title: m6A-IP from BrU-labeled non-fragmented nascent RNA; 0 min; supernatant rep A

description:
m6A-depleted nascent RNA
m6A-IP was performed subsequently to the BrU-IP (from the purified BrU-labeled, 0min chase, nascent RNA). This sample is the m6A-IP supernatant.


title: AMF_3

status: Public on Jul 14 2018

type: RNA

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: WT Alveolar Macrophage

hyb_protocol: All Methods listed in Scott et al.  Transcription Factor Zeb2 is required to maintain tissue-sepcific identities of macrophages. Immunity. 2018.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Bioconductor. Normalisation was done by RMA. All samples passed quality control, and the Robust Multi-array Average (RMA) procedure was used to normalize data within arrays (probeset summarization, background correction and log2-transformation) and between arrays (quantile normalization).

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Alveolar Mac _WT

tag: strain

tag: tissue

value: Lung

tag: cell type

value: alveolar macrophages

tag: genotype

value: wildtype


title: m6A-IP from BrU-labeled non-fragmented nascent RNA; 0 min; supernatant rep B

status: Public on Jun 19 2018

type: SRA

city: Heraklion

first: Evgenia

last: Ntini

address: Nik. Plastira 100

country: Greece

institute: IMBB-FORTH

library_source: transcriptomic

data_processing:
Reads were mapped to GRCh37/hg19 using STAR version 2.4.2a
Only uniquely aligned reads were kept.
bigWig files were generated with WigToBigWig from UCSC utilities
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigWig

organism: Homo sapiens

growth_protocol: HEK293T were grown in DMEM supplemented with 10% FBS

extract_protocol:
Trizol
Libraries were prepared according to TruSeq Stranded mRNA Library Preparation Kit instructions.

treatment_protocol: Cells were incubated with 2 mM bromouridine for 15 min and chased with 20 mM uridine for 0 min or 30 min.

tag: bru labeling time

tag: uridine chase time

tag: anti-brdu

value: BrU-IP (purified BrU-labeled nascent RNA, non-fragmented)

value: m6A-IP supernatant

tag: rip antibody (anti-brdu)

value: anti-BrdU (mouse monoclonal from BD Pharmigen)

tag: rip antibody (anti-m6a)

value: anti-m6A (rabbit polyclonal from Synaptic Systems)

tag: rip antibody (anti-brdu) vendor

value: BD Pharmigen

tag: rip antibody (anti-m6a) vendor

value: Synaptic Systems

tag: rip antibody (anti-brdu) cat. nr.

tag: rip antibody (anti-m6a) cat. nr.

tag: rip antibody (anti-brdu) lot #

tag: rip antibody (anti-m6a) lot #


title: BrU-labeled nascent RNA; non-fragmented; 30 min chase; Input rep A

description:
Nascent RNA (non-fragmented)
BrU-IP was performed from the 15min BrU-labeled—and—30 min chased total RNA. The BrU-IP eluate (purified nascent non-fragmented RNA) is the Input to the subsequent m6A-IP.


title: BrU-labeled nascent RNA - Input rep C

description:
Nascent RNA (fragmented)
BrU-IP was performed from the 15min BrU-labeled total fragmented RNA.

data_processing:
Reads were mapped to GRCh37/hg19 using STAR version 2.4.2a
Only uniquely aligned reads were kept.
bigWig files were generated with WigToBigWig from UCSC utilities
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigWig files (signal values represent normalized reads per million of mapped reads)

extract_protocol:
Trizol
Libraries were prepared according to TruSeq Stranded mRNA Library Preparation Kit instructions with some modifications. Started from the first strand synthesis step and use 3X Clean-NA-Beads beads volume after the first strand synthesis. Then continued as the manufacturer's instructions.

treatment_protocol: Cells were incubated with 2mM bromouridine for 15min.

value: BrU-IP


title: m6A-IP from BrU-labeled nascent RNA, rep C

description:
m6A-enriched nascent RNA fragments
m6A-IP was performed subsequently to the BrU-IP (from the purified BrU-labeled nascent RNA)


title: m6A-IP from BrU-labeled nascent RNA, rep B


title: BrU-labeled nascent RNA; non-fragmented; 0 min; Input rep A

description:
Nascent RNA (non-fragmented)
BrU-IP was performed from the 15min BrU-labeled total RNA. The BrU-IP eluate (purified nascent non-fragmented RNA) is the Input to the subsequent m6A-IP.


title: BrU-labeled nascent RNA - Input rep B


title: AMF_1

description: WT Alveolar Macrophage

label_protocol: All Methods listed in Scott et al.  Transcription Factor Zeb2 is required to maintain tissue-sepcific identities of macrophages. Immunity. 2018.


title: m6A-IP from BrU-labeled nascent RNA, rep A


title: AMF_2

description: WT Alveolar Macrophage

extract_protocol: All Methods listed in Scott et al.  Transcription Factor Zeb2 is required to maintain tissue-sepcific identities of macrophages. Immunity. 2018.


title: AMF_4

description: WT Alveolar Macrophage


title: 15min BrU-labeling; 60min uridine chase; replicate A

description:
Nascent RNA
BrU-IP was done from 15min BrU-labeled—and—60min uridine chased total RNA.

data_processing:
Reads were mapped to GRCh37/hg19 using STAR version 2.4.2a
Only uniquely aligned reads were kept.
bigWig files were generated with WigToBigWig from UCSC utilities
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files (signal values represent normalized reads per million of mapped reads)

extract_protocol:
Trizol
Libraries were prepared according to Illumina TruSeq Stranded totalRNA Library Preparation without Ribo-Minus.

treatment_protocol: Cells were treated with METTL3 siRNA (25 nM) for 72h. Cells were labeled with 2mM bromouridine for 15min and chased with 20mM uridine for 0min and 60min.

tag: sirna treatment

tag: labeling time

tag: chase with 20mm uridine

tag: rip antibody

tag: rip antibody vendor

tag: rip antibody cat. nr.

tag: rip antibody lot #


title: 15min BrU-labeling; 60min uridine chase; replicate B


title: BrU-labeled nascent RNA - Input rep A

tag: bru labeling time


title: 15min BrU-labeling; 0min uridine chase; replicate B

description:
Nascent RNA
BrU-IP was done from 15min BrU-labeled total RNA.

tag: anti-brdu


title: 15min BrU-labeling; 0min uridine chase; replicate A


title: BrU-labeled nascent RNA; non-fragmented; 0 min; Input rep B

tag: uridine chase time

tag: rip antibody (anti-brdu)


title: iOSE11 p52 Mock (Rep 2)

status: Public on May 25 2018

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

country: USA

institute: Moffitt Cancer Center

data_processing:
sequencing reads were aligned with Tophat v2.0.13 against human reference genome hs37d5.
Quantification of read counts aligned to the region associated with each gene was performed using HTSeq v0.6.1 based on National Center for Biotechnology information (NCBI) RefSeq gene model.
Read counts of all samples were normalized using the median-of-ratios method implemented in R/Bioconductor package DESeq2 v1.6.3.
Differential expression analysis between the two groups was performed by serial dispersion estimation and statistical model fitting procedures implemented in DESeq2.
Genome_build: hs37d5
Supplementary_files_format_and_content: Text file of normalized gene abundance by DESeq2

source_name: iOSE11 p52 Mock

growth_protocol: Cell lines were cultured in NOSE-CM Medium comprised of MCDB105 (Sigma; cat.no. M6395-1L):Medium 199 (Sigma; cat.no. M2154 ) (1 : 1) supplemented with 15% fetal bovine serum (Sigma; cat.no. F4135-500ML), 10 ng/ml epidermal growth factor (Invitrogen; cat.no PHG0311), 0.5 mg/ml hydrocortisone (Sigma; cat.no. H4001-1G), 5 mg/ml insulin (Sigma; cat.no. I9278-5ML), and 34 mg protein/ml bovine pituitary extract (Invitrogen; cat.no. 13028-014).

extract_protocol:
RNeasy Mini Kit (Qiagen, Hilde, Germany) following manufacturer's protocol, including the optional "on-column DNase digestion" step using freshly prepared DNase
100 ng of total RNA was used for library preparation using Ovation Human FFPERNA-seq multiplex system (NuGEN Technologies, San Carlos, CA); Sequencing was performed on an Illumina NextSeq500 instrument with 75 bp paired end reads.

treatment_protocol: Cells were plated on 100 mm plates and cultured for 24 h after plating to reach 80% confluency.  Cells were then briefly washed with PBS and fresh medium containing 10 µM Norepinephrine or vehicle (H2O) and incubated for 1 hr. Cells were harvested immediately after treatment and processed for total RNA extraction.

tag: cell line

tag: cell type

value: normal immortalized ovarian surface epithelial cells

tag: passage

tag: treatment

value: mock-treated

tag: treatment length

value: 1 h


title: iOSE11 p53 Mock (Rep 3)

source_name: iOSE11 p53 Mock


title: iOSE11 p52 NE (Rep 2)

source_name: iOSE11 p52 NE

value: 1 µM norepinephrine


title: iOSE11 p49 NE (Rep 1)

source_name: iOSE11 p49 NE


title: iOSE11 p49 Mock (Rep1)

source_name: iOSE11 p49 Mock


title: iFTE283 p53 Mock (Rep 3)

source_name: iFTE283 p53 Mock

value: immortalized fallopian tube surface epithelial cells


title: iFTE283 p53 NE (Rep 3)

source_name: iFTE283 p53 NE


title: iFTE283 p51 Mock (Rep 2)

source_name: iFTE283 p51 Mock


title: iFTE283 p49 NE (Rep 1)

source_name: iFTE283 p49 NE


title: iFTE283 p51 NE (Rep 2)

source_name: iFTE283 p51 NE


title: iFTE283 p49 Mock (Rep 1)

source_name: iFTE283 p49 Mock


title: MCF-7 total nucleoplasmic RNA-seq

status: Public on Feb 05 2018

data_processing:
Reads were mapped using STAR (Dobin et al., Bioinformatics 2013).
Reads were quality filtered (score 255).
Normalized genomic coverage from strand-specific bed files was generated with bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: mcf7NPtotal.minus.bw, bigWig file from nucleoplasmic RNA-seq reads mapped on the minus strand, MCF-7; mcf7NPtotal.plus.bw, bigWig file from nucleoplasmic RNA-seq reads mapped on the plus strand, MCF-7

source_name: nucleoplasmic total RNA

growth_protocol: MCF-7 cells grown in DMEM (10% FCS)

extract_protocol:
Cell fractionation and isolation of the nucleoplasmic fraction was after Conrad and Ørom, Methods Mol Biol 2017.
Libraries were constructed with the Illumina TruSeq Stranded Total RNA kit, including Ribo-Zero Gold extraction.

tag: tissue

value: breast adenocarcinoma


title: iOSE11 p53 NE (Rep 3)

source_name: iOSE11 p53 NE


title: MN_Coculture_1

status: Public on Jan 26 2018

city: Los Angeles

first: Shaughn

last: Bell

state: CA

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

data_processing:
fastq reads were alignd to the human genome (hg19) with tophat v2.0.8b with parameters --no-coverage-search
bam files for NCSC vs MESH were annotated using Partek software v7.17.0918 and RefSeq-release79 to generate RPKM numbers for each Refseq annotated gene
bam files for NCSC vs MN_Coculture were annotated using Partek software v 7.17.0918 and RefSeq-release68 to generate RPKM numbers for each Refseq annotated gene
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.  NCSC RPKMs are in both files but differ because of the RefSeq release version (release68 vs release79)

source_name: iPS cells

extract_protocol:
Total RNA was isolated using the PureLink™ RNA Mini Kit (Catalog # 12183018A) and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Ion Torrent protocols.  RNA sequencing libraries were constructed with the Ion Total RNA-Seq Kit.  Libraries were indexed with Ion Xpress RNA-Seq Barcodes and pooled for sequencing.

