title: Matching control of As-TM cells; HaCaT cells-unexposed sodium arsenite maintained for 28 weeks-replicate 1

description:
From Dr. Michael P. Waalkes, NIEHS
Permanent epithelial cell line from adult human maleskin, aneuploid, immortal, has a transformed phenotype in vitro but remains nontumorigenic, has been maintained for 28 weeks with no exposure as a match control for As-TM cells
The cells (matching control of As-TM cells) were obatained from Dr. Micheal Waalkes after 28 weeks of maintenance without sodium arsenite

value: unexposed maintained for 28 weeks


title: 15686

status: Public on Jan 23 2018

type: RNA

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of purified and labeled cRNA (Cy3 label: 825 ng; Cy5 label: 825 ng) was hybridised on the Agilent-021169 Arabidopsis 4 Oligo Microarray (V4) followed by (manual) washing, according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with SureScan High-Resolution Technology, and probe signals were quantified using Agilent's Feature Extraction software (version 10.7.3.1).

data_processing: We use the Agilent processed signal values (i.e., feature gProcessedSignal for the Cy3 signal and rProcessedSignal for the Cy5 signal) from Agilent Feature Extraction software v10.7.3.1 and compute log2-(Cy5/Cy3)-ratios. We remove Agilent control probes, as well as probes with signals below background on all arrays (absent spots). To decide whether a signal is significantly above background, we use the features gIsPosAndSignif and rIsPosAndSignif, also provided by the Agilent software. In case of multiple probes for the same Agilent ID, log2-(Cy5/Cy3)-ratios are averaged.

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 200 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double-stranded cDNA in a reverse transcription reaction. Subsequently, the sample was converted to antisense cRNA, amplified and labeled with Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer's protocol (Agilent).

growth_protocol: Seedlings were grown on half-strength MS medium without sucrose. 48h 4°C, 4 days in darkness 22°C.

extract_protocol: QIAGEN RNeasy Plant Mini Kit with on-column DNase digestion and four RPE washes.

tag: ecotype

value: Columbia 0

tag: genotype

value: elo3-6 mutant (GABI-KAT collection code GABI555_H06)

tag: age

value: 4 days

tag: tissue

value: seedling

tag: replicate

tag: treatment

value: darkness

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 200 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double-stranded cDNA in a reverse transcription reaction. Subsequently, the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer's protocol (Agilent).

value: wild type


title: HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 3

city: Louisville

first: J.

middle: Christopher

last: States

state: KY

address: 505 S. Hancock St., Rm 304

department: Department of Pharmacology & Toxicology

country: USA

institute: University of Louisville

description:
A generous gift from Dr. Tai Hao Quan, University of Michigan
Permanent epithelial cell line from adult human maleskin, aneuploid, immortal, has a transformed phenotype in vitro but remains nontumorigenic.
The cells were maintained for 7 weeks without 100 nM sodium arsenite

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C to Affymetrix Primeview Human arrays according to the GeneChip 3' array Hybridization User Manual from Affymetrix

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 4.0 (Affymetrix)

data_processing: The CEL files were imported into Partek software Version 6.6 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization. Contrast of interest were analyzed using a 2-way ANOVA considering treatment and time.

label: biotin

organism: Homo sapiens

source_name: Immortalized Human Keratinocytes (HaCaT)

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix 3' IVT Express Plus Reagent Kit from 250 ng total RNA

growth_protocol: HaCaT cells were cultured in 4 biological replicates in MEM alpha modification media supplemented with 10% fetal bovine serum, penicillin/streptomycin and glutamine. Cultures were maintained at 37°C in a humidified 5% CO2 atmosphere with 20% oxygen and were maintained separately for 3 and 7 weeks. A set of HaCaT cells maintained for 28 weeks (1 biological replicate) were obtained form Dr. Michael P. Waalkes.

extract_protocol: Total RNA was purified from the cells using the mirVana™ miRNA Isolation Kit.

treatment_protocol: cells maintained with and without 100 nM sodium arsenite from day 1 of plating.

tag: cell line

value: HaCaT cells

value: unexposed maintained for 7 weeks


title: 15680

growth_protocol: Seedlings were grown on half-strength MS medium without sucrose. 48h 4°C, 4 days in darkness 22°C, 1h red light.

value: red light


title: 15689

growth_protocol: Seedlings were grown on half-strength MS medium without sucrose. 48h 4°C, 4 days in darkness 22°C, 1h far-red light.

value: far-red light


title: 15681


title: 15690


title: 15679


title: HaCaT cells-unexposed sodium arsenite maintained for 3 weeks-replicate 4

description:
A generous gift from Dr. Tai Hao Quan, University of Michigan
Permanent epithelial cell line from adult human maleskin, aneuploid, immortal, has a transformed phenotype in vitro but remains nontumorigenic.
The cells were maintained for 3weeks without 100 nM sodium arsenite

value: unexposed maintained for 3 weeks


title: HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 1


title: 15678


title: HaCaT cells-unexposed sodium arsenite maintained for 3 weeks-replicate 2


title: 15676


title: 15677


title: HaCaT cells-unexposed sodium arsenite maintained for 3 weeks-replicate 3


title: HaCaT cells-unexposed sodium arsenite maintained for 3 weeks-replicate 1


title: HaCaT cells-exposed to 100 nM sodium arsenite for 7 weeks-replicate 4

description:
A generous gift from Dr. Tai Hao Quan, University of Michigan
Permanent epithelial cell line from adult human maleskin, aneuploid, immortal, has a transformed phenotype in vitro but remains nontumorigenic.
The cells were maintained for 7 weeks with 100 nM sodium arsenite

value: 100 nM sodium arsenite for 7 weeks


title: 15675


title: 15672


title: 15671


title: HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 2


title: HaCaT cells-exposed to 100 nM sodium arsenite for 7 weeks-replicate 2


title: 15673


title: 15674


title: HaCaT cells-exposed to 100 nM sodium arsenite for 3 weeks-replicate 4

description:
A generous gift from Dr. Tai Hao Quan, University of Michigan
Permanent epithelial cell line from adult human maleskin, aneuploid, immortal, has a transformed phenotype in vitro but remains nontumorigenic.
The cells were maintained for 3 weeks with 100 nM sodium arsenite

value: 100 nM sodium arsenite for 3 weeks


title: HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 4

hyb_protocol: Biotin-labeled samples were hybridized for 18 hr at 48C to Affymetrix miRNA 4.0 arrays according to the GeneChip 3' array Hybridization User Manual from Affymetrix

label_protocol: Biotinylated RNA were prepared according to the standard protocol for Affymetrix FlashTag Biotin HSR RNA labeling Kit from 800 ng total RNA


title: HaCaT cells-exposed to 100 nM sodium arsenite for 3 weeks-replicate 2

description:
A generous gift from Dr. Tai Hao Quan, University of Michigan
Permanent epithelial cell line from adult human male skin, aneuploid, immortal, has a transformed phenotype in vitro but remains nontumorigenic.
The cells were maintained for 3 weeks with 100 nM sodium arsenite


title: HaCaT cells-exposed to 100 nM sodium arsenite for 3 weeks-replicate 3


title: HaCaT cells-exposed to 100 nM sodium arsenite for 7 weeks-replicate 3


title: As-TM cells; HaCaT cells-exposed to 100 nM sodium arsenite for 7 weeks-replicate 1


title: 15670


title: HaCaT cells-exposed to 100 nM sodium arsenite for 3 weeks-replicate 1


title: HaCaT cells-exposed to 100 nM sodium arsenite for 28 weeks-replicate 1

description:
From Dr. Michael P. Waalkes, NIEHS
Permanent epithelial cell line from adult human maleskin, aneuploid, immortal, has transformed to malignancy by chronic (28 weeks) incubation in 100 nM sodium arsenite
The cells (As-TM cells) were obatained from Dr. Micheal Waalkes after 28 weeks of exposure to 100 nM sodium arsenite

value: 100 nM sodium arsenite for 28 weeks


title: Matching control of As-TM cells; HaCaT cells-unexposed sodium arsenite maintained for 28 weeks-replicate 1

description:
From Dr. Michael P. Waalkes, NIEHS
Permanent epithelial cell line from adult human maleskin, aneuploid, immortal, has a transformed phenotype in vitro but remains nontumorigenic, has been maintained for 28 weeks with no exposure as a match control for As-TM cells
The cells were obatained from Dr. Micheal Waalkes after 28 weeks of maintenance without sodium arsenite


description:
From Dr. Michael P. Waalkes, NIEHS
Permanent epithelial cell line from adult human maleskin, aneuploid, immortal, has transformed to malignancy by chronic (28 weeks) incubation in 100 nM sodium arsenite
The cells were obatained from Dr. Micheal Waalkes after 28 weeks of exposure to 100 nM sodium arsenite


title: HaCaT cells-unexposed sodium arsenite maintained for 3 weeks-replicate 4


title: p3-035a

type: SRA

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2
Demultiplexing with custom demultipler written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl GRCh38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text format

extract_protocol:
ACL remnants used in this study were harvested at the time of clinically indicated arthroscopic surgery from a discovery cohort of 28 patients, including 12 with an isolated injury pattern and 16 with a combined injury pattern in patients undergoing ACL reconstruction.  RNA was extracted and purified as previously described31. Briefly, ACL remnant was thawed, replenished with 1 mL of Trizol reagent and homogenized with the use of a Polytron homogenizer (Brinkmann Instruments). Aliquot of the homogenized suspension was transferred to a microfuge tube and incubated at room temperature for 5 min to permit the complete dissociation of nucleoprotein complexes. After addition of 200 μL of chloroform, the sample was mixed vigorously and the contents were transferred to phase lock gel tube and centrifuged for 15 min at 4°C. The clear aqueous layer was transferred to a fresh tube and 1 volume of 70% ethyl alcohol was added to precipitate RNA. RNA was collected using RNeasy spin columns (Qiagen Inc.) according to the instruction manual. RNA was quantified by using a NanoDrop ND-100 spectrophotometer (NanoDrop) while quality was assessed with use of Agilent Bioanalyzer (Agilent).
Sigma SeqPlex

tag: Sex

value: M

tag: height (inches)

tag: weight (lbs)

tag: bmi

tag: time from injury (weeks)

tag: smoker

value: No

tag: injury type

value: ACL injury only

value: ACL tears remnants


title: p3-18a

value: ACL injury with Meniscus_tear


title: p3-037a


title: p3-19a

value: Yes


title: p3-040a


title: p3-023a


title: p3-034a

value: F


title: p3-039a


title: HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 1


title: p3-033a


title: HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 3


title: p3-029a


title: p3-022a


title: p3-036a


title: p3-021a


title: p3-031a


title: p3-020a


title: p3-026a


title: p3-015a


title: p3-012a


title: p3-038a


title: p3-016a


title: p3-011a


title: p3-009a


title: p3-010a


title: p3-008a


title: p3-004a


title: p3-005a


title: p3-003a


title: p3-006a


title: Saline_M99183

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health.

