Mini Kit according to the manufacture instruction.

value: normal


title: PNT2-cellular

description: Cellular total RNA from PNT2 cells.

source_name: PNT2 cells_normal_cells


title: PC3M-exosome

description: Exosomal total RNA from PC3M cells

source_name: exosome from PC3M_cancer_cells

value: cancer


title: PC3M-cellular

description: Cellular total RNA from PC3M cells.

source_name: PC3M cells_cancer_cells


title: D30 DR ND Plasma on BN4

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data from Brown Norway Rats BN4 PBMCs stimulated with Day30 DR ND (normal diet) Rats Plasma

hyb_protocol: The Affymetrix GeneChip rat genome RG230 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Array images were normalized and analyzed with Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  Gene expression differences were also evaluated by principle component analyses, and the statistical significance of differential gene expression and false discovery rates (FDR) were derived through RankProduct (RP) statistic from Bioconductor (www.bioconductor.org).

organism: Rattus norvegicus

source_name: Diabetes inducible BB rats DR strain, no mutation at LYP locus

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: DR+/+, DRlyp/lyp, F+/+, and Flyp/lyp rats were maintained at The Medical College of Wisconsin (MCW) under specific pathogen-free conditions with standard light/dark cycles.  DR+/+ and DRlyp/lyp animals were propagated by mating Gimap5+/- breeders as described [12].  Rats were provided chow and water ad libitum.  All federal guidelines for use and care of laboratory animals (http://grants1.nih.gov/grants/olaw/references/phspol.htm) were followed.

extract_protocol: Total RNA was extracted with Trizol (Invitrogen, Carlsbad, CA, USA).  RNA was amplified/labeled using Affymetrix 3' IVT Express Kit (Affymetrix, Santa Clara, CA).

treatment_protocol: 20 day old littermates were weaned onto a normal diet (ND) consisting of plant and animal protein sources (LabDiet 5L0D, Purina, St. Louis, MO) or a hydrolyzed bovine casein diet (HCD, Modified AIN-93G diet, #103558GI, Dyets Inc., Bethlehem, PA).  A third group of BB littermates were provided ND and were treated with bacitracin and streptomycin (B/S) provided in the drinking water (0.5 g of each/250 ml, Sigma-Aldrich, St. Louis, MO, USA).    Blood was collected by heart puncture from rats under isofluorane anesthesia into EDTA vacutainer tubes (Becton-Dickinson, Franklin Lakes, NJ, USA).  Plasma was separated by centrifugation and stored at  -80°C.  All protocols were approved by the MCW Institutional Animal Care and Use Committee. Gene expression was accomplished by culturing Brown Norway PBMCs at 37°C in 5% CO2 stimulated with 40% of D30 DR ND, DR HCD, DR ND BS, and F+/+ plasma.  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: Brown Norway PBMCs

tag: age

value: 30 days old


title: D30 DR ND Plasma on BN3

description: Gene expression data from Brown Norway Rats BN3 PBMCs stimulated with Day30 DR ND (normal diet) Rats Plasma


title: D30 F+/+ ND control Plasma on BN4

description: Gene expression data from Brown Norway Rats BN4 PBMCs stimulated with Day30 F+/+ ND (normal diet) Rats Plasma

source_name: Healthy control Fisher rats F+/+ strain, no mutation at LYP locus


title: D30 F+/+ ND control Plasma on BN1

description: Gene expression data from Brown Norway Rats BN1 PBMCs stimulated with Day30 F+/+ ND (normal diet) Rats Plasma


title: D30 DR ND treated w/ B/S Plasma on BN2

description: Gene expression data from Brown Norway Rats BN2 PBMCs stimulated with Day30 DR ND (normal diet) Rats that treated w B/S in drinking water from age of day20 Plasma


title: Autologous BNrat_rep4 (BN4)

description: Gene expression data from BN (Brown Norway) Rat replicate1 - BN1 PBMCs stimulated with self plasma

source_name: Autologous BN (Brown Rorway) Rat, rep4

value: 180 days old


title: D30 F+/+ ND control Plasma on BN3

description: Gene expression data from Brown Norway Rats BN3 PBMCs stimulated with Day30 F+/+ ND (normal diet) Rats Plasma


title: D30 DR ND Plasma on BN1

description: Gene expression data from Brown Norway Rats BN1 PBMCs stimulated with Day30 DR ND (normal diet) Rats Plasma


