title: TNBC14

type: SRA

city: Nashville

first: Thomas

middle: Paul

last: Stricker

state: TN

address: 1161 21st Ave South, CC3309A

department: Pathology, Microbiology and Immunology

institute: Vanderbilt University

library_source: transcriptomic

data_processing:
Paired end reads were aligned to the human reference genome (build 36) using TopHat.  Tophat was run with an estimated mean and standard deviation insert size of 200 and 50 bases, respectively. We also provided the gene models to the aligner at this step for faster and accurate resolution of known splice junctions.
Read alignments with mapping qualities less than 10 were removed.   Alignments generated from more than one sequencing lane were merged with Picard MergeSamFiles.
Transcript quantification on the aligned bams is performed using cufflinks-2.0.0 (all default parameters).
Transcript expression levels were estimated directly from each lane of RNAseq data, as Fragments Per Kilobase per Million mapped reads (FPKM) using cufflinks (http://cufflinks.cbcb.umd.edu/) for transcript assembly and quantitation, with RefSeq gene models as a reference annotation set.  FPKM distributions were quantile normalized across lanes.
Genome_build: Hg18
Supplementary_files_format_and_content: log2 FPKM

source_name: breast cancer

extract_protocol:
Briefly, frozen section slides cut from each block were used to select areas with high tumor cell concentration. These areas of the frozen block were then punched using a sharpened 1mm tissue microarray punch.  OCT was removed from the ends of this punch via a scalpel, and the frozen core was ground to a fine powder under liquid nitrogen.  Total RNA and gDNA was then extracted from frozen tissue samples using Qiagen QiaShredder/RNeasy and DNeasy Blood and Tissue kits.
RNA quality was confirmed using an Agilent Bioanalyzer, no RNA with a RIN < 7.5 was used.  Poly-adenylated RNA was purified with the micropolyA purist kit (Ambion), ethanol precipitated, and resuspended in 10 uL RNAse free water.  First strand reverse transcription was primed with random nonomers, using SuperscriptII RT (Invitrogen). Second strand synthesis was performed with RNAse H and DNA Polymerase I.  Double stranded cDNA was repaired and polished with T4 DNA polymerase, Klenow, and T4 polynucleotide kinase.  Adenosine was added to 3' ends with Klenow and paired end Illumina adapters ligated with T4 DNA ligase.  Ligation reactions were size selected for 400-500 bp fragments after agarose gel electrophoresis and PCR amplified for 15 cycles using Illumina PCR primers and Pfx polymerase.  Paired end Illumina sequencing was performed according to the manufacturer's instructions.

tag: status

value: Triple Negative


title: TNBC11

status: Public on Feb 15 2017

country: USA

molecule: total RNA

organism: Homo sapiens


title: TNBC13


title: TNBC10


title: HSC_Chrm1KO_3

type: RNA

city: Bronx

first: Halley

middle: C

last: Pierce

state: NY

address: 1301 Morris Park Ave.

department: Ruth L. and David S. Gottesman Stem Cell Institutue

institute: Albert Einstein College of Medicine

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Analysis was performed by first processing the chip through Transcriptome analysis center (TAC) software (Affymetrix) to determine fold changes and p-values which were then analyzed by gene set enrichment analysis (GSEA).

label: biotin

organism: Mus musculus

source_name: steady state bone marrow HSC (LSKF) Chrm1-/-

label_protocol: Affymetrix protocol

extract_protocol: Qiagen Rneasy plus microkit RNA extraction from FACS sorted HSCs

treatment_protocol: steady state bone marrow sorted HSCs

tag: genotype/variation

tag: strain

tag: tissue

value: bone marrow HSC


title: TNBC12


title: Pre 10781006

city: Cambridge

first: Karl

middle: George

last: Wassmann

state: MA

address: 245 First Street Suite 1800-109

institute: CheckPoint Sciences Inc.

description: Phase III biomarker study, Advanced Melanoma, chemotherapy naïve

data_processing:
The normalized data is reported in delta CT units. 18S rRNA is the sole endogenous control gene. With each heating/cooling cycle, the real time PCR assay detects fluorescent signal accumulation. The Ct (cycle threshold) is the number of cycles required for the fluorescent signal to exceed background level. Thermal cycling goes through 40 cycles, and 18S rRNA is measured at the 14th cycle. Delta Ct is measured up to 26 cycles from the point endogenous control is recognized. Raw CT data is automatically processed to delta CT data by a software program subtracting the 18S CT value from the raw data CT value for each triplicate well. Triplicate test results are used to identify and eliminate data points that are statistical “outliers”; such data points are those that differ by a percentage greater than 3% of the average of all three values. If more than one data point in a set of three is excluded by this procedure, then all data for the relevant constituent is discarded.
Normalized signal (against 18S housekeeping gene). All normalized data was reported and analyzed as delta CT units and fold change was not calculated.

source_name: Whole Blood, Pretreatment

label_protocol: First-strand complementary DNA was synthesized from random hexamer-primed RNA templates using TaqMan® reverse-transcription reagents. Synthesis of first strand cDNA for use in PCR amplification used Applied Biosystems TAQMAN Reverse Transcription Reagents Kit (P/N 808-0234). Individual target-gene amplification was multiplexed with the 18S rRNA endogenous control and run in triplicate in 384-well format on the 7900HT fast real-time PCR system.  PCR procedures followed ABI Prism® 7900 Sequence Detection System instructions. Applied Biosystems (Foster City, Calif.)

extract_protocol: Total RNA was stabilized in PAXgene tubes and was extracted using vendor PreAnalytics PAXgene™ Blood RNA System to process the RNA to meet quality and integrity standards (RNA integrity number ≥6.3) per the Bioanalyzer 2100 in combination with the RNA 6000 Nano or Pico Series II LabChip

treatment_protocol: Post-treatment blood samples taken 30-days after immunotherapy treatment with 15 mg/kg dose of tremelimumab

value: Venous blood from arm

tag: gender

value: MALE

tag: age

tag: cancer stage

value: IV M1B

tag: worst diarrhea grade

tag: immunotherapy response (responder=1 nonresponder=0)

tag: survival status 12 months (1=alive 0=dead)


title: HSC_WT_3

source_name: steady state bone marrow HSC (LSKF) WT C67Bl/6

value: WT


title: TNBC9


title: THP-1 macrophages incubated with non-hydrolysis products_replicate 2

city: St. John's

first: Sherri

middle: L

last: Christian

state: Newfoundland

address: 232 Elizabeth Ave

department: Biochemistry

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: After terminal labeling with biotin, cRNA were hybridized for 16-18 hours at 45°C on Affymetrix GeneChips by TCAG.

scan_protocol: GeneChips were scanned at TCAG using an Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data analysis was performed using the Oligo package (v1.32.0) from Bioconductor using R (v3.2.0). The data were normalized using the RMA.

label: Biotin

source_name: THP-1 monocyte-derived macrophages_non-hydrolysis products

label_protocol: Biotinylated cRNA were prepared at The Centre for Applied Genomics (TCAG; Toronto, Ontario, Canada) from 250 ng of total RNA using the Affymetrix WT PLUS Reagent Kit, according to manufacturer's instructions.

growth_protocol: THP-1 monocytes were cultured in RPMI media supplemented with 10% fetal bovine serum and 1% Antibiotic/Antimycotic (Hyclone). Cells were incubated at 37°C with 5% CO2.

extract_protocol: Total RNA was isolated from cells using TRIzol; genomic DNA contamination was removed using the TURBO DNA-free kit (Ambion). The DNase-treated RNA samples were further purified using a Qiagen spin column.

treatment_protocol: THP-1 monocytes were differentiated into macrophages using 100 nM PMA for 72 hours. The differentiated macrophages were incubated for 18 hours with total lipoproteins that were treated with heparinized media from control HEK-293T cells or HEK-293T cells that expressed human LPL.

tag: cell type

value: THP-1 monocyte-derived macrophages

tag: incubated with

value: non-hydrolysis products for 18hrs


title: TNBC8


title: TNBC7


title: TNBC6


title: Pre 10781001

value: FEMALE

value: IV M1C


title: HSC_WT_1


title: TNBC5


title: Pre 10761008


title: Pre 10761005


title: TNBC4


title: TNBC3


title: TNBC2


title: HSC_WT_2


title: ERBC11

value: Estrogen receptor +


title: Pre 10761002


title: TNBC1


title: ERBC9


title: ftlctx_reelin

city: Boston

first: Uwe

last: Beffert

address: 24 Cummington Mall

department: Biology

institute: Boston University

description: Gene expression data from one lobe of 21 day old mouse frontal cortex

hyb_protocol: Biotin labeled cRNA are hybridized with Mouse 430 array using Affymetrix Standard Protocol.

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

data_processing: Raw data were processed with the Expression Console (Affymetrix) for MAS5 summarization and Quantile normalization.

source_name: mouse frontal cortex from Reln KO

label_protocol: Amplified and biotinylated cRNA was generated from total RNA using 3' IVT PLUS kit from (Affymetrix)

growth_protocol: Male mice were identified by their Reeler phenotype and sacrificed at 21 days of age; the frontal cortical lobes were microdissected and snap frozen. One lobe was used per sample.

extract_protocol: Total RNA was extracted using RNA-Stat60 according to manufacturer’s protocol.

treatment_protocol: No treatment

value: mixture of C57BL/6 and 129

value: male

value: 21 days old

value: brain, frontal cortex

value: REELIN KO


title: Pre 10751003


title: ftlctx_dab1

source_name: mouse frontal cortex from Dab1 KO

value: DAB1 KO


title: Pre 10751002


title: ftlctx_apoer2vldlr

source_name: mouse frontal cortex from double apoER2 and VLDLR knockout mice from Vldlr / apoer2 double-het cross

value: APOER2-VLDLR KO


title: ftlctx_apoer2

source_name: mouse frontal cortex from apoER2 KO from Vldlr / apoer2 double-het cross

value: APOER2 KO


title: ERBC7


title: ftlctx_wt

source_name: mouse frontal cortex from wild-type littermates from Vldlr / apoer2 double-het cross

value: Wild type


title: ERBC8


title: ftlctx_vldlr

source_name: mouse frontal cortex from Vldlr KO from Vldlr / apoer2 double-het cross

value: VLDLR KO


title: ERBC4


title: ERBC3


title: Pre 10741017

value: Venous blood from arm

value: IIIC


title: Pre 10741018

value: IV M1A


title: Pre 10701018

value: MALE

value: IV M1B


title: ERBC2


title: ERBC6


title: Pre 10701011

value: IV M1C


title: ERBC10

value: Estrogen receptor +


title: Pre 10701003


title: Pre 10701005

value: FEMALE


title: Pre 10701008


title: Pre 10681011


title: ERBC5


title: Pre 10681008


title: Pre 10681005


title: Pre 10681003


title: Pre 10681002


title: Pre 10601001


title: Pre 10661003


title: Pre 10561003


title: Pre 10561004


title: Pre 10501004


title: Pre 10271001


title: Pre 10291001


title: Pre 10361001


title: Pre 10471001


title: Pre 10561002


title: Pre 10211003


title: Pre 10211005


title: Pre 10161014


title: Pre 10161015


title: ERBC1


title: Pre 10161005


title: Pre 10081001


title: Pre 10081014


title: Pre 10081004


title: Pre 10081006


title: Pre 10081002


title: Pre 10161011


title: Pre 10081012


title: Pre 10041011


title: Pre 10041012


title: Pre 10021013


title: Pre 10021015


title: Pre 10041001


title: Pre 10041002


title: Pre 10021016


title: Pre 10041003


title: Pre 10021006


title: Pre 10021007


title: Pre 10021010


title: cell_control_rep1

city: Shanghai

first: Chunzhi

last: Qin

state: Shanghai

address: 180 Fenglin Road

department: General surgery

country: China

institute: Zhongshan Hospital

description: Gene expression data from DLD1 cells transfected with control-shRNA-expressing lentivirus

