title: TIF32 (36 C)

description:
DY178F
TIF32 (36 C)
Ribosome-protected RNA 25-34 nt

data_processing:
Library strategy: Ribo-seq
Base calling and demultiplexing were performed at the NHLBI DNA Sequencing and Genomics Core at the NIH Intramural program, Bethesda, MD.
Files were demultiplexed and filtered to remove low-quality reads. They were then trimmed to the start of the linker sequence. Contaminating sequences that corresponded to gel markers were eliminated.
Reads were aligned to a library of RNA genes and those not matching were retained. PCR duplicates were removed using UMIs added during linker ligation. UMIs were then trimmed.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009). For footprints, reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

extract_protocol:
Ribosome profiling lysates were clarified, RNase treated, and run over sucrose gradients to extract the monosome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos in some cases. In others, Ribo-Zero was used. RNA-Seq samples were prepared with the Illumina TruSeq Stranded ribo-zero kit.


title: PB6 Mock

status: Public on May 29 2019

type: RNA

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

description: Untreated

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Genome Studio (Illumina) was used to subtract background from raw gene expression intensity data. Standard normalization procedures for 1-color array data and data analysis to identify differentially expressed genes were performed using the GeneSpring GX software, version 12.5 (Agilent Technologies). Significantly regulated genes (p<0.05 with a cutoff of 1.5-fold change in treated compared to untreated samples) were analyzed with IPA and GSEA.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Untreated

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: Total RNA isolated with Trizol following manufacturer's recommendations

treatment_protocol: Human PBMCs isolated from healthy donors (10^7 per condition) were treated for 48 hours with the indicated flaviviruses or adjuvants

tag: cell type

value: PBMC

tag: donor

value: donor 2

tag: treatment

value: Untreated


title: PB6 D2 16681

description: Flavivirus

source_name: pathogenic DENV-2 16681, MOI=1

value: pathogenic DENV-2 16681, 10^6 PFUs


title: hcr1∆ sc HCR1_rep1

status: Public on May 23 2019

type: SRA

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

country: USA

institute: National Institutes of Health

description:
DY174F
hcr1∆ sc HCR1
Ribosome-protected RNA 25-34 nt
Biological replicate of DY175F.
Wig files composed of combination of two biological replicates (DY174F and DY175F):
processed data file: DY174F175F_plus.wig
processed data file: DY174F175F_minus.wig

library_source: transcriptomic

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD of ~0.6 and harvested.

treatment_protocol: Cells were rapidly vacuum filtered and flash frozen. Ribosome profiling samples were lysed in a freezer mill with lysis buffer. Total RNA for mRNA-Seq was extracted from whole cells.

tag: strain

value: hcr1<delta> sc HCR1


title: hcr1∆ sc hcr1-NTA1_rep1

description:
DY176F
hcr1∆ sc hcr1-NTA1
Ribosome-protected RNA 25-34 nt
Biological replicate of DY177F.
Wig files composed of combination of two biological replicates (DY176F and DY177F):
processed data file: DY176F177F_plus.wig
processed data file: DY176F177F_minus.wig

value: hcr1<delta> sc hcr1-NTA1


title: hcr1∆ sc HCR1_rep2

description:
DY175F
hcr1∆ sc HCR1
Ribosome-protected RNA 25-34 nt
Biological replicate of DY174F.
Wig files composed of combination of two biological replicates (DY174F and DY175F):
processed data file: DY174F175F_plus.wig
processed data file: DY174F175F_minus.wig


title: hcr1∆ sc hcr1-NTA1_rep2

description:
DY177F
hcr1∆ sc hcr1-NTA1
Ribosome-protected RNA 25-34 nt
Biological replicate of DY176F.
Wig files composed of combination of two biological replicates (DY176F and DY177F):
processed data file: DY176F177F_plus.wig
processed data file: DY176F177F_minus.wig


title: hcr1∆ YCplac33

description:
DY179F
hcr1∆ YCplac33
Ribosome-protected RNA 25-34 nt

value: hcr1<delta> YCplac33


title: tif32-R731I (36 C)_rep2

description:
DY173F
tif32-R731I (36 C)
Ribosome-protected RNA 25-34 nt
Biological replicate of DY172F.
Wig files composed of combination of two biological replicates (DY172F and DY173F):
processed data file: DY172F173F_plus.wig
processed data file: DY172F173F_minus.wig


title: tif32-H725P (36 C)_rep2

description:
DY171F
tif32-H725P (36 C)
Ribosome-protected RNA 25-34 nt
Biological replicate of DY170F.
Wig files composed of combination of two biological replicates (DY170F and DY171F):
processed data file: DY170F171F_plus.wig
processed data file: DY170F171F_minus.wig


title: tif32-R731I (36 C)_rep1

description:
DY172F
tif32-R731I (36 C)
Ribosome-protected RNA 25-34 nt
Biological replicate of DY173F.
Wig files composed of combination of two biological replicates (DY172F and DY173F):
processed data file: DY172F173F_plus.wig
processed data file: DY172F173F_minus.wig


title: PB7 R848

description: TLR7/8 agonist

value: donor 3

value: TLR7/8 agonist


title: PB6 ODN 2006

description: TLR9 agonist

source_name: 5µg/ml ODN2006

value: TLR9 agonist


title: 231_i27w_2

status: Public on May 11 2019

city: St. Louis

first: Dennis

last: Zhu

state: MO

address: 4905 Children’s Place

department: Molecular Microbiology

institute: Washington University

description: rRNA-depleted mRNA

data_processing:
RNA is sequenced using Illumina HiSeq 2500; then basecalls are made using Illumina Casava 1.8 software
Single-end reads were pseudoaligned to the Mtb H37Rv genome and quantified using kallisto with the following parameters --single -l 50 -s 5 -b 100
Genome_build: GenBank assembly GCA_000195955.2
Supplementary_files_format_and_content: tab-delimited processed files show count and tpm (transcripts per million) normalized data for each Mtb transcript

organism: Mycobacterium tuberculosis

source_name: 30mL bacteria culture

growth_protocol: All M. tuberculosis strains were grown at 37° C in Sauton's Broth media (0.5 g L-1 KH2PO4, 0.5 g L-1 MgSO4, 4g L-1 L-asparagine, 60 mL glycerol, 0.05 g L-1 ferric ammonium citrate, 2.0 g L-1 citric acid, 0.1 ml L-1 1% ZnSO4, 0.05% Tween 80, pH 7.0)

extract_protocol:
RNA was prepared from 30mL of log-phase M. tuberculosis using Trizol reagent after bead beating to lyse cells.
RNA was DnaseI treated using the TURBO DNA-free kit from Thermo-Fisher. Ribo-zero was used to deplete ribosomal RNA. Then the RNA library was prepared using standard Illumina protocols.

value: Erdman

tag: genotype

value: CardD i27w


title: Mouse1-Channel8

status: Public on May 02 2019

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

library_source: genomic

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts implemented in the bap-barcode module.
Paired-end reads were aligned to mm10 using bwa.
Duplicate reads and all downstream processing was performed using the bead-based scATAC-seq processing (bap) tool.
NA
Genome_build: mm10
Supplementary_files_format_and_content: Decomposed counts matrix. CountsData is indexed by peak (row), cell (column), and count where the Bed file and CellData provide annotations for rows and columns. Barcode translate file maps raw sequence barcode (many) to cell barcode (one) from the bap output. The BarcodeLogic Excel file contains the information needed to parse the cell barcode from the sequencing data.

molecule: genomic DNA

organism: Mus musculus

source_name: Whole adult mouse brain

growth_protocol: Flash frozen adult mouse whole brain tissue was purchased from BrainBits (SKU: C57AWB)

extract_protocol:
Nuclei isolation was performed using the Omni-ATAC protocol for isolation of nuclei from frozen tissues. Nuclei were resuspended in Whole Cell Tagmentation Mix containing 0.1% Tween-20, 0.01% Digitonin, 1X PBS supplemented with 0.1% BSA, ATAC Tagmentation Buffer and ATAC Tagmentation Enzyme (parts of the SureCell ATAC-Seq Library Prep Kit - 17004620, Bio-Rad). Cells were mixed and agitated on a ThermoMixer for 30 min at 37°C. Tagmented cells were kept on ice prior to encapsulation.
Tagmented nuclei were loaded onto a ddSEQ Single-Cell Isolator (12004336, Bio-Rad). Single-cell ATAC-Seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ddSEQ Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing was performed in a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module (1851197, Bio-Rad): 37°C for 30 min, 85°C for 10 min, 72°C for 5 min, 98°C for 30 sec, 8 cycles of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. Emulsions were broken and products cleaned up using Ampure XP beads (A63880, Beckman Coulter). Barcoded ATAC amplicons were further amplified using a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 98°C for 30 sec, 6-9 cycles (cycle number depending on the cell input, Section 4 Table 3 of the User Guide) of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer (G2939BA, Agilent) using the High-Sensitivity DNA kit (5067-4626, Agilent). Libraries were loaded at 1.5 pM on a NextSeq 550 (SY-415-1002, Illumina) using the NextSeq High Output Kit (150 cycles; 20024907, Illumina) and sequencing was performed using the following read protocol: Read 1 118 cycles, i7 index read 8 cycles, and Read 2 40 cycles. A custom sequencing primer is required for Read 1 (16005986, Bio-Rad; included in the kit).

tag: mouse id

tag: celltype

value: Whole adult mouse brain

tag: bead concentration


title: Mouse2-Channel4

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts implemented in the bap-barcode module.
Paired-end reads were aligned to mm10 using bwa.
Duplicate reads and all downstream processing was performed using the bead-based scATAC-seq processing (bap) tool.
Genome_build: mm10
Supplementary_files_format_and_content: Decomposed counts matrix. CountsData is indexed by peak (row), cell (column), and count where the Bed file and CellData provide annotations for rows and columns. Barcode translate file maps raw sequence barcode (many) to cell barcode (one) from the bap output. The BarcodeLogic Excel file contains the information needed to parse the cell barcode from the sequencing data.
Supplementary_files_format_and_content: mousebrain_BarcodeLogic.xlsx: BeadStructure

tag: tissue

value: whole brain


title: Mouse2-Channel1


title: Mouse1-Channel4


title: Mouse1-Channel5


title: Mouse2-Channel2


title: Mouse1-Channel6


title: Mouse1-Channel3


title: tif32-H725P (36 C)_rep1

description:
DY170F
tif32-H725P (36 C)
Ribosome-protected RNA 25-34 nt
Biological replicate of DY171F.
Wig files composed of combination of two biological replicates (DY170F and DY171F):
processed data file: DY170F171F_plus.wig
processed data file: DY170F171F_minus.wig


title: Mouse2-Channel3


title: Mouse1-Channel1


title: HumanBoneMarrow-ht-sciATAC-seq-Channel13

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts implemented in the bap-barcode module.
Paired-end reads were aligned to hg19 using bwa.
Duplicate reads and all downstream processing was performed using the bead-based scATAC-seq processing (bap) tool.
Genome_build: hg19
Supplementary_files_format_and_content: Decomposed counts matrix. CountsData is indexed by peak (row), cell (column), and count where the Bed file and CellData provide annotations for rows and columns. Barcode translate file maps raw sequence barcode (many) to cell barcode (one) from the bap output. The BarcodeLogic Excel file contains the information needed to parse the cell barcode from the sequencing data. The Tn5 table provides a key for the biological condition encoded by the Tn5 barcode

source_name: Human bone marrow mononuclear cells

growth_protocol: Cryopreserved human bone marrow mononuclear cells were purchased from Allcells.

