title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833085_R04C01


title: Th0 MigR1 rep2

status: Public on Feb 06 2018

type: SRA

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

country: USA

institute: University of Pittsburgh

description: processed data file: RNAseq_Blimp1RV_poholek.txt

library_source: transcriptomic

data_processing:
Raw sequencing data were decoded and demultiplexed with CASAVA 1.8.2 to generate FastQ files, mapped onto the mouse genome build mm9 using Tophat2.0.8 and gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Cufflinks 2.2. All downstream statistical analyses were performed with Partek Genomics Suite 6.6.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: RNAseq_Blimp1RV_poholek.txt: Tab-delimited text file includes RPKM values.

molecule: total RNA

organism: Mus musculus

source_name: CD4 T cell

growth_protocol:
Cell isolation: Cells from spleen and lymph node were obtained by mechanical disruption and sort purified for naïve phenotype: CD4+ CD44lo CD62L+ CD25neg.
In vitro protocol: All cells were stimulated in RPMI medium with 10% FCS, 2mM glutamine, 100 IU/ml penicillin, 0.1mg/ml streptomycin, 20mM HEPES buffer pH 7.2-7.5, and 2mM β-mercaptoethanol. Cells were activated by plate-bound α-CD3 and α-CD28 (10ug/ml) for 3 days under neutral conditions, α-IL-4 (10ug/ml) and α-IFNg (10ug/ml).

extract_protocol:
Approximately 0.5e6 cells were isolated by sorting GFP+ cells from three independent biological replicates of CD4 T cells transduced with Empty Vector or Blimp-1 expressing retrovirus. Total RNA was prepared by using mirVana miRNA Isolation Kit (AM1560, ABI).
A fraction of total RNA (2 μg) was processed into mRNA-seq library by using TruSeq RNA sample prep kit (FC-122-1001, Illumina). The libraries were sequenced for 50 cycles (single read) with a HiSeq 2000 (Illumina).

treatment_protocol: RV transduction: Blimp-1 cDNA was cloned into MigR1 expression vector that uses GFP as a selection marker. Sorted naïve CD4+ T cells from WT were cultured in the presence of plate-bound α-CD3 (10ug/ml), α-CD28 (10ug/ml) with α-IFN-γ (10ug/ml) and α-IL-4 for 36 hrs, then transduced with control (empty vector, MigR1), or Blimp-1 expressing retrovirus and cultured for two days. Cells were sorted for RNA isolation (GFP+).

tag: strain/background

tag: genotype/variation

value: WT

tag: cell type

value: Th0 activated T cells

tag: transduction

value: empty vector


title: Th0 MigR1 rep1


title: KMS-11-HR_Hypoxia_24h_cell1

type: RNA

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

country: Japan

institute: Tokyo Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip® human Gene 2.0 ST Array, and washed according to the protocol described in WT PLUS Reagent Kit User Manual (P/N 703174 Rev. 2).

scan_protocol: GeneChips were and stained, and scanned by Scanner 3000 7G system according to the protocol described in WT PLUS Reagent Kit User Manual (P/N 703174 Rev. 2).

data_processing: The data were analyzed with Command Console Software ver. 3.2 and Expression Console Software ver. 1.3.0 using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Homo sapiens

source_name: hypoxia-resistant-Multiple Myeloma-derived subl line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng of total RNA.

growth_protocol: Parental cells (RPMI8226, KMS-11, U266, IM-9) and HR cells (RPMi8226-HR, KMS-11-HR, U266-HR, IM-9-HR) were seeded at a density of 5 × 10^5 cells/ml, and cultured for 24 hours under normoxia conditions (20% O2) and hypoxic conditions (1% O2, 5% CO2, 94% N2) in a humidified gas-sorted hypoxic incubator (MCO-5M, Sanyo, Osaka, Japan), respectively.

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

tag: cell line

value: KMS-11 (hypoxia-resistant)

tag: condition

value: hypoxia (1% O2)


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833085_R03C01

type: genomic

city: North Ryde

first: Peter

middle: Laurence

last: Molloy

state: NSW

address: 11 Julis Ave

department: Health and Biosecurity

country: Australia

institute: CSIRO

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing: Data was normalized using Bioconductor package 'wateRmelon'. Bioconductor package 'Harman' was used for batch correction. The raw data are available in the .idat files and in the file "signal_intensities_369samples.csv". The batch corrected and normalized beta values are available in the file "processed_369samples.csv" on the series record.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Neonatal blood spot,Control supplement

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from 3x3mm dried blood spot punches using GenSolve technology followed by purification using the QIAamp DNA micro kit and an additional ethanol precipitation step

tag: gender

value: Male

tag: tissue

value: neonatal blood spot


title: KMS-11_Normoxia_24h_cell1

source_name: Multiple Myeloma-derived cell line

value: Multiple Myeloma-derived cell line

value: normoxia (20% O2)


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833085_R02C01

source_name: Neonatal blood spot,Fish oil supplement

value: Female


title: KMS-11_Normoxia_24h_cell2


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833079_R06C02


title: RPMI8226-HR_Hypoxia_24h_cell2

value: RPMI8226 (hypoxia-resistant)

value: hypoxia-resistant-Multiple Myeloma-derived subl line


title: RPMI8226_Normoxia_24h_cell2


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833079_R04C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833079_R05C02


title: RPMI8226-HR_Hypoxia_24h_cell1


title: RPMI8226_Normoxia_24h_cell1


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833079_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833079_R06C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833079_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833079_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833079_R02C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833079_R01C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833079_R04C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833065_R06C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833079_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833065_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833065_R04C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833065_R03C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833065_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833085_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833065_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833065_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833065_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833079_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833065_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833065_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833065_R02C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833064_R06C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833065_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833064_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833064_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833064_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833064_R04C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833064_R02C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833064_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833064_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833064_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833064_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833062_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833062_R05C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833064_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833062_R06C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833062_R04C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833062_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833062_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833062_R04C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833062_R03C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833062_R02C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833062_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833007_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833007_R05C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833007_R02C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833064_R02C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833007_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833062_R01C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833007_R04C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833007_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833062_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833007_R06C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833007_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833007_R03C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005771156_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833007_R02C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005771156_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833007_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833007_R04C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005771156_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005771156_R04C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005771156_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005771156_R03C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005771156_R05C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005771156_R01C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005771156_R02C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886146_R06C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886146_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886146_R04C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886146_R03C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886146_R02C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886146_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886146_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886146_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886146_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886146_R04C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886146_R02C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886105_R06C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005771156_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886146_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886105_R01C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005771156_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886105_R04C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886105_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886105_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005771156_R04C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886105_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886105_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886105_R02C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886104_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886104_R04C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886105_R05C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886105_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886105_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886104_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886104_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886105_R05C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886104_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886104_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886104_R05C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886104_R02C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886104_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886104_R02C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886104_R03C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886068_R06C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886104_R01C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886068_R05C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886068_R04C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886068_R05C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886068_R01C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886068_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886068_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886068_R06C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886068_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886068_R02C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833073_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886068_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886068_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833073_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833073_R04C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833073_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833073_R01C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833073_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833073_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833073_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833073_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833073_R01C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833043_R04C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833043_R06C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833043_R06C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833043_R03C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833073_R02C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833073_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833043_R02C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833043_R02C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833035_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833043_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833043_R05C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833043_R01C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833035_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833043_R03C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833043_R05C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833043_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833035_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833035_R06C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833035_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833035_R05C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833035_R03C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833035_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833035_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833032_R05C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833032_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833032_R04C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833032_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833032_R02C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833032_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833032_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833032_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833032_R02C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833032_R03C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833035_R04C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886027_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833032_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833035_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886027_R05C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886027_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886027_R02C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886027_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886027_R05C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886027_R04C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833035_R02C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886027_R06C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833032_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886027_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886023_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886023_R04C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886023_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886023_R02C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886023_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886023_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886023_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886016_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886023_R01C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886023_R03C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886027_R04C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886016_R04C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886016_R02C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886016_R06C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886027_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886027_R02C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886016_R03C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886016_R01C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886023_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886016_R02C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886016_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886016_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886016_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886014_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886016_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886023_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886023_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886014_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886014_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886014_R04C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886014_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886014_R03C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886014_R05C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886014_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886014_R02C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886051_R06C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886014_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886051_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886016_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886051_R03C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886051_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886051_R02C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886051_R04C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886051_R05C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886028_R06C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886051_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886051_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886028_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886051_R02C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886028_R05C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886051_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886051_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886028_R01C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886028_R04C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886028_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886028_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886014_R02C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886028_R05C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886014_R04C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886028_R03C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886028_R02C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003885150_R06C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886028_R01C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003885150_R04C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003885150_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003885150_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003885150_R01C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003885150_R06C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003885150_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003885150_R01C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003885150_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003885149_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886028_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003885149_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003885150_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003885149_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003885149_R03C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003885149_R01C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003885149_R04C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003885149_R06C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003885150_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003885149_R04C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003885149_R01C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003885149_R02C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003885149_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003885149_R05C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003885150_R02C01


title: 5500994232094102715084_F02

city: Atlanta

first: Hanjoong

last: Jo

state: GA

address: 1760 Haygood Drive, Health Sciences Research Bldg E170

department: Coulter Department of Biomedical Engineering

institute: Georgia Tech and Emory Univ

hyb_protocol: Biotin-labeled cRNA was generated from the cDNA and used to probe a Human Genome U219 array (Affymetrix, Sunnyvale, CA, USA) Array hybridization, washing, and scanning were performed according to the manufacturer’s recommendations.

