title: SHAE004_dORF6_48h_1


title: SHAE004_H1N1_0h_2

status: Public on Jul 30 2013

type: RNA

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

country: USA

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

molecule: total RNA

organism: Homo sapiens

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: Human airway epithelium cultures (HAE) were generated by provision of an air-liquid interface for 6 to 8 weeks to form well-differentiated , polarized cultures that resemble in vivo pseudo-stratified mucociliary epithelium.

extract_protocol: At 0, 12, 24, 36, 48, 60, 72, 84 and 96 hours post-infection (hpi) (SARS viruses) or 0, 6, 12, 18, 24, 36 and 48 hpi (H1N1) triplicate/quadruplicate wells of infected cells or mock infected were washed with 1X PBS and lysed directly with 1 ml of Trizol (Invitrogen) according to the manufacturer’s recommendation.  The resulting lysates were stored at -80°C until further processing.  All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA).  RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for quantitative PCR (qPCR) and microarray analyses.

treatment_protocol: Cells were seeded in 6-well plates (1 x 10e6 cells/well) two days prior to infection.  Immediately preceding infection, cell monolayers were washed with fresh medium and inoculated with either SARS viruses (MOI = 2) or A/CA/04/2009 (MOI = 1) and subsequently incubated at 37°C for 40 minutes.  Mock-infected controls were inoculated with culture medium only.  Following the incubation, cell monolayers were washed 3X with 1X PBS and fresh medium was added to the wells prior to time 0.

tag: cell type

value: Human airway epithelium cells (HAE)

tag: infection code

tag: sample material

value: cells

tag: timepoint

tag: biological replicate


title: SHAE004_dORF6_48h_3


title: SHAE004_dORF6_48h_2


title: SHAE004_dORF6_60h_1


title: SHAE004_dORF6_36h_3


title: SHAE004_dORF6_36h_1


title: SHAE004_dORF6_24h_2


title: SHAE004_dORF6_36h_2


title: SHAE004_dORF6_0h_1


title: SHAE004_dORF6_12h_2


title: SHAE004_dORF6_0h_2


title: SHAE004_dORF6_12h_1


title: SHAE004_dORF6_24h_1


title: SHAE004_dORF6_24h_3


title: SHAE004_BAT_96h_2

value: BatSRBD


title: SHAE004_BAT_96h_1


title: SHAE004_BAT_84h_2


title: SHAE004_BAT_72h_2


title: SHAE004_BAT_84h_3


title: SHAE004_dORF6_12h_3


title: SHAE004_BAT_72h_3


title: SHAE004_BAT_60h_2


title: SHAE004_BAT_48h_1


title: SHAE004_BAT_84h_1


title: SHAE004_BAT_96h_3


title: SHAE004_BAT_36h_1


title: SHAE004_BAT_36h_3


title: SHAE004_BAT_36h_2


title: SHAE004_BAT_48h_3


title: SHAE004_BAT_60h_3


title: SHAE004_BAT_48h_2


title: SHAE004_BAT_72h_1


title: SHAE004_dORF6_0h_3


title: SHAE004_BAT_60h_1


title: SHAE004_BAT_12h_3


title: SHAE004_BAT_12h_1


title: SHAE004_BAT_0h_3


title: SHAE004_BAT_0h_2


title: SHAE004_BAT_0h_1


title: SHAE003_dORF6_84hr_4

extract_protocol: At 0, 12, 24, 36, 48, 60, 72, 84 and 96 hours post-infection (hpi) (SARS-CoV virus),  0, 24, 48, 60, 72, 84 and 96 hours post-infection (hpi) (SARS ddORF6 and BatSRBD viruses) or 0, 6, 12, 18, 24, 36 and 48 hpi (H1N1) triplicate/quadruplicate wells of infected cells or mock infected were washed with 1X PBS and lysed directly with 1 ml of Trizol (Invitrogen) according to the manufacturer’s recommendation.  The resulting lysates were stored at -80°C until further processing.  All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA).  RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for quantitative PCR (qPCR) and microarray analyses.

treatment_protocol: Cells were seeded in 6-well plates (1 x 10e6 cells/well) two days prior to infection.  Immediately preceding infection, cell monolayers were washed with fresh medium and inoculated with either SARS viruses or A/CA/04/2009 at an MOI of 2 and subsequently incubated at 37°C for 40 minutes.  Mock-infected controls were inoculated with culture medium only.  Following the incubation, cell monolayers were washed 3X with 1X PBS and fresh medium was added to the wells prior to time 0.


title: SHAE003_dORF6_84hr_2


title: SHAE004_BAT_24h_1


title: SHAE003_dORF6_96hr_3


title: SHAE003_dORF6_84hr_3


title: SHAE003_dORF6_72hr_2


title: SHAE003_dORF6_84hr_1


title: SHAE003_dORF6_60hr_1


title: SHAE003_dORF6_96hr_1


title: SHAE003_dORF6_60hr_3


title: SHAE003_dORF6_72hr_3


title: SHAE003_dORF6_24hr_3


title: SHAE003_dORF6_48hr_4


title: SHAE003_dORF6_72hr_4


title: SHAE003_dORF6_96hr_4


title: SHAE003_dORF6_96hr_2


title: SHAE003_dORF6_60hr_4


title: SHAE003_dORF6_48hr_1


title: SHAE003_dORF6_72hr_1


title: SHAE003_dORF6_24hr_2


title: SHAE003_dORF6_60hr_2


title: SHAE003_dORF6_48hr_2


title: SHAE003_Mock_84hr_2

value: Mock


title: SHAE003_Mock_96hr_2


title: SHAE003_Mock_96hr_3


title: SHAE003_Mock_84hr_1


title: SHAE003_dORF6_0hr_2


title: SHAE003_dORF6_48hr_3


title: SHAE003_dORF6_24hr_1


title: SHAE003_dORF6_0hr_3


title: SHAE003_Mock_84hr_3


title: SHAE003_dORF6_0hr_4


title: SHAE003_Mock_96hr_1


title: SHAE003_Mock_72hr_3


title: SHAE003_Mock_72hr_1


title: SHAE003_Mock_18hr_3


title: SHAE003_Mock_60hr_3


title: SHAE003_Mock_36hr_3


title: SHAE003_Mock_60hr_1


title: SHAE003_Mock_60hr_2


title: SHAE003_Mock_48hr_3


title: SHAE003_Mock_36hr_1


title: SHAE003_dORF6_0hr_1


title: SHAE003_Mock_48hr_1


title: SHAE003_Mock_36hr_2


title: SHAE003_Mock_24hr_3


title: SHAE003_Mock_24hr_2


title: SHAE003_Mock_24hr_1


title: SHAE003_Mock_48hr_2


title: SHAE004_BAT_24h_2


title: SHAE003_Mock_72hr_2


title: SHAE003_Mock_12hr_1


title: SHAE004_BAT_12h_2


title: SHAE003_Mock_12hr_3


title: SHAE003_Mock_18hr_1


title: SHAE003_Mock_6hr_2


title: SHAE003_Mock_0hr_3


title: SHAE003_icSARS_72hr_2

value: icSARS


title: SHAE003_icSARS_72hr_3


title: SHAE003_icSARS_84hr_2


title: SHAE003_icSARS_96hr_2


title: SHAE003_Mock_0hr_2


title: SHAE003_Mock_6hr_3


title: SHAE003_Mock_12hr_2


title: SHAE003_icSARS_84hr_3


title: SHAE003_icSARS_84hr_4


title: SHAE003_Mock_0hr_1


title: SHAE003_icSARS_96hr_4


title: SHAE003_icSARS_96hr_3


title: SHAE003_icSARS_84hr_1


title: SHAE003_icSARS_72hr_4


title: SHAE003_Mock_6hr_1


title: SHAE003_icSARS_60hr_4


title: SHAE003_icSARS_48hr_4


title: SHAE003_icSARS_60hr_3


title: SHAE003_icSARS_72hr_1


title: SHAE003_icSARS_48hr_3


title: SHAE003_icSARS_60hr_1


title: SHAE003_icSARS_96hr_1


title: SHAE003_icSARS_24hr_1


title: SHAE003_icSARS_48hr_1


title: SHAE003_icSARS_48hr_2


title: SHAE003_icSARS_60hr_2


title: SHAE003_icSARS_24hr_3


title: SHAE003_icSARS_24hr_4


title: SHAE003_icSARS_0hr_4


title: SHAE003_icSARS_0hr_2


title: SHAE003_H1N1_36hr_2


title: SHAE003_H1N1_24hr_4


title: SHAE003_icSARS_0hr_3


title: SHAE003_H1N1_36hr_4


title: SHAE003_icSARS_0hr_1


title: SHAE003_icSARS_24hr_2


title: SHAE003_H1N1_48hr_2


title: SHAE003_H1N1_36hr_1


title: SHAE003_H1N1_36hr_3


title: SHAE003_H1N1_48hr_3


title: SHAE003_H1N1_48hr_4


title: SHAE003_H1N1_24hr_2


title: SHAE003_H1N1_24hr_3


title: SHAE003_H1N1_24hr_1


title: SHAE003_H1N1_48hr_1


title: SHAE003_H1N1_18hr_4


title: SHAE003_H1N1_18hr_2


title: SHAE003_H1N1_12hr_4


title: SHAE003_H1N1_18hr_3


title: SHAE003_H1N1_18hr_1


title: SHAE003_H1N1_6hr_3


title: SHAE003_H1N1_12hr_1


title: SHAE003_H1N1_12hr_3


title: SHAE003_H1N1_0hr_3


title: SHAE003_H1N1_0hr_4


title: SHAE003_H1N1_6hr_4


title: SHAE003_H1N1_12hr_2


title: SHAE003_H1N1_6hr_2


title: SHAE003_BAT_96hr_3


title: SHAE003_BAT_60hr_4


title: SHAE003_BAT_96hr_4


title: SHAE003_BAT_72hr_1


title: SHAE003_BAT_72hr_4


title: SHAE003_BAT_84hr_3


title: SHAE003_BAT_84hr_2


title: SHAE003_H1N1_6hr_1


title: SHAE003_BAT_96hr_2


title: SHAE003_BAT_96hr_1


title: SHAE003_BAT_60hr_1


title: SHAE003_BAT_48hr_4


title: SHAE003_BAT_72hr_2


title: SHAE003_BAT_60hr_2


title: SHAE003_BAT_72hr_3


title: SHAE003_BAT_24hr_4


title: SHAE003_BAT_48hr_1


title: SHAE003_BAT_60hr_3


title: SHAE003_BAT_48hr_3


title: SHAE003_H1N1_0hr_1


title: SHAE003_BAT_84hr_1


title: SHAE003_BAT_48hr_2


title: SHAE003_BAT_84hr_4


title: SHAE003_BAT_0hr_3


title: SHAE002_H1N1_18h_3


title: SHAE003_BAT_0hr_1


title: SHAE003_BAT_0hr_2


title: SHAE003_BAT_0hr_4


title: SHAE003_BAT_24hr_3


title: SHAE002_H1N1_36h_3


title: SHAE002_icSARS_60h_3


title: SHAE002_BAT_84h_1


title: SHAE002_icSARS_12h_3


title: SHAE002_BAT_60h_2


title: SHAE002_mock_24h_2


title: SHAE002_icSARS_84h_2


title: SHAE002_icSARS_84h_1


title: SHAE002_icSARS_96h_2


title: SHAE002_icSARS_72h_3


title: SHAE002_icSARS_96h_1


title: SHAE002_icSARS_72h_1


title: SHAE002_icSARS_72h_4


title: SHAE002_icSARS_96h_3


title: SHAE002_icSARS_60h_4


title: SHAE002_icSARS_84h_4


title: SHAE002_icSARS_96h_4


title: SHAE002_icSARS_72h_2


title: SHAE002_icSARS_60h_2


title: SHAE002_icSARS_84h_3


title: SHAE003_H1N1_0hr_2


title: SHAE002_icSARS_60h_1


title: SHAE002_icSARS_48h_3


title: SHAE002_icSARS_48h_4


title: SHAE002_icSARS_36h_2


title: SHAE002_icSARS_48h_2


title: SHAE002_icSARS_24h_4


title: SHAE002_icSARS_24h_2


title: SHAE002_icSARS_36h_1


title: SHAE002_icSARS_48h_1


title: SHAE002_icSARS_24h_3


title: SHAE002_icSARS_24h_1


title: SHAE002_icSARS_12h_4


title: SHAE002_icSARS_12h_2


title: SHAE002_icSARS_12h_1


title: SHAE002_icSARS_0h_3


title: SHAE002_icSARS_0h_1


title: SHAE002_icSARS_0h_2


title: SHAE002_icSARS_0h_4


title: SHAE002_dORF6_96h_4


title: SHAE002_dORF6_96h_1


title: SHAE002_dORF6_96h_2


title: SHAE002_dORF6_84h_4


title: SHAE002_dORF6_96h_3


title: SAKK 19/05, blood, baseline, patient 095

city: St. Gallen

first: Florent

last: Baty

address: Rorschacherstrasse 95

department: Lung Center

country: Switzerland

institute: Cantonal Hospital St. Gallen

description: Exon expression of peripheral blood samples at baseline (treatment naive) in late stage NSCLC patients.