title: D30 F+/+ ND control Plasma on BN2

description: Gene expression data from Brown Norway Rats BN2 PBMCs stimulated with Day30 F+/+ ND (normal diet) Rats Plasma


title: Autologous BNrat_rep1 (BN1)

source_name: Autologous BN (Brown Rorway) Rat, rep1


title: D30 DR ND treated w/ B/S Plasma on BN3

description: Gene expression data from Brown Norway Rats BN3 PBMCs stimulated with Day30 DR ND (normal diet) Rats that treated w B/S in drinking water from age of day20 Plasma


title: Autologous BNrat_rep3 (BN3)

source_name: Autologous BN (Brown Rorway) Rat, rep3


title: D30 DR ND treated w/ B/S Plasma on BN4

description: Gene expression data from Brown Norway Rats BN4 PBMCs stimulated with Day30 DR ND (normal diet) Rats that treated w B/S in drinking water from age of day20 Plasma


title: D30 DR HCD Plasma on BN2

description: Gene expression data from Brown Norway Rats BN2 PBMCs stimulated with Day30 DR Rats fed with HCD (hydrolyzed bovine casein diet) from age of day20 Plasma


title: D30 DR ND treated w/ B/S Plasma on BN1

description: Gene expression data from Brown Norway Rats BN1 PBMCs stimulated with Day30 DR ND (normal diet) Rats that treated w B/S in drinking water from age of day20 Plasma


title: D30 DR HCD Plasma on BN4

description: Gene expression data from Brown Norway Rats BN4 PBMCs stimulated with Day30 DR Rats fed with HCD (hydrolyzed bovine casein diet) from age of day20 Plasma


title: Autologous BNrat_rep2 (BN2)

source_name: Autologous BN (Brown Rorway) Rat, rep2


title: F+/+ (RT1u) day50, replicate2

description: Gene expression data of F344 Healthy Control rats F+/+  at day50, replicates2

source_name: F344 Healthy Control rats F+/+ strain, no mutation at LYP locus

treatment_protocol: 20 day old littermates were weaned onto a normal diet (ND) consisting of plant and animal protein sources (LabDiet 5L0D, Purina, St. Louis, MO).  All protocols were approved by the MCW Institutional Animal Care and Use Committee.

value: pancreatic islets

value: 50 days old


title: F+/+ (RT1u) day50, replicate3

description: Gene expression data of F344 Healthy Control rats F+/+  at day50, replicates3


title: D30 DR HCD Plasma on BN1

description: Gene expression data from Brown Norway Rats BN1 PBMCs stimulated with Day30 DR Rats fed with HCD (hydrolyzed bovine casein diet) from age of day20 Plasma


title: D30 DR HCD Plasma on BN3

description: Gene expression data from Brown Norway Rats BN3 PBMCs stimulated with Day30 DR Rats fed with HCD (hydrolyzed bovine casein diet) from age of day20 Plasma


title: F+/+ (RT1u) day50, replicate1

description: Gene expression data of F344 Healthy Control rats F+/+  at day50, replicates1


title: Flyplyp (FAM) day50, replicate2

description: Gene expression data of F344 Healthy Control rats Flyp/lyp  at day50, replicates2

source_name: F344 Healthy Control rats Flyp/lyp strain, with mutation at LYP locus


title: DR+/+ (DR) day50, replicate3

description: Gene expression data of Diabetes inducible BB rats DR+/+  at day50, replicates3

source_name: Diabetes inducible BB rats DR+/+ strain, no mutation at LYP locus


title: DRlyplyp (DP) day50, replicate3

description: Gene expression data of Spontaneously Diabetic BB rat DRlyplyp at day50, replicates3

source_name: Spontaneously Diabetic BB rats DRlyp/lyp strain, with mutation at LYP locus


title: Flyplyp (FAM) day50, replicate3

description: Gene expression data of F344 Healthy Control rats Flyp/lyp  at day50, replicates3


title: Flyplyp (FAM) day50, replicate1

description: Gene expression data of F344 Healthy Control rats Flyp/lyp  at day50, replicates1


title: DR+/+ (DR) day50, replicate2

description: Gene expression data of Diabetes inducible BB rats DR+/+  at day50, replicates2


title: DR+/+ (DR) day50, replicate1

description: Gene expression data of Diabetes inducible BB rats DR+/+  at day50, replicates1