value: iPSC-derived Neural Crest Stem Cells

tag: differentiation

value: NCSC cocultured with iPSC-derived Motor Neurons

tag: age of culture when rna harvested

value: 11 to 14 days to NCSC, then cocultured for 14 days, replated (to kill MN) and cultured for 7 more days


title: NCSC_3

description:
NCSC_vs_MESH_RPKM.txt
NCSC_vs_MN_Coculture_RPKM.txt

value: 11 to 14 days to NSCS


title: MESH_3

value: NCSC treated with MesenPRO with Heregulin

value: 11 to 14 days to NCSC, then 40 days in MesenPRO with Heregulin media


title: MESH_2


title: MESH_1


title: MESH_4


title: NCSC_1


title: PRMT1_ChIPseq_Ctrl_Abcam

status: Public on Feb 02 2018

city: Stanford

first: Douglas

last: Porter

address: 269 Campus Drive

department: Dermatology

institute: Stanford

description: ChIP-seq in undifferentiated keratinocytes

library_source: genomic

data_processing:
Reads were mapped to UCSC hg19 using bowtie,
ChIPseq peaks were called using MACS14.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in standard bed/whole bed format

molecule: genomic DNA

source_name: human keratinoctyes expressing HA-PRMT1

growth_protocol: neonatal keratinocyte were isolated from discarded foreskin, cultured in KSF and 154 keratinocyte medium

extract_protocol:
For ChIP-seq, HA-PRMT1 expressing primary keratinocytes were crosslinked with 1% formaldehyde and DSG, sonicated, and immunoprecipiated with antibodies recognizing the HA tag.
For ChIP-seq, NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina was used for library construction.

treatment_protocol: HA-PRMT1 were expressed using pBABE retroviral vector at near endogenous level. D4476 were added to 60uM final concentration for 48 hours before crosslinking

value: primary human neonatal keratinocytes

tag: antibody

value: HA (Abcam Ab9110)


title: PRMT1_ChIPseq_D4476_Abcam

description: ChIP-seq in undifferentiated keratinocytes with D4476


title: PRMT1_ChIPseq_Ctrl_rbmab

value: HA (cell signaling C29F4)


title: NCSC_2


title: MN_Coculture_3


title: PRMT1_ChIPseq_D4476_rbmab


title: MN_Coculture_2


title: RNA-seq siRNA control in C42B rep1

status: Public on Jan 24 2018

first: Suhn

middle: K

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

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

source_name: Human prostate cancer cell line C42B

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

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

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

value: Human prostate cancer cell line C42B

tag: chip antibody

tag: sirna

value: siCtrl


title: RNA-seq siZFX in C42B rep3

value: siZFX


title: RNA-seq siRNA control in C42B rep2


title: RNA-seq siRNA control in C42B rep3


title: RNA-seq siZFX in C42B rep1


title: ZFX ChIP-seq in C42B rep2

value: ZFX


title: ChIP-seq Input in C42B rep2


title: ZFX ChIP-seq in C42B rep1


title: keratinocytes with Ctrl shRNA-1 (CSNK1a)

status: Public on Jan 25 2018

description: CTRL knockdown

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA normalization using justRMA package in R 2.11.1

label: biotin

source_name: primary human keratinocytes

label_protocol: Ambion WT Expression kit was used to generate ssDNA targets. Fragmentation and biotin-labeling were performed using Afymetrix WT Terminal Labeling and Hybridization kit.

growth_protocol: Primary human keratinocytes grow in differentiated culture condition (1.2mM Ca2+)

extract_protocol: qiagen RNeasyPlus kit was used to isolate total RNA.

treatment_protocol: shRNA using pSMP retroviral expression vector.

value: control shRNA


title: keratinocytes with PRMT1 shRNA-B

description: PRMT1 shB knockdown

source_name: primary human kerationcytes

value: PRMT1 shRNA-B knockdown


title: RNA-seq siZFX in C42B rep2


title: keratinocytes with Ctrl shRNA-2 (CSNK1a)

description: CTRL knockdown


title: keratinocytes with CSNK1a1 shRNA-B

description: CSNK1a1 shB knockdown

value: CSNK1a1 shRNA-B knockdown


title: keratinocytes with Ctrl shRNA-1 (PRMT1)

description: CTRL knockdown


title: keratinocytes with CSNK1a1 shRNA-A

description: CSNK1a1 shA knockdown

value: CSNK1a1 shRNA-A knockdown


title: keratinocytes with Ctrl shRNA-2 (PRMT1)

description: CTRL knockdown


title: ChIP-seq Input in C42B rep1


title: keratinocytes with PRMT1 shRNA-A

description: PRMT1 shA knockdown

value: PRMT1 shRNA-A knockdown


title: Breast_T364

status: Public on Dec 31 2017

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: IRON normalization was performed on the dataset, batch corrected for RNA quality using PLS

source_name: Breast adenocarcinoma

label_protocol: Samples were amplified and labeled using a custom automated version of the NuGEN Ovation v2 with WB (whole blood) reagents protocol (using Ribo-SPIA amplification). The labeled molecules are biotinylated-cRNA. Sample amplification and labeling were performed by LabCorp Clinical Trials-Genomic Services in Seattle, Washington.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification. Isolated total RNA samples were assayed for quality (Agilent Bioanalyzer) and yield (Ribogreen) metrics prior to amplification.

value: Breast adenocarcinoma

tag: pathological tnm, group stage

tag: grade/differentiation

tag: er status

tag: pr status

tag: her2 status (ihc or fish)

tag: recurrence (yes/no)

tag: vital status

tag: rfs (months)

tag: os (months)


title: Breast_T360


title: Breast_T353

value: x


title: Breast_T352


title: Breast_T357


title: Breast_T356


title: Breast_T363


title: Breast_T361

value: 99 UNK


title: Breast_T365


title: Breast_T366


title: Breast_T362


title: Breast_T358


title: Breast_T355


title: Breast_T339


title: Breast_T350


title: Breast_T342


title: Breast_T344


title: Breast_T347


title: Breast_T354


title: Breast_T341


title: Breast_T345


title: Breast_T349


title: Breast_T348


title: Breast_T351


title: Breast_T338


title: Breast_T340


title: Breast_T359


title: Breast_T343


title: Breast_T337


title: Breast_T346


title: Breast_T335


title: Breast_T336


title: Breast_T326


title: Breast_T330


title: Breast_T331


title: Breast_T325


title: Breast_T321


title: Breast_T324


title: Breast_T320


title: Breast_T333


title: Breast_T334


title: Breast_T329


title: Breast_T328


title: Breast_T317


title: Breast_T313


title: Breast_T322


title: Breast_T318


title: Breast_T319


title: Breast_T323


title: Breast_T312


title: Breast_T310


title: Breast_T327


title: Breast_T332


title: Breast_T315


title: Breast_T309


title: Breast_T308


title: Breast_T316


title: Breast_T307


title: Breast_T314


title: Breast_T311


title: Breast_T305


title: Breast_T304


title: Breast_T303


title: Breast_T301


title: Breast_T292


title: Breast_T306


title: Breast_T291


title: Breast_T299


title: Breast_T297


title: Breast_T298


title: Breast_T289


title: Breast_T288


title: Breast_T296


title: Breast_T281


title: Breast_T284


title: Breast_T282


title: Breast_T302


title: Breast_T294


title: Breast_T285


title: Breast_T290


title: Breast_T295


title: Breast_T278


title: Breast_T287


title: Breast_T280


title: Breast_T283


title: Breast_T300


title: Breast_T277


title: Breast_T286


title: Breast_T279


title: Breast_T293


title: Breast_T274


title: Breast_T275


title: Breast_T276


title: Breast_T273


title: Breast_T268


title: Breast_T269


title: Breast_T271


title: Breast_T267


title: Breast_T272


title: Breast_T263


title: Breast_T270


title: Breast_T264


title: Breast_T258


title: Breast_T254


title: Breast_T249


title: Breast_T250


title: Breast_T260


title: Breast_T256


title: Breast_T253


title: Breast_T261


title: Breast_T257


title: Breast_T266


title: Breast_T262


title: Breast_T265


title: Breast_T259


title: Breast_T252


title: Breast_T248


title: Breast_T251


title: Breast_T245


title: Breast_T246


title: Breast_T247


title: Breast_T255


title: Breast_T242


title: Breast_T240


title: Breast_T241


title: Breast_T235


title: Breast_T239


title: Breast_T238


title: Breast_T237


title: Breast_T236


title: Breast_T232


title: Breast_T233


title: Breast_T229


title: Breast_T226


title: Breast_T234


title: Breast_T219


title: Breast_T220


title: Breast_T224


title: Breast_T231


title: Breast_T222


title: Breast_T215


title: Breast_T221


title: Breast_T228


title: Breast_T223


title: Breast_T218


title: Breast_T225


title: Breast_T214


title: Breast_T216


title: Breast_T230


title: Breast_T244


title: Breast_T217


title: Breast_T212


title: Breast_T210


title: Breast_T213


title: Breast_T209


title: Breast_T211


title: Breast_T207


title: Breast_T208


title: Breast_T205


title: Breast_T201


title: Breast_T203


title: Breast_T204


title: Breast_T206


title: Breast_T202


title: Breast_T199


title: Breast_T197


title: Breast_T227


title: Breast_T190


title: Breast_T195


title: Breast_T187


title: Breast_T193


title: Breast_T189


title: Breast_T191


title: Breast_T196


title: Breast_T183


title: Breast_T186


title: Breast_T185


title: Breast_T192


title: Breast_T188


title: Breast_T194


title: Breast_T200


title: Breast_T198


title: Breast_T184


title: Breast_T181


title: Breast_T243


title: Breast_T182


title: Breast_T179


title: Breast_T177


title: Breast_T178


title: Breast_T176


title: Breast_T175


title: Breast_T170


title: Breast_T171


title: Breast_T173


title: Breast_T174


title: Breast_T168


title: Breast_T169


title: Breast_T160


title: Breast_T161


title: Breast_T164


title: Breast_T166


title: Breast_T162


title: Breast_T165


title: Breast_T172


title: Breast_T159


title: Breast_T156


title: Breast_T158


title: Breast_T163


title: Breast_T167


title: Breast_T155


title: Breast_T151


title: Breast_T152


title: Breast_T154


title: Breast_T157


title: Breast_T150


title: Breast_T180


title: Breast_T149


title: Breast_T145


title: Breast_T143


title: Breast_T144


title: Breast_T147


title: Breast_T141


title: Breast_T139


title: Breast_T153


title: Breast_T136


title: Breast_T140


title: Breast_T142


title: Breast_T148


title: Breast_T146


title: Breast_T134


title: Breast_T133


title: Breast_T130


title: Breast_T129


title: Breast_T128


title: Breast_T131


title: Breast_T137


title: Breast_T124


title: Breast_T126


title: Breast_T123


title: Breast_T127


title: Breast_T125


title: Breast_T122


title: Breast_T121


title: Breast_T114


title: Breast_T117


title: Breast_T119


title: Breast_T132


title: Breast_T110


title: Breast_T115


title: Breast_T111


title: Breast_T113


title: Breast_T112


title: Breast_T138


title: Breast_T107


title: Breast_T99


title: Breast_T116


title: Breast_T120


title: Breast_T105


title: Breast_T101


title: Breast_T109


title: Breast_T102


title: Breast_T104


title: Breast_T108


title: Breast_T103


title: Breast_T100


title: Breast_T118


title: Breast_T97


title: Breast_T96


title: Breast_T98


title: Breast_T95


title: Breast_T106


title: Breast_T94


title: Breast_T90


title: Breast_T91


title: Breast_T89


title: Breast_T93


title: Breast_T83


title: Breast_T86


title: Breast_T92


title: Breast_T81


title: Breast_T87


title: Breast_T84


title: Breast_T80


title: Breast_T75


title: Breast_T88


title: Breast_T135


title: Breast_T71


title: Breast_T69


title: Breast_T76


title: Breast_T78


title: Breast_T74


title: Breast_T73


title: Breast_T85


title: Breast_T77


title: Breast_T70


title: Breast_T68


title: Breast_T72


title: Breast_T66


title: Breast_T82


title: Breast_T65


title: Breast_T67


title: Breast_T62


title: Breast_T64


title: Breast_T63


title: Breast_T59


title: Breast_T50


title: Breast_T51


title: Breast_T60


title: Breast_T61


title: Breast_T53


title: Breast_T57


title: Breast_T56


title: Breast_T58


title: Breast_T52


title: Breast_T48


title: Breast_T55


title: Breast_T79


title: Breast_T40


title: Breast_T44


title: Breast_T46


title: Breast_T39


title: Breast_T38


title: Breast_T37


title: Breast_T42


title: Breast_T47


title: Breast_T41


title: Breast_T54


title: Breast_T45


title: Breast_T43


title: Breast_T31


title: Breast_T28


title: Breast_T35


title: Breast_T29


title: Breast_T23


title: Breast_T30


title: Breast_T34


title: Breast_T24


title: Breast_T27


title: Breast_T26


title: Breast_T18


title: Breast_T36


title: Breast_T21


title: Breast_T14


title: Breast_T9


title: Breast_T22


title: Breast_T32


title: Breast_T19


title: Breast_T20


title: Breast_T17


title: Breast_T25


title: Breast_T16


title: Breast_T33


title: Breast_T13


title: Breast_T15


title: Breast_T12


title: Breast_T10


title: Breast_T11


title: Breast_T2


title: Breast_T5


title: Breast_T3


title: Breast_T4


title: Breast_T8


title: Breast_T6


title: Breast_T7


title: TG3-13

city: Suwon, Korea

first: Jung Woo

last: Eun

state: Korea

address: Department of Gastroenterology

country: South Korea

institute: Ajou University of Korea

description: SAMPLE 106

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with GenPlex 3.0

source_name: liver tissue

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

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen). RNA quality control was performed with Bio-Rad Experion.