hyb_protocol: Target synthesis was led starting from 200ng total RNA (lung biopsies) using the WT expression kit (Ambion) following standard recommendations, except that 12µg cRNA was used instead of 10µg for entering the second reverse transcription. Synthesis reaction were carried out using a PCR machine (Tprofessional Biometra) in 0.2ml tubes. 200µl cocktail (25ng/µl DNA) was loaded on Human Exon 1.0ST Array (Affymetrix) and hybridized for 17 hours (45°C, 60rpm) in Hybridization oven 645 (Affymetrix).

scan_protocol: GeneChips were processed with an Affymetrix GeneChip Scanner 3000 7G.

data_processing: DAT images and CEL files of the microarrays were generated using Affymetrix GeneChip Command Control 3.0.0.1214. The exon and gene level probesets were pre-processed, quality checked and normalized using the RMA procedure.

label: biotin

source_name: Blood at baseline from NSCLC patients

label_protocol: Fragmentation and labeling of amplified cDNA were performed using the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Circulating RNA from peripheral blood samples was extracted using PAXgene Blood RNA Kit (Qiagen) followed by further purification on Qiagen RNeasy MinElute Cleanup Kit (Qiagen), and by the depletion of Alpha and Beta Globins using GlobinClear Human Kit (Ambion) according to standard recommendations with the following exception: 5µg RNA Cleanup kit (Zymo) was used for cleaning the depleted RNA instead of the magnetic beads provided in the Ambion kit, which significantly increased the recovery of RNA.

tag: ID

tag: age (y)

tag: gender

value: M

tag: disease state

value: advanced non-small cell lung cancer

tag: tissue

value: blood

tag: treatment

value: baseline


title: SAKK 19/05, blood, baseline, patient 099


title: SAKK 19/05, blood, baseline, patient 103

value: F


title: SHAE002_dORF6_84h_3


title: SAKK 19/05, blood, baseline, patient 094


title: SHAE002_dORF6_84h_2


title: SAKK 19/05, blood, baseline, patient 098


title: SAKK 19/05, blood, baseline, patient 102


title: SAKK 19/05, blood, baseline, patient 090


title: SAKK 19/05, blood, baseline, patient 096


title: SAKK 19/05, blood, baseline, patient 087


title: SAKK 19/05, blood, baseline, patient 101


title: SAKK 19/05, blood, baseline, patient 088


title: SAKK 19/05, blood, baseline, patient 093


title: SAKK 19/05, blood, baseline, patient 086


title: SAKK 19/05, blood, baseline, patient 085


title: SHAE002_dORF6_84h_1


title: SHAE002_dORF6_72h_4


title: SHAE002_dORF6_72h_3


title: SAKK 19/05, blood, baseline, patient 081


title: SHAE002_dORF6_72h_2


title: SAKK 19/05, blood, baseline, patient 079


title: SHAE002_dORF6_60h_4


title: SAKK 19/05, blood, baseline, patient 082


title: SHAE002_dORF6_72h_1


title: SHAE002_dORF6_60h_3


title: SAKK 19/05, blood, baseline, patient 089


title: SAKK 19/05, blood, baseline, patient 091


title: SAKK 19/05, blood, baseline, patient 078


title: SHAE002_dORF6_60h_2


title: SAKK 19/05, blood, baseline, patient 092


title: SHAE002_dORF6_60h_1


title: SHAE002_dORF6_48h_4


title: SHAE002_dORF6_48h_2


title: SHAE002_dORF6_48h_1


title: SAKK 19/05, blood, baseline, patient 075


title: SAKK 19/05, blood, baseline, patient 083


title: SHAE002_dORF6_48h_3


title: SHAE002_dORF6_36h_4


title: SHAE002_dORF6_36h_3


title: SAKK 19/05, blood, baseline, patient 074


title: SHAE002_dORF6_36h_2


title: SAKK 19/05, blood, baseline, patient 080


title: SHAE002_dORF6_24h_4


title: SAKK 19/05, blood, baseline, patient 072


title: SHAE002_dORF6_24h_1


title: SHAE002_dORF6_36h_1


title: SAKK 19/05, blood, baseline, patient 077


title: SAKK 19/05, blood, baseline, patient 084


title: SHAE002_dORF6_12h_4


title: SHAE002_dORF6_12h_3


title: SHAE002_dORF6_24h_2


title: SAKK 19/05, blood, baseline, patient 073


title: SHAE002_dORF6_12h_2


title: SHAE002_dORF6_12h_1


title: SAKK 19/05, blood, baseline, patient 069


title: SAKK 19/05, blood, baseline, patient 070


title: SHAE002_dORF6_0h_3


title: SHAE002_dORF6_0h_1


title: SAKK 19/05, blood, baseline, patient 066


title: SHAE002_dORF6_0h_4


title: SAKK 19/05, blood, baseline, patient 068


title: SHAE002_dORF6_0h_2


title: SAKK 19/05, blood, baseline, patient 064


title: SAKK 19/05, blood, baseline, patient 061


title: SAKK 19/05, blood, baseline, patient 063


title: SAKK 19/05, blood, baseline, patient 057


title: SAKK 19/05, blood, baseline, patient 067


title: SHAE002_mock_96h_4

value: mock


title: SHAE002_mock_96h_3


title: SAKK 19/05, blood, baseline, patient 060


title: SAKK 19/05, blood, baseline, patient 058


title: SAKK 19/05, blood, baseline, patient 059


title: SHAE002_mock_96h_2


title: SHAE002_mock_84h_3


title: SAKK 19/05, blood, baseline, patient 065


title: SAKK 19/05, blood, baseline, patient 053


title: SAKK 19/05, blood, baseline, patient 056


title: SAKK 19/05, blood, baseline, patient 055


title: SAKK 19/05, blood, baseline, patient 049


title: SAKK 19/05, blood, baseline, patient 054b


title: SAKK 19/05, blood, baseline, patient 050


title: SAKK 19/05, blood, baseline, patient 040


title: SHAE002_mock_72h_4


title: SHAE002_mock_84h_4


title: SHAE002_mock_72h_3


title: SHAE002_mock_84h_1


title: SHAE002_mock_72h_2


title: SHAE002_mock_96h_1


title: SHAE002_mock_72h_1


title: SHAE002_mock_84h_2


title: SAKK 19/05, blood, baseline, patient 044b


title: SAKK 19/05, blood, baseline, patient 042


title: SAKK 19/05, blood, baseline, patient 047b


title: SAKK 19/05, blood, baseline, patient 051


title: SHAE002_mock_60h_4


title: SHAE002_mock_6h_3


title: SHAE002_mock_60h_3


title: SHAE002_mock_6h_1


title: SHAE002_mock_60h_2


title: SHAE002_mock_6h_2


title: SAKK 19/05, blood, baseline, patient 037b


title: SHAE002_mock_60h_1


title: SAKK 19/05, blood, baseline, patient 038


title: SAKK 19/05, blood, baseline, patient 030


title: SAKK 19/05, blood, baseline, patient 029


title: SHAE002_mock_48h_3


title: SHAE002_mock_48h_1


title: SHAE002_mock_36h_3


title: SAKK 19/05, blood, baseline, patient 026


title: SHAE002_mock_48h_4


title: SAKK 19/05, blood, baseline, patient 027


title: SHAE002_mock_36h_1


title: SHAE002_mock_36h_2


title: SHAE002_mock_24h_3


title: SAKK 19/05, blood, baseline, patient 028


title: SHAE002_mock_18h_3


title: SHAE002_mock_24h_1


title: SHAE002_mock_18h_2


title: SAKK 19/05, blood, baseline, patient 039


title: SAKK 19/05, blood, baseline, patient 025


title: SAKK 19/05, blood, baseline, patient 020


title: SAKK 19/05, blood, baseline, patient 018


title: SAKK 19/05, blood, baseline, patient 015


title: SHAE002_mock_12h_3


title: SAKK 19/05, blood, baseline, patient 021


title: SAKK 19/05, blood, baseline, patient 014


title: SHAE002_mock_18h_1


title: SAKK 19/05, blood, baseline, patient 016


title: SAKK 19/05, biopsy, patient 102

description: Exon expression of human lung biopsies sampled at baseline (treatment naive) in late stage NSCLC patients.

source_name: Bronchoscopic lung biopsies from NSCLC patients

extract_protocol: Total RNA from bronchoscopic biopsy were extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's recommendations.

value: lung biopsy


title: SHAE002_mock_12h_1


title: SAKK 19/05, blood, baseline, patient 008


title: SAKK 19/05, blood, baseline, patient 009


title: SHAE002_mock_12h_2


title: SHAE002_mock_0h_3


title: SAKK 19/05, blood, baseline, patient 003


title: SAKK 19/05, blood, baseline, patient 007


title: SAKK 19/05, blood, baseline, patient 019


title: SAKK 19/05, blood, baseline, patient 023


title: SHAE002_mock_0h_2


title: SHAE002_mock_0h_1


title: SHAE002_H1N1_6h_2


title: SHAE002_H1N1_6h_3


title: SHAE002_H1N1_6h_1


title: SAKK 19/05, biopsy, patient 098


title: SAKK 19/05, biopsy, patient 103


title: SAKK 19/05, biopsy, patient 101


title: SAKK 19/05, biopsy, patient 099


title: SHAE002_H1N1_48h_1


title: SHAE002_H1N1_36h_2


title: SHAE002_H1N1_48h_3


title: SHAE002_H1N1_36h_1


title: SAKK 19/05, biopsy, patient 096


title: SAKK 19/05, biopsy, patient 097


title: SHAE002_H1N1_48h_2


title: SAKK 19/05, blood, baseline, patient 002


title: SAKK 19/05, biopsy, patient 093


title: SHAE002_H1N1_24h_3


title: SHAE002_H1N1_24h_2


title: SAKK 19/05, biopsy, patient 094


title: SAKK 19/05, biopsy, patient 095


title: SAKK 19/05, biopsy, patient 091


title: SHAE002_H1N1_48h_4


title: SHAE002_H1N1_18h_1


title: SHAE002_H1N1_12h_3


title: SHAE002_H1N1_24h_1


title: SAKK 19/05, biopsy, patient 090


title: SHAE002_H1N1_12h_1


title: SHAE002_H1N1_18h_2


title: SAKK 19/05, biopsy, patient 084


title: SHAE002_H1N1_0h_3


title: SHAE002_H1N1_12h_2


title: SAKK 19/05, biopsy, patient 087


title: SHAE002_H1N1_0h_2


title: SAKK 19/05, biopsy, patient 078


title: SHAE002_H1N1_0h_1


title: SHAE002_BAT_96h_4


title: SAKK 19/05, biopsy, patient 077


title: SAKK 19/05, biopsy, patient 088


title: SAKK 19/05, biopsy, patient 082


title: SHAE002_BAT_96h_2


title: SAKK 19/05, biopsy, patient 075


title: SHAE002_BAT_96h_1


title: SAKK 19/05, biopsy, patient 081


title: SAKK 19/05, biopsy, patient 076


title: SAKK 19/05, biopsy, patient 080


title: SAKK 19/05, biopsy, patient 070


title: SHAE002_BAT_84h_4


title: DLY, lung at 30-day-old, biological rep2

city: Tai’an

first: Yunliang

last: Jiang

state: Shandong

address: No. 61 Daizong Avenue

department: College of Animal Science and Veterinary Medicine

country: China

institute: Shandong Agricultural University

description: Gene expression data from lungs at 30-day-old weaned pigs

hyb_protocol: The labeled RNA was hybridized in an Affymetrix Hybridization Oven 640. After hybridization, the microarray slides were washed and dyed using the Affymetrix Fluidics Station 450.