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Robust multi-array average (RMA) using a non-linear correction based upon a convolution model.

source_name: cells transfected with control shRNA

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

growth_protocol: DLD1 cells were maintained in RPMI1640.The media were supplemented with 10% fetal bovine serum in an incubator with 5% CO2 at 37°C.

extract_protocol: Total RNA from control and RNAi DLD1 was prepared with TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Cells were transfected with control-shRNA-expressing lentivirus or CDKL1-shRNA-expressing lentivirus.

value: colorectal cell line

tag: cell line


title: Pre 10021004


title: cell_knockdown_rep1

description: Gene expression data from DLD1 cells transfected with CDKL1-shRNA-expressing lentivirus

source_name: cells transfected with CDKL1-shRNA


title: Pre 10021001


title: Pre 10021003


title: cell_control_rep2


title: Hepatocytes_High-fat diet_anti-VLA-4

city: Bunko-ku

first: Yasutaka

last: Miyachi

state: Tokyo

address: 1-5-45 Yushima

department: Molecular Endocrinology and Metabolism

country: Japan

institute: Tokyo Medical and Dental University

hyb_protocol: Cy3 labeled and fragmented cRNA was hybridized on Whole Mouse Genome Microarray 4X44K (Agilent) using a hybridization oven for 17 h at 65°C.

scan_protocol: Slide was scanned on the Agilent DNA Microarray Scanner (G2505C).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Ailent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026655_D_F_20100123). Raw data were normalized to the 75th percentile signal intensity. Features flagged in Feature Extraction as Feature Non-uniform outliers and below background were excluded.

source_name: Hepatocytes from HFD-fed mice treated with anti-VLA-4 antibody

label_protocol: Cy3 labeled cRNA was prepared using the Low Input Quick Amp Labelling Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was extracted using QIAzol, and purified with Rneasy Plus Mini Kit.

value: Hepatocytes

value: male


title: cell_control_rep3


title: Pre 10021009


title: cell_knockdown_rep3


title: cell_knockdown_rep2


title: Hepatocytes_High-fat diet_IgG

source_name: Hepatocytes from HFD-fed mice treated with IgG


title: ob/ob LSEC

source_name: ob/ob Liver sinusoidal endothelial cells

value: Liver sinusoidal endothelial cells


title: Hepatocytes_Standard diet

source_name: Hepatocytes from SD-fed mice


title: HeLa_5J/m^2 UVC_12h_rep 1

city: Changsha

first: Zheng

last: Zhou

address: Lushan Road (S), Yuelu District

institute: Hunan University

description: Expression data of HeLa cells were treated with 5J/m^2 of UVC light.

hyb_protocol: The microarray slides were prehybridized at 42℃ for 1 h and hybridized at 42℃ for 16 h.

scan_protocol: Microarrays were scanned using Axon GenePix 4000B.

data_processing: The microarray data were normalized using standard global media normalization.

source_name: HeLa cells, 5J/m^2 UVC treated, recovery 12h

label_protocol: Total RNA was dephosphorylated and ligated to the same 3’ adapter oligonucleotide. For each sample, 1 µg ligated RNA was used to create cRNA according to the following description. The ligated ncRNAs were reverse transcribed using an oligonucleotide complementary to the 3’ adapter before extending with a 5’ end T7 promoter sequence extension. The cRNA was purified and labeled with Cy3 using the CyDye mono-reactive NHS Esters kit (Amersham Biosciences) followed by purifying with the Qiagen Rneasy mini kit.

growth_protocol: HeLa cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco) supplemented with 10% (v/v) Fetal Bovine Serum (Gibco) and 1% (v/v) Penicillin/Streptomycin (Gibco).

extract_protocol: Total RNA was extrated with TRIzol agent (Invitrogen) following the manufacturer’s instructions.

treatment_protocol: Before UVC treatments, HeLa cells were washed with PBS for 3 times.Then, cells were treated as the indicate dose of UVC. For MMS treatment, HeLa cells were treated with 0.005% MMS in DMEM for 30min followed by washing with PBS for 3 times.

value: HeLa

tag: treatment

value: 5J/m^2 UVC

tag: recovery time


title: WT LSEC

source_name: WT Liver sinusoidal endothelial cells


title: HeLa_10J/m^2 UVC_12h_rep 1

description: Expression data of HeLa cells were treated with 10J/m^2 of UVC light.

source_name: HeLa cells, 10J/m^2 UVC treated, recovery 12h

value: 10J/m^2 UVC


title: Pre 10011001

source_name: Whole Blood, Pretreatment


title: HeLa_0.005% MMS_12h_rep 1

description: Expression data of HeLa cells were treated with 0.005% MMS.

source_name: HeLa cells, 0.005% MMS treated for 30min, recovery 12h

value: 0.005% MMS for 30min


title: BT07 (aCGH)

status: Public on Feb 14 2017

type: genomic

city: Los Angeles

middle: G.

last: Graeber

state: CA

address: 570 Westwood Plaza, Bldg 114, Room 4341 CNSI

department: Mol & Med Pharmacology

institute: UCLA

description:
Same biomaterial as that in GSM530561 (BT07) from Series GSE21217
DNA copy number
brca_hg19_seg.mean.seg.txt

hyb_protocol: DNA was hybridized to Agilent Human Genome cGH 244A arrays at the Genomics Core of Memorial-Sloan Kettering Cancer Center.

scan_protocol: Per manufacturer's instructions

data_processing:
Log2 ratios were processed by Circular Binary Segmentation and the segmented values used for further analysis. Segment Log2 ratios for each unique RefSeq gene (~ 19,000 genes) were generated by collapsing multiple gene transcripts to the largest union of gene boundaries and viewed using IGV.
brca_hg19_seg.mean.seg.txt (reporting normalized log10 Cy5/Cy3 ratios) is linked as a supplementary file on the Series record.

molecule: genomic DNA

source_name: primary breast tumor

label_protocol: Bioprime Array CGH labeling kit (Invitrogen) using Cy3/Cy5

growth_protocol: Genomic DNA were extracted from macrodissected frozen tumor samples.

extract_protocol: Genome DNA was extracted from all samples with standard proteinase K digestion and phenol/chloroform extraction.

treatment_protocol: All patients fasted for at least six hours prior to imaging and pre-examination blood glucose levels were obtained. Patients were injected with 370 – 555 MBq (10-15 mCi) pyrogen-free 18F-FDG.  Imaging was performed 50 to 60 minutes later on an ADVANCE (General Electric Medical Systems) whole body PET/CT scanner in accordance with the MSKCC PET protocol. CT data were used for attenuation correction. All images were iteratively reconstructed using post-emission transmission attenuation-corrected data sets.  A standard ROI analysis tool provided with the scanner was used to calculate the maximal FDG concentration within the primary tumor mass. SUVmax values were obtained by correcting for the injected dose and patient weight, again using the standard software tools. Only FDG uptake in the primary site was analyzed. We did not correct for partial volume effect based on the resolution of our GE Advance FDG-PET scanner, which is 5-7 mm, depending on the distance from the center of the field. Count recovery even for the 1.4 cm, small tumor will be >90% (9). For the patient with anaplastic astrocytoma, preoperative anatomical MRI images were uploaded to the BrainLAB VectorVision® neuronavigation system, a frameless stereotaxy and image-guided surgical navigation systecontoured by the neurosurgeon conventionally, based on the anatomic MRI. Afterwards, 18FDG PET-MRI studies were uploaded and registered by a radiologist. During surgery, location was tracked by frameless stereotaxy. The stereotactic system was used to mark sites of biopsy as 3D points in the space of the navigational image. The navigational image was updated with intraoperative MRI prior to deep region of interest (ROI) biopsies to ensure accurate annotation of the biopsy site in relation to the tumor mass despite brain shift during resection.  m. Planned resection volume was

tag: tumor type

value: primary tumor

tag: disease status

value: breast cancer

tag: FDG uptake

value: low

tag: suv max

source_name: Promega reference DNA

tag: reference

value: Promega reference DNA

value: normal


title: BT11 (aCGH)

description:
Same biomaterial as that in GSM530565 (BT11) from Series GSE21217
DNA copy number
brca_hg19_seg.mean.seg.txt

value: high


title: BT12 (aCGH)

description:
Same biomaterial as that in GSM530566 (BT12) from Series GSE21217
DNA copy number
brca_hg19_seg.mean.seg.txt


title: HeLa_Untreated

description: Expression data of untreated samples.

source_name: HeLa cells, untreated

value: No treatment.

value: No recovery


title: BT10 (aCGH)

description:
Same biomaterial as that in GSM530564 (BT10) from Series GSE21217
DNA copy number
brca_hg19_seg.mean.seg.txt


title: BT09 (aCGH)

description:
Same biomaterial as that in GSM530563 (BT09) from Series GSE21217
DNA copy number
brca_hg19_seg.mean.seg.txt


title: BT08 (aCGH)

description:
Same biomaterial as that in GSM530562 (BT08) from Series GSE21217
DNA copy number
brca_hg19_seg.mean.seg.txt


title: BT02 (aCGH)

description:
Same biomaterial as that in GSM530557 (BT02) from Series GSE21217
DNA copy number
brca_hg19_seg.mean.seg.txt


title: BT03 (aCGH)

description:
Same biomaterial as that in GSM530558 (BT03) from Series GSE21217
DNA copy number
brca_hg19_seg.mean.seg.txt


title: BT05 (aCGH)

description:
Same biomaterial as that in GSM530560 (BT05) from Series GSE21217
DNA copy number
brca_hg19_seg.mean.seg.txt


title: BT04 (aCGH)

description:
Same biomaterial as that in GSM530559 (BT04) from Series GSE21217
DNA copy number
brca_hg19_seg.mean.seg.txt


title: L050 CD52 low

city: Nagasaki

first: Masataka

last: Umeda

state: Nagasaki

department: Unit of Advanced Preventive Medical Sciences

institute: Nagasaki University Graduate School of Biomedical Sciences

hyb_protocol: 2.0ug of Cy3-labelled cDNA was filled up to 50 ul containing 1x Agilent blocking agent and 1x Agilent hybridization buffer, and hybridized to SurePrint G3 Human 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), then dried immediately.