value: liver

tag: phenotype

value: hepatocellular carcinoma (TG3)


title: TG3-09

description: SAMPLE 102


title: TG3-11

description: SAMPLE 104


title: TG3-07

description: SAMPLE 100


title: TG3-10

description: SAMPLE 103


title: Breast_T1


title: TG3-08

description: SAMPLE 101


title: TG3-01

description: SAMPLE 94


title: TG3-03

description: SAMPLE 96


title: TG2-11

description: SAMPLE 92

value: hepatocellular carcinoma (TG2)


title: TG3-14

description: SAMPLE 107


title: TG3-05

description: SAMPLE 98


title: TG3-12

description: SAMPLE 105


title: TG2-09

description: SAMPLE 90


title: TG2-07

description: SAMPLE 88


title: TG2-12

description: SAMPLE 93


title: TG3-04

description: SAMPLE 97


title: TG3-06

description: SAMPLE 99


title: TG2-01

description: SAMPLE 82


title: TG1-08

description: SAMPLE 80

value: hepatocellular carcinoma (TG1)


title: TG3-02

description: SAMPLE 95


title: TG2-08

description: SAMPLE 89


title: Breast_T49


title: TG2-05

description: SAMPLE 86


title: TG1-07

description: SAMPLE 79


title: TG2-10

description: SAMPLE 91


title: TG1-09

description: SAMPLE 81


title: TG2-06

description: SAMPLE 87


title: TG2-03

description: SAMPLE 84


title: TG1-06

description: SAMPLE 78


title: TG1-04

description: SAMPLE 76


title: TG2-02

description: SAMPLE 83


title: TG2-04

description: SAMPLE 85


title: TG1-03

description: SAMPLE 75


title: TG1-05

description: SAMPLE 77


title: eHCC-04

description: SAMPLE 71

value: earyl hepatocellular carcinoma


title: TG1-01

description: SAMPLE 73


title: TG1-02

description: SAMPLE 74


title: eHCC-03

description: SAMPLE 70


title: eHCC-01

description: SAMPLE 68


title: eHCC-02

description: SAMPLE 69


title: eHCC-05

description: SAMPLE 72


title: DH-06

description: SAMPLE 62

value: Dysplastic nodules with high grade


title: DH-03

description: SAMPLE 59


title: DH-08

description: SAMPLE 64


title: DH-09

description: SAMPLE 65


title: DH-04

description: SAMPLE 60


title: DH-11

description: SAMPLE 67


title: DH-07

description: SAMPLE 63


title: DH-10

description: SAMPLE 66


title: DH-02

description: SAMPLE 58


title: DH-05

description: SAMPLE 61


title: DL-07

description: SAMPLE 52

value: Dysplastic nodules with low grade


title: DL-05

description: SAMPLE 50


title: DL-09

description: SAMPLE 54


title: DL-04

description: SAMPLE 49


title: DH-01

description: SAMPLE 57


title: DL-10

description: SAMPLE 55


title: DL-08

description: SAMPLE 53


title: DL-06

description: SAMPLE 51


title: DL-02

description: SAMPLE 47


title: DL-01

description: SAMPLE 46


title: DL-11

description: SAMPLE 56


title: DL-03

description: SAMPLE 48


title: CS-10

description: SAMPLE 43

value: Cirrhosis


title: CS-08

description: SAMPLE 41


title: CS-11

description: SAMPLE 44


title: CS-09

description: SAMPLE 42


title: CS-12

description: SAMPLE 45


title: CS-07

description: SAMPLE 40


title: CS-03

description: SAMPLE 36


title: CS-06

description: SAMPLE 39


title: CS-05

description: SAMPLE 38


title: CS-01

description: SAMPLE 34


title: FL-06

description: SAMPLE 19

value: Choronic Hepatitis with low grade


title: FH-03

description: SAMPLE 24

value: Choronic Hepatitis with high grade


title: CS-04

description: SAMPLE 37


title: FL-04

description: SAMPLE 17


title: FH-12

description: SAMPLE 33


title: FH-11

description: SAMPLE 32


title: CS-02

description: SAMPLE 35


title: FL-08

description: SAMPLE 21


title: FH-07

description: SAMPLE 28


title: FH-10

description: SAMPLE 31


title: FH-09

description: SAMPLE 30


title: FH-05

description: SAMPLE 26


title: FH-08

description: SAMPLE 29


title: FH-06

description: SAMPLE 27


title: FL-05

description: SAMPLE 18


title: FH-01

description: SAMPLE 22


title: FH-02

description: SAMPLE 23


title: N-13

description: SAMPLE 13

value: Normal


title: FL-03

description: SAMPLE 16


title: FL-07

description: SAMPLE 20


title: FH-04

description: SAMPLE 25


title: N-11

description: SAMPLE 11


title: N-12

description: SAMPLE 12


title: FL-01

description: SAMPLE 14


title: N-08

description: SAMPLE 8


title: N-09

description: SAMPLE 9


title: FL-02

description: SAMPLE 15


title: N-10

description: SAMPLE 10


title: N-06

description: SAMPLE 6


title: N-04

description: SAMPLE 4


title: N-07

description: SAMPLE 7


title: N-02

description: SAMPLE 2


title: N-05

description: SAMPLE 5


title: SCL-II over expressing miR-497

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

country: Israel

institute: Sheba Medical Center at Tel HaShomer

description: Gene expression data from SCL-II over expressing miR-497

hyb_protocol: Affymetrix 3' IVT labeling protocol  https://www.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf

data_processing: RMA (Partek)

source_name: SCL-II cells were derived from primary an undifferentiated SCC lesion from the face (Cancer Res. 1983 Dec;43(12 Pt 1):5995-6011.)

label_protocol: Affymetrix biotin labeling_ wt kit  (Affymetrix)

growth_protocol: Cell were grown in DMEM medium supplemented with 10% fetal bovine serum (FBS), 1% Penicillin–Streptomycin (P/S) antibiotics and 1% L-glutamine. Cultures were maintained in a 5% CO2 incubator at 37oC

extract_protocol: Total RNA was extracted from cell lines using Total RNA Purification Kit (Norgen)according to the manufacturer's instructions.

treatment_protocol: miR-497 or empty control vector with the Lipofectamine™ 2000 Transfection Reagent. Cells were grown in the present of G418 antibiotic.

tag: cell type

value: tumor cell line


title: N-03

description: SAMPLE 3

tag: tissue


title: N-01

description: SAMPLE 1


title: Alveolar macrophages from MWCNT-exposed mice_AM_MWCNT_4

status: Public on Dec 01 2017

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

department: Medicine

institute: University of Washington

hyb_protocol: Hybridization to microarrays were performed per Illumina protocols.

scan_protocol: Illumina iScan system

data_processing: Microarray data was assessed for quality, followed by variance stabilization and quantile normalization using the Bioconductor package lumi.

label_protocol: High quality RNA samples were converved to cDNA and biotin-labaled

extract_protocol: Total RNA from macrophages was isolated and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Control mice underwent oropharyngeal instillation of 35% surfactant/saline and experimental animals were exposed to 35% surfactant/saline solution containing 100 μg of MWCNT.

tag: strain background

tag: animal identification number

value: MWCNT C57Bl/6 mouse 4

tag: treated with

value: multiwall carbon nanotube (MWCNT)

value: Murine alveolar macrophage


title: SCL-II over expressing pcDNA3.1

description: Gene expression data from SCL-II over expressing pcDNA3.1

scan_protocol: Affymetrix 3' IVT labeling protocol  https://www.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf


title: PPB Xn sample_1

description: Sample name: D493_P4(A5)

hyb_protocol: Affymetrix biotin labeling_ wt kit  (Affymetrix)

scan_protocol: Affymetrix wt scanning protocol  as described in http://media.affymetrix.com/support/downloads/manuals/3_IVT_PLUS_Reagent_Kit_User_Manual.pdf

data_processing: Analysis was performed using RMA in PARTEK. log2 RMA was used to represent intensity values. The file analysis file for pulmonary blastoma.xls contains the log2 RMA values, the non-log transformed RMA values and probe set annotation. This file is available on the series record.

label_protocol: RNA samples were used to prepare biotinylated target DNA, according to manufacturer’s recommendations. The target complementary DNA (cDNA) generated from each sample was processed as per manufacturer’s recommendation using an Affymetrix GeneChip Instrument System

extract_protocol: Total RNA was extracted from each of the samples using TRIZOL .

value: Pleuropulmonary blastoma (PPB)

tag: developmental stage

value: adult


title: PPB Xn sample_2

description: Sample name: D494_P8(A8)


title: Alveolar macrophages from MWCNT-exposed mice_AM_MWCNT_1

value: MWCNT C57Bl/6 mouse 1


title: PPB primary sample

description: Sample name: D492_PT

source_name: Pleuropulmonary blastoma (PPB)


title: Alveolar macrophages from MWCNT-exposed mice_AM_MWCNT_6

value: MWCNT C57Bl/6 mouse 6


title: Alveolar macrophages from control mice_AM_Control_3

source_name: Alveolar macrophages from control mice

value: Control C57Bl/6 mouse 3

value: none (control)


title: Alveolar macrophages from MWCNT-exposed mice_AM_MWCNT_5

value: MWCNT C57Bl/6 mouse 5


title: Alveolar macrophages from MWCNT-exposed mice_AM_MWCNT_2

value: MWCNT C57Bl/6 mouse 2


title: Alveolar macrophages from MWCNT-exposed mice_AM_MWCNT_3

value: MWCNT C57Bl/6 mouse 3


title: PPB Xn sample_3

description: Sample name: D495_P12(A12)


title: Fetal lung

description: Sample name: D496_FL

source_name: fetal lung

value: lung

value: fetus


title: Alveolar macrophages from control mice_AM_Control_2

value: Control C57Bl/6 mouse 2


title: MET1 over expressing miR-497

description: Gene expression data from MET1 over expressing miR-497

source_name: (MET1) were established from forehead skin a primary SCC lesion (British Journal of Cancer (2006) 94, 1446–1451. doi:10.1038/sj.bjc.6603135)


title: MET1 over expressing pcDNA3.1

description: Gene expression data from MET1 over expressing pcDNA3.1


title: Adult lung

description: Sample name: D497_AL

source_name: Adult lung


title: Alveolar macrophages from control mice_AM_Control_1

value: Control C57Bl/6 mouse 1


title: Alveolar macrophages from control mice_AM_Control_6

value: Control C57Bl/6 mouse 6


title: Alveolar macrophages from control mice_AM_Control_5

value: Control C57Bl/6 mouse 5


title: Alveolar macrophages from control mice_AM_Control_4

value: Control C57Bl/6 mouse 4


title: Day 5 post injury replicate 4

status: Public on Nov 21 2017

hyb_protocol: Illumina TotalPrep RNA Amplification kit

data_processing: Microarray data was assessed for quality, followed by background subtraction (based on control probes), variance stabilization and quantile normalization using the Bioconductor package lumi.

source_name: CoRL after injury day 5

extract_protocol: Total RNA from FACS isolated ZsGreen CoRL was isolated using Qiagen RNeasy Plus Mini Kit according to the manufacturers protocol. Extracted RNA yield and purity were determined using a NanoDrop ND-1000. RNA integrity was determined using an Agilent 2100 Bioanalyzer, samples with RIN ≥ 8 were considered to be of sufficient quality for microarray analysis.

treatment_protocol: Experimental FSGS was induced in Ren1cCre×Rs-ZsGreen-R mice with a cytotoxic anti-glomerular antibody, as we have previously reported. Briefly, two doses of sheep anti-glomerular antibody at 12 mg/20g of body weight via intraperitoneal injection, 24 hours apart, induced abrupt podocyte depletion. Mice were euthanized 5 days following the second dose of sheep anti-glomerular antibody (n = 4). Age matched mice which did not receive sheep anti-glomerular antibody were used as baseline controls (n = 4).