scan_protocol: The probe arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: The signal intensities of the spots on each image were quantified by the Affymetrix GeneChip Operating Software Version 1.4 (GCOS 1.4) and the data were adjusted and normalized by the dChip software.

organism: Sus scrofa

source_name: Sus scrofa lung after weaning

label_protocol: RNA was prepared using the GeneChip (AFF-900623)　one cycle target for the labeling and control reagents

growth_protocol: All animal procedures were performed according to protocols approved by the Animal Care and Use Committee of Shandong Agricultural University.

extract_protocol: Total RNA was isolated using standard protocols (Trizol) from lung tissue samples  and purified using an RNeasy Mini kit according to the manufacturer’s protocol.

treatment_protocol: Pigs were randomly assigned into two groups and reared in separate places: the PRRSV-infected group consisted of 11 DPL and 10 DLY pigs, and the control group consisted of five DPL and five DLY pigs. Infections in the pigs proceeded via inoculation with 2 ml of a viral suspension of PRRSV (at a tissue culture infectious dose of 105) by dripping the solution into the nasal cavity of each pig. The control group was treated with an identical volume of PBS by the same method.

value: lung

tag: breed

value: DLY (Duroc×Landrace×Yorkshire)

tag: age

value: 30-day-old weaned pig


title: SHAE002_BAT_84h_3


title: SHAE002_BAT_96h_3


title: DLY, lung at 30-day-old, biological rep1


title: SAKK 19/05, biopsy, patient 068


title: SAKK 19/05, biopsy, patient 074


title: SAKK 19/05, biopsy, patient 065


title: DPL, lung at 30-day-old, biological rep1

value: DPL (Chinese indigenous pig breed)


title: SHAE002_BAT_72h_3


title: DLY, lung at 30-day-old, biological rep3


title: SAKK 19/05, biopsy, patient 063


title: DPL, lung at 30-day-old, biological rep3


title: SHAE002_BAT_72h_2


title: SHAE002_BAT_84h_2


title: SAKK 19/05, biopsy, patient 069


title: SHAE002_BAT_60h_4


title: SHAE002_BAT_72h_4


title: SAKK 19/05, biopsy, patient 061


title: SHAE002_BAT_60h_3


title: SAKK 19/05, biopsy, patient 060


title: SAKK 19/05, biopsy, patient 064


title: SHAE002_BAT_48h_4


title: HCC79N-Nsp

type: genomic

city: shanghai

first: Zeguang

last: Han

address: No.351,Guoshoujing Rd.,Zhangjiang Hi-Tech Park

institute: Chinese National Genome Center at Shanghai

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.

label: Biotin

molecule: genomic DNA

source_name: hepatocellular carcinoma

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from hepatocellular carcinoma and their adjacent liver tissues using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: hepatocellular carcinoma

tag: sample id


title: SHAE002_BAT_60h_1

value: Human airway epithelium cells (HAE)


title: SHAE002_BAT_48h_1

value: cells


title: DPL, lung at 30-day-old, biological rep2


title: HCC75N-Nsp

description: Hybridized to 250K_Nsp


title: SAKK 19/05, biopsy, patient 067


title: HCC77N-Nsp

description: Hybridized to 250K_Nsp


title: SHAE002_BAT_48h_3

value: BatSRBD


title: HCC67N-Nsp

description: Hybridized to 250K_Nsp


title: SAKK 19/05, biopsy, patient 057


title: SAKK 19/05, biopsy, patient 056


title: HCC71N-Nsp

description: Hybridized to 250K_Nsp


title: SAKK 19/05, biopsy, patient 051


title: SAKK 19/05, biopsy, patient 055


title: SHAE002_BAT_36h_2


title: SHAE002_BAT_36h_1


title: HCC73N-Nsp

description: Hybridized to 250K_Nsp


title: SHAE002_BAT_36h_3


title: SHAE002_BAT_24h_4


title: HCC63N-Nsp

description: Hybridized to 250K_Nsp


title: SHAE002_BAT_24h_3


title: HCC61N-Nsp

description: Hybridized to 250K_Nsp


title: HCC69N-Nsp

description: Hybridized to 250K_Nsp


title: SHAE002_BAT_36h_4


title: SHAE002_BAT_72h_1


title: SAKK 19/05, biopsy, patient 049


title: SAKK 19/05, biopsy, patient 083


title: SHAE002_BAT_24h_2


title: SAKK 19/05, biopsy, patient 038


title: HCC55N-Nsp

description: Hybridized to 250K_Nsp


title: HCC65N-Nsp

description: Hybridized to 250K_Nsp


title: SHAE002_BAT_12h_4


title: SHAE002_BAT_12h_3


title: HCC53N-Nsp

description: Hybridized to 250K_Nsp


title: SHAE002_BAT_0h_4


title: SHAE002_BAT_0h_2


title: SHAE002_BAT_0h_3


title: SAKK 19/05, biopsy, patient 023


title: SHAE002_BAT_24h_1


title: HCC49N-Nsp

description: Hybridized to 250K_Nsp


title: HCC51N-Nsp

description: Hybridized to 250K_Nsp


title: SAKK 19/05, biopsy, patient 002


title: ky13 Replicate 3

city: Princeton

first: Leonid

last: Kruglyak

state: NJ

address: 110 Carl Ichan Laboratory

institute: Princeton University

description: ky13 Biological Replicate 3

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B Scanner

data_processing: Median signal processed in R using limma, background corrected, within array loess normalization, and Gquantile between array normalization, replicate probes averaged

organism: Caenorhabditis elegans

source_name: Reference (mixed stage, mixed N2:CB4856)

label_protocol: RNA was labeled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent, San Jose CA) according to the manufacturer's instructions

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: whole worm

tag: strain

value: reference (mixed stage, mixed N2:CB4856)

tag: genetic background/npr-1 allele

value: N2 (putative null allele)


title: N2 Replicate 2

description: N2 Biological Replicate 2


title: SHAE002_BAT_12h_2


title: HCC45N-Nsp

description: Hybridized to 250K_Nsp


title: qgIR1 Replicate 3

description: qgIR1 Biological Replicate 2

value: N2 (CB4856 introgression)


title: HCC39N-Nsp

description: Hybridized to 250K_Nsp


title: SHAE002_BAT_0h_1


title: HCC41N-Nsp

description: Hybridized to 250K_Nsp


title: HCC35N-Nsp

description: Hybridized to 250K_Nsp


title: HCC27N-Nsp

description: Hybridized to 250K_Nsp


title: kyIR9 Replicate 2

description: kyIR9 Biological Replicate 2

value: CB4856 (N2 introgression)


title: qgIR1 Replicate 2

description: qgIR1 Biological Replicate 2


title: HCC47N-Nsp

description: Hybridized to 250K_Nsp


title: N2 Replicate 1

description: N2 Biological Replicate 1


title: SHAE002_BAT_12h_1


title: HCC19N-Nsp

description: Hybridized to 250K_Nsp


title: HCC21N-Nsp

description: Hybridized to 250K_Nsp


title: ad609 Replicate 2

description: ad609 Biological Replicate 2


title: HCC43N-Nsp

description: Hybridized to 250K_Nsp


title: HCC25N-Nsp

description: Hybridized to 250K_Nsp


title: HCC17N-Nsp

description: Hybridized to 250K_Nsp


title: ky13 Replicate 2

description: ky13 Biological Replicate 2


title: kyIR9 Replicate 3

description: kyIR9 Biological Replicate 3


title: HCC127N-Nsp

description: Hybridized to 250K_Nsp


title: HCC15N-Nsp

description: Hybridized to 250K_Nsp


title: HCC13N-Nsp

description: Hybridized to 250K_Nsp


title: qgIR1 Replicate 1

description: qgIR1 Biological Replicate 1


title: CB4856 Replicate 2

description: CB4856 Biological Replicate 2


title: CB4856 Replicate 1

description: CB4856 Biological Replicate 1


title: ky13 Replicate 1

description: ky13 Biological Replicate 1


title: HCC125N-Nsp

description: Hybridized to 250K_Nsp


title: HCC121N-Nsp

description: Hybridized to 250K_Nsp


title: ad609 Replicate 1

description: ad609 Biological Replicate 1


title: HCC11N-Nsp

description: Hybridized to 250K_Nsp


title: kyIR9 Replicate 1

description: kyIR9 Biological Replicate 1


title: SAKK 19/05, biopsy, patient 058

value: advanced non-small cell lung cancer

value: baseline


title: PBMC_1_W14_6h_Gag-

city: Creteil

first: hakim

last: hocini

address: Hopital Henri Mondor, 51, Avenue du Maréchal De Lattre De Tassigny

country: France

institute: inserm

description: SAMPLE 43

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Assay

scan_protocol: iScan Illumina scanning protocol using iScan control software

data_processing:
neqc of limma package
Background correction with normexp (using negative controls) + offset adding + log2 transformation + normalisation by quantiles including controls

source_name: PBMC

label_protocol: In vitro transcription was generated from 150 ng of RNA using Ambion Illumina TotalPrep RNA Amplification Kits (Applied Biosystems/Ambion).

extract_protocol: RNA were purified using RNeasy Plus Micro Kit (Qiagen, France) and quantified using a ND-8000 spectrophotometer (NanoDrop Technologies) before being checked for integrity on the 2100 BioAnalyzer (Agilent Technologies).

tag: time

tag: incubation

tag: stimulation

value: Gag-

tag: volunteer

tag: ChIP


title: HCC111N-Nsp

description: Hybridized to 250K_Nsp


title: PBMC_1_W14_24h_Gag-

description: SAMPLE 44


title: HCC119N-Nsp

description: Hybridized to 250K_Nsp


title: HCC113N-Nsp

description: Hybridized to 250K_Nsp


title: PBMC_1_W14_24h_Gag+

description: SAMPLE 40

value: Gag+


title: PBMC_1_W14_6h_LIPO5

description: SAMPLE 35


title: HEK293, stable PRL-1 transfectant, biological replicate 2

city: Indianapolis

first: Carmen

middle: M.

last: Dumaual

state: IN

address: 723 West Michigan St., Room SL306

department: Biology

institute: Indiana University-Purdue University Indianapolis

description: PRL-1 Overexpressing

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Affymetrix HG U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were processed with R-project software version 2.13.1 through the Rstudio interface version 0.94.92.  Intensity values were read using the affy library of the Bioconductor package  version 2.8.  Normalizaton and calls were made using the mas5 procedure under default parameters.

source_name: HEK293 cells stably transfected with pcDNA4-PRL-1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Affymetrix Genechip Expression Analysis Technical Manual, 2002, Affymetrix).

growth_protocol: HEK293 cells stably overexpressing PRL-1 or transfected with empty pcDNA4 vector were grown in 100mm plates in DMEM supplemented with 10% (v/v) fetal bovine serum, 50 units/ml penicillin, and 50ug/ml streptomycin.

extract_protocol: Total RNA was extracted using the TRIzol reagent (Life Technologies) and further purified with a Qiagen Rneasy Mini Kit, following the manufacturers' instructions for both.

tag: cell line


title: Cecum-Sham-16h-rep3

city: Charlottesville

first: Kevin

middle: Michael

last: D'Auria

state: VA

address: 415 Lane Road, Room 2041

department: Biomedical Engineering

institute: University of Virginia

hyb_protocol: RNA was hybridized to Mouse 430 2.0 chips, washed, and stained according to the recommended Affymetrix protocols.

scan_protocol: A GeneChip Scanner 3000 7G was used

data_processing: Each array was RMA background corrected. All arrays were then loess normalized on the probe level. Loess normalization was again applied after median polish probe set summarization.