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.
Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: peripheral blood CD4+ T cells

label_protocol: cDNA were amplified by Ovation® Pico WTA System V2（NuGEN Technologies) from 3ng total RNA according to the manufacturer's instructions. Amplified cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer. Cyanine-3 (Cy3) labeled cDNA was prepared with SureTag Complete DNA Labeling Kit (Agilent) according to the manufacturer's instructions, followed by Amicon Ultra-0.5 mL Centrifugal Filters for DNA Purification and Concentration (Merck Millipore). Dye incorporation and cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: The RNA was obtained from CD3+ CD45+ CD4+ CD8− CD52high and CD3+ CD45+ CD4+ CD8− CD52low T cells. Total cellular RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany)following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: tissue

value: sorted CD3+CD4+ CD52 low T cells

value: female

tag: diagnosis

value: Systemic Lupus Erythematosus


title: L050 CD52 high

value: sorted CD3+CD4+ CD52 high T cells

tag: gender


title: L048 CD52 high


title: L038 CD52 high


title: L048 CD52 low


title: L041 CD52 low


title: whole blood genomic DNA of sample SE1125

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
ChAMP
The 'Matrix_processed.txt' contains Average Beta (normalized using ChAMP) values

label: Cy5 and Cy3

source_name: non-smoker whole blood genomic DNA

label_protocol: 500 ng of DNA was bisulfite converted using the EZ-DNA Methylation kit (Zymo Research)

extract_protocol: Nucleated DNA from whole blood was collected after sucrose-induced osmotic lysis of cells followed by phenol-chloroform extraction and DNA was stored in Tris-EDTA buffer at -20°C.

tag: subject status

value: non-smoker

value: whole blood


title: L037 CD52 high


title: L041 CD52 high


title: L037 CD52 low


title: whole blood genomic DNA of sample SE1301


title: whole blood genomic DNA of sample SE1479

source_name: smoker whole blood genomic DNA

value: smoker


title: whole blood genomic DNA of sample SE1090


title: L038 CD52 low


title: whole blood genomic DNA of sample SE1223


title: whole blood genomic DNA of sample SE1236


title: whole blood genomic DNA of sample SE0274


title: whole blood genomic DNA of sample SE1058


title: Wild-type seedlings, rep2

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

description: Gene expression data from control wild-type Arabidopsis seedlings

hyb_protocol: Following fragmentation, 12.5 microgram of cRNA were hybridized for 16 h at 45 degree C on the rice Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChip were scanned using Affymetrix scanner

data_processing: CEL files were imported into Genespring software and probe summarization and normalization was performed using MAS5 algorithm

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

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

growth_protocol: Wild-type and transgenic Arabidopsis seedlings were grown on MS medium for 10 days in a culture room with a daily photoperiodic cycle of 14 h light and 10 h dark

extract_protocol: Total RNA was extracted using TRI reagent according to the manufacturer's instructions

treatment_protocol: Seedlings were grown under normal control conditions

tag: genotype/variation

value: wild type

tag: ecotype

value: Columbia

value: Seedlings

tag: age

value: 10 day old


title: whole blood genomic DNA of sample SE1539


title: whole blood genomic DNA of sample SE1302


title: OsHOX24-overexpression seedlings, rep1

description: Gene expression data from control OsHOX24 overexpression Arabidopsis seedlings


title: OsHOX24-overexpression seedlings, rep3


title: OsHOX24-overexpression seedlings, rep2


title: whole blood genomic DNA of sample SE1491


title: whole blood genomic DNA of sample SE1566


title: Wild-type seedlings, rep3


title: Wild-type seedlings, rep1


title: whole blood genomic DNA of sample SE1573


title: whole blood genomic DNA of sample SE2000


title: whole blood genomic DNA of sample SE1089


title: whole blood genomic DNA of sample SE0975


title: whole blood genomic DNA of sample SE1485


title: whole blood genomic DNA of sample SE1115


title: whole blood genomic DNA of sample SE1095


title: whole blood genomic DNA of sample SE1346


title: whole blood genomic DNA of sample SE1308


title: whole blood genomic DNA of sample SE1092


title: whole blood genomic DNA of sample SE1268


title: whole blood genomic DNA of sample SE1489


title: whole blood genomic DNA of sample SE1093


title: whole blood genomic DNA of sample SE1081


title: whole blood genomic DNA of sample SE1113


title: whole blood genomic DNA of sample SE1110


title: whole blood genomic DNA of sample SE1078


title: whole blood genomic DNA of sample SE1320


title: whole blood genomic DNA of sample SE1251


title: whole blood genomic DNA of sample SE1322


title: whole blood genomic DNA of sample SE1063


title: whole blood genomic DNA of sample SE1116


title: whole blood genomic DNA of sample SE1076


title: whole blood genomic DNA of sample SE1141


title: whole blood genomic DNA of sample SE0984


title: whole blood genomic DNA of sample SE1174


title: whole blood genomic DNA of sample SE1325


title: whole blood genomic DNA of sample SE1309


title: whole blood genomic DNA of sample SE0748


title: whole blood genomic DNA of sample SE1299


title: MDA-MB-231-LB-4w

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

description:
Cy3 (unmethylated)/Cy5 (methylated)
Treated cells for 28 days

hyb_protocol: Infinium HD Methylation Assay Protocol (Illumina, Inc., San Diego, CA). Briefly, resuspended DNA samples onto BeadChips. Incubate the BeadChips in the Illumina Hybridization Oven to hybridize the samples onto the BeadChips.

scan_protocol: Illumina iScan (Illumina, Inc., San Diego, CA)

data_processing: Data was extracted using the R package methylumi. The ‘noob’ function in the R package minfi was used to process the data and then the ‘dasen’ function in the R package wateRmelon for normalization and dye-bias correction.

source_name: Invasive breast carcinoma

label_protocol: Infinium HD Methylation Assay Protocol (Illumina, Inc., San Diego, CA). Briefly, allele-specific single base extension of the probes incorporates a biotin nucleotide (C and G) or a dinitrophenyl labeled nucleotide (A and T)

growth_protocol: Cells were cultured at 37C in RPMI-1640 supplemented with 10mM HEPES, 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin-streptomycin (Full RPMI).

extract_protocol: Genomic DNA was extracted using the Quick-gDNA MiniPrep kit (cat# D3025; Zymo Research, Irvine, CA)

treatment_protocol: Control cells were maintained in full RPMI + DMSO for 28 days, treated cells were maintained for 4 cycles of 5 days incubation in full RPMI + 10nM LBH589 followed by 2 days of incubation in full RPMI + DMSO.