extract_protocol:
Lysis was performed simultaneously with tagmentation. Washed and pelleted cells were resuspended in Whole Cell Tagmentation Mix containing 0.1% Tween-20, 0.01% Digitonin, 1X PBS supplemented with 0.1% BSA, ATAC Tagmentation Buffer and ATAC Tagmentation Enzyme (parts of the SureCell ATAC-Seq Library Prep Kit - 17004620, Bio-Rad). Cells were mixed and agitated on a ThermoMixer for 30 min at 37°C. Tagmented cells were kept on ice prior to encapsulation.
Tagmented cells were loaded onto a ddSEQ Single-Cell Isolator (12004336, Bio-Rad). Single-cell ATAC-Seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ddSEQ Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing was performed in a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module (1851197, Bio-Rad): 37°C for 30 min, 85°C for 10 min, 72°C for 5 min, 98°C for 30 sec, 8 cycles of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. Emulsions were broken and products cleaned up using Ampure XP beads (A63880, Beckman Coulter). Barcoded ATAC amplicons were further amplified using a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 98°C for 30 sec, 6-9 cycles (cycle number depending on the cell input, Section 4 Table 3 of the User Guide) of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer (G2939BA, Agilent) using the High-Sensitivity DNA kit (5067-4626, Agilent). Libraries were loaded at 1.5 pM on a NextSeq 550 (SY-415-1002, Illumina) using the NextSeq High Output Kit (150 cycles; 20024907, Illumina) and sequencing was performed using the following read protocol: Read 1 118 cycles, i7 index read 8 cycles, and Read 2 40 cycles. A custom sequencing primer is required for Read 1 (16005986, Bio-Rad; included in the kit).

treatment_protocol: Bone marrow mononuclear cells were quickly thawed in a 37°C water bath, rinsed with culture medium (RPMI 1640 medium supplemented with 15% FBS and 1% Pen/Strep) and then treated with 0.2 U/μL DNase I in 10 mL of culture medium at 37°C for 30 min. After DNase I treatment, cells were washed with medium once, filtered with a 35 μm cell strainer and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter. Cell viability was greater than 90% for all samples. Cells were plated at a concentration of 1 x 10^6 cell/mL, rested at 37°C and 5% CO2 for 1 h and then either incubated in serum containing media (RPMI 1640 medium supplemented with 15% FBS and 1% Pen/Strep) at 37°C and 5% CO2 for 6 h (Serum stimulation) or treated with 20 ng/mL Lipopolysaccharide (LPS) (tlrl-3pelps, Invivogen) for 6 h (LPS stimulation). After stimulation, cells were washed twice with ice cold 1x PBS + 0.1% BSA and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter. As a control, we processed cells immediately after counting, without any incubation.

value: Human bone marrow mononuclear cells


title: HumanBoneMarrow-ht-sciATAC-seq-Channel15


title: HumanBoneMarrow-ht-sciATAC-seq-Channel16


title: Mouse1-Channel2


title: HumanBoneMarrow-ht-sciATAC-seq-Channel12


title: HumanBoneMarrow-ht-sciATAC-seq-Channel8


title: HumanBoneMarrow-ht-sciATAC-seq-Channel7


title: HumanBoneMarrow-ht-sciATAC-seq-Channel11


title: HumanBoneMarrow-ht-sciATAC-seq-Channel10


title: HumanBoneMarrow-ht-sciATAC-seq-Channel5


title: Mouse1-Channel7


title: HumanBoneMarrow-ht-sciATAC-seq-Channel9


title: HumanBoneMarrow-ht-sciATAC-seq-Channel6


title: HumanBoneMarrow-ht-sciATAC-seq-Channel4


title: HumanBoneMarrow-ht-sciATAC-seq-Channel3


title: HumanBoneMarrow-ht-sciATAC-seq-Channel2


title: HumanBoneMarrow-ht-sciATAC-seq-Channel1


title: Human-PBMC-Channel4

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts implemented in the bap-barcode module.
Paired-end reads were aligned to hg19 using bwa.
Duplicate reads and all downstream processing was performed using the bead-based scATAC-seq processing (bap) tool.
Per-library outputs were combined into a single ranged summarized experiment for downstream analyses, as represented in the output data
Genome_build: hg19
Supplementary_files_format_and_content: Decomposed counts matrix. CountsData is indexed by peak (row), cell (column), and count where the Bed file and CellData provide annotations for rows and columns. Barcode translate file maps raw sequence barcode (many) to cell barcode (one) from the bap output. The BarcodeLogic Excel file contains the information needed to parse the cell barcode from the sequencing data.

source_name: Peripheral blood mononuclear cells

growth_protocol: Cryopreserved human peripheral blood mononuclear cells were purchased from Allcells. Cells were quickly thawed in a 37°C water bath, rinsed with culture medium (IMDM medium supplemented with 10% FBS and 1% Pen/Strep) and then treated with 0.2 U/μL DNase I (Thermo Fisher Scientific) in 10 mL of culture medium at 37°C for 30 min. After DNase I treatment, cells were washed with medium once and then twice with ice cold 1x PBS + 0.1% BSA. Cells were then filtered with a 35 μm cell strainer (Corning) and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter (Bio-Rad). Cell viability was greater than 80% for all samples.

value: Peripheral blood mononuclear cells

value: PBMC Donor2


title: Human-PBMC-Channel6

value: PBMC Donor3


title: Human-PBMC-Channel3


title: Human-PBMC-Channel1


title: Human-PBMC-Channel5


title: HumanBoneMarrow-ht-sciATAC-seq-Channel14


title: RNA from anagen phase hair follicles, rep 2

status: Public on Apr 01 2019

city: Utrecht

first: Onur

last: BASAK

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the total number of reads for every transcript.
Genome_build: mm10
Supplementary_files_format_and_content: *Epi_org*.csv: Comma separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column names indicate the GeneID and primer number of the sample. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: skin

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer’s instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq2 technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: passages

tag: source

value: tissue


title: RNA from anagen phase hair follicles, rep 1


title: Human-PBMC-Channel2


title: PB7 Alum

description: Aluminium hydroxide

source_name: Alhydrogel 2%

value: PBMC

value: Aluminium hydroxide


title: RNA from bulk cells of organoids, within 3 mo in culture, 7 d after culture, with TgfB inhibitor, rep 2

value: cells from cultured organoids


title: RNA from anagen phase hair follicles, rep 3


title: RNA from bulk cells of organoids, within 3 mo in culture, 7 d after culture, with TgfB inhibitor, rep 1


title: RNA from bulk cells of organoids, within 3 mo in culture, 7 d after culture, with Forskolin and Fgf1, rep 2


title: RNA from bulk cells of organoids, within 3 mo in culture, 7 d after culture, with Forskolin and TgfB inhibitor, rep 2


title: RNA from bulk cells of organoids, within 3 mo in culture, 7 d after culture, with Forskolin and TgfB inhibitor, rep 4


title: RNA from bulk cells of organoids, within 3 mo in culture, 7 d after culture, with Forskolin and TgfB inhibitor, rep 3


title: RNA from bulk cells of organoids, within 3 mo in culture, 7 d after culture, with Forskolin and TgfB inhibitor, rep 1


title: RNA from bulk cells of organoids, within 3 mo in culture, 7 d after last passage, with Forskolin and Fgf10, rep 3


title: RNA from bulk cells of organoids, within 3 mo in culture, 7 d after last passage, with Forskolin and Fgf10, rep 2


title: RNA from bulk cells of organoids, within 3 mo in culture, 7 d after last passage, with Forskolin and Fgf10, rep 4


title: RNA from bulk cells of organoids, not passaged, 7 d after culture, with Forskolin and Fgf10, rep 1


title: RNA from bulk cells of organoids, within 3 mo in culture, 7 d after last passage, with Forskolin and Fgf10, rep 1


title: RNA from bulk cells of organoids, not passaged, 7 d after culture, with Forskolin and TgfB inhibitor, rep 1


title: RNA from bulk cells of organoids, within 3 mo in culture, 7 d after culture, with Forskolin and Fgf1, rep 1


title: RNA from bulk cells of organoids, not passaged, 7 d after culture, with TgfB inhibitor, rep 1


title: RNA from bulk cells of organoids, not passaged, 7 d after culture, with Forskolin and Fgf1, rep 1


title: s_16_Lo_6

status: Public on Mar 26 2019

city: Rochester

first: Larry

last: Pease

state: MN

address: 200 First St SW

department: Immunology

institute: Mayo Clinic

data_processing:
Raw sequencing data was processed from the MAPRSeq pipeline (v 2.0.0)
Alignment was performed by TopHat 2.0.12 against the mouse genome mm10
Gene expression were obtained by featureCounts v1.4.4
Genome_build: hg19
Supplementary_files_format_and_content: table delimited gene count file

source_name: Her2/neu-driven breast tumors from F1 mice

extract_protocol:
miRNeasy
TruSeq mRNA library prep kit

value: [BALB/c-neuT x FVB/J] F1

value: breast tumor


title: s_19_Hi_5


title: s_22_Hi_11


title: s_13_Lo_1


title: s_21_Hi_8


title: s_18_Hi_1


title: s_20_Hi_7


title: s_17_Lo_11


title: s_8_Hi_6


title: s_12_Hi_10


title: s_14_Lo_4


title: s_4_Lo_8


title: s_2_Lo_3


title: s_11_Hi_9


title: s_1_Lo_2


title: RNA from bulk cells of organoids, not passaged, 7 d after culture, with Forskolin, rep 1


title: s_7_Hi_4


title: s_5_Hi_2


title: s_6_Hi_3


title: s_3_Lo_7


title: s_9_Lo_9


title: siSTK25-1

status: Public on Mar 20 2019

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from hTERT-RPE-1 cells  treated with siSTK25.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezgcdf R package (version 17.0.0).