data_processing: CEL files from the Affymetrix Array Station were processed and normalized by the Robust Multi-Array Average (RMA) algorithm. No batch correction was performed in this version of RMA and it is suggested for an integrated analysis.

source_name: Whole blood

label_protocol: Double-stranded cDNAs were synthesized from 1 μg of total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and converted to double-strand using the cDNA Synthesis System (Invitrogen). Biotin-labeled cRNA was generated from the cDNA. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix.

extract_protocol: Total RNA was isolated, treated with DNase I, and cleaned up using a Qiagen RNeasy MinElute Cleanup Kit. RNA concentrations were determined using NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA) and RNA quality was evaluated using the Experion electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA).

treatment_protocol: PAXgene tubes were stored at -20C until processing for RNA extraction. RNA extraction and Affy profiling were performed in 4 different batches, noted in the experiment design.

tag: disease

value: RA

tag: batch

tag: glucocorticoids

value: TRUE

tag: Sex

value: F

value: peripheral blood from SLE and RA patients were collected directly into PAXgene tubes.


title: 5500994232094102715084_A05

scan_protocol: Array hybridization, washing, and scanning were performed according to the manufacturer’s recommendations.

value: SLE

value: FALSE


title: 5500994232094102715084_G03


title: 5500994232094102715084_D01

value: Normal


title: 5500994232094102715084_A04


title: 5500994232094102715084_C02


title: 5500994232094102715084_H02


title: 5500994232094102715084_B02


title: 5500994232094102715084_C04


title: 5500994232094102715084_B05

value: M


title: 5500994232094102715084_G06


title: 5500994232094102715084_H06


title: 5500994232094102715084_A06


title: 5500994232094102715084_H01


title: 5500994232094102715084_C06


title: 5500994232094102715084_F03


title: 5500994232094102715084_G04


title: 5500994232094102715084_G07


title: 5500994232094102715084_F01


title: 5500994232094102715084_C07


title: 5500994232094102715084_F06


title: 5500994232094102715084_F04


title: 5500024077142060710629_B01

hyb_protocol: Biotin-labeled cRNA was generated from the cDNA and used to probe a Human Genome HT_HG-U133A plate (Affymetrix, Sunnyvale, CA, USA) Array hybridization, washing, and scanning were performed according to the manufacturer’s recommendations.

data_processing: CEL files from the Affymetrix Array Station were processed and normalized by the Robust Multi-Array Average (RMA) algorithm

treatment_protocol: PAXgene tubes were stored at -20C until processing for RNA extraction.

value: 4 hour

tag: trial

tag: tx

value: PCBO

tag: dose

value: Male NHVs were randomly assigned to receive either a placebo of polyethylene glycol (PEG)-400 solution; a single daily oral dose of BMS-791826 (150 or 300 mg) as a PEG-400 solution; or a single daily dose of 10 mg prednisolone. PAXgene tubes were collected before dosing and at 4 hours postdose on day 1.


title: 5500024077142060710629_D06


title: 5500024077142060710629_B04


title: 5500024077142060710629_G02


title: 5500994232094102715084_D06


title: 5500024077142060710629_C01

value: 0 hour


title: 5500024077142060710629_H01

value: PRED


title: 5500024077142060710629_A05


title: 5500024077142060710629_B05


title: 5500024077142060710629_E05


title: 5500024077142060710629_A03


title: 5500024077142060710629_E07


title: 5500994232094102715084_B01


title: 5500994232094102715084_B04


title: 5500024077142060710629_E04


title: 5500024077142060710629_D08


title: 5500994232094102715084_E01


title: 5500024077142060710629_C05


title: 5500024077142060710629_B02


title: 5500024077142060710629_B07


title: 5500024077142060710629_E02


title: 5500024077142060710629_B03


title: 5500024077142060710629_F05


title: 5500024077142060710629_G04


title: 5500024077142060710629_H05


title: 5500994232094102715084_G02


title: 5500024077142060710629_H07


title: 5500024077142060710629_D01


title: 5500024077142060710629_D02


title: 5500994232094102715084_G05


title: 5500024077142060710629_D03


title: 5500024077142060710629_H06


title: 5500994232094102715084_D04


title: 5500994232094102715084_D02


title: 5500994232094102715084_E07


title: 5500994232094102715084_E06


title: 5500994232094102715084_E04


title: 5500994232094102715084_H05


title: 5500024077142060710629_D07


title: 5500994232094102715084_A01


title: 5500024077142060710629_E01


title: 5500024077142060710629_B08


title: 5500024077142060710629_A06


title: 5500024077142060710629_H04


title: 5500024077142060710629_F03


title: 5500024077142060710629_A02


title: 5500994232094102715084_C05


title: 5500024077142060710629_A08


title: 5500024077142060710629_B06


title: 5500024077142060710629_C04


title: 5500024051907020909371_H11

tag: time

value: Male NHVs were randomly assigned to receive daily doses of 5, 10, or 30 mg prednisolone for 9 days. Two participants received placebo. PAXgene tubes were collected before dosing and at 2, 4, 8, 48, 144, and 216 hours postdose.


title: 5500024077142060710629_G06


title: 5500994232094102715084_B03


title: 5500024051907020909371_H12


title: 5500994232094102715084_D03


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title: 5500994230972102515825_D12


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title: 5500024051907020909371_H04


title: 5500024051907020909372_H03


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title: 5500024051907020909371_H02


title: 5500994230972102515825_H03


title: 5500024051907020909372_H01


title: 5500994230972102515825_A08


title: 5500024051907020909371_H03


title: 5500024051907020909371_G11


title: 5500024051907020909371_H01


title: 5500024051907020909371_G12


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title: 5500024051907020909372_G04


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title: 5500024051907020909371_G02


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title: 5500024051907020909372_G03


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title: 5500024051907020909372_F03


title: 5500024051907020909372_F02


title: 5500994230972102515825_A02


title: 5500994230972102515825_F09


title: 5500024051907020909371_F01


title: 5500994230972102515825_C02


title: 5500024051907020909371_F04


title: 5500994230972102515825_G01


title: 5500024051907020909372_F01


title: 5500024051907020909371_E12


title: 5500994230972102515825_A05


title: 5500994230972102515825_F11


title: 5500994230972102515825_D10


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title: 5500024051907020909371RE_D07


title: 5500024051907020909371RE_D08


title: 5500024051907020909371_E01


title: 5500994230972102515825_H07


title: 5500994230972102515825_G12


title: 5500994230972102515825_G06


title: 5500994230972102515825_G08


title: 5500024051907020909371_D06


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title: 5500994230972102515825_A03


title: 5500024051907020909371_C11


title: 5500994230972102515825_H11


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title: 5500994230972102515825_E05


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title: 5500024051907020909371_D09


title: 5500024051907020909372_C06


title: 5500024051907020909372_C07


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title: 5500024051907020909371_C06


title: 5500024051907020909372_C04


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title: 5500024051907020909371_C02


title: 5500994230972102515825_A12


title: 5500024051907020909371_B09


title: 5500024051907020909372_C03


title: 5500994230972102515825_E02


title: 5500024051907020909371_B11


title: 5500024051907020909371_C05


title: 5500994230972102515825_E08


title: 5500024051907020909371_B08


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title: 5500994230972102515825_D06


title: 5500024051907020909371_C03


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title: 5500994230972102515825_H08


title: 5500994230972102515825_E07


title: 5500994230972102515825_E03


title: 5500024051907020909371_C01


title: 5500994230972102515825_B03


title: 5500994230972102515825_F06


title: 5500024051907020909371_B05


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title: 5500024051907020909371_B04


title: 5500024051907020909372_B08


title: 5500024051907020909372_B07


title: 5500024051907020909371_B06


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title: 5500024051907020909371_A09