tag: disease subtype

value: Triple-negative breast cancer

value: LBH589 (10nM) for 28 days


title: whole blood genomic DNA of sample SE1300


title: whole blood genomic DNA of sample SE1478


title: whole blood genomic DNA of sample SE1591


title: whole blood genomic DNA of sample SE0268


title: whole blood genomic DNA of sample SE1122


title: whole blood genomic DNA of sample SE1468


title: whole blood genomic DNA of sample SE1146


title: whole blood genomic DNA of sample SE1353


title: whole blood genomic DNA of sample SE1341


title: whole blood genomic DNA of sample SE1066


title: whole blood genomic DNA of sample SE1492


title: whole blood genomic DNA of sample SE0839


title: MDA-MB-231-LB-96hs

description:
Cy3 (unmethylated)/Cy5 (methylated)
Treated cells for 96 hs

value: LBH589 (10nM) for 96 hours


title: whole blood genomic DNA of sample SE1271


title: whole blood genomic DNA of sample SE1318


title: whole blood genomic DNA of sample SE1337


title: whole blood genomic DNA of sample SE1042


title: whole blood genomic DNA of sample SE1401


title: whole blood genomic DNA of sample SE0912


title: whole blood genomic DNA of sample SE1027


title: HCC1806-DMSO

description:
Cy3 (unmethylated)/Cy5 (methylated)
Untreated control

value: DMSO


title: HCC1806-LB-96hs


title: MDA-MB-231-DMSO


title: whole blood genomic DNA of sample SE1011


title: whole blood genomic DNA of sample SE1175


title: whole blood genomic DNA of sample SE1550


title: whole blood genomic DNA of sample SE1055


title: whole blood genomic DNA of sample SE1560


title: whole blood genomic DNA of sample SE0682


title: whole blood genomic DNA of sample SE1387


title: whole blood genomic DNA of sample SE1154


title: whole blood genomic DNA of sample SE1068


title: whole blood genomic DNA of sample SE1595


title: whole blood genomic DNA of sample SE1120


title: whole blood genomic DNA of sample SE1107


title: whole blood genomic DNA of sample SE1249


title: whole blood genomic DNA of sample SE1465


title: whole blood genomic DNA of sample SE1118


title: whole blood genomic DNA of sample SE1285


title: whole blood genomic DNA of sample SE1070


title: whole blood genomic DNA of sample SE1490


title: whole blood genomic DNA of sample SE1361


title: whole blood genomic DNA of sample SE1352


title: whole blood genomic DNA of sample SE1155


title: whole blood genomic DNA of sample SE1421


title: whole blood genomic DNA of sample SE1131


title: whole blood genomic DNA of sample SE0996


title: whole blood genomic DNA of sample SE1207


title: whole blood genomic DNA of sample SE0885


title: HCC1806-LB-4w


title: whole blood genomic DNA of sample SE1119


title: whole blood genomic DNA of sample SE1555


title: whole blood genomic DNA of sample SE0222


title: whole blood genomic DNA of sample SE1511


title: whole blood genomic DNA of sample SE1527


title: whole blood genomic DNA of sample SE1234


title: whole blood genomic DNA of sample SE1338


title: whole blood genomic DNA of sample SE0757


title: whole blood genomic DNA of sample SE1414


title: whole blood genomic DNA of sample SE0669


title: whole blood genomic DNA of sample SE1399


title: whole blood genomic DNA of sample SE1161


title: whole blood genomic DNA of sample SE1194


title: whole blood genomic DNA of sample SE0916


title: whole blood genomic DNA of sample SE1505


title: whole blood genomic DNA of sample SE0875


title: whole blood genomic DNA of sample SE0805


title: whole blood genomic DNA of sample SE1371


title: whole blood genomic DNA of sample SE1486


title: whole blood genomic DNA of sample SE1565


title: whole blood genomic DNA of sample SE0498


title: whole blood genomic DNA of sample SE0795


title: whole blood genomic DNA of sample SE1409


title: whole blood genomic DNA of sample SE1276


title: whole blood genomic DNA of sample SE1283


title: whole blood genomic DNA of sample SE1004


title: whole blood genomic DNA of sample SE1077


title: whole blood genomic DNA of sample SE0930


title: whole blood genomic DNA of sample SE1540


title: whole blood genomic DNA of sample SE1191


title: whole blood genomic DNA of sample SE0972


title: whole blood genomic DNA of sample SE1313


title: whole blood genomic DNA of sample SE1350


title: whole blood genomic DNA of sample SE1562


title: whole blood genomic DNA of sample SE1460


title: whole blood genomic DNA of sample SE2045


title: whole blood genomic DNA of sample SE0787


title: whole blood genomic DNA of sample SE1152


title: whole blood genomic DNA of sample SE1265


title: whole blood genomic DNA of sample SE1176


title: whole blood genomic DNA of sample SE1431


title: whole blood genomic DNA of sample SE1586


title: whole blood genomic DNA of sample SE1564


title: whole blood genomic DNA of sample SE1003


title: whole blood genomic DNA of sample SE1295


title: whole blood genomic DNA of sample SE1483


title: whole blood genomic DNA of sample SE0822


title: whole blood genomic DNA of sample SE1466


title: whole blood genomic DNA of sample SE1626


title: whole blood genomic DNA of sample SE1389


title: whole blood genomic DNA of sample SE1458


title: whole blood genomic DNA of sample SE1099


title: whole blood genomic DNA of sample SE0576


title: whole blood genomic DNA of sample SE1031


title: whole blood genomic DNA of sample SE1149


title: whole blood genomic DNA of sample SE1123


title: whole blood genomic DNA of sample SE1196


title: whole blood genomic DNA of sample SE1153


title: whole blood genomic DNA of sample SE1380


title: whole blood genomic DNA of sample SE1407


title: whole blood genomic DNA of sample SE1117


title: whole blood genomic DNA of sample SE1523


title: whole blood genomic DNA of sample SE1553


title: whole blood genomic DNA of sample SE1261


title: whole blood genomic DNA of sample SE1439


title: whole blood genomic DNA of sample SE0196


title: whole blood genomic DNA of sample SE1109


title: whole blood genomic DNA of sample SE1474


title: whole blood genomic DNA of sample SE1315


title: whole blood genomic DNA of sample SE1544


title: whole blood genomic DNA of sample SE1062


title: whole blood genomic DNA of sample SE1391


title: whole blood genomic DNA of sample SE1587


title: whole blood genomic DNA of sample SE1574


title: whole blood genomic DNA of sample SE1232


title: whole blood genomic DNA of sample SE1306


title: whole blood genomic DNA of sample SE1147


title: whole blood genomic DNA of sample SE1298


title: whole blood genomic DNA of sample SE1133


title: whole blood genomic DNA of sample SE0884


title: whole blood genomic DNA of sample SE1144


title: whole blood genomic DNA of sample SE1388


title: whole blood genomic DNA of sample SE1124


title: whole blood genomic DNA of sample SE1599


title: whole blood genomic DNA of sample SE1589


title: whole blood genomic DNA of sample SE1426


title: whole blood genomic DNA of sample SE1020


title: whole blood genomic DNA of sample SE1245


title: whole blood genomic DNA of sample SE0982


title: whole blood genomic DNA of sample SE13691


title: whole blood genomic DNA of sample SE1420


title: whole blood genomic DNA of sample SE1470


title: whole blood genomic DNA of sample SE1135


title: whole blood genomic DNA of sample SE1244


title: whole blood genomic DNA of sample SE1585


title: whole blood genomic DNA of sample SE0881


title: whole blood genomic DNA of sample SE1425


title: whole blood genomic DNA of sample SE2017


title: whole blood genomic DNA of sample SE1317


title: whole blood genomic DNA of sample SE1510


title: whole blood genomic DNA of sample SE1212


title: whole blood genomic DNA of sample SE1192


title: whole blood genomic DNA of sample SE1584


title: whole blood genomic DNA of sample SE1554


title: whole blood genomic DNA of sample SE1592


title: whole blood genomic DNA of sample SE1286


title: whole blood genomic DNA of sample SE1558


title: whole blood genomic DNA of sample SE1247


title: whole blood genomic DNA of sample SE1552


title: whole blood genomic DNA of sample SE1370


title: whole blood genomic DNA of sample SE1190


title: whole blood genomic DNA of sample SE1578


title: whole blood genomic DNA of sample SE1583


title: whole blood genomic DNA of sample SE1158


title: whole blood genomic DNA of sample SE1195


title: whole blood genomic DNA of sample SE1596


title: whole blood genomic DNA of sample SE1231


title: whole blood genomic DNA of sample SE1160


title: whole blood genomic DNA of sample SE1428


title: whole blood genomic DNA of sample SE1400


title: whole blood genomic DNA of sample SE0939


title: whole blood genomic DNA of sample SE1429


title: whole blood genomic DNA of sample SE1282


title: whole blood genomic DNA of sample SE1228


title: whole blood genomic DNA of sample SE2010


title: whole blood genomic DNA of sample SE1403


title: whole blood genomic DNA of sample SE1513


title: whole blood genomic DNA of sample SE1272


title: whole blood genomic DNA of sample SE1495


title: whole blood genomic DNA of sample SE1150


title: whole blood genomic DNA of sample SE1083


title: whole blood genomic DNA of sample SE1440


title: whole blood genomic DNA of sample SE2033


title: whole blood genomic DNA of sample SE0173


title: whole blood genomic DNA of sample SE1257


title: whole blood genomic DNA of sample SE0664


title: whole blood genomic DNA of sample SE1305


title: whole blood genomic DNA of sample SE2054


title: whole blood genomic DNA of sample SE1542


title: whole blood genomic DNA of sample SE1535


title: whole blood genomic DNA of sample SE1621


title: whole blood genomic DNA of sample SE1252


title: whole blood genomic DNA of sample SE1449


title: whole blood genomic DNA of sample SE1543


title: whole blood genomic DNA of sample SE1619


title: whole blood genomic DNA of sample SE0681


title: whole blood genomic DNA of sample SE1581


title: whole blood genomic DNA of sample SE1630


title: whole blood genomic DNA of sample SE1393


title: whole blood genomic DNA of sample SE1216


title: whole blood genomic DNA of sample SE1642


title: whole blood genomic DNA of sample SE0356


title: whole blood genomic DNA of sample SE1496


title: whole blood genomic DNA of sample SE1240


title: whole blood genomic DNA of sample SE1091


title: whole blood genomic DNA of sample SE1605


title: whole blood genomic DNA of sample SE1327


title: whole blood genomic DNA of sample SE0545


title: whole blood genomic DNA of sample SE1545


title: whole blood genomic DNA of sample SE1467


title: whole blood genomic DNA of sample SE1284


title: whole blood genomic DNA of sample SE2049


title: whole blood genomic DNA of sample SE1603


title: whole blood genomic DNA of sample SE1519


title: whole blood genomic DNA of sample SE1218


title: whole blood genomic DNA of sample SE09501


title: Zncl2 6h

first: Zhaoqing

last: Chu

address: 3888 Chenhua Road, Songjiang

institute: Shanghai Chenshan Plant Science Research Center, CAS

description:
SAMPLE 20
Test

data_processing:
The expression profiles were calculated with –ΔΔCT values. Fold changes were also calculated with the formula “fold change = 2–ΔΔCT”.
Fold Change worksheet reports test/control.
Signals normalized against housekeeping genes.

label: SYBR Green

organism: Brachypodium distachyon

source_name: Brachypodium distachyon seedling

label_protocol: The cDNA was synthesized with 2.0 µg of total RNA by using PrimeScript Reverse Transcriptase (TAKARA). The reaction mixtures were diluted 20 times with distilled water and used as templates for quantitative real-time PCR. The primers used in this paper were listed in Supplementary Table S2. The qPCR was conducted and repeated three times. The reaction condition was as follows: 95°C for 3 mins, 40 cycles of 95°C for 10 s, 60°C for 30s.

growth_protocol: The seeds of B. distachyon were surface sterilized with 20% NaClO and planted on 0.6% agar containing 0.5× Murashige and Skoog and 0.3% Sucrose. Plants were grown at 22°C under 16-h-light/8-h-dark conditions and the light intensity was 120 µm m-2 s-1.

extract_protocol: The total RNA was extracted from plant tissues and seedlings using RNAiso Plus (Takara, Dalian, China) according to the manufacturer's instruction.

treatment_protocol: 2-week-old seedlings were treated with 4 major treatment groups including group 1- environmental factors ( cold, heat, H2O2, PEG, and NaCl), group 2-heavy metals ( Zn and Cd) , group 3-phytohormones (SA, ABA, and MeJA) and group 4-biotic treatments(PH14,Guy11 and F0968) (As for detailed treatments, please refer to Supplementary Table S1).

tag: developmental stage

value: Seedling

value: 2 weeks

tag: stress

tag: time


title: CK 6h-salt

description:
SAMPLE 22
Control
CK 6h-salt is the control for SAMPLES 24.

value: control (CK-salt)


title: Nacl 3h

description:
SAMPLE 23
Test

value: Nacl


title: Zncl2 3h

description:
SAMPLE 19
Test


title: Cdcl2 3h

description:
SAMPLE 17
Test


title: SA 3h

description:
SAMPLE 15
Test

value: SA


title: PH14 12h

description:
SAMPLE 27
Test


title: Cdcl2 6h

description:
SAMPLE 18
Test


title: Root

description:
SAMPLE 32
Test

value: Root


title: Leaf

description:
SAMPLE 34
Test

value: Leaf


title: F0968 4h

description:
SAMPLE 30
Test


title: PH14 4h

description:
SAMPLE 26
Test


title: Guy11 4h

description:
SAMPLE 28
Test


title: Seedling

description:
SAMPLE 35
Test


title: F0968 12h

description:
SAMPLE 31
Test


title: MeJA 3h

description:
SAMPLE 13
Test

value: MeJA


title: Mock

description:
SAMPLE 25
Control
Mock is the control for SAMPLES 26, 27, 28, 29, 30, 31, 32, 33, 34, 35.

value: control (Mock)

value: Mock


title: Guy11 12h

description:
SAMPLE 29
Test


title: ABA 6h

description:
SAMPLE 12
Test

value: ABA


title: Nacl 6h

description:
SAMPLE 24
Test


title: Stem

description:
SAMPLE 33
Test

value: Stem


title: ABA 3h

description:
SAMPLE 11
Test


title: H2O2 6h

description:
SAMPLE 10
Test


title: H2O2 3h

description:
SAMPLE 9
Test


title: CK 3h-salt

description:
SAMPLE 21
Control
CK 3h-salt is the control for SAMPLES 23.


title: SA 6h

description:
SAMPLE 16
Test


title: MeJA 6h

description:
SAMPLE 14
Test


title: PBMCs_unvacci_72h_biological rep3 [exon-level]

city: Bonn

first: Chritiane

last: Neuhoff

state: NRW

address: Endenicher Allee 15

department: Institute of Animal Science

country: Germany

institute: University of Bonn

hyb_protocol: The hybridization of microarray probes followed by washing and staining was performed with the GeneChip® Hybridization, Wash and Stain kit (P/N 900720, Affymetrix Inc., Santa Clara, CA).

scan_protocol: Arrays were scanned by the Affymetrix GeneChip® scanner 3000 7G. The Affymetrix GeneChip® Command Console™ (AGCC) software was used to evaluate the array images and to export the reports of spot intensity data in .CEL file format.

data_processing:
Normalization and statistical analyses of microarray dataset were performed using packages of Bioconductor-platform implemented in R-project software (v3.1.2). The ‘oligo’ package was implemented for the RMA (Robust Multi-array Average) based quantile normalization of microarray data. The transcript level matrix was generated using core and the exon level matrix was generated using the probeset as target option. The differential gene expression analysis was performed using the linear analysis of microarray technique from the ‘limma’ package with empirical Bayes adjustment to the variance, followed by Benjamini and Hochberg (BH) correction for multiple testing. Genes with an FDR≤5% and a fold-change ≥1.5 were selected. In addition, To characterize the differences of transcriptional responses between pigs of vaccinated and unvaccinated group, the annotated gene expression profiles of PBMCs were subjected to an exploratory functional analysis through gene set enrichment analysis (GSEA) algorithm implemented in GSEA-P tool.
PorGene-1_0-st‐v1
PorGene-1_0-st-v1.na34.sscr2.transcript.csv (for gene-level) and PorGene-1_0-st-v1.na34.sscr2.probeset.csv (for exon-level)
Each column header represents one array sample. The left mostrow  of the matrix-gene represents the transcript IDs and left most row of the matrix-exon represent the exon IDs. Values in each cells of both matrices represent the log2 transformed normalized expression of gene or exon for the corresponding row.

organism: Sus scrofa

source_name: PBMCs at 72 h post PRRSV vaccination

label_protocol: The biotin-labeled probes (sense-strand cDNA) were prepared for microarray hybridization using the GeneChip® WT PLUS Reagent kit (P/N 902281; Affymetrix Inc., Santa Clara, CA, USA)

growth_protocol: Piglets were housed at research station at Frankenforst, University of Bonn, Germany and maintained with standard feeding and husbandry protocol.

extract_protocol: The total RNA was extracted from PBMCs using the miRNeasy mini kit (P/N 217004, Qiagen, Hilden, Germany) along with on column Dnase treatment (P/N 79254, Qiagen, Hilden, Germany)

treatment_protocol: PBMCs were isolated from anticoagulated blood samples collected within three days following PRRSV vaccination in 28 days old German Landrace pigs and age-matched unvaccinated pigs

tag: immunization status

value: Unvaccinated

tag: breed

value: German Landrace

value: Female


title: PBMCs_unvacci_72h_biological rep2 [exon-level]


title: PBMCs_unvacci_72h_biological rep1 [exon-level]


title: 4℃ 6h

description:
SAMPLE 4
Test

value: 4℃


title: 45℃ 6h

description:
SAMPLE 6
Test


title: 4℃ 3h

description:
SAMPLE 3
Test


title: PEG 3h

description:
SAMPLE 7
Test

value: PEG


title: PBMCs_vacci_72h_biological rep3 [exon-level]

value: Vaccinated


title: CK 6h

description:
SAMPLE 2
Control
CK 6h is the control for SAMPLES 4, 6, 8, 10, 12, 14, 16, 18, 20.

value: Seedling

value: 2 weeks

value: control (CK)


title: PEG 6h

description:
SAMPLE 8
Test


title: CK 3h

description:
SAMPLE 1
Control
CK 3h is the control for SAMPLES 3, 5, 7, 9, 11, 13, 15, 17, 19.