data_processing: RMA normalization log2 transformed, using the oligo package of Bioconductor

organism: Macaca nemestrina

source_name: fetal cardiac tissue

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Rhesus Macaque Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA was extracted from tissue samples using the Qiagen RNeasy kit, following the manufacturer's recommendations. Quality and quantity were assessed using an Agilent 2100 Bioanalyzer and NanoDrop 8000 spectrophotometer, respectively.

tag: developmental stage

value: fetal

value: heart

value: Saline

tag: treatment location

value: Choriodecidual inoculation

tag: labor

value: normal


title: Saline_M05267


title: GBS_A10016

value: Group B streptococcus

value: delivered


title: GBS_K02151

value: preterm


title: Saline_5109


title: Saline_4105


title: GBS_A12263


title: GBS_5106

value: E. coli

value: Intra-amniotic


title: Saline_5081


title: V16D_HP1α_rep2

status: Public on Jan 22 2018

city: Vancouver

first: Yuzhuo

last: Wang

state: BC

address: 2660 Oak Street

department: Vancouver Prostate Centre

country: Canada

institute: University of British Columbia

description: Gene expression in stable cell lines with puromycin selection after culture in complete media for 14 days

hyb_protocol: Labeled, fragmented cRNA was hybridized to Agilent SurePrint G3 Human Gene Expression v3 8x60K array following manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides at 3um scan resolution.

data_processing: Image data were processed with Agilent Feature Extraction 11.0.1.1. Processed signals were quantile normalized with Agilent GeneSpring 12.0.

source_name: V16D, HP1α, FBS 14d, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Agilent’s One-Colour Microarray-Based Gene Expression Analysis Low Input Quick Amp Labelling v6.0 (Agilent Technologies, Santa Clara, CA).

growth_protocol: NCI-H660 cells were obtained from ATCC, and cultured in RPMI-1640 medium with supplements as follows: 5% FBS, 10 nM beta-estradiol, 10 nM Hydrocortisone, 1% Insulin-Transferrin-Selenium. V16D cell was a CRPC cell line derived from LNCaP, constructed by Dr. Amina Zoubeidi's laboratory, and cultured in  RPMI-1640 medium with 10% FBS.

extract_protocol: Total RNA was isolated using Trizol (Thermo Fisher)

treatment_protocol: Lentiviral particles delivering shRNA or gene overexpressing plasmids were added to the culture media of parental cells,  puromycin was used at 1 μg/ml to select for infected cells and to maintain stable cell populations. To induce neuroendocrine phenotype in V16D cell, cells were starved with phenol-red free RPMI-1640  containing 10% Charcoal-Stripped Serum for 24 hours, then cultured with the addition of 10 μM enzalutamide for 14 days, in parallel, control cells were cultured in complete media for 14 days.

tag: cell type

value: prostate cancer

tag: genotype/variation

value: HP1alpha overexpression

value: FBS complete media 14 days


title: V16D_HP1α_EnZrep1

description: Gene expression in stable cell lines with puromycin selection after culture in phenol-red free media with CSS and 10 μM enzalutamide for 14 days

source_name: V16D, HP1α, EnZ 14d, replicate 1

value: CSS with 10 μM enzalutamide media 14 days


title: 69one1

city: Torrevieja

first: Ramon

middle: G

last: Manzano

state: Alicante

address: Partida la Loma s/n

department: Unidad de Consejo Genetico, Plataforma de Oncologia

country: Spain

institute: Hospital Quiron Torrevieja

description: Two color microarray from which only Cy5 data are analyzed after dye-bias correction

hyb_protocol: As described in Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp labeling) v 5.7 [Manual G4140-90050]

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent G2505B fluorescent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction (v9.5) software.

data_processing: Only Cy5 data were analyzed after dye bias correction (Feature extraction software version 9.5). Preprocessing consisted of: background correction (normexp, offset=50), quantile normalization, base 2 logarithmic transformation. Obtention of the median intensity values of the 264 non-control probes that are replicated 9 times in each microarray. The R statistical environment was used for preprocessing.

extract_protocol: QIAGEN Rneasy kit

tag: gender

value: Male

tag: dataset

value: Training set

value: Colorectal cancer

source_name: Normal universal tissue

value: Normal universal tissue


title: 73one2

label_protocol: As described in Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp labeling) v 5.7 [Manual G4140-90050]

tag: tissue

value: Lung cancer


title: 62one3

value: Bile duct cancer


title: 61one2

value: Pancreatic cancer

source_name: Normal pancreas

value: Normal pancreas


title: V16D_ctrl_rep2

source_name: V16D, control, FBS 14d, replicate 2

value: control overexpression

tag: treatment


title: V16D_HP1α_rep1

source_name: V16D, HP1α, FBS 14d, replicate 1

tag: cell line


title: V16D_ctrl_EnZ_rep1

source_name: V16D, control, EnZ 14d, replicate 1


title: GBS_A10033

value: fetal

value: heart

value: Group B streptococcus

value: Choriodecidual inoculation


title: 63one1

value: Female

source_name: Normal colon

value: Normal colon


title: 61one1


title: 73one4

value: Urothelial cancer


title: 64one3

value: Ovarian cancer

source_name: Normal ovary

value: Normal ovary


title: 62one1

value: Male

value: Training set


title: V16D_HP1α_EnZ_rep2

source_name: V16D, HP1α, EnZ 14d, replicate 2

value: prostate cancer

value: HP1alpha overexpression

value: CSS with 10 μM enzalutamide media 14 days


title: V16D_ctrl_rep1

source_name: V16D, control, FBS 14d, replicate 1

value: FBS complete media 14 days


title: V16D_ctrl_EnZ_rep2

source_name: V16D, control, EnZ 14d, replicate 2


title: Infected 1

city: Stanford

first: Mark

middle: M.

last: Davis

state: CA

address: 279 Campus Drive

department: Department of Microbiology and Immunology

institute: Stanford University

data_processing:
Read quality was determined with FastQC 0.11.4.
Using STAR 2.4.2a, we aligned the reads to the mouse reference genome (NCBI37/mm9), with splice junctions defined by the GTF file (UCSC).
Gene expression was determined by calculating fragments per kilobase per million aligned reads (FPKM) using Cufflinks 2.2.1.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Tab-delimited text files with FPKM values.

organism: Mus musculus

source_name: Spleen

extract_protocol:
gamma-delta T cells were bulk sorted directly into RNAprotect Cell Reagent (Qiagen). RNA was extracted with an RNeasy Plus Micro Kit (Qiagen).
After analysis on the 2100 Bioanalyzer, the sequencing libraries were prepared using the RiboGone Mammalian rRNA Depletion Kit (Clontech) and the SMARTer Stranded RNA-Seq Kit (Clontech).

value: Spleen

tag: strain

value: gamma-delta T cell

tag: infection

value: Plasmodium chabaudi chabaudi AJ

tag: time point

value: 19 days post-infection

tag: infection status

value: Infected


title: Uninfected 3

value: Uninfected


title: Uninfected 2


title: Uninfected 1


title: Uninfected 4


title: Infected 4


title: Infected 3


title: Infected 2


title: 60one2

value: Lung cancer

source_name: Normal lung

value: Normal lung


title: 60one1

value: Female


title: H660_sh40

description:
KD_3
Gene expression in stable cell lines with puromycin selection

source_name: H660_HP1α knockdown

treatment_protocol: Lentiviral particles delivering shRNA or gene overexpressing plasmids were added to the culture media of parental cells,  puromycin was used at 1 ug/ml to select for infected cells and to maintain stable cell populations. To induce neuroendocrine phenotype in V16D cell, cells were starved with phenol-red free RPMI-1640  containing 10% Charcoal-Stripped Serum for 24 hours, then cultured with the addition of 10 uM enzalutamide for 14 days, in parallel, control cells were cultured in complete media for 14 days.

value: Neuroendocrine prostate cancer (NEPC) cell line

value: HP1alpha KD


title: 59one1

value: Ovarian cancer

value: Normal ovary


title: 55one3

value: Training set

value: Cervical cancer

source_name: Normal cervix

value: Normal cervix


title: 56one1

value: Soft tissue sarcoma

source_name: Normal skeletal muscle

value: Normal skeletal muscle


title: 51one3

value: Thyroid cancer

source_name: Normal thyroid

value: Normal thyroid


title: 53one2

value: Breast cancer

source_name: Normal breast

value: Normal breast


title: 45one3

value: Male

value: Pancreatic cancer

source_name: Normal universal tissue

value: Normal universal tissue


title: H660_shcontrol_rep1

description:
control_1
Gene expression in stable cell lines with puromycin selection

value: control KD


title: 50one1

value: Female


title: 53one1

source_name: Normal pancreas

value: Normal pancreas


title: 52one3

value: Kidney cancer

source_name: renal

value: Normal renal


title: 53one4

value: Training set

value: Head&neck cancer


title: 48one1

value: Lung cancer

value: Normal lung


title: H660_sh39

description:
KD_2
Gene expression in stable cell lines with puromycin selection

value: Neuroendocrine prostate cancer (NEPC) cell line

value: HP1alpha KD


title: 42one4

value: Testes cancer


title: 52one1

value: Ovarian cancer

value: Normal ovary


title: 45one4

value: Colorectal cancer

value: Normal colon


title: H660_sh38

description:
KD_1
Gene expression in stable cell lines with puromycin selection


title: 45one2

value: Pancreatic cancer


title: 50one3

value: Soft tissue sarcoma

value: Normal skeletal muscle


title: 46one1

value: Male


title: H660_shcontrol_rep2

description:
control_2
Gene expression in stable cell lines with puromycin selection

value: control KD


title: ATII_Tert3

city: Madrid

first: Gonzalo

last: Gomez-Lopez

state: Madrid

address: Calle Melchor Fdez Almagro 3

department: Structural Biology

institute: CNIO

hyb_protocol: Microarray: Mouse Gene Expression G3 60K (Agilent microarray design ID 028005, P/N G4852A). Microarray sequences and annotations are listed in sheet '028005_mm9_20121126'. Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 600 ng. Volume: 50 µL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analyzed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and background subtraction by spatial detrending algorithms.

data_processing: Microarray background subtraction was carried out using normexp method. To normalize the dataset, we performed loess within arrays normalization and quantiles between arrays normalization.