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title: 5500024051907020909372_B05


title: 5500024051907020909372_B01


title: 5500024051907020909372_B02


title: 5500024051907020909372_B06


title: 5500024051907020909371_B03


title: 5500994230972102515825_H05


title: 5500024051907020909371_B01


title: 5500024051907020909372_B04


title: 5500024051907020909371_B02


title: 5500994232093102615054_A02


title: 5500024051907020909371_A10


title: 5500024051907020909372_A08


title: 5500994232093102615054_A07


title: 5500994232093102615054_C02


title: 5500994232093102615054_G08


title: 5500994232093102615054_G09


title: 5500994232093102615054_B10


title: 5500024051907020909371_A08


title: 5500994232093102615054_C11


title: 5500024051907020909372_A07


title: 5500994232093102615054_H05


title: 5500024051907020909371_A07


title: 5500024051907020909371_A06


title: 5500024051907020909371_A05


title: 5500994232093102615054_H04


title: 5500024051907020909372_A05


title: 5500024051907020909372_A04


title: 5500024051907020909372_A02


title: 5500024051907020909372_A06


title: 5500024051907020909372_A03


title: 5500994232093102615054_D08


title: 5500024051907020909371_A01


title: 5500024051907020909371_A04


title: 5500024051908013009382_E02

hyb_protocol: Biotin-labeled cRNA was generated from the cDNA and used to probe a Human Genome HT_HG-U133A plate (Affymetrix, Sunnyvale, CA, USA), consisting of 96 single HG-U133A arrays in a 96-well plate. Array hybridization, washing, and scanning were performed according to the manufacturer’s recommendations.

tag: treatment

tag: donor

value: D

value: Whole blood was preserved anticoagulant citrate dextrose solution !Sample_treatment_protocol = whole blood from 4 NHVs was cultured with either DMSO vehicle, 5 μM prednisolone, 5 μM BMS-791826, or 10 μM BMS-776532 for 5 hours, followed by transfer to a PAXgene tube.


title: 5500024051908013009382_G01

value: Pred


title: 5500994232093102615054_E08

value: RA


title: 5500024051908013009382_F02

value: Vehicle


title: 5500024051907020909371_A02


title: 5500024051907020909371_A03


title: 5500024051908013009382_G02


title: 5500994232093102615054_F12

value: F


title: 5500994232093102615054_H07

value: TRUE

value: peripheral blood from SLE and RA patients were collected directly into PAXgene tubes.


title: 5500994232093102615054_D05

value: FALSE


title: 5500994232093102615054_C08

value: SLE


title: 5500994232093102615054_F01


title: 5500024051908013009382_B03

value: C


title: 5500024051908013009382_B01


title: 5500994232093102615054_D12


title: 5500024051908013009382_C02


title: 5500994232093102615054_D03


title: 5500024051908013009382_A05

value: B


title: 5500024051908013009382_B02


title: 5500024051908013009382_C04


title: 5500024077142060710621_H07

source_name: peripheral blood mononuclear cells (PBMCs)

label_protocol: Double-stranded cDNAs were synthesized from 1 µg of total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and converted to double-strand using the cDNA Synthesis System (Invitrogen). Biotin-labeled cRNA was generated from the cDNA. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix.

extract_protocol: RNA was isolated using the Qiagen RNeasy isolation kit according to manufacturer’s instructions.

treatment_protocol: Cells were cultured at 5 million lymphocytes/well of a 96-well flat-bottom block plate (Qiagen, Hilden, Germany) in 500 µl assay media (RPMI-1640 with GlutaMAX, 10% charcoal-stripped fetal bovine serum; Gibco Laboratories, Gaithersburg, MD, USA). Cells were cultured for 6 hours with either dimethyl sulfoxide (DMSO) vehicle or 1 μM prednisolone. After 6 hours, cells were pelleted and resuspended in 1 ml nucleic acid purification lysis solution (Applied Biosystems, Foster City, CA, USA) diluted 1:2 with calcium-free and magnesium-free phosphate-buffered saline (Invitrogen, Carlsbad, CA, USA). Cells were incubated in lysis buffer for 10 minutes at room temperature followed by storage at –80°C.

value: PBMCs were isolated from the blood of 8 independent donors using Ficoll gradient centrifugation. Samples were collected and profiled in 4 batches as indicated in the experimental design.


title: 5500024051908013009382_G03

value: A


title: 5500024051908013009382_B05


title: 5500024051908013009382_D04


title: 5500994230972102515825_C09

value: Normal


title: 5500024076091050610804_D03


title: 5500024077142060710628_H05


title: 5500024051908013009382_F04


title: 5500994232093102615054_D02

value: M


title: 5500994232093102615054_F10


title: 5500994232093102615054_B04


title: 5500994232093102615054_C04


title: 5500024076091050610804_A02


title: 5500024077142060710628_F04


title: 5500994232093102615054_D09


title: 5500994232093102615054_G10


title: 5500024076091050610804_C01

value: DMSO


title: 5500994232093102615054_H08


title: 5500024077142060710628_D06


title: 5500024077142060710628_F05


title: 5500024077142060710628_C05


title: 5500024077142060710621_B07


title: 5500994232093102615054_B02


title: 5500994232093102615054_A05


title: 5500024051907020909372_A01

value: Male NHVs were randomly assigned to receive daily doses of 5, 10, or 30 mg prednisolone for 9 days. Two participants received placebo. PAXgene tubes were collected before dosing and at 2, 4, 8, 48, 144, and 216 hours postdose.


title: 5500024077142060710621_A07


title: 5500024063070081409289_G05


title: 5500024063070081409289_D07


title: 5500024063070081409289_H04


title: 5500024063070081409289_G11


title: 5500024063802093009566_H11


title: 5500024077142060710628_B03


title: 5500994232093102615054_H03


title: 5500024077142060710621_C07


title: 5500994232093102615054_G06


title: 5500994232093102615054_C09


title: 5500024063070081409289_F11


title: 5500994230972102515825_E01


title: 5500024063802093009566_G11


title: 5500994232093102615054_D06


title: 5500994232093102615054_G03


title: 5500024063070081409289_D09


title: 5500024063070081409289_B08


title: 5500024076091050610804_B02


title: 5500024063070081409289_E03


title: 5500994232093102615054_F09


title: 5500024063070081409289_E11


title: 5500024063070081409289_F05


title: 5500024063070081409289_C07


title: 5500994232093102615054_C03


title: 5500024063070081409289_H02


title: 5500994232093102615054_D10


title: 5500024051908013009382_G05

value: Whole blood was preserved anticoagulant citrate dextrose solution !Sample_treatment_protocol = whole blood from 4 NHVs was cultured with either DMSO vehicle, 5 μM prednisolone, 5 μM BMS-791826, or 10 μM BMS-776532 for 5 hours, followed by transfer to a PAXgene tube.


title: 5500994232093102615054_E05


title: 5500024036519102508685_D10

value: Pred


title: 5500994232093102615054_F11


title: 5500024036519102508685_G11


title: 5500024036519102508685_E11


title: 5500024036519102508685_B11


title: 5500024036519102508685_G07


title: 5500994232093102615054_F04


title: 5500024036519102508685_E09


title: 5500024036519102508685_G09


title: 5500994232093102615054_B12


title: 5500994232093102615054_B05

value: RA


title: 5500994232093102615054_B08


title: 5500024036519102508685_C10


title: 5500024036519102508685_H10


title: 5500024036519102508685_F10


title: 5500024036519102508685_G08


title: 5500024017802120306173_A12


title: 5500024017802120306173_G09


title: VA2

city: Kyoto

first: Yukiko

last: Hiramatsu

state: Kyoto

address: 54 Shogoin-Kawahara-cho, Sakyo-ku

department: Department of Gastroenterology and Hepatology

institute: Kyoto University Graduate School of Medicine

description: gene expression of isolated crypts of Villin-Cre; Arid1a f/f mouse intestines

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Data were normalized   on GeneSpring GX 14.5 (Agilent). Features flagged in Feature Extraction as not positive and significant or not above background were excluded.

source_name: Arid1a f/f

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 20ug Total RNA using the Pico WTA System(Ovation) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: isolated crypts

tag: strain

value: mixed

tag: genotype

value: Arid1a f/f


title: 5500024036519102508685_E08


title: 5500024017802120306173_A06


title: 5500994232093102615054_A03

value: F

value: peripheral blood from SLE and RA patients were collected directly into PAXgene tubes.


