title: P674T


title: P294T

status: Public on Oct 03 2018

type: SRA

city: Nijmegen

first: Suzan

last: Stelloo

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

library_source: transcriptomic

data_processing:
Strand-specific libraries were generated with the TruSeq Stranded mRNA sample preparation kit (Illumina, Part # 15031047 Rev. E) and sequenced on a HiSeq2500
Sequencing data was aligned to hg38 using TopHat and number of reads per gene were measured with HTSeq count.
EdgeR-Limma workflow was used for gene expression analysis. The ComBat normalization method within the R package SVA was used to correct the batch effects observed by day of RNA isolation. Genes with >1 count per million in at least 10 samples were included. Normalized data is provided in the table Porto_ge_table
Genome_build: hg38
Supplementary_files_format_and_content: Expression table of samples (columns) by transcript (rows) reporting normalized counts.

molecule: total RNA

organism: Homo sapiens

source_name: primary prostate cancer

growth_protocol: fresh frozen material

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA universal kit (Qiagen) according to the manufacturer’s instruction with Qiagen’s QIAcube robot. Samples with a RIN>8 were considered for library preparation.
Strand-specific libraries were generated with the TruSeq Stranded mRNA sample preparation kit (Illumina, Part # 15031047 Rev. E).

treatment_protocol: prostatectomy samples, labeled according to recurrence status (case/control/exclude) and ERG expression (low/high)

tag: patient id

tag: erg expression

value: high

tag: case/control

value: Case

tag: tissue

value: primary prostate cancer


title: Loxp_T2.5_LPS Loxp T2.5 LPS 3 SAM24331099

city: South San Francisco

first: Sarah

middle: K

last: Kummerfeld

state: CA

address: 1 DNA Way

country: USA

institute: Genentech

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

molecule: polyA RNA

organism: Mus musculus

source_name: RNA from BMDMs from mice that are COP1-wt Rosa26-CreERT2 or COP1-floxed Rosa26-CreERT2

extract_protocol: At day 7 of differentiation, BMDMs were treated with 100 ng/ml of LPS or not. BMDMs were directly harvested in lysis buffer (from Qiagen RNeasy mini kit) at different time points following LPS stimulation. Total RNA was isolated using the Qiagen RNeasy mini kit as per manufacturer’s protocol including the on-column DNase digestion

tag: group

tag: genotype

value: Loxp

tag: time

tag: treatment

value: LPS

tag: individual

tag: cell type

value: BMDMs


title: WT_T0_Untreated WT T0 Untreated 1 SAM24331068

value: WT

value: Untreated


title: P276T


title: WT_T13_LPS WT T13 LPS 3 SAM24331085


title: P257T

value: low

value: Control


title: P245T


title: WT_T2.5_LPS WT T2.5 LPS 1 SAM24331069


title: P297T


title: P268T


title: WT_T4_LPS WT T4 LPS 2 SAM24331076


title: Loxp_T9_LPS Loxp T9 LPS 2 SAM24331096


title: P329T


title: Loxp_T4_LPS Loxp T4 LPS 1 SAM24331088


title: P423T


title: WT_T6_LPS WT T6 LPS 2 SAM24331077


title: P348T


title: WT_T4_LPS WT T4 LPS 3 SAM24331082


title: P227T


title: Loxp_T0_Untreated Loxp T0 Untreated 2 SAM24331092


title: P252T


title: Loxp_T13_LPS Loxp T13 LPS 3 SAM24331103


title: P223T


title: P336T_H3K27me3

library_source: genomic

data_processing:
Sequences were generated by the Illumina Hiseq 2500 (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.
Peak calling over input control (mixed inputs) was performed using DFilter and MACS for AR, H3K27ac, H3K4me3 ChIP-seq samples. The peaks called by both peak callers were used for analysis.
H3K27me3 ChIP-seq peaks were called by genome segmentation using ChromHMM chosing the state with high H3K27me3 signal (binary data, no quantitative data)
Genome_build: hg19
Supplementary_files_format_and_content: bed

molecule: genomic DNA

extract_protocol:
Chromatin immunoprecipitations were performed as described previously with minor changes (Zwart et al., 2013). Samples were crosslinked in solution A with 2mM DSG (CovaChem) for 25 minutes at room temperature. After 25 minutes, 1% formaldehyde was added for 20 minutes and subsequently quenched with glycine. Samples were lysed as described (Schmidt et al., 2009) and sonicated for at least 10 cycles of 30s on, 30s off using a Diagenode Bioruptor Pico. For each ChIP, 5ug of antibody was conjugated with 50ul Protein A magnetic beads. Antibodies used were AR (sc-816, Santa Cruz), H3K27ac (39133, Active Motif), H3K4me3 (Ab8580, Abcam) and H3K27me3 (39155, Active Motif). Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).

treatment_protocol: prostatectomy samples, labeled according to recurrence status (case/control/exclude)

tag: chip antibody

value: H3K27me3 (Active Motif, catalog# 39155, lot# 31814017)


title: P228T


title: P295T_H3K27me3


title: P291T_H3K27me3

value: Exclude


title: P279T_H3K27me3


title: P272T_H3K27me3


title: P274T_H3K27me3


title: P263T_H3K27me3


title: P254T_H3K27me3


title: P229T


title: P249T_H3K27me3


title: P230T_H3K27me3


title: P695T_H3K27me3


title: P265T


title: P680T_H3K27me3


title: P294T_H3K27me3


title: P355T_H3K27me3


title: P280T_H3K27me3


title: P544T_H3K27me3


title: P603T_H3K27me3


title: P555T_H3K27me3


title: P560T_H3K27me3


title: P593T_H3K27me3


title: P559T_H3K27me3


title: P531T_H3K27me3


title: P452T_H3K27me3


title: HeLa: pullscram_1

city: Chippendale

first: Darya

middle: Pavlovna

last: Vanichkina

state: New South Wales

address: 32 Queen Street

country: Australia

institute: University of Sydney

data_processing:
Read alignment: STAR version 2.3.0
gencode 19 annotations
Genome_build: hg19
Supplementary_files_format_and_content: mapped bw files;  count table

source_name: pulldown sample with scrambled mimic transfected oligo

growth_protocol: Cells were maintained in DMEM media supplemented with 10% (v/v) FBS and 2 mM L-glutamine. All cells were obtained from American Type Culture Collection and cultured at 37°C and 5% (v/v) CO 2 . All cells were tested negative for mycoplasma contamination (MycoAlert Mycoplasma Detection Kit, Lonza).

extract_protocol:
mirVana miRNA Extraction Kit (Life Technologies).
1:1 mix of RH and oligo-dT primers
TotalScript RNA-seq Kit

treatment_protocol: One million cells were reverse transfected with equimolar amounts of CNV K-miR-29b and CNV K-scram oligos (Nihon Techno Service) per well in a 6-well plate using Lipofectamine RNAiMax reagent (Life Technologies) according to the manufacturer's instructions. Unless mentioned otherwise in the methods, mimics were transfected at a final concentration of 10 nM. Cells were topped up with 2 ml of complete growth media 24 h after transfection, and were allowed to recover for an additional 8 h before harvesting. To prepare deep sequencing libraries from pulldown RNA, approximately 9 × 10 6 cells were transfected with CNV K mimics.

tag: cell line

value: HeLa

tag: input rna amount

value: 5 ng

tag: kit used

value: TotalScript RNA-seq Kit (Epicentre), using a mix of Random hexamer and Oligo-dT primers


title: HeLa: pull29b_3

source_name: pulldown sample with miR-29b mimic transfected oligo


title: P464T_H3K27me3


title: HeLa: pullscram_3


title: HeLa: pull29b_2


title: P779T_H3K27me3


title: HeLa: inputscram_3

source_name: input sample with scrambled mimic transfected oligo


title: HeLa: inputscram_2


title: P747T_H3K27me3


title: HeLa: pull29b_1


title: P832T_H3K27me3


title: P265T_H3K27me3


title: P737T_H3K27me3


title: HeLa: pullscram_2


title: P660T_H3K27me3


title: HeLa: inputscram_1


title: P717T_H3K27me3


title: HeLa: input29b_3

source_name: input sample with miR-29b mimic transfected oligo


title: HeLa: input29b_2


title: HeLa: input29b_1


title: P536T_H3K27me3


title: P268T_H3K27me3


title: P309T_H3K27me3


title: P310T_H3K27me3


title: BT474, T47D, ZR75 (inDrop)

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
Mixed samples include:
BT474
BT474.C70
T47D
T47D.C70
ZR75
ZR75.C70

data_processing:
Single-cell RNA-seq data were generated using inDrop version 3. In FASTQ files, read numbers are labeled as R1, R2, R3 and R4, where R1 is the biological read, R2 carries the first half of the hydrogel bead barcode (8 bp), R3 carries the library index (8 bp), and R4 carries the second half of the hydrogel bead barcode (8 bp), followed by the UMI (6 bp). FASTQ files were processed using the indrops pipeline developed by the Klein laboratory (https://github.com/indrops/indrops, v.0.3.1.1, commit 7979ee8a212fcec5ba726a8ccf8b7b8fa9db52cf, using Python 2.7, Rsem 1.3.0, Bowtie 1.1.1, Samtools 1.3.1, JDK 1.8.0_45) (https://www.ncbi.nlm.nih.gov/pubmed/27929523). Default parameters were applied (for Bowtie, m: 200, n: 1, l:15, e: 80; for Trimmomatic, LEADING: "28", SLIDINGWINDOW: "4:20", MINLEN: "16"; for UMI quantification, m: 10, u: 1, d: 600, split-ambigs: False, min_non_polyA: 15; for low complexity filter, max_low_complexity_fraction: 0.50; for output: output_unaligned_reads_to_other_fastq: False, filter_alignments_to_softmasked_regions: False).
Sequences originating from pooled libraries were demultiplexed using the following indices:  T47D-1, CTTAATAG; T47D.C70-1, ATAGCCTT; ZR75-1, TAAGGCTC; ZR75.C70-1, TCGCATAA; BT474-1, TTACCTCC; BT474.C70-1, CAGTTATG; T47D.C70-2, CCTTTACT; T47D-2, GAGACGGA; ZR75.C70-2, AGAAAGCT; ZR75-2, ACGCTCTT; BT474.C70-2, CGCATTCT; BT474-2, ATAGAGAG.
Alignment was performed against cDNA from Ensembl GRCh38.85 release. Empty or improductive droplets were filtered out based on the low abundance of reads per barcode, with a threshold set manually for each dataset after inspection of the barcode abundance distribution.
To get a reliable single cell transcriptome dataset, we exclude the cells with less than 1,000 genes expressed (UMI > 0), and exclude the genes if they meet both of the criteria: expressed in less than 5% of all single cells and less than 50% of single cells of the same type. The filtered data is then normalized by using scran (Lun et al., 2016) with deconvolution within each cell type followed by rescaling across cell types by using parameter “clusters” in computeSumFactors function. This setting can largely avoid the influence of differentially expressed genes across cell types on the normalization accuracy (detail refers to scran paper).
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files contain the raw UMIs for each gene

source_name: breast cancer cells (BT474, T47D, ZR75) untreated or treated with C70

growth_protocol: MCF7 and C70R cells were cultured in DMEM supplemented with 10% FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin. FULVR cells are cultured in RPMI without phenol red supplemented with 10% charcoal-stripped FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin. SUM159 cells are cultured in DMEM/F12 supplemented with 5% FBS, 10 mM HEPES, 10 μg ml−1 hydrocortisone, 5 μg ml−1 insulin and 1% penicillin/streptomycin.