tag: strain

tag: mouse group

value: experimentally induced focal segmental glomerulosclerosis (FSGS)

value: cells of renin lineage (CoRL)


title: 40minE2_BS

status: Public on Oct 19 2017

description: Bisulfite converted gDNA

data_processing:
Reads were mapped with bowtie2.
Reads deduplication and methylation calling with Bismark (Krueger and Andrews, Bioinformatics 2011).
Genome_build: hg19
Supplementary_files_format_and_content: etoh.BS.bed; 40minE2.BS.bed; Score column in the bed files represents b-value (b-value*1000).

growth_protocol: MCF-7 cells, normally grown in DMEM (10% FCS), were placed in hormone-free medium i.e. high glucose DMEM without phenol red supplemented with 5% charcoal stripped FCS for 72h before induction.

extract_protocol:
Genomic DNA was extracted with Qiagen kit.
According to the instructions of the SureSelect MethylSeq Target Enrichment System (Agilent).

treatment_protocol: Hormone starved cells were treated either with etoh (ctrl) or 100nM estradiol for 40min.

tag: cell line

tag: estradiol treatment (min)

value: breast adenocarcinoma


title: etoh_chrRNAseq

description: chromatin-associated total RNA

data_processing:
Reads were mapped using STAR (Dobin et al., Bioinformatics 2013).
Reads were quality filtered (score 255).
Normalized genomic coverage from strand-specific bed files was generated with bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: etoh_minus.bw, bigWig file from chromatin-associated RNA-seq reads mapped on the minus strand, control MCF-7; etoh_plus.bw, bigWig file from chromatin-associated RNA-seq reads mapped on the plus strand, control MCF-7; 40minE2_minus.bw, bigWig file from chromatin-associated RNA-seq reads mapped on the minus strand, 40min estradiol treated MCF-7; 40minE2_plus.bw, bigWig file from chromatin-associated RNA-seq reads mapped on the plus strand, 40min estradiol treated MCF-7.

molecule: nuclear RNA

extract_protocol:
Cell fractionation and isolation of the chromatin fraction was after Bhatt et al., (Cell 2012). Chromatin-associated total RNA was extracted with Trizol.
Libraries were constructed with the Illumina TruSeq Stranded Total RNA kit, including Ribo-Zero Gold extraction.


title: 40minE2_chrRNAseq

description: chromatin-associated total RNA


title: etoh_BS

description: Bisulfite converted gDNA


title: 15min BrU-labeling; 0min uridine chase

status: Public on Aug 22 2017

data_processing:
Reads were mapped to GRCh37/hg19 using STAR version 2.4.2a
Only uniquely aligned reads were kept.
bigWig files were generated with WigToBigWig from UCSC utilities
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files (signal values represent normalized reads per million)

growth_protocol: HEK293T were grown in DMEM supplemented with 10% FCS

treatment_protocol: Cells were labeled with 2mM bromouridine for 15min and chased with 20mM uridine for different time intervals (0min, 15min, 30min and 60min).

tag: labeling time

tag: chase with 20mm uridine

tag: anti-brdu

value: BrU-IP

tag: rip antibody

value: anti-BrdU (mouse monoclonal from BD Pharmigen)

tag: rip antibody vendor

value: BD Pharmigen

tag: rip antibody cat. nr.

tag: rip antibody lot #


title: 15min BrU-labeling; 60min uridine chase


title: 15min BrU-labeling; 15min uridine chase

description:
Nascent RNA
BrU-IP was done from 15min BrU-labeled—and—15min uridine chased total RNA.


title: Day 5 post injury replicate 3

tag: cell type


title: Day 5 post injury replicate 1


title: Uninjured replicate 3

source_name: CoRL baseline

value: uninjured (baseline)


title: H9_30_2_RNA-seq

status: Public on Jul 10 2017

city: Clemson

first: Qing

last: Liu

state: SC

address: Jordan Hall

department: Biological Sciences

institute: Clemson University

description: biological replicate 2

data_processing:
RNA-seq fastq data were aligned with Tophat (version 2.0.9) to GRCh39/hg19 Homo sapiens reference genome from the UCSC Genome Browser.
Cuffdiff of the Cufflinks software (version 2.2.1) and GRCh39/hg19 Homo sapiens gtf file from UCSC Genome Browser were used to estimate abundances of transcripts and generate their FPKM values.
Table of FPKM values of all samples were created using cummeRbund package in R.
Genome_build: hg19
Supplementary_files_format_and_content: text file with FPKM values.

source_name: hESC-derived cells

growth_protocol: Both hESCs and hiPSCs were grown in Matrigel (Corning)-coated 12-well plates with Essential 8™ Medium (Thermo Fisher Scientific).

extract_protocol:
Total RNA from approximately 3-5 million cells were extracted using QIAzol lysis ralleagent (QIAGEN), and then were subjected to DNase I digestion and purified by AllPrep DNA/RNA Mini Kit (QIAGEN) according to the manufacturer’s instructions.
RNA-seq libraries were constructed using ScriptSeq™ v2 RNA-Seq Library Preparation kit (Epicentre Biotechnologies) according to the manufacturer’s instructions.

treatment_protocol: The cardiomyocyte differentiation was initiated using a monolayer differentiation method with PSC Cardiomyocyte Differentiation kit (Thermo Fisher Scientific).

value: hESC-derived cells

tag: differentiation time (days)


title: H9_4_1_RNA-seq

description: biological replicate 1


title: H9_4_2_RNA-seq

description: biological replicate 2


title: H9_30_1_RNA-seq

description: biological replicate 1


title: H9_2_1_RNA-seq

description: biological replicate 1


title: Uninjured replicate 2


title: Uninjured replicate 4


title: H9_2_2_RNA-seq

description: biological replicate 2


title: Day 5 post injury replicate 2


title: H9_0_2_RNA-seq

description: biological replicate 2

source_name: hESC

value: hESC


title: FTS AG 2

status: Public on Aug 11 2017

description: single cell suspension lymphocytes that were cultured  with HSP65 antigen (5µg/ml) for 72 hrs

data_processing: RMA PARTEK. Background Correction: RMA Background Correction  Normalization: Quantile Normalization  Log Probes using Base: 2  Probeset Summarization: Median Polish

organism: Rattus norvegicus

source_name: FTS AG

growth_protocol: For drug therapy, we randomly divided the rats into three groups. Rats in the first group were treated daily (starting on day +1 after AIA induction) with oral FTS (100 mg/kg). Rats in the second group received  only the oral vehicle CMC control (0.5% carboxymethyl cellulose).At experiment end, the rats were sacrificed and their spleens were  harvested for further testing. Single cell suspensions of spleen were cultured with HSP65 (AG stimulation) or control media (Med group) for 72 hrs.

extract_protocol: Direct-zol™ RNA MiniPrep w/ TRI-Reagent kits (Zymo Research Corp.)

treatment_protocol: Eight-week-old Lewis rats have been injected at the base of the tail with 100 μl CFA prepared by suspending heat-killed M. tuberculosis (Difco) in mineral oil at 10 mg/ml. For determining the clinical outcomes, we measured starting day +9 the ankle diameter and score all paws on a scale of 0–4 for degree of swelling, redness, and deformity of the joints. For drug therapy, we randomly divided the rats into two groups. Rats in the first group we treated daily (starting on day +1 after AIA induction) with oral FTS (100 mg/kg). Rats in the second group of control Rats received only the oral vehicle CMC control (0.5% carboxymethyl cellulose).   At experiment end, the we sacrificed and their spleens have been harvested for in-vitro testing. Single cell suspensions of spleen has been cultured with HSP65 (AG stimulation) or control media (Med group) for 72 hrs. At culture termination, we harvested the cells and isolated the CD4+ T cell population using Rat CD4 MicroBeads and the MACS cell separation platform (Miltenyi Biotec, Germany), according to the manufacturer’s instructions.The purified CD4+ T cell were lysed with the TRIzol® Reagent (Invitrogen, Carlsbad, CA) and total RNA was purified using the Direct-zol™ RNA Kit (Zymo Research Corporation, Irvine, CA) for subsequent downstream analysis

value: Lewis

tag: agent

value: FTS

tag: tissue

value: spleen

value: single cell suspension lymphocytes

tag: treatment

value: cultured with HSP65 antigen for 72 hrs (AG stimulation)


title: FTS med 1

description: single cell suspension lymphocytes that were cultured without HSP65 antigen (5µg/ml) for 72 hrs

source_name: FTS med

value: cultured without HSP65 antigen for 72 hrs


title: 15min BrU-labeling; 30min uridine chase

description:
Nascent RNA
BrU-IP was done from 15min BrU-labeled—and—30min uridine chased total RNA.

extract_protocol:
Trizol
Libraries were prepared according to Illumina TruSeq Stranded totalRNA Library Preparation without Ribo-Minus.


title: FTS AG 1


title: FTS med 2


title: CMC AG 2

source_name: CMC AG

value: CMC


title: CMC AG 1


title: H9_0_1_RNA-seq

description: biological replicate 1


title: H1_30_1_RNA-seq

description: biological replicate 1


title: H1_4_2_RNA-seq

description: biological replicate 2


title: H1_30_2_RNA-seq

description: biological replicate 2


title: CMC med 2

source_name: CMC med


title: Uninjured replicate 1


title: H1_4_1_RNA-seq

description: biological replicate 1


title: H1_2_2_RNA-seq

description: biological replicate 2


title: H1_2_1_RNA-seq

description: biological replicate 1


title: H1_0_2_RNA-seq

description: biological replicate 2


title: H1_0_1_RNA-seq

description: biological replicate 1


title: C20_4_1_RNA-seq

description: biological replicate 1

source_name: hiPSC-derived cells

value: hiPSC-derived cells


title: C15_30_2_RNA-seq

description: biological replicate 2


title: C20_4_2_RNA-seq

description: biological replicate 2


title: C20_2_1_RNA-seq

description: biological replicate 1


title: C20_0_1_RNA-seq

description: biological replicate 1

source_name: hiPSC

value: hiPS cell


title: C20_0_2_RNA-seq

description: biological replicate 2


title: C20_30_2_RNA-seq

description: biological replicate 2


title: C15_4_1_RNA-seq

description: biological replicate 1


title: C20_2_2_RNA-seq

description: biological replicate 2


title: C20_30_1_RNA-seq

description: biological replicate 1


title: C15_4_2_RNA-seq

description: biological replicate 2


title: C15_30_1_RNA-seq

description: biological replicate 1


title: C15_0_2_RNA-seq

description: biological replicate 2


title: H9_30_2_ATAC-seq

description: biological replicate 2

data_processing:
Library strategy: ATAC-seq
The raw data was then trimmed to remove the adapter sequences (CTGTCTCTTATACACATCT) with in house script.  The trimmed files were mapped to the human genome (hg19 GRCh37) using Bowtie2 (2.1.0) with default parameters.  Read pairs, which aligned concordantly to the genome and had a mapping quality greater than 10, were kept for following analysis. Read pairs mapped to mitochondria DNA were discarded. Redundancy read pairs from PCR amplification were also removed afterward using Picard tools (version 1.79). The finally filtered bam files were converted into normalized BigWig files using Bedtools (2.25.0) for visualization of the peaks.
To estimate global enrichment of open accessible-regions of the ATAC-seq data, the ATAC-seq signal around 2KB of transcription start sties of RefGenes (UCSC hg19) was compared to an upstream 4KB window. The maximum enrichment sites were taken as the enrichment score for each library and used to represent the quality of ATAC-seq library.
Open accessible-regions for each library were defined by the peaks called by MACS2 (2.1.0) with the parameters “-g hs --nomodel --shift 0 –q 0.01”.  Peaks located at blacklist genomics regions were removed using bedtools (2.25.0).
Genome_build: hg19
Supplementary_files_format_and_content: bed file

extract_protocol:
About 50,000 cells were collected and pelleted by centrifugation for 15 min at 500 g and 4°C. Cell pellets were washed once with ice-cold 1x PBS and then pelleted again by centrifugation at the previous settings. Cell pellets were re-suspended in 25 μl of ice-cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630), and nuclei were pelleted by centrifugation for 30 min at 500g, 4°C
The nuclei were re-suspended in 50 μl reaction buffer (2 μl of Tn5 transposase and 12.5 μl of TD buffer from a Nextera DNA Library Prep Kit from Illumina, and 22.5 μl nuclease-free H2O). The reaction was incubated at 37°C for 30 min, and subsequently the reaction mixture was purified using MinElute PCR Purification Kit (Qiagen). The purified transposed DNA was amplified with NEBNext High-Fidelity 2 X PCR Master Mix (New England Biolabs) and custom-designed primers with barcodes (Buenrostro et al. 2013). Gel electrophoresis was used to remove primer dimers from the PCR products with 2% E-Gel EX Agarose Gels (Thermo Fisher Scientific), and then the PCR products were purified using QIAquick PCR Purification Kit (Qiagen). DNA concentration was measured with a Qubit Fluorometer (Thermo Fisher Scientific) and library sizes were determined using Agilent High Sensitivity DNA kit on Agilent 2100 Bioanalyzer. The ATAC-seq libraries were sequenced with a HiSeq 2000 sequencer (Illumina) with 2 X101 cycles.