title: A1

description: gene expression of isolated crypts of Arid1a f/f mouse intestines


title: 5500024036519102508685_A11


title: A2


title: 5500024036519102508685_H09


title: 5500024017802120306173_D03


title: VA3

source_name: Villin-Cre; Arid1a f/f

value: Villin-Cre; Arid1a f/f


title: 5500994232093102615054_B07

value: SLE

value: FALSE


title: 5500994232093102615054_G12


title: 5500994232093102615054_A01


title: 5500994232093102615054_F06

value: TRUE


title: 5500994232093102615054_E10


title: 5500024017802120306173_D07

value: PBMCs were isolated from the blood of 8 independent donors using Ficoll gradient centrifugation. Samples were collected and profiled in 4 batches as indicated in the experimental design.


title: A3


title: VA1


title: 5500994232093102615054_F07


title: 5500994232093102615054_C12


title: 5500994232093102615054_F02


title: 5500024017802120306173_G03


title: 5500024017802120306173_F12


title: KMS-27

city: Muraoka-Higashi 2-chome Fujisawa

first: Kazuhide

last: Nakayama

state: Kanagawa

department: Regenerative medicine Unit

institute: Takeda Pharmaceutical Company Limited

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.0.4.0).
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, then mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
RPM (reads per million) data were calculated using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (read count) for each sample.

growth_protocol: NCI-H929 cells were cultured in RPMI1640 medium containing 10%FBS and 0.05mM 2-Mercaptoethanol. U266B1 cells were cultured in RPMI1640 medium containing 15% FBS. RPMI8226, MM.1S, MM.1R, OPM2, KMM-1, KMS-11, KMS-20, KMS-21BM, KMS-26, KMS-27, KMS-28BM cells were cultured in RPMI1640 containing 10% FBS.

extract_protocol:
Total RNA was isolated and purified from cultured cells using an RNeasy Mini kit (QIAGEN).
A total of 10 ng RNA was reverse transcribed using the Ion AmpliSeq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific) following the manufacturer’s protocol. cDNA libraries were amplified and barcoded using Ion AmpliSeq Transcriptome Human Gene Expression core panel and Ion Xpress Barcode Adapter (Thermo Fisher Scientific).

tag: cell type

value: Multiple myeloma cell line


title: KMS-28BM

tag: cell line


title: KMS-26


title: 5500994232093102615054_D04

value: Normal


title: KMS-20


title: 5500024017802120306173_H08

value: DMSO


title: 5500024017802120306173_A05


title: 5500024017802120306173_F04


title: 5500024017802120306173_A11


title: 5500994232093102615054_A12


title: 5500994232093102615054_F05

value: M


title: 5500994232093102615054_H01


title: KMS-11


title: 5500994232093102615054_C10


title: 5500994232093102615054_A08


title: 5500024017802120306173_E05


title: 5500024017802120306173_D02


title: 5500024017802120306173_H02


title: 5500994232093102615054_B01


title: 5500994232093102615054_D07


title: KMM-1


title: 5500024017802120306173_D08


title: OPM2


title: 5500994232093102615054_G01


title: 5500024017802120306173_E11


title: KMS-21BM


title: MM.1R


title: 5500994232093102615054_A04


title: 5500994232093102615054_C06


title: 5500994232093102615054_E01


title: N2

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

description:
N_160727_2_1
processed data column: N1

data_processing:
Low quality portions of paired-end reads were trimmed using Trim galore (version 0.4.2; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with cutadapt (version 1.1.2)
Sequenced reads were mapped to the human genomes (hg38) using STAR (version 2.5.2b).
The abundances of known genes (GENCODE comprehensive gene annotation, version 27; https://www.gencodegenes.org/releases/current.html) were estimated using Cufflink (version 2.2.1)
Genome_build: hg38
Supplementary_files_format_and_content: Text file

source_name: Adjacent normal tissue

extract_protocol:
Poly(A) RNA was purified from 1 g total RNA of each sample, and cDNA was synthesized using SuperScript II (Invitrogen).
Sequencing libraries were prepared using the TruSeq RNA Library preparation kit (Illumina) and sequenced by using HiSeq 2500 (Illumina).

value: adjacent normal tissue


title: N3

description:
N_160727_3_1
processed data column: N2


title: MM.1S


title: U266B1


title: N1

description:
N_160727_1_1
processed data column: N0


title: RPMI8226


title: C8

description:
C_160727_8_1
processed data column: C8

source_name: Breast cancer tissue

value: breast cancer tissue

tag: cancer type

value: Invasive ductal carcinoma

tag: cancer subtype

value: Luminal B type


title: C9

description:
C_160727_9_1
processed data column: C9

tag: tissue


title: BJ_WGBS

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

library_source: genomic

data_processing:
The libraries were sequenced with 100-bp paired-end reads on an Illumina HiSeq 2500 instrument. 10 bp was clipped from the WGBS raw sequencing reads at either end.
BiSeq raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) or bsmap 2.7 (Xi et al. 2009) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: bed. Column headers are: Chr, Start, End, methylatedCpG/TotalCpG, Score, Strand

source_name: BJ Fibroblasts

growth_protocol: Clonal FOXA2 doxycycline inducible cells lines were derived from an immortalized BJ foreskin fibroblast cell line from ATCC (BJ-5ta; CRL-4001).  Cells were cultured in MEM-Alpha (Life technologies: 32561-037) with 10% FBS, 1% pen-strep, .01mg/mL hygromycin B and 5ng/mL bFGF.  Derived BJFOXA2 lines were grown in the same conditions plus .5ug/mL Puromycin.

extract_protocol:
PureLink DNA extraction
Swift kit

tag: cell line background

tag: genotype/variation

value: FOXA2 doxycycline inducible cell line

tag: treated with

value: none (uninduced)


title: C7

description:
C_160727_7_1
processed data column: C7


title: C6

description:
C_160727_6_1
processed data column: C6


title: NCI-H929


title: C4

description:
C_160727_4_1
processed data column: C4


title: C5

description:
C_160727_5_1
processed data column: C5


title: C3

description:
C_160727_3_1
processed data column: C3


title: C2

description:
C_160727_2_1
processed data column: C2


title: 5500994232093102615054_G04

tag: disease

tag: batch

tag: glucocorticoids

tag: Sex

value: F


title: C0

description:
C_160727_0_1
processed data column: C0


title: 5500994232093102615054_E07

value: peripheral blood from SLE and RA patients were collected directly into PAXgene tubes.


title: 5500994232093102615054_D01


title: 5500994232093102615054_B03

value: RA


title: 5500994232093102615054_G11


title: 5500994232093102615054_E04


title: 5500994232093102615054_B11


title: 5500994232093102615054_H02

value: SLE


title: 5500994232093102615054_E03

value: FALSE


title: 5500994232093102615054_C05


title: 5500994226366082015802_E04

value: TRUE


title: 5500994232093102615054_G02


title: 5500994226366082015802_D01


title: 5500994226366082015802_D03


title: 5500994226366082015802_H01


title: 5500994226366082015802_F09


title: 5500994232093102615054_E12


title: 5500994226366082015802_A07


title: 5500994232093102615054_E09


title: 5500994226366082015802_H05


title: C1

description:
C_160727_1_1
processed data column: C1


title: 5500994226366082015802_F01


title: 5500994226366082015802_A10


title: 5500994226366082015802_C08


title: 5500994226366082015802_B07


title: 5500994226366082015802_A04


title: 5500994226366082015802_B06


title: 5500994226366082015802_A08


title: 5500994226366082015802_A11


title: 5500994226366082015802_A05


title: 5500994226366082015802_F06


title: 5500994226366082015802_H08


title: 5500994226366082015802_B09


title: 5500994226366082015802_E05


title: TAC_1 [transcriptome]

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
TAC_1
RNA extracted from tacrolimus-treated mouse kidneys (Replicate 1).

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours.