source_name: hTERT-RPE-1 cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: All cell lines were maintained in DMEM/F-12 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol: Total RNA extraction was performed using the Qiagen Rneasy Mini Kit according to the manufacturer's protocol when cells were treated for 48 hours.

treatment_protocol: All cell lines were treated with their respective siRNA or miRNA pre-mir mimics using 50 nM siRNA with Lipofectamine RNAi MAX according to the manufacturer's instructions.


title: miR24-3

description: Gene expression data from hTERT-RPE-1 cells  treated with miR24.


title: siC-1

description: Gene expression data from hTERT-RPE-1 cells  treated with siC.

value: siC


title: siC-3


title: miR24-1


title: TAZ 4SA 8

description: Gene expression data from retinal pigment epithelium cell line RPE-7 treated with TAZ 4SA.

extract_protocol: Total RNA extraction was performed using the Qiagen Rneasy Mini Kit according to the manufacturer's protocol from exponentially growing hTERT-RPE-1 cells when they reached 70% confluence.

treatment_protocol: All cell lines were stably expressing their respective constructs.

tag: group

value: TAZ 4SA


title: siSTK25-3


title: siSTK25-2


title: RPE1 control 1

description: Gene expression data from retinal pigment epithelium cell line RPE-1 treated with RPE.

value: RPE


title: YAP S5A 5

description: Gene expression data from retinal pigment epithelium cell line RPE-5 treated with YAP S5A.

value: YAP S5A


title: TAZ 4SA 9

description: Gene expression data from retinal pigment epithelium cell line RPE-8 treated with TAZ 4SA.


title: U87_LXR623

status: Public on Feb 05 2019

description: SAMPLE 2

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezg R package (version 17.0.0).

source_name: U87 glioblastoma cells

growth_protocol: Human glioma cells (HCT116) were cultured in DMEM (Corning, New York, USA) supplemented with 10 % FBS at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Hiden, Germany) according to the manufacturer's protocol.

treatment_protocol: After one day of cell seeding, U87 cells were treared with 20 uM of LXR623 for 24 hours in DMEM supplemented with 1.5% FBS.

tag: cell line

value: glioma cancer cells

tag: treated with

value: LXR623 20uM for 24h


title: OTX015 2

status: Public on Jan 09 2019

description: Gene expression data from NCH644 glioblastoma cells in neurosphere culture treated with OTX015.

growth_protocol: NCH644 glioma cells were cultured in MG-43 medium (CLS, Heidelberg, Germany).

extract_protocol: RNAs of the NCH644 cells in different culture media were collected and extracted at the same time with RNeasy Mini Kit (Qiagen Cat No./ID: 74104).

treatment_protocol: Drugs or DMSO were added 24 hours before RNA collection. OTX015: 5uM, Panobinostat: 5uM, or the combination: OTX015 5uM+ Panobinostat 5uM.


title: RPE1 control 2

description: Gene expression data from retinal pigment epithelium cell line RPE-2 treated with RPE.


title: HCT116_Control

description: SAMPLE 1

source_name: HCT116 colon carcinoma cells

growth_protocol: Human colon cancer cells (HCT116) were cultured in RPMI (Corning, New York, USA) supplemented with 10 % FBS at 37°C in 5% CO2.

treatment_protocol: After one day of cell seeding, HCT116 cells were treared with 20 uM of LXR623 for 24 hours in RPMI supplemented with 1.5% FBS.

value: colon carcinoma cells

value: 0.1% DMSO


title: panobinostat 1

description: Gene expression data from NCH644 glioblastoma cells in neurosphere culture treated with panobinostat.

value: panobinostat


title: miR24-2


title: YAP S5A 4

description: Gene expression data from retinal pigment epithelium cell line RPE-4 treated with YAP S5A.


title: siC-2


title: panobinostat 2

source_name: NCH644 glioblastoma cells in neurosphere culture


title: DMSO 2

description: Gene expression data from NCH644 glioblastoma cells in neurosphere culture treated with DMSO.

value: DMSO


title: panobinostat

description: Gene expression data from GBM43 glioblastoma from mice treated with panobinostat.

source_name: mice implanted with patient derived xenograft glioblastoma G43

growth_protocol: Patient derived GBM43 glioblastoma were harvested and equal amout of tumor mess were implanted subcutaneously to Nude mice.

extract_protocol: Tumors were minced and RNA were collected and extracted at the same time with RNeasy Mini Kit (Qiagen Cat No./ID: 74104).

treatment_protocol: Mice were either treated with 6 doses of DMSO or 6 doses of 15mg/kg panobinostat (3 times a week). Tumors were harvested from the two groups at the end of the treatment.

value: GBM43 glioblastoma


title: RPE1 control 3

description: Gene expression data from retinal pigment epithelium cell line RPE-3 treated with RPE.


title: YAP S5A 6

description: Gene expression data from retinal pigment epithelium cell line RPE-6 treated with YAP S5A.


title: OTX015+panobinostat 2

description: Gene expression data from NCH644 glioblastoma cells in neurosphere culture treated with OTX015+panobinostat.


title: OTX015+panobinostat 1


title: OTX015 1


title: B6 Pi[-] d35 #2, batch E

status: Public on Dec 25 2018

description: Gene expression data from right femur of B6 Pi[-] animal at day 35 following experimental fracture.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene10stmmentrezg R package (version 16.0.0).

source_name: Femur bone following experimental fracture

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

growth_protocol: In vivo animal model

extract_protocol: Total RNAs were isolated from each fracture callus using procedures developed for murine bones (Wang et al., Matrix Biology, 2006; 25(5):271-81).  In order to both achieve an optimal balance in biological replicate variability and repeatability RNA from every two of the six fracture calluses were randomly pooled to generate three assay samples.

treatment_protocol: Pi group: Phosphate deficiency (Pi) was initiated 2 days prior to fracture and was maintained for 15 days by supplying the mice with a low phosphate diet (Harlan Laboratories, Madison, WI). Phosphate was then replenished and bone healing was allowed to continue until 35 days. For the three strains of mice, control groups were included where the mice were given normal diet throughout the study.

value: bone fracture callus

tag: gender

value: male

tag: batch

value: batch E

tag: diet

tag: timepoint

value: day 35

tag: animal


title: HCT116_LXR623

description: SAMPLE 2

tag: cell type


title: DMSO 1

tag: treatment


title: DMSO

description: Gene expression data from GBM43 glioblastoma from mice treated with DMSO.


title: U87_Conrol

description: SAMPLE 1


title: B6 Pi[-] d10 #1, batch E

description: Gene expression data from right femur of B6 Pi[-] animal at day 10 following experimental fracture.

tag: strain

value: day 10


title: B6 Pi[-] d14 #3, batch E

description: Gene expression data from right femur of B6 Pi[-] animal at day 14 following experimental fracture.

value: day 14


title: B6 Pi[-] d5 #1, batch E

description: Gene expression data from right femur of B6 Pi[-] animal at day 5 following experimental fracture.

value: day 5


title: B6 Pi[-] d28 #2, batch E

description: Gene expression data from right femur of B6 Pi[-] animal at day 28 following experimental fracture.

value: day 28


title: B6 Pi[-] d21 #2, batch E

description: Gene expression data from right femur of B6 Pi[-] animal at day 21 following experimental fracture.

value: day 21


title: B6 control d5 #3, batch E

description: Gene expression data from right femur of B6 control animal at day 5 following experimental fracture.

value: control


title: B6 Pi[-] d5 #3, batch E


title: B6 Pi[-] d18 #3, batch E

description: Gene expression data from right femur of B6 Pi[-] animal at day 18 following experimental fracture.

value: day 18


title: B6 control d7 #1, batch E

description: Gene expression data from right femur of B6 control animal at day 7 following experimental fracture.

value: day 7


title: B6 control d10 #1, batch E

description: Gene expression data from right femur of B6 control animal at day 10 following experimental fracture.


title: B6 control d14 #2, batch E

description: Gene expression data from right femur of B6 control animal at day 14 following experimental fracture.


title: C3H Pi[-] d28 #3, batch E

description: Gene expression data from right femur of C3H Pi[-] animal at day 28 following experimental fracture.


title: B6 control d21 #1, batch E

description: Gene expression data from right femur of B6 control animal at day 21 following experimental fracture.


title: B6 control d28 #2, batch E

description: Gene expression data from right femur of B6 control animal at day 28 following experimental fracture.


title: C3H Pi[-] d10 #3, batch E

description: Gene expression data from right femur of C3H Pi[-] animal at day 10 following experimental fracture.


title: B6 control d0 #1, batch E

description: Gene expression data from right femur of B6 control animal at baseline.

source_name: Control femur bone

value: bone

value: day 0


title: C3H Pi[-] d18 #2, batch E

description: Gene expression data from right femur of C3H Pi[-] animal at day 18 following experimental fracture.


title: B6 control d35 #1, batch E

description: Gene expression data from right femur of B6 control animal at day 35 following experimental fracture.


title: B6 control d0 #3, batch E


title: C3H Pi[-] d5 #2, batch E

description: Gene expression data from right femur of C3H Pi[-] animal at day 5 following experimental fracture.


title: C3H Pi[-] d7 #1, batch E

description: Gene expression data from right femur of C3H Pi[-] animal at day 7 following experimental fracture.


title: C3H Pi[-] d5 #3, batch E


title: C3H Pi[-] d18 #3, batch E


title: C3H control d35 #2, batch E

description: Gene expression data from right femur of C3H control animal at day 35 following experimental fracture.


title: C3H control d28 #2, batch E

description: Gene expression data from right femur of C3H control animal at day 28 following experimental fracture.


title: C3H control d14 #3, batch E

description: Gene expression data from right femur of C3H control animal at day 14 following experimental fracture.


title: C3H control d21 #2, batch E

description: Gene expression data from right femur of C3H control animal at day 21 following experimental fracture.


title: C3H control d21 #1, batch E


title: C3H control d10 #1, batch E

description: Gene expression data from right femur of C3H control animal at day 10 following experimental fracture.


title: C3H control d5 #3, batch E

description: Gene expression data from right femur of C3H control animal at day 5 following experimental fracture.


title: AJ Pi[-] d14 #2, batch E

description: Gene expression data from right femur of AJ Pi[-] animal at day 14 following experimental fracture.

value: AJ


title: AJ Pi[-] d3 #3, batch E

description: Gene expression data from right femur of AJ Pi[-] animal at day 3 following experimental fracture.

value: day 3


title: AJ Pi[-] d28 #1, batch E

description: Gene expression data from right femur of AJ Pi[-] animal at day 28 following experimental fracture.


title: AJ Pi[-] d35 #2, batch E

description: Gene expression data from right femur of AJ Pi[-] animal at day 35 following experimental fracture.


title: C3H control d7 #2, batch E

description: Gene expression data from right femur of C3H control animal at day 7 following experimental fracture.