organism: Mus musculus

source_name: Cecal epithelial-layer cells, Sham, 16h

label_protocol: RNA was labeled using the Affymetrix 3’ IVT expression kit and protocol

growth_protocol: Mice (male C57BL/6J, 8 weeks old from Jackson Laboratories) were fed Harlan LM-485 diet

extract_protocol: Ceca were rinsed with Hank’s Balanced Salt Solution (HBSS), placed in a solution (HBSS, 50mM EDTA, 1mM DTT) and shaken (250 rpm) for 30 minutes (37°C) to remove epithelial layer cells. The digested tissue was strained (100µm cell strainer) and filtrate centrifuged (1,000g, 4°C, 10min).  Cells were resuspended in red cell lysis beffer (150mM NH4Cl, 10mM NaHCO3, 0.1 mM EDTA) and pelleted cells stored (-80°C). RNA was isolated using the RNeasy mini kit (Qiagen) with on-column DNase digestion according to manufacturer’s instructions. An Agilent 2100 BioAnalyzer was used to assess RNA integrity.

treatment_protocol: Mice were anesthetized with ketamine/xylazine in preparation for surgery.  A midline laparotomy was performed to locate the cecum, 20 µg toxin injected into the distal tip, and incisions sutured.  A total of 100 uL was injected into the cecum of each animal. Sham injected animals received only saline.

tag: hours

tag: injection

value: Sham

tag: background strain


title: PBMC_1_W0_24h_NS

description: SAMPLE 46

value: NS


title: HCC115N-Nsp

description: Hybridized to 250K_Nsp

tag: disease state


title: PBMC_1_W14_6h_NS

description: SAMPLE 47


title: PBMC_1_W0_24h_Gag+

description: SAMPLE 38


title: HCC105N-Nsp

description: Hybridized to 250K_Nsp


title: Cecum-Sham-16h-rep2


title: HEK293, stable PRL-1 transfectant, biological replicate 1

description: PRL-1 Overexpressing


title: Cecum-Sham-16h-rep1


title: HCC101N-Nsp

description: Hybridized to 250K_Nsp

tag: sample type


title: HCC109N-Nsp

description: Hybridized to 250K_Nsp


title: HCC107N-Nsp

description: Hybridized to 250K_Nsp


title: PBMC_1_W0_6h_Gag-

description: SAMPLE 41


title: PBMC_1_W0_24h_LIPO5

description: SAMPLE 34


title: Cecum-Sham-16h-rep4


title: PBMC_1_W14_24h_LIPO5

description: SAMPLE 36


title: HCC123N-Nsp

description: Hybridized to 250K_Nsp


title: PBMC_1_W0_6h_NS

description: SAMPLE 45


title: PBMC_1_W0_6h_LIPO5

description: SAMPLE 33


title: 12_G_14_Cy3

city: Miami

first: David

middle: I

last: Dayan

state: Florida

address: 4600 Rickenbacker CSWY

institute: University of Miami

hyb_protocol: Labeled aRNA samples (2 pmol dye/ul) were hybridized to slides in 10 ul of hybridization buffer [50% formamide buffer, 5x SSPE, 1% sodium dodecyl sulfate, 0.2 mg/ml bovine serum albumin, 1 mg/ml denatured salmon sperm DNA (Sigma), and 1 mg/ml RNase-free poly(A) RNA (Sigma)] for 44 hours at 42º C.

scan_protocol: Arrays were scanned using a ScanArray Express 4000 (Perkin Elmer). Resulting 16 bit Tiff Images were quantified using ImaGene® (Biodiscovery, Inc.) spotfinding software.

data_processing: Log2 measures of gene expression were normalized using a linear mixed model in JMP Genomics 3.2 (SAS, Cary, NC, USA) to remove the effects of dye (fixed effect) and array (random effect) following a joint regional and spatial Lowess transformation to account for both intensity and spatial bias. The model was of the form yij = μ + Ai + Dj + (AxD)ij + εij, where yij is the signal from the ith array with dye j, μ is the sample mean, Ai and Dj are the overall variation in arrays (arrays 1-80) and dyes (Cy3 and Cy5), (AxD)ij is the array x dye interaction and εij is the stochastic error.

organism: Fundulus heteroclitus

source_name: Glycolytic muscle, Georgia, 12C

label_protocol: RNA for hybridization was prepared by one round of amplification (aRNA) using the Amino Allyl MessageAmp aRNA Kit (Ambion, Austin, TX, USA) to form copy template RNA by T7 amplification. Amino-allyl UTP was incorporated into targets during T7 transcription, and resulting amino-allyl aRNA was coupled to Cy3 and Cy5 dyes (GE Healthcare, Piscataway, NJ, USA).

growth_protocol: Individual fundulus were collected from wild populations in Maine, Georgia, and Florida (F. grandis), and common gardened for 6 weeks before treatment.

extract_protocol: RNA was extracted using a Trizol buffer (Invitrogen, Carlsbad, CA, USA) followed by purification using the Qiagen RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA).

treatment_protocol: Common gardened Fundulus were acclimated to 12, 20 or 28C for 4 weeks.