title: Sample_A10

city: San Francisco

first: Srilaxmi

last: Nerella

address: HSE1355A, 513 Parnassus ave

department: Department of Medicine

institute: UCSF

data_processing:
We mapped reads onto the human transcriptome (Ensembl GRCh37) and genome reference (Ensembl hg19) using TopHat2 (v 2.0.13) with the default parameters. TopHat2 was supplied with a set of known transcripts (as a GTF formatted file, Ensembl GRCh37) using –G option.
The mapped reads of each sample are stored in a binary format (.bam). ROP (gprofile.py) categorizes the reads into genomic categories (junction read, CDS, intron, UTR3, UTR5, introns, inter-genic read, deep a deep inter-genic read, mitochondrial read, and multi-mapped read) based on their compatibility with the features defined by Ensembl (GRCh37) gene annotations.
ROP (rprofile.py) categorizes reads into repeat elements (classes and families) based on their compatibility with repeat instances defined by RepeatMasker annotation (RepeatMasker v3.3, Repeat Library 20120124).
We count the number of reads overlapping variable(V), diversity (D), joining (J), and constant (C) gene segments of B cell receptor (BCR) and T cell receptor (TCR) loci using htseq-count (HTSeq v0.6.1).
We remapped the remaining unmapped reads to the human reference genome (hg19) and transcriptome (known transcripts, Ensembl GRCh37) using Megablast (BLAST+ 2.2.30).
The remaining unmapped reads were mapped to the reference repeat sequences using Megablast (BLAST+ 2.2.30). The reference repeat sequences were downloaded from Repbase v20.07 (http://www.girinst.org/repbase/). Human repeat elements (humrep.ref and humsub.ref) were merged into a single reference.
. We used IgBlast (v. 1.4.0) with a stringent e-value threshold (e-value < 10-20) to map the remaining unmapped reads onto the V(D)J gene segments of the of the B cell receptor (BCR) and T cell receptor (TCR) loci. Gene segments of B cell receptors (BCR) and T cell receptors (TCR) were imported from IMGT version: 3.1.17 (International ImMunoGeneTics information system). The IMGT database contains: variable (V) gene segments; diversity (D) gene segments; and joining (J) gene segments.
We used Megablast (BLAST+ 2.2.30) to align remaining unmapped reads onto the collection of bacterial, viral, and eukaryotic reference genomes. Bacterial and viral genomes were downloaded from NCBI (ftp://ftp.ncbi.nih.gov/). Genomes of eukaryotic pathogens were downloaded from EuPathDB (http://eupathdb.org/eupathdb/). We used MetaPhlAn2 (Metagenomic Phylogenetic Analysis, v 2.0) to obtain the taxonomic profile of microbial communities present in the sample.
Genome_build: GRCh37/hg19

source_name: airway epithelium

extract_protocol:
RNA was extracted from the epithelial brushing samples using the Qiagen RNeasy mini-kit.
Libraries were constructed and barcoded with the TruSeq Stranded Total RNA using a Ribo-Zero Human/Mouse/Rat library preparation kit, per manufacturer’s protocol

value: airway epithelium

value: Female

tag: diagnosis

value: Asthmatic


title: Sample_C06


title: F+/+ (RT1u) day40, replicate1

description: Gene expression data of F344 Healthy Control rats F+/+  at day40, replicates1

value: 40 days old


title: Sample_B06

value: Male


title: Sample_H03


title: F+/+ (RT1u) day40, replicate2

description: Gene expression data of F344 Healthy Control rats F+/+  at day40, replicates2


title: F+/+ (RT1u) day40, replicate3

description: Gene expression data of F344 Healthy Control rats F+/+  at day40, replicates3


title: DRlyplyp (DP) day50, replicate1

description: Gene expression data of Spontaneously Diabetic BB rat DRlyplyp at day50, replicates1


title: Flyplyp (FAM) day40, replicate2

description: Gene expression data of F344 Healthy Control rats Flyp/lyp  at day40, replicates2


title: Flyplyp (FAM) day40, replicate3

description: Gene expression data of F344 Healthy Control rats Flyp/lyp  at day40, replicates3


title: Flyplyp (FAM) day40, replicate1

description: Gene expression data of F344 Healthy Control rats Flyp/lyp  at day40, replicates1


title: DRlyplyp (DP) day50, replicate2

description: Gene expression data of Spontaneously Diabetic BB rat DRlyplyp at day50, replicates2