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and differential analysis using Limma package in R / Bioconductor.

source_name: Kidney, tacrolimus

label_protocol: Agilent - Low RNA input QuickAmp.

extract_protocol: Total RNAs were extracted from kidneys using miRNeasy Mini kit (Qiagen).

treatment_protocol: CD-1 mice were treated with Tacrolimus (1mg/kg/d for 28 days) or physiological serum as control.

tag: strain/background

value: Kidney (total)

value: Tacrolimus

tag: amount in (ug)

tag: rin number


title: CTL_4 [transcriptome]

description:
CTL_4
RNA extracted from control mouse kidneys (Replicate 4).

source_name: Kidney, control

tag: treatment

value: Physiological serum


title: TAC_4 [transcriptome]

description:
TAC_4
RNA extracted from tacrolimus-treated mouse kidneys (Replicate 4).


title: 5500994226366082015802_D02


title: CTL_2 [transcriptome]

description:
CTL_2
RNA extracted from control mouse kidneys (Replicate 2).


title: 5500994226366082015802_D04


title: 5500994226366082015802_C10


title: TAC_3 [transcriptome]

description:
TAC_3
RNA extracted from tacrolimus-treated mouse kidneys (Replicate 3).


title: 5500994226366082015802_E03


title: 5500994226366082015802_F04


title: 5500994226366082015802_F07


title: N-myc-low

city: Shanghai

first: Hao

last: Gu

address: 280 South Chongqing Road, Shanghai

country: China

institute: Shanghai Jiao Tong University School of Medicine

description: gene expression

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole mouse Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for array slides (Scan Area 61x21.6 mm, Scan resolution 5 μm, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: SoNar-low B-ALL cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 μg RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit purification (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: SoNar-high and SoNar-low B-ALL were lysed by TRIzol reagent for extraction of RNA. RNA was prepared using RNasey Mini Kit(Qiagen p/n 74104) according to  the manufacturer's recommendations. After clean-up, RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored by RNA electrophoresis.

treatment_protocol: SoNar-high and SoNar-low B-ALL cells were sorted from bone marrow based on ratio F405/F488 nm.

value: bone marrow

tag: age

value: 8 weeks

tag: strain


title: 5500994226366082015802_G11


title: 5500994226366082015802_D05


title: 5500994226366082015802_B03


title: 5500994226366082015802_B12


title: 5500994226366082015802_G09

value: M


title: D2C2-FL-HIGH

description: gene expression

source_name: SoNar-high fetal liver blood cells

extract_protocol: SoNar-high and SoNar-low fetal liver blood cells were lysed by TRIzol reagent for extraction of RNA. RNA was prepared using RNasey Mini Kit(Qiagen p/n 74104) according to  the manufacturer's recommendations. After clean-up, RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored by RNA electrophoresis.

treatment_protocol: SoNar-high and SoNar-low fetal liver blood cells were sorted from E13.5 fetal liver based on ratio F405/F488 nm.

value: fetal liver blood cells


title: M615 T1 -- MLN128

city: Los Angeles

first: David

last: Shackelford

state: CA

address: 10833 LeConte Avenue

department: Division of Pulmonary and Critical Care Medicine

institute: UCLA - David Geffen School of Medicine

description: Gene expression data from lung  squamous cell carcinomas dissected form Kras;Lkb1 mice treated with 1mg/kg MLN128 for 8 weks

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Lung squamous cell carcinoma from mouse that was treated daily with 1mg/kg MLN128 for 8 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tumors were induced in Kras LSL-G12D; Lkb1 fl/fl mice by intranasal administration of Adenoviral Cre.

extract_protocol: Extraction of total RNA was performed with Qiagen RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Four weeks after tumor induction, mice were randomly assigned into two groups and treated daily with either Vehicle or 1mg/kg MLN128 for 8 weeks. At the end of the study, mice were euthanized and tumors were dissected out from lung and snap frozen in liquid nitrogen. Frozen tumors were stored in -80C freezer.

value: lung squamous cell carcinoma

tag: genotype

value: Kras LSL-G12D; Lkb1 f/fl; LSL-Luc


title: 5500994226366082015802_C06


title: CTL_3 [transcriptome]

description:
CTL_3
RNA extracted from control mouse kidneys (Replicate 3).


title: 5500994226366082015802_B01


title: TAC_2 [transcriptome]

description:
TAC_2
RNA extracted from tacrolimus-treated mouse kidneys (Replicate 2).


title: 5500994226366082015802_E07


title: 5500994226366082015802_C09


title: 5500994232093102615054_A11


title: M651 T1 -- Vehicle

description: Gene expression data from lung  squamous cell carcinomas dissected form Kras;Lkb1 mice treated with Vehicle for 8 weks

source_name: Lung squamous cell carcinoma from mouse that was treated daily with Vehicle for 8 weeks

value: Vehicle


title: 5500994232093102615054_B09

value: Normal


title: D2C2-FL-LOW

description: gene expression

source_name: SoNar-low fetal liver blood cells


title: 5500994226366082015802_A02


title: M570 T3 -- Vehicle


title: Th1

city: Fukuoka

first: Mitsuhiro

last: Kanamori

state: Fukuoka

address: Higashi-ku Maidashi 3-1-1

department: Allergy and Immunology

institute: Kyushu University

hyb_protocol: Expression Hybridization Kit (#5188-5242; Agilent)

scan_protocol: DNA Microarray Scanner (Agilent)

data_processing:
Feature Extraction ver 10.7.1.1 (Agilent)
GeneSpring GX 12.0 (Agilent) with Threshold raw signals to 1.0, Normalization algorithm: Percentile Shift, and Shift to percentile: 75

source_name: Splenic naïve CD4 T cells

label_protocol: Quick-Amp Labeling Kit (#51900612; Agilent)

extract_protocol: Total RNA was purified with ReliaPrep RNA Cell Miniprep System (Promega)

treatment_protocol: Th1 cells were induced from splenic naïve CD4 T cells by culturing for 4 days under the Th1-inducing condition (anti-CD3/CD28, anti-IL-4, IL-2 and IL-12)

tag: cell type

value: Splenic naïve CD4 T cells

tag: cell subtype


title: Th1reg

treatment_protocol: Th1reg cells were prepared by culturing rested cells for 4 days under the iTreg-inducing condition (anti-CD3/CD28, anti-IFNg/IL-4, IL-2 and TGF-b)


title: 5500994226366082015802_H06

value: F

value: peripheral blood from SLE and RA patients were collected directly into PAXgene tubes.


title: rested

treatment_protocol: Rested cells were prepared by culturing Th1 cells for 4 days with anti-IFN-g/IL-4 and IL-2

value: rested Th1


title: Th1+TGFb

treatment_protocol: Th1+TGFb cells were prepared by culturing Th1 cells for 4 days under the iTreg-inducing condition (anti-CD3/CD28, anti-IFNg/IL-4, IL-2 and TGF-b)

value: Th1 cultured under the iTreg condition


title: iTreg

treatment_protocol: iTreg cells were induced from splenic naïve CD4 T cells by culturing for 4 days under the  iTreg-inducing condition (anti-CD3/CD28, anti-IFNg/IL-4, IL-2 and TGF-b)

value: iTreg


title: 5500994226366082015802_E11

value: SLE

value: FALSE


title: CTL_1 [transcriptome]

description:
CTL_1
RNA extracted from control mouse kidneys (Replicate 1).

tag: tissue

value: Kidney (total)

value: Physiological serum


title: 5500994226366082015802_E02


title: HD_MCF7_siER_Rep3

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

description:
siRNA_ER_3
Sample_siRNA_ERa_C

data_processing:
Raw RNA-Seq reads were aligned using using TopHat v2. Gencode v24 was used as reference set of gene annotations and hg38 as referenge genomic sequence.
Read count was performed using featureCounts algorithm in default settings and read count tables were normalized with DESeq2 package.
Differentially expression between siCTR and siERα-treated MCF-7 was performed using DESeq2 in default settings.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include the normalized read counts for each sample

molecule: polyA RNA

growth_protocol: MCF-7 were growth in hormone-depleted (HD) media obtained from phenol red-free DMEM supplemented with 5% charcoal-dextran-treated serum.

extract_protocol: The starting RNA-seq datasets were obtained from libraries generated with the TruSeq stranded library preparation kit (Illumina) using as input material polyA(+) RNA fraction.

treatment_protocol: MCF-7 cells were grown 4 days in this media before being transfected with siRNAs using Lipofectamine2000 (Life Technologies), according to the reverse transfection protocol. Stealth RNAi™ siRNAs from Invitrogen were used to target ERα mRNA (ESR1HSS103376, ESR1HSS103377, ESR1HSS176619); stealth RNAi™ siRNA Negative Control medium GC was used as a control (siCTR).

tag: cell line

value: breast cancer cell line

tag: transfected with

value: siER


title: HD_MCF7_siCTR_Rep1

description:
siRNA_CTRL_1
Sample_siRNA_CTRL_A

value: siCTR


title: HD_MCF7_siCTR_Rep2

description:
siRNA_CTRL_2
Sample_siRNA_CTRL_B


title: HD_MCF7_siER_Rep2

description:
siRNA_ER_2
Sample_siRNA_ERa_B


title: HD_MCF7_siER_Rep1

description:
siRNA_ER_1
Sample_siRNA_ERa_A


title: HD_MCF7_siCTR_Rep3

description:
siRNA_CTRL_3
Sample_siRNA_CTRL_C


title: 5500994226366082015802_F05


title: 5500994226366082015802_E10

value: RA


title: F695 T1 -- MLN128

value: lung squamous cell carcinoma

value: Kras LSL-G12D; Lkb1 f/fl; LSL-Luc


title: 5500994226366082015802_G05

value: TRUE


title: 5500994226366082015802_G02


title: H1299 cells_mock_24h_rep3

city: hefei

first: Wanglai

last: Hu

address: 81 Meishan road

institute: Anhui Medical University

description: lncRNA expression after 24h in mock-treated human lung adenocarcinoma cell H1299

hyb_protocol: The labeled samples were hybridized with Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) in Agilent’s SureHyb Hybridization Chambers according to the manufacturer’s standard protocols (Agilent Technologies).

scan_protocol: The arrays were scanned by the Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: TP53-null H1299 human lung adenocarcinoma cells,24h,mock,replicate3

label_protocol: The toatl RNA were labled with the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instruction.

growth_protocol: Cells were cultured with DMEM medium with 10% heat-inactivated fetal bovine serum and incubated at 37 ºC in a humidified incubator with 5% CO2.