tag: population

value: Georgia

tag: tissue

value: glycolytic muscle

tag: acclimation temperature


title: PBMC_3_W14_24h_NS

description: SAMPLE 192


title: 12_M_20_Cy5

source_name: Glycolytic muscle, Maine, 12C

value: Maine


title: Cecum-TcdB-16h-rep2

source_name: Cecal epithelial-layer cells, TcdB, 16h

value: TcdB


title: PBMC_3_W14_6h_Gag-

description: SAMPLE 187


title: HCC103N-Nsp

description: Hybridized to 250K_Nsp

value: hepatocellular carcinoma

tag: sample id


title: HEK293, empty pcDNA4 vector, biological replicate 2

description: Control

source_name: HEK293 cells stably transfected with empty pcDNA4 vector


title: PBMC_3_W14_6h_NS

description: SAMPLE 191


title: PBMC_3_W14_24h_Gag-

description: SAMPLE 188


title: 20_G_17_Cy5

source_name: Glycolytic muscle, Georgia, 20C


title: 20_M_17_Cy3

source_name: Glycolytic muscle, Maine, 20C


title: Cecum-Sham-6h-rep3

source_name: Cecal epithelial-layer cells, Sham, 6h


title: Cecum-TcdA-16h-rep1

source_name: Cecal epithelial-layer cells, TcdA, 16h

value: TcdA


title: Cecum-TcdB-16h-rep1


title: Cecum-TcdB-16h-rep3


title: PBMC_3_W0_6h_LIPO5

description: SAMPLE 177


title: PBMC_3_W0_6h_NS

description: SAMPLE 189


title: PBMC_3_W0_24h_Gag+

description: SAMPLE 182


title: PBMC_3_W0_24h_Gag-

description: SAMPLE 186


title: PBMC_3_W14_6h_LIPO5

description: SAMPLE 179


title: PBMC_3_W14_24h_LIPO5

description: SAMPLE 180


title: PBMC_3_W0_24h_NS

description: SAMPLE 190


title: HEK293, empty pcDNA4 vector, biological replicate 3

description: Control


title: Cecum-TcdA-16h-rep2


title: HCC117N-Nsp

description: Hybridized to 250K_Nsp


title: HCC23N-Nsp

description: Hybridized to 250K_Nsp


title: 20_M_17_Cy5


title: Cecum-TcdA+TcdB-6h-rep1

source_name: Cecal epithelial-layer cells, TcdA+TcdB, 6h

value: TcdA+TcdB


title: 28_G_17_Cy3

source_name: Glycolytic muscle, Georgia, 28C


title: Cecum-Sham-6h-rep1


title: PBMC_9_W14_6h_LIPO5

description: SAMPLE 19


title: 12_M_13_Cy3


title: 12_M_19_Cy5


title: 28_M_12_Cy3

source_name: Glycolytic muscle, Maine, 28C


title: PBMC_3_W0_6h_Gag-

description: SAMPLE 185


title: PBMC_9_W14_24h_NS

description: SAMPLE 32


title: PBMC_3_W0_6h_Gag+

description: SAMPLE 181


title: HEK293, empty pcDNA4 vector, biological replicate 1

description: Control


title: PBMC_9_W14_6h_Gag-

description: SAMPLE 27


title: Cecum-TcdB-6h-rep3

source_name: Cecal epithelial-layer cells, TcdB, 6h


title: PBMC_9_W14_6h_Gag+

description: SAMPLE 23


title: Cecum-Sham-6h-rep2


title: 28_P_15_Cy5

organism: Fundulus grandis

source_name: Glycolytic muscle, Florida, 28C

value: Florida


title: PBMC_9_W14_24h_Gag-

description: SAMPLE 28


title: PBMC_9_W14_6h_NS

description: SAMPLE 31


title: 12_M_13_Cy5


title: Cecum-TcdA-6h-rep3

source_name: Cecal epithelial-layer cells, TcdA, 6h


title: PBMC_9_W0_6h_NS

description: SAMPLE 29

source_name: PBMC


title: PBMC_9_W0_6h_Gag+

description: SAMPLE 21


title: PBMC_9_W0_6h_Gag-

description: SAMPLE 25


title: PBMC_9_W0_24h_Gag+

description: SAMPLE 22


title: PBMC_9_W0_24h_Gag-

description: SAMPLE 26


title: PBMC_9_W0_24h_LIPO5

description: SAMPLE 18


title: Cecum-TcdB-6h-rep2


title: Cecum-TcdB-6h-rep1


title: 20_G_12_Cy3


title: 12_G_11_Cy5


title: 20_M_12_Cy3


title: 12_G_12_Cy5


title: 20_G_18_Cy3


title: PBMC_9_W0_6h_LIPO5

description: SAMPLE 17


title: 28_G_14_Cy5


title: PBMC_9_W0_24h_NS

description: SAMPLE 30


title: PBMC_6_W14_6h_LIPO5

description: SAMPLE 163


title: 20_G_15_Cy3


title: Cecum-Sham-2h-rep3

source_name: Cecal epithelial-layer cells, Sham, 2h


title: Cecum-Sham-2h-rep2


title: Cecum-Sham-2h-rep1


title: PBMC_6_W14_6h_Gag+

description: SAMPLE 167


title: PBMC_6_W14_24h_NS

description: SAMPLE 176


title: Cecum-TcdA-6h-rep2


title: Cecum-TcdA-6h-rep1


title: PBMC_6_W0_6h_NS

description: SAMPLE 173


title: PBMC_6_W0_24h_Gag+

description: SAMPLE 166


title: PBMC_6_W0_24h_NS

description: SAMPLE 174


title: PBMC_6_W14_6h_Gag-

description: SAMPLE 171


title: PBMC_6_W0_6h_Gag-

description: SAMPLE 169


title: PBMC_6_W14_24h_LIPO5

description: SAMPLE 164


title: PBMC_6_W14_6h_NS

description: SAMPLE 175


title: PBMC_6_W0_6h_LIPO5

description: SAMPLE 161


title: 12_G_19_Cy5


title: PBMC_6_W0_24h_LIPO5

description: SAMPLE 162


title: Cecum-TcdA+TcdB-2h-rep1

source_name: Cecal epithelial-layer cells, TcdA+TcdB, 2h


title: 28_G_15_Cy3


title: Cecum-TcdA+TcdB-2h-rep2


title: 12_G_14_Cy5

source_name: Glycolytic muscle, Georgia, 12C


title: PBMC_10_W14_6h_LIPO5

description: SAMPLE 115


title: PBMC_10_W14_24h_LIPO5

description: SAMPLE 116


title: 12_M_17_Cy3

source_name: Glycolytic muscle, Maine, 12C


title: Cecum-TcdB-2h-rep2

source_name: Cecal epithelial-layer cells, TcdB, 2h


title: Cecum-TcdB-2h-rep3


title: PBMC_10_W14_24h_Gag-

description: SAMPLE 124


title: PBMC_10_W14_6h_Gag-

description: SAMPLE 123


title: 20_P_15_Cy5

source_name: Glycolytic muscle, Florida, 20C


title: PBMC_10_W14_6h_Gag+

description: SAMPLE 119


title: Cecum-TcdA-16h-rep3


title: 12_P_15_Cy3

source_name: Glycolytic muscle, Florida, 12C


title: Cecum-TcdB-2h-rep1


title: PBMC_10_W14_24h_NS

description: SAMPLE 128


title: 20_P_16_Cy5


title: PBMC_10_W0_6h_NS

description: SAMPLE 125


title: PBMC_3_W14_6h_Gag+

description: SAMPLE 183


title: Cecum-TcdA-2h-rep3

source_name: Cecal epithelial-layer cells, TcdA, 2h


title: PBMC_10_W0_24h_Gag-

description: SAMPLE 122


title: Cecum-TcdA-2h-rep2


title: PBMC_10_W0_6h_Gag-

description: SAMPLE 121


title: PBMC_10_W0_24h_LIPO5

description: SAMPLE 114


title: PBMC_5_W14_6h_NS

description: SAMPLE 159


title: PBMC_10_W14_24h_Gag+

description: SAMPLE 120


title: Cecum-TcdA-2h-rep1


title: PBMC_10_W0_6h_LIPO5

description: SAMPLE 113


title: PBMC_10_W0_24h_Gag+

description: SAMPLE 118


title: PBMC_10_W0_6h_Gag+

description: SAMPLE 117


title: 12_P_12_Cy3


title: 28_M_14_Cy5


title: 20_M_18_Cy3

source_name: Glycolytic muscle, Maine, 20C


title: 20_M_11_Cy3


title: 28_M_11_Cy5


title: PBMC_5_W14_24h_NS

description: SAMPLE 160


title: PBMC_5_W14_24h_Gag+

description: SAMPLE 152


title: 20_M_12_Cy5


title: 20_G_11_Cy3

source_name: Glycolytic muscle, Georgia, 20C


title: 28_G_11_Cy3


title: 20_G_12_Cy5


title: 12_G_15_Cy5


title: PBMC_5_W14_24h_LIPO5

description: SAMPLE 148


title: PBMC_5_W14_6h_Gag-

description: SAMPLE 155


title: PBMC_5_W14_24h_Gag-

description: SAMPLE 156


title: PBMC_5_W0_6h_Gag-

description: SAMPLE 153


title: 20_P_16_Cy3


title: PBMC_4_W14_24h_NS

description: SAMPLE 112


title: PBMC_5_W14_6h_LIPO5

description: SAMPLE 147


title: PBMC_5_W0_6h_LIPO5

description: SAMPLE 145


title: PBMC_5_W0_24h_LIPO5

description: SAMPLE 146


title: PBMC_5_W0_24h_Gag+

description: SAMPLE 150


title: PBMC_5_W0_24h_NS

description: SAMPLE 158


title: PBMC_5_W14_6h_Gag+

description: SAMPLE 151


title: PBMC_5_W0_6h_NS

description: SAMPLE 157


title: PBMC_5_W0_6h_Gag+

description: SAMPLE 149


title: PBMC_4_W14_6h_NS

description: SAMPLE 111


title: PBMC_4_W14_6h_LIPO5

description: SAMPLE 99


title: 28_G_16_Cy5


title: PBMC_4_W14_6h_Gag+

description: SAMPLE 103


title: PBMC_4_W0_24h_NS

description: SAMPLE 110


title: 20_G_22_Cy3


title: PBMC_4_W0_6h_Gag+

description: SAMPLE 101


title: 20_G_21_Cy3


title: 28_G_15_Cy5


title: PBMC_4_W0_24h_LIPO5

description: SAMPLE 98


title: PBMC_7_W14_24h_NS

description: SAMPLE 96


title: PBMC_4_W0_6h_LIPO5

description: SAMPLE 97


title: 20_P_12_Cy5


title: Cecum-TcdA+TcdB-2h-rep3


title: PBMC_4_W14_24h_LIPO5

description: SAMPLE 100


title: right EC, biological rep3

city: New York

first: Diego

middle: E

last: Berman

state: NY

department: Pathology and Cell Biology

institute: Columbia University

description: Gene expression data from right mouse EC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Genechip Mouse gene 2.0 ST arrays. 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: Microarrays data were analyzed through the use of Ingenuity® iReport (Ingenuity® Systems, www.ingenuity.com). Please see attached file with the list of genes ordered according to their fold change and p values.

source_name: right entorhinal cortex of a 6 month-old C57BL/6 wild-type mouse

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: Mice were kept in the animal facility in a 12/12 hour light/dark cycle.

extract_protocol: Dissected lef and right cortical samples were immediately processed for RNA extraction by using the RNeasy Kit from QIAGEN according to manufacturer’s instructions. Before running the microarrays, RNA quality and integrity was monitored on an Agilent BioAnalyzer.

treatment_protocol: Mice were not subjected to any treatment.

value: right entorhinal cortex

tag: genotype

value: wild-type

tag: age

value: 6 month

tag: strain


title: 28_P_16_Cy3


title: PBMC_7_W14_24h_Gag-

description: SAMPLE 92

tag: time

tag: incubation


title: PBMC_7_W14_24h_LIPO5

description: SAMPLE 84

tag: stimulation

tag: volunteer


title: PBMC_7_W14_6h_NS

description: SAMPLE 95

tag: ChIP


title: 20_P_11_Cy3


title: PBMC_7_W14_24h_Gag+

description: SAMPLE 88


title: right EC, biological rep1


title: PBMC_7_W0_24h_Gag+

description: SAMPLE 86


title: 12_P_17_Cy5


title: PBMC_7_W0_6h_Gag+

description: SAMPLE 85


title: PBMC_7_W0_24h_NS

description: SAMPLE 94


title: PBMC_7_W0_6h_Gag-

description: SAMPLE 89


title: PBMC_7_W0_24h_Gag-

description: SAMPLE 90


title: left EC, biological rep3

description: Gene expression data from left mouse EC

source_name: left entorhinal cortex of a 6 month-old C57BL/6 wild-type mouse

value: left entorhinal cortex


title: PBMC_2_W14_24h_NS

description: SAMPLE 80


title: PBMC_7_W0_6h_NS

description: SAMPLE 93


title: right EC, biological rep2


title: PBMC_2_W14_6h_NS

description: SAMPLE 79


title: PBMC_7_W14_6h_Gag-

description: SAMPLE 91


title: 20_P_11_Cy5


title: 28_P_15_Cy3


title: PBMC_2_W14_24h_Gag-

description: SAMPLE 76


title: left EC, biological rep1

description: Gene expression data from left mouse EC

value: lef entorhinal cortex


title: left EC, biological rep2

description: Gene expression data from left mouse EC


title: PBMC_2_W14_24h_Gag+

description: SAMPLE 72


title: 20_M_15_Cy5


title: 12_M_18_Cy3


title: 20_M_14_Cy3


title: PBMC_2_W14_6h_Gag-

description: SAMPLE 75

value: Gag-


title: PBMC_2_W14_6h_LIPO5

description: SAMPLE 67


title: PBMC_2_W14_6h_Gag+

description: SAMPLE 71

value: Gag+


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_ms1_mutant_pooled_sample3

city: Tsukuba

first: Norihiro

last: Futamura

state: Ibaraki

address: 1 Matsunosato

country: Japan

institute: Forestry and Forest Products Research Institute (FFPRI)

description: This pooled RNA sample was collected from male strobili of seven male-sterile individuals derived from Toyama 1 half-sib F2 pedigree at the end of October, 2008. It is the third of three sterile male strobilus samples containing disrupted microspores.

hyb_protocol: Hybridization was performed by Roche NimbleGen Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) and quantile normalization (Bolstad et al. Bioinformatics 19(2):185). Arrays devived from individual samples and pooled samples were normalized separately.

organism: Cryptomeria japonica

source_name: Cryptomeria japonica ms1 mutant mix3

label_protocol: Labeling was performed by Roche NimbleGen Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
Trees, from 4 to 6 years old, were treated with 100 ppm gibberellic acid GA3 at the end of July to induce flowering. Male strobili of male-fertile (MF) and male-sterile (MF) Cryptomeria japonica were collected at seven-days intervals from September to November.
The collected male strobili were observed by light microscopy, and classified into four types: pre-meiosis (PM) stage, meiosis (MEI) stage, tetrad (TET) stage and uninuclear microspore (UM) stage, according to their stage of pollen development.

extract_protocol: Total RNA was extracted using the a modified CTAB method (Futamura et al. BMC Genomics 9(1): 383) and purified with the SV Total RNA Isolating Sysytem (Promega, Madison, WI, USA). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

value: Toyama ms1 mutant

tag: phenotype

value: male sterile

tag: accession

value: male strobili containing uninuclear microspore


title: PBMC_2_W0_6h_Gag-

description: SAMPLE 73


title: 12_M_12_Cy3

value: glycolytic muscle


title: 20_M_19_Cy5

value: Maine


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_ms1_mutant_pooled_sample1

description: This pooled RNA sample was collected from male strobili of six male-sterile individuals derived from Toyama 1 half-sib F2 pedigree in the middle of November, 2006. It is the first of three sterile male strobilus samples containing disrupted microspores.

source_name: Cryptomeria japonica ms1 mutant mix1


title: PBMC_2_W0_6h_NS

description: SAMPLE 77

value: NS


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_wild-type_pooled_sample3

description: This pooled RNA sample was collected from male strobili of seven wild-type individuals derived from Toyama 1 half-sib F2 pedigree at the end of October, 2008. It is the third of three fertile male strobilus samples containing uninuclear microspores.

source_name: Cryptomeria japonica wild-type mix3

value: Wild-type

value: normal


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_ms1_mutant_pooled_sample2

description: This pooled RNA sample was collected from male strobili of four male-sterile individuals derived from Toyama 1 half-sib F2 pedigree at the beginning of November, 2007. It is the second of three sterile male strobilus samples containing disrupted microspores.

source_name: Cryptomeria japonica ms1 mutant mix2


title: PBMC_2_W14_24h_LIPO5

description: SAMPLE 68

source_name: PBMC


title: 28_M_5_Cy5

source_name: Glycolytic muscle, Maine, 28C


title: PBMC_2_W0_24h_Gag-

description: SAMPLE 74


title: PBMC_2_W0_6h_LIPO5

description: SAMPLE 65


title: PBMC_2_W0_6h_Gag+

description: SAMPLE 69


title: 12_M_12_Cy5


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_wild-type_pooled_sample2

description: This pooled RNA sample was collected from male strobili of four wild-type individuals derived from Toyama 1 half-sib F2 pedigree at the beginning of November, 2007. It is the second of three fertile male strobilus samples containing uninuclear microspores.

source_name: Cryptomeria japonica wild-type mx2


title: PBMC_2_W0_24h_NS

description: SAMPLE 78


title: PBMC_2_W0_24h_LIPO5

description: SAMPLE 66


title: PBMC_11_W14_24h_Gag+

description: SAMPLE 136


title: PBMC_11_W14_6h_NS

description: SAMPLE 143


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_wild-type_pooled_sample1

description: This pooled RNA sample was collected from male strobili of six wild-type individuals derived from Toyama 1 half-sib F2 pedigree in the middle of November, 2006. It is the first of three fertile male strobilus samples containing uninuclear microspores.

source_name: Cryptomeria japonica wild-type mix1


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_ms1_mutant_pooled_sample3

description: This pooled RNA sample was collected from male strobili of seven male-sterile individuals derived from Toyama 1 half-sib F2 pedigree in the middle of October, 2008. It is the third of three sterile male strobilus samples with tetrad stage of pollen development.

value: male strobili with tetrad stage of pollen development


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_ms1_mutant_pooled_sample1

description: This pooled RNA sample was collected from male strobili of six male-sterile individuals derived from Toyama 1 half-sib F2 pedigree in the latter half of October, 2006. It is the first of three sterile male strobilus samples with tetrad stage of pollen development.


title: PBMC_2_W0_24h_Gag+

description: SAMPLE 70


title: PBMC_11_W14_24h_Gag-

description: SAMPLE 140


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_ms1_mutant_pooled_sample2

description: This pooled RNA sample was collected from male strobili of four male-sterile individuals derived from Toyama 1 half-sib F2 pedigree in the middle of October, 2007. It is the second of three sterile male strobilus samples with tetrad stage of pollen development.


title: PBMC_11_W14_24h_LIPO5

description: SAMPLE 132


title: PBMC_11_W14_24h_NS

description: SAMPLE 144


title: 28_M_13_Cy3


title: 12_G_11_Cy3

source_name: Glycolytic muscle, Georgia, 12C

value: Georgia


title: 20_G_11_Cy5


title: 28_G_14_Cy3

source_name: Glycolytic muscle, Georgia, 28C


title: 20_G_18_Cy5


title: 28_G_17_Cy5


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_wild-type_pooled_sample3

description: This pooled RNA sample was collected from male strobili of seven wild-type individuals derived from Toyama 1 half-sib F2 pedigree in the middle of October, 2008. It is the third of three fertile male strobilus samples with tetrad stage of pollen development.