title: AJ Pi[-] d18 #3, batch E

description: Gene expression data from right femur of AJ Pi[-] animal at day 18 following experimental fracture.


title: AJ control d28 #3, batch E

description: Gene expression data from right femur of AJ control animal at day 28 following experimental fracture.


title: C3H control d0 #3, batch E

description: Gene expression data from right femur of C3H control animal at baseline.


title: AJ control d18 #3, batch E

description: Gene expression data from right femur of AJ control animal at day 18 following experimental fracture.


title: AJ control d10 #3, batch E

description: Gene expression data from right femur of AJ control animal at day 10 following experimental fracture.


title: AJ control d10 #1, batch E


title: AJ control d28 #2, batch E


title: AJ control d5 #2, batch E

description: Gene expression data from right femur of AJ control animal at day 5 following experimental fracture.


title: AJ Pi[-] d7 #1, batch E

description: Gene expression data from right femur of AJ Pi[-] animal at day 7 following experimental fracture.


title: B6 Pi[-] d14 #1, batch D

description: Gene expression data from right femur of B6 Pi[-] animal at day 14 following experimental fracture.

value: batch D


title: AJ control d35 #3, batch E

description: Gene expression data from right femur of AJ control animal at day 35 following experimental fracture.

value: bone fracture callus


title: B6 Pi[-] d28 #2, batch D

description: Gene expression data from right femur of B6 Pi[-] animal at day 28 following experimental fracture.

value: male


title: AJ Pi[-] d3 #1, batch E

value: batch E


title: B6 Pi[-] d7 #3, batch D

description: Gene expression data from right femur of B6 Pi[-] animal at day 7 following experimental fracture.


title: B6 Pi[-] d5 #1, batch D

description: Gene expression data from right femur of B6 Pi[-] animal at day 5 following experimental fracture.


title: B6 Pi[-] d14 #3, batch D


title: B6 control d28 #2, batch D

description: Gene expression data from right femur of B6 control animal at day 28 following experimental fracture.


title: B6 Pi[-] d3 #3, batch D

description: Gene expression data from right femur of B6 Pi[-] animal at day 3 following experimental fracture.


title: B6 control d14 #3, batch D

description: Gene expression data from right femur of B6 control animal at day 14 following experimental fracture.


title: B6 Pi[-] d21 #3, batch D

description: Gene expression data from right femur of B6 Pi[-] animal at day 21 following experimental fracture.


title: B6 control d35 #2, batch D

description: Gene expression data from right femur of B6 control animal at day 35 following experimental fracture.

value: day 35


title: AJ control d3 #1, batch E

description: Gene expression data from right femur of AJ control animal at day 3 following experimental fracture.


title: B6 control d7 #2, batch D

description: Gene expression data from right femur of B6 control animal at day 7 following experimental fracture.


title: B6 Pi[-] d35 #3, batch D

description: Gene expression data from right femur of B6 Pi[-] animal at day 35 following experimental fracture.


title: B6 control d21 #2, batch D

description: Gene expression data from right femur of B6 control animal at day 21 following experimental fracture.


title: B6 control d7 #1, batch D


title: B6 control d0 #3, batch D

description: Gene expression data from right femur of B6 control animal at baseline.


title: C3H Pi[-] d35 #2, batch D

description: Gene expression data from right femur of C3H Pi[-] animal at day 35 following experimental fracture.


title: C3H Pi[-] d18 #2, batch D

description: Gene expression data from right femur of C3H Pi[-] animal at day 18 following experimental fracture.


title: C3H Pi[-] d5 #1, batch D

description: Gene expression data from right femur of C3H Pi[-] animal at day 5 following experimental fracture.


title: C3H control d28 #2, batch D

description: Gene expression data from right femur of C3H control animal at day 28 following experimental fracture.


title: C3H control d35 #1, batch D

description: Gene expression data from right femur of C3H control animal at day 35 following experimental fracture.


title: C3H Pi[-] d7 #1, batch D

description: Gene expression data from right femur of C3H Pi[-] animal at day 7 following experimental fracture.


title: C3H Pi[-] d10 #2, batch D

description: Gene expression data from right femur of C3H Pi[-] animal at day 10 following experimental fracture.

value: day 10


title: C3H Pi[-] d28 #2, batch D

description: Gene expression data from right femur of C3H Pi[-] animal at day 28 following experimental fracture.


title: C3H Pi[-] d5 #3, batch D


title: B6 control d3 #3, batch D

description: Gene expression data from right femur of B6 control animal at day 3 following experimental fracture.


title: C3H control d10 #1, batch D

description: Gene expression data from right femur of C3H control animal at day 10 following experimental fracture.


title: C3H control d21 #2, batch D

description: Gene expression data from right femur of C3H control animal at day 21 following experimental fracture.


title: C3H control d21 #3, batch D


title: AJ Pi[-] d35 #2, batch D

description: Gene expression data from right femur of AJ Pi[-] animal at day 35 following experimental fracture.


title: C3H control d0 #2, batch D

description: Gene expression data from right femur of C3H control animal at baseline.


title: C3H control d7 #3, batch D

description: Gene expression data from right femur of C3H control animal at day 7 following experimental fracture.


title: AJ Pi[-] d28 #2, batch D

description: Gene expression data from right femur of AJ Pi[-] animal at day 28 following experimental fracture.


title: C3H Pi[-] d18 #1, batch D


title: C3H control d14 #1, batch D

description: Gene expression data from right femur of C3H control animal at day 14 following experimental fracture.

value: day 14


title: AJ Pi[-] d10 #1, batch D

description: Gene expression data from right femur of AJ Pi[-] animal at day 10 following experimental fracture.


title: AJ Pi[-] d3 #2, batch D

description: Gene expression data from right femur of AJ Pi[-] animal at day 3 following experimental fracture.


title: AJ Pi[-] d18 #1, batch D

description: Gene expression data from right femur of AJ Pi[-] animal at day 18 following experimental fracture.


title: AJ Pi[-] d7 #2, batch D

description: Gene expression data from right femur of AJ Pi[-] animal at day 7 following experimental fracture.


title: AJ control d18 #2, batch D

description: Gene expression data from right femur of AJ control animal at day 18 following experimental fracture.


title: AJ control d21 #2, batch D

description: Gene expression data from right femur of AJ control animal at day 21 following experimental fracture.


title: AJ Pi[-] d3 #1, batch D


title: AJ control d28 #2, batch D

description: Gene expression data from right femur of AJ control animal at day 28 following experimental fracture.


title: AJ control d35 #3, batch D

description: Gene expression data from right femur of AJ control animal at day 35 following experimental fracture.


title: AJ control d5 #1, batch D

description: Gene expression data from right femur of AJ control animal at day 5 following experimental fracture.

value: day 5


title: AJ control d10 #3, batch D

description: Gene expression data from right femur of AJ control animal at day 10 following experimental fracture.


title: B6 Pi[-] d18 #1, batch C

description: Gene expression data from right femur of B6 Pi[-] animal at day 18 following experimental fracture.

value: batch C


title: B6 Pi[-] d10 #3, batch C

description: Gene expression data from right femur of B6 Pi[-] animal at day 10 following experimental fracture.


title: B6 Pi[-] d3 #1, batch C

description: Gene expression data from right femur of B6 Pi[-] animal at day 3 following experimental fracture.


title: B6 control d18 #3, batch C

description: Gene expression data from right femur of B6 control animal at day 18 following experimental fracture.


title: B6 Pi[-] d7 #1, batch C

description: Gene expression data from right femur of B6 Pi[-] animal at day 7 following experimental fracture.


title: B6 control d28 #1, batch C

description: Gene expression data from right femur of B6 control animal at day 28 following experimental fracture.

value: day 28


title: B6 Pi[-] d28 #3, batch C

description: Gene expression data from right femur of B6 Pi[-] animal at day 28 following experimental fracture.


title: AJ control d0 #1, batch D

description: Gene expression data from right femur of AJ control animal at baseline.

value: control


title: C3H Pi[-] d21 #1, batch C

description: Gene expression data from right femur of C3H Pi[-] animal at day 21 following experimental fracture.

value: day 21


title: B6 control d7 #1, batch C

description: Gene expression data from right femur of B6 control animal at day 7 following experimental fracture.

value: day 7


title: B6 control d5 #1, batch C

description: Gene expression data from right femur of B6 control animal at day 5 following experimental fracture.


title: B6 control d3 #1, batch C

description: Gene expression data from right femur of B6 control animal at day 3 following experimental fracture.


title: AJ control d10 #2, batch D


title: C3H Pi[-] d35 #1, batch C

description: Gene expression data from right femur of C3H Pi[-] animal at day 35 following experimental fracture.


title: B6 control d10 #3, batch C

description: Gene expression data from right femur of B6 control animal at day 10 following experimental fracture.


title: C3H Pi[-] d5 #3, batch C

description: Gene expression data from right femur of C3H Pi[-] animal at day 5 following experimental fracture.


title: B6 control d0 #3, batch C

description: Gene expression data from right femur of B6 control animal at baseline.

value: bone


title: B6 control d28 #2, batch C


title: B6 Pi[-] d28 #2, batch C


title: B6 Pi[-] d14 #3, batch C

description: Gene expression data from right femur of B6 Pi[-] animal at day 14 following experimental fracture.


title: C3H Pi[-] d14 #2, batch C

description: Gene expression data from right femur of C3H Pi[-] animal at day 14 following experimental fracture.


title: B6 Pi[-] d5 #1, batch C

description: Gene expression data from right femur of B6 Pi[-] animal at day 5 following experimental fracture.


title: C3H Pi[-] d18 #2, batch C

description: Gene expression data from right femur of C3H Pi[-] animal at day 18 following experimental fracture.

value: day 18


title: C3H Pi[-] d7 #1, batch C

description: Gene expression data from right femur of C3H Pi[-] animal at day 7 following experimental fracture.


title: C3H control d3 #1, batch C

description: Gene expression data from right femur of C3H control animal at day 3 following experimental fracture.


title: C3H control d21 #2, batch C

description: Gene expression data from right femur of C3H control animal at day 21 following experimental fracture.


title: C3H control d28 #1, batch C

description: Gene expression data from right femur of C3H control animal at day 28 following experimental fracture.


title: AJ Pi[-] d21 #2, batch C

description: Gene expression data from right femur of AJ Pi[-] animal at day 21 following experimental fracture.

value: AJ


title: AJ Pi[-] d5 #2, batch C

description: Gene expression data from right femur of AJ Pi[-] animal at day 5 following experimental fracture.


title: AJ Pi[-] d3 #1, batch C

description: Gene expression data from right femur of AJ Pi[-] animal at day 3 following experimental fracture.