title: PBMCs_unvacci_24h_biological rep3 [exon-level]

source_name: PBMCs at 24 h post PRRSV vaccination


title: 45℃ 3h

description:
SAMPLE 5
Test


title: PBMCs_vacci_72h_biological rep2 [exon-level]


title: PBMCs_vacci_72h_biological rep1 [exon-level]


title: PBMCs_vacci_24h_biological rep2 [exon-level]


title: PBMCs_unvacci_24h_biological rep1 [exon-level]


title: PBMCs_vacci_24h_biological rep3 [exon-level]


title: PBMCs_unvacci_6h_biological rep3 [exon-level]

source_name: PBMCs at 6 h post PRRSV vaccination


title: PBMCs_vacci_24h_biological rep1 [exon-level]


title: anti-PD-1_Progressing_rep2

city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

description:
sample from distinct melanoma skin metastasis from one patient
M10

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Signal intensity quantification was performed using an Illumina BeadStation 500GX Genetic Analysis Systems scanner, using the standard Illumina scanning protocol.

data_processing:
For each sample, a single intensity (expression) value for each Illumina probe on the array was obtained using
Illumina GenomeStudio software with standard settings and no background correction.
For the data matrices, the ID_REF is the Illumina Probe_ID, and the Detection Pval is as provided by the Illumina software.
Detection Pvalues < 0.01 were taken to indicate Present  (i.e., the corresponding expression level was considered to be above background).
Normalization of the expression values in each sample was done by scaling: for each sample all its expression values were
multiplied by the constant which made the median of the expression values for that sample equal to 256. The scaled values
were then log base 2 transformed.
Note the sample names are as designated in the paper associated with this dataset.

source_name: melanoma skin metastasis

label_protocol: Total RNA was biotin labeled with the WG-DASL pre 1 MCS4 w/UDG Kit according to the manufacturers suggested protocol.

extract_protocol: Sample acquisition and RNA isolation from FFPE melanoma skin metastasis specimens were performed as described in the reference above.

tag: response to anti-pd-1 (nivolumab) immunotherapy (regression or progression)

value: Progression


title: PBMCs_vacci_ 0h_biolgical rep1 [exon-level]

source_name: PBMCs at just before PRRSV vaccination


title: anti-PD-1_Progressing_rep4

description:
sample from distinct melanoma skin metastasis from one patient
M12


title: PBMCs_unvacci_6h_biological rep1 [exon-level]


title: PBMCs_vacci_6h_biological rep1 [exon-level]


title: anti-PD-1_Progressing_rep3

description:
sample from distinct melanoma skin metastasis from one patient
M11


title: PBMCs_vacci_6h_biological rep3 [exon-level]


title: PBMCs_unvacci_6h_biological rep2 [exon-level]


title: anti-PD-1_Progressing_rep1

description:
sample from distinct melanoma skin metastasis from one patient
M9


title: PBMCs_vacci_0h_biological rep3 [exon-level]


title: anti-PD-1_Regressing_rep3

description:
sample from distinct melanoma skin metastasis from one patient
M5

value: Regression


title: anti-PD-1_Regressing_rep5

description:
sample from distinct melanoma skin metastasis from one patient
M7


title: PBMCs_unvacci_24h_biological rep2 [exon-level]


title: anti-PD-1_Regressing_rep4

description:
sample from distinct melanoma skin metastasis from one patient
M6


title: anti-PD-1_Regressing_rep6

description:
sample from distinct melanoma skin metastasis from one patient
M8


title: PBMCs_vacci_0h_biological rep2 [exon-level]


title: anti-PD-1_Regressing_rep2

description:
sample from distinct melanoma skin metastasis from one patient
M4


title: PBMCs_vacci_6h_biological rep2 [exon-level]


title: PBMCs_vacci_72h_biological rep3 [gene-level]


title: PBMCs_unvacci_72h_biological rep3 [gene-level]


title: PBMCs_vacci_72h_biological rep1 [gene-level]


title: PBMCs_unvacci_24h_biological rep3 [gene-level]


title: PBMCs_unvacci_72h_biological rep2 [gene-level]


title: PBMCs_unvacci_72h_biological rep1 [gene-level]


title: PBMCs_unvacci_24h_biological rep2 [gene-level]


title: PBMCs_vacci_72h_biological rep2 [gene-level]


title: PBMCs_unvacci_6h_biological rep3 [gene-level]


title: PBMCs_unvacci_24h_biological rep1 [gene-level]


title: PBMCs_vacci_24h_biological rep2 [gene-level]


title: PBMCs_unvacci_6h_biological rep2 [gene-level]


title: PBMCs_vacci_6h_biological rep3 [gene-level]


title: S. solea 33 dph 33d_B

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

description: Solea solea

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol hyb protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%) scan protocol

data_processing: Data processed with FeatureExtraction v9.5 and quantile normalized using R2.6.1 statistical software data processing

label: Cyanine 3

organism: Solea solea

source_name: whole larvae collected at 33 dph

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol label protocol

growth_protocol: growth protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples extract protocol

treatment_protocol: treatment protocol

tag: condition

value: pool of 5 larvae collected at 33 dph


title: PBMCs_unvacci_6h_biological rep1 [gene-level]


title: PBMCs_vacci_6h_biological rep2 [gene-level]


title: PBMCs_vacci_0h_biological rep3 [gene-level]


title: PBMCs_vacci_0h_biological rep2 [gene-level]


title: PBMCs_vacci_24h_biological rep3 [gene-level]


title: S. solea 33 dph 33d_D

description: Solea solea


title: S. solea 24 dph 24d_D

description: Solea solea

source_name: whole larvae collected at 24 dph

value: pool of 5 larvae collected at 24 dph


title: PBMCs_vacci_ 0h_biolgical rep1 [gene-level]


title: S. solea 33 dph 33d_A

description: Solea solea


title: PBMCs_vacci_24h_biological rep1 [gene-level]


title: S. solea 24 dph 24d_C

description: Solea solea


title: S. solea 24 dph 24d_A

description: Solea solea


title: S. solea 24 dph 24d_B

description: Solea solea


title: S. solea 18 dph 18d_D

description: Solea solea

source_name: whole larvae collected at 18 dph

value: pool of 5 larvae collected at 18 dph


title: S. solea 18 dph 18d_C

description: Solea solea


title: S. solea 18 dph 18d_A

description: Solea solea


title: S. solea 33 dph 33d_C

description: Solea solea


title: PBMCs_vacci_6h_biological rep1 [gene-level]


title: S. solea 18 dph 18d_B

description: Solea solea


title: S. solea 15 dph 15d_B

description: Solea solea

label: Cyanine 5

source_name: whole larvae collected at 15 dph

value: pool of 10 larvae collected at 15 dph


title: S. solea 13 dph 13d_D

description: Solea solea

source_name: whole larvae collected at 13 dph

value: pool of 10 larvae collected at 13 dph


title: S. solea 15 dph 15d_C

description: Solea solea

label: Cyanine 6


title: S. solea 15 dph 15d_A

description: Solea solea

label: Cyanine 4


title: Exogenous ENO2, CD1 mouse embryonic fibroblast subline E1 rep.2

description: Sample name: CD1_eno2_E1_P33

hyb_protocol: 55 μl 2X Hi-RPM hybridization buffer, 11 μl 10X aCGH blocking agent, 5 μl Cot-1 DNA (1.0 mg/ml) were added to the test and reference gDNA mix and ran 3 mins at 95°C, 30 mins at 37°C to promote binding of the gDNA targets to the probes and to prevent nonspecific binding. The mix was then allowed to hybridize to the microarray slide at 65°C for 24 hrs. After hybridization, slides were washed sequentially using Agilent Oligo aCGH/ChIP-on-Chip Washer Buffers.

scan_protocol: Microarrays were scanned using an Agilent Technologies Scanner G2505C. The raw data was extracted using Agilent Feature Extraction 11.5.1.1.

data_processing:
Bioconductor analysis tools were used for data processing: background correction and print-tip loess normalization were performed in snapCGH package; circular binary segmentation was performed on log2(test/reference)-transformed copy-number profiles using DNAcopy package.
File processed_data_seg.mean.seg.txt is linked to the Series record. "seg.mean" indicates the metric that is used for the copy number information.  ".seg" allows the file to be dragged and dropped into the Integrative Genome Viewer (IGV).

source_name: CD1 mouse embryonic fibroblasts

label_protocol: The Agilent SureTag DNA Labeling Kit was used to fragment, amplify, label, purify, and prepare the gDNA for hybridization.  Only samples with greater than 1.6 260/280 ratio and with validated DNA integrity (by running a 1% agarose gel for 30 mins at 85V) were used. Restriction digestion using Alu I (10 μg/μl) and RSA I (10 μg/μl) and stabilizing acetylated BSA (10 μg/μl) was run on samples for 2 hrs at 37°C, 20 mins at 65°C to fragment isolated gDNA. 5 μl Random Primers were added to the 24 μl of the restriction digest and sample mix for 3 mins at 95°C, 10 mins on ice to anneal to the ssDNA fragments. To amplify the gDNA while generating labeled targets for array hybridization 1 μl of Exo-Klenow fragment of DNA polymerase, 5 μl 10XdNTPs, and 3 μl Cy5-dUTP (Cy3-dUTP) were added to the restriction digest and test (reference) sample mix and ran for 2 hrs at 37°C, 10 mins at 65°C. Unreacted dye and unincorporated nucleotides were removed from the labeled gDNA using Amicon 30 kDa column purification.  The degree of labeling and concentration was then determined, and the test and reference gDNA mixed at a 1:1 ratio.

growth_protocol: CD1 mouse embryonic fibroblasts, E14.5, were purchased from Stem Cell Technologies. p53fl/fl MEFs were obtained at day E14.5 from p53fl/fl (FVB.129P2-Trp53tm1Brn/Nci) crossed with C57BL/6-129/SV mice. MEF cells were maintained in Dulbecco’s Modified Eagle’s Medium without pyruvate and supplemented with 10% FBS and 1% SPF. Cells were lifted and re-plated at a density of 9 x 105 viable cells / 60 mm dish every 3-4 days (ie, 3T9 protocol).

extract_protocol: Genomic DNA was harvested using the DNeasy kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Overexpression of HK1, HK2, kinase-dead HK2 (HK2 KD, D209A / D657A) or ENO2 glycolysis enzymes and the MYC oncogene or the control protein RFP in CD1 MEFs was accomplished by transduction of non-immortalized cells with pDS-FB-neo retrovirus, followed by selection in 600 μg/ml G418. Deletion of p53 in p53fl/fl MEFs was induced by infection of non-immortalized cells with either retroviral Cre-GFP or Cre-ERT2 plus treatment with 1 μM 4-OHT. To protect cells from reactive oxygen species (ROS), cells were cultured either at physiological oxygen concentrations (3% O2), with 2,500 U/ ml catalase from bovine liver (Sigma-Aldrich), or with both 3% O2 and catalase.