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

treatment_protocol: Cells were cultured with medium with and without additional 1 ug doxycycline for 24h.

value: human lung adenocarcinoma cells

tag: p53-inducible system

value: doxycycline inducible Tet-on system


title: F612 T1 -- MLN128


title: H1299 cells_mock_24h_rep2

source_name: TP53-null H1299 human lung adenocarcinoma cells,24h,mock,replicate2


title: N-myc-high

description: gene expression

source_name: SoNar-high B-ALL cells

value: bone marrow

value: 8 weeks


title: H1299 cells_doxycycline_24h_rep3

description: lncRNA expression after 24h in doxycycline-treated human lung adenocarcinoma cell H1299

source_name: TP53-null H1299 human lung adenocarcinoma cells,24h,doxyclycine,replicate3


title: 5500994226366082015802_E08

source_name: Whole blood

tag: disease

value: F

value: peripheral blood from SLE and RA patients were collected directly into PAXgene tubes.


title: M578 T4 -- Vehicle

value: Vehicle


title: 5500994226366082015802_G03

tag: batch

value: FALSE


title: 5500994226366082015802_B02

value: Normal

tag: glucocorticoids


title: H1299 cells_doxycycline_24h_rep2

source_name: TP53-null H1299 human lung adenocarcinoma cells,24h,doxyclycine,replicate2


title: H1299 cells_mock_24h_rep1

source_name: TP53-null H1299 human lung adenocarcinoma cells,24h,mock,replicate1


title: H1299 cells_doxycycline_24h_rep1

source_name: TP53-null H1299 human lung adenocarcinoma cells,24h,doxyclycine,replicate1


title: 5500994226366082015802_D10

tag: Sex


title: 5500994226366082015802_F03


title: 5500994226366082015802_D06


title: 5500994226366082015802_D11


title: 5500994226366082015802_G01


title: 5500994226366082015802_D08


title: 5500994226366082015802_H04

value: M


title: dsaeR.3

city: Chicago

first: Laura

last: Cook

state: IL

address: 900 S. Ashland Avenue (870)

department: College of Pharmacy

institute: University of Illinois at Chicago

description: GBS A909dsaeR colonizing the murine vaginal tract 48 h post-inoculation Rep 3

data_processing:
Basecalls performed using Illumina Basespace
Adaptors and low-quality reads were trimmed using trimGalore 0.4.0
Short reads were aligned to the Streptococcus agalactiae A909 reference genome assembly with BWA mem 0.7.15
Raw counts of the reads of genes were quantified using featureCounts in Subread 1.5.1
Genome_build: NC_007432.1, Streptococcus agalactiae A909, complete genome
Supplementary_files_format_and_content: txt files were generated by featureCounts in Subread 1.5.1. Each column represent one sample. Each row represent one gene

organism: Streptococcus agalactiae A909

source_name: GBS A909

growth_protocol: Samples grown in liquid medium were grown overnight, diluted and then grown to mid-log phase. In the vaginal tract, samples were inoculated at 10^7 CFU/mouse and bacteria were collected by vaginal lavage at 48 hours post-inoculation

extract_protocol:
RNA was extracted from liquid cultures or vaginal lavage fluid using the Ambion Ribopure Bacterial RNA prep kit (Thermofisher AM1925), for mouse samples, eukaryotic RNA was depleted using MICROBEnrich kit (Thermo Fisher AM1901) rRNA was removed via the MICROBExpress kit (Thermo Fisher AM1905)
cDNA libraries were constructed using the KAPA Stranded RNA-Seq Library Preparation Kit for Illumina Platforms (KAPABiosystems, KR0934).

tag: genotype/variation

value: mutant


title: 5500994226366082015802_E09


title: 5500994226366082015802_D09


title: dsaeR.2

description: GBS A909dsaeR colonizing the murine vaginal tract 48 h post-inoculation Rep 2


title: dsaeR.1

description: GBS A909dsaeR colonizing the murine vaginal tract 48 h post-inoculation Rep 1


title: 5500994226366082015802_H10


title: 5500994226366082015802_G08


title: dsaeR_THY.1

description: GBS A909dsaeR grown in THY Rep 1


title: 5500994226366082015802_C03


title: dsaeR_THY.2

description: GBS A909dsaeR grown in THY Rep 2


title: dsaeR_CDM.1

description: GBS A909dsaeR grown in chemically defined medium Rep 1


title: dsaeR_CDM.3

description: GBS A909dsaeR grown in chemically defined medium Rep 3


title: dsaeR_CDM.2

description: GBS A909dsaeR grown in chemically defined medium Rep 2


title: A909.3

description: GBS A909 colonizing the murine vaginal tract 48 hours post-inoculation Rep 3

value: wildtype


title: 5500994226366082015802_H07


title: 5500994226366082015802_G06


title: CAL-1_shRUNX2_#1

city: Kumamoto

first: Goro

last: Sashida

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: IRCMS

institute: Kumamoto University

description: Gene expression in RUNX2 knocked down CAL-1 cells 3 days post transduction

hyb_protocol: 600 ng of the labeled cRNA was hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray ver.3. The process of hybridization and washing was performed using an Expression Hybridization Kit (Agilent) and a Gene Expression Wash Pack (Agilent), respectively.

scan_protocol: GeneChips were scanned using a DNA microarray scanner and Feature Extraction ver 10.7.1.1 (Agilent Technologies)

data_processing: Standard Agilent protocol using GeneSpringGX14.5 (Agilent Technologies): Threshold raw signals to 1.0. Normalizsation algorithm, Pertentile Shift. Shift to percentile, 75.

source_name: CAL-1, shRNA RUNX2 vector #1, replicate 1

label_protocol: 100 ng of total RNA was mixed with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent), amplified and labeled with Cyanine 3 using a Low Input Amp Labeling Kit (Agilent) according to the manufacturer's instructions, which generated single-color labeled cRNA.

extract_protocol: RNeasy Plus Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: CAL-1 cells were infected by either shRNA-Luciferase or shRNA-RUNX2 IRES-GFP retrovirus vectors, and then GFP-expressing CAL-1 cells were sorted 3 days post infection by using FACSAriaII (BD).

tag: cells

value: BPDCN

tag: runx2 knock down

value: YES


title: CAL-1_shRUNX2_#2

source_name: CAL-1, shRNA RUNX2 vector #2, replicate 1


title: A909.1

description: GBS A909 colonizing the murine vaginal tract 48 hours post-inoculation Rep 2


title: A909_CDM.3

description: GBS A909 grown in chemically defined medium Rep 3


title: 5500994226366082015802_H11


title: A909.2

description: GBS A909 colonizing the murine vaginal tract 48 hours post-inoculation Rep 1


title: A909_CDM.2

description: GBS A909 grown in chemically defined medium Rep 1


title: A909_CDM.1

description: GBS A909 grown in chemically defined medium Rep 2


title: 5500994226366082015802_A01


title: 5500994226366082015802_C07


title: TAC_4 [miRNome]

description:
TAC_4
RNA extracted from tacrolimus-treated mouse kidneys (Replicate 4).

hyb_protocol: Agilent : 100.0 ng at 55 degree_C during 20 hours.

data_processing: The R package AgiMicroRna was used to extract the TotalGenesignal value from the Agilent result files. Quantile normalization and differential analysis were performed using Limma package in R / Bioconductor.