value: day 3


title: AJ control d28 #2, batch C

description: Gene expression data from right femur of AJ control animal at day 28 following experimental fracture.


title: C3H control d5 #2, batch C

description: Gene expression data from right femur of C3H control animal at day 5 following experimental fracture.


title: C3H control d28 #2, batch C


title: C3H Pi[-] d3 #3, batch C

description: Gene expression data from right femur of C3H Pi[-] animal at day 3 following experimental fracture.


title: AJ control d35 #3, batch C

description: Gene expression data from right femur of AJ control animal at day 35 following experimental fracture.


title: AJ Pi[-] d35 #1, batch C

description: Gene expression data from right femur of AJ Pi[-] animal at day 35 following experimental fracture.


title: C3H control d10 #3, batch C

description: Gene expression data from right femur of C3H control animal at day 10 following experimental fracture.


title: AJ control d35 #2, batch C


title: C3H control d18 #3, batch C

description: Gene expression data from right femur of C3H control animal at day 18 following experimental fracture.


title: AJ Pi[-] d35 #2, batch C


title: C3H control d10 #1, batch C


title: AJ Pi[-] d14 #1, batch C

description: Gene expression data from right femur of AJ Pi[-] animal at day 14 following experimental fracture.


title: C3H Pi[-] d7 #3, batch C


title: AJ Pi[-] d10 #2, batch C

description: Gene expression data from right femur of AJ Pi[-] animal at day 10 following experimental fracture.


title: AJ control d10 #3, batch C

description: Gene expression data from right femur of AJ control animal at day 10 following experimental fracture.


title: AJ control d21 #1, batch C

description: Gene expression data from right femur of AJ control animal at day 21 following experimental fracture.


title: AJ control d7 #2, batch C

description: Gene expression data from right femur of AJ control animal at day 7 following experimental fracture.


title: AJ control d3 #3, batch C

description: Gene expression data from right femur of AJ control animal at day 3 following experimental fracture.


title: AJ control d0 #3, batch C

description: Gene expression data from right femur of AJ control animal at baseline.

value: day 0


title: B6 Pi[-] d18 #2, batch B

description: Gene expression data from right femur of B6 Pi[-] animal at day 18 following experimental fracture.

value: bone fracture callus

value: batch B


title: B6 control d21 #3, batch B

description: Gene expression data from right femur of B6 control animal at day 21 following experimental fracture.

value: male


title: AJ control d14 #1, batch C

description: Gene expression data from right femur of AJ control animal at day 14 following experimental fracture.


title: B6 control d28 #2, batch B

description: Gene expression data from right femur of B6 control animal at day 28 following experimental fracture.


title: B6 Pi[-] d28 #2, batch B

description: Gene expression data from right femur of B6 Pi[-] animal at day 28 following experimental fracture.


title: B6 control d0 #2, batch B

description: Gene expression data from right femur of B6 control animal at baseline.


title: C3H Pi[-] d18 #2, batch B

description: Gene expression data from right femur of C3H Pi[-] animal at day 18 following experimental fracture.


title: C3H Pi[-] d7 #1, batch B

description: Gene expression data from right femur of C3H Pi[-] animal at day 7 following experimental fracture.


title: B6 Pi[-] d10 #2, batch B

description: Gene expression data from right femur of B6 Pi[-] animal at day 10 following experimental fracture.


title: C3H Pi[-] d7 #2, batch B


title: B6 control d7 #1, batch B

description: Gene expression data from right femur of B6 control animal at day 7 following experimental fracture.


title: B6 Pi[-] d5 #1, batch B

description: Gene expression data from right femur of B6 Pi[-] animal at day 5 following experimental fracture.


title: B6 Pi[-] d28 #1, batch B


title: B6 control d18 #2, batch B

description: Gene expression data from right femur of B6 control animal at day 18 following experimental fracture.


title: B6 control d5 #2, batch B

description: Gene expression data from right femur of B6 control animal at day 5 following experimental fracture.


title: B6 Pi[-] d5 #2, batch B


title: B6 control d0 #3, batch B


title: C3H Pi[-] d14 #1, batch B

description: Gene expression data from right femur of C3H Pi[-] animal at day 14 following experimental fracture.


title: B6 control d35 #3, batch B

description: Gene expression data from right femur of B6 control animal at day 35 following experimental fracture.

value: day 35


title: C3H Pi[-] d21 #3, batch B

description: Gene expression data from right femur of C3H Pi[-] animal at day 21 following experimental fracture.


title: C3H control d3 #2, batch D

description: Gene expression data from right femur of C3H control animal at day 3 following experimental fracture.

value: batch D


title: C3H Pi[-] d5 #3, batch B

description: Gene expression data from right femur of C3H Pi[-] animal at day 5 following experimental fracture.


title: B6 control d10 #2, batch B

description: Gene expression data from right femur of B6 control animal at day 10 following experimental fracture.

value: day 10


title: C3H control d18 #1, batch B

description: Gene expression data from right femur of C3H control animal at day 18 following experimental fracture.


title: C3H Pi[-] d28 #1, batch B

description: Gene expression data from right femur of C3H Pi[-] animal at day 28 following experimental fracture.


title: B6 Pi[-] d14 #3, batch B

description: Gene expression data from right femur of B6 Pi[-] animal at day 14 following experimental fracture.

value: day 14


title: C3H control d28 #2, batch B

description: Gene expression data from right femur of C3H control animal at day 28 following experimental fracture.


title: C3H control d21 #2, batch B

description: Gene expression data from right femur of C3H control animal at day 21 following experimental fracture.


title: C3H control d10 #2, batch B

description: Gene expression data from right femur of C3H control animal at day 10 following experimental fracture.


title: C3H Pi[-] d3 #1, batch B

description: Gene expression data from right femur of C3H Pi[-] animal at day 3 following experimental fracture.


title: AJ Pi[-] d3 #1, batch B

description: Gene expression data from right femur of AJ Pi[-] animal at day 3 following experimental fracture.


title: C3H control d28 #3, batch B


title: C3H control d10 #1, batch B


title: AJ Pi[-] d21 #1, batch B

description: Gene expression data from right femur of AJ Pi[-] animal at day 21 following experimental fracture.


title: C3H control d5 #1, batch B

description: Gene expression data from right femur of C3H control animal at day 5 following experimental fracture.

value: day 5


title: C3H control d0 #1, batch B

description: Gene expression data from right femur of C3H control animal at baseline.


title: AJ control d7 #1, batch B

description: Gene expression data from right femur of AJ control animal at day 7 following experimental fracture.


title: AJ Pi[-] d35 #2, batch B

description: Gene expression data from right femur of AJ Pi[-] animal at day 35 following experimental fracture.


title: AJ control d28 #2, batch B

description: Gene expression data from right femur of AJ control animal at day 28 following experimental fracture.

value: day 28


title: AJ control d14 #2, batch B

description: Gene expression data from right femur of AJ control animal at day 14 following experimental fracture.

value: control


title: AJ Pi[-] d28 #3, batch B

description: Gene expression data from right femur of AJ Pi[-] animal at day 28 following experimental fracture.


title: AJ Pi[-] d5 #3, batch B

description: Gene expression data from right femur of AJ Pi[-] animal at day 5 following experimental fracture.


title: AJ control d28 #1, batch B


title: B6 Pi[-] d35 #1, batch A

description: Gene expression data from right femur of B6 Pi[-] animal at day 35 following experimental fracture.

value: batch A


title: AJ Pi[-] d7 #3, batch B

description: Gene expression data from right femur of AJ Pi[-] animal at day 7 following experimental fracture.

value: day 7


title: AJ control d35 #3, batch B

description: Gene expression data from right femur of AJ control animal at day 35 following experimental fracture.


title: AJ control d18 #1, batch B

description: Gene expression data from right femur of AJ control animal at day 18 following experimental fracture.


title: AJ Pi[-] d14 #3, batch B

description: Gene expression data from right femur of AJ Pi[-] animal at day 14 following experimental fracture.


title: AJ control d10 #3, batch B

description: Gene expression data from right femur of AJ control animal at day 10 following experimental fracture.


title: AJ control d3 #2, batch B

description: Gene expression data from right femur of AJ control animal at day 3 following experimental fracture.


title: B6 Pi[-] d14 #3, batch A

description: Gene expression data from right femur of B6 Pi[-] animal at day 14 following experimental fracture.


title: B6 Pi[-] d28 #2, batch A

description: Gene expression data from right femur of B6 Pi[-] animal at day 28 following experimental fracture.


title: B6 Pi[-] d14 #2, batch A


title: B6 Pi[-] d5 #1, batch A

description: Gene expression data from right femur of B6 Pi[-] animal at day 5 following experimental fracture.


title: B6 Pi[-] d3 #2, batch A

description: Gene expression data from right femur of B6 Pi[-] animal at day 3 following experimental fracture.


title: B6 Pi[-] d21 #1, batch A

description: Gene expression data from right femur of B6 Pi[-] animal at day 21 following experimental fracture.

value: day 21


title: B6 control d28 #3, batch A

description: Gene expression data from right femur of B6 control animal at day 28 following experimental fracture.


title: B6 Pi[-] d7 #2, batch A

description: Gene expression data from right femur of B6 Pi[-] animal at day 7 following experimental fracture.


title: B6 control d28 #2, batch A


title: B6 control d14 #1, batch A

description: Gene expression data from right femur of B6 control animal at day 14 following experimental fracture.


title: C3H Pi[-] d21 #2, batch A

description: Gene expression data from right femur of C3H Pi[-] animal at day 21 following experimental fracture.


title: B6 control d18 #1, batch A

description: Gene expression data from right femur of B6 control animal at day 18 following experimental fracture.

value: day 18


title: C3H Pi[-] d10 #1, batch A

description: Gene expression data from right femur of C3H Pi[-] animal at day 10 following experimental fracture.


title: B6 control d7 #3, batch A

description: Gene expression data from right femur of B6 control animal at day 7 following experimental fracture.


title: B6 control d7 #1, batch A


title: B6 control d3 #2, batch A

description: Gene expression data from right femur of B6 control animal at day 3 following experimental fracture.


title: C3H Pi[-] d35 #3, batch A

description: Gene expression data from right femur of C3H Pi[-] animal at day 35 following experimental fracture.


title: C3H control d28 #2, batch A

description: Gene expression data from right femur of C3H control animal at day 28 following experimental fracture.


title: C3H control d18 #2, batch A

description: Gene expression data from right femur of C3H control animal at day 18 following experimental fracture.


title: C3H Pi[-] d3 #2, batch A

description: Gene expression data from right femur of C3H Pi[-] animal at day 3 following experimental fracture.


title: B6 control d0 #3, batch A

description: Gene expression data from right femur of B6 control animal at baseline.