title: H9_4_2_ATAC-seq

description: biological replicate 2


title: H9_30_1_ATAC-seq

description: biological replicate 1


title: H9_2_2_ATAC-seq

description: biological replicate 2


title: C15_2_2_RNA-seq

description: biological replicate 2


title: H9_2_1_ATAC-seq

description: biological replicate 1


title: H9_4_1_ATAC-seq

description: biological replicate 1


title: C15_2_1_RNA-seq

description: biological replicate 1


title: C15_0_1_RNA-seq

description: biological replicate 1


title: H9_0_1_ATAC-seq

description: biological replicate 1


title: H1_30_2_ATAC-seq

description: biological replicate 2


title: H1_30_1_ATAC-seq

description: biological replicate 1


title: H1_4_2_ATAC-seq

description: biological replicate 2


title: H1_4_1_ATAC-seq

description: biological replicate 1


title: H1_2_2_ATAC-seq

description: biological replicate 2


title: H1_0_1_ATAC-seq

description: biological replicate 1


title: C20_30_1_ATAC-seq

description: biological replicate 1


title: C20_4_2_ATAC-seq

description: biological replicate 2


title: C20_4_1_ATAC-seq

description: biological replicate 1


title: H1_2_1_ATAC-seq

description: biological replicate 1


title: C20_2_1_ATAC-seq

description: biological replicate 1


title: H9_0_2_ATAC-seq

description: biological replicate 2


title: CMC med 1


title: C20_0_2_ATAC-seq

description: biological replicate 2


title: C20_0_1_ATAC-seq

description: biological replicate 1


title: C20_30_2_ATAC-seq

description: biological replicate 2


title: C15_30_2_ATAC-seq

description: biological replicate 2


title: C20_2_2_ATAC-seq

description: biological replicate 2


title: C15_30_1_ATAC-seq

description: biological replicate 1


title: C15_4_2_ATAC-seq

description: biological replicate 2


title: C15_4_1_ATAC-seq

description: biological replicate 1


title: C15_0_2_ATAC-seq

description: biological replicate 2


title: C15_0_1_ATAC-seq

description: biological replicate 1


title: C15_2_2_ATAC-seq

description: biological replicate 2


title: C15_2_1_ATAC-seq

description: biological replicate 1


title: H1_0_2_ATAC-seq

description: biological replicate 2


title: VCaP R1881 24h 3

status: Public on Jun 06 2017

city: Oslo

first: Alfonso

last: Urbanucci

state: Oslo

address: Trondheimsveien 8

country: Norway

institute: Oslo University Hospital

hyb_protocol: Hybridisation of cRNA onto the Illumina HumanHT-12 v.4 Expression BeadChips (Illumina Inc, California, USA) was carried out as per manufacturer's instructions

scan_protocol: After scanning, the iScan software extracts signal intensities and saves all files for each BeadChip. Raw data is imported to Illumina’s GenomeStudio software V2011.1, Gene Expression module v. 1.9.0. Here the quality of each array and scan is investigated, and text files with both non-normalized and quantile normalized data exported.

data_processing: Data extraction, quantile normalization and initial quality control of the bead summary raw data were performed using GenomeStudio v2011.1 from Illumina and the Gene Expression module v1.9.0. The data were annotated using the HumanHT-12_V4_0_R2_15002873_B.bgx annotation file from Illumina.

source_name: VCaP

label_protocol: Labelling was performed with Illumina® TotalPrep™-96 RNA Amplification Kit according to manufacturer's instructions

growth_protocol: cells were maintained as recommended by the ATCC

extract_protocol: RNA was collected using the Rneasy kit (Qiagen) according to manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Cells were kept in phenol red-free medium +10% charcoal-stripped serum (CSS) for 72 h prior to treatment with 1nM R1881 or 1nM R1881+125nM JQ1

tag: time point


title: VCaP R1881+JQ1 24h 2


title: VCaP R1881 24h 1


title: VCaP R1881+JQ1 24h 1


title: VCaP R1881 24h 2


title: VCaP R1881+JQ1 24h 3


title: VCaP R1881+JQ1 12h 3


title: VCaP R1881+JQ1 12h 1


title: VCaP R1881 12h 3


title: VCaP R1881 5h 2


title: VCaP R1881+JQ1 5h 1


title: VCaP R1881 12h 1


title: VCaP R1881 5h 1


title: LNCaP R1881 12h 3

source_name: LNCaP


title: VCaP R1881+JQ1 5h 3


title: LNCaP R1881 12h 2


title: LNCaP R1881+JQ1 12h 1


title: LNCaP R1881 12h 1


title: VCaP R1881+JQ1 12h 2


title: LNCaP R1881+JQ1 24h 2


title: LNCaP R1881+JQ1 12h 3


title: VCaP R1881+JQ1 5h 2


title: LNCaP R1881 24h 3


title: LNCaP R1881+JQ1 24h 3


title: LNCaP R1881+JQ1 24h 1


title: VCaP R1881 12h 2


title: VCaP R1881 5h 3


title: LNCaP R1881 24h 1


title: LNCaP R1881 24h 2


title: LNCaP R1881+JQ1 12h 2


title: CRPC-530-input

data_processing:
The raw reads were aligned using novoalign (http://www.novocraft.com, V2.08.02) with default parameters on the human genome version 19 (hg19).
Filter to SAM quality 20 was applied and only a maximum of 5 duplicated reads were kept. The peak detection (i.e. Detection of open chromatin sites) was performed using MACS with default parameters using inputs samples as controls. Morever, Fseq was also used with ploidy information derived from input controls, and background correction. Peaks detected with MACS and Fseq (2 iterations) were then intersected. for cell-lines replicates were available and were also intersected to find a consensus map of open region upon the given conditions.
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing genomic regions of open chromatin

source_name: castrate resistant prostate cancer

growth_protocol: PC cells were maintained in media supplemented with 10% FBS. Tissue was frozen.

extract_protocol:
Lysates were clarified from sonicated nuclei and naked DNA was isolated with 3 subsequent Phenol:Chloroform:Isoamyl Alcohol extractions were performed, see study for more information.
Libraries were prepared according Illumina's instructions accompanying the TruSeq library preparation kit. Cell lines and tissue samples were sequenced separately.

treatment_protocol: Cells were kept in phenol red-free media +10% charcoal-stripped serum (CSS) for 72 h prior to treatment with 1nM R1881 for 4h. Tissues were snap forzen, 10 x 10um sections per sample was used.

value: prostate tissue


title: CRPC-542


title: LNCaP R1881+JQ1 5h 3


title: CRPC-542-input


title: CRPC-530


title: PCa-18307-input

source_name: primary prostate cancer


title: PCa-18307


title: PCa-19403-input


title: PCa-19403


title: LNCaP R1881 5h 2


title: BPH-688-input

source_name: benign prostate hyperplasia


title: LNCaP R1881 5h 1


title: LNCaP R1881+JQ1 5h 1


title: LNCaP R1881+JQ1 5h 2


title: LNCaP R1881 5h 3


title: BPH-677


title: VCaP_1nM_R1881_1_3d_input

description:
prostate cancer cell line
unique_peaks_VCaP_1nM_R1881_3d_sorted_merged.bed

value: VCaP


title: VCaP_1nM_R1881_2_3d_input


title: VCaP_1nM_R1881_2_3d


title: CRPC-278


title: BPH-677-input


title: BPH-659-input


title: BPH-659


title: VCaP_0M_1_3d_input

description:
prostate cancer cell line
unique_peaks_VCaP_0M_3d_sorted_merged.bed


title: VCaP_1nM_R1881_1_3d


title: VCaP_0M_2_3d_input


title: VCaP_0M_2_3d


title: LNCaP_1nM_R1881_2_3d

description:
prostate cancer cell line
unique_peaks_LNCaP_1nM_R1881_3d_sorted_merged.bed

value: LNCaP


title: VCaP_0M_1_3d


title: PCa-10286-input


title: LNCaP_1nM_R1881_2_3d_input


title: CRPC-278-input


title: BPH-688


title: LNCaP_1nM_R1881_1_3d_input


title: LNCaP_1nM_R1881_1_3d


title: LNCaP_0M_2_3d

description:
prostate cancer cell line
unique_peaks_LNCaP_0M_3d_sorted_merged.bed


title: LNCaP_0M_1_3d_input


title: LNCaP_0M_1_3d


title: LNCaP_0M_2_3d_input


title: human MONO from ARDS day 1 [Mn_B1_16]

status: Public on Apr 30 2017

description: Sample name: Mn_B1_16

hyb_protocol: MessageAmp II-96 Kit, Version C amplification Kit (Applied Biosciences, Foster City, CA)

source_name: Human peripheral blood monocyte

growth_protocol: Human BALF and peripheral blood were collected from ARDS patients.  AMs and peripheral blood monocytes were isolated by antibody-based negative selection via magnetic autoMacs columns (Miltenyi).  RNA was isolated and hybridized to the Illumina HumanRef-8 BeadChip v3.

extract_protocol: Total RNA was isolated by ABI Prism 6100 Nucleic Acid PrepStation (Applied Biosciences, Foster City, CA)

tag: patient identification number

value: ARDS patient number 16

tag: diagnosis

value: Acute Respiratory Distress Syndrome (ARDS)

value: blood

value: Human peripheral blood monocyte

tag: age

tag: gender

value: Female


title: human MONO from ARDS day 1 [Mn_B1_36]

description: Sample name: Mn_B1_36

value: ARDS patient number 36

value: Male


title: human MONO from ARDS day 1 [Mn_B1_23]

description: Sample name: Mn_B1_23

value: ARDS patient number 23


title: human MONO from ARDS day 1 [Mn_B1_33]

description: Sample name: Mn_B1_33

value: ARDS patient number 33


title: human MONO from ARDS day 1 [Mn_B1_49]

description: Sample name: Mn_B1_49

value: ARDS patient number 49


title: human MONO from ARDS day 1 [Mn_B1_38]

description: Sample name: Mn_B1_38

value: ARDS patient number 38


title: human MONO from ARDS day 1 [Mn_B1_40]

description: Sample name: Mn_B1_40

value: ARDS patient number 40


title: human MONO from ARDS day 1 [Mn_B1_24]

description: Sample name: Mn_B1_24

value: ARDS patient number 24


title: human MONO from ARDS day 1 [Mn_B1_29]

description: Sample name: Mn_B1_29

value: ARDS patient number 29


title: human MONO from ARDS day 1 [Mn_B1_25]

description: Sample name: Mn_B1_25

value: ARDS patient number 25


title: human MONO from ARDS day 1 [Mn_B1_19]

description: Sample name: Mn_B1_19

value: ARDS patient number 19


title: human MONO from ARDS day 1 [Mn_B1_34]

description: Sample name: Mn_B1_34

value: ARDS patient number 34


title: human MONO from ARDS day 1 [Mn_B1_28]

description: Sample name: Mn_B1_28

value: ARDS patient number 28


title: human MONO from ARDS day 1 [Mn_B1_9]

description: Sample name: Mn_B1_9

value: ARDS patient number 9

value: Acute Respiratory Distress Syndrome (ARDS)


title: human MONO from ARDS day 1 [Mn_B1_44]

description: Sample name: Mn_B1_44

value: ARDS patient number 44

value: blood

value: Human peripheral blood monocyte


title: human MONO from ARDS day 1 [Mn_B1_18]

description: Sample name: Mn_B1_18

value: ARDS patient number 18

value: Male


title: human MONO from ARDS day 1 [Mn_B1_47]