source_name: AAV9-Tert vector

label_protocol:
Amount of nucleic acid labeled: 100ng. Commercial One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.7 kit by following manufacturer instructions. Agilent manual G4140-90040 of Sep2014. Amplification: by RNA polymerases.
Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of Cy3-CTP fluorophore.
Labeled samples are purified with silica-based spin columns.

extract_protocol: ATII cells were sorted by FACS from mouse lungs of both groups AAV9-Tert and AAV9-empty vector. Lungs were extracted and introduced in HBBS buffer with antibiotic and 1% BSA. Separate the lobules of the lung on a dish mince them with a scalpel. Transfer them to a GentleMacs tube with HBBS, antibiotics, 1% BSA, DNAse I (60 units/mL) (Sigma, DN25) and collagenase type I (70 units/mL) (GIBCO, Cat. Number 17100). Then we run the GentleMac program “lung 1”, after the program incubate the sample at 37ºC for 30 minutes and at the end we run the GentleMac program “lung 2”. Cell suspension was filtered through a 40μm stainer and then centrifuge 1200 rpm 5 min. Cells were resuspended in 2 mL ACK Lysis Buffer to lyse red blood cells. Incubate 4 min. at room temperature. We added DMEM without serum to wash, centrifugate and discard supernatant. At the end, resuspend cells in PBS with EDTA (1mM), Hepes (25 mM) and 3% FBS to start staining with LysoTracker as described in commercial protocol (Molecular Probes, LysoTracker Green DND-26, Cat. Num. L7526) and the following antibodies from Pharmingen (BD Biosciences, San Jose CA): PE antimouse CD45, PE antimouse CD31, APC antimouse EpCAM. DAPI (Sigma, St Louis MO) was used to identify dead cells. Data was collected and the defined populations (CD45-CD31-EpCAM+ LysoTracker+ and LysoTracker-) were sorted using an InFlux cell sorted (BD, San Jose CA), we excluded cell aggregates by using pulse processing in the scatter signals and dead cells in the basis of DAPI staining. All data was analyzed using FlowJo software v9.8.5 (Treestar, Ahsland OR). RNA was extracted from post-caval lobe frozen lungs with RNeasy kit following manufacturer instruction (Qiagen, cat. Nº 73504) and RNA integrity analyzed in an Agilent Bioanalyzer. cDNA was synthesised and analyzed on Agilent´s Mouse Genome DNA microarray, following the manufacturer´s instructions. Microarray background subtraction was carried out using normexp method.

treatment_protocol: Mice with pulmonary fibrosis were treated with either AAV9-Tert or empty vector and were sacrificed 1 week post-virus inoculation. ATII cells were sorted by FACS from mouse lungs of both groups AAV9-Tert and AAV9-empty vector.

value: Alveolar epithelial type II cells sorted by FACS

value: male

tag: disease state

value: pulmonary fibrosis


title: 44one4

value: Female

value: Training set

value: Vaginal cancer

value: Normal universal tissue


title: 42one2

value: Breast cancer

value: Normal breast


title: 40one3

value: Lung cancer

value: Normal lung


title: 35one1

value: Esophagus cancer

source_name: Normal stomach

value: Normal stomach


title: 35one3

value: Soft tissue sarcoma


title: ATII_Tert2


title: 37one2

value: Normal skeletal muscle


title: ATII_Tert1


title: twentysix4

value: Male

value: Merkel cell carcinoma

source_name: Normal esophagus

value: Normal esophagus


title: M20 rna-seq

city: Charlottesville

first: Alexander

middle: Fritz

last: Koeppel

state: VA

address: 1640 Jefferson Park Avenue

department: School of Medicine

institute: University of Virginia

description: RNA-seq data for Male Chorionic villus sample M20

data_processing:
align to genome with STAR
count reads mapping to genes with featureCounts
Genome_build: grch38
Supplementary_files_format_and_content: gene counts, txt

source_name: Chorionic villus

extract_protocol:
CVS tissue was thawed on ice with 600 μl of RTL Plus lysis buffer (QIAGEN) and 1% β-mercaptoethanol added to each sample. Cells were homogenized by passing at least 10 times through single-use needles with decreasing gauge (22G, 25G, then 27G) attached to a 1 mL sterile, RNase-free syringe. The homogenates were loaded onto AllPrep spin columns and the remainder of the protocol was performed following manufacturer instructions. DNA and RNA were extracted using the commercial AllPrep DNA/RNA Extraction Mini Kit (QIAGEN) for RNA-seq. RNA was eluted with 30 μl of the kit-provided RNase-free water at room temperature, then the elution was passed through the column a second time to increase RNA yield. DNA was eluted with 100 μl of the kit-provided EB buffer warmed to 70°C
RNA-Seq libraries were constructed from 200 ng of total RNA using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kits (Illumina, Carlsbad, CA). Constructed libraries contained RNAs >200 nt (both unpolyadenylated and 140 polyadenylated) and were depleted of cytoplasmic and mitochondrial rRNAs.

value: Chorionic villus

tag: Sex

tag: gestational age


title: twentyeight4


title: twentyseven3


title: twentythree2

value: Ovarian cancer

source_name: Normal ovary

value: Normal ovary


title: Case_21

city: Burlington

first: Nicholas

middle: H

last: Farina

state: VT

address: 89 Beaumont Avenue

department: Biochemistry

institute: University of Vermont Cancer Center

description:
Circulating miRNA profile of serum from a CASE woman
HRBP447

hyb_protocol: Samples were combined with a hybridization mix, injected into arrays, and placed in the Affymetrix® GeneChip® Hybridization Oven 645 at 48° C and 60 RPM for 42 hours.

scan_protocol: Arrays were stained using the Affymetrix® GeneChip® Fluidics Station 450 and scanned with the Affymetrix® GeneChip® Scanner 3000.

data_processing: Raw CEL files were processed individually using the apt-probeset-summarize function within the Affymetrix Power Tools v1.18.0 software package. Simplified Expression Analysis (SEA) algorithm was used to summarize probesets and the Detectable Above BackGround (DABG) algorithm was used to assign p-values to probeset intensities. Following probeset summarization, the average of 95 anti-genomic probesets was subtracted from each RNA expression probeset. Any value less than 0, below microarray background, was set to 0. For present/absent calls, all probesets with a DABG p > 0.05 were set to 0.

label_protocol: Exactly 8ul of RNA was tagged with a Poly-A tail, using an ATP driven reaction from the Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kit.  Samples were then labeled with a biotinylated molecule using a ligation reaction.  Efficiency of the biotin ligation reaction was verified using NeutrAvidin (10mg/mL) with a gel-shift assay.

growth_protocol: not applicable

extract_protocol: RNA was isolated from a 200μL serum aliquot using the miRNeasy Serum Plasma kit with ce-miR-39 spike-in (QIAGEN), QIAcube (QIAGEN) automation, and eluted with 14uL of nuclease-free water. Multiple serum aliquots from the same patient were processed simultaneously, RNA pooled, and stored in small aliquots to isolate sufficient RNA for downstream applications.

treatment_protocol: Serum is obtained from coagulated whole blood samples by centrifugation at 3000 rpm for 10 minutes. Serum aliquots are stored at -80°C within 1 hour of blood draw. Serum samples did not undergo previous freeze/thaw cycles.

value: serum

tag: group

value: case

value: female


title: ATII_Empty3

source_name: empty vector

value: Alveolar epithelial type II cells sorted by FACS

value: male

value: pulmonary fibrosis


title: twentyfour1

value: Training set

value: Thyroid cancer

value: Normal thyroid


title: twentytwo1

value: Malignant Mesothelioma

value: Normal lung


title: twentyeight3

value: Female

value: Soft tissue sarcoma

value: Normal breast


title: M21 rna-seq

description: RNA-seq data for Male Chorionic villus sample M21

treatment_protocol: CVS tissue was thawed on ice with 600 μl of RTL Plus lysis buffer (QIAGEN) and 1% β-mercaptoethanol added to each sample. Cells were homogenized by passing at least 10 times through single-use needles with decreasing gauge (22G, 25G, then 27G) attached to a 1 mL sterile, RNase-free syringe. The homogenates were loaded onto AllPrep spin columns and the remainder of the protocol was performed following manufacturer instructions. DNA and RNA were extracted using the commercial AllPrep DNA/RNA Extraction Mini Kit (QIAGEN) for RNA-seq. RNA was eluted with 30 μl of the kit-provided RNase-free water at room temperature, then the elution was passed through the column a second time to increase RNA yield. DNA was eluted with 100 μl of the kit-provided EB buffer warmed to 70°C

value: Chorionic villus

value: Male

value: other


title: ATII_Empty1


title: twentyfive3

value: Testes cancer

value: Normal stomach


title: ATII_Empty2


title: nineteen3

value: Unknown primary


title: twentyfive4

value: Non Hodgkin lymphoma

source_name: Normal spleen

value: Normal spleen


title: Case_20

description:
Circulating miRNA profile of serum from a CASE woman
HRBP399

value: serum

value: case

value: female


title: twenty1

value: Training set

value: Ovarian cancer

value: Normal ovary


title: Control_18

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP393

value: control


title: M22 rna-seq

description: RNA-seq data for Male Chorionic villus sample M22


title: Control_24

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP455


title: 32one2

value: Lung cancer

value: Normal lung


title: Case_23

description:
Circulating miRNA profile of serum from a CASE woman
HRBP420


title: Control_23

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP500


title: M19 rna-seq

description: RNA-seq data for Male Chorionic villus sample M19

value: Chorionic villus


title: twentyeight2

value: Male

value: Colorectal cancer

source_name: Normal colon

value: Normal colon


title: M18 rna-seq

description: RNA-seq data for Male Chorionic villus sample M18


title: twentysix2

description: Two color microarray from which only Cy5 data are analyzed after dye-bias correction

