title: experiment 4 control samples at 51 h 4c51

source_name: experiment 4 control samples at 51 h

value: control


title: DNA infertile 80

status: Public on Oct 01 2012

type: genomic

city: Florence

first: Chiara

last: Chianese

address: viale Pieraccini. 6

country: Italy

institute: Univerity of Florence

description: severe oligozoospermia

hyb_protocol: After sample denaturation and pre-annealing with 5µl of Human Cot-1 DNA (Invitrogen, Carlsbad, CA), hybridization was performed at 65°C with shaking for 24 hours. After two washing steps, the array was analyzed through the Agilent scanner and the Feature Extraction software (v10 1.1.1).

scan_protocol: Scanned on an Agilent G2539A scanner. Images were quantified using Agilent Feature Extraction Software (version 10 1.1.1).

data_processing: Agilent Feature Extraction Software (version 10 1.1.1) was used for background subtraction and LOWESS normalization. Graphical overview was obtained using the DNA Analytics (v4.0.73). All the array experiments were analysed using the ADM-2 algorithm at threshold 5. Text aberration summaries were analyzed to calculate the average log2 ratios of each Copy Number Variation and we considered at least 3 adjacent oligonucleotides needed for a reliable call. The positions of oligomeres refer to the Human Genome March 2006 assembly (hg18).

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA extracted from lymphocytes of an infertile patient

label_protocol: 300ng of test DNA and control DNA  were double-digested with RsaI and AluI (Promega) for 1 hour at 37°C. After digestion, samples were incubated at 65°C for 20 minutes to inactivate the enzymes, then labeled by random priming (Agilent Technologies) for 2 hours using Cy5-dUTP for the test DNA and Cy3-dUTP (Agilent Technologies) for the control DNA. Labeled DNAs were incubated at 65°C for 10 minutes and then purified with Microcon YM-30 filter units (Millipore, Billerica, USA). Every purified sample was brought to a total volume of 9.5µl in 1XTE (pH 8.0, Promega), and yield and specific activity were determined for each sample using a NanoDrop ND-1000 UV-VIS Spectrophotometer (Labtech International LTD). The appropriate cyanine 5- and cyanine 3-labeled samples were combined in a total volume of 16μl.

extract_protocol: Genomic DNA extracted using QIAamp DNA mini kit or Salting out procedure following manufacturer's instructions

tag: gender

value: Male

tag: phenotype

value: severe oligozoospermia

tag: cell type

value: lymphocyte

tag: cnv count

source_name: genomic DNA extracted from lymphocytes of the reference normozoospermic control subject

value: normozoospermic

value: male


title: DNA infertile 76

description: severe oligozoospermia

tag: cnv code


title: experiment 4 control samples at 48 h 4c48

type: RNA

city: Durham

first: Joel

last: Meyer

state: NC

address: Box 90328 LSRC A354

country: USA

institute: Duke University

hyb_protocol: Affymetrix GeneChip Hybridization, Wash protocol (Affymetrix, Santa Clara, CA)

scan_protocol: Affymetrix GeneChip Scan protocol (Affymetrix, Santa Clara, CA)

data_processing: Data were normalized using RMA (quantile normalization) in both Rosetta Resolver and GeneSpring (GX 11). Next, using nonfiltered Rosetta Resolver RMA-normalized data, six samples were excluded from the analysis based on their identification as outliers using PCA: 18630_6C48, 18634_6c51, 18631_6u48, 18636_6u51, 18616_5e48, 15921_7e51. The Matrix spreadsheet contains the data generated by and analyzed in GeneSpring for the remaining 69 samples.

label: biotin

molecule: total RNA

organism: Caenorhabditis elegans

source_name: experiment 4 control samples at 48 h

label_protocol: MessageAmp Premier RNA  Amplification Kit Cat#4385821

growth_protocol: Age-synchronized L1-stage wildtype (N2 Bristol strain) C. elegans were prepared by egg prep and overnight hatch, plated on K agar plates without food (to continue L1 arrest), and after the third UVC exposure placed on K agar plates with a lawn of OP50 bacteria.

extract_protocol: Nematodes were frozen by dripping 3,000-5,000 pelleted nematodes suspended in about 500 μl K-medium into liquid nitrogen, and stored at -80°C. The pellets were ground into fine powder with a liquid nitrogen-cooled mortar and pestle and RNA was extracted using an RNeasy kit (Qiagen, Valencia, CA, USA).

treatment_protocol: The growth-arrested L1 larvae were exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total), or maintained under normal lab light (mostly dark, in incubators). Half of the UVC and no-UVC samples were also exposed to EtBr (5ug/mL in agar). Nematodes were sampled for RNA 3 h after the first UVC dose (3 h), just prior to the second dose (24 h), just prior to the third dose (48 h), and 3 h after the final dose (51 h), which is also 3 h after being placed on food. The entire experiment was repeated 7 times, with a subset of samples (final n = 4-6 per time and treatment) chosen for microarray analysis based on yield and quality of RNA.

tag: tissue

value: pooled whole-body extracts

tag: treatment

tag: time

tag: strain

value: N2 Bristol


title: Patient 9 -Dose 6 -3-hr-blood - mAdbID:107467

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 107467

hyb_protocol: Sample Hybridization Protocol Other: Combine Cy3 and Cy5 labeled target (adjust the color to purple), add 1/10 volume of 10 X fragmentation buffer (Ambion # 8740) and incubate for 15 min at 70 C. Add 3 ul of stop solution (Ambion # 8730) and complete dry the sample by speed vacuum. Add 19 ul of the following mixture to the dried target: 15 ul Kreatech hybridization buffer (Kraetech Diagnostics), 2 ul poly dA (8mg/ml Pharmacia Cat# 27-7988-01) 2 ul yeast tRNA (4mg/ml Sigma Cat# R8759). Incubate for 3 min at 99 C and subsequently add 44.5 ul of the following mixture: 12.5 ul 20X SSC, 2ul 10% SDS, 30 ul formamide. Apply target mixture to array slide, add coverslip, place in humidified hyb chamber, and hybridize at 42C for 20 hrs.

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505B US45103062 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B US45103062, Agilent).

data_processing:
BRB Array Tools Data Processing Protocol
Calculation Method: Gene expression analysis was performed using NCI BRB-Array Tools Version 4.1.0 developed by the NCI Biometric Research Branch (Bethesda, MD). Each array was normalized using a median over the entire array. The data were filtered by intensity>=100 in both channel or override if one channel <100. Spot size>10um. Minimum fold change: less than 5% of expression data values have at least a 1.5 fold change in either direction from the gene median value. Excluded missing values present in less than 50% of samples across the entire data set.
FeatureExtractor_Version: 9.5.1.1
Protocol_Name: GE2-NonAT_95_Feb07 (Read Only)

source_name: Blood Specimen - Dose 6 - 3-hour blood

label_protocol:
Cy5 Labeling Protocol
Other: Sample aRNA was labelled with cy5 using ULS aRNA Fluorescent Labeling kit (Kreatech).

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was extracted using Trizol reagent (Invitrogen or Gibco BRL).

treatment_protocol:
Treatment type: compound
Agent: rIL-2 (Proleukin,®Prometheus Laboratories, San Diego, CA)
Treatment dose: 600,000 International Units/kg (0.037 mg
Treatment time: every 8 hours by a 15-minute intravenous
In-vitro treatment: Patients were hospitalized in a monitored hematology-oncology unit at the University of Virginia Medical Center and received 600,000 International Units/kg (0.037 mg/kg) of rIL-2 (Proleukin,®Prometheus Laboratories, San Diego, CA) every 8 hours by a 15-minute intravenous infusion for a maximum of 14 doses. Following 9 days of rest, the schedule was repeated for up to 14 doses, for a maximum of 28 doses per course, as tolerated. During administration of therapy, doses were frequently withheld for severe toxicity. Patients were medicated with cephalexin, famotidine, ibuprofen and acetaminophen on a scheduled basis to reduce the risk of infection and cytokine-release symptoms.

value: blood

tag: disease state

value: metastatic malignant melanoma

tag: other

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) 3 hours after the sixth dose of rIL-2 to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.

source_name: Pooled Normal Donor PBMC

label_protocol:
Cy3 Labeling Protocol
Other: Reference aRNA was labelled with cy3 using ULS aRNA Fluorescent Labeling kit (Kreatech).

value: Blood

value: PBMC

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.