title: DR+/+ (DR) day40, replicate1

description: Gene expression data of Diabetes inducible BB rats DR+/+  at day40, replicates1


title: DR+/+ (DR) day40, replicate3

description: Gene expression data of Diabetes inducible BB rats DR+/+  at day40, replicates3


title: F+/+ (RT1u) day30, replicate3

description: Gene expression data of F344 Healthy Control rats F+/+  at day30, replicates3


title: DR+/+ (DR) day40, replicate2

description: Gene expression data of Diabetes inducible BB rats DR+/+  at day40, replicates2


title: DRlyplyp (DP) day40, replicate1

description: Gene expression data of Spontaneously Diabetic BB rat DRlyplyp at day40, replicates1


title: DRlyplyp (DP) day40, replicate3

description: Gene expression data of Spontaneously Diabetic BB rat DRlyplyp at day40, replicates3


title: Sample_C09


title: DRlyplyp (DP) day40, replicate2

description: Gene expression data of Spontaneously Diabetic BB rat DRlyplyp at day40, replicates2


title: F+/+ (RT1u) day30, replicate2

description: Gene expression data of F344 Healthy Control rats F+/+  at day30, replicates2


title: Flyplyp (FAM) day30, replicate3

description: Gene expression data of F344 Healthy Control rats Flyp/lyp  at day30, replicates3


title: Sample_H09


title: Flyplyp (FAM) day30, replicate2

description: Gene expression data of F344 Healthy Control rats Flyp/lyp  at day30, replicates2


title: Sample_E05


title: Sample_G09


title: Sample_C05


title: DR+/+ (DR) day30, replicate2

description: Gene expression data of Diabetes inducible BB rats DR+/+  at day30, replicates2


title: DR+/+ (DR) day30, replicate3

description: Gene expression data of Diabetes inducible BB rats DR+/+  at day30, replicates3


title: Sample_D09


title: DRlyplyp (DP) day30, replicate3

description: Gene expression data of Spontaneously Diabetic BB rat DRlyplyp at day30, replicates3


title: Sample_H08


title: Flyplyp (FAM) day30, replicate1

description: Gene expression data of F344 Healthy Control rats Flyp/lyp  at day30, replicates1


title: DRlyplyp (DP) day30, replicate1

description: Gene expression data of Spontaneously Diabetic BB rat DRlyplyp at day30, replicates1


title: F+/+ (RT1u) day30, replicate1

description: Gene expression data of F344 Healthy Control rats F+/+  at day30, replicates1


title: Sample_G12


title: Flyplyp (FAM) day20, replicate3

description: Gene expression data of F344 Healthy Control rats Flyp/lyp  at day20, replicates3

value: 20 days old


title: DRlyplyp (DP) day30, replicate2

description: Gene expression data of Spontaneously Diabetic BB rat DRlyplyp at day30, replicates2


title: Sample_G05


title: Sample_B04


title: DR+/+ (DR) day30, replicate1

description: Gene expression data of Diabetes inducible BB rats DR+/+  at day30, replicates1


title: Flyplyp (FAM) day20, replicate2

description: Gene expression data of F344 Healthy Control rats Flyp/lyp  at day20, replicates2


title: DR+/+ (DR) day20, replicate2

description: Gene expression data of Diabetes inducible BB rats DR+/+  at day20, replicates2


title: Sample_G11


title: DRlyplyp (DP) day20, replicate3

description: Gene expression data of Spontaneously Diabetic BB rat DRlyplyp at day20, replicates3


title: Sample_D04


title: Flyplyp (FAM) day20, replicate1

description: Gene expression data of F344 Healthy Control rats Flyp/lyp  at day20, replicates1


title: D40 F+/+ ND, replicate2

description: Gene expression Data of Day40 Fisher F+/+ ND (normal diet) Healthy Control Rat

hyb_protocol: The Affymetrix GeneChip Rat Genome RG230 2.0 array was selected for these studies for its overall comprehensive coverage.

data_processing: Array images were quantified with Affymetrix Expression Console Software and normalized with Robust Multichip Analysis (Bioconductor - www.bioconductor.org) to determine signal log ratios [26].  Gene expression differences were also evaluated by principle component analyses, and the statistical significance of differential gene expression and false discovery rates (FDR) were derived through RankProduct (RP) statistic from Bioconductor.