value: Esophagus cancer

value: Normal esophagus


title: twentyfour3

value: Female

value: Breast cancer

value: Normal breast


title: M16 rna-seq

description: RNA-seq data for Male Chorionic villus sample M16

value: other


title: M17 rna-seq

description: RNA-seq data for Male Chorionic villus sample M17


title: twentytwo2

value: Head&neck cancer


title: M15 rna-seq

description: RNA-seq data for Male Chorionic villus sample M15


title: Control_07

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP390

value: serum

value: female


title: M14 rna-seq

description: RNA-seq data for Male Chorionic villus sample M14


title: Case_19

description:
Circulating miRNA profile of serum from a CASE woman
HRBP389

value: case


title: nineteen4

value: Training set


title: nineteen1

value: Gastric cancer

value: Normal stomach


title: seventeen4


title: M13 rna-seq

description: RNA-seq data for Male Chorionic villus sample M13

value: Chorionic villus


title: Control_21

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP371

value: control


title: Control_08

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP363


title: M12 rna-seq

description: RNA-seq data for Male Chorionic villus sample M12

value: Male


title: Control_05

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP356


title: seventeen2

value: Soft tissue sarcoma

source_name: Normal fat

value: Normal fat


title: M09 rna-seq

description: RNA-seq data for Male Chorionic villus sample M09


title: M11 rna-seq

description: RNA-seq data for Male Chorionic villus sample M11


title: M10 rna-seq

description: RNA-seq data for Male Chorionic villus sample M10


title: M07 rna-seq

description: RNA-seq data for Male Chorionic villus sample M07


title: fifteen3

value: Colorectal cancer

value: Normal colon


title: sixteen4

value: Pancreatic cancer

value: Normal pancreas


title: seventeen1

value: Female

value: Normal skeletal muscle


title: Case_17

description:
Circulating miRNA profile of serum from a CASE woman
HRBP344

value: serum


title: Case_18

description:
Circulating miRNA profile of serum from a CASE woman
HRBP351

value: female


title: fifteen4

description: Two color microarray from which only Cy5 data are analyzed after dye-bias correction

value: Ovarian cancer

value: Normal ovary


title: ten2

value: Training set

value: Cervix cancer

value: Normal cervix


title: Case_15

description:
Circulating miRNA profile of serum from a CASE woman
HRBP319

value: case


title: twelve1

value: Male


title: forteen4

value: Breast cancer

value: Normal breast


title: Case_22

description:
Circulating miRNA profile of serum from a CASE woman
HRBP293


title: eight1

value: Malignant Melanoma

value: Normal fat


title: Case_13

description:
Circulating miRNA profile of serum from a CASE woman
HRBP234


title: Case_16

description:
Circulating miRNA profile of serum from a CASE woman
HRBP338


title: Case_14

description:
Circulating miRNA profile of serum from a CASE woman
HRBP267


title: M08 rna-seq

description: RNA-seq data for Male Chorionic villus sample M08

value: Chorionic villus


title: eight2

value: Endometrial cancer


title: Case_12

description:
Circulating miRNA profile of serum from a CASE woman
HRBP209


title: M05 rna-seq

description: RNA-seq data for Male Chorionic villus sample M05

value: other


title: M06 rna-seq

description: RNA-seq data for Male Chorionic villus sample M06


title: Case_24

description:
Circulating miRNA profile of serum from a CASE woman
HRBP507


title: Control_17

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP230

value: control


title: M02 rna-seq

description: RNA-seq data for Male Chorionic villus sample M02


title: Cells treated with forskolin, biological replicate 2

city: Worcester

first: Silvia

last: Corvera

state: MA

address: 373 Platantion Street

department: Molecular Medicine

institute: UMASS Medical School

description: gene expression

hyb_protocol: Affymetrix protocols were followed for the preparation of cRNA, which was hybridized to HG-U133v2 Chips.

scan_protocol: Raw expression data collected from an Affymetrix HP GeneArrayScanner

data_processing: The data were analyzed with Affymetrix Expression Console_1_4_0

source_name: adipocytes from human vascular progenitors treated with forskolin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Adipose tissue from two individuals was cultured in hydogel under pro-angiogenic conditions. Capillary networks emerging from the explants were subcultured on plastic, grown to confluence, subjected to adipogenic differentiation and after 12 days treated with vehicle or forskolin for 7 days

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

treatment_protocol: vehicle or forskolin 50 uM for 7 days

value: forskolin

tag: sample type

value: cultured primary cells


title: M04 rna-seq

description: RNA-seq data for Male Chorionic villus sample M04


title: seven4

value: Lung cancer

source_name: Normal lung

value: Normal lung


title: six1

value: Female

value: Training set

value: Colorectal cancer

value: Normal colon


title: six2

value: Head&neck cancer

source_name: Universal normal

value: Universal normal


title: M03 rna-seq

description: RNA-seq data for Male Chorionic villus sample M03

value: Male


title: F16 rna-seq

description: RNA-seq data for Female Chorionic villus sample F16


title: Cells treated with forskolin, biological replicate 1

description: gene expression

value: adipocytes from human vascular progenitors


title: Cells treated with vehicle, biological replicate 2

description: gene expression

source_name: adipocytes from human vascular progenitors treated with vehicle


title: Case_11

description:
Circulating miRNA profile of serum from a CASE woman
HRBP181

value: serum

value: case

value: female


title: M01 rna-seq

description: RNA-seq data for Male Chorionic villus sample M01

value: Chorionic villus


title: Control_02

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP180

value: control


title: Case_10

description:
Circulating miRNA profile of serum from a CASE woman
HRBP176


title: F15 rna-seq

description: RNA-seq data for Female Chorionic villus sample F15


title: six3

description: Two color microarray from which only Cy5 data are analyzed after dye-bias correction

value: Esophagus cancer

value: Normal esophagus


title: five4

value: Ovarian cancer

value: Normal ovary


title: Case_09

description:
Circulating miRNA profile of serum from a CASE woman
HRBP148


title: esofagone4


title: one3a

value: Pancreatic cancer

value: Normal pancreas


title: F17 rna-seq

description: RNA-seq data for Female Chorionic villus sample F17

value: Female

value: other


title: Control_15

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP178


title: Control_16

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP165


title: Cells treated with vehicle, biological replicate 1

description: gene expression

value: cultured primary cells


title: F11 rna-seq

description: RNA-seq data for Female Chorionic villus sample F11


title: F14 rna-seq

description: RNA-seq data for Female Chorionic villus sample F14


title: Control_20

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP159


title: F12 rna-seq

description: RNA-seq data for Female Chorionic villus sample F12


title: F13 rna-seq

description: RNA-seq data for Female Chorionic villus sample F13


title: Control_14

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP147


title: Control_13

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP162


title: F08 rna-seq

description: RNA-seq data for Female Chorionic villus sample F08


title: 91one2

source_name: esofagus cancer

value: Validation set

tag: biopsy location

value: Retroperitoneal implant

source_name: Normal esofagus

value: Normal esofagus


title: 92one4

source_name: bileduct cancer2

source_name: Universal normal tissue

value: Universal normal tissue


title: 85one2

source_name: breast cancer2

value: Lymph node


title: 88one1

source_name: endometrial cancer

source_name: Normal cervix

value: Normal cervix


title: F10 rna-seq

description: RNA-seq data for Female Chorionic villus sample F10

source_name: Chorionic villus

tag: cell type

value: Chorionic villus


title: 90one1

source_name: ovarian cancer2


title: 85one1

source_name: ovarian cancer1

source_name: Normal ovary


title: Case_04

description:
Circulating miRNA profile of serum from a CASE woman
HRBP127

value: serum

value: case

value: female


title: F07 rna-seq

description: RNA-seq data for Female Chorionic villus sample F07


title: Case_06

description:
Circulating miRNA profile of serum from a CASE woman
HRBP134


title: F09 rna-seq

description: RNA-seq data for Female Chorionic villus sample F09


title: Case_07

description:
Circulating miRNA profile of serum from a CASE woman
HRBP140


title: Case_08

description:
Circulating miRNA profile of serum from a CASE woman
HRBP145


title: Case_05

description:
Circulating miRNA profile of serum from a CASE woman
HRBP132


title: F06 rna-seq

description: RNA-seq data for Female Chorionic villus sample F06


title: F03 rna-seq

description: RNA-seq data for Female Chorionic villus sample F03


title: 92one2

description: Two color microarray from which only Cy5 data are analyzed after dye-bias correction

source_name: ovarian cancer3


title: 84one4

source_name: Pancreatic cancer2

value: Male

value: Liver


title: F02 rna-seq

description: RNA-seq data for Female Chorionic villus sample F02


title: F01 rna-seq

description: RNA-seq data for Female Chorionic villus sample F01


title: 83one4

source_name: breast cancer1

source_name: Normal breast

value: Normal breast


title: Control_22

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP107

value: control


title: Control_10

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP090


title: F05 rna-seq

description: RNA-seq data for Female Chorionic villus sample F05

value: Female


title: Control_09

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP123


title: Control_06

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP031


title: 83one1

source_name: bileduct cancer1

value: Primary


title: Primary_hepatocytes_DMSO

city: Kuopio

first: Jaana

last: Rysae

address: Yliopistonranta 1C

department: School of Pharmacy

country: Finland

institute: University of Eastern Finland

description: Gene expression data from DMSO treated mouse primary hepatocytes.

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing:
Expression estimates were calculated using GCRMA (v2.2.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
Probe sets were redefined according to Dai et al. (Nucleic Acids Res. 33, e175, 2005) using remapped Chip Definition File v9, based on the Entrez Gene database (build 36, v2). Expression estimates were done as described previously Buler, M. et al. J. Biol. Chem. 287, 1847–1860 (2012).

label: Biotin

source_name: primary hepatocyte

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, pooled from 3 different samples.

growth_protocol: Primary hepatocytes were isolated from a male 9-week-old C57BL/6 mouse and cultured as described in Arpiainen, S. et al. Toxicol. Appl. Pharmacol. 232, 135–141 (2008).

extract_protocol: Total RNA was isolated using TRI-Reagent (Sigma-Aldrich) according to the manufacturer’s protocol and treated with DNase.

treatment_protocol: The cultures were maintained for 24 h before treatment with vehicle (dimethyl sulfoxide) or 10 μmol/l pregnenolone 16α-carbonitrile (PCN) for 12 h, after which cells were collected and RNA isolated.

value: DMSO

value: male


title: Control_19

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP034


title: Primary_hepatocytes_PCN

description: Gene expression data from PCN treated mouse primary hepatocytes.

value: 10 umol/l PCN


title: Control_01

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP112


title: Control_04

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP041


title: Control_03

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP098


title: Case_03

description:
Circulating miRNA profile of serum from a CASE woman
HRBP081


title: PpNAC1_RNAi_plantlets_PN5_C

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

institute: Universidad de Málaga

description: Gene expression in PpNAC1 RNAi plantlets line PN5

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 mL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 mL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the microarrays. They were incubated in SureHyb microarray hybridization chambers with gasket slides (Agilent Technologies) at 65ºC for 17 h in an rotary oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 s with acetonitrile and 30 s in Agilent's stabilization and drying solution, then air dried.

scan_protocol: Hybridized slides were scanned at 5 μm resolution and their signal intensities were detected by a GenePix 4100A microarray scanner (Molecular devices, Sunnyvale, CA, USA).