extract_protocol:
Single-cell RNA-seq was performed using the inDrop protocol on a custom system as described in [https://www.ncbi.nlm.nih.gov/pubmed/27929523]. Hydrogel beads with version 3 oligonucleotide design were purchased from the Harvard Single Cell Core (https://iccb.med.harvard.edu/single-cell-core). Microfluidic encapsulation chips were purchased from 1CellBio (part no. 10080; https://1cell-bio.com/).
Library preparation was performed as described in [https://www.ncbi.nlm.nih.gov/pubmed/27929523].

treatment_protocol: Cells were treated with inhibitors: fulvestrant (1 μM) or KDM5-C70 (10 μM).

value: mixed sample (non-demultiplexed)


title: P450T_H3K27me3


title: SUM159_2 20180214 (RNA-Seq)

data_processing:
Raw RNA-seq reads are aligned to version hg19 of human genome by using Tophat2 (PMID: 23618408) with the default parameters.
Gene counts are quantified by using RSEM with REFSEQ annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Gene quantification files (*.genes.results) are generated using RSEM

source_name: breast cancer cells

growth_protocol: MCF7, C70R and C49R cells were cultured in DMEM supplemented with 10% FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin. FULVR and TAMR cells are cultured in RPMI without phenol red supplemented with 10% charcoal-stripped FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin. For the analysis between MCF7, FULVR and TAMR, MCF7 cells are cultured in RPMI without phenol red supplemented with 10% charcoal-stripped FBS, 1% penicillin/streptomycin and 10 μg ml−1 insulin. Cells were cultured in RPMI without phenol red supplemented with 10% charcoal-stripped FBS, 1% penicillin/streptomycin for E2 and its corresponding control.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols.

treatment_protocol: MCF7, C70R, C49R, FULVR and TAMR cells were treated with E2 (100 nM) or three different inhibitors: fulvestrant (1 μM), KDM5-C70 (10 μM) and KDM5-C49 (10 μM).

value: control


title: T47D_C70_d07_2 20180214 (RNA-Seq)


title: ZR75_C70_d07_2 20180214 (RNA-Seq)


title: SUM159_C70_d07_2 20180214 (RNA-Seq)


title: T47D_2 20180214 (RNA-Seq)


title: P823T_H3K27me3


title: P305T_H3K27me3


title: FULVR_2 20180214 (RNA-Seq)

value: FULVR


title: BT474_2 20180214 (RNA-Seq)


title: BT474_C70_d07_2 20180214 (RNA-Seq)


title: P349T_H3K27me3


title: P343T_H3K27me3

value: Case


title: P328T_H3K27me3

value: primary prostate cancer


title: ZR75_C70_d07_3 21118 (RNA-Seq)


title: ZR75_C70_d07_1 21118 (RNA-Seq)


title: P324T_H3K27me3


title: P301T_H3K27me3


title: ZR75_3 21118 (RNA-Seq)


title: P300T_H3K27me3


title: P457T_H3K27me3


title: ZR75_1 21118 (RNA-Seq)


title: T47D_C70_d07_3 21118 (RNA-Seq)


title: FULVR_C70_d07_2 20180214 (RNA-Seq)


title: T47D_C70_d07_1 21118 (RNA-Seq)


title: P444T_H3K27me3


title: P261T_H3K27me3


title: P431T_H3K27me3


title: T47D_3 21118 (RNA-Seq)


title: T47D_1 21118 (RNA-Seq)


title: SUM159_C70_d07_3 21118 (RNA-Seq)


title: SUM159_C70_d07_1 21118 (RNA-Seq)


title: P427T_H3K27me3


title: SUM159_3 21118 (RNA-Seq)


title: P449T_H3K27me3


title: P342T_H3K27me3


title: SUM159_1 21118 (RNA-Seq)


title: FULVR_C70_d07_3 21118 (RNA-Seq)


title: P456T_H3K27me3


title: FULVR_C70_d07_1 21118 (RNA-Seq)


title: P730T_H3K27me3


title: P618T_H3K27me3


title: FULVR_3 21118 (RNA-Seq)


title: P710T_H3K27me3


title: FULVR_1 21118 (RNA-Seq)


title: BT474_C70_d07_3 21118 (RNA-Seq)


title: P507T_H3K27me3


title: P527T_H3K27me3


title: P643T_H3K27me3


title: P500T_H3K27me3


title: P552T_H3K27me3


title: P509T_H3K27me3


title: BT474_3 21118 (RNA-Seq)


title: P475T_H3K27me3


title: BT474_C70_d07_1 21118 (RNA-Seq)


title: P466T_H3K27me3


title: FULVR_FULV_2 20171012 (RNA-Seq)

value: FULV


title: P534T_H3K27me3


title: P513T_H3K27me3


title: P811T_H3K27me3


title: BT474_1 21118 (RNA-Seq)


title: FULVR_FULV_1 20171012 (RNA-Seq)


title: P533T_H3K27me3


title: FULVR_2 20171012 (RNA-Seq)


title: FULVR_3 20171012 (RNA-Seq)


title: FULVR_1 20171012 (RNA-Seq)


title: P511T_H3K27me3


title: MCF7_FULV_3 20171012 (RNA-Seq)


title: P352T_H3K27me3


title: P276T_H3K27me3


title: P506T_H3K27me3


title: P245T_H3K27me3


title: P229T_H3K27me3


title: P228T_H3K27me3


title: P223T_H3K27me3


title: FULVR_FULV_3 20171012 (RNA-Seq)


title: P327T_H3K27me3


title: MCF7_1 20171012 (RNA-Seq)


title: MCF7_FULV_1 20171012 (RNA-Seq)


title: Group15_MCF7_KDM5B_KO_N2_input (ChIP-Seq)

data_processing:
Adapter sequences of ChIP-seq raw reads are removed by using cutadapt (DOI:10.14806/ej.17.1.200).
Trimmed reads are aligned by bowtie2 using default parameters to version hg19 of human genome. The samtools (PMID: 19505943) and picard (http://broadinstitute.github.io/picard) are used to sort and remove duplicated reads to avoid PCR bias from the sequencing process.
Each group of libraries after the above pre-processing is down-sampled (without replacement) to a fixed number of reads, which shown in the file names, such as "ds20000000".
Peak calling (identification of regions of ChIP-seq enrichment over background) is performed by using MACS2 (PMID: 18798982) with parameters of “--extsize=146 –nomodel”.
The “broad peak” option is on when identifying binding regions of KDM5B, H3K4me3 and H3K4me2. The typical-enhancers and super-enhancers are identified from H3K27ac enrichment by using ROSE pipeline with parameters described in PMID: 23582322.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig of downsampled signals & bed files of called peaks are generated using MACS2

extract_protocol:
For KDM5B ChIP-seq, 1 × 10^7 cells were fixed with 2mM DSG (Thermo scientific 20593) for 30 min at room temperature. DSG was then removed and replaced with fixing buffer (50 mM HEPES-NaOH (pH 7.5), 100 mM NaCl, 1mM EDTA) containing 1% paraformaldehyde (Electron Microscopy Sciences, 15714) and crosslinked for 10 min at 37 °C.  For histone modification ChIP-seq, 5 × 10^6 cells were fixed with 1% paraformaldehyde for 10 min at room temperature. For ER ChIP-seq, 1 × 10^7 cells were fixed with 1% paraformaldehyde for 10 min at 37 °C. Crosslinking was quenched by adding glycine to a final concentration of 0.125 M. The cells were washed with ice-cold PBS, harvested in PBS. The nuclear fraction was extracted by first resuspending the pellet in 1 ml of lysis buffer (50 mM HEPES-NaOH (pH 8.0), 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4 °C. Cells were pelleted, and washed in 1 ml of wash buffer (10 mM Tris-HCL (pH 8.0), 200 mM NaCl, 1 mM EDTA) for 10 min at 4 °C. Cells were then pelleted and resuspended in 1 ml of shearing buffer (10 mM Tris-HCl (pH 8), 1 mM EDTA, 0.1% SDS) and sonicated in a Covaris sonicator. Lysate was centrifuged for 5 min at 14,000 rpm to purify the debris. Then 100 µl of 10% Triton X-100 and 30 µl of 5M NaCl were added. The sample was then incubated with 20 µl of Dynabeads Protein G (LifeTechnologies,10003D) for 1 h at 4 °C. Primary antibodies were added to each tube and immunoprecipitation (IP) was conducted overnight in the cold room. Cross-linked complexes were precipitated with Dynabeads Protein G for 2 hr at 4 °C. The beads were then washed in low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C, high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C and LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C. DNA was eluted in elution buffer (100 mM sodium bicarbonate and 1% SDS). Cross-links were reversed overnight at 65 °C. RNA and protein were digested with 0.2 mg ml−1 RNase A for 30 min at 37 °C followed by 0.2 mg ml−1 Proteinase K for 1 h at 55 °C. DNA was purified with phenol-chloroform extraction and isopropanol precipitation.
ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from 1 ng of purified ChIP DNA or input DNA according to the manufacturer’s protocol.

treatment_protocol: MCF7, C70R, C49R, FULVR and TAMR cells were treated with E2 (100 nM) or three different inhibitors: fulvestrant (10 μM), KDM5-C70 (10 μM) and KDM5-C49 (10 μM).