title: Patient 9 -Pre-therapy Dose 0 -blood - mAdbID:107466

description: mAdb experiment ID: 107466

source_name: Blood Specimen - Pre-therapy - Dose 0

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) pre-therapy to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: experiment 4 UVC- and EtBr-exposed samples at 24 h 4eu24

value: UVC- and EtBr-exposed


title: Patient 8 -Pre-therapy Dose 0 -tumor - mAdbID:107462

description: mAdb experiment ID: 107462

source_name: Tumor Biopsy - Pre-therapy - Dose 0

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained pre-therapy. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


title: DNA infertile 75

description: azoospermia

value: azoospermia


title: Patient 8 -Pre-therapy Dose 0 -blood - mAdbID:107461

description: mAdb experiment ID: 107461


title: experiment 4 control samples at 24 h 4c24

source_name: experiment 4 control samples at 24 h

value: control


title: P514 WM plasma cells_GPL91

city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

description: human peripheral blood B cells  P514 WM plasma cells_GPL91

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

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

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.

label: Biotin

source_name: P514 WM plasma cells_GPL91

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

extract_protocol: RNeasy Mini Kit(50)

tag: P514 WM plasma cells_GPL91


title: W1 WM plasma cells_GPL91

description: human peripheral blood B cells  W1 WM plasma cells_GPL91

source_name: W1 WM plasma cells_GPL91

tag: W1 WM plasma cells_GPL91


title: experiment 4 EtBr-exposed samples at 24 h 4e24

value: EtBr-exposed


title: DNA infertile 72

description: azoospermia

value: Male

value: lymphocyte


title: P541 MM plasma cells_GPL91

description: human peripheral blood B cells  P541 MM plasma cells_GPL91

source_name: P541 MM plasma cells_GPL91

tag: P541 MM plasma cells_GPL91


title: P485 WM plasma cells_GPL91

description: human peripheral blood B cells  P485 WM plasma cells_GPL91

source_name: P485 WM plasma cells_GPL91

tag: P485 WM plasma cells_GPL91


title: Patient 7 -Dose 5 -tumor - mAdbID:107460

description: mAdb experiment ID: 107460

source_name: Tumor Biopsy - Dose 5 - 3 hours later

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained 3 hours after the 5th dose of rIL-2. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


title: experiment 4 UVC-exposed samples at 24 h 4u24

value: pooled whole-body extracts

value: UVC-exposed


title: experiment 4 UVC- and EtBr-exposed samples at 3 h 4eu3

value: 3 h

value: N2 Bristol


title: DNA infertile 74

description: azoospermia

value: normozoospermic

value: male


title: P513 MM plasma cells_GPL91

description: human peripheral blood B cells  P513 MM plasma cells_GPL91

source_name: P513 MM plasma cells_GPL91

tag: P513 MM plasma cells_GPL91


title: DNA infertile 70

description: azoospermia


title: P542 WM plasma cells_GPL91

description: human peripheral blood B cells  P542 WM plasma cells_GPL91

source_name: P542 WM plasma cells_GPL91

tag: P542 WM plasma cells_GPL91


title: Patient 7 -Dose 5 -3-hr-blood - mAdbID:107459

description: mAdb experiment ID: 107459

value: Blood

value: PBMC

source_name: Blood Specimen - Dose 5 - 3-hour blood

value: blood

value: metastatic malignant melanoma

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) 3 hours after the 5th dose of rIL-2 to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: Patient 7 -Pre-therapy Dose 0 -tumor - mAdbID:107458

description: mAdb experiment ID: 107458

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained pre-therapy. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.


title: P445 WM plasma cells_GPL91

description: human peripheral blood B cells  P445 WM plasma cells_GPL91

source_name: P445 WM plasma cells_GPL91

tag: P445 WM plasma cells_GPL91


title: DNA infertile 71

description: severe oligozoospermia

source_name: genomic DNA extracted from lymphocytes of an infertile patient

tag: gender

tag: phenotype

value: severe oligozoospermia


title: experiment 4 EtBr-exposed samples at 3 h 4e3

value: EtBr-exposed


title: experiment 4 UVC-exposed samples at 3 h 4u3

source_name: experiment 4 UVC-exposed samples at 3 h


title: P488 WM plasma cells_GPL91

description: human peripheral blood B cells  P488 WM plasma cells_GPL91

source_name: P488 WM plasma cells_GPL91

tag: P488 WM plasma cells_GPL91


title: DNA infertile 73

description: mild oligozoospermia

value: Male

value: mild oligozoospermia

tag: cell type

value: lymphocyte

tag: cnv count

source_name: genomic DNA extracted from lymphocytes of the reference normozoospermic control subject


title: DNA infertile 69

description: azoospermia

value: azoospermia


title: P326 WM plasma cells_GPL91

description: human peripheral blood B cells  P326 WM plasma cells_GPL91

source_name: P326 WM plasma cells_GPL91

tag: P326 WM plasma cells_GPL91


title: experiment 4 UVC-exposed samples at 48 h 4u48

tag: tissue

value: pooled whole-body extracts

tag: treatment

value: UVC-exposed

tag: time


title: DNA infertile 67

description: mild oligozoospermia

value: normozoospermic


title: DNA infertile 68

description: azoospermia

tag: cnv code

value: male


title: experiment 4 control samples at 3 h 4c3

source_name: experiment 4 control samples at 3 h

value: control

value: 3 h

tag: strain

value: N2 Bristol


title: Patient 7 -Pre-therapy Dose 0 -blood - mAdbID:107457

description: mAdb experiment ID: 107457

source_name: Blood Specimen - Pre-therapy - Dose 0

value: blood

tag: disease state

value: metastatic malignant melanoma

tag: other

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) pre-therapy to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.

source_name: Pooled Normal Donor PBMC

value: Blood

value: PBMC


title: Patient 6 -Pre-therapy Dose 0 -blood -repeat 2 - mAdbID:107452

description: mAdb experiment ID: 107452

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.


title: Patient 6 -Pre-therapy Dose 0 -blood -repeat 1 - mAdbID:107451

description: mAdb experiment ID: 107451


title: P250 MM plasma cells_GPL91

description: human peripheral blood B cells  P250 MM plasma cells_GPL91

source_name: P250 MM plasma cells_GPL91

tag: P250 MM plasma cells_GPL91


title: Patient 5 -Dose 6 -3-hr-blood - mAdbID:107449

description: mAdb experiment ID: 107449

source_name: Blood Specimen - Dose 6 - 3-hour blood

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) 3 hours after the sixth dose of rIL-2 to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: Patient 6 -Dose 8 -tumor - mAdbID:107456

description: mAdb experiment ID: 107456

scan_protocol: Scan_MicronsPerPixelX: 10 Scan_MicronsPerPixelY: 10 Scan_ScannerName: Agilent Technologies Scanner G2505B US45103062 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B US45103062, Agilent).

source_name: Tumor Biopsy - Dose 8 - 3 hours later

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained 3 hours after the 8th dose of rIL-2. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


title: P251 MM plasma cells_GPL91

description: human peripheral blood B cells  P251 MM plasma cells_GPL91

source_name: P251 MM plasma cells_GPL91

tag: P251 MM plasma cells_GPL91


title: experiment 2 UVC- and EtBr-exposed samples at 51 h  2eu51

value: UVC- and EtBr-exposed


title: experiment 2 control samples at 51 h  2c51

source_name: experiment 2 control samples at 51 h


title: P124 MM plasma cells_GPL91

description: human peripheral blood B cells  P124 MM plasma cells_GPL91

source_name: P124 MM plasma cells_GPL91

tag: P124 MM plasma cells_GPL91


title: Patient 6 -Dose 7 -3-hr-blood - mAdbID:107454

description: mAdb experiment ID: 107454

source_name: Blood Specimen - Dose 7 - 3-hour blood

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) 3 hours after the seventh dose of rIL-2 to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: experiment 2 EtBr-exposed samples at 51 h  2e51