data_processing: The raw data preprocessing, quantile normalization and differential expressed gene analysis were done with the Limma package for R.

organism: Pinus pinaster

source_name: PpNAC1 RNAi plantlets line PN5 replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by    NucleoSpin® Gel and PCR Clean-up column purification (Macherey-Nagel, Düren, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Somatic embryos were germinated for 60 days on MLV medium supplemented with 87 mM sucrose.Two RNAi transgenic lines, PN5 and PN9, as well as three control lines, PN519, were used, with 3 biological replicates per line and 6 whole plantlets per replicate.

extract_protocol: Total RNA was isolated following the method of Chang S et al. Plant Mol Biol Rep 1993, 11:113–116

tag: developmental stage

value: 60 days plantlets

tag: genotype

value: PpNAC1 RNAi


title: PpNAC1_RNAi_plantlets_PN9_C

description: Gene expression in PpNAC1 RNAi plantlets line PN9

source_name: PpNAC1 RNAi plantlets line PN9 replicate 2


title: Control_11

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP002

tag: gender


title: PpNAC1_RNAi_plantlets_PN9_B

source_name: PpNAC1 RNAi plantlets line PN9 replicate 1


title: five2

description: Two color microarray from which only Cy5 data are analyzed after dye-bias correction

tag: dataset

value: Training set

tag: tissue

value: Breast cancer


title: WT_60_days_plantlets_C

description: Gene expression in WT 60 days plantlets

source_name: WT 60 days plantlets replicate 3

value: Wild type


title: 82one1

source_name: Pancreatic cancer1

value: Validation set

source_name: Normal pancreas

value: Normal pancreas


title: Control_12

description:
Circulating miRNA profile of serum from a CONTROL woman
HRBP015

value: serum

value: female


title: F04 rna-seq

description: RNA-seq data for Female Chorionic villus sample F04

value: Chorionic villus

value: other


title: pdx KrasG12D TGIFL/L p53L/L, cancer cell, biological rep1

city: Chiayi

first: Weng

middle: Ching

last: Chieh

address: No.168, Sec. 1, University Rd., Minhsiung

department: Department of Biomedical Sciences

country: Taiwan

institute: National Chung Cheng University

description: Kras mutantion, TGIF1 deletion and P53 deletion

hyb_protocol: Samples were hybridized to Mouse Gene ST 1.0 arrays using Affymetrix hybridization kit materials, according to the manufacturrer's instructions. Sample cocktails were heated at 99°C for 5 minutes, then 45°C for 5 minutes, centrifuged at max speed for 1 minute. Eighty ul of hyb solution was transferred to each array, and hybridized 17 hours at 45°C at 60rpm. Fluidics washing protocol used was FS450_0007.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data generated were analyzed using Affymetrix Transcriptome Analysis Console software with Gene Level Differential Expression Analysis.
We are using RMA normalization from the Affymatrix Expression Console software.
MoGene-1_0-st-v1.na34.mm10.probeset.csv
MoGene-1_0-st-v1.na34.mm10.transcript.csv

source_name: pdx KrasG12D TGIFL/L p53L/L

label_protocol: WT expression kit (Ambion), WT Terminal Labeling Kit (Affymetrix), according to the manufatcturer's instructions

growth_protocol: Mouse primary PDAC cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, nonessential amino acids, 100 units/ml penicillin and 100 μg/ml streptomycin at 37 °C in a 5% CO2 incubator.

extract_protocol: RNEasy Micro kit (Qiagen), following manufatcturer's instructions

tag: genotype/variation

value: pdx KrasG12D TGIFL/L p53L/L


title: 79one1

source_name: Renal cancer

value: Female

value: Lymph node

source_name: Normal kidney

value: Normal kidney


title: Case_01

description:
Circulating miRNA profile of serum from a CASE woman
HRBP005

value: case


title: PpNAC1_RNAi_plantlets_PN5_A

source_name: PpNAC1 RNAi plantlets line PN5 replicate 1


title: Control rep3

city: Pamplona

first: Juan Roberto

last: Rodriguez-Madoz

state: Navarra

address: PIO XII 55

department: Cell Therapy Program

institute: Foundation For Applied Medical Research

description: Gene expression data from non treated BJ cells

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized with Bioconductor software using RMA algorithm.

source_name: Human newborn foreskin fibroblasts

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: BJ human fibroblast cells (ATCC, CRL-2522) were cultured in DMEM high glucose supplemented with 10% FBS, 2 mM L-glutamine, 1% NEAA and 100 UI/ml Penicillin/Streptomycin.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: BJ cells were incubated during 48h with CM272 small molecule compound at 0.2 uM.

value: skin; foreskin

value: fibroblast

tag: disease

value: normal

tag: age

value: newborn

value: male

tag: cell line

value: BJ (ATCC CRL-2522)


title: Case_02

description:
Circulating miRNA profile of serum from a CASE woman
HRBP022


title: pdx KrasG12D p53L/L, cancer cell, biological rep1

description: Kras mutantion and P53 deletion

source_name: pdx KrasG12D p53L/L

value: pdx KrasG12D p53L/L


title: pdx KrasG12D TGIFL/L p53L/L, cancer cell, biological rep2


title: PpNAC1_RNAi_plantlets_PN5_B

source_name: PpNAC1 RNAi plantlets line PN5 replicate 2

value: 60 days plantlets

value: PpNAC1 RNAi


title: Control rep2


title: WT_60_days_plantlets_B

description: Gene expression in WT 60 days plantlets

source_name: WT 60 days plantlets replicate 2

value: Wild type


title: 77one3

source_name: Lung cancer

value: Male

value: Validation set

value: Lung

source_name: Normal lung

value: Normal lung


title: Bj272 rep1

description: Gene expression data from BJ cells treated for 48h with CM272  (200nM)

source_name: Human newborn foreskin fibroblasts treated with CM272


title: Control rep1


title: pdx KrasG12D p53L/L, cancer cell, biological rep2

description: Kras mutantion and P53 deletion


title: WT_60_days_plantlets_A

description: Gene expression in WT 60 days plantlets

source_name: WT 60 days plantlets replicate 1


title: Bj272 rep3


title: Bj272 rep2


title: BB-z CAR-T cells stimulated for 72 hours, rep 2

status: Public on Jan 21 2018

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

country: Japan

institute: Keio University

description: BB-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 72 hours by CD19, rep2

hyb_protocol: Samples were hybridized with Affymetrix Human Gene 2.0 ST array for 16-18 hr at 45°C.

scan_protocol: Affymetrix GeneChip Scanner 3000 (Scanner #4)

data_processing: Raw intensity files were processed using Affymetrix Expression Console (version 1.4.1). RMA data.

source_name: BB-z CAR-T cells stimulated for 72 hours, biological replicate #2

label_protocol: Samples were labeled with Biotin Allonamide Triphosphate.

growth_protocol: Human CD8+ T cells were cultured in vitro (RPMI supplemented with 10% human AB serum).

extract_protocol: Stimulated T cells were collected 4 hours, 24 hours and 72 hours later and CAR+ CD8+ T cells were isolated by flow cytometry. The CAR+ T cells were detected by the expression of DNGFR. RNA was isolated from the purified CAR-T cells with the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: CD8+ T cells were retrovirally transduced with individual anti-CD19 CAR genes (28-z, BB-z and 28-DIL2RB-z (YXXQ)) linked with truncated nerve growth factor receptor (DNGFR) and were stimulated with NALM-6.

value: CD8+ T cells

tag: car gene

value: BB-z

tag: donor

tag: stimulation time

value: 72 hours


title: BB-z CAR-T cells stimulated for 72 hours, rep 3

description: BB-z anti-CD19 CAR-transduced CD8+ T cells stimulated by for 72 hours CD19, rep3

source_name: BB-z CAR-T cells stimulated for 72 hours, biological replicate #3


title: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 72 hours, rep 4

description: 28-DIL2RB-z (YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated for 72 hours by CD19, rep4

source_name: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 72 hours, biological replicate #4

value: 28-DIL2RB-z (YXXQ)


title: 28-z CAR-T cells stimulated for 72 hours, rep 2

description: 28-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 72 hours by CD19, rep2

source_name: 28-z CAR-T cells stimulated for 72 hours, biological replicate #2


title: BB-z CAR-T cells stimulated for 72 hours, rep 1

description: BB-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 72 hours by CD19, rep1

source_name: BB-z CAR-T cells stimulated for 72 hours, biological replicate #1


title: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 72 hours, rep 3

description: 28-DIL2RB-z (YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated for 72 hours by CD19, rep3

source_name: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 72 hours, biological replicate #3


title: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 72 hours, rep 2

description: 28-DIL2RB-z (YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated for 72 hours by CD19, rep2

source_name: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 72 hours, biological replicate #2


title: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 24 hours, rep 4

description: 28-DIL2RB-z (YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated for 24 hours by CD19, rep4

source_name: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 24 hours, biological replicate #4

value: 24 hours


title: BB-z CAR-T cells stimulated for 72 hours, rep 4

description: BB-z anti-CD19 CAR-transduced CD8+ T cells stimulated by for 72 hours CD19, rep4

source_name: BB-z CAR-T cells stimulated for 72 hours, biological replicate #4


title: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 72 hours, rep 1

description: 28-DIL2RB-z (YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated for 72 hours by CD19, rep1

source_name: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 72 hours, biological replicate #1


title: 28-z CAR-T cells stimulated for 72 hours, rep 3

description: 28-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 72 hours by CD19, rep3

source_name: 28-z CAR-T cells stimulated for 72 hours, biological replicate #3


title: 28-z CAR-T cells stimulated for 72 hours, rep 1

description: 28-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 72 hours by CD19, rep1

source_name: 28-z CAR-T cells stimulated for 72 hours, biological replicate #1


title: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 24 hours, rep 3

description: 28-DIL2RB-z (YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated for 24 hours by CD19, rep3

source_name: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 24 hours, biological replicate #3


title: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 24 hours, rep 2

description: 28-DIL2RB-z (YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated for 24 hours by CD19, rep2

source_name: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 24 hours, biological replicate #2


title: BB-z CAR-T cells stimulated for 24 hours, rep 2

description: BB-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 24 hours by CD19, rep2

source_name: BB-z CAR-T cells stimulated for 24 hours, biological replicate #2


title: 28-z CAR-T cells stimulated for 24 hours, rep 4

description: 28-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 24 hours by CD19, rep4

source_name: 28-z CAR-T cells stimulated for 24 hours, biological replicate #4


title: BB-z CAR-T cells stimulated for 24 hours, rep 4

description: BB-z anti-CD19 CAR-transduced CD8+ T cells stimulated by for 24 hours CD19, rep4

source_name: BB-z CAR-T cells stimulated for 24 hours, biological replicate #4


title: Breast milk-supernatant-mother3-2

first: Nobuyoshi

last: Kosaka

address: 5-1-1, Tsukiji, Chuo-ku

department: Research of Molecular Functions and Targets

institute: National Cancer Center

description: miRNA expression from breast milk supernatant

hyb_protocol: Labeled RNA was hybridized to the Human miRNA Microarray version 2 8x15K (G4470B Agilent Technologies) with the miRNA Complete Labeling Reagent and Hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.