tag: antibody


title: P832T_H3K4me3

value: H3K4me3 (Abcam, catalog# Ab8580, lot# GR240214-2)


title: MCF7_2 20171012 (RNA-Seq)


title: P823T_H3K4me3


title: Group15_MCF7_KDM5B_KO_N2_H3K4me3 (ChIP-Seq)

value: anti-H3K4me3 (abcam, ab1012)


title: Group15_MCF7_KDM5B_KO_N2_H3K4me2 (ChIP-Seq)

value: anti-H3K4me2 (Millipore, 07-030)


title: MCF7_FULV_2 20171012 (RNA-Seq)


title: Group15_MCF7_KDM5B_KO_N1_input (ChIP-Seq)


title: Group15_MCF7_KDM5B_KO_N1_H3K4me3 (ChIP-Seq)


title: P730T_H3K4me3


title: MCF7_3 20171012 (RNA-Seq)


title: Group15_MCF7_KDM5A_KO_N2_input (ChIP-Seq)


title: P717T_H3K4me3


title: P737T_H3K4me3


title: Group15_MCF7_KDM5B_KO_N1_H3K4me2 (ChIP-Seq)


title: Group15_MCF7_KDM5A_KO_N2_H3K4me3 (ChIP-Seq)


title: Group15_MCF7_KDM5A_KO_N2_H3K4me2 (ChIP-Seq)


title: P680T_H3K4me3


title: P710T_H3K4me3


title: P695T_H3K4me3


title: Group15_MCF7_KDM5A_KO_N1_H3K4me3 (ChIP-Seq)


title: P660T_H3K4me3


title: P779T_H3K4me3


title: P544T_H3K4me3


title: P555T_H3K4me3


title: Group15_MCF7_KDM5A_KO_N1_H3K4me2 (ChIP-Seq)


title: P747T_H3K4me3


title: Group15_MCF7_H3K4me2 (ChIP-Seq)


title: Group14_FULVR_C70_CTCF (ChIP-Seq)

value: anti-CTCF


title: Group15_MCF7_H3K4me3 (ChIP-Seq)


title: P540T_H3K4me3


title: P536T_H3K4me3


title: P541T_H3K4me3


title: Group15_MCF7_KDM5A_KO_N1_input (ChIP-Seq)


title: Group14_FULVR_input (ChIP-Seq)


title: P534T_H3K4me3


title: Group14_MCF7_CTCF (ChIP-Seq)


title: Group14_FULVR_CTCF (ChIP-Seq)


title: P527T_H3K4me3


title: Group13_MCF7_H3K79me2 (ChIP-Seq)


title: Group14_MCF7_input (ChIP-Seq)


title: P643T_H3K4me3


title: Group14_MCF7_C70_CTCF (ChIP-Seq)


title: P507T_H3K4me3


title: P533T_H3K4me3


title: P511T_H3K4me3


title: P509T_H3K4me3


title: Group13_MCF7_C70_H3K79me2 (ChIP-Seq)


title: Group15_MCF7_input (ChIP-Seq)


title: P500T_H3K4me3


title: P506T_H3K4me3


title: P462T_H3K4me3


title: Group12_ZR75_C70_d14_H3K4me3 (ChIP-Seq)


title: Group13_MCF7_input (ChIP-Seq)


title: Group12_ZR75_C70_d07_H3K4me3 (ChIP-Seq)


title: Group12_ZR75_C70_d00_H3K4me3 (ChIP-Seq)


title: P456T_H3K4me3


title: P449T_H3K4me3


title: Group12_ZR75_C70_d14_H3K4me2 (ChIP-Seq)


title: Group12_ZR75_C70_d02_H3K4me3 (ChIP-Seq)


title: P431T_H3K4me3


title: P355T_H3K4me3


title: Group12_ZR75_C70_d00_H3K4me2 (ChIP-Seq)


title: Group12_ZR75_C70_d07_H3K4me2 (ChIP-Seq)


title: P310T_H3K4me3


title: P336T_H3K4me3


title: Group12_T47D_C70_d07_H3K4me3 (ChIP-Seq)


title: P309T_H3K4me3


title: Group12_ZR75_input (ChIP-Seq)


title: Group12_T47D_C70_d14_H3K4me3 (ChIP-Seq)


title: P328T_H3K4me3


title: Group12_T47D_C70_d02_H3K4me3 (ChIP-Seq)


title: P301T_H3K4me3


title: Group12_T47D_C70_d00_H3K4me3 (ChIP-Seq)


title: P298T_H3K4me3


title: Group12_T47D_C70_d14_H3K4me2 (ChIP-Seq)


title: ZR75_2 20180214 (RNA-Seq)


title: Group12_T47D_C70_d07_H3K4me2 (ChIP-Seq)


title: Group12_T47D_C70_d02_H3K4me2 (ChIP-Seq)


title: P295T_H3K4me3


title: P291T_H3K4me3


title: P280T_H3K4me3


title: Group12_T47D_input (ChIP-Seq)


title: P433T_H3K4me3


title: Group12_T47D_C70_d00_H3K4me2 (ChIP-Seq)


title: Group12_ZR75_C70_d02_H3K4me2 (ChIP-Seq)


title: Group12_SUM159_C70_d14_H3K4me3 (ChIP-Seq)


title: Group12_SUM159_C70_d07_H3K4me3 (ChIP-Seq)


title: Group12_SUM159_C70_d02_H3K4me3 (ChIP-Seq)


title: Group12_SUM159_C70_d14_H3K4me2 (ChIP-Seq)


title: P300T_H3K4me3


title: P294T_H3K4me3


title: Group12_SUM159_C70_d00_H3K4me3 (ChIP-Seq)


title: P274T_H3K4me3


title: P263T_H3K4me3


title: Group12_SUM159_C70_d02_H3K4me2 (ChIP-Seq)


title: Group12_SUM159_C70_d07_H3K4me2 (ChIP-Seq)


title: P272T_H3K4me3


title: P276T_H3K4me3


title: P261T_H3K4me3


title: P265T_H3K4me3


title: P254T_H3K4me3


title: P249T_H3K4me3


title: Group12_SUM159_input (ChIP-Seq)


title: Group12_FULVR_C70_d07_H3K4me3 (ChIP-Seq)


title: P230T_H3K4me3


title: Group12_FULVR_C70_d02_H3K4me3 (ChIP-Seq)


title: P229T_H3K4me3


title: Group12_FULVR_C70_d14_H3K4me2 (ChIP-Seq)


title: P227T_H3K4me3


title: Group12_FULVR_C70_d00_H3K4me3 (ChIP-Seq)


title: Group12_FULVR_C70_d14_H3K4me3 (ChIP-Seq)


title: P223T_H3K4me3


title: Group12_SUM159_C70_d00_H3K4me2 (ChIP-Seq)


title: Group12_FULVR_C70_d07_H3K4me2 (ChIP-Seq)


title: Group12_FULVR_C70_d02_H3K4me2 (ChIP-Seq)


title: P336T_H3K27ac

value: H3K27ac (Active Motif, catalog# 39133, lot# 31814008)


title: Group12_FULVR_C70_d00_H3K4me2 (ChIP-Seq)


title: Group12_FULVR_input (ChIP-Seq)


title: P230T_H3K27ac


title: P268T_H3K4me3


title: Group12_BT474_C70_d14_H3K4me3 (ChIP-Seq)


title: P279T_H3K4me3

value: Control


title: P291T_H3K27ac


title: Group12_BT474_C70_d00_H3K4me3 (ChIP-Seq)


title: Group12_BT474_C70_d07_H3K4me3 (ChIP-Seq)


title: P272T_H3K27ac


title: P249T_H3K27ac


title: Group12_BT474_C70_d02_H3K4me3 (ChIP-Seq)


title: P279T_H3K27ac


title: Group12_BT474_C70_d14_H3K4me2 (ChIP-Seq)


title: P254T_H3K27ac


title: Group12_BT474_C70_d07_H3K4me2 (ChIP-Seq)


title: Group12_BT474_input (ChIP-Seq)


title: P295T_H3K27ac


title: Group12_BT474_C70_d00_H3K4me2 (ChIP-Seq)


title: P274T_H3K27ac


title: P298T_H3K27ac


title: P680T_H3K27ac


title: P674T_H3K27ac


title: P280T_H3K27ac


title: P355T_H3K27ac


title: P294T_H3K27ac


title: P660T_H3K27ac


title: P555T_H3K27ac


title: P265T_H3K27ac


title: P611T_H3K27ac


title: P540T_H3K27ac


title: P263T_H3K27ac


title: Group12_BT474_C70_d02_H3K4me2 (ChIP-Seq)


title: P695T_H3K27ac


title: P559T_H3K27ac


title: P603T_H3K27ac


title: P832T_H3K27ac


title: P560T_H3K27ac


title: P452T_H3K27ac


title: P464T_H3K27ac


title: P531T_H3K27ac


title: P779T_H3K27ac


title: P747T_H3K27ac


title: P593T_H3K27ac


title: P737T_H3K27ac


title: P643T_H3K27ac


title: P268T_H3K27ac


title: P717T_H3K27ac


title: P544T_H3K27ac


title: P536T_H3K27ac


title: P309T_H3K27ac


title: P506T_H3K27ac


title: P310T_H3K27ac


title: P450T_H3K27ac


title: P266T_H3K27ac


title: P297T_H3K27ac


title: P823T_H3K27ac


title: P301T_H3K27ac


title: P328T_H3K27ac


title: P343T_H3K27ac


title: P324T_H3K27ac


title: P444T_H3K27ac


title: P431T_H3K27ac


title: P433T_H3K27ac


title: P300T_H3K27ac


title: P426T_H3K27ac


title: P462T_H3K27ac


title: P261T_H3K27ac


title: P342T_H3K27ac


title: P427T_H3K27ac


title: P457T_H3K27ac


title: P449T_H3K27ac


title: P305T_H3K27ac


title: P500T_H3K27ac


title: P552T_H3K27ac


title: P348T_H3K27ac


title: P618T_H3K27ac


title: P416T_H3K27ac


title: P730T_H3K27ac


title: P509T_H3K27ac


title: P507T_H3K27ac


title: P475T_H3K27ac


title: P456T_H3K27ac


title: P710T_H3K27ac


title: P466T_H3K27ac


title: P533T_H3K27ac


title: P811T_H3K27ac


title: P352T_H3K27ac


title: P534T_H3K27ac


title: P513T_H3K27ac


title: P527T_H3K27ac


title: P262T_H3K27ac


title: P245T_H3K27ac


title: P511T_H3K27ac


title: P252T_H3K27ac


title: P257T_H3K27ac


title: P255T_H3K27ac


title: P228T_H3K27ac


title: neutrophilic asthma_IV_25

type: RNA

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

description: Gene expression data from whole lungs of Balb/c mice with neutrophilic allergic airway inflammation

hyb_protocol: 5 ug of fragmented biotin labeled aRNA was used with hybridization cocktails on GeneChipTM Mouse Gene 1.0 ST microarray (Affymetrix, Santa Clara, CA) following manufacturer protocols.