tag: strain

tag: passage

tag: type

source_name: C57BL/6J mouse tissue

value: reference


title: S. solea 11 dph 11d_C

description: Solea solea

source_name: whole larvae collected at 11 dph

value: pool of 10 larvae collected at 11 dph


title: S. solea 15 dph 15d_D

description: Solea solea

label: Cyanine 7


title: S. solea 8 dph 8d_D

description: Solea solea

source_name: whole larvae collected at 8 dph

value: pool of 10 larvae collected at 8 dph


title: S. solea 11 dph 11d_B

description: Solea solea


title: S. solea 8 dph 8d_C

description: Solea solea


title: S. solea 11 dph 11d_D

description: Solea solea


title: Exogenous kinase-dead HK2 (HK2 KD, D209A / D657A), CD1 mouse embryonic fibroblast subline Lx

description: Sample name: CD1_hk2.kd_Lx_P43

value: hk2 (kinase-dead)


title: Exogenous kinase-dead HK2 (HK2 KD, D209A / D657A), CD1 mouse embryonic fibroblast subline K2

description: Sample name: CD1_hk2.kd_K2_P63


title: S. solea 11 dph 11d_A

description: Solea solea


title: S. solea 8 dph 8d_A

description: Solea solea


title: Exogenous HK2, CD1 mouse embryonic fibroblast subline L2

description: Sample name: CD1_hk2_L2_P47


title: S. solea 8 dph 8d_B

description: Solea solea


title: S. solea 13 dph 13d_C

description: Solea solea


title: S. solea 6 dph 6d_D

description: Solea solea

source_name: whole larvae collected at 6 dph

value: pool of 10 larvae collected at 6 dph


title: anti-PD-1_Regressing_rep1

description:
sample from distinct melanoma skin metastasis from one patient
M3


title: Exogenous HK2, CD1 mouse embryonic fibroblast subline L1

description: Sample name: CD1_hk2_L1_P34


title: Exogenous HK2, CD1 mouse embryonic fibroblast subline K3

description: Sample name: CD1_hk2_K3_P36


title: EES12

city: Columbia

first: Martina

middle: SJ

last: McDermott

state: SC

address: 715 Sumter Street

department: Dept of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

hyb_protocol: 300 ng of Cy3-labelled cRNA and 300 ng of Cy5-labelled cRNA was mixed and 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 instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to  Agilent SurePrint G3 Human Gene Expression 8x60K Microarrays (G4851A-28004) 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 immersed in acetonitrile and dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channels set to 20 bit).

data_processing: Agilent feature extraction data were processed with Limma package in R. Background correction was performed using backgroundCorrect function with method normexp. Normalization of intensity values for between array comparisons was performed with the normalizeBetweenArrays function using a cyclic loess method. In order to perform between array comparisons, within-block correlations were calculated with the function intraspotCorrelation. Linear model was fit to individual channels using the lmscFit function.

source_name: MCF7 breast cancer cells, Estrogen plus Senexin treated, 12hrs

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

growth_protocol: MCF7 cells weregrown in phenol-red free DMEM/Hams F12 with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine, 1 mM sodium pyruvate (Sigma) and 5 mg insulin (Sigma). After three days, cells were plated in either phenol-red free RPMI-1640 or phenol-red free DMEM/Hams F12 with 10% charcoal-dextran-stripped FBS (Fisher Scientific), (with all additives indicated above) and allowed to grow for 24-72 hours prior to treatment.

extract_protocol: Total RNA was extracted using RNAeasy Mini Kit (Qiagen) and RNA quality was tested using Bioanalyser.

treatment_protocol: Cells were seeded in biological duplicates under ED conditions, treated with 2.5 µM Senexin A for 24 hours and then treated with 10 nM E2 for 12 hours.

tag: cell line

tag: tissue

value: breast cancer

source_name: MCF7 breast cancer cells, Estrogen , 12hrs


title: S. solea 13 dph 13d_B

description: Solea solea


title: S. solea 6 dph 6d_C

description: Solea solea


title: S. solea 6 dph 6d_B

description: Solea solea


title: S. solea 6 dph 6d_A

description: Solea solea


title: S. solea 4 dph 4d_D

description: Solea solea

source_name: whole larvae collected at 4 dph

value: pool of 10 larvae collected at 4 dph


title: Exogenous HK2, CD1 mouse embryonic fibroblast subline K2

first: Thomas

description: Sample name: CD1_hk2_K2_P34


title: Exogenous HK2, CD1 mouse embryonic fibroblast subline K1

description: Sample name: CD1_hk2_K1_P40


title: Exogenous ENO2, CD1 mouse embryonic fibroblast subline E1 rep.1

description: Sample name: CD1_eno2_E1_P25


title: S. solea 4 dph 4d_C

description: Solea solea


title: S. solea 4 dph 4d_B

description: Solea solea


title: Exogenous HK2, CD1 mouse embryonic fibroblast subline G1 rep.2

description: Sample name: CD1_hk2_G1_P52


title: S12

source_name: MCF7 breast cancer cells, Senexin treated, 12hrs

source_name: MCF7 breast cancer cells, Untreated, 12hrs


title: Exogenous HK2, CD1 mouse embryonic fibroblast subline G1 rep.1

description: Sample name: CD1_hk2_G1_P29


title: ES12

source_name: MCF7 breast cancer cells, Estrogen, 12hrs


title: E12


title: Exogenous RFP, CD1 mouse embryonic fibroblast subline K2

description: Sample name: CD1_rfp_K2_P50

value: control (rfp)


title: Exogenous RFP, CD1 mouse embryonic fibroblast subline K1

description: Sample name: CD1_rfp_K1_P34


title: Exogenous MYC, pMIG-Cre p53fl/fl mouse embryonic fibroblast subline Db (DMEM with 25mM glucose)

description: Sample name: p53ko_myc_Db_P15

source_name: p53fl/fl mouse embryonic fibroblasts

value: p53fl/fl (FVB.129P2-Trp53tm1Brn/Nci) crossed with C57BL/6-129/SV

value: myc


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline A1 (DMEM with 25mM glucose, then DMEM with 25mM galactose)

description: Sample name: p53ko_glc.to.gal_A1_P22

value: glucose to galactose media


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline B4 rep.1 (DMEM with 25mM fructose)

description: Sample name: p53ko_frc_B4_P9

value: fructose media


title: p53fl/fl mouse embryonic fibroblast diploid wild type control

description: Sample name: p53wt_ctrl_A0_P2

value: control (diploid, early passage, pre-senescence)


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline A2 rep.1 (DMEM with 25mM glucose)

description: Sample name: p53ko_ctrl_A2_P8

value: control


title: S. solea 1 dph 1d_B

description: Solea solea

source_name: whole larvae collected at 1 dph

value: pool of 10 larvae collected at 1 dph


title: S. solea 1 dph 1d_A

description: Solea solea


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline B3 (DMEM with 25mM fructose)

description: Sample name: p53ko_frc_B3_P21


title: S. solea 4 dph 4d_A

description: Solea solea


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline D1 (DMEM with 25mM pyruvate and 1mM glucose)

description: Sample name: p53ko_pyr.glc_D1_P47

value: pyruvate and glucose media


title: S. solea 1 dph 1d_C

description: Solea solea


title: pMIG-Cre + Exogenous RFP, p53fl/fl mouse embryonic fibroblast subline E4 (DMEM with 25mM glucose)

description: Sample name: p53ko_rfp_E4_P13


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline B4 (DMEM with 25mM glucose)

description: Sample name: p53ko_ctrl_B4_P23


title: pMIG-Cre + Exogenous RFP, p53fl/fl mouse embryonic fibroblast subline Db rep.1 (DMEM with 25mM glucose)

description: Sample name: p53ko_rfp_Db_P8


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline B5 (DMEM with 25mM glucose)

description: Sample name: p53ko_ctrl_B5_P23


title: Exogenous HK1, CD1 mouse embryonic fibroblast subline K3

description: Sample name: CD1_hk1_K3_P37


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline B4 rep.2 (DMEM with 25mM fructose)

description: Sample name: p53ko_frc_B4_P23


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline D1 (DMEM with 25mM lactate and 1mM glucose)

description: Sample name: p53ko_lac.glc_D1_P45

value: lactate and low glucose media


title: Exogenous HK1, CD1 mouse embryonic fibroblast subline K1

description: Sample name: CD1_hk1_K1_P60

value: reference


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline Da (DMEM with 25mM glucose)

description: Sample name: p53ko_ctrl_Da_P33


title: S. solea 1 dph 1d_D

description: Solea solea


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline A1 rep.1 (DMEM with 25mM fructose)

description: Sample name: p53ko_frc_A1_P22


title: pMIG-Cre + Exogenous RFP, p53fl/fl mouse embryonic fibroblast subline Db rep.2 (DMEM with 25mM glucose)

description: Sample name: p53ko_rfp_Db_P15


title: pMIG-Cre + Exogenous RFP, p53fl/fl mouse embryonic fibroblast subline E1 (DMEM with 25mM glucose)

description: Sample name: p53ko_rfp_E1_P13


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline A1 (DMEM with 25mM glucose, then DMEM with 5mM pyruvate)

description: Sample name: p53ko_glc.to.pyr_A1_P33

value: glucose to pyruvate media


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline A2 rep.2 (DMEM with 25mM glucose)

description: Sample name: p53ko_ctrl_A2_P31


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast single cell clone from subline C6 rep.2 (DMEM with 25mM glucose)

description: Sample name: p53ko_scc_C6.3_P27

value: single cell clone


title: HMEC-1_EPC_24 hours_rep3

first: Qing

last: Li

address: 600 YiShan Road

institute: Institute of Microsurgery on Extremities

description: Gene expression data from HMEC-1 treated with EPC-Exos

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: HMEC-1 treated with EPC-Exos

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: HMECs (1 × 10^6 cells per well) were seeded in 25-cm2 culture flask and incubated in serum-free MCDB131 cell culture media at 37 °C, 5% CO2.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: HMECs were treated with 1 × 10^11 particles/mL of EPC-Exos or an equal volume of PBS for 24 hours..Total RNA from HMECs was extracted for hybridization on Affymetrix microarrays.

tag: cell type

value: endothelial cells


title: HMEC-1_EPC_24 hours_rep1


title: HMEC-1_PBS_24 hours_rep3

description: Gene expression data from HMEC-1 treated with PBS

source_name: HMEC-1 treated with PBS


title: pERT-Cre + 4OHT p53fl/fl mouse embryonic fibroblast subline A1 (DMEM with 25mM fructose)

description: Sample name: p53ko_pERT.tam.frc_A1_P27


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast single cell clone from subline C6 rep.1 (DMEM with 25mM glucose)

description: Sample name: p53ko_scc_C6.2_P27


title: pMIG-Cre + Exogenous RFP, p53fl/fl mouse embryonic fibroblast subline Db rep.3 (DMEM with 25mM glucose)

description: Sample name: p53ko_rfp_Db_P24


title: HMEC-1_PBS_24 hours_rep2


title: pMIG-Cre + Exogenous RFP, p53fl/fl mouse embryonic fibroblast subline E3 (DMEM with 25mM glucose)

description: Sample name: p53ko_rfp_E3_P13


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline A1 (DMEM with 25mM glucose)

description: Sample name: p53ko_ctrl_A1_P22


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline D3 (DMEM with 1mM glucose supplemented with additional 2.5mM AAs)

description:
[original title] pMIG-Cre p53fl/fl mouse embryonic fibroblast subline D3 (DMEM with 1mM glucose supplemented with an additional 2.5mM of glycine, alanine, asparagine, aspartic acid, glutamic acid, proline, and serine)
Sample name: p53ko_neaa.glc_D3_P44

value: non-essential amino acids + low glucose


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast single cell clone from subline A2 rep.1 (DMEM with 25mM glucose)

description: Sample name: p53ko_scc_A2.1_P107


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline B3 (DMEM with 25mM glucose)

description: Sample name: p53ko_ctrl_B3_P23


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline A2 rep.3 (DMEM with 25mM glucose)

description: Sample name: p53ko_ctrl_A2_P59


title: pMIG-Cre + Exogenous RFP, p53fl/fl mouse embryonic fibroblast subline E2 (DMEM with 25mM glucose)

description: Sample name: p53ko_rfp_E2_P13


title: pMIG-Crep53fl/fl mouse embryonic fibroblast subline D2 (DMEM with 5mM glucose)

description: Sample name: p53ko_low.glc_D2_P41

value: low glucose


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline A1 rep.2 (DMEM with 25mM fructose)

description: Sample name: p53ko_frc_A1_P59


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline A2 rep.4 (DMEM with 25mM glucose)

description: Sample name: p53ko_ctrl_A2_P107


title: eGFP-DC-cy3_vs_eGFP-M-cy5

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

hyb_protocol: Hybridized on Agilent-014868 Whole Mouse Genome Microarrays.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: eGFP-M

label_protocol: Manufacturer's instructions.