data_processing: Images were quantified using Agilent Feature Extraction software version 10.5.1.1 (Agilent) using default parameters (Grid: 019118_D_20080214) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Supernatant of breast milk, mother 3, 6 months after deliver

label_protocol: 70 ng of each RNA sample was labeled with the miRNA Complete Labeling Reagent and Hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: Total RNA extracted using mirVana miRNA isolation kit following manufacturer's instructions

value: breast milk

tag: breast milk component

value: supernatant


title: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 24 hours, rep 1

description: 28-DIL2RB-z (YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated for 24 hours by CD19, rep1

source_name: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 24 hours, biological replicate #1


title: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 4 hours, rep 3

description: 28-DIL2RB-z (YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated for 4 hours by CD19, rep3

source_name: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 4 hours, biological replicate #3

value: 4 hours


title: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 4 hours, rep 4

description: 28-DIL2RB-z (YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated for 4 hours by CD19, rep4

source_name: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 4 hours, biological replicate #4


title: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 4 hours, rep 2

description: 28-DIL2RB-z (YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated for 4 hours by CD19, rep2

source_name: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 4 hours, biological replicate #2


title: 28-z CAR-T cells stimulated for 72 hours, rep 4

description: 28-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 72 hours by CD19, rep4

source_name: 28-z CAR-T cells stimulated for 72 hours, biological replicate #4


title: 28-z CAR-T cells stimulated for 24 hours, rep 3

description: 28-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 24 hours by CD19, rep3

source_name: 28-z CAR-T cells stimulated for 24 hours, biological replicate #3


title: Breast milk-supernatant-mother2-2

source_name: Supernatant of breast milk, mother 2, 8 months after deliver


title: BB-z CAR-T cells stimulated for 24 hours, rep 3

description: BB-z anti-CD19 CAR-transduced CD8+ T cells stimulated by for 24 hours CD19, rep3

source_name: BB-z CAR-T cells stimulated for 24 hours, biological replicate #3


title: 28-z CAR-T cells stimulated for 24 hours, rep 2

description: 28-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 24 hours by CD19, rep2

source_name: 28-z CAR-T cells stimulated for 24 hours, biological replicate #2


title: Breast milk-supernatant-mother3-1

source_name: Supernatant of breast milk, mother 3, 5 months after deliver


title: Breast milk-supernatant-mother2-1

source_name: Supernatant of breast milk, mother 2, 6 months after deliver


title: Breast milk-supernatant-mother1-1

source_name: Supernatant of breast milk, mother 1, 4 days after deliver


title: BB-z CAR-T cells stimulated for 4 hours, rep 4

description: BB-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 4 hours by CD19, rep4

source_name: BB-z CAR-T cells stimulated for 4 hours, biological replicate #4


title: 28-z CAR-T cells stimulated for 24 hours, rep 1

description: 28-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 24 hours by CD19, rep1

source_name: 28-z CAR-T cells stimulated for 24 hours, biological replicate #1


title: BB-z CAR-T cells stimulated for 24 hours, rep 1

description: BB-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 24 hours by CD19, rep1

source_name: BB-z CAR-T cells stimulated for 24 hours, biological replicate #1


title: BB-z CAR-T cells stimulated for 4 hours, rep 2

description: BB-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 4 hours by CD19, rep2

source_name: BB-z CAR-T cells stimulated for 4 hours, biological replicate #2


title: input DNA

city: Wuhan

first: Saifeng

last: Cheng

state: Hubei

address: No.1,Shizishan Street

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University

library_source: genomic

data_processing:
Sequence reads from all libraries were filtered by Trimmomatic (version 0.32)
Clean reads were mapped to the MSU 7.0 rice genome using Bowtie 2 (version 2.1.0)
Samtools (version 0.1.17) was used to remove potential PCR duplicates
MACS software (39) was used to call peaks with the default parameters
Genome_build: MSU 7.0
Supplementary_files_format_and_content: wig files and text file with called peaks.

molecule: genomic DNA

organism: Oryza sativa Japonica Group

source_name: rice shoot apex

growth_protocol: Seeds with indicated genotypes were surface-sterilized and germinated in media containing 0.3% phytagel supplemented with 2% (w/v) sucrose at 28 °C (in light) and 24 °C (in dark) with a 14 h light/10 h dark cycle for 5 days, then the shoot apex were taken  with a scalpel under a dissecting microscope.

extract_protocol:
Shoot apex were cross-linked in 1% formaldehyde under vacuum. Chromatin was extracted and fragmented to 200 to 500 bp by sonication, and ChIP was performed using the anti-FLAG antibody.
Libraries were constructed following the Illumina TruSeq ChIP Sample Prep Set A protocol.

value: 2-3 mm shoot apex from 5-day-old shoot

value: JMJ705 overexpression in the wildtype background

tag: chip antibody


title: wox11/oxJ5 ChIP-seq

value: JMJ705 overexpression in the wox11 mutant background

value: anti-FLAG (Sigma, F1804)


title: BB-z CAR-T cells stimulated for 4 hours, rep 3

description: BB-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 4 hours by CD19, rep3

source_name: BB-z CAR-T cells stimulated for 4 hours, biological replicate #3


title: oxJ5 ChIP-seq


title: Dropseq E14.5 wildtype1

status: Public on Jan 20 2018

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

data_processing:
Read2 was aligned with bowtie2-2.2.7 using the -k 1 option
The aligned reads were tagged with their corresponding UMI and barcode from read1
Each aligned read was tagged with its gene name
An expression matrix was generated by counting the number of unique UMIs per gene per cell
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited gene counts per cell

source_name: kidney

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: wildtype

tag: strain

value: mixed, mostly CD-1 and 129


title: Dropseq E14.5 mutant2


title: Dropseq E14.5 mutant1


title: Dropseq E14.5 wildtype2


title: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 4 hours, rep 1

description: 28-DIL2RB-z (YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated for 4 hours by CD19, rep1

source_name: 28-DIL2RB-z (YXXQ) CAR-T cells stimulated for 4 hours, biological replicate #1


title: Breast milk-supernatant-mother1-2

source_name: Supernatant of breast milk, mother 1, 18 days after deliver


title: 28-z CAR-T cells stimulated for 4 hours, rep 2

description: 28-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 4 hours by CD19, rep2

source_name: 28-z CAR-T cells stimulated for 4 hours, biological replicate #2


title: BB-z CAR-T cells stimulated for 4 hours, rep 1

description: BB-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 4 hours by CD19, rep1

source_name: BB-z CAR-T cells stimulated for 4 hours, biological replicate #1


title: 28-z CAR-T cells stimulated for 4 hours, rep 1

description: 28-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 4 hours by CD19, rep1

source_name: 28-z CAR-T cells stimulated for 4 hours, biological replicate #1


title: 28-z CAR-T cells stimulated for 4 hours, rep 4

description: 28-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 4 hours by CD19, rep4

source_name: 28-z CAR-T cells stimulated for 4 hours, biological replicate #4


title: e20 embryo, biological replicate 4

city: Newark

first: Chuming

last: Chen

state: DE

address: 15 Innovation Way, Suite 205

department: Computer and Information Sciences

institute: University of Delaware

description: embryo; male

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: R/Bioconductor software packages were used for data processing in this study. Expression values were normalized using Robust Multi-Array Averaging (RMA) method. We used the LIMMA (Version 3.30.13) to assess differentially expressed genes. Statistical significance was adjusted for multiple testing by controlling false discovery rate at 5%. Analyses were performed with affylmGUI (Version 1.48.0). Affymetrix chicken annotation data (Version 3.6) was used to annotate the differentially expressed genes.

organism: Gallus gallus

source_name: liver, e20 embryo

label_protocol: standard Affymetrix protocol

growth_protocol: Fertile eggs from Ross x Ross broiler (meat-type) chickens were purchased from a commercial hatchery (Moyer’s Hatchery, Quakertown, PA).  The eggs were incubated in an automated incubator (Jamesway) at 39 C and 95% relative humidity. At e20, eggs containing viable embryos were transferred to hatching trays to determine the approximate time of hatch. Chicks hatched within a 4 hr period on the 21st day of incubation were wing-banded and held in the incubator for 24 hr (i.e., until d1). Day-old (d1) chicks were vaccinated against Marek’s disease virus and transferred to a heated battery brooder (Petersime Incubator Co.) maintained at 33 C.  The chicks received a commercial starter ration (22% crude protein and 3100 kcal ME/kg) and water ad libitum throughout the experiment.  After continuous light for the first two days, the birds were maintained on a 20 hr light: 4 hr dark (20L:4D) photoperiod. All protocols used in this study were in accordance to guidelines approved by the University of Delaware Animal Care and Use Committee (ACUC).

extract_protocol: Liver RNA samples from four embryos or hatchling chicks per age were used for isolation of total RNA using a RNeasy Midi Kit (Qiagen) following the manufacturer’s protocol, followed by on column DNAse treatment.

treatment_protocol: Four male embryos were used for collection of liver tissue at day 16 (e16) , e18, and e20 of embryonic development and six male chicks at 1, 3 and 9 day (d) of age. The d1 liver samples were taken from unfed chicks in the hatching incubator (38 C) just prior to removal of the remaining chicks for vaccination and transfer to a heated battery brooder. Four male embryos were used for collection of liver tissue at day 16 (e16) , e18, and e20 of embryonic development and six male chicks at 1, 3 and 9 day (d) of age. The d1 liver samples were taken from unfed chicks in the hatching incubator (38 C) just prior to removal of the remaining chicks for vaccination and transfer to a heated battery brooder maintained at 33 C. After visual verification of sex (presence of testes), each male liver was quickly removed, placed into a 15 ml Nalgene cryogenic vial and snap frozen in liquid nitrogen. The remaining chicks were provide with feed and water ad libitum and maintained under a 20L:4D photoperiod.  The frozen liver samples were transferred to an ultra-low freezer (-85 C) and stored until isolation of total RNA.