scan_protocol: Chips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: Raw data were normalized using RMA in Affymetrix Expression Console and presented as log transformed signal intensity; One way ANOVA and contrasts to test the significance of individual comparisons between groups were performed using R statistical package.

label: Biotin

source_name: Whole lungs of high dose HDM intranasal-treated mice

label_protocol: Gene Chip WT Plus Reagent Kit was used for the synthesis of cDNA and cRNA an biotin-labeled cRNA. 300 ng of tRNA was utilized as starting material following manufacturer protocol.

growth_protocol: Three different asthma phenotypes- eosinophilic, mixed, and neutrophilic, were induced in Balb/c mice via different ways of house dust mite sensitization.

extract_protocol: After the end of the treatment mice were sacrificed and lung samples were snap frozen in liquid nitrogen for transcriptome analyses. Snap frozen lung samples were placed in RNAlater-ICE for transitioning before tissue homogenisation in RLT buffer (Qiagen) with beta-mercaptoethanol (Sigma-Aldrich) using gentleMACS Dissociator (Miltenyi Biotec) according to manufacturer’s instructions. Total RNA was isolated using the RNeasy Mini kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: Allergic inflammation was induced in mice by exposure to a mixture of standardized Der p (Dermatophagoides pteronissinus) and Der f (Dermatophagoides farina) allergen extracts (ALK-Abelló A/S, Horsholm, Denmark). The extracts were standardized against an in-house reference and amounts are expressed in development units (DU). For eosinophilic asthma mice were sensitized by three intraperitoneal (i.p.) injections of HDM extract containing 0.75 DU Der f and 0.75 DU Der p (ALK-Abelló A/S) adsorbed to 1.5 mg Al(OH)3 (Pierce, Rockford, IL, USA)  in 200 µl PBS on days 0, 7 and 21. On days 26 to 28, mice were challenged intranasally (i.n.) with the similar dose of HDM extract dissolved in 50 µl PBS. For induction of the mixed or neutrophilic endotype mice were i.n. sensitized/challenged with the HDM extract (0.75 DU Der f /0.75 DU Der p or 7.5 DU Der f/7.5 DU Der p, respectively) in 50 µl PBS once a week a total of four times  Intranasal application of only PBS served as a control. All animal procedures were performed with approval from the University of Marburg local authorities (Regierungspräsidium Gießen).

tag: asthma phenotype

value: neutrophilic asthma

tag: strain

value: Balb/c

value: whole lung


title: P313T_H3K27ac

tag: patient id


title: mixed asthma_III_16

description: Gene expression data from whole lungs of Balb/c mice with mixed allergic airway inflammation

source_name: Whole lungs of low dose HDM iintranasal-treated mice

value: mixed asthma


title: mixed asthma_III_17

source_name: Whole lungs of low dose HDM intranasal-treatedmice


title: neutrophilic asthma_IV_23

source_name: Whole lungs of high dose HDM iintranasal-treated mice


title: P832T_AR

value: AR (Santa Cruz, catalog# sc-816, mix of 4 lot#s B2114, H2914, A0515, J0614)


title: P229T_H3K27ac


title: P227T_H3K27ac


title: P327T_H3K27ac


title: eosinophilic asthma_II_9

description: Gene expression data from whole lungs of Balb/c mice with eosinophilic allergic airway inflammation

source_name: Whole lungs of low dose HDM intraperitoneal and intranasal-treated mice

value: eosinophilic


title: control_I_1

description: Gene expression data from whole lungs of control Balb/c mice

source_name: Whole lungs of PBS-treated mice


title: P276T_H3K27ac


title: eosinophilic asthma_II_8


title: XY (20110126) E_coli_1

city: Bethesda

first: Gisela

last: Storz

state: MD

address: 49 Convent Drive

department: Division of Molecular and Cellular Biology

institute: NICHD

description: MgtS overexpression (2)

hyb_protocol: The hybridization was conducted for the Affymetrix E. coli Genome 2.0 array as described in Affymetrix manual Section 3: Prokaryotic Sample and array Processing (www.affymetrix.com/support/downloads/manuals/expression_s3_manual.pdf)

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 7G according to manufacturer's instruction

data_processing: Affymetrix GeneChip operating software was used to extract the arbitrary fluorescence values

label: biotoin

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli strain GSO818 transformed with pBAD24-MgtS, grown in LB

label_protocol: The cDNA was prepared for the Affymetrix E. coli Genome 2.0 array as described in Affymetrix manual Section 3: Prokaryotic Sample and array Processing (www.affymetrix.com/support/downloads/manuals/expression_s3_manual.pdf)

growth_protocol: GSO818 MG1655 ∆mgtS araEcon (kan) (GSO818) cells harboring pBAD24 or pBAD24-MgtS grown to OD600 ~0.5 in LB at 37°C with shaking.

extract_protocol: Total RNA was prepared as described previously (Durand & Storz, 2010).

treatment_protocol: At OD600 ~0.5, were induced with 0.2% arabinose for 7.5 min, after which cells were pelleted by centrifugation and harvested for RNA extraction.

tag: protocol

value: 0.2% arabinose induction for 7.5 min

value: MgtS overexpression


title: neutrophilic asthma_IV_24


title: eosinophilic asthma_II_7


title: control_I_2


title: P811T_AR

tag: case/control

value: Case


title: P223T_H3K27ac

tag: tissue

value: primary prostate cancer


title: BC301: bl-206

city: Daejeon

first: Bic-Na

last: Song

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

department: Korean Bioinformation Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC301

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array data processing were performed on Illumina GenomeStudio software. We normalized gene expression data using Quantile normalization and log2 transformation.

label: biotin

source_name: Primary bladder cancer

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX).

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer's protocol. RNA quality and integrity were confirmed by electrophoresis on agarose gel stained with ethidium bromide and examined under ultraviolet light.

value: Primary bladder cancer

tag: gender

value: F

tag: invasiveness

value: non-muscle invasive

tag: Stage

value: Ta

tag: grade

value: low grade


title: XY (20110126) E_coli_2

description: Empty vector (2)

source_name: E. coli strain GSO818 transformed with pBAD24, grown in LB

value: Empty vector


title: mixed asthma_III_15

source_name: Whole lungs of low dose HDM intranasal-treated mice


title: ECH (20091218) Sample_2_empty_vector

description: Empty vector (1)


title: control_I_3


title: ECH (20091218) Sample_1_yneM_overexpressed

description: MgtS overexpression (1)


title: BC446: bl-26

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC446

value: M

value: muscle invasive

value: high grade


title: BC289: bl-155

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC289


title: BC297: bl-187

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC297


title: BC442: bl-333

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC442


title: P737T_AR

source_name: primary prostate cancer


title: BC443: bl-2

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC443


title: P747T_AR

value: Control


title: P730T_AR


title: BC441: bl-328

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC441


title: P779T_AR


title: BC439: bl-293

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC439

source_name: Recurrent bladder tumor

value: Recurrent bladder tumor


title: P717T_AR

value: AR (Santa Cruz, catalog# sc-816, mix of 4 lot#s B2114, H2914, A0515, J0614)


title: BC447: bl-41

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC447


title: BC435: bl-258

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC435


title: P695T_AR


title: BC351: bl-491

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC351


title: BC345: bl-444

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC345


title: BC326: bl-342

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC326


title: BC350: bl-485

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC350


title: BC329: bl-355

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC329


title: P674T_AR


title: BC328: bl-351

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC328


title: BC438: bl-279

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC438


title: P643T_AR


title: BC436: bl-263

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC436


title: P680T_AR


title: BC325: bl-339

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC325


title: BC319: bl-302

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC319


title: P618T_AR


title: BC320: bl-307

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC320


title: BC318: bl-294

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC318


title: BC304: bl-215

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC304


title: BC352: bl-503

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC352


title: BC355: bl-513

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC355


title: BC430: bl-173

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC430


title: P603T_AR


title: P593T_AR


title: P560T_AR


title: BC354: bl-510

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC354


title: BC348: bl-473

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC348

value: Not determined

value: papilloma


title: BC349: bl-475

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC349


title: P559T_AR


title: BC347: bl-466

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC347

value: small cell ca


title: BC344: bl-434

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC344


title: P555T_AR


title: P552T_AR

value: Case


title: P544T_AR

value: primary prostate cancer


title: BC346: bl-457

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC346


title: P536T_AR


title: P540T_AR


title: BC341: bl-416

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC341

value: Primary bladder cancer


title: BC414: bl-64

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC414


title: BC403: bl-14

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC403


title: BC343: bl-429

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC343

value: F


title: BC339: bl-404

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC339


title: BC415: bl-74

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC415

value: non-muscle invasive


title: BC342: bl-426

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC342


title: BC409: bl-43

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC409


title: BC401: bl-1

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC401

value: Ta


title: BC396: bl-187

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC396


title: BC360: bl-14

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC360


title: BC397: bl-192

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC397


title: BC398: bl-196

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC398


title: BC389: bl-155

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC389


title: P533T_AR


title: BC357: bl-1

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC357

value: low grade


title: BC394: bl-175

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC394


title: P527T_AR


title: P534T_AR


title: P513T_AR


title: P531T_AR


title: BC338: bl-401

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC338


title: BC337: bl-398

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC337


title: BC334: bl-375

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC334


title: BC336: bl-391

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC336


title: BC335: bl-385

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC335


title: P511T_AR


title: P509T_AR


title: P507T_AR


title: BC324: bl-334

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC324


title: BC333: bl-370

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC333

value: low high grade


title: BC327: bl-348

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC327

value: M


title: BC429: bl-168

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC429


title: P506T_AR


title: P500T_AR


title: P475T_AR


title: BC321: bl-316

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC321


title: P466T_AR


title: P464T_AR


title: BC426: bl-147

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC426

value: muscle invasive


title: BC317: bl-285

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC317

value: high grade


title: BC419: bl-105

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC419


title: BC428: bl-163

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC428


title: BC423: bl-129

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC423


title: BC421: bl-114

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC421


title: BC418: bl-100

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC418


title: BC427: bl-158

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC427


title: BC417: bl-89

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC417


title: P456T_AR

value: Control


title: BC420: bl-110NM

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC420

value: Recurrent bladder tumor


title: BC425: bl-138

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC425


title: BC413: bl-58

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC413


title: BC314: bl-259

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC314


title: BC315: bl-266

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC315


title: BC331: bl-363

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC331


title: BC312: bl-248

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC312


title: P452T_AR

value: AR (Santa Cruz, catalog# sc-816, mix of 4 lot#s B2114, H2914, A0515, J0614)