source_name: Kidney, tacrolimus

tag: strain/background

value: Kidney (total)

tag: treatment

value: Tacrolimus

tag: amount in (ug)

tag: rin number


title: MDA-MB-231_shNC_2015-03-11

status: Public on Feb 05 2018

city: Austin

first: Blerta

last: Xhemalce

state: Texas

address: 2500 Speedway

institute: University of Texas at Austin

data_processing:
For all datasets, sequence quality was verified by FastQC, and no adapter trimming was performed due to a lack of detectable contamination in either ChIP-seq or RNA-seq.
For all datasets, reads were aligned to the hg38 reference genome using Tophat2 running Bowtie2 using the "--sensitive" set of options.
For RNA-seq data, all alignments marked as secondary by Tophat2 or with a mapping quality below 5 were removed, and the resulting BAM file was quantified using HTSeq based on Gencode v21 annotations. Later analysis of differential expression was performed in edgeR, as described in the manuscript.
For ChIP-seq data, PCR and optical duplicates were marked and discarded using Picard, and alignments with a mapping quality beow 5 were removed. Each read was then extended 200 base pairs (corresponding to the estimated fragment length). The extended alignments were then used to generate bigwig files, first by conversion to bedGraph format using the genomeCoverageBed tool in the Bedtools suite, followed by conversion to bigWig format using the bedGraphToBigWig utility provided by the UCSC Genome Browser.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files contain the density per million of reads at each genomic position, and are present for all ChIP-seq datasets. Tab delimited text fiels contain the total number of reads (obtained from HTSeq) within each gene, and are present for all RNA-seq datasets.

source_name: MDA-MB-231 cell line

growth_protocol: MDA-MB-231 cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, 100 μg/ml streptomycin and 2 mM L-glutamine (PSQ).

extract_protocol:
Total RNA and protein extraction was performed with the RNA/Protein purification kit from Norgen (#23000).
1.5 µg of total RNA (RIN=10) was used per RNA-Seq library (TruSeq stranded Total RNA) according to the standard Illumina protocol. 8 barcoded libraries were sequenced per lane with a HiSeq2000 instrument to obtain paired-end, 75 bp reads.

treatment_protocol: MDA-MB-231 cells stably expressing shNC or shMePCE were obtained by infection with retroviral particles produced in 293T cells by cotransfection of pSuper.Retro.Puro-shRNA with pCL-Ampho and selection 1µg/ml of puromycin.

tag: shRNA status

value: shNC


title: Hela-S3-GFP_MePCE_N-Ter

source_name: HeLa-S3 cell line

growth_protocol: Hela-S3-Flp-In cells were grown in spinner flasks at 75 rpm in RPMI+10%FBS+PSQ supplemented with 200 µg/ml of Zeocin (parental) or 400 µg/ml hygromycin (GFP and MePCE-Flag).

extract_protocol:
Cells were fixed with 0.37% formaldehyde for 10 minutes at room temperature and quenched with 20 mM Glycine for 5 min. Cells were washed 2 times with cold PBS supplemented with EDTA-free Complete Protease Inhibitor cocktail from Roche (PIC), and scraped 2 times with 2.5 ml of cold PBS+PIC w/o EDTA. Pellets were suspended in 1.6 ml of RIPA buffer (50 mM Tris-HCl (pH 8), 150 mM NaCl, 2 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS and PIC), sonicated in 15 ml conical tubes 3 times for 10 min at high 10 sec on/off cycles in a cooled Bioruptor and cleared by centrifugation for 15 min at 20,000 g at 4°C. The chromatin was quantified and the quality of DNA shearing was checked on a 1% agarose gel. The chromatin was diluted with RIPA Buffer to contain the equivalent of 10 ng/µl of DNA. 1 ml of chromatin corresponding to 10 µg of DNA was incubated with the appropriate antibodies O/N at 4°C, then with 25 µl of pre-washed Protein G Dynabeads® for 3 h at room temperature. The beads were washed for 5 min at RT with 1 ml of TSE-150 (0.1% SDS, 1% Triton X-100, 150 mM NaCl, 2 mM EDTA, 20 mM Tris-HCl, pH 8), TSE-500 (0.1% SDS, 1% Triton X-100, 500 mM NaCl, 2 mM EDTA, 20 mM Tris-HCl, pH 8), LiCl buffer (0.25 M LiCl, 1% NP-40, 1% DOC, 1 mM EDTA, 10 mM Tris, pH 8) and TE (10 mM Tris-HCl, pH8, 0.1 mM EDTA). The immuno-complexes were eluted from the beads using a total of 125 µl of elution buffer (100 mM sodium bicarbonate, 1% SDS) for 30 min at 30°C and de-crosslinked overnight at 65°C. The ChIP samples were purified with the Qiaquick® PCR purification kit (Qiagen) and the DNA was eluted from the columns with 50 µl of water.
10 ng of DNA (size ~200 bp) from inputs and ChIP was used per ChIP-Seq library (Bioo ChIP-Seq kit) following manufacturers instructions. 8 barcoded libraries were sequenced in one lane with a HiSeq2000 instrument to obtain single-end, 36 bp reads.

treatment_protocol: HeLa-S3-FlpIn cells were previously described (Xhemalce et al., 2012). Isogenic HeLa-S3-FlpIn cell lines containing either GFP or MePCE-Flag inserted at the single FRT site were constructed according to the protocol provided with the Flp-In™ system.

tag: chip antibody

value: Anti-MePCE, Origene, Catalog #TA590479, Lot #T01235A02


title: MDA-MB-231_shMePCE_2015-03-11

value: shMePCE


title: Hela-S3-GFP_Input


title: MDA-MB-231_shMePCE_2015-03-09


title: MDA-MB-231_shNC_2015-03-09


title: Hela-S3-GFP_Beads


title: TAC_1 [miRNome]

description:
TAC_1
RNA extracted from tacrolimus-treated mouse kidneys (Replicate 1).

tag: tissue


title: 5500994226366082015802_C04

extract_protocol: Total RNA was isolated, treated with DNase I, and cleaned up using a Qiagen RNeasy MinElute Cleanup Kit. RNA concentrations were determined using NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA) and RNA quality was evaluated using the Experion electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA).

treatment_protocol: PAXgene tubes were stored at -20C until processing for RNA extraction. RNA extraction and Affy profiling were performed in 4 different batches, noted in the experiment design.


title: MDA-MB-231_shMePCE_RNAPII-S2

tag: cell line

value: Anti-RNAPII-S2P, Abcam, Catalog #ab5095, Lot #733314


title: MDA-MB-231_shMePCE_RNAPII-S5

value: Anti-RNAPII-S5P, Abcam, Catalog #ab5131, Lot #690055


title: MDA-MB-231_shMePCE_MePCE-N-ter


title: prostatesRNA_control_30d_rep1

city: Nanjing

first: Ruitong

last: Han

address: No. 22, Hankou Road, Gulou District

institute: Nanjing University

description: piRNA expression data from mouse prostates

hyb_protocol: The labeled samples were hybridized onto Arraystar Mouse piRNA Array in Agilent’s SureHyb Hybridization Chambers according to the manufacturer’s standard protocols (Agilent Technologies).

scan_protocol: The arrays were scanned by the Agilent Scanner G2505C.

source_name: prostatesRNA, control, 30d, replicate 1

label_protocol: Kit and instrument:  RNeasy Mini Kit (Qiagen p/n 74104)  NanoDrop ND-1000    Procedure:  1.Add 20 μL of nuclease-free water to your cRNA sample, for a total volume of 100 μL.  2.Add 350 μL of Buffer RLT and mix well by pipetting.  3.Add 250 μL of ethanol (100% purity) and mix thoroughly by pipetting. Do not centrifuge.  4.Transfer the 700 μL of the cRNA sample to an RNeasy mini column in a 2 mL collection tube. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through and collection tube.  5.Transfer the RNeasy column to a new collection tube and add 500 μL of buffer RPE (containing ethanol) to the column. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through. Re-use the collection tube.  6.Add another 500 μL of buffer RPE to the column. Centrifuge the sample at 4°C for 60 seconds at 13,000 rpm. Discard the flow-through and the collection tube.  7.Elute the cleaned cRNA sample by transferring the RNeasy column to a new 1.5 mL collection tube. Add appropriate RNase-free water (Passed-please see report ”Labeling Efficiency-QC”) directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm.  8.Maintain the cRNA sample-containing flow-through on ice. Discard the RNeasy column.  9. Take 1.5 μl of each sample to determine the yield and specific activity by using the NanoDrop ND-1000( Passed-please see report ”Labeling Efficiency-QC”).  From the main menu, choose MicroArray Measurement. Go to the Sample Type pull-down menu and select DNA-50.  Blank the instrument with 1.5 μL of 1x labeling solution.  Use 1.5 μL of purified labeled genomic DNA for quantitation. Measure the absorbance at A260nm (DNA), A550nm (cyanine 3).  The specific activity (pmol dyes per μg genomic DNA) of the labeled genomic DNA can be obtained by the following calculation:  (Concentration of Cy3)  Specific Activity =——————————————— = pmol Cy3 per μg cRNA  (Concentration of cRNA) * 1000  * If the yield is <1.65 μg and the specific activity is <9.0 pmol Cy3 per μg cRNA do not proceed to the hybridization step. Repeat cRNA preparation.