description: Sample name: Mn_B1_47

value: ARDS patient number 47


title: human MONO from ARDS day 1 [Mn_B1_11]

description: Sample name: Mn_B1_11

value: ARDS patient number 11

value: Female


title: human MONO from ARDS day 1 [Mn_B1_43]

description: Sample name: Mn_B1_43

value: ARDS patient number 43


title: human MONO from ARDS day 1 [Mn_B1_32]

description: Sample name: Mn_B1_32

value: ARDS patient number 32


title: human AM from ARDS day 1 [AM_B1_49]

description: Sample name: AM_B1_49

source_name: Human alveolar macrophage

value: ARDS patient number 49

value: bronchoalveolar lavage fluid (BALF)

value: Human alveolar macrophage


title: human MONO from ARDS day 1 [Mn_B1_46]

description: Sample name: Mn_B1_46

value: ARDS patient number 46


title: human AM from ARDS day 1 [AM_B1_9]

description: Sample name: AM_B1_9


title: human MONO from ARDS day 1 [Mn_B1_37]

description: Sample name: Mn_B1_37

value: ARDS patient number 37


title: human MONO from ARDS day 1 [Mn_B1_15]

description: Sample name: Mn_B1_15

value: ARDS patient number 15


title: human MONO from ARDS day 1 [Mn_B1_3]

description: Sample name: Mn_B1_3

value: ARDS patient number 3

value: Acute Respiratory Distress Syndrome (ARDS)


title: human MONO from ARDS day 1 [Mn_B1_42]

description: Sample name: Mn_B1_42

value: ARDS patient number 42

value: blood


title: human MONO from ARDS day 1 [Mn_B1_10]

description: Sample name: Mn_B1_10

value: ARDS patient number 10

value: Human peripheral blood monocyte


title: Input_R1881_Dox

status: Public on Apr 14 2017

data_processing:
The raw reads were aligned using novoalign (http://www.novocraft.com, V2.08.02) or bowtie (version 1.1.1) (for histone ChIPs) with default parameters on the human genome version 19 (hg19).
Filter to SAM quality 20 was applied and only a maximum of 5 duplicated reads were kept. The peak detection (i.e. binding site detection) was performed using MACS with default parameters using inputs samples as controls.
Genome_build: hg19
Supplementary_files_format_and_content: bwig files

source_name: LNCaP MYC cells

growth_protocol: LNCaP cells were maintained in RPMI media supplemented with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies, see study for more information.
Libraries were prepared according to published instructions for the ChIP-exo libraries (AR/MYC, see study for details) and Illumina's instructions accompanying the TruSeq library preparation kit for the histone ChIP-seqs.

treatment_protocol: Cells were kept in phenol red-free RPMI +10% charcoal-stripped serum (CSS) for 72 h prior to treatment with 1nM R1881 and/or 2 ug/mL Doxycycline (Dox) for 16h

tag: cell line

value: c-Myc overexpressing LNCaP

tag: antibody


title: H3K27ac_R1881_Dox

value: anti-H3K27ac, diagenode (pAb-196-050)


title: H3K27me3_R1881_Dox

value: anti-H3K27me3, diagenode (pAb-195-050)


title: H3K27me3_R1881


title: human AM from ARDS day 1 [AM_B1_46]

description: Sample name: AM_B1_46

value: Female


title: human AM from ARDS day 1 [AM_B1_44]

description: Sample name: AM_B1_44

value: ARDS patient number 44


title: human AM from ARDS day 1 [AM_B1_36]

description: Sample name: AM_B1_36

value: ARDS patient number 36

value: Male


title: human AM from ARDS day 1 [AM_B1_43]

description: Sample name: AM_B1_43

value: ARDS patient number 43

value: bronchoalveolar lavage fluid (BALF)

value: Human alveolar macrophage


title: human AM from ARDS day 1 [AM_B1_16]

description: Sample name: AM_B1_16

value: ARDS patient number 16


title: human AM from ARDS day 1 [AM_B1_11]

description: Sample name: AM_B1_11

value: ARDS patient number 11


title: human AM from ARDS day 1 [AM_B1_23]

description: Sample name: AM_B1_23

value: ARDS patient number 23

value: Acute Respiratory Distress Syndrome (ARDS)


title: human AM from ARDS day 1 [AM_B1_29]

description: Sample name: AM_B1_29

value: ARDS patient number 29


title: human AM from ARDS day 1 [AM_B1_42]

description: Sample name: AM_B1_42

value: ARDS patient number 42


title: human AM from ARDS day 1 [AM_B1_3]

description: Sample name: AM_B1_3

value: ARDS patient number 3


title: human AM from ARDS day 1 [AM_B1_33]

description: Sample name: AM_B1_33

value: ARDS patient number 33


title: human AM from ARDS day 1 [AM_B1_34]

description: Sample name: AM_B1_34

value: ARDS patient number 34


title: human AM from ARDS day 1 [AM_B1_40]

description: Sample name: AM_B1_40

value: ARDS patient number 40


title: human AM from ARDS day 1 [AM_B1_28]

description: Sample name: AM_B1_28

value: ARDS patient number 28


title: human AM from ARDS day 1 [AM_B1_47]

description: Sample name: AM_B1_47

value: ARDS patient number 47


title: Input_R1881

value: c-Myc overexpressing LNCaP


title: human AM from ARDS day 1 [AM_B1_10]

description: Sample name: AM_B1_10

value: ARDS patient number 10

value: Female


title: human AM from ARDS day 1 [AM_B1_18]

description: Sample name: AM_B1_18

value: ARDS patient number 18

value: bronchoalveolar lavage fluid (BALF)

value: Male


title: human AM from ARDS day 1 [AM_B1_24]

description: Sample name: AM_B1_24

value: ARDS patient number 24

value: Human alveolar macrophage


title: human AM from ARDS day 1 [AM_B1_32]

description: Sample name: AM_B1_32

value: ARDS patient number 32

value: Acute Respiratory Distress Syndrome (ARDS)


title: human AM from ARDS day 1 [AM_B1_37]

description: Sample name: AM_B1_37

value: ARDS patient number 37


title: human AM from ARDS day 1 [AM_B1_25]

description: Sample name: AM_B1_25

value: ARDS patient number 25


title: human AM from ARDS day 1 [AM_B1_38]

description: Sample name: AM_B1_38

value: ARDS patient number 38


title: human AM from ARDS day 1 [AM_B1_15]

description: Sample name: AM_B1_15

value: ARDS patient number 15


title: human AM from ARDS day 1 [AM_B1_19]

description: Sample name: AM_B1_19

value: ARDS patient number 19


title: H3K4me3_R1881_Dox

value: anti-H3K4me3, diagenode (C154100003)


title: H3K27ac_R1881

value: anti-H3K27ac, diagenode (pAb-196-050)


title: H3K4me1_R1881_Dox

value: c-Myc overexpressing LNCaP

value: anti-H3K4me1, diagenode (pAb-194-050)


title: PCa-10286

value: prostate tissue


title: H3K4me3_R1881


title: H3K4me1_R1881


title: Input_R1881_2


title: MYC_R1881_Dox_2

value: anti-MYC, RnD (AF3696)


title: MYC_R1881_2


title: MYC_R1881_1


title: AR_R1881_Dox_1

value: anti-AR, santa cruz (scbt-816X)


title: AR_R1881_1


title: Input_R1881_Dox_1


title: MYC_R1881_Dox_1


title: AR_R1881_Dox_2


title: AR_R1881_2


title: RWPE-1_ECI1_2

status: Public on Mar 03 2017

description: processed data file: 04_cuffdiff_RWPE_ECI1_vs_Scr.tar.gz

data_processing:
tophat (v2.0.10) with samtools (v0.1.18.0) and bowtie (v2.1.0.0) using default parameters was used to map reads to hg19. Cufflinks (v2.1.1) and CuffDiff (v2.2.1) to build transcriptome for each individual cell line considering biological replicates, and find differentially expressed genes of each siRNAs versus the respective scrumble siRNA.
both significantly and non significanttly differentially expressed genes are given in the processed files
Genome_build: hg19
Supplementary_files_format_and_content: folders containing multiple text files output from CuffDiff. gene_exp.diff files in each folder contains info on the differentially expressed genes.

growth_protocol: LNCaP cells were maintained in RPMI media supplemented with 10% FBS. RWPE-1 cells were maintained in Keratinocyte Serum Free Medium supplemented with bovine pituitary extract and human recombinant epidermal growth factor, according to ATCC recommendations

extract_protocol:
mRNA was collected with illustraMiniSpin kit (GE Healthcare) according to manufacturer's instructions.
Libraries were prepared according Illumina's instructions
multiplexed 6 samples per lane

treatment_protocol: Reverse transfections were performed with Lipofectamine® RNAiMAX Transfection Reagent according to manufacturer's recommendations. ECI2 targeting siRNAs were obtained from Qiagen (SI04202282 and SI04201848).

value: normal prostate epithelium cell line

tag: transfected with

value: siRNAs targeting ECI2


title: RWPE-1_ECI2_2

description: processed data file: 04_cuffdiff_RWPE_ECI2_vs_Scr.tar.gz


title: R1881_Dox_12h_2

source_name: LNCaP MYC

treatment_protocol: Cells were kept in phenol red-free RPMI +10% charcoal-stripped serum (CSS) for 72 h prior to treatment with vehicle, 1nM R1881 and/or 2 ug/mL Doxycycline (Dox)


title: RWPE-1_Scr_2

description: processed data file: 04_cuffdiff_RWPE_ECI1_vs_Scr.tar.gz; 04_cuffdiff_RWPE_ECI2_vs_Scr.tar.gz

value: scrambled siRNA


title: Dox 12h_3

value: Doxycycline


title: R1881_Dox_5h_1


title: R1881_12h_3


title: R1881_5h_3


title: Dox 12h_1


title: R1881_Dox_5h_2


title: EtOH 5h_3

value: EtOH


title: Dox 5h_3


title: R1881_12h_2


title: R1881_Dox_5h_3


title: Dox 5h_2


title: EtOH 12h_2


title: EtOH 5h_2


title: Dox 12h_2


title: EtOH 5h_1


title: RWPE-1_ECI2_1


title: EtOH 12h_3


title: R1881_5h_1


title: R1881_Dox_12h_3


title: R1881_Dox_12h_1


title: RWPE-1_ECI1_1


title: RWPE-1_Scr_1


title: R1881_12h_1


title: LNCaP_ECI2_2

description: processed data file: 04_cuffdiff_LNCaP_ECI2_vs_Scr.tar.gz

value: LNCaP

value: prostate cancer cell line


title: LNCaP_ECI1_2

description: processed data file: 04_cuffdiff_LNCaP_ECI1_vs_Scr.tar.gz


title: EtOH 12h_1


title: Dox 5h_1


title: R1881_5h_2


title: LNCaP_Scr_2

description: processed data file: 04_cuffdiff_LNCaP_ECI1_vs_Scr.tar.gz; 04_cuffdiff_LNCaP_ECI2_vs_Scr.tar.gz


title: LNCaP_ECI1_1


title: LNCaP_ECI2_1


title: LNCaP_Scr_1


title: wild type exposed to room air replicate 3

status: Public on Feb 18 2017

hyb_protocol: Ambion’s Illumina TotalPrep RNA Amplification kit

data_processing: Microarray data was assessed for quality, followed by background adjustment, variance stabilization and quantile normalization using the Bioconductor package lumi.

source_name: Whole lung homogenate

extract_protocol: Total RNA was isolated from mouse lung homogenates using Rneasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Age- and gender- matched C57BL/6 and Mmp28-/- (on a C57BL/6 background) mice were used for all experiments. At 7-9 weeks, mice were exposed to cigarette smoke from University of Kentucky 3R4F Reference Brand cigarettes using a JB-2082 cigarette smoke machine (CH Technologies). The smoke exposures were three hours in duration for five days per week at a concentration of 250 tpm/m3 for a total of 3 months. Controls were kept in the same facility and exposed to room air within a similar chamber.

tag: genotype

value: WT


title: wild type exposed to cigarette smoke replicate 2


title: knock out exposed to room air replicate 3

value: KO Mmp28-/-


title: knock out exposed to cigarette smoke replicate 4


title: wild type exposed to room air replicate 2


title: UMB cell line

status: Public on Feb 28 2017

description: Gene expression data from UMB cell line

hyb_protocol: Affymetrix wt scanning protocol  as described in http://media.affymetrix.com/support/downloads/manuals/3_IVT_PLUS_Reagent_Kit_User_Manual.pdf

data_processing: RMA

source_name: UMB cell line

growth_protocol: UMB cells were grown in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Invitrogen), 1% Penicillin–streptomycin 100M and 1% L‐glutamine (both from Biological Industries. Human bone marrow-derived MSCs were isolated and grown as previously described (Resnick et al, 2013). The cells demonstrated the typical expression of surface markers and differentiated into adipocytes and osteoblasts under appropriate culture conditions. T1 and T4-Xn RNA were derived directly from Xn tumor tissue.