title: P710T_AR


title: P450T_AR


title: BC310: bl-240

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC310


title: BC313: bl-253

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC313


title: P449T_AR


title: BC307: bl-231

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC307


title: BC308: bl-233

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC308


title: BC309: bl-235

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC309


title: P462T_AR


title: BC311: bl-243

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC311

value: Not determined


title: BC306: bl-222

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC306


title: P433T_AR


title: P431T_AR


title: P444T_AR


title: P427T_AR


title: BC410: bl-48

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC410

value: papiiloma


title: BC412: bl-52

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC412


title: BC411: bl-178

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC411


title: P416T_AR


title: P426T_AR


title: BC405: bl-25

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC405


title: BC395: bl-178

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC395


title: P355T_AR


title: BC392: bl-169

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC392


title: BC406: bl-32

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC406


title: BC391: bl-161

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC391


title: BC393: bl-171

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC393


title: BC404: bl-20

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC404


title: BC303: bl-212

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC303


title: BC408: bl-40

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC408


title: BC390: bl-157

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC390


title: P352T_AR


title: P348T_AR


title: P343T_AR


title: BC316: bl-277

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC316


title: P349T_AR


title: P336T_AR


title: BC305: bl-219

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC305


title: P342T_AR


title: BC296: bl-182

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC296


title: P324T_AR


title: BC302: bl-209

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC302


title: P327T_AR


title: BC291: bl-162

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC291


title: BC290: bl-159

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC290


title: BC361: bl-24

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC361


title: BC287: bl-142

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC287


title: P328T_AR


title: BC288: bl-146

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC288


title: BC356: bl-522

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC356


title: BC358: bl-7

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC358


title: BC359: bl-10

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC359


title: BC300: bl-201

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC300

value: sarcomatoid ca


title: BC294: bl-177

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC294


title: BC292: bl-172

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC292


title: BC295: bl-179

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC295


title: P310T_AR

value: Case


title: P313T_AR

value: primary prostate cancer


title: P309T_AR


title: BC388: bl-152

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC388

value: Primary bladder cancer


title: P305T_AR


title: P301T_AR


title: P300T_AR


title: BC386: bl-139

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC386


title: BC384: bl-132

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC384

value: F


title: BC387: bl-144

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC387

value: non-muscle invasive


title: genomic DNA from UACC-3199

type: genomic

description: cell line

hyb_protocol: DNA methylation profiling was carried out on the Illumina Infinium HumanMethylation450K BeadChip arrays according to Illumina protocol

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

data_processing:
Illumina GenomeStudio software (GSGX v1.1.0)
The raw_data.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Labeling was performed at the Harvard Medical School-Partners HealthCare Center for Genetics and Genomics according to Illimina protocol

growth_protocol: 59 cell lines were grown in corresponding media described in Table S1

extract_protocol: DNA was isolated using QIAamp DNA Mini kit (QIAGEN, cat# 51304)


title: genomic DNA from VCaP

description: cell line

source_name: VCaP

value: VCaP


title: P298T_AR


title: BC383: bl-128

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC383

value: Ta


title: P297T_AR


title: BC382: bl-118

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC382


title: BC385: bl-135

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC385


title: BC380: bl-102

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC380


title: genomic DNA from UOCB1

description: cell line


title: P295T_AR


title: genomic DNA from TTC642

description: cell line


title: P294T_AR


title: genomic DNA from TTC549

description: cell line


title: BC379: bl-99

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC379

value: low grade


title: P280T_AR


title: genomic DNA from TTC709

description: cell line


title: BC377: bl-94

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC377

value: M


title: BC376: bl-91

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC376


title: genomic DNA from SUM159

description: cell line


title: BC378: bl-96

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC378

value: muscle invasive


title: P274T_AR


title: genomic DNA from SUM159R treated with JQ1

description: cell line


title: BC373: bl-74

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC373

value: high grade


title: P279T_AR

value: Control


title: genomic DNA from SW1222

description: cell line


title: BC372: bl-70

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC372


title: genomic DNA from SUM159R

description: cell line


title: P272T_AR


title: BC374: bl-78

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC374


title: P268T_AR


title: genomic DNA from SUM149

description: cell line


title: genomic DNA from SUM149R treated with JQ1

description: cell line


title: BC375: bl-82

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC375


title: BC370: bl-57

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC370


title: P265T_AR


title: genomic DNA from SMS-KCN

description: cell line

source_name: SMS-KCN


title: BC371: bl-64

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC371

value: papilloma


title: P266T_AR

value: AR (Santa Cruz, catalog# sc-816, mix of 4 lot#s B2114, H2914, A0515, J0614)


title: genomic DNA from TM87

description: cell line


title: P276T_AR


title: genomic DNA from SMS-SAN

description: cell line

source_name: SMS-SAN


title: BC367: bl-43

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC367

value: Recurrent bladder tumor


title: P263T_AR


title: genomic DNA from Nalm14

description: cell line


title: P262T_AR


title: P291T_AR

value: Exclude


title: genomic DNA from NGP

description: cell line

source_name: NGP

value: NGP


title: P261T_AR

value: Case


title: P255T_AR

value: primary prostate cancer


title: P254T_AR


title: BC362: bl-27

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC362

value: Primary bladder cancer


title: P257T_AR


title: genomic DNA from NLF

description: cell line

source_name: NLF

value: NLF


title: BC365: bl-41

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC365

value: F

value: non-muscle invasive


title: BC363: bl-34

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC363


title: P252T_AR


title: genomic DNA from NB69

description: cell line


title: P249T_AR


title: BC465: bl-118

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC465


title: genomic DNA from MDA-IBC-3

description: cell line


title: BC464: bl-113

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC464


title: genomic DNA from MHH-NB-11

description: cell line


title: genomic DNA from PMC42

description: cell line


title: BC364: bl-38

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC364

value: Ta


title: P229T_AR


title: genomic DNA from MOLM14

description: cell line


title: genomic DNA from SUM149R

description: cell line


title: P228T_AR


title: BC366: bl-41

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC366

value: low grade


title: P230T_AR


title: P227T_AR


title: genomic DNA from LNCaP-abl

description: cell line

source_name: LNCaP-abl


title: BC463: bl-108

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC463

value: M


title: genomic DNA from LIM2405

description: cell line


title: BC460: bl-93

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC460

value: muscle invasive

value: clear cell ca


title: BC459: bl-83

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC459


title: genomic DNA from LNCaP

description: cell line

source_name: LNCaP

value: LNCaP


title: dms with puromycin 72hr post infection

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description: number of read per position per nucelotide, and mutation rate

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
Wig files were then generated by summing the number of mismatches and total reads  obtained for each position in the human genome. For this, each read was counted for each bp.
Genome_build: refSeq Genome + NC_006273.2
Supplementary_files_format_and_content: txt files, contains aligned reads following the described pre-processing steps

source_name: Primary fibroblasts

growth_protocol: HFFs cells were grown in DMED high glucose media in 37c  5%CO2. HFFs were either mock or 72h infected with HCMV Merlin strain passage 3 with MOI 5 prior to DMS treatment

extract_protocol:
total RNA was extracted using TRI ragent and phase separated using chloroform. mRNA was isolated using polyA selection kit (Ambion)
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circularized and PCR amplified.

treatment_protocol: 6% DMS for 5min in 37c. Discard medium and neutralization with 30% BME. Harvesting with TRI reagent

tag: infection

value: human cytomegalovirus (HCMV) - Merlin - 72 hours

tag: treatment

value: DMS with puromycin

value: Primary fibroblasts


title: genomic DNA from LS

description: cell line

source_name: LS

value: LS


title: genomic DNA from LAPC-4

description: cell line


title: P223T_AR

tag: chip antibody

value: AR (Santa Cruz, catalog# sc-816, mix of 4 lot#s B2114, H2914, A0515, J0614)


title: dms without puromycin 72hr post infection

value: DMS without puromycin

tag: cell type


title: BC462: bl-103

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC462

value: Recurrent bladder tumor

value: high grade


title: BC458: bl-78

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC458

value: Primary bladder cancer


title: genomic DNA from LIM1899

description: cell line

tag: cell line


title: BC457: bl-76

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC457


title: NIH3T3: pullscram_cyt

data_processing:
Read alignment: STAR version 2.3.0
gencode M2 annotations
Genome_build: mm10
Supplementary_files_format_and_content: mapped bw files;  count tables csv

source_name: cytoplasmic pulldown sample with scrambled mimic transfected oligo

tag: input rna amount

value: 5 ng

tag: kit used

value: TotalScript RNA-seq Kit (Epicentre), using a mix of Random hexamer and Oligo-dT primers