value: pooled whole-body extracts

value: EtBr-exposed


title: P120 MM plasma cells_GPL91

description: human peripheral blood B cells  P120 MM plasma cells_GPL91

source_name: P120 MM plasma cells_GPL91

tag: P120 MM plasma cells_GPL91


title: P122 MM plasma cells_GPL91

description: human peripheral blood B cells  P122 MM plasma cells_GPL91

source_name: P122 MM plasma cells_GPL91

tag: P122 MM plasma cells_GPL91


title: experiment 1 EtBr-exposed samples at 51 h  1e51


title: P121 MM plasma cells_GPL91

description: human peripheral blood B cells  P121 MM plasma cells_GPL91

source_name: P121 MM plasma cells_GPL91

tag: P121 MM plasma cells_GPL91


title: experiment 1 UVC-exposed samples at 51 h  1u51

value: UVC-exposed


title: DNA infertile 63

description: azoospermia

source_name: genomic DNA extracted from lymphocytes of an infertile patient

tag: gender

value: Male

tag: phenotype

value: azoospermia

value: lymphocyte

value: normozoospermic

value: male


title: P008 MM plasma cells_GPL91

description: human peripheral blood B cells  P008 MM plasma cells_GPL91

source_name: P008 MM plasma cells_GPL91

tag: P008 MM plasma cells_GPL91


title: experiment 1 UVC- and EtBr-exposed samples at 51 h  1eu51

value: N2 Bristol


title: DNA infertile 64

description: azoospermia

tag: cell type

tag: cnv count

source_name: genomic DNA extracted from lymphocytes of the reference normozoospermic control subject


title: DNA infertile 61

description: azoospermia


title: DNA infertile 66

description: mild oligozoospermia

value: mild oligozoospermia


title: DNA infertile 65

description: severe oligozoospermia

value: severe oligozoospermia


title: DNA infertile 62

description: azoospermia


title: experiment 1 control samples at 51 h  1c51

source_name: experiment 1 control samples at 51 h

tag: tissue

tag: treatment

value: control


title: Patient 8 -Dose 6 -3-hr-blood - mAdbID:107463

description: mAdb experiment ID: 107463

value: blood

value: metastatic malignant melanoma

value: Blood

value: PBMC

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.


title: Patient 5 -Pre-therapy Dose 0 -blood - mAdbID:107447

description: mAdb experiment ID: 107447

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) pre-therapy to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: P006 MM plasma cells_GPL91

description: human peripheral blood B cells  P006 MM plasma cells_GPL91

source_name: P006 MM plasma cells_GPL91

tag: P006 MM plasma cells_GPL91


title: P002 MM plasma cells_GPL91

description: human peripheral blood B cells  P002 MM plasma cells_GPL91

source_name: P002 MM plasma cells_GPL91

tag: P002 MM plasma cells_GPL91


title: Patient 4 -Pre-therapy Dose 0 -blood - mAdbID:107443

description: mAdb experiment ID: 107443

source_name: Blood Specimen - Pre-therapy - Dose 0

tag: disease state

source_name: Pooled Normal Donor PBMC


title: experiment 1 UVC- and EtBr-exposed samples at 48 h  1eu48

value: pooled whole-body extracts

value: UVC- and EtBr-exposed

tag: time

tag: strain


title: BrdU_WT_MMS_60_min

city: Montpellier

first: Philippe

last: Pasero

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics - CNRS

hyb_protocol: DNA was hybridized to the Affymetrix GeneChip® S. cerevisiae Tiling 1.0R Array (P/N. 900645) following the manufacturer's protocol.

scan_protocol: Tiling arrays were scanned with the GeneChip scanner 3000 7G.

data_processing:
Signals were normalized with TAS 1.1.02 (Affymetrix) using quantile normalisation. Analysis results were stored in log2 scale for signal intensity and in -10Log10 for p-values. Probe signals were analysed using perfect matches only with a bandwidth of 300. P-value intervals were generated using the following parameters: cutoff: 10-5, max gap: 80 and min run: 40. Significant intervals were scored as active origins when signal intensity was above a threshold arbitrarily determined as 50% of the signal range and when BrdU tracks were larger than 1 kb. Replication profiles (signal log ratio) were displayed with IGB 6.1. BrdU peaks overlapping with replication origins referenced in OriDB were scored with Galaxy. BrdU peaks that overlap with repetitive sequences such as transposons and subtelomeric repeats were not used in this study.

Signal bar files generated for each ChIP are expressed in log2 (IP/Input) ratio for signal intensity.

organism: Saccharomyces cerevisiae W303

source_name: BrdU-IP from wild-type cells in 0.1% MMS 60 min

label_protocol: 7.5 µg of amplified DNA was fragmented and labelled using the GeneChip WT Double-Stranded DNA Terminal Labelling kit (Affymetrix, PN 900812) following the manufacturer's recommendations.

growth_protocol: Cells were cultured in YPD, synchronized in G1 using alpha-factor at 25°C and then released into S phase (16°C), or at 25°C in the presence of HU, MMS or nocodazole.

extract_protocol: For immunoprecipitation of BrdU-labelled DNA, 1.5x10^9 cells were lysed for 5 x 2 minutes in NIB buffer (17 % glycerol, 50 mM MOPS buffer, 150mM potassium acetate, 2 mM magnesium chloride, 500 µM spermidine and 150 µM spermine, pH7.2) with Zirconium beads on a Vibrax (VXR basic, Ika) at 4°C. DNA was isolated using the Qiagen Genomic DNA extraction kit and sonicated to reach an average DNA size of 300-600 bp. For each immunoprecipitation, 10 µl of mouse anti-BrdU IgG1 (BDBioscience 555627, lot: 07461) was prebound to Dynabeads M-280 Sheep anti-mouse IgG (Invitrogen 112.02) and added to the denatured purified DNA.

treatment_protocol: Samples were taken either in S phase + 200 mM HU (hydroxyurea) or 0.1% MMS (methyl methanesulfonate) or taken in G2-arrested cells with 7.5ug/ml nocodazole.

tag: genotype

value: wild-type

tag: antibody

value: mouse anti-BrdU IgG1

tag: antibody vendor

value: BD Biosciences

tag: antibody catalog #

tag: antibody lot #

source_name: Input DNA from wild-type cells


title: BrdU_rad50sch_60_min

source_name: BrdU-IP from rad50sch cells in HU 60 min

value: rad50sch mutant


title: B35 WM B cells_GPL91

description: human peripheral blood B cells  B35 WM B cells_GPL91

source_name: B35 WM B cells_GPL91

tag: B35 WM B cells_GPL91


title: B34 WM B cells_GPL91

description: human peripheral blood B cells  B34 WM B cells_GPL91

source_name: B34 WM B cells_GPL91

tag: B34 WM B cells_GPL91


title: experiment 1 EtBr-exposed samples at 48 h  1e48

value: EtBr-exposed


title: DNA infertile 58

description: azoospermia

tag: gender

value: Male

tag: phenotype

value: azoospermia

value: lymphocyte

value: normozoospermic

value: male


title: B33 WM B cells_GPL91

description: human peripheral blood B cells  B33 WM B cells_GPL91

source_name: B33 WM B cells_GPL91

tag: B33 WM B cells_GPL91


title: P001 MM plasma cells_GPL91

description: human peripheral blood B cells  P001 MM plasma cells_GPL91

source_name: P001 MM plasma cells_GPL91

tag: P001 MM plasma cells_GPL91


title: DNA infertile 60

description: azoospermia

tag: cell type

tag: cnv count


title: B32 WM B cells_GPL91

description: human peripheral blood B cells  B32 WM B cells_GPL91

source_name: B32 WM B cells_GPL91

tag: B32 WM B cells_GPL91


title: experiment 1 UVC-exposed samples at 48 h 1u48

tag: tissue

tag: treatment

value: UVC-exposed

value: N2 Bristol


title: BrdU_rad50C687G_60_min

source_name: BrdU-IP from rad50C687G cells in HU 60 min

tag: strain

value: rad50C687G mutant


title: Patient 3 -Pre-therapy Dose 0 -blood -repeat 2 - mAdbID:107438

description: mAdb experiment ID: 107438

value: blood

tag: disease state

value: metastatic malignant melanoma

tag: other

value: Blood

value: PBMC

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.