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_wild-type_pooled_sample2

description: This pooled RNA sample was collected from male strobili of four wild-type individuals derived from Toyama 1 half-sib F2 pedigree in the middle of October, 2007. It is the second of three fertile male strobilus samples with tetrad stage of pollen development.

source_name: Cryptomeria japonica wild-type mix2


title: 20_G_3_Cy3


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_wild-type_pooled_sample1

description: This pooled RNA sample was collected from male strobili of six wild-type individuals derived from Toyama 1 half-sib F2 pedigree in the latter half of October, 2006. It is the first of three fertile male strobilus samples with tetrad stage of pollen development.


title: PBMC_11_W0_6h_LIPO5

description: SAMPLE 129


title: PBMC_11_W0_24h_Gag-

description: SAMPLE 138


title: PBMC_11_W0_6h_NS

description: SAMPLE 141


title: PBMC_11_W14_6h_Gag+

description: SAMPLE 135


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_ms1_mutant_pooled_sample3

description: This pooled RNA sample was collected from male strobili of seven male-sterile individuals derived from Toyama 1 half-sib F2 pedigree in the end of September, 2008. It is the third of three three pooled sterile male strobilus samples with pre-meiotic stage of pollen development.

value: male strobili with pre-meiotic stage of pollen development


title: 28_G_16_Cy3


title: PBMC_8_W14_24h_NS

description: SAMPLE 64


title: PBMC_11_W0_24h_LIPO5

description: SAMPLE 130


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_ms1_mutant_pooled_sample2

description: This pooled RNA sample was collected from male strobili of eight male-sterile individuals derived from Toyama 1 half-sib F2 pedigree between the end of September and the beginning of October, 2007. It is the second of three pooled sterile male strobilus samples with pre-meiotic stage of pollen development.


title: PBMC_8_W14_6h_Gag-

description: SAMPLE 59


title: PBMC_8_W14_6h_Gag+

description: SAMPLE 55


title: PBMC_8_W14_6h_NS

description: SAMPLE 63


title: 12_M_17_Cy5

source_name: Glycolytic muscle, Maine, 12C


title: PBMC_11_W0_24h_Gag+

description: SAMPLE 134


title: PBMC_11_W0_6h_Gag+

description: SAMPLE 133


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_wild-type_pooled_sample3

description: This pooled RNA sample was collected from male strobili of seven wild-type individuals derived from Toyama 1 half-sib F2 pedigree in the end of September, 2008. It is the third of three pooled fertile male strobilus samples with pre-meiotic stage of pollen development.


title: PBMC_8_W14_24h_LIPO5

description: SAMPLE 52


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_ms1_mutant_pooled_sample1

description: This pooled RNA sample was collected from male strobili of six male-sterile individuals derived from Toyama 1 half-sib F2 pedigree between the end of September and the beginning of October, 2006. It is the first of three pooled sterile male strobilus samples with pre-meiotic stage of pollen development.


title: PBMC_8_W14_24h_Gag+

description: SAMPLE 56


title: PBMC_8_W14_6h_LIPO5

description: SAMPLE 51


title: PBMC_8_W14_24h_Gag-

description: SAMPLE 60


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_wild-type_pooled_sample2

description: This pooled RNA sample was collected from male strobili of eight wild-type individuals derived from Toyama 1 half-sib F2 pedigree between the end of September and the beginning of October, 2007. It is the second of three pooled fertile male strobilus samples with pre-meiotic stage of pollen development.


title: PBMC_8_W0_24h_NS

description: SAMPLE 62


title: 28_P_14_Cy3

source_name: Glycolytic muscle, Florida, 28C

value: Florida


title: 12_P_15_Cy5

source_name: Glycolytic muscle, Florida, 12C


title: 28_P_16_Cy5


title: 28_P_17_Cy3


title: PBMC_11_W0_6h_Gag-

description: SAMPLE 137


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_ms1_mutant_sample7

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 13 derived from Toyama 1 half-sib F2 pedigree on October 30th, 2007. It is the seventh of seven sterile male strobilus samples containing disrupted microspores.

source_name: Cryptomeria japonica ms1 mutant 13

value: male strobili containing disrupted microspores


title: 12_P_12_Cy5


title: 20_P_18_Cy3

source_name: Glycolytic muscle, Florida, 20C


title: PBMC_8_W0_6h_Gag-

description: SAMPLE 57


title: PBMC_8_W0_24h_Gag+

description: SAMPLE 54


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_wild-type_pooled_sample1

description: This pooled RNA sample was collected from male strobili of six wild-type individuals derived from Toyama 1 half-sib F2 pedigree between the end of September and the beginning of October, 2006. It is the first of three pooled fertile male strobilus samples with pre-meiotic stage of pollen development.


title: PBMC_12_W14_24h_NS

description: SAMPLE 16


title: PBMC_8_W0_24h_Gag-

description: SAMPLE 58


title: PBMC_8_W0_6h_NS

description: SAMPLE 61


title: 20_M_15_Cy3

source_name: Glycolytic muscle, Maine, 20C


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_ms1_mutant_sample6

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 11 derived from Toyama 1 half-sib F2 pedigree on November 2nd, 2007. It is the sixth of seven sterile male strobilus samples containing disrupted microspores.

source_name: Cryptomeria japonica ms1 mutant 11


title: PBMC_12_W14_6h_Gag-

description: SAMPLE 11


title: 20_M_18_Cy5


title: PBMC_8_W0_6h_LIPO5

description: SAMPLE 49


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_ms1_mutant_sample5

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 6 derived from Toyama 1 half-sib F2 pedigree on October 30th, 2007. It is the fifth of seven sterile male strobilus samples containing disrupted microspores.

source_name: Cryptomeria japonica ms1 mutant 6


title: PBMC_12_W14_6h_Gag+

description: SAMPLE 7


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_ms1_mutant_sample4

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 3 derived from Toyama 1 half-sib F2 pedigree on October 28th, 2007. It is the fourth of seven sterile male strobilus samples containing disrupted microspores.

source_name: Cryptomeria japonica ms1 mutant 3


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_ms1_mutant_sample1

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 21 derived from Toyama 1 half-sib F2 pedigree on October 27th, 2005. It is the first of seven sterile male strobilus samples containing disrupted microspores.

source_name: Cryptomeria japonica ms1 mutant 21


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_ms1_mutant_sample3

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 97 derived from Toyama 1 half-sib F2 pedigree on November 10th, 2006. It is the third of seven sterile male strobilus samples containing disrupted microspores.

source_name: Cryptomeria japonica ms1 mutant 97


title: PBMC_12_W0_24h_NS

description: SAMPLE 14

source_name: PBMC


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_ms1_mutant_sample2

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 17 derived from Toyama 1 half-sib F2 pedigree on November 10th, 2006. It is the second of seven sterile male strobilus samples containing disrupted microspores.

source_name: Cryptomeria japonica ms1 mutant 17


title: PBMC_12_W14_24h_Gag-

description: SAMPLE 12


title: PBMC_12_W14_6h_LIPO5

description: SAMPLE 3


title: PBMC_12_W14_24h_LIPO5

description: SAMPLE 4


title: PBMC_12_W0_24h_Gag-

description: SAMPLE 10


title: PBMC_12_W0_24h_Gag+

description: SAMPLE 6


title: PBMC_12_W0_6h_NS

description: SAMPLE 13


title: 12_M_19_Cy3


title: 28_M_12_Cy5

source_name: Glycolytic muscle, Maine, 28C


title: 20_M_19_Cy3


title: PBMC_8_W0_6h_Gag+

description: SAMPLE 53


title: 12_M_15_Cy5


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_wild-type_sample7

description: This RNA sample was collected from male strobili of a wild-type individual no. 42 derived from Toyama 1 half-sib F2 pedigree on October 28th, 2007. It is the seventh of seven fertile male strobilus samples containing uninuclear microspores.

source_name: Cryptomeria japonica wild-type 42

value: male strobili containing uninuclear microspores


title: 28_M_11_Cy3


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_wild-type_sample6

description: This RNA sample was collected from male strobili of a wild-type individual no. 41 derived from Toyama 1 half-sib F2 pedigree on October 30th, 2007. It is the sixth of seven fertile male strobilus samples containing uninuclear microspores.

source_name: Cryptomeria japonica wild-type 41


title: Raji_rep3

city: Berlin

first: Lora

last: Dimitrova

state: Berlin

address: Hindenburgdamm 30

department: Institute of Pathology

country: Germany

institute: Charité-University Medicine Berlin

hyb_protocol: 2.5 ug of ss cDNA were hybridized for 16 hr at 45°C on Human Gene ST 1.0 Arrays (Affymetrix). Arrays were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000

data_processing:
Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

source_name: Burkitt lymphoma cell line

label_protocol: Single strand cDNA was prepared from 250 ng total RNA according to the standard Ambion protocol (WT Expression kit) and fragmentation and biotin labeling  was done according to the standard Affymetrix protocol (WT terminal labeling kit)

growth_protocol: The Burkitt lymphoma cell lines Raji and Namalwa (designated as B-cell lines throughout the manuscript) and the Hodgkin cell line L428 were grown in RPMI 1640 (PAA Laboratories) supplemented with 10% fetal calf serum (PAN-Biotech). For the cultivation of the cell line L428-PAX5, 25 mM HEPES (Life Technologies/Invitrogen) was added supplementary. The cell lines were incubated at 37 °C and 5% CO2.

extract_protocol: RNA was isolated as described by Ehlers et al.(2008).

treatment_protocol: PAX5 expression was induced in the cell line L428-PAX5 prior to the treatment with 5-aza-2′-deoxycytidine (5-aza-dC; Sigma-Aldrich, St. Louis, MO, USA), a DNA demethylating reagent and Trichostatin A (TSA; Sigma-Aldrich), a histone deacetylase inhibitor. After 2 days of incubation with 0.25 nM mifepristone, the medium was partially replaced and only the freshly added medium was supplemented with mifepristone. 5-aza-dC was subsequently added at a concentration of 3 µM and the cells were incubated for further 3 days. TSA was added at concentration 640 nM 24 h prior to harvesting.

tag: cell line

value: Raji

tag: treatment

tag: duration of treatment

value: no treatment


title: L425-PAX5+MAT_rep3

source_name: Hodgkin lymphoma cell line

value: Mifepristone + 5-aza-2′-deoxycytidine + Trichostatin A (MAT)

value: 5 days


title: L428+MAT_rep2


title: PBMC_12_W0_6h_Gag+

description: SAMPLE 5

value: Gag+


title: L425-PAX5+MAT_rep1


title: L425-PAX5+MAT_rep2


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_wild-type_sample4

description: This RNA sample was collected from male strobili of a wild-type individual no. 31 derived from Toyama 1 half-sib F2 pedigree on October 28th, 2007. It is the fourth of seven fertile male strobilus samples containing uninuclear microspores.

source_name: Cryptomeria japonica wild-type 31


title: L428+MAT_rep3


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_wild-type_sample5

description: This RNA sample was collected from male strobili of a wild-type individual no. 37 derived from Toyama 1 half-sib F2 pedigree on October 30th, 2007. It is the fifth of seven fertile male strobilus samples containing uninuclear microspores.

source_name: Cryptomeria japonica wild-type 37


title: L428+MAT_rep1


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_wild-type_sample2

description: This RNA sample was collected from male strobili of a wild-type individual no. 30 derived from Toyama 1 half-sib F2 pedigree on November 7th, 2006. It is the second of seven fertile male strobilus samples containing uninuclear microspores.

source_name: Cryptomeria japonica wild-type 30


title: PBMC_12_W0_6h_LIPO5

description: SAMPLE 1


title: PBMC_12_W0_6h_Gag-

description: SAMPLE 9

value: Gag-


title: 12_G_21_Cy3

source_name: Glycolytic muscle, Georgia, 12C

tag: population

value: glycolytic muscle


title: PBMC_12_W0_24h_LIPO5

description: SAMPLE 2


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_wild-type_sample1

description: This RNA sample was collected from male strobili of a wild-type individual no. 28 derived from Toyama 1 half-sib F2 pedigree on October 27th, 2005. It is the first of seven fertile male strobilus samples containing uninuclear microspores.