tag: molecule subtype

value: cytoplasmic RNA


title: BC451: bl-187

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC451

value: small cell ca


title: BC455: bl-63

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC455

value: M

value: non-muscle invasive

value: Ta

value: low grade


title: NIH3T3: inputscram_nuc

source_name: nuclear input sample with scrambled mimic transfected oligo

value: nuclear RNA


title: NIH3T3: pull29b_nuc

source_name: nuclear pulldown sample with miR-29b mimic transfected oligo


title: NIH3T3: pull29b_cyt

source_name: cytoplasmic pulldown sample with miR-29b mimic transfected oligo


title: genomic DNA from LIM2551

description: cell line


title: NIH3T3: inputscram_cyt

source_name: cytoplasmic input sample with scrambled mimic transfected oligo


title: NIH3T3: pullscram_nuc

source_name: nuclear pulldown sample with scrambled mimic transfected oligo


title: NIH3T3: pullscram_4

source_name: pulldown sample with scrambled mimic transfected oligo


title: genomic DNA from KOPT-K1

description: cell line


title: NIH3T3: input29b_cyt

source_name: cytoplasmic input sample with miR-29b mimic transfected oligo


title: NIH3T3: pullscram_3


title: genomic DNA from HCT116 ARID1A KO

description: cell line

source_name: HCT116 ARID1A KO


title: BC454: bl-3/10

description:
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.
BC454

source_name: Primary bladder cancer

value: F


title: NIH3T3: pullscram_2


title: genomic DNA from Kelly

description: cell line

source_name: Kelly

value: Kelly


title: genomic DNA from HCT116 ARID1A HET

description: cell line

source_name: HCT116 ARID1A HET


title: NIH3T3: pullscram_1


title: NIH3T3: pull29b_4

source_name: pulldown sample with miR-29b mimic transfected oligo


title: genomic DNA from HCC3153

description: cell line


title: NIH3T3: pull29b_3


title: NIH3T3: inputscram_4

source_name: input sample with scrambled mimic transfected oligo


title: NIH3T3: pull29b_1


title: NIH3T3: inputscram_2


title: genomic DNA from HCA24

description: cell line


title: genomic DNA from HCT116 ARID1A WT

description: cell line

source_name: HCT116 ARID1A WT


title: NIH3T3: inputscram_1


title: genomic DNA from HCA7

description: cell line


title: Dam-Sd Rep1

city: Clayton

first: Jan

last: Schroeder

state: VIC

address: Building 75 Innovation Walk

department: Anatomy & Developmental Biology

institute: Monash University

data_processing:
Library strategy: DamID-seq
DamID alignment: Subread and featureCounts
DamID analysis: process with EdgeR in R for differentially methylated GATC motifs
DamID analysis: generate peaks from adjacent mehtylated sites, find closest gene with Bedtools
ATAC alignment: Bowtie2
ATAC analysis: peak calling with MACS2; intersection of peaks with Bedtools
RNA alignment: subread and featureCounts
RNA analysis: edgeR to compute RPKM
Genome_build: dm6
Supplementary_files_format_and_content: DamID_peaks_nf1.bed contains DamID signficantly methylated Nerfin-1 peaks and the closest gene within 5kbp in BED format
Supplementary_files_format_and_content: DamID_peaks_sd.bed contains DamID signficantly methylated Scalloped peaks and the closest gene within 5kbp in BED format
Supplementary_files_format_and_content: ATAC_intersected_peaks.bed contains peaks generated by intersecting results from three replicates
Supplementary_files_format_and_content: RNA_expressed.txt contains list of expressed genes (selected at RPKM>=10) with the raw counts from the replicates

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: Crosses producing larvae with the indicated genotype were allowed to lay eggs o/n at 25°C. Eggs were transferred to the non-permissive temperature (18°C) for 4 days. To restrict expression of the TaDa transgenes to a defined period, larvae were transferred to the permissive temperature (29°C) 24 hours before dissection.

extract_protocol:
CNSs were treated with protK, RNase A followed by phenol chloroform DNA extraction. DNA was ethanol precipitated, washed and dissolved, followed by DpnI digestion, DamID adaptors ligation, DpnII digestion and PCR amplification.
MePCR product was sonicated using a Covaris S2 device to generate fragments of 100-500bp, with an average of 300bp. DNA was purified using Agencourt AMPure beads purification. Illumina sequencing libraries were prepared using KAPA Hyper prep kit (Kapa Biosystems) and 300ng starting material. Five to seven cycles of PCR were performed.

tag: genotype

value: w; tubGal80TS/+; GMR31H08-Gal4, UAS-GFP/p[pUAST-LT3-Dam-Sd] attP2

value: CNS

tag: developmental stage

value: Wandering third instar larvae


title: NIH3T3: inputscram_3


title: NIH3T3: pull29b_2


title: genomic DNA from HCA2

description: cell line


title: NIH3T3: input29b_4

source_name: input sample with miR-29b mimic transfected oligo

value: 6 ng


title: NIH3T3: input29b_3


title: NIH3T3: input29b_2


title: genomic DNA from FC-IBC02

description: cell line


title: Dam-only Rep1

value: w; tubGal80TS/+; GMR31H08-Gal4, UAS-GFP/p[pUAST-LT3-Dam] attP2


title: RNA-Neuron Rep3

data_processing:
DamID alignment: Subread and featureCounts
DamID analysis: process with EdgeR in R for differentially methylated GATC motifs
DamID analysis: generate peaks from adjacent mehtylated sites, find closest gene with Bedtools
ATAC alignment: Bowtie2
ATAC analysis: peak calling with MACS2; intersection of peaks with Bedtools
RNA alignment: subread and featureCounts
RNA analysis: edgeR to compute RPKM
Genome_build: dm6
Supplementary_files_format_and_content: DamID_peaks_nf1.bed contains DamID signficantly methylated Nerfin-1 peaks and the closest gene within 5kbp in BED format
Supplementary_files_format_and_content: DamID_peaks_sd.bed contains DamID signficantly methylated Scalloped peaks and the closest gene within 5kbp in BED format
Supplementary_files_format_and_content: ATAC_intersected_peaks.bed contains peaks generated by intersecting results from three replicates
Supplementary_files_format_and_content: RNA_expressed.txt contains list of expressed genes (selected at RPKM>=10) with the raw counts from the replicates

growth_protocol: Flies were reared at 25°C

extract_protocol:
Cells were pelleted and resuspended in Trizol. RNA was isolated according to manufacturer’s protocol. Samples from sorts executed on different days were pooled into three different samples containing 180-330ng RNA.
Libraries prepared according to standard protocols (TruSeq RNA, Illumina).

value: P[nerfin-1.GFP-NLS.SV-40] iA

value: FACS sorted GFP+ cells from CNS


title: genomic DNA from GI-ME-N

description: cell line

source_name: GI-ME-N


title: genomic DNA from CWR_22RV1

description: cell line


title: genomic DNA from CHP134

description: cell line


title: genomic DNA from COG-N-278

description: cell line


title: RNA-Neuron Rep2


title: NIH3T3: input29b_1

value: 5 ng

value: TotalScript RNA-seq Kit (Epicentre), using a mix of Random hexamer and Oligo-dT primers


title: ATAC-Nf Rep1

extract_protocol:
Cells were lysed and nuclei pelleted. Nuclei were subjected to tagmentation (Nextera kit, Illumina). PCR amplification of purified DNA was performed using forward and reverse indexing primers and HotStart KAPA ready mix (13 cycles).
Fragments between 200-700bp of the amplified and purified libraries were size-selected using a Pippin Prep instrument.


title: RNA-Neuron Rep1


title: Dam-only Rep2


title: genomic DNA from C80

description: cell line


title: Neutrophil_BCRX_0.2mg/kg_No.34_day7

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

country: Japan

institute: Iwate University

description: Gene expression in peripheral neutrophil from cattle No.34 with 0.2mg/kg of BCRX on day 7

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 018964_D_F_2008110) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 200 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the peripheral neutrophil and liver tissue using Trizol reagent (Invitrogen) according to the manufacturer's instructions.

tag: breed

value: Holstein

tag: individual

value: cattle No.34

value: Peripheral neutrophil

tag: agent

value: β-CRX

tag: dose

value: 0.2 mg/kgBW

tag: time

tag: experiment type

value: In vivo


title: genomic DNA from C99

description: cell line


title: Dam-Nf Rep1

value: w; tubGal80TS/+; GMR31H08-Gal4, UAS-GFP/p[pUAST-LT3-Dam-Nerfin-1] attP2

tag: tissue


title: ATAC-Nf Rep2


title: genomic DNA from C4-2B

description: cell line


title: Dam-Nf Rep2


title: genomic DNA from Blin1

description: cell line


title: ATAC-Nf Rep3


title: genomic DNA from 21MT1

description: cell line


title: genomic DNA from 21NT

description: cell line


title: Neutrophil_BCRX_0.2mg/kg_No.25_day7

description: Gene expression in peripheral neutrophil from cattle No.25 with 0.2mg/kg of BCRX on day 7

value: cattle No.25


title: genomic DNA from 21PT

description: cell line


title: Neutrophil_BCRX_0.2mg/kg_No.32_day7

description: Gene expression in peripheral neutrophil from cattle No.32 with 0.2mg/kg of BCRX on day 7

value: cattle No.32


title: Neutrophil_BCRX_0.2mg/kg_No.34_day0

description: Gene expression in peripheral neutrophil from cattle No.34 with 0.2mg/kg of BCRX on day 0


title: genomic DNA from BE(2)-C

description: cell line


title: genomic DNA from CHP-126

description: cell line


title: genomic DNA from C32

description: cell line


title: Dam-Sd Rep2

value: w; tubGal80TS/+; GMR31H08-Gal4, UAS-GFP/p[pUAST-LT3-Dam-Sd] attP2

value: CNS


title: genomic DNA from BT12

description: cell line


title: genomic DNA from C4-2

description: cell line


title: Left ventricle atorvastatin rep3

city: Berlin

first: Georgios

last: Kararigas

address: Hessische Str. 3-4

country: Germany

institute: Charite University Hospital

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

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

source_name: Left ventricle atorvastatin

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: The mice were kept on a 12-hour light, 12-hour dark cycle in temperature-controlled rooms with water ad libitum.

extract_protocol: Total RNA was isolated using the RNeasy Fibrous Tissue Mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Left ventricles were snap frozen in liquid nitrogen and stored at -80°C until further analysis.