title: Patient 1 -Dose 6 -3-hr-blood - mAdbID:107428

description: mAdb experiment ID: 107428

source_name: Blood Specimen - Dose 6 - 3-hour blood

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) 3 hours after the sixth dose of rIL-2 to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: Patient 2 -Pre-therapy Dose 0 -blood -repeat 1 - mAdbID:107430

description: mAdb experiment ID: 107430

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) pre-therapy to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: DNA infertile 56

description: azoospermia

source_name: genomic DNA extracted from lymphocytes of an infertile patient

tag: cnv code


title: DNA infertile 55

description: azoospermia

source_name: genomic DNA extracted from lymphocytes of the reference normozoospermic control subject


title: DNA infertile 53

description: azoospermia


title: Patient 3 -Dose 6 -3-hr-blood -repeat 1 - mAdbID:107441

description: mAdb experiment ID: 107441


title: Patient 3 -Pre-therapy Dose 0 -blood -repeat 1 - mAdbID:107437

description: mAdb experiment ID: 107437


title: Patient 2 -Dose 6 -3-hr-blood - mAdbID:107433

description: mAdb experiment ID: 107433


title: experiment 1 control samples at 48 h  1c48

source_name: experiment 1 control samples at 48 h

value: pooled whole-body extracts

value: control

tag: time


title: BrdU_rad50delta_60_min

source_name: BrdU-IP from rad50delta cells in HU 60 min

tag: genotype

value: rad50delta mutant

tag: antibody

value: mouse anti-BrdU IgG1

tag: antibody vendor

value: BD Biosciences

tag: antibody catalog #

tag: antibody lot #

value: wild-type


title: DNA infertile 54

description: azoospermia

tag: gender

value: Male

tag: phenotype

value: azoospermia

value: lymphocyte

value: normozoospermic

value: male


title: DNA infertile 57

description: azoospermia

tag: cell type


title: DNA infertile 59

description: azoospermia

tag: cnv count


title: Patient 1 -Pre-therapy Dose 0 -tumor - mAdbID:107427

description: mAdb experiment ID: 107427

source_name: Tumor Biopsy - Pre-therapy - Dose 0

value: blood

value: metastatic malignant melanoma

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained pre-therapy. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


title: B31 WM B cells_GPL91

description: human peripheral blood B cells  B31 WM B cells_GPL91

source_name: B31 WM B cells_GPL91

tag: B31 WM B cells_GPL91


title: Rad50_WT_G2_60_min

source_name: Rad50-HA6 ChIP from wild-type cells in nocodazole 120 min

extract_protocol: For chromatin immunoprecipitation (Rad50-HA6 and Scc1-PK9), 1X10^9 cells were lysed using a Multi-Beads Shocker (MB400U, YASUI KIKAI, Osaka) in Lysis Buffer (50 mM HEPES-KOH pH7.5, 140 mM Nacl, 1 mM EDTA, 1% TritonX-100, 0.1% Na-deoxycholate, 1X protease Inhibitors and 1 mM PMSF). Extracts were sonicated using a Bioruptor to reach an average DNA size of 300-600 bp. Protein A Dynabeads were coupled to anti-PK (MCA1360, AbD serotec, lot: 1009A) or anti-HA (F-7: sc-7392, Santa Cruz, lot: E1910) antibodies.

tag: chip antibody

value: anti-HA (F-7)

value: Santa Cruz


title: DNA infertile 52

description: azoospermia


title: BrdU_WT_Sphase_16°C

source_name: BrdU-IP from wild-type cells in S phase, 70 min at 16°C


title: Rad50_WT_HU_60_min

source_name: Rad50-HA6 ChIP from wild-type cells in HU 60 min

source_name: Input DNA from wild-type cells


title: B28 WM B cells_GPL91

description: human peripheral blood B cells  B28 WM B cells_GPL91

source_name: B28 WM B cells_GPL91

tag: B28 WM B cells_GPL91


title: Scc1_rad50sch_60_min

source_name: Scc1-PK9 ChIP from rad50sch cells in HU 60 min

tag: strain

value: rad50sch mutant

value: anti-PK

value: AbD Serotec

source_name: Input DNA from rad50delta cells


title: B30 WM B cells_GPL91

description: human peripheral blood B cells  B30 WM B cells_GPL91

source_name: B30 WM B cells_GPL91

tag: B30 WM B cells_GPL91


title: Scc1_rad50C687G_60_min

source_name: Scc1-PK9 ChIP from rad50C687G cells in HU 60 min

value: rad50C687G mutant

value: rad50delta mutant


title: Patient 1 -Pre-therapy Dose 0 -blood - mAdbID:107426

description: mAdb experiment ID: 107426

source_name: Blood Specimen - Pre-therapy - Dose 0

tag: tissue

tag: disease state

tag: other

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) pre-therapy to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.

source_name: Pooled Normal Donor PBMC

value: Blood

value: PBMC

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.


title: Scc1_rad50delta_60_min

source_name: Scc1-PK9 ChIP from rad50delta cells in HU 60 min

tag: genotype


title: DNA infertile 51

description: azoospermia

source_name: genomic DNA extracted from lymphocytes of an infertile patient

value: Male

value: azoospermia

value: lymphocyte

source_name: genomic DNA extracted from lymphocytes of the reference normozoospermic control subject


title: Scc1_WT_MMS_60_min

source_name: Scc1-PK9 ChIP from wild-type cells in 0.1% MMS 60 min

value: wild-type


title: B24 WM B cells_GPL91

description: human peripheral blood B cells  B24 WM B cells_GPL91

source_name: B24 WM B cells_GPL91

tag: B24 WM B cells_GPL91


title: B04 WM B cells_GPL91

description: human peripheral blood B cells  B04 WM B cells_GPL91

source_name: B04 WM B cells_GPL91

tag: B04 WM B cells_GPL91


title: B11 WM B cells_GPL91

description: human peripheral blood B cells  B11 WM B cells_GPL91

source_name: B11 WM B cells_GPL91

tag: B11 WM B cells_GPL91


title: B15 WM B cells_GPL91

description: human peripheral blood B cells  B15 WM B cells_GPL91

source_name: B15 WM B cells_GPL91

tag: B15 WM B cells_GPL91


title: B23 WM B cells_GPL91

description: human peripheral blood B cells  B23 WM B cells_GPL91

source_name: B23 WM B cells_GPL91

tag: B23 WM B cells_GPL91


title: Testes_Germ Cell-Specific Sin3a Hemizygous_rep 1

city: Chicago

first: Christopher

middle: J.

last: Payne

address: 2430 N. Halsted St.

institute: Northwestern University Feinberg School of Medicine

description: Gene expression in total testicular tissue of a mouse containing one functional Sin3a allele in the germ cells at postnatal day 0

hyb_protocol: Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit. 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours at 65 degrees C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Scanned on an Agilent G2565AA scanner Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1)

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization

organism: Mus musculus

source_name: whole testes, Vasa-cre;Sin3a<deleted/+> mice (HEMI), biological replicate 1

label_protocol: For the linear T7-based amplification step, 100 ng of each total RNA sample was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: Total RNA extracted using the Rneasy Mini Kit (Qiagen) following the manufacturer's protocol.

tag: gender

value: male

tag: age

value: Postnatal Day 0

value: whole testis

value: FVB.129/Sv mixed

tag: genotype/variation

value: Sin3a hemizygous (HEMI)


title: DNA infertile 47

description: azoospermia

tag: phenotype

tag: cell type

tag: cnv count

value: normozoospermic


title: DNA infertile 46

description: azoospermia

tag: cnv code


title: DNA infertile 45

description: azoospermia


title: Testes_Sin3a Wild Type_rep 2

description: Gene expression in total testicular tissue of a mouse containing two functional Sin3a alleles in all cells at postnatal day 0

source_name: whole testes, Vasa-cre;Sin3a<+/+> mice (WT), biological replicate 2

tag: strain

value: Vasa-cre;Sin3a<+/+> (WT)


title: Scc1_h2aS129A_HU_60_min

source_name: Scc1-PK9 ChIP from h2aS129A cells in HU 60 min

value: h2aS129A mutant

tag: chip antibody

value: anti-PK

tag: antibody vendor

value: AbD Serotec

tag: antibody catalog #

tag: antibody lot #


title: DNA infertile 49

description: azoospermia


title: DNA infertile 50

description: azoospermia


title: Testes_Germ Cell-Specific Sin3a Hemizygous_rep 2

source_name: whole testes, Vasa-cre;Sin3a<deleted/+> mice (HEMI), biological replicate 2

tag: tissue


title: DNA infertile 48

description: azoospermia


title: Testes_Germ Cell-Specific Sin3a KO_rep 2

description: Gene expression in total testicular tissue of a mouse lacking two functional Sin3a alleles in the germ cells at postnatal day 0

source_name: whole testes, Vasa-cre;Sin3a<deleted/floxed> mice (VSKO), biological replicate 2