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

treatment_protocol: UMB cells and MSCs grown in adherent culture were detached using trypsin, centrifuged, washed with PBS, centrifuged again and suspended in TRIzol reagent (Life Technologies). T1 and T4-Xn tissues were suspended in TRIzol reagent (Life Technologies).

value: human kidney


title: knock out exposed to cigarette smoke replicate 1


title: knock out exposed to cigarette smoke replicate 2


title: knock out exposed to room air replicate 2


title: wild type exposed to room air replicate 1


title: human MSCs

description: Gene expression data from human MSCs

source_name: primary human BM-derived MSCs

value: human bone-marrow


title: wild type exposed to cigarette smoke replicate 5


title: knock out exposed to room air replicate 1


title: wild type exposed to cigarette smoke replicate 3


title: AML Xn 4th generation

description: Gene expression data from 4th generation of human AML Xn

source_name: 4th generation of human AML Xn


title: AML Xn 1st generation

description: Gene expression data from 1st generation of human AML Xn

source_name: 1st generation of human AML Xn


title: knock out exposed to cigarette smoke replicate 5


title: wild type exposed to cigarette smoke replicate 1


title: wild type exposed to cigarette smoke replicate 4


title: knock out exposed to cigarette smoke replicate 3


title: S-035

status: Public on Jan 01 2017

description: SAMPLE 20

data_processing: The data were normalized using quantile normalization with GenPlex 3.0

source_name: Human Blood

extract_protocol: Blood samples for total RNA extraction were collected from patients at 48 hrs after CA and harvested in blood RNA tube (PAXgene, Qiagen BD Company, UK) for RNA isolation. Total RNA extracted from PAXgene™ tubes was used to study gene expression by microarrays.

tag: disease state

value: patient resuscitated after cardiac arrest

tag: neurological outcome (cerebral performance category)

value: peripheral blood


title: S-027

description: SAMPLE 14


title: S-036

description: SAMPLE 21


title: S-030

description: SAMPLE 17


title: S-028

description: SAMPLE 15


title: S-026

description: SAMPLE 13


title: S-032

description: SAMPLE 18


title: S-037

description: SAMPLE 22


title: S-029

description: SAMPLE 16


title: S-034

description: SAMPLE 19


title: PC-3 + rtTA2 + TTP-tdTom + Dox #2

status: Public on Nov 08 2016

description: infected with a pRetroX-Tet-On-Advanced retrovirus, then a second pRetroX-Tight-TTP-pPGK-tdTomato retrovirus

data_processing:
BASECALLING was performed by Illumina BaseSpace Sequence Hub
READ TRIMMING & CLEANUP were performed by Illumina BaseSpace Sequence Hub
Read alignment using TopHat v2.0.13
Abundance (Reads Per Kilobase of exon per Megabase of library size --RPKM) calculation using cufflinks v2.2.1
Differential expression calculation using cufflinks.
Genome_build: hs375d
Supplementary_files_format_and_content: cufflinks output

source_name: prostate cancer cells

growth_protocol: RPMI + 10% FBS, 1x glutamine, 1% penicillin/streptomycin at 37°C, 5% CO2

extract_protocol:
RNA was extracted from cells using the Macherey-Nagel NucleoSpin RNA kit (Ref # 740955).
RNA-Seq was performed using the NuGen Ovation Encore Complete kit.  Briefly, 100 ng of RNA was used to generate cDNA and a strand-specific library following the manufacturer’s protocol (NuGEN Technologies, Inc., San Carlos, CA).  ).  Quality control steps including analysis on the BioAnalyzer RNA chip and quantitative RT-PCR for library quantification were performed.  The libraries were then sequenced on the Illumina NextSeq 500 sequencer with a 75-base paired-end run in order to generate 40-50 million read pairs per sample.

treatment_protocol: 300 ng/ml doxycycline (Dox) for 4h prior to collection

value: prostate; derived from metastatic site:bone

value: epithelial

tag: disease

value: adenocarcinoma

tag: disease stage

value: grade IV


title: PC-3 + rtTA2 + TTP-tdTom + Dox #3

tag: cell type


title: PC-3 + rtTA2 + tdTom + Dox #1

description: infected with a pRetroX-Tet-On-Advanced retrovirus, then a second pRetroX-Tight-pPGK-tdTomato retrovirus


title: PC-3 + rtTA2 + tdTom + Dox #2


title: PC-3 + rtTA2 + TTP-tdTom + Dox #1


title: PC-3 + rtTA2 + tdTom + Dox #3


title: S-015

description: SAMPLE 8


title: S-022

description: SAMPLE 10


title: S-025

description: SAMPLE 12


title: S-013

description: SAMPLE 6


title: 3.5 ppm MeHg group compares to control S48_top

status: Public on Sep 27 2016

hyb_protocol: Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning.

scan_protocol: Arrays were scanned using an ScanArray Express (PerkinElmer) scanner.

data_processing: Raw data were extracted by Imagene version 6.0 software and analyzed by R version 2.9., Bioconductor 2.4, specifically limma 2.18.3. Graph 1.22.5 and Igraph 0.5.1 were used for network analysis which is visualized by Cytoscape 2.6.1.

organism: Danio rerio

source_name: 3.5ppm MeHg exposed zebrafish embryos

label_protocol: cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) Targets were labeled with Cy3 and Cy5 using the Array 50 Expression Array Detection kit (Genisphere)

growth_protocol: Fish were reared in 28℃ dechlorinated, filtered municipal water (DFMW) in the UWM MFB Sciences Center animal facility and fed Biodiet Starter (Bio-Oregon) 4% of body weight per day.

extract_protocol: Total RNA of pooled embryos (N=100) from Control, Low and High groups was isolated using Trizol reagent  (Invitrogen) and was further purified using the RNeasy MiniElute cleanup kit (Qiagen)

treatment_protocol: Female TL zebrafish were fed by wild-caught and lyophilized walleye fillets following Low and High MeHg (1 and 3.5 ppm), then bred with male GL fish which were fed normal food. Eggs were collect after 24 hpf.

tag: stage

value: 24 hpf

source_name: Control zebrafish embryos


title: 3.5 ppm MeHg group compares to control S48_bot


title: S-011

description: SAMPLE 4

tag: tissue


title: S-023

description: SAMPLE 11


title: S-008

description: SAMPLE 2


title: 3.5 ppm MeHg group compares to control S38_top


title: 1 ppm MeHg group compares to control S5_top

source_name: 1ppm MeHg exposed zebrafish embryos


title: 3.5 ppm MeHg group compares to control S38_bot


title: S-021

description: SAMPLE 9


title: 1 ppm MeHg group compares to control S5_bot


title: S-014

description: SAMPLE 7


title: S-012

description: SAMPLE 5


title: 1 ppm MeHg group compares to control S17_top


title: S-001

description: SAMPLE 1


title: S-010

description: SAMPLE 3


title: D305_HiL1_nonTBS

status: Public on Dec 31 2016

description: Gene expression data from SEGA originating from a patient with no Tuberous Sclerosis with high MEI (Hil1)

hyb_protocol: Affymetrix wt labeling protocol  as described in  https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

scan_protocol: Affymetrix wt scanning protocol  as described in  https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

data_processing: RMA (PARTEK)

source_name: subependymal giant cell astrocytomas (SEGAs)

tag: individual

value: Patient with no Tuberous Sclerosis

value: SEGA with high MEI (Hil1)


title: 1 ppm MeHg group compares to control S17_bot


title: D303_LoL1

description: Gene expression data from  Tuberous Sclerosis patient SEGA with normal MEI number (LoL1)

value: Tuberous Sclerosis patient

value: SEGA with normal MEI number (LoL1)


title: D304_HiL1

description: Gene expression data from  Tuberous Sclerosis patient SEGA with high MEI (Hil1)


title: D302_HiL1


title: Long Sleep MZ Twin 6

status: Public on Sep 09 2016

data_processing: Microarray data was assessed for quality, followed by quantile normalization using the Bioconductor package lumi. The dataset was initially filtered by flagging probes that fell below a low-signal threshold, which was defined by the 75th percentile of the negative control probe signals within each array. The full dataset was subsequently processed using a variance filter (i.e., “shorth” function in the Bioconductor package genefilter).  Approximately 10,000 transcripts passed the above filtering steps and underwent further analysis.

source_name: Long Sleep MZ Twin 6, PBL

label_protocol: Illumina

extract_protocol: Total RNA was isolated from PBLs using Paxgene Blood RNA kit (Qiagen, Valencia, CA)

tag: twin pair

tag: sleep duration

value: long

value: peripheral blood leukocytes (PBL)


title: Short Sleep MZ Twin 5

source_name: Short Sleep MZ Twin 5, PBL

value: short


title: Long Sleep MZ Twin 8

source_name: Long Sleep MZ Twin 8, PBL


title: Short Sleep MZ Twin 7

source_name: Short Sleep MZ Twin 7, PBL


title: Long Sleep MZ Twin 10

source_name: Long Sleep MZ Twin 10, PBL


title: Long Sleep MZ Twin 4

source_name: Long Sleep MZ Twin 4, PBL


title: Short Sleep MZ Twin 8

source_name: Short Sleep MZ Twin 8, PBL


title: Long Sleep MZ Twin 11

source_name: Long Sleep MZ Twin 11, PBL


title: Long Sleep MZ Twin 3

source_name: Long Sleep MZ Twin 3, PBL


title: Short Sleep MZ Twin 2

source_name: Short Sleep MZ Twin 2, PBL


title: Short Sleep MZ Twin 6

source_name: Short Sleep MZ Twin 6, PBL


title: Long Sleep MZ Twin 9

source_name: Long Sleep MZ Twin 9, PBL


title: Short Sleep MZ Twin 9

source_name: Short Sleep MZ Twin 9, PBL


title: Short Sleep MZ Twin 11

source_name: Short Sleep MZ Twin 11, PBL


title: Short Sleep MZ Twin 10

source_name: Short Sleep MZ Twin 10, PBL


title: Short Sleep MZ Twin 4

source_name: Short Sleep MZ Twin 4, PBL


title: Long Sleep MZ Twin 5

source_name: Long Sleep MZ Twin 5, PBL


title: Long Sleep MZ Twin 2

source_name: Long Sleep MZ Twin 2, PBL


title: Long Sleep MZ Twin 7

source_name: Long Sleep MZ Twin 7, PBL


title: Short Sleep MZ Twin 3

source_name: Short Sleep MZ Twin 3, PBL


title: Short Sleep MZ Twin 1

source_name: Short Sleep MZ Twin 1, PBL


title: Long Sleep MZ Twin 1

source_name: Long Sleep MZ Twin 1, PBL


title: knockout treated with rhPTX-2 replicate 4

status: Public on Aug 11 2016

description: KO+PTX2 REP 4

data_processing: Microarray data was assessed for quality, followed by variance stabilization and quantile normalization using the Bioconductor package lumi. Mouse and human microarrays were analyzed separately.

source_name: knockout treated with rhPTX-2, whole kidney homogenate

growth_protocol: Human adult PTECs and fetal epithelial cells were isolated from discarded human kidneys that were digested using a collagenase-based method as previously described and purified by MACS column (Miltenyi) affinity for anti-Epcam antibodies and LTL attached to magnetic beads. Confluent monolayers were studied and passaged up to 4 times, from at least 3 separate donors.

extract_protocol: Total RNA was isolated from mouse kidney homogenates or human PTECs using Rneasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: 1. Mice received rhPTX-2 (10 mg/kg) or vehicle (10 mM sodium phosphate, 5% (w/v) sorbitol, 0.01% (w/v) polysorbate 20, pH 7.5) by intraperitoneal injection from 24d (3.5wk) after birth at the first three days daily and then 2/wk and ending at 9 weeks at which time they were killed and kidneys harvested. 2. Primary PTECs, pre-treated 1hr with 25 μg/mL rhPTX-2 or human IgG (Jackson ImmunoResearch) then challenged with 10% human plasma (Sigma-Aldrich) for 16 hours.