tag: strain background

value: mixed; SV129/Black Swiss and C57BL/6

tag: gender

value: male

tag: treated with

value: atorvastatin

value: left ventricle


title: genomic DNA from 21MT2

description: cell line


title: genomic DNA from COG-N-367

description: cell line


title: Neutrophil_BCRX_0.2mg/kg_No.25_day0

description: Gene expression in peripheral neutrophil from cattle No.25 with 0.2mg/kg of BCRX on day 0

tag: cell type


title: genomic DNA from 2004

description: cell line

tag: cell line


title: Left ventricle atorvastatin rep2


title: Neutrophil_BCRX_0.2mg/kg_No.26_day0

description: Gene expression in peripheral neutrophil from cattle No.26 with 0.2mg/kg of BCRX on day 0

value: cattle No.26


title: Liver_BCRX_0.2mg/kg_No.61_day7

description: Gene expression in liver tissue from cattle No.61 with 0.2mg/kg of BCRX on day 7

value: cattle No.61

value: Liver


title: Left ventricle atorvastatin rep1


title: Liver_BCRX_0.2mg/kg_No.66_day7

description: Gene expression in liver tissue from cattle No.66 with 0.2mg/kg of BCRX on day 7

value: Holstein

value: cattle No.66


title: 336-No2

city: Versailles

first: HAKIM

last: MIREAU

address: Route de Saint-Cyr

country: France

institute: INRAE

description:
Ribosome Footprints
27 nt to 30 nt RNA

data_processing:
Library strategy: Ribo-Seq
bcl2fastq2-2.18.12 (demultiplex), Cutadapt 1.15 (adapter trimming)
Reads between 27 to 30 nt were selected and then mapped to mitochondrial genome of the Col-0 Arabidopsis acccession using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated RPKM were calculated based on the number of reads mapping to mitochondrial coding  sequences (CDSs) after normalization to the number of reads mapping to nuclear CDSs. Mitochondrial mRNA translation efficiencies were evaluated by dividing RPKM values by mitochondrial  mRNA abundances which were determined by RT- quantitative PCR.
mitochondrial genome of the Col-0 Arabidopsis acccession JF729201
Genome_build: Col-0 mitochondrial genome of Arabidopsis thaliana
Supplementary_files_format_and_content: Excel file with number of reads per exon for each genotype

organism: Arabidopsis thaliana

source_name: Flowers

growth_protocol: Greenhouse, long day conditions

extract_protocol:
Total ribosome footprints were prepared from a mix of flower buds and open flowers. About 2.5 g of flowers were ground in liquid nitrogen and resuspended in 15 ml of ribosome extraction buffer (0.2 M sucrose, 0.2 M KCl, 40 mM Tris-acetate, pH 8, 10 mM MgCl2, 10 mM b-mercaptoethanol, 2% polyoxyethylene 10 tridecyl ether, 1% Triton X-100, 100 mg/ml chloramphenicol and 100 mg/ml cycloheximide). The obtained solution was centrifuged twice for 10 min at 15 000 g at 4◦C to remove the cell debris and the supernatant was transferred to a new tube. To estimate the RNA concentration contained in the supernatant, total RNA was extracted from a 0.5 ml aliquot using the TRI Reagent® (Sigma- Aldrich) following the manufacturer’s instructions. The su- pernatant was then digested with 10 U/OD260nm/ml of RNAse I (Ambion), and incubated 1 h at 25◦C to de- grade unprotected RNA. The solution was then layered on an equal volume of a sucrose cushion (1 M Sucrose, 0.1 M KCl, 40 mM Tris-acetate, pH 8, 15 mM MgCl2, 5 mM b-mercaptoethanol, 100 mg/ml chloramphenicol and 100 mg/ml cycloheximide) and centrifuged for 3 h at 55 000 g at 4◦C in a TFT 65-13 rotor (Kontron). The ob- tained pellet was resuspended in 0.6 ml of RNA extrac- tion buffer I (0.1 M EGTA pH 8, 0.1 M NaCl, 1% sodium dodecyl sulphate (SDS), 10 mM Tris–HCl pH 8 and 1 mM ethylenediaminetetraacetic acid (EDTA)), and RNAs were extracted with the TRI Reagent® (Sigma-Aldrich) following the manufacturer’s recommendations. Ribosomal footprints were further purified on 17% (v/v) acrylamide- bisacrylamide (19:1) gel made with 7 M urea and 1 × Tris- acetate-EDTA (TAE) buffer. For this, 600 mg of RNAs were electrophoresed in two separated 15 cm-wide wells. The gel was pre-run for 1 h at 50◦C and then run for 15–16 h at 90 V at the same temperature. A mix comprising 100 ng of 27- mer and 33-mer RNA oligonucleotides was loaded on both gel extremities and used as size marker. After staining for 30 min in 1× SYBR Gold (Life Technologies) diluted in 1× TAE, RNA contained in the 27 and 33 nt regions were sep- arately excised from the gel. The gels slices were stored at least 2 h at -20◦C and then physically disrupted by centrifu- gation through a needle hole made in a 0.5 ml microcen- trifuge tube nested in an outer 1.5 ml collection microtube. The tube assembly was centrifuged at maximum speed for 5 min. RNAs were eluted overnight from gel fragments by passive diffusion in 5 ml of RNA extraction buffer II (10 mM Tris–HCl pH 8, 1 mM EDTA, 0.1 M NaCl, and 0.2%SDS) at 4◦C on a rotating wheel. The recovered RNAs were then isolated with the TRI Reagent® (Sigma-Aldrich) fol- lowing the manufacturer’s instructions, resuspended in 30 ml of RNAse-free water and stored at −80◦C until use.Ribosome footprints were depleted from ribosomal RNA with the Ribo-Zero Plant kit (Illumina) following manufacturer’s recommendations.
TruSeq Small kit from Illumina  (single end, 50 nt)

value: PPR336 mutant

value: flower


title: Liver_BCRX_0.2mg/kg_No.58_day7

description: Gene expression in liver tissue from cattle No.58 with 0.2mg/kg of BCRX on day 7

value: cattle No.58

value: β-CRX

value: 0.2 mg/kgBW

value: In vivo


title: Liver_BCRX_0.2mg/kg_No.66_day0

description: Gene expression in liver tissue from cattle No.66 with 0.2mg/kg of BCRX on day 0


title: NIH3T3: input29b_nuc

source_name: nuclear input sample with miR-29b mimic transfected oligo

tag: input rna amount

value: 5 ng

value: TotalScript RNA-seq Kit (Epicentre), using a mix of Random hexamer and Oligo-dT primers

value: nuclear RNA


title: 336-No1

description:
Ribosome Footprints
27 nt to 30 nt RNA


title: ColO-No2

description:
Ribosome Footprints
27 nt to 30 nt RNA


title: Liver_BCRX_0.2mg/kg_No.61_day0

description: Gene expression in liver tissue from cattle No.61 with 0.2mg/kg of BCRX on day 0


title: ColO-No1

description:
Ribosome Footprints
27 nt to 30 nt RNA


title: Liver_BCRX_0.2mg/kg_No.58_day0

description: Gene expression in liver tissue from cattle No.58 with 0.2mg/kg of BCRX on day 0


title: Left ventricle plac rep3

source_name: Left ventricle plac

value: mixed; SV129/Black Swiss and C57BL/6

value: male

value: Plac


title: CiprofloxacinTreatedBiofilm_3

city: Bozeman

first: Kerry

middle: S

last: Williamson

state: Montana

address: 109 Lewis Hall

department: Microbiology and Immunology

institute: Montana State University

description:
Biofilm cells grown in a drip flow reactor at 33C with CWE flowing at 10 ml/hour for 72 hours, followed by flow of CWE containing 1 mg/liter ciprofloxacin at 10 ml/hour for an additional 24 hours.
CiprofloxacinTreatedBiofilm_rep3

hyb_protocol: Labeled cDNA was hybridized to Affymetrix P. aeruginosa microarrays (part 900339) for 16 h at 50˚C with constant rotational mixing at 60 rpm.

scan_protocol: Microarrays were stained using a GCOS Fluidics Station 450 and scanned with an Affymetrix 7G scanner.

data_processing: Affymetrix GCOS v1.4 was used to generate CEL files, which were imported into FlexArray v1.6.1 for quality control and data analysis. Microarray data from three independent biological replicates from each condition (planktonic, biofilm, and treated biofilm) was background corrected and normalized using the GC-RMA algorithm in Flexarray 1.6.1.

organism: Pseudomonas aeruginosa

source_name: 4 day old antibiotic treated biofilm

label_protocol: 8 μg of turbo DNase treated RNA was reverse transcribed, fragmented, and labeled according to the Affymetrix prokaryotic target labeling protocol (GeneChip expression analysis technical manual, November 2004).

growth_protocol: P. aeruginosa PAO1 was cultured at 33C using a medium designed to mimic chronic wound exudate (CWE).  CWE was composed of a basal salts solution of: KCl (4.40 mM), NaCl (99.93 mM), Na2SO4 (300 μM), Na2HPO4 (1.27 mM), urea (9.60 mM), NaNO2 (58 μM), and TRIS (413 μM). The salt solution was adjusted to 7.5 pH and sterilized by autoclaving.  Stock solutions of amino acids and carbon sources were filter sterilized using 0.2 μm pore size PES bottle-top filters (Fisher Scientific, Waltham, MA).  The carbon sources were L-lactate (13.4 mM), glucose (1.8 mM), and amino acids.  The concentrations of each amino acid were: L-alanine (786 μM), L-arginine (88 μM), L-asparagine (45 μM), L-aspartate (451 μM), L-cysteine (495 μM), L-glutamate (460 μM), L-glutamine (589 μM), L-glycine (641 μM), L-histidine (167 μM), L-isoleucine (281 μM), L-leucine (561 μM), L-lysine (631 μM), L-methionine (77 μM), L-phenylalanine (280 μM), L-proline (1,720 μM), L-serine (317 μM), L-threonine (291 μM), L-valine (502 μM), L-tryptophan (376 μM), and L-tyrosine (616 μM). Sterile MgCl2 (940 μM), and CaCl2 (557 μM) were added to the basal salts solution.  A vitamin solution and iron solution were added to give final concentrations of thiamine (7.5 μM), nicotinic acid (16 μM), and FeSO4•7H2O (0.36 μM).

extract_protocol: After a 3 minute incubation with lysozyme, cells were incubated in 650 μL of Tri-reagent for 5 minutes, and then RNA extraction was carried out according to the Direct-zol™ RNA MiniPrep RNA Purification protocol (Zymo Research, Irvine CA).