value: bone


title: C3H Pi[-] d5 #3, batch A

description: Gene expression data from right femur of C3H Pi[-] animal at day 5 following experimental fracture.


title: C3H control d21 #2, batch A

description: Gene expression data from right femur of C3H control animal at day 21 following experimental fracture.


title: C3H Pi[-] d18 #2, batch A

description: Gene expression data from right femur of C3H Pi[-] animal at day 18 following experimental fracture.


title: C3H Pi[-] d7 #1, batch A

description: Gene expression data from right femur of C3H Pi[-] animal at day 7 following experimental fracture.


title: BMS

description: SAMPLE 4

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

source_name: airway smooth muscle cells

growth_protocol: N/A (cells were sorted by flow cytometry)

extract_protocol: Extraction of total RNA using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: hrGFP+DsRED- (airway smooth muscle) cells from adult mouse lungs isolated by flow cytometry from the double transgenic mice.  VAS mice were fed with routine vitamin-A sufficient diet; VAD mice were fed with vitamin A deficient diet for 5 days before their airway smooth muscles were Mouse ASMs were isolated from Acta2-hrGFP;Cspg4-DsRED adult mice using flow cytometry.  VAS mice were given normal, vitamin A-sufficient diet (15 IU vitamin/g) while the VAD mice were given 3 days of vitamin A-deficient diet (< 0.1 IU vitamin/g).  CTR/BMS mouse ASMs were also isolated from Acta2-hrGFP;Cspg4-DsRED adult mice using flow cytometry.  CTR mice were given 3 days of powdered, vitamin A sufficient diet mixed with vehicles (corn oil) while the BMS diet were given 3 days of powdered, vitamin A sufficient diet mixed with a potent pan-RA-receptor antagonist (BMS, 5 mcg/g).

tag: genotype/variation

value: BMS:3 days of powdered, vitamin A sufficient diet mixed with a potent pan-RA-receptor antagonist (BMS, 5 mcg/g)

value: airway smooth muscle (ASM) cells


title: CTR

description: SAMPLE 3

value: CTR:3 days of powdered, vitamin A sufficient diet mixed with vehicles (corn oil)


title: C3H control d14 #2, batch A

description: Gene expression data from right femur of C3H control animal at day 14 following experimental fracture.

value: bone fracture callus


title: C3H Pi[-] d14 #3, batch A

description: Gene expression data from right femur of C3H Pi[-] animal at day 14 following experimental fracture.

value: male


title: AJ Pi[-] d35 #3, batch A

description: Gene expression data from right femur of AJ Pi[-] animal at day 35 following experimental fracture.

value: AJ

value: day 35


title: AJ Pi[-] d35 #2, batch A


title: C3H control d3 #3, batch A

description: Gene expression data from right femur of C3H control animal at day 3 following experimental fracture.

value: day 3


title: C3H control d35 #3, batch A

description: Gene expression data from right femur of C3H control animal at day 35 following experimental fracture.


title: VAS

description: SAMPLE 1

value: VAS:normal, vitamin A-sufficient diet


title: AJ Pi[-] d18 #2, batch A

description: Gene expression data from right femur of AJ Pi[-] animal at day 18 following experimental fracture.


title: AJ Pi[-] d21 #3, batch A

description: Gene expression data from right femur of AJ Pi[-] animal at day 21 following experimental fracture.


title: C3H control d10 #1, batch A

description: Gene expression data from right femur of C3H control animal at day 10 following experimental fracture.

value: day 10


title: C3H control d7 #1, batch A

description: Gene expression data from right femur of C3H control animal at day 7 following experimental fracture.


title: AJ Pi[-] d10 #3, batch A

description: Gene expression data from right femur of AJ Pi[-] animal at day 10 following experimental fracture.


title: VAD

description: SAMPLE 2

value: VAD:3 days of vitamin A-deficient diet


title: AJ Pi[-] d5 #1, batch A

description: Gene expression data from right femur of AJ Pi[-] animal at day 5 following experimental fracture.

value: day 5


title: AJ Pi[-] d3 #1, batch A

description: Gene expression data from right femur of AJ Pi[-] animal at day 3 following experimental fracture.

value: batch A


title: AJ control d14 #3, batch A

description: Gene expression data from right femur of AJ control animal at day 14 following experimental fracture.

value: control

value: day 14


title: AJ control d28 #2, batch A

description: Gene expression data from right femur of AJ control animal at day 28 following experimental fracture.

value: day 28


title: AJ control d7 #3, batch A

description: Gene expression data from right femur of AJ control animal at day 7 following experimental fracture.

value: day 7


title: AJ control d10 #3, batch A

description: Gene expression data from right femur of AJ control animal at day 10 following experimental fracture.


title: AJ control d5 #3, batch A

description: Gene expression data from right femur of AJ control animal at day 5 following experimental fracture.


title: AJ control d35 #1, batch A

description: Gene expression data from right femur of AJ control animal at day 35 following experimental fracture.


title: AJ control d0 #2, batch A

description: Gene expression data from right femur of AJ control animal at baseline.

value: bone

value: day 0


title: AJ control d21 #3, batch A

description: Gene expression data from right femur of AJ control animal at day 21 following experimental fracture.

value: day 21


title: Donor 2 - BMS

description: SAMPLE 4

source_name: ASM cells_BMS

growth_protocol: De-identified primary human ASM cells, provided by Gift of Hope Foundation (Itasca, IL) were cultured in 75 cm2 culture flasks containing DMEM/F12 supplement with 10% FBS, 1x antibiotic/antimycotic mixture to 80% confluency.  Cells from each donor were counted and split into four wells of 22,000 cells per well and cultured

treatment_protocol: Cells were cultured in control medium (CTR) or medium containing a pan-RA receptor inhibitor BMS 493 (10-6M) for 24 hours.

tag: donor id

value: Donor 2

value: airway smooth muscle (ASM) cells

tag: culture condition

value: medium containing a pan-RA receptor inhibitor BMS 493 (1 uM)

value: BMS


title: Donor 3 - BMS

description: SAMPLE 6

value: Donor 3


title: Donor 3 - CTR

description: SAMPLE 5

source_name: ASM cells_control

value: control medium (CTR)

value: CTR


title: AJ control d35 #3, batch A

tag: tissue

value: bone fracture callus

value: male

value: AJ

value: day 35


title: Cre+ 24h 3

status: Public on Dec 12 2018

description: Gene expression data from Lck-Cre+;Ikzf-/- splenic T cells treated for 24h with anti-CD3 and anti-CD28.

growth_protocol: Cells were cultured in RPMI 1640 medium (GE Healthcare HyClone) supplemented with 10% fetal bovine serum, 50 μM β-mercaptoethanol, 4 mM L-glutamine, 50 U/ml of penicillin and 50 μg/ml streptomycin.

extract_protocol: RNA was isolated using the Qiagen RNeasy Minikit.

treatment_protocol: The cells were either left untreated or activated for 24 hours with plate bound anti-CD3 and soluble anti-CD28.

value: spleen

value: CD4+ T cells

tag: genotype

value: Lck-Cre+;Ikzf-/-

tag: state

value: activated


title: Cre- 24h 1

description: Gene expression data from Lck-Cre-;Ikzf+/+ splenic T cells treated for 24h with anti-CD3 and anti-CD28.

value: Lck-Cre-;Ikzf+/+


title: Donor 1 - BMS

description: SAMPLE 2

value: Donor 1


title: Cre+ 0h 2

description: Gene expression data from Lck-Cre+;Ikzf-/- splenic T cells at baseline.

value: baseline


title: Cre+ 0h 1

source_name: Lck-Cre+;Ikzf-/- splenic T cells at baseline.


title: Cre- 0h 3

description: Gene expression data from Lck-Cre-;Ikzf+/+ splenic T cells at baseline.


title: Donor 2 - CTR

description: SAMPLE 3

value: Donor 2

value: airway smooth muscle (ASM) cells


title: Cre- 24h 3

source_name: Lck-Cre-;Ikzf+/+ splenic T cells treated for 24h with anti-CD3 and anti-CD28.


title: Donor 1 - CTR

description: SAMPLE 1


title: Cre+ 0h 3


title: Cre+ 24h 1

source_name: Lck-Cre+;Ikzf-/- splenic T cells treated for 24h with anti-CD3 and anti-CD28.


title: Subject 4

status: Public on Nov 26 2018

description: Gene expression data from right dorsolateral prefrontal cortex of subject with bipolar disorder with psychotic features.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hgu133plus2hsentrezgcdf R package (version 14.0.0).

source_name: dorsolateral prefrontal cortex of post-mortem brain tissue

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

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen).

tag: disease state

tag: laterality

value: right


title: Cre+ 24h 2


title: Cre- 24h 2


title: Subject 64


title: Subject 62

description: Gene expression data from left dorsolateral prefrontal cortex of subject with bipolar disorder with psychotic features.

value: left


title: Subject 34


title: Subject 2

description: Gene expression data from left dorsolateral prefrontal cortex of subject with bipolar disorder without psychotic features.


title: Subject 102


title: Subject 82

description: Gene expression data from right dorsolateral prefrontal cortex of subject with schizophrenia.

value: SCZ


title: Subject 6


title: Subject 74


title: Subject 57


title: Subject 45


title: Cre- 0h 2

source_name: Lck-Cre-;Ikzf+/+ splenic T cells at baseline.


title: Subject 36


title: Cre- 0h 1


title: Subject 25


title: Subject 9


title: Subject 93

description: Gene expression data from left dorsolateral prefrontal cortex of subject with schizophrenia.


title: Subject 22


title: Subject 80

description: Gene expression data from right dorsolateral prefrontal cortex of control subject.

value: control


title: Subject 47


title: Subject 78


title: Subject 38


title: Subject 35


title: Subject 15


title: Subject 62

type: genomic

description: Methylation data from left dorsolateral prefrontal cortex of subject with bipolar disorder with psychotic features.

hyb_protocol: Overnight hybridization to BeadChip arrays.

scan_protocol: Next day staining of hybridized arrays produced methylation-dependent differential fluorescence that was detected via an Illumina iScan array scanner.

data_processing: Raw intensities in the green and red channels of the fluorescent signal were read and converted to methylation status by the methylumIDAT function in the methylumi R package (version 2.20.0), which generated beta values and detection p values.

label: Cy5 and Cy3

label_protocol: 0.5 micrograms of bisulfite-converted DNA was amplified and fragmented using standard Illumina protocol.

extract_protocol: DNA was extracted using a phenol-chloroform protocol.


title: Subject 27

description: Gene expression data from left dorsolateral prefrontal cortex of control subject.


title: Subject 65


title: Subject 49


title: Subject 102

description: Methylation data from left dorsolateral prefrontal cortex of subject with bipolar disorder without psychotic features.