treatment_protocol: 20 day old littermates were weaned onto a normal diet (ND) consisting of plant and animal protein sources (LabDiet 5L0D, Purina, St. Louis, MO) or a hydrolyzed bovine casein diet (HCD, Modified AIN-93G diet, #103558GI, Dyets Inc., Bethlehem, PA).  A third group of BB littermates were provided ND and were treated with bacitracin and streptomycin (B/S) provided in the drinking water (0.5 g of each/250 ml, Sigma-Aldrich, St. Louis, MO, USA).  Pancreata were harvested and islets isolated following standard published methodology. All protocols were approved by the MCW Institutional Animal Care and Use Committee.


title: Sample_H04


title: D40 F+/+ ND, replicate1


title: D40 DR ND, pool2 replicate2

description: Gene expression Data of Day40 DR ND (normal diet) control Rat


title: F+/+ (RT1u) day20, replicate2

description: Gene expression data of F344 Healthy Control rats F+/+  at day20, replicates2


title: Sample_F04


title: F+/+ (RT1u) day20, replicate3

description: Gene expression data of F344 Healthy Control rats F+/+  at day20, replicates3


title: DR+/+ (DR) day20, replicate3

description: Gene expression data of Diabetes inducible BB rats DR+/+  at day20, replicates3


title: Sample_E04


title: Sample_B05


title: F+/+ (RT1u) day20, replicate1

description: Gene expression data of F344 Healthy Control rats F+/+  at day20, replicates1


title: DR+/+ (DR) day20, replicate1

description: Gene expression data of Diabetes inducible BB rats DR+/+  at day20, replicates1


title: Sample_E08


title: DRlyplyp (DP) day20, replicate1

description: Gene expression data of Spontaneously Diabetic BB rat DRlyplyp at day20, replicates1


title: D40 DR ND, pool2 replicate1


title: Sample_E10


title: Sample_B09


title: Sample_D05


title: Sample_F11


title: Sample_C04


title: Sample_E06


title: Sample_A06


title: D40 DR HCD replicate1

description: Gene expression data of Day40 DR Rat fed with HCD (hydrolyzed bovine casein diet) from age of day20


title: D40 DR ND B/S replicate1

description: Gene expression Data of Day40 DR ND (normal diet) Rat that treated w B/S in drinking water from age of day20


title: Sample_A05

value: Healthy


title: DRlyplyp (DP) day20, replicate2

description: Gene expression data of Spontaneously Diabetic BB rat DRlyplyp at day20, replicates2


title: D40 DR HCD replicate2


title: D30 DR ND Plasma on BN2

description: Gene expression data from Brown Norway Rats BN2 PBMCs stimulated with Day30 DR ND (normal diet) Rats Plasma


title: 8323_N2-14_20160216

city: Basel

first: Verdon

last: Taylor

address: Mattenstrasse 28

department: Department Biomedicine

country: Switzerland

institute: University of Basel

description: Gene expression data of Notch2 cKO animals

hyb_protocol: Affymetrix,  Small Sample Service, was performed by ATLAS Biolabs, Full Service, Fabeckstraße 60-62, 14195 Berlin, Germany

data_processing: Samples were analsysed using  Lasergene DNA-Star program using preset Microarray default settings

source_name: 8-10 week old Notch2 cKO animals, 5days post Tamoxifen administration

extract_protocol: Animals were sacrificed, SVZ was microdissected, dissociation was performed in Papain Ovomucoid for 30 minutes (according to Giachino et al. 2009)

treatment_protocol: Adult (p56) animals (Hes5::CreERT2, Notch2 floxed) were treated for 5 days with Tamoxifen to induce recombination and deletion of Notch2.

value: adult subventricular zone

tag: genotype

value: Notch2 cKO

tag: cell type

value: NSCs


title: 8323_C19_20160216

description: Gene expression data of Control animals

scan_protocol: Affymetrix,  Small Sample Service, was performed by ATLAS Biolabs, Full Service, Fabeckstraße 60-62, 14195 Berlin, Germany

source_name: 8-10 week old Control animals, 5days post Tamoxifen administration

value: wildtype control


title: 8323_C5_20151125

description: Gene expression data of Control animals

label_protocol: Affymetrix,  Small Sample Service, was performed by ATLAS Biolabs, Full Service, Fabeckstraße 60-62, 14195 Berlin, Germany