tag: breed

value: Ross x Ross

value: liver

tag: Sex

value: male

value: e16 embryo

tag: feeding status

value: in ovo


title: day 9, hatchling, biological replicate 1

description: hatchling; male

source_name: liver, day 9 hatchling

tag: developmental stage

value: day 9 hatchling

value: feed & water ad libituim


title: day 3, hatchling, biological replicate 1

description: hatchling; male

source_name: liver, day 3 hatchling

value: day 3 hatchling


title: 28-z CAR-T cells stimulated for 4 hours, rep 3

description: 28-z anti-CD19 CAR-transduced CD8+ T cells stimulated for 4 hours by CD19, rep3

source_name: 28-z CAR-T cells stimulated for 4 hours, biological replicate #3

tag: cell type

value: CD8+ T cells


title: day 3, hatchling, biological replicate 3

description: hatchling; male


title: day 9, hatchling, biological replicate 2

description: hatchling; male


title: day 9, hatchling, biological replicate 4

description: hatchling; male


title: day 1, hatchling, biological replicate 4

description: hatchling; male

source_name: liver, day 1 hatchling

value: day 1 hatchling

value: water ad libitum


title: day 1, hatchling, biological replicate 2

description: hatchling; male


title: day 3, hatchling, biological replicate 2

description: hatchling; male


title: e20 embryo, biological replicate 3

description: embryo; male


title: day 1, hatchling, biological replicate 1

description: hatchling; male


title: e18 embryo, biological replicate 4

description: embryo; male

source_name: liver, e18 embryo


title: e20 embryo, biological replicate 1

description: embryo; male


title: day 1, hatchling, biological replicate 3

description: hatchling; male


title: e20 embryo, biological replicate 2

description: embryo; male


title: day 9, hatchling, biological replicate 3

description: hatchling; male


title: e18 embryo, biological replicate 2

description: embryo; male


title: e18 embryo, biological replicate 1

description: embryo; male


title: e16 embryo, biological replicate 4

description: embryo; male

source_name: liver, e16 embryo


title: e18 embryo, biological replicate 3

description: embryo; male


title: day 3, hatchling, biological replicate 4

description: hatchling; male


title: Control

city: Shanghai

first: Bingjun

last: Qian

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

data_processing:
Low-quality reads (>30% of bases with Phred score <20) were firstly removed from raw reads with scythe sofeware.
3’ adapter sequences were firstly removed from raw reads with sickle sofeware.
The redundant reads were removed to retain only the unique reads using our perl scripts.
With our perl scripts, the reads with length longer than 17 nt and shorter than 27 nt were finally retained for the identification of miRNAs.
MiRBase 21.0 which included 765 rat miRNAs was downloaded to identify known miRNAs in rat small RNA libraries, and the filtered reads from each sRNA libraries were mapped onto the rat miRNAs.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: fasta, unique sRNA reads
the processed data ( .fasta files), and the copy number of each reads were included in the processed data, in which the  name of reads were saved as their order and copy number. And apart from that, we don't have any quantitative processed data for our submission.

organism: Rattus norvegicus

source_name: aortas

growth_protocol: Sprague-Dawley (SD) male rats (8 weeks of age) from Shanghai Slac Laboratory Animal Co., Ltd. (Shanghai, China) were housed in cages, and they were maintained under specific pathogen-free conditions with a 12 h light/dark cycle at Center of Experimental Animal, Jiangsu Vocational College of Medicine. The temperature and humidity in the cages were controlled at 24 ± 1°C and 60 ± 5%, respectively.

extract_protocol:
The SHRs were euthanized 1.5 h post administration, and their aortas were separated and cut into pieces with 2 mm of length followed by being froze with liquid nitrogen. Then, the samples were shipped with a dry ice transport container to Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China). TRIzol reagent (Invitrogen, CA, USA) was used to extract the total RNAs from each sample.
Then the extracted total RNAs from three samples within each group were mixed in equal amount, and the small RNA libraries were constructed as previously described [20]. Each small RNA library was sequenced in individual lane for 36 cycles using Illumina Genome Analyser II

treatment_protocol: Three SHRs were randomly chosen to form three groups, defined as HD group (fed with EGCG at high dose, 300 mg/kg BW), LD group (fed with EGCG at low dose, 30 mg/kg BW) and Control group (fed with 0.7% saline solution).

tag: group

value: aortas with 2 mm of length

value: Sprague-Dawley


title: e16 embryo, biological replicate 3

description: embryo; male

tag: tissue


title: e16 embryo, biological replicate 1

description: embryo; male


title: e16 embryo, biological replicate 2

description: embryo; male


title: QHDG

description: HD group (fed with EGCG at high dose, 300 mg/kg BW)


title: mdmxER-Cre;C463A/WT MEFs treated with 4OHT, biological rep2

city: Boston

first: Zhi-Min

last: Yuan

state: Massachusetts

address: Goldenson Building, Long wood Ave.

department: School of Public Health

institute: Harvard University

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

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

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

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

growth_protocol: Cells were cultured at 37°C and 5% CO2 in DMEM medium (Corning, Cat.No 10013CV) with 10% fetal bovine serum (Gibco, Cat.No 10082147) and 1% penicillin-streptomycin until about 80% confluent.

extract_protocol: Followed standard  manufacturer's instructions of RNeasy MinElut kit

treatment_protocol: EtOH or 4OHT were added into the media for 24 hours. After replaced with fresh medium for 48 hours, cells were harvested.

value: Mouse Embryonic Fibroblasts

tag: genotype/varation

tag: treated with

value: 4OHT for 24hrs


title: MCF7C463A/WT cells, biological rep1

description: MCF7 MT-1

source_name: MCF7C463A/WT cells

treatment_protocol: No additional treatment applied.

value: Breast cancer cell line

tag: genotype/variation

value: MDMX C463A mutation


title: MCF7 wile type cells, biological rep2

description: MCF7 WT-2

source_name: MCF7 wile type cells

tag: cell line

value: wild type


title: mdmxER-Cre;C463A/WT MEFs treated with 4OHT, biological rep1


title: mdmxER-Cre;C463A/WT MEFs treated with EtOH, biological rep2

value: EtOH for 24hrs


title: MCF7C463A/WT cells, biological rep2

description: MCF7 MT-2


title: MCF7C463A/WT cells, biological rep3

description: MCF7 MT-3


title: QLDG

description: LD group (fed with EGCG at low dose, 30 mg/kg BW)

value: male


title: Non-tumor of Patient 5

city: Guangzhou

first: Feng

last: He

state: Guangdong

address: 1# Panfu Road

department: Department of General Surgery

institute: Guangzhou First People's Hospital, the Second Affiliated Hospital of South China University of Technology

description:
Gene expression of non-tumor colorectal tissue from patient5
D907028N

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Patient5: Female, 53yrs, TNM stage : II

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

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen) and purified using the RNeasy Mini Kit (Qiagen). Complementary DNA was synthesized, labeled, purified, and hybridized to the microarray (Arraystar).

treatment_protocol: Fresh colorectal tumor samples and matched non-tumor samples (obtained from unaffected colorectal at least 5 cm from the tumor) from 6 colorectal cancer patients were individually profiled.

tag: individual

value: Colorectal tissue

tag: gender

value: Female

tag: age

tag: tnm stage

value: II


title: Colorectal tumors of Patient 6

description:
Gene expression of colorectal cancer tissue from patient6
D907993ca

source_name: Patient6: Female, 63yrs, TNM stage : IIIA

value: Colorectal cancer tissue

value: IIIA


title: Sunitinib_6h_replicate2

city: Wien

first: Georg

middle: E

last: Winter

state: Austria

address: Lazarettgasse 14, AKH BT25.3

country: Austria

institute: CeMM - Research Institute for Molecular Medicine of the Austrian Academy of Sciences

description: MOLT4 T-ALL cell line

data_processing:
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. FPKM values were ERCC normalized. See methods for further details
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript

molecule: polyA RNA

source_name: RNA-seq after 6hr MI-389 (0.1 µM) treatment

growth_protocol: MOLT4 cells were grown in RPMI medium supplemented with 10%FBS and 1% Pen/Strep

extract_protocol:
RNA was isolated using miRvana kit according to the manufacturer's instructions. External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using SMARTer v4 Low Input RNA Kit from Clontech; following barcodes were used for multiplexing (DMSO_6h_replicate1:ATCACG; DMSO_6h_replicate2:TTAGGC; DMSO_6h_replicate3:ACTTGA; MI_3_89_6h_replicate1:GTGGCC; MI_3_89_6h_replicate2:GTTTCG; MI_3_89_6h_replicate3:CGTACG; Sunitinib_6h_replicate1:GATCAG; Sunitinib_6h_replicate2:TAGCTT; Sunitinib_6h_replicate3:GGCTAC)

value: T-ALL


title: Sunitinib_6h_replicate1

description: MOLT4 T-ALL cell line


title: Sunitinib_6h_replicate3

description: MOLT4 T-ALL cell line


title: DMSO Control rep2

city: Antwerp

first: Boris

last: Krivoshiev

address: Groenenborgerlaan 171

institute: University of Antwerp

data_processing:
Alignment, mapping, and annotation steps were performed with CLC Genomics Workbench (CLC Bio, DEN) using default parameters.
Samples were normalized by quantile normalization before being mapped.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with Expression values|Normalized expression values|Gene name|Transcripts annotated|Detected transcripts|Exon length|Gene ID|Unique gene reads|Total gene reads|Unique exon reads|Total exon reads|Unique exon-exon reads|Total exon-exon reads|Unique intron reads|Total intron reads |Exons|RPKM|Chromosome|Chromosome region start|Chromosome region end.

source_name: Human Hepatocellular Carcinoma Cell Line (HepG2)

growth_protocol: HepG2 cells (ATCC HB-8065) were cultured in minimum essential medium supplemented with Earle's salts (Gibco, Carlsbad, CA, USA), 1 mm sodium pyruvate, 4 mm l-glutamine, 1% non-essential amino acids, 50 IU ml–1penicillin, 50 mg ml–1 streptomycin and 10% heat-inactivated fetal bovine serum. Cells were not allowed to exceed maximum of 25 passages.