title: Subject 57

description: Methylation data from right dorsolateral prefrontal cortex of subject with bipolar disorder with psychotic features.


title: Subject 2


title: Subject 67


title: Subject 67

description: Methylation data from left dorsolateral prefrontal cortex of control subject.


title: Subject 15

description: Methylation data from right dorsolateral prefrontal cortex of control subject.


title: Subject 66


title: Subject 49


title: Subject 82

description: Methylation data from right dorsolateral prefrontal cortex of subject with schizophrenia.


title: Subject 71


title: Subject 45


title: Subject 70


title: TBI 739

status: Public on Nov 08 2018

description: Gene expression data from Lung collected 48 hours after mild traumatic brain injury treated with TBI.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene10stmmentrezgcdf R package (version 16.0.0).

growth_protocol: Female ICR mice were allowed to mature as normal in a temperature/humidity controlled diurnal light room with ad libitum access to water and food.

extract_protocol: After RNAlater fixation, a section from each of the two lung samples were placed in 600 μL of buffer RLT (Qiagen, Hilden, Germany) with 6 μL of 14.3 M beta-mercaptoethanol (Sigma) then homogenized using the TissueLyser II at 30 Hz for four minutes. RNA was then extracted from the homogenate using the QiaCube equipped with the RNeasy Plus Mini Kit.

treatment_protocol: When mice reached 22-28 grams (6-8 weeks of age) they received either mild traumatic brain injury or tail trauma. We used tail trauma as our control to determine if any sort of trauma (not necessarily specific to the brain) could provide a response. 48 hours after the respective trauma, the mice were sacrificed and RNA was extracted to analyze via microarray.

value: lung

value: TBI


title: TBI 738

source_name: Lung collected 48 hours after mild traumatic brain injury


title: Subject 68


title: Subject 25


title: NON-RELAPSE IN 3 YEAR (7)

status: Public on Oct 27 2018

city: Chongqing

first: Liang

last: Zhang

address: No. 10 Changjiang Zhi Rd., Yuzhong Dist

country: China

institute: Cancer Center of Daping Hospital, Third Military Medical University

description:
Human lung tissue RFS>3 year   7
RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with  GeneChip® Human Transcriptome Array 2.0 (Affymetrix, Santa Clara, CA).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data were processed by Affymetrix® Transcriptome Analysis Console software 3.0. We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.

source_name: Early stage NSCLC RFS>3 Year

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: The formalin-fixed and paraffin-embedded (FFPE) tissues of early stage NSCLC were selected accroding the RFS .Clinical data were acquired from medical records or telephone follow up.

extract_protocol: RNA was extracted from deparaffinized and proteinase K–treated FFPE tissue (20–40 mg) using the RNA prep Pure FFPE Kit (QIAGEN, Valencia, CA) according to the manufacturer’s instructions. RNA concentration and quality were assessed by absorbance spectrometry on a NanoDrop (Thermo Fisher Scientific, Wilmington, DE).

treatment_protocol: The LUAD FFPE tissue samples were cut into 8 micrometer sections, 5-8 pieces in total.

tag: diagnosis

value: early stage NSCLC

value: Lung

tag: adjuvant chemotherapy

value: yes


title: Subject 65


title: NON-RELAPSE IN 3 YEAR (5)

description:
Human lung tissue RFS>3 year   5
RMA expression value derived from Expression Console software; core-exon analysis


title: NON-RELAPSE IN 3 YEAR (4)

description:
Human lung tissue RFS>3 year   4
RMA expression value derived from Expression Console software; core-exon analysis


title: TT 741

description: Gene expression data from Lung collected 48 hours after tail trauma as a control for trauma treated with TT.

value: TT


title: NON-RELAPSE IN 3 YEAR (3)

description:
Human lung tissue RFS>3 year   3
RMA expression value derived from Expression Console software; core-exon analysis


title: TT 742

source_name: Lung collected 48 hours after tail trauma as a control for trauma


title: NON-RELAPSE IN 3 YEAR (6)

description:
Human lung tissue RFS>3 year   6
RMA expression value derived from Expression Console software; core-exon analysis


title: TT 740


title: NON-RELAPSE IN 3 YEAR (1)

description:
Human lung tissue RFS>3 year   1
RMA expression value derived from Expression Console software; core-exon analysis


title: RELAPSE IN 1 YEAR (7)

description:
Human lung tissue RFS<1 year  7
RMA expression value derived from Expression Console software; core-exon analysis

source_name: Early stage NSCLC RFS<1 Year


title: RELAPSE IN 1 YEAR (5)

description:
Human lung tissue RFS<1 year  5
RMA expression value derived from Expression Console software; core-exon analysis


title: RELAPSE IN 1 YEAR (6)

description:
Human lung tissue RFS<1 year  6
RMA expression value derived from Expression Console software; core-exon analysis


title: RELAPSE IN 1 YEAR (3)

description:
Human lung tissue RFS<1 year  3
RMA expression value derived from Expression Console software; core-exon analysis

value: no


title: RELAPSE IN 1 YEAR (4)

description:
Human lung tissue RFS<1 year  4
RMA expression value derived from Expression Console software; core-exon analysis


title: RELAPSE IN 1 YEAR (1)

description:
Human lung tissue RFS<1 year  1
RMA expression value derived from Expression Console software; core-exon analysis


title: NON-RELAPSE IN 3 YEAR (2)

description:
Human lung tissue RFS>3 year   2
RMA expression value derived from Expression Console software; core-exon analysis


title: DPSC 1

status: Public on Oct 22 2018

description: Gene expression data from primary dental pulp stem cells (DPSCs).

source_name: dental pulp stem cells (DPSCs)

growth_protocol: Undifferentiated hiPSCs were maintained on Matrigel (Corning) coated 6-well plates in TeSR-E8 medium (STEMCELL Technologies) with 100 μg/ml Primocin (1:500 dilution, Invivogen) in a 37°C incubator with 5% CO2.

extract_protocol: Cells were harvested from wells and RNA was extracted using using QIAshredder columns (QIAGEN, 79656) and the RNeasy Plus Mini Kit (QIAGEN, 74136) according to the QIAGEN manual instructions. Purified RNA was eluted in 30 µl nuclease-free water.

treatment_protocol: NCCs were passaged in TeSR-E7 basic medium supplemented with 0.5-1 µM CHIR99021 (CHIR), 10 ng/ml SB431542 (R&D Systems) and 100 μg/ml Primocin. All other cell types were passaged in alpha-modification of Eagle’s medium (Gibco/Invitrogen) supplemented with 10% FBS, 1 mM L-glutamine (Gibco/Invitrogen), and 100 μg/ml Primocin for 2-3 passages before RNA extraction for microarray analysis.

value: DPSC


title: SCAP 1

description: Gene expression data from primary stem cells of the apical papilla (SCAPs).

value: SCAP


title: WT 24 hr PCS rep2

status: Public on Oct 18 2018

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

description:
WT 24 hr PCS rep2
S5

data_processing:
Analysis was performed by the University of Delaware Bioinformatics Core Facility using a modified MAPRseq pipeline implemented on the BioMix compute cluster at the Center for Bioinformatics and Computational Biology/Delaware Biotechnology Institute
Sequence quality was assessed using FASTQC
Sequences were end-trimmed (Q30) and filtered (no ambiguous nucleotides, 35bp minimum length after trimming) using Trim Galore (v0.4.4)
Trimmed reads were aligned to the reference genome using Tophat v2.1.0
Mapping quality was assessed using RSeQC v2.3.7 and metrics extracted from BedTools v2.17 and SamTools v1.4
Feature counts were extracted using HtSeq v0.6.1p1
Pairwise differential expression analysis was performed on features with >1 cpm in at least 2 samples using EdgeR v 3.16.5
Genome_build: Mus musculus mm10 (UCSC tophat version as downloaded May 2017)
Supplementary_files_format_and_content: tab-delimited w/ the following columns: Chr, GeneID, Start, Stop, CodingLength, GeneCount, RPKM

source_name: Lens

extract_protocol:
By using in vivo mouse model of cataract surgery, lens fiber cells were removed from wild type (WT) via a central corneal incision, leaving behind the lens capsule and attached LECs, samples were harvested at 0 hour and 24 hours PCS, flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit (50) from Qiagen (Cat No./ID: 74104). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols for Stradeded TruSeq Library Preparation Kit for the Illumina HiSeq 2500

value: Lens capsule and attached LECs

tag: age

value: Adult 2 months old

value: wild type

value: 24 h after surgery


title: WT 24 hr PCS rep1

description:
WT 24 hr PCS rep1
S4


title: PCMP 7

description: Gene expression data from iPSC-derived putative craniofacial mesenchymal progenitors (PCMPs).

value: PCMP


title: PDLSC 2

description: Gene expression data from primary periodontal ligament stem cells (PDLSCs).

value: PDLSC


title: PDLSC 1

source_name: periodontal ligament stem cells (PDLSCs)


title: WT 0 hr PCS rep1

description:
WT 0 hr PCS rep1
S1

value: immediately after surgery


title: DPSC 2


title: Pineal_Gland_Night_2 [OriginalRef]

status: Public on Oct 05 2018

first: Joseph

middle: Charles

last: Mays

state: NY

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU School of Medicine

description: Animals were sacrificed during the "night" part of their light cycle (ZT1800)

data_processing:
Base-calling was performed using Illumina RTA v1.18.64.
Sequenced reads were aligned to the Rnor6.0 genome using CellRanger v2.1.0 with default parameters, once with the Ensembl 6.0.90 annotation, and again with a custom (ExtendedRef) annotation.
Cell barcodes predicted not to be associated with a cell were filtered using CellRanger v2.1.0 with default parameters.
Transcript counts were normalized to 10,000 molecules per cell. Additional manual filtering was performed to remove barcodes thought to be associated with multiple cells.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: tab-delimited text files in which each row is one gene, each column is one cell, and each entry is the library size-normalized transcript count value for a given gene in a given cell.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Pineal Gland

extract_protocol:
Rat pineal glands were extracted following sacrifice and dissocated into a single-cell suspension using the Papain Dissociation System, following manufacturer's instructions. PolyA mRNA was extracted using the 10X Genomics Chromium 3' v2 kit and manufacturer's protocol.
cDNA libraries were constructed and prepared for Illumina sequencing from ployA mRNA using the 10X Genomics Chromium 3' v2 kit and manufacturer's protocol.

value: Night

value: Sprague Dawley


title: WT 24 hr PCS rep3

description:
WT 24 hr PCS rep3
S6


title: Pineal_Gland_Night_1 [OriginalRef]


title: WT 0 hr PCS rep3

description:
WT 0 hr PCS rep3
S3


title: NCC 3

description: Gene expression data from iPSC-derived neural crest cells (NCCs).