title: Scc1_mec1_tel1_sml1_HU_60_min

source_name: Scc1-PK9 ChIP from mec1 tel1 sml1 cells in HU 60 min

tag: genotype

value: mec1 tel1 sml1 mutant

source_name: Input DNA from rad50delta cells

value: rad50delta mutant


title: B7 tonsil B cells_GPL91

description: human peripheral blood B cells  B7 tonsil B cells_GPL91

source_name: B7 tonsil B cells_GPL91

tag: B7 tonsil B cells_GPL91


title: Testes_Sin3a Wild Type_rep 1

source_name: whole testes, Vasa-cre;Sin3a<+/+> mice (WT), biological replicate 1


title: Testes_Germ Cell-Specific Sin3a KO_rep 1

source_name: whole testes, Vasa-cre;Sin3a<deleted/floxed> mice (VSKO), biological replicate 1


title: Scc1_mec1_sml1_HU_60_min

source_name: Scc1-PK9 ChIP from mec1 sml1 cells in HU 60 min

value: mec1 sml1 mutant


title: Scc1_WT_HU_60_min, rep2

description:
Control for MT027_IP* Scc1 ChIPs.
MT027_IPA

source_name: Scc1-PK9 ChIP from wild-type cells in HU 60 min


title: B6 tonsil B cells_GPL91

description: human peripheral blood B cells  B6 tonsil B cells_GPL91

source_name: B6 tonsil B cells_GPL91

tag: B6 tonsil B cells_GPL91


title: Scc1_WT_G2 after HU

source_name: Scc1-PK9 ChIP from wild-type cells in G2 cells realeased from HU


title: Scc1_WT_Sphase_16°C

source_name: Scc1-PK9 ChIP from wild-type cells in S phase, 70 min, 16°C


title: B25 tonsil B cells_GPL91

description: human peripheral blood B cells  B25 tonsil B cells_GPL91

source_name: B25 tonsil B cells_GPL91

tag: B25 tonsil B cells_GPL91


title: Scc1_WT_HU_60_min, rep1

description:
Control for non-MT027_IP* Scc1 ChIPs.
MT002_IPA


title: B19 tonsil B cells_GPL91

description: human peripheral blood B cells  B19 tonsil B cells_GPL91

source_name: B19 tonsil B cells_GPL91

tag: B19 tonsil B cells_GPL91


title: DNA infertile 44

description: azoospermia

source_name: genomic DNA extracted from lymphocytes of an infertile patient

tag: gender

value: Male

source_name: genomic DNA extracted from lymphocytes of the reference normozoospermic control subject


title: DNA infertile 43

description: azoospermia

value: azoospermia


title: DNA infertile 42

description: azoospermia

value: lymphocyte


title: Lung_M. tuberculosis infected_10weeks_sample 2

city: New Delhi

first: Anil

middle: K

last: Tyagi

state: Delhi

address: Benito Juarez Road

department: Biochemistry

country: India

institute: University of Delhi South Campus

description: Gene expression in guinea pig lungs at 10 weeks post-M. tuberculosis infection

hyb_protocol: 1650ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software v 10.7 of Agilent and Normalized using Agilent GeneSpring GX v 11.5 software. The normalization performed is 75^th percentile shift Normalization.

organism: Cavia porcellus

source_name: M. tuberculosis infected_10weeks_Guine pig Lung 2

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: Total RNA was isolated from tissues by using Qiagen Total RNA Isolation Rneasy Mini kit as per the manufacturer’s instructions.

treatment_protocol: Guinea pigs were aerosol infected with M. tuberculosis, lungs were harvested from infected and un-infected guinea pigs at 10 weeks post-infection and stored in RNA later for RNA isolation.

tag: infection

value: Mycobacterium tuberculosis

value: Lung

value: Female

value: Dunkin Hartley


title: Lung_M. tuberculosis infected_10weeks_sample 1

source_name: M. tuberculosis infected_10weeks_Guine pig Lung 1


title: Lung_M. tuberculosis infected_10weeks_sample 3

source_name: M. tuberculosis infected_10weeks_Guine pig Lung 3


title: B18 tonsil B cells_GPL91

description: human peripheral blood B cells  B18 tonsil B cells_GPL91

source_name: B18 tonsil B cells_GPL91

tag: B18 tonsil B cells_GPL91


title: B17 tonsil B cells_GPL91

description: human peripheral blood B cells  B17 tonsil B cells_GPL91

source_name: B17 tonsil B cells_GPL91

tag: B17 tonsil B cells_GPL91


title: DNA infertile 40

description: azoospermia

tag: phenotype

tag: cell type

tag: cnv count

value: male


title: peripheral blood B cells 6_GPL91

description: human peripheral blood B cells  peripheral blood B cells 6_GPL91

source_name: peripheral blood B cells 6_GPL91

tag: peripheral blood B cells 6_GPL91


title: DNA infertile 41

description: azoospermia

tag: cnv code


title: B16 tonsil B cells_GPL91

description: human peripheral blood B cells  B16 tonsil B cells_GPL91

source_name: B16 tonsil B cells_GPL91

tag: B16 tonsil B cells_GPL91


title: AH6 HPC_Rat Old

city: Marseille

first: PABAN

last: Veronique

address: 3 place V. Hugo

institute: Aix-Marseille Universite

description: Gene expression in hippocampus of LOU/C/Jall rat at 26 months old

hyb_protocol: Hybridization was performed in a hybridization oven at 65◦C for 17 hr  at 10rpm into SurePrint G3 Rat GE microarray slides (8×60K G4853A, Agilent Technologies, Santa Clara, CA) containing 60,000 oligonucleotide probes.

scan_protocol: Hybridized microarray slides were then washed according to manufacturer’s instructions and scanned using an AgilentMicroarray Scanner, using the Agilent Feature Extraction Software (Agilent Technologies).

data_processing: Quantification files derived from the Agilent Feature Extraction Software were analyzed using the AgiND package (http://tagc.univmrs.fr/AgiND). We also used the AgiND R package for quality control and normalization. Quantile methods and a background correction were used for data normalization.

organism: Rattus norvegicus

source_name: Hippocampus old LOU/C/Jall rat

label_protocol: Sample amplification and labeling followed the one-color microarray-based gene expression analysis (low input quick amp labeling) protocol (version 6.5, May 2010) recommended by Agilent Technologies.  In brief, 100 ng of each total RNA sample was reverse transcribed into cDNA using oligo dT-T7 promoter primer. Labeled cRNA was synthesized from the cDNA. The reaction was performed in a solution containing dNTP mix, cyanine 3-dCTP, and T7 RNA Polymerase, and incubated at 40◦C for 2 hr. Qiagen’s RNeasy mini spin columns are used for purification of the amplified cRNA samples. cRNA are quantited using NanoDrop Spectrophotometer version 3.2.1. 600ng of cyanine 3-labeled, linearly amplified cRNA are used for hybrization.

extract_protocol: Hippocampus and frontal cortex tissues were homogenized and purified with mirVana miRNA Kit (AB Applied-Ambion, France) according to the manufacturer’s protocol.

treatment_protocol: Rats were anesthetized with isoflurane (5% in N2O/O2 (2/1)), decapitated, and the brain was removed. Hippocampus and frontal cortex were dissected out in 2 hemi-structures and immediately frozen in liquid nitrogen.

tag: strain

value: LOU/C/Jall

value: brain

tag: brain region

value: hippocampus

tag: age

value: 26 months


title: DNA infertile 39

description: azoospermia

value: normozoospermic


title: Scc1_WT_G2_nocodazole

source_name: Scc1-PK9 ChIP from wild-type cells in nocodazole 120 min

tag: genotype

value: wild-type

tag: chip antibody

value: anti-PK

tag: antibody vendor

value: AbD Serotec

tag: antibody catalog #

tag: antibody lot #

source_name: Input DNA from rad50delta cells


title: AA4 CF_Rat Young

description: Gene expression in frontal cortex of LOU/C/Jall rat at 5 months old

source_name: Frontal cortex young LOU/C/Jall rat

tag: tissue

value: frontal cortex

tag: gender

value: 5 months


title: DNA infertile 37

description: azoospermia

value: Male

value: azoospermia


title: peripheral blood B cells 7_GPL91

description: human peripheral blood B cells  peripheral blood B cells 7_GPL91

source_name: peripheral blood B cells 7_GPL91

tag: peripheral blood B cells 7_GPL91


title: AI4 CF_Rat Old

description: Gene expression in frontal cortex of LOU/C/Jall rat at 26 months old

source_name: Frontal cortex old LOU/C/Jall rat


title: Z6 HPC_Rat Young

description: Gene expression in hippocampus of LOU/C/Jall rat at 5 months old

source_name: Hippocampus young LOU/C/Jall rat


title: AB4 CF_Rat Young


title: 6DTon

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

description: 16S rRNA genes are PCR amplified from DNA extracts using 16S rRNA universal forward and reverse primers and labeled via incorporation of Cy3-dCTP in a second nested PCR.