extract_protocol:
To ensure for high quality and good yield of RNA, the combined TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy (Qiagen, Hilden, Germany) approach was adopted. Briefly, this involved lysing cells and extracting total RNA by phase separation using TRIzol as per the manufacturer's instructions. The aqueous phase containing the crude total RNA extraction was then subjected to clean up using the RNeasy kit according to the manufacturer's instructions, resulting in pure total RNA.
The TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA, USA) was used following the manufacturer's protocol to construct sequencing libraries. Briefly, 4 μg total RNA was subjected to purification using poly-T oligo-attached magnetic beads to purify for poly-A containing mRNA. mRNA was then fragmented using divalent cations and exposure to high temperatures. Fragments were then reverse transcribed into first-strand cDNA using random hexamer primers followed by second-strand cDNA synthesis to create blunt-ended, double-stranded cDNA. Unconverted RNA was then depleted by RNase H incubation. Fragment 3′ ends were then adenylated to prevent ligation to one another during adaptor ligation. Successful adaptor-ligated fragments were purified and enriched by means of PCR using primers that annealed to adaptors to create the final cDNA library.
Constructed sequencing libraries were then paired-end sequenced (2 × 50 bp) using the Illumina HiSeq 1500 platform (Illumina).

treatment_protocol: HepG2 cells were seeded in six-well plates and allowed to culture for 72 hours for acclimatization after detachment/reattachment. Cells were treated with TCEP at concentrations 25 or 250 μm, or to TCIPP at concentrations 2.5 or 25 μm (assigned as low- and high-dose TCEP or TCIPP, respectively, from here on out). Negative controls were treated with 0.1% DMSO only. Treatments were conducted for 72 hours. Treatments were done in triplicate for each condition involving separate cell seeding, cell growth, treatments and RNA extractions per triplicate.

value: Hepatocellular carcinoma cell line

tag: treatment

value: DMSO

tag: concentration

tag: treatment duration

tag: passages


title: MI_3_89_6h_replicate2

description: MOLT4 T-ALL cell line

source_name: RNA-seq after 6hr sunitinib (1 µM) treatment


title: MI_3_89_6h_replicate3

description: MOLT4 T-ALL cell line


title: Non-tumor of Patient 4

description:
Gene expression of non-tumor colorectal tissue from patient4
D907020N

source_name: Patient4: Male, 59yrs, TNM stage : IIIA

value: Male


title: Non-tumor of Patient 6

description:
Gene expression of non-tumor colorectal tissue from patient6
D907993N


title: Non-tumor of Patient 3

description:
Gene expression of non-tumor colorectal tissue from patient3
D906882N

source_name: Patient3: Female, 56yrs, TNM stage : IIIB

value: IIIB


title: Colorectal tumors of Patient 4

description:
Gene expression of colorectal cancer tissue from patient4
D907020ca


title: MI_3_89_6h_replicate1

description: MOLT4 T-ALL cell line


title: Colorectal tumors of Patient 5

description:
Gene expression of colorectal cancer tissue from patient5
D907028ca


title: Non-tumor of Patient 2

description:
Gene expression of non-tumor colorectal tissue from patient2
D896032N

source_name: Patient2: Male, 61yrs, TNM stage : IVA

value: IVA


title: DMSO_6h_replicate3

description: MOLT4 T-ALL cell line

source_name: RNA-seq after 6hr DMSO (0.1%) treatment


title: MCF7 wile type cells, biological rep1

description: MCF7 WT-1


title: DMSO Control rep1


title: MCF7 wile type cells, biological rep3

description: MCF7 WT-3


title: TCIPP 2.5uM rep3

value: TCIPP


title: DMSO_6h_replicate1

description: MOLT4 T-ALL cell line


title: TCIPP 2.5uM rep2


title: Ctrl-Sal rep3

city: San Diego

first: Kefeng

last: Li

address: 9500 Gilman Dr

institute: University of California, San Diego

description: Rats without exposure to chronic stress and treated with saline

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rattus norvegicus whole genome (rn6) using TopHat2
Fragments per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell C et al., Nature Biotechnology, 2010.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Rat hippocampi were collected, snap-frozen in liquid nitrogen. RNA was extracted using TRIzol kit. A total of 3 µg of RNA was used for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Sprague Dawley

value: Hippocampus

value: 6-7 weeks old


title: DMSO_6h_replicate2

description: MOLT4 T-ALL cell line


title: TCIPP 2.5uM rep1


title: TCIPP 25uM rep1

value: 25 uM


title: Ctrl-Sal rep2

source_name: Rats without exposure to chronic stress and treated with saline


title: Colorectal tumors of Patient 3

description:
Gene expression of colorectal cancer tissue from patient3
D906882ca


title: Colorectal tumors of Patient 2

description:
Gene expression of colorectal cancer tissue from patient2
D896032ca


title: TCEP 25uM rep3

value: TCEP


title: Colorectal tumors of Patient 1

description:
Gene expression of colorectal cancer tissue from patient1
D653416ca

source_name: Patient1: Male, 55yrs, TNM stage : II


title: DMSO Control rep3


title: TCIPP 25uM rep2


title: CUMS-Flx rep3

description: Rats exposed to chronic stress and treated with fluoxetine (10 mg/kg/d) for 7 days


title: CUMS-Flx rep2

source_name: Rats exposed to chronic stress and treated with fluoxetine (10 mg/kg/d) for 7 days


title: CUMS-Flx rep1


title: TCIPP 25uM rep3


title: TCEP 25uM rep1


title: TCEP 25uM rep2


title: TCEP 250uM rep3


title: CUMS-Alb rep3

description: Rats exposed to chronic stress and treated with albiflorin (7 mg/kg/d) for 7 days


title: CUMS-Sal rep2

description: Rats exposed to chronic stress and treated with saline


title: Ctrl-Sal rep1


title: CUMS-Alb rep1

source_name: Rats exposed to chronic stress and treated with albiflorin (7 mg/kg/d) for 7 days


title: CUMS-Sal rep3

source_name: Rats exposed to chronic stress and treated with saline


title: human primary OA chondrocyte transfected with siRNA control

city: MONTPELLIER

first: Paul

last: CHUCHANA

address: 80 rue Augustin Fliche

country: France

institute: CNRS

description: pool of 3 independent equimolar RNA samples

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on the Affymetrix® MG-430v2. StripChips were washed and stained on the fluidic station of the Affymetrix GeneAtlas system with HWS kit.

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

data_processing: The files were generated with the "rma-alt-splicing" algorithm. Only transcripts having opposite sign between chondrocytes treated with Klotho (normalized to untreated chondrocytes) and chondrocytes transfected with siRNA Klotho (normalized relative to the control siRNA) were selected.

source_name: OA patients

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix GeneAtlas IVT Express protocol from 100 ng total RNA (GeneAtlas 3'IVT ExpressTechnical Manual, 2010, P/N702833 Rev4 Affymetrix).

growth_protocol: DMEM + 10% Fetal calf serum in monolayer culture

extract_protocol: RNA was isolated from 5x10^5 chondrocytes  with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: double transfection of siRNA or 7 days treatment with recombinant protein with changes every 2 days.

value: cartilage

tag: disease status

value: osteoarthritis


title: Sample 11_n199-infected MRC5 cells_12h

city: Pittsburgh

first: Neal

last: DeLuca

state: PA

address: 450 Technology Dr

institute: Univ. of Pittsburgh

description:
12n199_S5_L006_R1_001
processed data file: n199 2.xlsx

data_processing:
reads were trimmed, and mapped to the HSV genome using the RNA seq software in the CLC workbench V9
RNA seq experiments were exported from CLC workbench to Excell
raw read totals were normalized to total read count and size in excell and graphs were made for the abundance of selected IE, E, BG, and L genes
graphs were combined into a single figure using Adobe Illustrator
Genome_build: Herpes simplex virus type 1
Supplementary_files_format_and_content: KOS 2.xlsx is an exported CLC workbench RNAseq experiment giving the raw data for samples 1-6 (sheet 1), normalization factor for total reads (sheet 2), normalized reads (sheet 3), and graphs of reads adjusted to gene size for HSV IE, E, BG, and late genes along with graphic representation of the knietics of expression (sheets 4-7).
Supplementary_files_format_and_content: n199 2.xlsx is an exported CLC workbench RNAseq experiment giving the raw data for samples 7-12 (sheet 1), normalization factor for total reads (sheet 2), normalized reads (sheet 3), and graphs of reads adjusted to gene size for HSV IE, E, BG, and late genes along with graphic representation of the kinetics of expression(sheets 4-7).

organism:
Homo sapiens
Human alphaherpesvirus 1

source_name: n199-infected MRC5 cells

extract_protocol: 1 ug of total RNA from each sample was used to create sequencing libraries using the TruSeq RNA Sample Prep kit (Illumina).

tag: infected with

value: n199 (ICP22 mutant)

tag: time post infection


title: TCEP 250uM rep1

tag: cell type


title: CUMS-Alb rep2

tag: tissue


title: CUMS-Sal rep1


title: Sample 12_n199-infected MRC5 cells_16h

description:
16n199_S6_L006_R1_001
processed data file: n199 2.xlsx


title: Kidney at adulthood (12 years)

city: San Antonio

first: Laura

middle: L

last: Cox

state: Texas

department: Genetics

institute: Texas Biomedical Research Institute

description:
Baboon_Kidney_Adult_2
Gene expression data from Papio hamadryas whole kidney at adulthood.

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16hr at 45oC to Affymetrix Human Genome U133A Arrays (adult samples) or to Affymetrix Human Genome U133A 2.0 Arrays (gestational samples). Arrays were washed and stained with phycoerythrein-conjugated streptavidin (Molecular Probes) using a Fluidics Station 450 (Affymetrix) according to the manufacturer’s recommended procedures.

scan_protocol: GeneChips were scanned using the GCS 3000 high-resolution confocal laser scanner (Affymetrix).

data_processing: The scanned images were analyzed using programs resident in GeneChip Operating System v1.4 (GCOS; Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity of 250 for all arrays used. The expression data were analyzed by statistical algorithms resident in GCOS; in short, the signal intensity for each gene was calculated as the average intensity difference, represented by [Σ(PM - MM)/(number of probe pairs)], where PM and MM denote perfect-match and mismatch probes (Lockhart et al., 1996, Nat. Biotechnol. 14:1675-1680; Liu et al., 2002, Bioinformatics 18:1593-9; Hubbell et al., 2002, Bioinformatics 18(12):1585-92). GCOS-generated detection and change calls were used to identify robust expression changes. Array data were all-median normalized using GeneSifter software (GeneSifter.Net, VizX Labs, Seattle, WA).

organism: Papio hamadryas

source_name: whole kidney at adulthood

label_protocol: Biotinylated cRNA were prepared using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and Bioarray™ HighYield™ RNA Transcript Labeling Kit (ENZO Diagnostics Inc.) as per the manufacturer’s instructions from 6 ug total RNA.

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

value: whole kidney

value: 12 years