growth_protocol: B16F1-GFP-M and B16F1-GFP-D murine melanoma cells were cultured in DMEM plus 10% FCS and 1% antibiotics. Cells were grown at 37°C in 5% CO2 and split 1:3 when reached 80% confluency. All cells were refed every other day with a fresh medium.

extract_protocol: Total RNA extracted using manufacturer's instructions.

treatment_protocol: No treatment. Comparison of the 2 cell lines.

value: melanoma cells

source_name: eGFP-DC

value: derived dormant melanoma cells


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline B2 (DMEM with 25mM galactose)

description: Sample name: p53ko_gal_B2_P94

value: p53fl/fl (FVB.129P2-Trp53tm1Brn/Nci) crossed with C57BL/6-129/SV

value: galactose media


title: Wild type CD1 mouse embryonic fibroblast subline H2 rep.3

description: Sample name: CD1_ctrl_H2_P35

source_name: CD1 mouse embryonic fibroblasts


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline B2 (DMEM with 25mM fructose, then DMEM with 25mM glucose)

description: Sample name: p53ko_frc.to.glc_B2_P94

value: fructose to glucose media

source_name: C57BL/6J mouse tissue


title: Wild type CD1 mouse embryonic fibroblast subline H2 rep.1

description: Sample name: CD1_ctrl_H2_P18


title: Wild type CD1 mouse embryonic fibroblast subline E2

description: Sample name: CD1_ctrl_E2_P54


title: HMEC-1_EPC_24 hours_rep2


title: Wild type CD1 mouse embryonic fibroblast subline F4

description: Sample name: CD1_ctrl_F4_P29


title: Exogenous RFP, CD1 mouse embryonic fibroblast subline E2

description: Sample name: CD1_rfp_E2_P33

value: control (rfp)


title: Wild type CD1 mouse embryonic fibroblast subline H2 rep.2

description: Sample name: CD1_ctrl_H2_P25


title: Wild type CD1 mouse embryonic fibroblast subline A2 rep.2

description: Sample name: CD1_ctrl_A2_P52


title: Exogenous MYC, CD1 mouse embryonic fibroblast subline G1

description: Sample name: CD1_myc_G1_P29

value: myc


title: HMEC-1_PBS_24 hours_rep1


title: Wild type CD1 mouse embryonic fibroblast subline B7

description: Sample name: CD1_ctrl_B7_P99

value: control


title: Wild type CD1 mouse embryonic fibroblast subline A1

description: Sample name: CD1_ctrl_A1_P25


title: Exogenous RFP, CD1 mouse embryonic fibroblast subline E1

description: Sample name: CD1_rfp_E1_P31


title: Catalase protected CD1 mouse embryonic fibroblast subline H1

description: Sample name: CD1_cat_H1_P25

value: catalase


title: Hypoxia + catalase protected CD1 mouse embryonic fibroblast subline I1 rep.2

description: Sample name: CD1_cat.3O2_I1_P32

value: catalase + 3% O2


title: Hypoxia + catalase protected CD1 mouse embryonic fibroblast subline I1 rep.1

description: Sample name: CD1_cat.3O2_I1_P19


title: Hypoxia + catalase protected CD1 mouse embryonic fibroblast subline I2

description: Sample name: CD1_cat.3O2_I2_P22


title: Hypoxia protected CD1 mouse embryonic fibroblast subline F1

description: Sample name: CD1_3O2_F1_P13


title: Wild type CD1 mouse embryonic fibroblast subline F3

description: Sample name: CD1_ctrl_F3_P22


title: Hypoxia protected CD1 mouse embryonic fibroblast subline H1 rep.1

description: Sample name: CD1_3O2_H1_P13


title: CD1 mouse embryonic fibroblast diploid wild type control

description: Sample name: CD1_ctrl_A0_P1

value: control (diploid, early passage, pre-senescence)


title: Wild type CD1 mouse embryonic fibroblast subline D9

description: Sample name: CD1_ctrl_D9_P36

value: reference


title: Wild type CD1 mouse embryonic fibroblast subline G1

description: Sample name: CD1_ctrl_G1_P29


title: Wild type CD1 mouse embryonic fibroblast subline A2 rep.1

description: Sample name: CD1_ctrl_A2_P25


title: Wild type CD1 mouse embryonic fibroblast subline F1 rep.1

description: Sample name: CD1_ctrl_F1_P13


title: wt mouse Keratinocytes PQ 1

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

hyb_protocol: Affymetrix GeneChip® Mouse Gene 2.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.3.1.187

source_name: mouse Keratinocytes (Atg7 f/f K14::Cre -)

label_protocol: 100ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Catalog Number 902281, Affymetrix, Santa Clara, CA)

growth_protocol: Autophagy deficient and competent mouse Keratinocytes were grown in KGM-2 medium

extract_protocol: RNA was extracted with TriFast Reagent (VWR International, Radnor, PA) and subsequent RNA cleanup and concentration was performed using the Rneasy MinElure Cleanup Kit (Qiagen, Venlo, Netherlands)

treatment_protocol: When the cells reached 50% confluence, they were sujected to paraquat 20µM (PQ) or were sham treated. RNA was isolated after 48h post treatment.

tag: cells

value: mouse Keratinocytes

tag: agent

value: Paraquat


title: wt mouse Keratinocytes PQ 3


title: Hypoxia protected CD1 mouse embryonic fibroblast subline H2

description: Sample name: CD1_3O2_H2_P13


title: KO mouse Keratinocytes PQ 1

source_name: mouse Keratinocytes (Atg7 f/f K14::Cre +)


title: DR4 mouse embryonic fibroblast diploid wild type control

description: Sample name: DR4_ctrl_A0_P1

source_name: DR4 mouse embryonic fibroblasts


title: KO mouse Keratinocytes PQ 3


title: KO mouse Keratinocytes PQ 2


title: wt mouse Keratinocytes PQ 2


title: KO mouse Keratinocytes ctrl 3

value: sham control


title: Hypoxia + catalase protected CD1 mouse embryonic fibroblast subline H1 rep.2

description: Sample name: CD1_cat.3O2_H1_P25


title: Hypoxia + catalase protected CD1 mouse embryonic fibroblast subline H1 rep.1

description: Sample name: CD1_cat.3O2_H1_P10


title: Wild type CD1 mouse embryonic fibroblast subline D10

description: Sample name: CD1_ctrl_D10_P36


title: KO mouse Keratinocytes ctrl 2


title: Hypoxia protected CD1 mouse embryonic fibroblast subline H1 rep.2

description: Sample name: CD1_3O2_H1_P25


title: wt mouse Keratinocytes ctrl 3


title: KO mouse Keratinocytes ctrl 1


title: Wild type CD1 mouse embryonic fibroblast subline F2

description: Sample name: CD1_ctrl_F2_P22


title: Wild type DR4 mouse embryonic fibroblast subline A1 rep.1

description: Sample name: DR4_ctrl_A1_P23


title: wt mouse Keratinocytes ctrl 2


title: Hypoxia + catalase protected CD1 mouse embryonic fibroblast subline H1 rep.3

description: Sample name: CD1_cat.3O2_H1_P60


title: Wild type CD1 mouse embryonic fibroblast subline F1 rep.2

description: Sample name: CD1_ctrl_F1_P23


title: Exogenous RFP, CD1 mouse embryonic fibroblast subline J2

description: Sample name: CD1_rfp_J2_P24


title: Wild type CD1 mouse embryonic fibroblast subline I1 rep.1

description: Sample name: CD1_ctrl_I1_P22


title: wt mouse Keratinocytes ctrl 1


title: Exogenous MYC, CD1 mouse embryonic fibroblast subline E2

description: Sample name: CD1_myc_E2_P37


title: Exogenous RFP, CD1 mouse embryonic fibroblast subline L2

description: Sample name: CD1_rfp_L2_P29


title: Catalase protected CD1 mouse embryonic fibroblast subline C1

description: Sample name: CD1_cat_C1_P39


title: Exogenous RFP, CD1 mouse embryonic fibroblast subline E3

description: Sample name: CD1_rfp_E3_P33


title: Exogenous RFP, CD1 mouse embryonic fibroblast subline G2

description: Sample name: CD1_rfp_G2_P50


title: Wild type CD1 mouse embryonic fibroblast subline A4 rep.1

description: Sample name: CD1_ctrl_A4_P25


title: Exogenous MYC, CD1 mouse embryonic fibroblast subline E1

description: Sample name: CD1_myc_E1_P33


title: Exogenous RFP, CD1 mouse embryonic fibroblast subline J4

description: Sample name: CD1_rfp_J4_P24


title: Wild type CD1 mouse embryonic fibroblast subline I2

description: Sample name: CD1_ctrl_I2_P42


title: Wild type CD1 mouse embryonic fibroblast subline A6

description: Sample name: CD1_ctrl_A6_P40


title: Wild type CD1 mouse embryonic fibroblast subline I1 rep.2

description: Sample name: CD1_ctrl_I1_P32


title: Wild type DR4 mouse embryonic fibroblast subline A1 rep.2

description: Sample name: DR4_ctrl_A1_P47


title: Wild type CD1 mouse embryonic fibroblast subline A4 rep.2

description: Sample name: CD1_ctrl_A4_P40


title: Wild type CD1 mouse embryonic fibroblast subline C8

description: Sample name: CD1_ctrl_C8_P40


title: Exogenous RFP, CD1 mouse embryonic fibroblast subline G1

description: Sample name: CD1_rfp_G1_P29


title: Wild type CD1 mouse embryonic fibroblast subline A3 rep.1

description: Sample name: CD1_ctrl_A3_P25

treatment_protocol: Overexpression of the MYC oncogene or the control protein RFP in CD1 MEFs was accomplished by transduction of non-immortalized cells with pDS-FB-neo retrovirus, followed by selection in G418 for 8 days. Deletion of p53 in p53fl/fl MEFs was induced by infection of non-immortalized cells with retroviral Cre-GFP. To protect cells from reactive oxygen species (ROS), cells were cultured either at physiological oxygen concentrations (3% O2), with 2,500 U/ ml catalase from bovine liver (Sigma-Aldrich), or with both 3% O2 and catalase.


title: Wild type CD1 mouse embryonic fibroblast subline A5

description: Sample name: CD1_ctrl_A5_P36


title: Wild type CD1 mouse embryonic fibroblast subline A3 rep.2

description: Sample name: CD1_ctrl_A3_P40


title: Wild type CD1 mouse embryonic fibroblast subline E1

description: Sample name: CD1_ctrl_E1_P45


title: eGFP-M-cy3_vs_eGFP-DC-cy5


title: Wild type CD1 mouse embryonic fibroblast subline H1 rep.1

description: Sample name: CD1_ctrl_H1_P25


title: Wild type CD1 mouse embryonic fibroblast subline C9 rep.1

description: Sample name: CD1_ctrl_C9_P42


title: Wild type CD1 mouse embryonic fibroblast subline H1 rep.2

description: Sample name: CD1_ctrl_H1_P36


title: Wild type CD1 mouse embryonic fibroblast subline H1 rep.3

description: Sample name: CD1_ctrl_H1_P49


title: Wild type CD1 mouse embryonic fibroblast subline C9 rep.2

description: Sample name: CD1_ctrl_C9_P78


title: Mammary sample from cow 8520

city: Beijing

first: Dengpan

last: Bu

address: No.2 Yuanmingyuan West Rd,Haidian District

institute: Institute of Animal Science,Chinese Academy of Agricultural Sciences

description: Gene expression of mammary sample

hyb_protocol: Each slide was hybridized with 1.65 μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, US, Cat#5188-5242). Hybridization was carried out with a hybridization oven (Agilent technologies, US) for 17 hours.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, US) with default settings (i.e., dye channel: Green, Scan resolution= 5 μm, PMT, 100%, 10%, 16bit).