hyb_protocol: Prior to hybridization, slides were blocked with sodium borohydride (NaBH4, 1X PBS, 99% ethanol) in order to reduce unreactive aldehyde groups, thus minimizing the fluorescent background. Fourteen microliter of each labeled and purified PCR sample were mixed with 6 µl of hybridization buffer containing 2X SSC, 0.2 µg/µl yeast tRNA, 0.1% SDS, and heated for 5 minutes at 100C. After that, 10 µl of each solution were loaded slowly at one corner and under the cover slip, allowing capillary action to pull the solution over the array. Slides were then placed on incubation racks in a humidified chamber, and hybridization was then performed at 55C for 16 h in a microarray incubator. Slides were removed from the hybridization chamber and sunk into a water bath containing a washing solution (2X SSC, 10%SDS, at 55C) to remove the cover slips. The slides were washed using an automated microarray robotic instrument. A washing program was set up as follow: one washing in buffer (2X SSC, 10%SDS) at 55C for 2 minutes, a second washing in 2X SSC buffer at room temperature for 2 minutes, and a final washing in 0.1X SSC buffer at room temperature for 2 minutes. Once the slides are finished spinning in the centrifuge, they were removed and placed in a light-proof container until scanning.

scan_protocol: The microarray slides are scanned using an Axon 4000B scanner and crude data is extracted using GenePix Pro software. Data are normalized by comparing individual signal intensities to the average of signals from universal probes.

data_processing: Individual probe spot net intensity was calculated by subtracting the foreground intensity (F532) with background intensity (B532); intensity was set to 1 if net intensity is <1 or signal to noise ratio (F532/B532) < 2; between-the-array signal normalization was done based on mean universal 16S sequence probe intensities; signals were also scaled to be within the same minimal and maximal intensities range across arrays; normalized and scaled intensities of the same probe sequence were then averaged. The averaged unique probe intensities were then raised to the power of 0.3 and then converted to ordinal numbers on a 0-5 scale, with 0=not detected and 1 to 5 reflect increasing signal strength. For detail analysis procedure see: http://bioinformatics.forsyth.org/homim

source_name: oral sample

label_protocol: Two separate PCR reactions were set up with, respectively, forward primer 5'-CCA GAG TTT GAT YMT GGC-3' with reverse primer 5'-GAA GGA GGT GWT CCA RCC GCA -3', and forward primer 5'-GAC TAG AGT TTG ATY MTG GC-3' with reverse primer 5'-GYT ACC TTG TTA CGA CTT-3'. Two µl of genomic DNA template were added to the reaction mixture (final volume 25 µl) containing 20 pmol of each primer, 40 nmol of deoxytriphosphates, 1.5 mM Mg2+ and 1 U of Platinum High Fidelity Taq polymerase (Invitrogen, San Diego, CA). The samples were preheated at 94°C for 2 min, followed by 32 cycles of amplification under the following conditions: 94°C for 30 s, 55°C for 30 s, and 68°C for 1.5 min, with an additional 1 s for each cycle. A final 10 min elongation step at 68°C was added. The results of the PCR amplification were examined by electrophoresis in a 1% agarose gel. The two parallel PCR reactions were combined and the products purified with QIAquick PCR Purification Kit (Qiagen).Purified PCR products were labeled via the incorporation of Cy3-dCTP during a second reaction. Briefly, 7 μL of each product were added into a 25 μL reaction mixture containing 15 pmol of the forward primer 9F (5'-GAGTTTGATYMTGGCTCAG-3') , 5 pmol of the 1492R primer , 2.5 μL 10•X high fidelity PCR buffer, 2 mM MgSO4, 2.5 μL of deoxynucleotide triphosphate mixture without deoxycytidine triphosphate (10 mM, 0.2 mM final concentration of each deoxynucleotide), 2.5 μL of deoxycytidine triphosphate mixture (1 μL of 1 mM Cy3-dCTP + 4 μL of 2 mM dCTP, 0.2 mM final concentration), 0.25 μL 10% Triton X, and 1.25 U Taq polymerase. The PCR program included an initial denaturation step at 94C for 2 minutes, followed by 40 cycles of denaturation at 94oC for 30s, annealing at 55C for 30s, elongation at 68C for 1.5 minute with an additional 1 s for each cycle, and a final elongation step at 68C for 10 minutes.

growth_protocol: None; DNA was extracted directly from clinical samples

extract_protocol: Bacterial DNA was eluted from saliva that had been collected using a sterile oral suction device, supragingival plaque using sterile applicator, tongue and buccal brushing using a sterile cytotbrush respectively, per patient at each specimen collection time. Plaque, and tongue and buccal brushings were placed in 150 microliter of TE buffer. Genomic DNA was extracted using the Epicenter Masterpure Kit for DNA Extraction (Epicentre Biotechnologies, Madison, Wisconsin).

tag: time of specimen collection

value: after transplant

tag: sample type

value: tongue brushing

tag: developed respiratory signs/symptoms (rss) or no rss

value: RSS


title: 6DP

treatment_protocol: None; DNA was extracted directly from clinical samples

value: plaque


title: 6DS

value: saliva


title: 6DBuc

value: buccal brushings


title: DNA infertile 38

description: azoospermia

source_name: genomic DNA extracted from lymphocytes of an infertile patient

tag: phenotype

tag: cell type

value: lymphocyte

tag: cnv count

value: male


title: AG4 CF_Rat Old

tag: strain

value: LOU/C/Jall

value: brain

value: 26 months


title: DNA infertile 36

description: azoospermia

tag: cnv code

source_name: genomic DNA extracted from lymphocytes of the reference normozoospermic control subject

value: normozoospermic


title: peripheral blood B cells 5_GPL91

description: human peripheral blood B cells  peripheral blood B cells 5_GPL91

source_name: peripheral blood B cells 5_GPL91

tag: peripheral blood B cells 5_GPL91


title: DNA infertile 35

description: azoospermia


title: peripheral blood B cells 4_GPL91

description: human peripheral blood B cells  peripheral blood B cells 4_GPL91

source_name: peripheral blood B cells 4_GPL91

tag: peripheral blood B cells 4_GPL91


title: 6CP


title: 6BTon


title: Y4 CF_Rat Young

tag: brain region

tag: age


title: peripheral blood B cells 3_GPL91

description: human peripheral blood B cells  peripheral blood B cells 3_GPL91

source_name: peripheral blood B cells 3_GPL91

tag: peripheral blood B cells 3_GPL91


title: peripheral blood B cells 2_GPL91

description: human peripheral blood B cells  peripheral blood B cells 2_GPL91

source_name: peripheral blood B cells 2_GPL91

tag: peripheral blood B cells 2_GPL91


title: DNA infertile 34

description: severe oligozoospermia

value: severe oligozoospermia


title: peripheral blood B cells 1_GPL91

description: human peripheral blood B cells  peripheral blood B cells 1_GPL91

source_name: peripheral blood B cells 1_GPL91

tag: peripheral blood B cells 1_GPL91


title: DNA infertile 33

description: azoospermia

tag: gender


title: 6AP

value: before transplant


title: 6AS


title: DNA infertile 32

description: azoospermia


title: AA6 HPC_Rat Young

tag: tissue

value: hippocampus

value: 5 months


title: DNA infertile 31

description: azoospermia

value: Male

value: azoospermia


title: 6BBuc

tag: time of specimen collection

value: after transplant


title: Z4 CF_Rat Young

value: frontal cortex


title: AI6 HPC_Rat Old


title: PPM0 NS

city: Maastricht

first: Danitsja

last: van Leeuwen

address: PO Box 616

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

hyb_protocol: Agilent whole genome human 4x44k microarray

scan_protocol: ScanArrayExpress scanner (Perkin Elmer, Boston, MA) with a fixed laser power and a variable photomultiplier gain, such that no spots were saturated

data_processing: Raw data extraction from scanes in ImaGene version 7.0.0 (BioDiscorvery) and data preprocessing in GeneSight (BioDiscovery) where background correction, log2 transformation and LOWESS normalisation have been conducted. VALUES in data table represent LOWESS normalized log2 tranformed differences (smoker or non-smoker minus common reference).