title: D40 DR ND, pool1 replicate1


title: Sample_F06


title: 8323_N20_20160216


title: Sample_H05


title: Sample_A09


title: Sample_F09


title: Sample_D06


title: Sample_E09


title: D40 DR ND B/S replicate2


title: Sample_G06


title: Sample_B10


title: Sample_F03


title: D40 DR ND, pool1 replicate2


title: Sample_F08


title: Sample_H06


title: Sample_G04


title: Sample_D11


title: Sample_G10


title: 8323_N13_20151125


title: Sample_C12


title: Sample_F10


title: Sample_F05


title: Sample_E12


title: 15697

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of purified and labeled cRNA (Cy3 label: 825 ng; Cy5 label: 825 ng) was hybridised on the Agilent-021169 Arabidopsis 4 Oligo Microarray (V4) followed by (manual) washing, according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with SureScan High-Resolution Technology, and probe signals were quantified using Agilent's Feature Extraction software (version 10.7.3.1).

data_processing: We use the Agilent processed signal values (i.e., feature gProcessedSignal for the Cy3 signal and rProcessedSignal for the Cy5 signal) from Agilent Feature Extraction software v10.7.3.1 and compute log2-(Cy5/Cy3)-ratios. We remove Agilent control probes, as well as probes with signals below background on all arrays (absent spots). To decide whether a signal is significantly above background, we use the features gIsPosAndSignif and rIsPosAndSignif, also provided by the Agilent software. In case of multiple probes for the same Agilent ID, log2-(Cy5/Cy3)-ratios are averaged.

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 200 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double-stranded cDNA in a reverse transcription reaction. Subsequently, the sample was converted to antisense cRNA, amplified and labeled with Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer's protocol (Agilent).

growth_protocol: Seedlings were grown on half-strength MS medium without sucrose. 48h 4°C, 4 days in darkness 22°C.

extract_protocol: QIAGEN RNeasy Plant Mini Kit with on-column DNase digestion and four RPE washes.

tag: ecotype

value: Columbia 0

value: wild type

value: 4 days

value: seedling

tag: replicate

tag: treatment

value: darkness

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 200 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double-stranded cDNA in a reverse transcription reaction. Subsequently, the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer's protocol (Agilent).

growth_protocol: Seedlings were grown on half-strength MS medium without sucrose. 48h 4°C, 4 days in darkness 22°C, 1h far-red light.

value: far-red light


title: 15687

tag: tissue

growth_protocol: Seedlings were grown on half-strength MS medium without sucrose. 48h 4°C, 4 days in darkness 22°C, 1h red light.

value: red light


title: 15692

value: elo3-6 mutant (GABI-KAT collection code GABI555_H06)


title: 15685


title: 15696


title: 15683


title: 15694


title: 15695


title: 15688


title: 15691


title: 15693


title: HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 4

city: Louisville

first: J.

middle: Christopher

last: States

state: KY

address: 505 S. Hancock St., Rm 304

department: Department of Pharmacology & Toxicology

institute: University of Louisville

description:
A generous gift from Dr. Tai Hao Quan, University of Michigan
Permanent epithelial cell line from adult human maleskin, aneuploid, immortal, has a transformed phenotype in vitro but remains nontumorigenic.
The cells were maintained for 7 weeks without 100 nM sodium arsenite

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C to Affymetrix Primeview Human arrays according to the GeneChip 3' array Hybridization User Manual from Affymetrix

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 4.0 (Affymetrix)

data_processing: The CEL files were imported into Partek software Version 6.6 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization. Contrast of interest were analyzed using a 2-way ANOVA considering treatment and time.

source_name: Immortalized Human Keratinocytes (HaCaT)

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix 3' IVT Express Plus Reagent Kit from 250 ng total RNA

growth_protocol: HaCaT cells were cultured in 4 biological replicates in MEM alpha modification media supplemented with 10% fetal bovine serum, penicillin/streptomycin and glutamine. Cultures were maintained at 37°C in a humidified 5% CO2 atmosphere with 20% oxygen and were maintained separately for 3 and 7 weeks. A set of HaCaT cells maintained for 28 weeks (1 biological replicate) were obtained form Dr. Michael P. Waalkes.

extract_protocol: Total RNA was purified from the cells using the mirVana™ miRNA Isolation Kit.

treatment_protocol: cells maintained with and without 100 nM sodium arsenite from day 1 of plating.

tag: cell line

value: HaCaT cells

value: unexposed maintained for 7 weeks


title: 15682


title: 15684