data_processing: Data was acquired with Feature Extraction software 10.7 (Agilent technologies, US) and normalized by Quantile method with Gene Spring Software 11.0 (Agilent technologies, US)

organism: Bos taurus

source_name: Mammary, diet MF

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies, US Cat#5190-2305) according to the manufacturer’s instructions.

extract_protocol: RNA was extracted with TRIZOL Reagent (Cat#15596-018, Life technologies, Carlsbad, CA, US). Total RNA was purified by Rneasy mini kit (QIAGEN, Germany, Cat#74106) and RNase-Free DNase Set (QIAGEN, Germany, Cat#79254). The quality of RNA was analyzed with Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: 10 primiparous lactating Holstein cows (body weight, 558 ± 10 kg; days in milk, 136 ± 37d; daily milk yield, 21.1 ± 2.3 kg) were fed with 40% forage and 60% concentrate (CS; n=5) or 60% forage and 40% concentrate (MF; n=5) for 9 weeks. At the end of 9 weeks biopsy from mammary and liver were obtained.

value: Mammary


title: Mammary sample from cow 9004

description: Gene expression of mammary sample


title: Mammary sample from cow 8499

description: Gene expression of mammary sample

source_name: Mammary, diet CS


title: Mammary sample from cow 8500

description: Gene expression of mammary sample


title: Mammary sample from cow 8417

description: Gene expression of mammary sample


title: Mammary sample from cow 9006

description: Gene expression of mammary sample


title: Liver sample from cow 9004

description: Gene expression of liver sample

source_name: Liver, diet MF

value: Liver


title: Mammary sample from cow 8496

description: Gene expression of mammary sample


title: Mammary sample from cow 8446

description: Gene expression of mammary sample


title: Huh7 cells-transfected with empty vector [Control5]

city: Edinburgh

first: Cigdem

last: Selli

address: Little France Crescent

department: Centre for Reproductive Health

country: United Kingdom

institute: Queen's Medical Research Institute

description:
Control5
SAMPLE 9

hyb_protocol: Biotinylated cRNA (750 ng) was hybridized at 58 °C for 16 hrs to HumanHT-12 v3 expression BeadChip (Direct Hybridization Assay Kit, Illumina).

scan_protocol: BeadChip was washed, blocked, scanned using (Illumina BeadArray Reader), and Cy3 signal intensity was measured.

data_processing: The data were log2 transformed and normalised via quantile normalisation using lumi R package.

label_protocol: Total RNA (500 ng) was amplified and labelled with biotin using the Illumina Total Prep RNA Amplification Kit (Ambion).

growth_protocol: Huh7 cells were cultured in DMEMsupplemented with 10% fetal bovine serum , 2 mM L-glutamine , 0.1 mM non-essential aminoacid solution.

extract_protocol: Total RNA was isolated using High Pure RNA Isolation Kit (Roche Applied Science).

treatment_protocol: Cells were transfected with 2 µg vector using 6 microliter FugeneHD transfection reagent and incubated for 48 hours.

tag: transfection

value: empty vector

tag: cell line origin

value: a well differentiated hepatocyte derived cellular carcinoma cell line that was originally taken from a liver tumor


title: Mammary sample from cow 8507

description: Gene expression of mammary sample


title: Liver sample from cow 9006

description: Gene expression of liver sample


title: Liver sample from cow 8507

description: Gene expression of liver sample


title: Liver sample from cow 8520

description: Gene expression of liver sample


title: Huh7 cells-transfected with silencing vector [Silencing5]

description:
Silencing5
SAMPLE 10

value: TRPC1-silencing vector


title: Huh7 cells-transfected with empty vector [Control6]

description:
Control6
SAMPLE 11


title: Huh7 cells-transfected with silencing vector [Silencing6]

description:
Silencing6
SAMPLE 12


title: Huh7 cells-transfected with silencing vector [Silencing4]

description:
Silencing4
SAMPLE 8


title: Liver sample from cow 8446

description: Gene expression of liver sample

source_name: Liver, diet CS


title: Liver sample from cow 8500

description: Gene expression of liver sample


title: Liver sample from cow 8499

description: Gene expression of liver sample


title: Huh7 cells-transfected with empty vector [Control4]

description:
Control4
SAMPLE 7


title: Huh7 cells-transfected with silencing vector [Silencing2]

description:
Silencing2
SAMPLE 4


title: Huh7 cells-transfected with empty vector [Control3]

description:
Control3
SAMPLE 5


title: Liver sample from cow 8496

description: Gene expression of liver sample


title: Huh7 cells-transfected with silencing vector [Silencing3]

description:
Silencing3
SAMPLE 6


title: HCC-LM3 treated with GANT61 48hr

city: NANCAHNG

first: Shiwen

last: Luo

state: JiangXi

address: 17 Yong Wai street

department: Center for experimental medicine

institute: The Frist Affiliated Hospital of Nanchang University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label_protocol: Each biotinylated cRNA (750 ng) was hybridized to an Illumina Human HT expression BeadChip V4 (Illumina Inc., San Diego, CA). Following standard washing steps and staining with Streotavidin-Cy3, the arrays were scanned using an Illumina BeadArray Reader.

growth_protocol: Cells were cultured as recommended by the supplier in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: Total RNA from each sample was isolated by TRIzol (Invitrogen) according to the manufacturer's instructions. Double-stranded cDNA and biotin-labeled cRNA were synthesized from RNA (300 ng) using an Illumina TotalPrep RNA Amplification Kit (Ambion Inc., Austin, TX) according to the manufacturer’s protocol

treatment_protocol: HCC-LM3 cells were treated with GANT61 (20 μM for 48 hr), Cyclopamine (20μM for 48 hr) and control vehicle DMSO, respectively.

value: adenocarcinoma

tag: morphology

value: epithelial

tag: growth properties

value: adherent

tag: treated with

value: 20μM GANT61 for 48 hr


title: Liver sample from cow 8468

description: Gene expression of liver sample


title: Huh7 cells-transfected with silencing vector [Silencing1]

description:
Silencing1
SAMPLE 2


title: Liver sample from cow 8417

description: Gene expression of liver sample


title: HCC-LM3 treated with Cyclopamine 48hr

description: replicate 1

value: 20μM Cyclopamine for 48 hr


title: HCC-LM3 treated with DMSO 48hr

description: replicate 1

value: vehicle DMSO


title: Mammary sample from cow 8468

description: Gene expression of mammary sample


title: HeLa_Dp44mT_1

city: Wako

first: Makoto

last: Muroi

state: Saitama

department: Chemical Biology Group

institute: RIKEN CSRS

hyb_protocol: Following fragmentation, RNA were hybridized for 16 hr at 45°C on the Affymetrix Human U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Fluidics Station (Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Expression Console™ Software using Affymetrix default analysis settings.

source_name: HeLa cells treated with 5 µM of Dp44mT for 18h

label_protocol: Biotin-labeled RNA was prepared from 250ng total RNA according to the 3'IVT labeling kit protocol (Affymetrix).

growth_protocol: HeLa cells were maintained in DMEM containing 10% FCS, 50 units/ml penicillin G and 50 µg/ml streptomycin. The cells were seeded in 10-cm culture dishes and cultured overnight.

extract_protocol: Total RNA from the cells was prepared using Isogen (Nippon Gene, Japan) according to the manufacturer's instructions.

treatment_protocol: HeLa cells were treated with a compound for 18h.

value: HeLa

value: cervical cancer


title: F4/80lowPMO_co-infected_day14/5_rep3

city: Manchester

first: Dominik

middle: Andreas

last: Rückerl

address: Oxford Road

department: Faculty of Biology, Medicine and Health

institute: The University of Manchester

description: Gene expression data from bacterial infection induced, recruited, blood monocyte derived macrophages in co-infected animals

hyb_protocol: 5.5 ug of fragmented and labeled sscDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Partek Genomics Suite version 6.6 with the following options: probesets were quantile normalised and RMA background correction applied. Probesets were summarised to genes by calculating the means (log 2).

source_name: F4/80 low peritoneal macrophages from Heligmosomoides polygyrus / Salmonella Typhimurium (SL3261) consecutively co-infected C57BL/6 females 14 / 5 d.p.i.

label_protocol: Total RNA (10 ng) were converted to cDNA, fragmented and biotinylated using the GeneChip WT Pico Reagent kit (Affymetrix)  following the manufacturer's instruction.

growth_protocol: C57BL/6 female mice, aged approx 7-10 weeks at the start of the experiment housed in IVC cages under SPF conditions.

extract_protocol: Total RNA were extracted using the RNeasy Mini Kit (Qiagen) as described by the manufacturer.

treatment_protocol: Animals were infected with 200 L3 H.polygyrus and 9 days post infection co-infected with 3x10^4 cfu Salmonella Typhimurium (SL3261) and peritoneal macrophages analysed 5 days later (Day 14 p. H.polygyrus infection). As control uninfected (naïve) or single H.polygyrus / Salmonella Typhimurium infected animals were used. Whole peritoneal cells were isolated by peritoneal lavage and F4/80 high / low macrophages sorted by flow cytometry (CD19-TCRb-, SiglecF-, Ly6G-, CD11b+, CD115+, F4/80 high / low)

value: peritoneal cavity

tag: Sex

value: female

value: F4/80 low macrophages

tag: infection

value: co-infected


title: Huh7 cells-transfected with empty vector [Control1]

description:
Control1
SAMPLE 1


title: 48h flooded and infected replicate3

city: Pretoria

first: Bianca

last: Reeksting

address: 117 Lunnon Road

department: Department of Genetics

country: South Africa

institute: University of Pretoria

description: Biological replicate 3 of 3:48h flooded and infected

hyb_protocol: Hybridization was carried out according to the two-colour microarray-based gene expression analysis protocol (Agilent)

scan_protocol: Microarray slides were scanned using the Axon GenePix 400B scanner (Molecular devices)

data_processing: Axon GenePix6.0 software was used for image analysis. Normalization and statistical analysis was carried out in the R environment

organism: Persea americana

source_name: Root_48h flooded and infected

label_protocol: 4-6ug of RNA was transcribed into single stranded cDNA priming with random nonamer and oligo(dt) primers, using the Superscript III Reverse transcriptase. Samples labelled with Cy5 and References with Cy3 (CyDye Post-Labelling Reactive Dye Pack, GE Healthcare Life Sciences)

growth_protocol: Plants were grown under greenhouse conditions in 2l containers in soil-perlite mix (1:1)

extract_protocol: Total RNA extracted using phenol chloroform extraction

treatment_protocol: Split into one of four groups: control, flooded, infected, combination treatment

value: root

tag: rootstock

value: Dusa

tag: time-point

value: 48 hours

source_name: pooled reference

tag: reference type

value: Reference pool (0h, 8h, 22h, 48h, 96h, 7d)


title: F4/80lowPMO_SL3261_day5_rep2

description: Gene expression data from bacterial infection induced, recruited, blood monocyte derived macrophages

source_name: F4/80 low peritoneal macrophages from Salmonella Typhimurium (SL3261) infected C57BL/6 females 5 d.p.i.

tag: strain


title: F4/80lowPMO_SL3261_day5_rep4


title: 48h infected replicate3

description: Biological replicate 3 of 3:48h infected

source_name: Root_48h infected


title: F4/80lowPMO_co-infected_day14/5_rep4


title: F4/80lowPMO_SL3261_day5_rep1


title: HeLa_DMSO_1

source_name: HeLa cells treated with DMSO for18h


title: Huh7 cells-transfected with empty vector [Control2]

description:
Control2
SAMPLE 3

value: empty vector

value: a well differentiated hepatocyte derived cellular carcinoma cell line that was originally taken from a liver tumor


title: F4/80lowPMO_co-infected_day14/5_rep2


title: HeLa_CollismycinA_1

source_name: HeLa cells treated with 5 µM of Collismycin A for 18h