source_name: non-smoker blood

label_protocol: Agilent Low RNA Input Linear Amplification system

extract_protocol: Total RNA extracted from blood with PAXgene Blood RNA kit accoridng to manufacturer's instructions

treatment_protocol: Blood collection into PAXgene Blood RNA tubes, mixing and storage

value: blood

tag: smoking status

value: non-smoker

source_name: smoker blood

value: common reference smoker (pool of RNA from all smokers (n=22) in the study)


title: DNA infertile 30

description: azoospermia

value: lymphocyte


title: PP26 NS


title: AG6 HPC_Rat Old

source_name: Hippocampus old LOU/C/Jall rat

value: male


title: AB6 HPC_Rat Young

value: LOU/C/Jall


title: AF6 HPC_Rat Old

value: brain


title: PPC0 NS


title: DNA infertile 27

description: azoospermia


title: AF4 CF_Rat Old

value: 26 months


title: 6BP

tag: sample type

value: plaque

tag: developed respiratory signs/symptoms (rss) or no rss

value: RSS


title: PPD0 NS


title: 6ABuc

value: before transplant

value: buccal brushings


title: 31CTongue

value: tongue brushing


title: 31I1Tongue


title: Lung_Normal_Uninfected control

description: Gene expression in lungs of normal uninfected guine pig

source_name: Normal_Uninfected guinea pig lung

tag: infection

value: Uninfected control

value: Lung

value: Female

value: Dunkin Hartley


title: 31I1Buccal

value: after transplant


title: PPL0 NS

value: blood

value: non-smoker


title: DNA infertile 26

description: azoospermia

value: Male

tag: phenotype

value: azoospermia

tag: cell type

value: lymphocyte

tag: cnv count

value: normozoospermic


title: PPH0 NS

value: common reference smoker (pool of RNA from all smokers (n=22) in the study)


title: PP19 NS


title: AH4 CF_Rat Old

tag: strain

value: LOU/C/Jall

value: brain

value: frontal cortex

value: male

value: 26 months


title: DNA infertile 25

description: azoospermia

tag: cnv code


title: Y6 HPC_Rat Young

tag: brain region

value: hippocampus

value: 5 months


title: 31CSaliva

value: saliva

value: RSS


title: DNA infertile 28

description: severe oligozoospermia

value: severe oligozoospermia


title: 31ATongue

value: before transplant

value: tongue brushing


title: DNA infertile 29

description: azoospermia

value: Male


title: 31I1Plaque

value: after transplant

value: plaque


title: PP23 NS

value: blood

value: non-smoker


title: DNA infertile 24

description: azoospermia

value: azoospermia

value: lymphocyte

value: normozoospermic


title: PP17 NS

value: common reference smoker (pool of RNA from all smokers (n=22) in the study)


title: 31ASaliva1


title: 31CBuccal

value: buccal brushings


title: PP24 NS


title: DNA infertile 22

description: azoospermia

value: male


title: DNA infertile 23

description: azoospermia


title: DNA infertile 21

description: azoospermia


title: 31ABuccal


title: 18CTon

value: No RSS


title: 18CS

value: saliva


title: DNA infertile 20

description: azoospermia


title: DNA infertile 18

description: severe oligozoospermia


title: PPG0 NS


title: 31APlaque

value: RSS


title: 18CBuc


title: UCD 153 24h 3

city: Davis

first: Douglas

middle: D

last: Risser

state: California

address: One Shields Ave

department: Microbiology

institute: UC Davis

hyb_protocol: Two micrograms of labled cDNA were prepared for hybridization using the Nimblegen hybridization kit and sample tracking controls and hybridized to a Nimblegen 12x135k slide fitted with an HX12 mixer at 42C on a Nimblegen Hybridization System 4 hybridizer for 16-20h.

scan_protocol: Following hybridization slides were washed with Nimblegen wash buffer and scanned using a GenePix 4000B scanner using GenePix Pro-6.0 software (Molecular Devices).

data_processing: Scanned images (.tif) were imported into NimbleScan software (NimbleGen) where the image containing all 12 arrays on each slide was separated into 12 individual image files.  An automatic alignment was performed for each individual array and X, Y, and Signal files (.xys) were generated.  Normalization of .xys files was performed using the R package oligo (Carvalho et al, 2007. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 8:485-489) and the R package oneChannelGUI (Sanges et al, 2007. oneChannelGUI: A graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language. Bioinformatics 23:2406-3408) was used to compute a linear model fit and contrasts to generate top tables containing the change in expression between experimental and reference data points as M-values (Log2[experimental]-log2[reference]) along with statistical information such as p-, adjusted p- and B-values.  All data and statistical analyses were computed from three independent biological replicates.  Contrasts were computed for the patN-deletion strain using the wild-type strain as a reference at each time point (i.e. the ∆patN strain t = 3 h - wild type t = 3 h) (∆patN -wild type contrast) as well as for each time point using t = 0 of the same strain as a reference (i.e. the ∆patN strain t = 3 h – the ∆patN strain t = 0h) (∆patN or wild type time course contrast).  Differential expression of genes with B-values > 0 was considered statistically significant.  Heat maps were generated using Genesis (Sturn et al, 2002. Genesis: Cluster analysis of microarray data. Bioinformatics 18:207-208) with the M-values from top tables for each time point.

organism: Nostoc punctiforme PCC 73102

label_protocol: Ten micrograms  of total RNA were used for cDNA synthesis using SuperScript Double Stranded cDNA Synthesis Kit (Invitrogen). 0.5 ug of cDNA was labled with Cy3 dye using the Nimblegen One-color DNA labeling kit.

growth_protocol: Nostoc punctiforme strains were cultured in Allan and Arnon medium diluted four fould (AA/4), as previously described (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256) with the exception that cultures were supplemented with 30mM fructose.

extract_protocol: RNA extractions were performed as previously described with a bead beater and phenol (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256).

treatment_protocol: For nitrogen step-down culutres supplemented with 2.5 mM NH4Cl at a chlorophyl a concentration of 2-3 ug/ml were harvested at 1000xg for 5 min, washed 3x with AA/4 and resuspended in AA/4.

tag: genotype/variation

value: wild type


title: DNA infertile 16

description: severe oligozoospermia

value: severe oligozoospermia


title: UCD 524 24h 3

value: patN-deletion


title: PPE0 NS


title: UCD 153 120h 3


title: PP13 NS


title: DNA infertile 19

description: azoospermia

value: Male


title: UCD 524 120h 3


title: UCD 524 18h 3


title: DNA infertile 17

description: azoospermia


title: PP16 NS


title: PPB0 NS


title: PP12 NS


title: DNA infertile 14

description: azoospermia


title: PPA0 NS


title: PP7 NS


title: DNA infertile 15

description: azoospermia


title: PP10 NS


title: DNA infertile 13

description: azoospermia


title: DNA infertile 12

description: azoospermia


title: 18CP

value: after transplant


title: 18BTon

value: tongue brushing


title: 18BS


title: 18BP

value: plaque


title: 18BBuc


title: UCD 524 12h 3


title: UCD 153 18h 3


title: 18ATon

value: before transplant


title: UCD 153 12h 3


title: 18AP


title: 18ABuc


title: PP3 NS

value: blood

value: non-smoker


title: UCD 153 6h 3


title: UCD 524 6h 3


title: DNA infertile 11

description: mild oligozoospermia

value: mild oligozoospermia

value: lymphocyte

value: normozoospermic


title: DNA infertile 8

description: azoospermia

value: azoospermia

value: male


title: DNA infertile 9

description: azoospermia


title: UCD 153 3h 3


title: DNA infertile 10

description: azoospermia


title: DNA infertile 7

description: severe oligozoospermia


title: UCD 524 3h 3


title: PP1 NS

value: common reference smoker (pool of RNA from all smokers (n=22) in the study)


title: UCD 524 1h 3


title: 17DP

value: RSS


title: PP25 S

value: smoker


title: 17BTon


title: PPM1 S


title: DNA infertile 6

description: azoospermia


title: PP5 NS


title: PPD1 S


title: 17BS

value: saliva


title: UCD 524 0h 3

value: patN-deletion


title: 17BP


title: jhd2 antisense signals associated with CDSs and 500bp UP and DOWN

city: Toronto

first: Mengshu

last: Xu

state: ON

address: 1 King's College Circle

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: SK1 background

hyb_protocol: Affymetrix arrays were washed and biotin-labelled RNA was hybridized overnight at 45°C rotating at 65rpm. The array was then washed and stained using Affy fluidics stations.