source_name: Cryptomeria japonica wild-type 28


title: PBMC_12_W14_6h_NS

description: SAMPLE 15


title: 28_G_13_Cy5

source_name: Glycolytic muscle, Georgia, 28C

tag: tissue


title: 28_G_11_Cy5

tag: acclimation temperature


title: 20_G_24_Cy3

source_name: Glycolytic muscle, Georgia, 20C


title: Raji_rep2


title: Namalwa_rep3

value: Namalwa


title: Cryptomeria_japonica_male_strobili_pollen_development_UM_wild-type_sample3

description: This RNA sample was collected from male strobili of a wild-type individual no. 973 derived from Toyama 1 half-sib F2 pedigree on November 10th, 2006. It is the third of seven fertile male strobilus samples containing uninuclear microspores.

source_name: Cryptomeria japonica wild-type 973


title: 12_P_18_Cy5

source_name: Glycolytic muscle, Florida, 12C


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_ms1_mutant_sample6

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 13 derived from Toyama 1 half-sib F2 pedigree on October 23th, 2007. It is the sixth of seven sterile male strobilus samples with tetrad stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 13

value: Toyama ms1 mutant

value: male sterile


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_ms1_mutant_sample7

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 9 derived from Toyama 1 half-sib F2 pedigree on October 10th, 2008. It is the seventh of seven sterile male strobilus samples with tetrad stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 9


title: 28_P_12_Cy3

source_name: Glycolytic muscle, Florida, 28C


title: Namalwa_rep1


title: 12_P_20_Cy5


title: 20_P_12_Cy3

source_name: Glycolytic muscle, Florida, 20C


title: L428-PAX5+M_rep3

value: Mifepristone (M)


title: Raji_rep1


title: Namalwa_rep2


title: L428+M_rep2


title: 20_G_21_Cy5


title: L428-PAX5+M_rep1


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_ms1_mutant_sample4

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 3 derived from Toyama 1 half-sib F2 pedigree on October 19th, 2007. It is the fourth of seven sterile male strobilus samples with tetrad stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 3

value: male strobili with tetrad stage of pollen development


title: L428-PAX5+M_rep2


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_ms1_mutant_sample5

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 6 derived from Toyama 1 half-sib F2 pedigree on October 19th, 2007. It is the fifth of seven sterile male strobilus samples with tetrad stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 6


title: L428+M_rep3


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_ms1_mutant_sample3

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 97 derived from Toyama 1 half-sib F2 pedigree on October 20th, 2006. It is the third of seven sterile male strobilus samples with tetrad stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 97


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_ms1_mutant_sample2

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 17 derived from Toyama 1 half-sib F2 pedigree on October 20th, 2006. It is the second of seven sterile male strobilus samples with tetrad stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 17


title: 12_G_18_Cy3

value: Georgia


title: DCs cultured with IL-27

city: Boston

first: Francisco

last: Quintana

state: MA

address: 77 Ave Louis Pasteur

department: Center for Neurological Diseases

institute: Harvard Medical Institute

description: IL-27-treated DCs.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

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

data_processing:
Data were processed using GeneSpring 11.5 guided work flow. ExonRMA16 - summarization algorithm. Gene level expression were summarized after quantile normalization.
Probe group file: MoEx-1_0-st-v1.r.pgf
Meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: Wild type primary splenic dendritic cells, 8 weeks old, Il-27

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Mouse DCs isolated by flow cytometry from mouse spleen.

extract_protocol: Purified RNA was sent to Expression Analysis (http://www.expressionanalysis.com/) for preparation and hybridization.

treatment_protocol: DCs were treated ON with IL-27 or vehicle.

tag: strain/background

tag: genotype/variation

value: wild type

tag: cell type

value: primary splenic DCs

value: 8 weeks


title: L428+M_rep1

source_name: Hodgkin lymphoma cell line


title: 20_P_19_Cy5

value: Florida


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_ms1_mutant_sample1

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 14 derived from Toyama 1 half-sib F2 pedigree on October 17th, 2006. It is the first of seven sterile male strobilus samples with tetrad stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 14

tag: genotype


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_wild-type_sample7

description: This RNA sample was collected from male strobili of a wild-type individual no. 27 derived from Toyama 1 half-sib F2 pedigree on October 10th, 2008. It is the seventh of seven fertile male strobilus samples with tetrad stage of pollen development.

source_name: Cryptomeria japonica wild-type 27

value: Wild-type

value: normal


title: WT mouse skin treated daily with TPA during 4 days and collected 24 hr later, replicate 3

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

hyb_protocol: Mouse Gene 1.0 ST arrays (Affymetrix) under standard conditions

scan_protocol: Standard Affymetrix protocol

data_processing: Upon microarray hybridization, the raw data was normalized with RMA using RMAexpress software (v.1.0.5).

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 μg/sample) to generated labeled cRNA probes according to the manufacturer’s instructions (Affymetrix).

growth_protocol: This experiment has been done with animals.

extract_protocol: Total cellular RNA was extracted from three independent exponential cultures of the appropriate cell lines using the RNAeasy kit (Qiagen)

treatment_protocol:
Topic administration of TPA or acetone on the dorsal shaved skin of mice before extraction of skin.
WT mouse skin treated daily with TPA (phorbol ester 12-O-tetradecanoylphorbol-13 acetate, 6.8 nmol in 200 μl acetone) during 4 days and collected 24 hr later

tag: strain background

value: FVB

value: whole skin


title: WT mouse skin treated once with TPA and collected 24 hr later, replicate 3

treatment_protocol:
Topic administration of TPA or acetone on the dorsal shaved skin of mice before extraction of skin.
WT mouse skin treated once with TPA (phorbol ester 12-O-tetradecanoylphorbol-13 acetate, 6.8 nmol in 200 μl acetone) and collected 24 hr later


title: DCs cultured with medium

description: Control-treated DCs.

source_name: Wild type primary splenic dendritic cells, 8 weeks old, medium

tag: age

value: vehicle


title: WT mouse skin treated daily with TPA during 4 days and collected 24 hr later, replicate 2


title: WT mouse skin treated daily with TPA during 4 days and collected 24 hr later, replicate 1


title: WT mouse skin treated once with TPA and collected 24 hr later, replicate 2


title: 28_P_12_Cy5


title: 20_P_15_Cy3


title: 20_P_17_Cy5


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_wild-type_sample5

description: This RNA sample was collected from male strobili of a wild-type individual no. 37 derived from Toyama 1 half-sib F2 pedigree on October 16th, 2007. It is the fifth of seven fertile male strobilus samples with tetrad stage of pollen development.

source_name: Cryptomeria japonica wild-type 37


title: 12_P_18_Cy3


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_wild-type_sample6

description: This RNA sample was collected from male strobili of a wild-type individual no. 42 derived from Toyama 1 half-sib F2 pedigree on October 16th, 2007. It is the sixth of seven fertile male strobilus samples with tetrad stage of pollen development.

source_name: Cryptomeria japonica wild-type 42


title: DKO mouse skin treated daily with TPA during 4 days and collected 24 hr later, replicate 3

treatment_protocol:
Topic administration of TPA or acetone on the dorsal shaved skin of mice before extraction of skin.
DKO mouse skin treated daily with TPA (phorbol ester 12-O-tetradecanoylphorbol-13 acetate, 6.8 nmol in 200 μl acetone) during 4 days and collected 24 hr later


title: WT mouse skin treated once with acetone and collected 24 hr later, replicate 1

treatment_protocol:
Topic administration of TPA or acetone on the dorsal shaved skin of mice before extraction of skin.
WT mouse skin treated once with acetone and collected 24 hr later


title: WT mouse skin treated once with TPA and collected 24 hr later, replicate 1


title: DKO mouse skin treated daily with TPA during 4 days and collected 24 hr later, replicate 2


title: DKO mouse skin treated once with TPA and collected 24 hr later, replicate 2

treatment_protocol:
Topic administration of TPA or acetone on the dorsal shaved skin of mice before extraction of skin.
DKO mouse skin treated once with TPA (phorbol ester 12-O-tetradecanoylphorbol-13 acetate, 6.8 nmol in 200 μl acetone) and collected 24 hr later


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_wild-type_sample4

description: This RNA sample was collected from male strobili of a wild-type individual no. 31 derived from Toyama 1 half-sib F2 pedigree on October 16th, 2007. It is the fourth of seven fertile male strobilus samples with tetrad stage of pollen development.

source_name: Cryptomeria japonica wild-type 31


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_wild-type_sample3

description: This RNA sample was collected from male strobili of a wild-type individual no. 973 derived from Toyama 1 half-sib F2 pedigree on October 20th, 2006. It is the third of seven fertile male strobilus samples with tetrad stage of pollen development.

source_name: Cryptomeria japonica wild-type 973


title: 12_P_20_Cy3

source_name: Glycolytic muscle, Florida, 12C


title: WT mouse skin treated once with acetone and collected 24 hr later, replicate 2


title: WT mouse skin treated once with acetone and collected 24 hr later, replicate 3


title: DKO mouse skin treated once with TPA and collected 24 hr later, replicate 1


title: DKO mouse skin treated daily with TPA during 4 days and collected 24 hr later, replicate 1


title: DKO mouse skin treated once with TPA and collected 24 hr later, replicate 3


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_wild-type_sample2

description: This RNA sample was collected from male strobili of a wild-type individual no. 30 derived from Toyama 1 half-sib F2 pedigree on October 20th, 2006. It is the second of seven fertile male strobilus samples with tetrad stage of pollen development.

source_name: Cryptomeria japonica wild-type 30


title: 28_M_13_Cy5

source_name: Glycolytic muscle, Maine, 28C

value: Maine


title: 20_M_13_Cy3

source_name: Glycolytic muscle, Maine, 20C

value: glycolytic muscle


title: 20_M_11_Cy5


title: DKO mouse skin treated once with acetone and collected 24 hr later, replicate 1

treatment_protocol:
Topic administration of TPA or acetone on the dorsal shaved skin of mice before extraction of skin.
DKO mouse skin treated once with acetone and collected 24 hr later


title: DKO mouse skin treated once with acetone and collected 24 hr later, replicate 2


title: Cryptomeria_japonica_male_strobili_pollen_development_TET_wild-type_sample1

description: This RNA sample was collected from male strobili of a wild-type individual no. 25 derived from Toyama 1 half-sib F2 pedigree on October 10th, 2006. It is the first of seven fertile male strobilus samples with tetrad stage of pollen development.

source_name: Cryptomeria japonica wild-type 25


title: 12_M_20_Cy3

source_name: Glycolytic muscle, Maine, 12C


title: Cryptomeria_japonica_male_strobili_pollen_development_MEI_ms1_mutant_sample7

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 13 derived from Toyama 1 half-sib F2 pedigree on October 19th, 2007. It is the seventh of seven sterile male strobilus samples with meiotic stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 13

value: male strobili with meiotic stage of pollen development


title: 20_G_30a_Cy5

source_name: Glycolytic muscle, Georgia, 20C


title: Cryptomeria_japonica_male_strobili_pollen_development_MEI_ms1_mutant_sample6

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 11 derived from Toyama 1 half-sib F2 pedigree on October 16th, 2007. It is the sixth of seven sterile male strobilus samples with meiotic stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 11

value: Toyama ms1 mutant


title: purified adult mouse cardiomyocytes_rep 3

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

country: United Kingdom

institute: Cerevance ltd

description:
replicate 3
CMa_3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using RSN with lumi Bioconductor package (v.2.10.0) in R (v.2.15.3).

source_name: purified adult mouse cardiomyocytes

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

growth_protocol: no growth protocol

extract_protocol: RNA was extracted with Trizol reagent (Invitrogen), following manufacturer instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Diffuse myocardial damage was induced through a single injection (s.c.) of isoproterenol (ISO) to  mice (200mg kg-1).