source_name: neural crest cells (NCCs)

value: NCC


title: WT 0 hr PCS rep2

description:
WT 0 hr PCS rep2
S2


title: NCC 7


title: PCMP 3

source_name: putative craniofacial mesenchymal progenitors (PCMPs)


title: DPSC 3


title: Pineal_Gland_Night_2 [ExtendedRef]


title: BMSC 4

description: Gene expression data from primary bone marrow derived mesenchymal stromal cells (BMSCs).

value: BMSC


title: NCC 1


title: BMSC 1

source_name: bone marrow derived mesenchymal stromal cells (BMSCs)


title: BMSC 2


title: SCAP 2

source_name: stem cells of the apical papilla (SCAPs)


title: SCAP 4


title: Pineal_Gland_Night_1 [ExtendedRef]


title: PCMP 1


title: PDLSC 3


title: Pineal_Gland_Day_2 [ExtendedRef]

description: Animals were sacrificed during the "day" part of their light cycle (ZT0600)

value: Day


title: Pineal_Gland_Day_1 [ExtendedRef]


title: Pineal_Gland_Day_1 [OriginalRef]


title: Pineal_Gland_Day_2 [OriginalRef]


title: Cachectic 4

status: Public on Sep 28 2018

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

institute: Erasmus University Medical Center

hyb_protocol: Fluorescently labeled RNA was hybridized to custom Exiqon LNA capture probes (based on miRBase version 10, annotation version 13), spotted in duplicate on Nexterion E glass slides, for 16 hours at 60°C in a Tecan HS4800 hybridization station. The capture probe set consists of 1344 probes of which 577 are capable of detecting murine miRNAs.

scan_protocol: After hybridization, samples were washed and scanned using a Tecan LS Reloaded scanner. Image generation and feature extraction were performed using Imagene 6.0.

data_processing: The raw microRNA expression data, median signal minus median background, were normalized using quantile normalization. Obvious outliers were removed and murine miRNAs were selected with an average expression above background. Duplicate spots on the array were averaged.

source_name: C26 tumor-bearing cachectic mouse

label_protocol: 1 μg of total RNA of each separate sample was labelled with CY3 using the ULS™ aRNA Labeling Kit (Kreatech Diagnostics, the Netherlands)

growth_protocol: Male CD2F1 (BALB/c × DBA/2 F1) mice of 8 weeks (~ 25 grams) were obtained from Charles River, Maastricht, the Netherlands. Upon arrival, animals were housed in individually ventilated cages and maintained at 22 °C under a 12 h light-dark cycle with ad libitum access to CRM (P) chow (Special Diet Services, Witham, Essex, UK) and water (n = 3 – 4 animals per cage). Animals were acclimatized for one week prior to the start of the experiments. Animals allocated in tumour bearing (TB) groups received a subcutaneous (SC) inoculation in the right flank with 0.5 x 106 C26 adenocarcinoma cells in 100 μL sterile PBS under anaesthesia by isoflurane inhalation (5% isoflurane induction), a classic model of cancer cachexia.

extract_protocol: Total RNA was extracted from cell pellets using RNABee (BioConnect, the Netherlands) according to the manufacturer's instructions. All samples passed RNA quality control using Nanodrop 2000. MicroRNA profiling was performed as previously described (Pothof J. et al. 2009 EMBO J 28:2090-2099 / van Jaarsveld M.T.M. et al. 2013 Mol. Oncology 8:458-468)

treatment_protocol: SB431542 (Bio-connect BV, Huissen, The Netherlands) is a potent and selective inhibitor of the transforming growth factor-β type I receptors ALK4, ALK5, and ALK7. Dose: 10 mg/kg, schedule: daily, and route of administration: intraperitoneally (1 μL/g body weight)

value: CD2F1 (BALB/c x DBA/2 F1)

tag: gender

value: male

value: appr. 8 weeks

value: C26 tumor-bearing cachectic mouse

value: Gastrocnemicus muscle


title: Cachectic 3


title: SB431542 treated 3

source_name: C26 tumor-bearing treated for 21 days with daily dose of 10mg/kg SB431542

value: C26 tumor-bearing SB431542 treated mouse


title: Cachectic 2


title: SB431542 treated 1


title: Control 4

source_name: control

value: control


title: SB431542 treated 2


title: Control 1


title: Control 3


title: Experiment 1, NKX2-1-AS1siRNAs, biological replicate 2

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezg R package (version 16.0.0).

source_name: NCI-H441 cells

growth_protocol: NCI-H441 cells, derived from a papillary adenocarcinoma of the lung, were grown in the conditions recommended by ATCC.

extract_protocol: TRIzol RNA extraction was used to prepare samples for Experiment 1, while spin-column RNA extraction was used to prepare samples for Experiment 2. Total RNA was treated with DNA-Free kit.

treatment_protocol: Cells were transfected with custom made Silencer® Select siRNA designed to target the second exon of NKX2-1-AS1 and the region of the first exon not overlapping with the NKX2-1 sequence, or with non-silencing control.

tag: sirna

value: NKX2-1-AS1 siRNAs

tag: protocol

value: TRIzol


title: Control 2


title: Experiment 1, NKX2-1-AS1siRNAs, biological replicate 3


title: Experiment 1, Non-silencing control, biological replicate 2

value: control siRNA


title: Experiment 1, Non-silencing control, biological replicate 1


title: Experiment 2, Non-silencing control, biological replicate 3

value: spin-column


title: Experiment 2, Non-silencing control, biological replicate 2


title: Experiment 2, Non-silencing control, biological replicate 1


title: Cachectic 1


title: Experiment 2, NKX2-1-AS1siRNAs, biological replicate 3


title: Experiment 2, NKX2-1-AS1siRNAs, biological replicate 2


title: Experiment 2, NKX2-1-AS1siRNAs, biological replicate 1


title: d14 OVA+PorB 3

status: Public on Sep 26 2018

description: Gene expression data from the spleen of a mouse given a second vaccination with OVA+PorB.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor R package and the Brainarray mogene10stv1mmentrezg R package (version 14.0.0).

growth_protocol: 6 week old C57BL/6 were obtained from Jackson Labs (Bar Harbor, ME).

extract_protocol: Harvested spleens were homogenized, and RNA purified using and RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol.

treatment_protocol: Mice received vaccinations of 10ug ovalbumin, 10 ug PorB, or 10ug ovalbumin + 10ug PorB in 100uL PBS subcutaneously behind the neck on days -1, +13 and +27. Control mice received 100uL PBS only in a single vaccination. 24 hours post vaccination on the indicated date mice were euthanized and their spleens collected.

value: spleen

tag: timepoint

value: day 14

value: OVA+PorB

tag: group

value: d14 OVA+PorB


title: d14 OVA+PorB 1

source_name: spleen of a mouse given a second vaccination with OVA+PorB

tag: treatment


title: d28 OVA+PorB 1

description: Gene expression data from the spleen of a mouse given a third vaccination with OVA+PorB.

value: day 28

value: d28 OVA+PorB


title: d28 OVA+PorB 2

source_name: spleen of a mouse given a third vaccination with OVA+PorB


title: d14 OVA+PorB 2


title: d28 OVA+PorB 3


title: Experiment 1, Non-silencing control, biological replicate 3


title: Experiment 1, NKX2-1-AS1siRNAs, biological replicate 1


title: d0 OVA+PorB 1

description: Gene expression data from the spleen of a mouse given a single vaccination with OVA+PorB.

value: day 0

value: d0 OVA+PorB


title: d0 OVA+PorB 3

source_name: spleen of a mouse given a single vaccination with OVA+PorB


title: d14 PorB 1

description: Gene expression data from the spleen of a mouse given a second vaccination with PorB.

value: PorB

value: d14 PorB


title: d28 PorB 3

description: Gene expression data from the spleen of a mouse given a third vaccination with PorB.

value: d28 PorB


title: d14 PorB 2

source_name: spleen of a mouse given a second vaccination with PorB


title: d0 OVA+PorB 2


title: d14 PorB 3


title: d28 PorB 2

source_name: spleen of a mouse given a third vaccination with PorB


title: d0 PorB 1

description: Gene expression data from the spleen of a mouse given a single vaccination with PorB.

value: d0 PorB


title: d28 PorB 1


title: d0 PorB 3

source_name: spleen of a mouse given a single vaccination with PorB


title: d28 OVA 1

description: Gene expression data from the spleen of a mouse given a third vaccination with OVA.

value: OVA

value: d28 OVA


title: d28 OVA 2

source_name: spleen of a mouse given a third vaccination with OVA


title: d14 OVA 1

description: Gene expression data from the spleen of a mouse given a second vaccination with OVA.

value: d14 OVA


title: d0 OVA 3

description: Gene expression data from the spleen of a mouse given a single vaccination with OVA.

value: d0 OVA


title: d0 OVA 1

source_name: spleen of a mouse given a single vaccination with OVA


title: d14 OVA 2

source_name: spleen of a mouse given a second vaccination with OVA


title: d0 OVA 2


title: d14 OVA 3


title: ONC201

status: Public on Sep 25 2018

description: Gene expression data from U87 glioblastoma cells treated with ONC201 in 0.1% DMSO.

source_name: U87 glioblastoma cells treated with ONC20.1 in 0.1% DMSO

growth_protocol: Human glioma cells (U87) were cultured in DMEM (Corning, New York, USA) supplemented with 10% FBS at 37°C in 5% CO2.

treatment_protocol: After one day of cell seeding, U87 cells were treated with 200 nM of ONC201, ONC206, or ONC212 in 0.1% DMSO, or with 0.1% DMSO negative control, for 72 hours in DMEM supplemented with 1.5% FBS.

tag: cell line

tag: cell type

value: glioblastoma


title: PBS 3

description: Gene expression data from the spleen of a mouse given a single vaccination with PBS.

value: spleen

value: PBS


title: RELAPSE IN 1 YEAR (2)

description:
Human lung tissue RFS<1 year  2
RMA expression value derived from Expression Console software; core-exon analysis

source_name: Early stage NSCLC RFS<1 Year

value: early stage NSCLC

value: Lung

value: no


title: d0 PorB 2


title: d28 OVA 3

value: day 28


title: ONC212

description: Gene expression data from U87 glioblastoma cells treated with ONC212 in 0.1% DMSO.


title: ONC206

description: Gene expression data from U87 glioblastoma cells treated with ONC206 in 0.1% DMSO.


title: PBS 1

description: Gene expression data fr+L21:L43om the spleen of a mouse given a single vaccination with PBS.

value: day 0


title: Control

description: Gene expression data from U87 glioblastoma cells treated with 0.1% DMSO.

value: Control


title: PBS 2

source_name: spleen of a mouse given a single vaccination with PBS