growth_protocol: Pregnant mice were randomly divided into 2 groups: control group and MC-LR group, with each mouse kept separately. From gestation day 12 to postnatal day 21, 2 groups of pregnant mice were exposed to 0 and 10 μg/L of MC-LR through drinking water. The male offspring were breastfed after natural birth. 30 days after birth, the organs were promptly frozen in liquid nitrogen until further analysis.empty-2P, empty-4P, empty-5P were the three samples from 3 offsprings of different pregnant mice in control group. 10-3P, 10-4P, 10-7P were the three samples from 3 offsprings of different pregnant mice in MC-LR group.

treatment_protocol: Prostates were manually selected under the dissecting scope, and promptly frozen in liquid nitrogen.

tag: group

value: control

value: prostate

tag: gender

value: male

tag: age


title: MDA-MB-231_shNC_MePCE-N-ter


title: MDA-MB-231_shNC_H3K4me3

value: Anti-H3K4me3, Abcam, Catalog #ab8580, Lot #197627


title: MDA-MB-231_shNC_RNAPII-S5


title: MDA-MB-231_shNC_RNAPII-S2


title: MDA-MB-231_shMePCE_GFP

value: Anti-GFP, Invitrogen, Catalog #A11122, Lot #779558


title: TAC_2 [miRNome]

description:
TAC_2
RNA extracted from tacrolimus-treated mouse kidneys (Replicate 2).


title: ARID1Ahigh good prognosis pt 2

city: Gifu

first: Tamotsu

last: Takeuchi

address: Yanagido

department: Pathology and Translational Research

institute: Gifu University School of Medcine

description: Gene expression in cancer cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.  Signal value of raw data, which was obtained by Agilent Feature Extraction, was further processed for normalization. #1 control sample value was removed. #2 Mean signal value was obtained after removal of top 2% and bottom 5% signal. #3 Scaling factor (SF) was calculated as, 2500 (target signal constant)/ signal of each array. #4 Scale signal was obtained by SF x probe signal of each array.

source_name: Gastric cancer tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: total RNA was extracted from the co-cultured cells using RNeasy spin columns kit (Qiagen).

treatment_protocol: Gastric cancer tissues were obtained by surgical resection.

tag: individual

value: pt 2

value: gastric cancer

tag: histopathological type

value: Adenocarcinoma

value: ARID1Ahigh good prognosis


title: MDA-MB-231_shMePCE_Input


title: CTL_1 [miRNome]

description:
CTL_1
RNA extracted from control mouse kidneys (Replicate 1).

source_name: Kidney, control

treatment_protocol: CD-1 mice were treated with Tacrolimus (1mg/kg/d for 28 days) or physiological serum as control.

value: Physiological serum


title: ARID1Alow and poor prognosis pt 1

description: Gene expression in cancer cells

value: pt 1

value: ARID1Alow and poor prognosis


title: CTL_4 [miRNome]

description:
CTL_4
RNA extracted from control mouse kidneys (Replicate 4).

value: Kidney (total)


title: CTL_3 [miRNome]

description:
CTL_3
RNA extracted from control mouse kidneys (Replicate 3).


title: MDA-MB-231_shNC_Input

value: shNC


title: ARID1Alow and poor prognosis pt 2

description: Gene expression in cancer cells


title: CAL-1_Control

description: Gene expression in CAL-1 cells 3 days post transduction

source_name: CAL-1, shRNA Luciferase vector, replicate 1

value: BPDCN

value: NO


title: CTL_2 [miRNome]

description:
CTL_2
RNA extracted from control mouse kidneys (Replicate 2).


title: ARID1Ahigh good prognosis pt 1

description: Gene expression in cancer cells


title: MDA-MB-231_shNC_GFP


title: MDA-MB-231_shMePCE_H3K4me3

value: shMePCE


title: TAC_3 [miRNome]

description:
TAC_3
RNA extracted from tacrolimus-treated mouse kidneys (Replicate 3).

value: Tacrolimus


title: prostatesRNA_MC-LR_30d_rep1

source_name: prostatesRNA, MC-LR, 30d, replicate 1

value: MC-LR

value: prostate


title: prostatesRNA_MC-LR_30d_rep3

source_name: prostatesRNA, MC-LR, 30d, replicate 3

value: male


title: prostatesRNA_control_30d_rep3

source_name: prostatesRNA, control, 30d, replicate 3

value: control


title: prostatesRNA_MC-LR_30d_rep2

source_name: prostatesRNA, MC-LR, 30d, replicate 2


title: [mouse BM][leukemic CD19+AA4.1+ nilotinib treated][3]

city: Monrovia

first: Nora

last: Heisterkamp

address: 1218 S Fifth Avenue

department: Department of Systems Biology

institute: Beckman Research Institute City of Hope

description: Gene expression data from nilotinib treated leukemic CD19+AA4.1+ mouse bone marrow cells

hyb_protocol: Hybridization according to Affymetrix protocol.

scan_protocol: Not provided

data_processing: Processed using the RMA alogorithm for normalization and summarization after import into BRB Array tool.

source_name: leukemic nilotinib treated bone marrow

label_protocol: Biotinylated cRNA was generated and fragmented according to the Affymetrix protocol.

growth_protocol: Wild type and transgenic mice of <60 and >90 days of age.

extract_protocol: Total RNA from CD19+ AA4.1+cells used for microarray analysis was isolated by RNeasy (QIAGEN) purification.

treatment_protocol: Total bone marrow was flow sorted for Cd19+AA4.1+ cells.

tag: strain

value: leukemic nilotinib treated bone marrow


title: [mouse BM][leukemic CD19+AA4.1+ nilotinib treated][2]


title: [mouse BM][normal CD19+AA4.1+][3]

description: Gene expression data from normal CD19+AA4.1+ mouse bone marrow cells

source_name: normal bone marrow

value: normal bone marrow


title: Naïve T-injected moderately inflamed colon tissue, biological rep2

city: CAMBRIDGE

first: Jesse

last: Lyons

state: Ma

address: 77 Massachusetts Ave 16-343

department: Bioengineering

institute: Massachusetts Institute of Technology

description: Gene expression data from moderately inflamed colons

hyb_protocol: Following labeling, biotinylated cRNA was hybridized to the Mouse Genome 430 2.0 GeneChips®  for 16 hr at 45C in an Affymetrix HybridizationOven 645. GeneChips® were washed and stained in the Affymetrix Fluidics Station 450 using the GeneChip® Hybridization, Wash, and Stain Kit.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the Affymetrix expression console with RMA processing.

source_name: colon tissue from Naïve T-injected mice

label_protocol: The targets were prepared using the Affymetrix 3'IVT assay and labeled by biotinylation.

growth_protocol: Animals were injected with Tregs or naïve T cells at 10 weeks of age and sacrificed 2-3 months after injection.

treatment_protocol: Colons were excised and distal colon tissue (from rectum to proximal/distal junction) was snap frozen.

value: colon

tag: genotype

tag: injected cell type

value: Naïve T

value: 4-5 mos

tag: inflammation level

value: moderate


title: [mouse BM][preleukemic  CD19+AA4.1+][1]

description: Gene expression data from preleukemic CD19+AA4.1+ mouse bone marrow cells

source_name: preleukemic bone marrow

value: preleukemic bone marrow


title: [mouse BM][leukemic CD19+AA4.1+ nilotinib treated][1]


title: Naïve T-injected severely inflamed colon tissue, biological rep2

description: Gene expression data from severely inflamed colons

value: severe


title: [mouse BM][normal CD19+AA4.1+][1]


title: [mouse BM][leukemic CD19+AA4.1+][1]

description: Gene expression data from leukemic CD19+AA4.1+ mouse bone marrow cells

source_name: leukemic bone marrow

value: leukemic bone marrow


title: Naïve T-injected severely inflamed colon tissue, biological rep3


title: [mouse BM][normal CD19+AA4.1+][2]


title: [mouse BM][preleukemic CD19+AA4.1+][3]


title: Naïve T-injected moderately inflamed colon tissue, biological rep3


title: [mouse BM][leukemic CD19+AA4.1+][3]


title: Naïve T-injected severely inflamed colon tissue, biological rep1


title: Treg-injected negative control colon tissue, biological rep4

description: Gene expression data from non-inflamed colons

source_name: colon tissue from Treg-injected mice

value: Treg

value: non-inflamed


title: [mouse BM][preleukemic CD19+AA4.1+][2]


title: prostatesRNA_control_30d_rep2

source_name: prostatesRNA, control, 30d, replicate 2


title: [mouse BM][leukemic CD19+AA4.1+][2]


title: Treg-injected negative control colon tissue, biological rep3


title: Treg-injected negative control colon tissue, biological rep1


title: Treg-injected negative control colon tissue, biological rep2