tag: strain

value: heart

value: Normal adult cardiomyocytes (CMs)

tag: Stage

value: differentiated


title: purified adult mouse cardiomyocytes_rep 2

description:
replicate 2
CMa_2


title: purified myocytes derived by c-kitpos endogenous cardiac stem cells in vitro_rep 1

description:
replicate 1
YfpCM_1

source_name: the c-kitpos cell-derived YFPpos cardiomyocytes


title: purified adult mouse cardiomyocytes_rep 1

description:
replicate 1
CMa_1


title: Cryptomeria_japonica_male_strobili_pollen_development_MEI_ms1_mutant_sample5

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 6 derived from Toyama 1 half-sib F2 pedigree on October 16th, 2007. It is the fifth of seven sterile male strobilus samples with meiotic stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 6

value: male sterile


title: purified c-kitpos endogenous cardiac stem cells_rep 1

description:
replicate 1
c-kitpos eCSCs_1

source_name: c-kitpos eCSCs

value: c-kitpos endogenous cardiac stem cells (eCSCs)

value: undifferentiated


title: purified myocytes derived by c-kitpos endogenous cardiac stem cells in vitro_rep 2

description:
replicate 2
YfpCM_2

value: c-kitpos cell-derived YFPpos cardiomyocytes


title: 20_G_24_Cy5

value: Georgia


title: purified c-kitpos endogenous cardiac stem cells_rep 3

description:
replicate 3
c-kitpos eCSCs_3


title: Cryptomeria_japonica_male_strobili_pollen_development_MEI_ms1_mutant_sample4

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 3 derived from Toyama 1 half-sib F2 pedigree on October 13th, 2007. It is the fourth of seven sterile male strobilus samples with meiotic stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 3


title: GN+Water

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430A 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with protocol FS450_0002.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G Plus.

data_processing: The data were analyzed with the Affymetrix GeneChip Operating System (GCOS) software using the RMA method using Affymetrix default analysis settings.

source_name: whole kidney

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

treatment_protocol: 4 groups of 6 adult mice treated for 9 weeks with Saline injections + oral water, Saline + oral Captopril, Experimentally induced glomerulonephritis (GN) + oral water and GN + Captopril.

value: whole kidney

tag: gender

value: male

value: 17 week


title: GN+Captopril


title: 20_G_15_Cy5


title: Saline+Water


title: Saline+Captopril


title: 12_G_12_Cy3

source_name: Glycolytic muscle, Georgia, 12C


title: 28_G_13_Cy3

source_name: Glycolytic muscle, Georgia, 28C


title: Cryptomeria_japonica_male_strobili_pollen_development_MEI_ms1_mutant_sample3

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 97 derived from Toyama 1 half-sib F2 pedigree on October 17th, 2006. It is the third of seven sterile male strobilus samples with meiotic stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 97

tag: phenotype


title: Cryptomeria_japonica_male_strobili_pollen_development_MEI_ms1_mutant_sample2

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 17 derived from Toyama 1 half-sib F2 pedigree on October 17th, 2006. It is the second of seven sterile male strobilus samples with meiotic stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 17

tag: accession


title: purified myocytes derived by c-kitpos endogenous cardiac stem cells in vitro_rep 3

description:
replicate 3
YfpCM_3


title: 12_G_15_Cy3


title: purified c-kitpos endogenous cardiac stem cells_rep 2

description:
replicate 2
c-kitpos eCSCs_2


title: Cryptomeria_japonica_male_strobili_pollen_development_MEI_ms1_mutant_sample1

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 14 derived from Toyama 1 half-sib F2 pedigree on October 7th, 2005. It is the first of seven sterile male strobilus samples with meiotic stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 14


title: 12_G_20_Cy3


title: 20_G_22_Cy5


title: 12_G_19_Cy3


title: 20_P_18_Cy5

source_name: Glycolytic muscle, Florida, 20C

value: Florida


title: Cryptomeria_japonica_male_strobili_pollen_development_MEI_wild-type_sample6

description: This RNA sample was collected from male strobili of a wild-type individual no. 41 derived from Toyama 1 half-sib F2 pedigree on October 10th, 2007. It is the sixth of seven fertile male strobilus samples with meiotic stage of pollen development.

source_name: Cryptomeria japonica wild-type 41

value: Wild-type

value: normal


title: 12_M_18_Cy5

source_name: Glycolytic muscle, Maine, 12C

value: Maine

value: glycolytic muscle


title: Cryptomeria_japonica_male_strobili_pollen_development_MEI_wild-type_sample4

description: This RNA sample was collected from male strobili of a wild-type individual no. 31 derived from Toyama 1 half-sib F2 pedigree on October 13th, 2007. It is the fourth of seven fertile male strobilus samples with meiotic stage of pollen development.

source_name: Cryptomeria japonica wild-type 31

value: male strobili with meiotic stage of pollen development


title: 5103 female

city: Beijing

first: Yuepeng

last: Song

address: No. 35, Qinghua East Road

institute: Beijing Forestry University

description: Expression data from Andromonoecious poplar female flower

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

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

organism: Populus tomentosa

source_name: female flower of andromonoecious before flowering

growth_protocol: steady natural environment

extract_protocol: Total RNA was extracted using the RNeasy Plant mini kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.

treatment_protocol: No treatment

value: female flower


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_ms1_mutant_sample7

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 13 derived from Toyama 1 half-sib F2 pedigree on September 19th, 2007. It is the seventh of seven sterile male strobilus samples with pre-meiotic stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 13

value: Toyama ms1 mutant

value: male strobili with pre-meiotic stage of pollen development


title: Cryptomeria_japonica_male_strobili_pollen_development_MEI_wild-type_sample2

description: This RNA sample was collected from male strobili of a wild-type individual no. 30 derived from Toyama 1 half-sib F2 pedigree on October 17th, 2006. It is the second of seven fertile male strobilus samples with meiotic stage of pollen development.

source_name: Cryptomeria japonica wild-type 30


title: 5103 male

description: Expression data from Andromonoecious poplar male flower

source_name: male flower of andromonoecious before flowering

value: male flower


title: 20_G_3_Cy5

source_name: Glycolytic muscle, Georgia, 20C


title: Cryptomeria_japonica_male_strobili_pollen_development_MEI_wild-type_sample3

description: This RNA sample was collected from male strobili of a wild-type individual no. 973 derived from Toyama 1 half-sib F2 pedigree on October 13th, 2006. It is the third of seven fertile male strobilus samples with meiotic stage of pollen development.

source_name: Cryptomeria japonica wild-type 973


title: 2-14 female


title: 12_P_17_Cy3

source_name: Glycolytic muscle, Florida, 12C


title: 2-14 male


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_ms1_mutant_sample5

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 6 derived from Toyama 1 half-sib F2 pedigree on September 19th, 2007. It is the fifth of seven sterile male strobilus samples with pre-meiotic stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 6

value: male sterile


title: 28_M_5_Cy3

source_name: Glycolytic muscle, Maine, 28C


title: 20_M_13_Cy5

source_name: Glycolytic muscle, Maine, 20C


title: Cryptomeria_japonica_male_strobili_pollen_development_MEI_wild-type_sample5

description: This RNA sample was collected from male strobili of a wild-type individual no. 37 derived from Toyama 1 half-sib F2 pedigree on October 13th, 2007. It is the fifth of seven fertile male strobilus samples with meiotic stage of pollen development.

source_name: Cryptomeria japonica wild-type 37


title: Cryptomeria_japonica_male_strobili_pollen_development_MEI_wild-type_sample7

description: This RNA sample was collected from male strobili of a wild-type individual no. 42 derived from Toyama 1 half-sib F2 pedigree on October 10th, 2007. It is the seventh of seven fertile male strobilus samples with meiotic stage of pollen development.

source_name: Cryptomeria japonica wild-type 42


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_ms1_mutant_sample6

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 11 derived from Toyama 1 half-sib F2 pedigree on September 19th, 2007. It is the sixth of seven sterile male strobilus samples with pre-meiotic stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 11


title: 12_G_21_Cy5

source_name: Glycolytic muscle, Georgia, 12C


title: 12_M_15_Cy3


title: Cryptomeria_japonica_male_strobili_pollen_development_MEI_wild-type_sample1

description: This RNA sample was collected from male strobili of a wild-type individual no. 26 derived from Toyama 1 half-sib F2 pedigree on October 17th, 2005. It is the first of seven fertile male strobilus samples with meiotic stage of pollen development.

source_name: Cryptomeria japonica wild-type 26


title: C.elegans control sample replicate 3

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

description: Standard affymetrix recommended quality control parameters were used during entire experiment.

hyb_protocol: 10 μg of Biotin end labeled aRNA (amplified RNA) was fragmented and hybridized to the Affymetrix C. elegans GeneChips as recommended by Affymetrix. The quality & quantity of the aRNA probe preparation was assessed before hybridization using an Agilent 2100 bioanalyzer & Nanodrop-1000 spectrophotometer, receptively.

scan_protocol: Affymetrix GeneChip® Command Console (AGCC) software was used for the control of array washing (GeneChip Fluidics Station-450), data acquisition (Scanner 3000-7G), as well as for the preliminary data analysis.

data_processing:
Preprocessing of microarray raw data including probe-specific background correction, summarization of probe set values, and normalization was carried out using the GCRMA algorithm with CARMAweb 1.4, an R and Bioconductor based web service for microarray data analysis (Rainer et al., 2006).
Rainer J, Sanchez-Cabo F, Stocker G, Sturn A, Trajanoski Z (2006). CARMAweb: comprehensive R and Bioconductor based web service for microarray data analysis. Nucleic Acids Res 34:W498–W503

source_name: C.elegans control exposure, replicate 3

label_protocol: 200 ng of total RNA was subjected to aRNA amplification and Biotin labeling as described in the MessageAmpTM Premier RNA Amplification Kit (Ambion) for microarray analysis. aRNA cleanup was achieved using magnetic beads (Ambion).

growth_protocol: Caenorhabditis elegans were exposed (for 48h in liquid medium followed by a further 12h on plates containing nematode growth medium, NGM) to the slow releasing H2S donor drug, GYY4137 (morpholin-4-ium 4 methoxyphenyl (morpholino) phosphinodithioate, 100 uM).

extract_protocol: The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen), modified to include a homogenization step with 0.5 mm glass beads (Sigma) to maximize cell breakage. RNA was subsequently purified using an RNeasy kit (Qiagen) followed by a DNase digestion (Qiagen).

value: larvae (L4)

value: whole animal

value: N2 (Bristol)


title: 568_N.lepida_control_LR

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

description: AID 568, Neotoma lepida, control rabbit chow diet, Lytle Ranch, liver tissue

hyb_protocol: Standard Agilent 1-color gene expression hybridization protocol.

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

data_processing:
Images from scanned arrays were processed with Agilent Feature Extraction software version 10.5.1.1.
Data files were filtered to remove features flagged as nonuniform features or population outliers. Remaining intensity values for each probe were averaged, to yield single value for each unique probe sequence.
Intensity values were log base 2 transformed and normalized by median centering.

organism: Neotoma lepida

label_protocol: Agilent One-Color Quick Amp Labeling Kit

extract_protocol: Ambion RNAqueous (RNA extraction)

treatment_protocol: RNAlater (Sigma)

value: Lytle Ranch

tag: diet

value: control: rabbit chow

value: liver


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_ms1_mutant_sample3

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 17 derived from Toyama 1 half-sib F2 pedigree on September 26th, 2006. It is the third of seven sterile male strobilus samples with pre-meiotic stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 17


title: C.elegans hydrogen sulfide sample replicate 1

source_name: C.elegans hydrogen sulfide exposure, replicate 1

tag: treatment

value: hydrogen sulfide exposure


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_ms1_mutant_sample4

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 3 derived from Toyama 1 half-sib F2 pedigree on September 19th, 2007. It is the fourth of seven sterile male strobilus samples with pre-meiotic stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 3


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_ms1_mutant_sample2

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 97 derived from Toyama 1 half-sib F2 pedigree on September 22th, 2006. It is the second of seven sterile male strobilus samples with pre-meiotic stage of pollen development .

source_name: Cryptomeria japonica ms1 mutant 97


title: C.elegans control sample replicate 2

source_name: C.elegans control exposure, replicate 2


title: 548_N.lepida_control_LR

description: AID 548, Neotoma lepida, control rabbit chow diet, Lytle Ranch, liver tissue

value: female


title: 20_G_30a_Cy3

source_name: Glycolytic muscle, Georgia, 20C

value: Georgia