treatment_protocol: Planktonic culture conditions: Three independent P. aeruginosa planktonic cultures were prepared by inoculating 1.0 ml of an overnight culture into 100 mL of CWE medium in 500 mL baffled Erlenmeyer flasks. Cultures were incubated to early logarithmic phase (OD 0.250, 1x 108 CFU) at 33˚C (approximate wound temperature). Cultures were harvested by dividing into two 45 mL aliquots in 50 mL Falcon Tubes (Corning Inc., Corning, NY), and centrifuging at 5,125 x g for 5 minutes at 4˚C in an Allegra® X-15R Centrifuge (Beckman Coulter, Brea, CA). Cell pellets were frozen at -80˚C for use in metabolomic or transcriptomic studies.    Biofilm growth conditions:  P. aeruginosa biofilms were grown on hydroxyapatite-coated glass slides (Clarkson Chromatography, South Williamsport, PA) in a drip flow reactor (DFR) designed by Biosurface Technologies Corp., Bozeman, MT (Goeres). P. aeruginosa PAO1 was cultured overnight in CWE medium at 33˚C with shaking at 250 rpm. A 1:100 dilution of the overnight culture in CWE was incubated until the culture reached an OD600 of 1.0.  The culture was diluted 1:10 with CWE and 5 ml of this suspension was added to each channel of the DFR.  The DFR was incubated for one hour at 33˚C to allow cell attachment. Following batch phase, a MasterFlex® L/S™ model 7519-20 peristaltic pump (Cole-Parmer, Vernon Hills, IL) was started at a flow rate of 10 mL/hour, and biofilms were cultivated at 33˚C for 72 hours (Figure S1). CWE medium containing 1 mg/L ciprofloxacin was then pumped through the ciprofloxacin treatment chambers, while CWE without ciprofloxacin continued to flow through the untreated control chambers for 24 h. After a total of 96 h of growth, the P. aeruginosa PAO1 biofilms were harvested.  Each slide was removed from its chamber using sterile forceps and placed in a 50 mL Falcon Tube (Corning Inc., Corning, NY) containing 10 mL phosphate buffered saline (PBS). Slides were scraped using sterile GeneMate 18 cm Cell Lifters (BioExpress, Kaysville, UT). The cell suspension was homogenized by vortexing and passage through an 18 gauge, 1.5-inch long Precisionglide® needle and 20 mL syringe (Beckton Dickinson and Co., Franklin Lakes, NJ) twice slowly.  Aliquots (1 ml) were collected and centrifuged at 10,000 g for 1 min. The supernatant was removed by pipetting and discarded. Cell pellets were placed into the -80˚C freezer.

tag: strain

tag: growth type

value: Ciprofloxacin Treated Biofilm


title: Left ventricle plac rep4

value: left ventricle


title: CiprofloxacinTreatedBiofilm_2

description:
Biofilm cells grown in a drip flow reactor at 33C with CWE flowing at 10 ml/hour for 72 hours, followed by flow of CWE containing 1 mg/liter ciprofloxacin at 10 ml/hour for an additional 24 hours.
CiprofloxacinTreatedBiofilm_rep2


title: Left ventricle pravastatin rep5

source_name: Left ventricle pravastatin

value: pravastatin


title: CiprofloxacinTreatedBiofilm_1

description:
Biofilm cells grown in a drip flow reactor at 33C with CWE flowing at 10 ml/hour for 72 hours, followed by flow of CWE containing 1 mg/liter ciprofloxacin at 10 ml/hour for an additional 24 hours.
CiprofloxacinTreatedBiofilm_rep1


title: Cj11168_ΔFlhF_Rep3

city: Yangzhou

first: Fangzhe

last: Ren

state: Jiangsu

address: East Wenhui Road No.12

country: China

institute: Yangzhou university

description:
flhF mutant3
Gene expression profiles of C. jejuni strains grown in MH broth for 20h

hyb_protocol: Each Slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: Bacteria mutant, 20h

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: C. jejuni strains were grown in Mueller–Hinton (MH) broth for 20h under microaerobic condition (5% O2, 10% CO2, and 85% N2)

extract_protocol: C. jejuni strains were grown for 24 h, 1 ml of the culture was pelleted by centrifugation and lysised with lysozyme, total RNA was extracted using the RNeasy plus mini kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.

treatment_protocol: For C. jejuni flhF mutant, the flhF gene was inactivated by insertional mutagenesis

tag: genotype/variation

value: flhF mutant


title: Left ventricle plac rep1


title: Left ventricle pravastatin rep4


title: Biofilm_3

description:
Biofilm cells grown in a drip flow reactor at 33C with a CWE flowing at 10 ml/hour for 96 hours.
Biofilm_rep3

source_name: 4 day old untreated biofilm

value: Untreated Biofilm


title: Left ventricle pravastatin rep1


title: Left ventricle pravastatin rep2


title: Cj11168_ΔFlhF_Rep2

description:
flhF mutant2
Gene expression profiles of C. jejuni strains grown in MH broth for 20h


title: genomic DNA from COG-N-305

description: cell line


title: Left ventricle pravastatin rep3


title: Cj11168_WT_Rep3

description:
WT 3
Gene expression profiles of C. jejuni strains grown in MH broth for 20h

source_name: Bacteria WT, 20h

value: wild-type


title: Neutrophil_BCRX_0.2mg/kg_No.32_day0

description: Gene expression in peripheral neutrophil from cattle No.32 with 0.2mg/kg of BCRX on day 0

value: Holstein

value: cattle No.32

value: Peripheral neutrophil


title: Biofilm_2

description:
Biofilm cells grown in a drip flow reactor at 33C with a CWE flowing at 10 ml/hour for 96 hours.
Biofilm_rep2


title: Neutrophil_BCRX_0.2mg/kg_No.26_day7

description: Gene expression in peripheral neutrophil from cattle No.26 with 0.2mg/kg of BCRX on day 7

value: cattle No.26

value: β-CRX

value: 0.2 mg/kgBW


title: Biofilm_1

description:
Biofilm cells grown in a drip flow reactor at 33C with a CWE flowing at 10 ml/hour for 96 hours.
Biofilm_rep1


title: Planktonic_3

description:
Planktonic cells grown to early log phase (0.250 OD) at 33C in CWE.
Planktonic_rep3

source_name: Early log phase planktonic culture

value: Planktonic


title: Cj11168_ΔFlhF_Rep1

description:
flhF mutant1
Gene expression profiles of C. jejuni strains grown in MH broth for 20h


title: Left ventricle plac rep2


title: HepG2_3TFs_day7

status: Public on Oct 02 2018

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

data_processing:
The sequence reads were aligned to the mouse reference genome assembly (hg19) using tophat (v2.1.1) /Bowtie (v2.3.0.0).
Fragments per kilobase of exon per million mapped fragments (FPKM) was calculated from the aligned reads by using Cufflinks (v2.1.1).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

source_name: liver (hepatocellular carcinoma)

growth_protocol: A human hepatocellular carcinoma HepG2 cells were purchased from RIKEN BioResource Center CELL BANK. Cells were cultured using Dulbecco’s Modified Eagle’s Medium (DMEM, Nacalai Tesque) supplemented with 10% (v/v) fetal bovine serum (FBS, Gibco) in 5% CO2 incubator at 37 °C.

extract_protocol:
RNA was extracted using the NucleoSpin RNA II Kit (MACHEREY-NAGEL)
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA protocol

treatment_protocol: The HepG2 cells were tranduced with retroviruses that contained genes encoding indicated transcription factors.

value: liver (hepatocellular carcinoma)

tag: transfection

value: infected with HNF1A, HNF4A, and FOXA3

tag: Stage

value: 7 days after infection


title: HepG2_FOXA3_day14

value: infected with FOXA3

value: 14 days after infection


title: HepG2_HNF1A_day14

value: infected with HNF1A


title: HepG2_HNF4A_day14

value: infected with HNF4A


title: HepG2_EGFP_day7

value: infected with EGFP


title: Planktonic_2

description:
Planktonic cells grown to early log phase (0.250 OD) at 33C in CWE.
Planktonic_rep2


title: Tg rep2

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

description:
mywong_l2fpkm.txt
mywong_IntCts.txt
d5152

data_processing:
HiSeq2000 using v3 chemistry. Software: Control software version 2.0.12.0, RTA version 1.17.21.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Sequence aligned to hg19 with bowtie 1.0.1 and ensembl version 75 transcripts were quantified using rsem1.2.26
Genome_build: hg19
Supplementary_files_format_and_content: mywong_l2fpkm.txt is parsed fpkm from rsem output transformed to log2 space by adding 1 to FPKM and calculating the log2 value
Supplementary_files_format_and_content: mywong_IntCts.tx is integer count data for samples from rsem output

source_name: Tg, HeLaXBP1s cells

growth_protocol: HeLaXBP1s cells were plated in biological triplicate at a density of 6 × 10^5 cells per well in 6-well plates in complete DMEM supplemented with 10% fetal bovine serum (FBS), as well as geneticin sulfate (G418, 500 ug/ml)and allowed to adhere overnight before treatment.

extract_protocol:
RNeasy Plus Mini Kit (Qiagen)
Illumina Tru-seq

value: HeLaXBP1s cells

tag: treatment

value: 0.1% DMSO plus 750 nM Thapsigargin

value: 24hrs of treatment


title: Tg rep1

description:
mywong_l2fpkm.txt
mywong_IntCts.txt
d5151


title: Cj11168_WT_Rep1

description:
WT 1
Gene expression profiles of C. jejuni strains grown in MH broth for 20h

value: wild-type


title: HepG2_3TFs_day14


title: XBP1s rep2

description:
mywong_l2fpkm.txt
mywong_IntCts.txt
d5143

source_name: XBP1s, HeLaXBP1s cells

value: 0.1% DMSO plus 1 ug/ml dox

value: 48hrs of treatment


title: Planktonic_1

description:
Planktonic cells grown to early log phase (0.250 OD) at 33C in CWE.
Planktonic_rep1


title: Tg rep3

description:
mywong_l2fpkm.txt
mywong_IntCts.txt
d5153


title: HepG2_HNF4A_day7


title: HepG2_FOXA3_day7


title: HepG2_HNF1A_day7


title: Vehicle rep2

description:
mywong_l2fpkm.txt
mywong_IntCts.txt
d5140

source_name: Vehicle, HeLaXBP1s cells

value: 0.1% DMSO


title: Vehicle rep3

description:
mywong_l2fpkm.txt
mywong_IntCts.txt
d5141


title: XBP1s rep1

description:
mywong_l2fpkm.txt
mywong_IntCts.txt
d5142


title: Cj11168_WT_Rep2

description:
WT 2
Gene expression profiles of C. jejuni strains grown in MH broth for 20h


title: Vehicle rep1

description:
mywong_l2fpkm.txt
mywong_IntCts.txt
d5139


title: XBP1s rep3

description:
mywong_l2fpkm.txt
mywong_IntCts.txt
d5144