tag: genotype/variation

tag: treatment

value: whole kidney


title: knockout treated with rhPTX-2 replicate 2

description: KO+PTX2 REP 2


title: knockout treated with vehicle replicate 5

description: KO+VEH REP 5

source_name: knockout treated with vehicle, whole kidney homogenate

value: vehicle


title: knockout treated with rhPTX-2 replicate 1

description: KO+PTX2 REP 1


title: knockout treated with vehicle replicate 3

description: KO+VEH REP 3


title: knockout treated with rhPTX-2 replicate 3

description: KO+PTX2 REP 3


title: knockout treated with vehicle replicate 4

description: KO+VEH REP 4


title: knockout treated with vehicle replicate 2

description: KO+VEH REP 2


title: human proximal tubule epithelial cells exposed to human plasma, replicate 2

description: PLASMA(+) PTX2(-) REP2

source_name: exposed to human plasma, proximal kidney tubule epithelial cells

value: proximal kidney tubule epithelial cells (primary cell culture)

value: exposed to human plasma


title: human proximal tubule epithelial cells, no treatment, replicate 3

description: PLASMA(-) PTX2(-) REP3

source_name: no treatment, proximal kidney tubule epithelial cells

value: no treatment


title: human proximal tubule epithelial cells, treated with PTX2 then exposed to plasma, replicate 1

description: PLASMA(+) PTX2(+) REP1

source_name: treated with PTX2 then exposed to plasma, proximal kidney tubule epithelial cells


title: human proximal tubule epithelial cells, no treatment, replicate 1

description: PLASMA(-) PTX2(-) REP1


title: human proximal tubule epithelial cells exposed to human plasma, replicate 1

description: PLASMA(+) PTX2(-) REP1


title: wild type treated with vehicle replicate 2

description: WT+VEH REP 2

source_name: wild type treated with vehicle, whole kidney homogenate


title: human proximal tubule epithelial cells, treated with PTX2 then exposed to plasma, replicate 3

description: PLASMA(+) PTX2(+) REP3


title: human proximal tubule epithelial cells, no treatment, replicate 2

description: PLASMA(-) PTX2(-) REP2


title: human proximal tubule epithelial cells, treated with PTX2 then exposed to plasma, replicate 2

description: PLASMA(+) PTX2(+) REP2


title: human proximal tubule epithelial cells exposed to human plasma, replicate 3

description: PLASMA(+) PTX2(-) REP3


title: knockout treated with vehicle replicate 1

description: KO+VEH REP 1


title: P#321_Sarcoid

status: Public on Jul 22 2016

hyb_protocol: Affymetrix standard protocol

scan_protocol: GeneChip Operating System (GCOS)

data_processing: RMA algorithm with quantile normalization and background correction

source_name: BAL cells, Sarcoid

label_protocol: Affymetrix standard protocol

extract_protocol: RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: BAL cells were isolated from BAL fluid by centrifugation at 1,000 g for 10 minutes at 4°C. BAL cells were washed with hanks balanced salt solution, resuspended and counted with a hemocytometer. Mean viability of lavage cells was > 95% as determined by trypan blue dye exclusion.

value: Sarcoidosis Patient

value: BAL cells


title: P#346_Sarcoid


title: wild type treated with vehicle replicate 1

description: WT+VEH REP 1


title: P#159_Sarcoid


title: P#176_Sarcoid


title: P#3_Sarcoid


title: P#318_Sarcoid


title: P#232_Normal

source_name: BAL cells, Normal

value: Normal Control Subject


title: P#212_Sarcoid


title: P#238_Sarcoid


title: P#397_Sarcoid


title: P#390_Sarcoid


title: P#316_Sarcoid


title: P#217_Sarcoid


title: P#180_Normal


title: P#96_Sarcoid


title: P#129_Sarcoid


title: wild type treated with vehicle replicate 3

description: WT+VEH REP 3


title: P#197_Normal


title: P#198_Normal


title: P#193_Normal


title: P#179_Normal


title: P#188_Normal


title: P#163_Normal


title: P#187_Normal


title: P#150_Normal


title: SK-24h

status: Public on Jul 20 2016

description: 24h after JQ1 treatment

data_processing: The data were normalized using quantile normalization with GenPlex 3.0, and selected all Pcall on all arrays (P call = Detection P value < 0.1)

source_name: human liver cell line

growth_protocol: The human HCC cell line SK-Hep-1 were obtained from KCLB (Korean Cell Line Bank, Seoul, South Korea) and cell line was maintained in DMEM medium (Lonza, Walkersville, MD) supplemented with 10% fetal bovine serum (Sigma, St. Louis, MO) and 100 units/ ml of penicillin–streptomycin (Invitrogen, Carlsbad, CA). All cells were cultured at 37 °C in a humidiﬁed incubator with 5% CO2.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment and Quality control experiment performed

treatment_protocol: After treatment JQ1, cells were harvested for RNA at each time point.

tag: time point

tag: agent


title: SK-9h

description: 9h after JQ1 treatment

tag: cell line


title: SK-6h

description: 6h after JQ1 treatment


title: SK-48h

description: 48h after JQ1 treatment


title: SK-3h

description: 3h after JQ1 treatment


title: 252038210341_1_3

status: Public on Apr 05 2016

city: Napoli

first: Mario

last: Capasso

address: Via Gaetano Salvatore, 486

department: Dept. of  Molecular Medicine and Medical Biotechnology

country: Italy

institute: University of Napoli "Federico II" - CEINGE Biotecnologie Avanzate Scarl

hyb_protocol: Cy3-labeled cRNA was hybridized on the 4x44K arrays using Agilent’s High-RPM Gene Expression Hyb Kit. Hybridization was performed for 17 h at 65°C in a rotating hyb oven at 10 rpm.

scan_protocol: Images were acquired using the scanner: Agilent Technologies G5761A SG14245029. TIFF-images were processed using Agilent’s Feature Extraction software Version 11.5.1.1.

data_processing: Raw data were normalized using the quantile algorithm from limma.

source_name: snap-frozen neuroblastoma tissue

label_protocol: tumor RNA was linearily amplified and labeled with Cy3 using Agilent’s one-color Quick Amp Labeling Kit.

extract_protocol: After homogenization of tumor tissue by using the FastPrep FP120 cell disruptor (Qbiogene, Carlsbad, CA, USA) total RNA was isolated using the TRIzol reagent (Invitrogen, Karlsruhe, Germany). Integrity of the isolated RNA was assessed using the 2100 Bioanalyzer (Agilent Technologies) and only samples with an RNA integrity number of at least 7.5 were considered for further processing.

tag: tumor type

value: Neuroblastoma

tag: chemotherapy

value: No

tag: tumor stage (inss)

value: stage 4


title: P#393_Normal


title: 252038210344_1_4


title: 252038210334_1_4


title: 252038210334_1_2


title: SK-0h-1

description: 0h after JQ1 treatment


title: SK-14h

description: 14h after JQ1 treatment


title: 252038210343_1_1


title: 252038210338_1_3


title: P#192_Normal


title: SK-0h-0

description: 0h after JQ1 treatment


title: 252038210326_1_4


title: 252038210334_1_3


title: 252038210338_1_2


title: 252038210334_1_1


title: 252038210335_1_2


title: 252038210338_1_1


title: 252038210326_1_3


title: 252038210324_1_4


title: 252038210295_1_2


title: 252038210295_1_3


title: 252038210290_1_3


title: 252038210297_1_2


title: 252038210290_1_4


title: 252038210291_1_3


title: 252038210290_1_2


title: 252038210282_1_2


title: 252038210295_1_1


title: 252038210291_1_2


title: 252038210289_1_4


title: 252038210290_1_1


title: 252038210291_1_1


title: HIVpos_NL EX0056

status: Public on Apr 01 2016

hyb_protocol: Hybridized to Affymetrix PrimeView Human Gene Expression arrays using the Affymetrix standard protocol.

scan_protocol: GeneChip Operating System (GCOS).

data_processing: RMA algorithm with quantile normalization and background correction (RMAExpress).

source_name: Peripheral blood leukocytes, HIV+, preserved DLCO

label_protocol: Affymetrix standard protocol.

extract_protocol: Total RNA was isolated from PBLs using PAXgene Blood RNA kit (Qiagen, Valencia, CA).

value: peripheral blood leukocytes

tag: gender

value: male

tag: smoker status

value: current

tag: disease status

value: HIV-positive

tag: dlco

value: normal


title: HIVpos_NL EX0081

tag: cell type


title: HIVpos_NL EX0322


title: HIVpos_LO EX0150

source_name: Peripheral blood leukocytes, HIV+, low DLCO

value: low


title: HIVneg_NL EX0229

source_name: Peripheral blood leukocytes, HIV-, preserved DLCO

value: HIV-negative


title: HIVneg_NL EX0113


title: HIVpos_NL EX0066


title: HIVpos_NL EX0305


title: HIVneg_NL EX0232


title: HIVneg_NL EX0036


title: HIVpos_LO EX0116


title: HIVneg_NL EX0213


title: HIVneg_NL EX0145


title: HIVpos_LO EX0115


title: HIVpos_NL EX0201


title: P#239_Sarcoid


title: HIVneg_NL EX0032


title: HIVneg_NL EX0358


title: HIVpos_LO EX0148


title: HIVpos_LO EX0044


title: HIVpos_LO EX0164


title: HIVpos_LO EX0122


title: HIVpos_LO EX0064


title: HIVpos_NL EX0297


title: HIVpos_LO EX0123


title: HIVpos_NL EX0089


title: HIVneg_NL EX0327


title: HIVneg_LO EX0155

source_name: Peripheral blood leukocytes, HIV-, low DLCO


title: HIVpos_LO EX0050


title: HIVpos_NL EX0249


title: HIVneg_LO EX0182


title: HIVneg_LO EX0171


title: HIVneg_LO EX0080


title: HIVneg_LO EX0085


title: HIVneg_LO EX0219


title: HIVneg_LO EX0129


title: HIVneg_LO EX0031


title: HIVneg_LO EX0053


title: HIVneg_LO EX0197


title: D107_2144_11

status: Public on Dec 31 2015

description: microRNA expression data

hyb_protocol: FlashTag™ Biotin HSR RNA Labeling Kit  (Affymetrix) http://media.affymetrix.com/support/downloads/manuals/flashtag_user_guide.pdf

data_processing: RMA quantile normalization

source_name: FFPE Human melanoma

growth_protocol: Melanoma samples were derived from metastatic melanoma patients  treated with ipilimumab.

extract_protocol: Total RNA was isolated using miRNeasy FFPE kit (Qiagen)  according to the manufacture guidelines.

treatment_protocol: Samples were prepared as Formalin fixed paraffin embedded (FFPE) tissues and stained with hematoxilin and eosin. Non-tumor tissue was removed.

tag: tissue

value: tumor


title: D108_20330_10

description: microRNA expression data

scan_protocol: FlashTag™ Biotin HSR RNA Labeling Kit  (Affymetrix) http://media.affymetrix.com/support/downloads/manuals/flashtag_user_guide.pdf


title: D111_12819

description: microRNA expression data

label_protocol: FlashTag™ Biotin HSR RNA Labeling Kit  (Affymetrix) http://media.affymetrix.com/support/downloads/manuals/flashtag_user_guide.pdf


title: D112_17968

description: microRNA expression data


title: HIVneg_LO EX0026


title: Monocyte extracted from adult (wk6-12) Bone Marrow, biological replicate 4

status: Public on Mar 01 2016

description: Monocyte extracted from Bone Marrow

hyb_protocol: Standard Affymetrix protocol. cDNA was hybrised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays (GPL6246).

data_processing:
Data were processed using Bioconductor. Normalisation was done by RMA.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: Monocyte, extracted from Bone Marrow (BM)

label_protocol: Affymetrix WT Terminal Labeling Kit

growth_protocol: Tissues were isolated from the mice at the indicated ages.

extract_protocol: Single cell suspensions were prepared by organ digestion (yolk sac and fetal liver) with 1 mg/ml collagenase A and 10 U/ml DNA (30 and 5 minutes at 37oC), crushing (bones) or flushing of the lungs (broncholaveolar lavage). 2x104 cells were FACS purified into RLT buffer (Qiagen) containing 10 ml/ml 2-mercaptoethanol. RNA was isolated using the RNA isolation kit micro (Qiagen no74034).

treatment_protocol: not applicable

tag: strain

value: Bone Marrow

tag: age