scan_protocol: Affymetrix scanner 3000 7G

data_processing:
Cross-quantile normalization and median centering was done with Tiling Analysis Software (TAS).
Log2 transformed values.  In each spreadsheet, the column headers represent coordinates (in bp) relative to CDSs. Columns "-500" to"-25" and "25" to "500" represent signal from regions flanking CDSs. "CDS 1...20" columns represents signal associated with CDSs that have been scaled into 20 bins.  Note that antisense signals for each CDS are in the reverse orientation to the coding orientation of that gene.

organism: Saccharomyces cerevisiae

source_name: terminally sporulated cells

label_protocol: Biotin labelling with TdT

growth_protocol: Standard budding yeast sporulation protocols

extract_protocol: RNA was prepared by bead beating cell pellets (Mini Bead beater, Biospec Products)  for 4 x 2.5 minutes in Trizol (Invitrogen) with 5 min incubations on ice between cycles. After addition of chloroform and phase separation, RNA was further purified by extraction with acidic phenol at 65°C for 30 min.

treatment_protocol: 50 O.D. pellets were collected and flash frozen in liquid nitrogen.

value: SK1 background

tag: sporulation timepoint


title: DNA infertile 5

description: severe oligozoospermia

value: Male

value: severe oligozoospermia


title: 17BBuc

value: after transplant

value: buccal brushings


title: UCD 153 1h 3

value: wild type


title: jhd2 sense signals associated with CDSs and 500bp UP and DOWN

description: SK1 background


title: PPC1 S

value: blood


title: 17ATon

value: before transplant

value: tongue brushing


title: UCD 153 0h 3


title: DNA infertile 4

description: severe oligozoospermia

value: lymphocyte

value: normozoospermic


title: PPL1 S


title: WT antisense signals associated with CDSs and 500bp UP and DOWN

description: SK1 background


title: UCD 524 24h 2


title: PP22 S


title: DNA infertile 3

description: severe oligozoospermia

value: male


title: WT sense signals associated with CDSs and 500bp UP and DOWN

description: SK1 background


title: DNA infertile 2

description: azoospermia

value: azoospermia


title: UCD 153 24h 2


title: DNA infertile 1

description: azoospermia


title: UCD 524 120h 2


title: UCD 153 120h 2


title: PP18 S

value: common reference smoker (pool of RNA from all smokers (n=22) in the study)


title: PP20 S

value: smoker


title: PPH1 S


title: jhd2 Sporulation timepoint 16h

hyb_protocol: 5ug of mononucleosomal DNA was hybridized per array.

data_processing: Cross-quantile normalization and median centering was done with Tiling Analysis Software (TAS)

source_name: sporulating cells

label_protocol: Mono-nucleosomal DNA was DNase I digested to 50-90bp fragments, then end labelled with biotin.

extract_protocol: Crosslinked cell pellets were lysed by first sonication using a Diagenode Bioruptor for two cycles of 15min with a 15min rest on ice. For samples from 8h of sporulation or later, cells were then vortexed for 1h at 4°C. This was followed by bead beating for 7 cycles of 1 min with 2 min rests on ice. Mononucleosomal DNA was prepared from these extracts as described in Lee et al. 2007 "A high-resolution atlas of nucleosome occupancy in yeast"

treatment_protocol: 200 O.D. pellets were collected at each timepoint, crosslinked with methanol-free formaldehyde at 1% for 15min at room temperature. Crosslinking reaction was quenched by adding Glycine to 125mM for 10 min. Cells were washed twice with PBS buffer and flash frozen in liquid nitrogen.

tag: timepoint


title: jhd2 Sporulation timepoint 12h


title: PP15 S


title: 17ABuc

value: RSS


title: 16BS

value: saliva


title: PP21 S


title: 16AP

value: plaque


title: 16AS


title: jhd2 Sporulation timepoint 10h

value: SK1 background


title: jhd2 Sporulation timepoint 8h


title: jhd2 Sporulation timepoint 6h


title: 16ABuc


title: jhd2 Sporulation timepoint 4h


title: 15CS

value: No RSS


title: jhd2 Sporulation timepoint 0h


title: UCD 524 18h 2

value: patN-deletion


title: 15CP

value: after transplant


title: UCD 153 12h 2

value: wild type


title: UCD 524 6h 2


title: UCD 153 18h 2


title: UCD 524 12h 2


title: UCD 524 3h 2


title: PPE1 S

value: blood


title: PPB1 S


title: PP14 S


title: UCD 153 6h 2


title: PPG1 S


title: PPA1 S


title: jhd2 Vegetative cells in YPD media

source_name: Vegetative cells

value: Vegetative log phase


title: PP11 S


title: 15BTon

value: tongue brushing


title: 15BS


title: WT Sporulation timepoint 16h

value: WT


title: UCD 153 3h 2


title: WT Sporulation timepoint 12h


title: PP8 S


title: 15BP


title: PP9 S


title: PP6 S


title: WT Sporulation timepoint 10h


title: PP4 S


title: UCD 153 1h 2


title: 15ATon

value: before transplant


title: 15BBuc

value: buccal brushings


title: WT Sporulation timepoint 8h


title: WT Sporulation timepoint 6h


title: PP2 S


title: 15AS


title: UCD 153 120h 1


title: WT Sporulation timepoint 0h


title: UCD 524 1h 2


title: UCD 524 120h 1


title: 15ABuc


title: 14CS


title: 16ATon


title: WT Vegetative cells in YPD media


title: UCD 524 24h 1


title: 14CP


title: WT Sporulation timepoint 4h


title: UCD 153 24h 1


title: UCD 524 0h 2


title: UCD 153 0h 2


title: 15AP


title: Comparison B_Deep CV vs Surface female_rep5

city: Groton

first: Ebru

last: Unal

state: CT

address: 1080 Shennecossett Road

department: Department of Marine Sciences

institute: University of Connecticut

hyb_protocol: Printed slides were pre-hybridized following the manufacturer’s instructions (Pronto Microarray Hybridization Kit, Corning). After addition of the hybridization buffer (Pronto, Corning), the samples were loaded into slides and incubated in a MAUI Hybridization Chamber (BioMicro) overnight at 42ºC for ~15 hours.

scan_protocol: The slides were scanned by using Genepix Pro Ver. 4.1 (Molecular Devices, Union City, CA) scanner with AutoPMT setting. At the completion of each scan, images were visually checked to align the features in a specific block to their appropriate location on a deconvolution file.

data_processing: The normalization, quality control and gene filtering of the microarray data were performed by using Acuity 4.0 Microarray Informatics Software (Molecular Devices, Inc.). The Lowess normalization (with data centering) was performed for individual slides by using print-tip (block-by-block) normalization, with a smoothing factor of 0.4 for 4 iterations (Yang et al. 2002). The Lowess normalized median Log2 ratios of the individual dye intensities were used for subsequent analysis. Following normalization of each slide, pre-processing of the microarrays was performed, including the spot quality analysis and array scaling.

label: Alexa Fluor 647

organism: Calanus finmarchicus

source_name: Deep copepodite-5 (CV) stages

label_protocol: Fluorescently labeled cDNA was generated using SurperScriptTM Plus Direct cDNA Labeling System (Invitrogen). First-strand cDNA synthesis was performed on samples using SuperScript III RT and labeled using Alexa Fluor 647-aha-dUTP nucleotide with red fluorescent emission.

extract_protocol: RNeasy Mini Kit (Qiagen) following the instructions of the manufacturer, with a final elution volume of 30 µl.

treatment_protocol: Stratified samples were collected in April 17, 2008 from Wilkinson Basin in the Gulf of Maine. Live identified copepods were individually frozen in liquid nitrogen. 9-10 female individuals were pooled for subsequent RNA extraction.

tag: Stage

value: Copepodite-5 (CV)

tag: location

value: Whole copepod, multiple individuals pooled

label: Alexa Fluor 555

source_name: Adult surface females

label_protocol: Fluorescently labeled cDNA was generated using SurperScriptTM Plus Direct cDNA Labeling System (Invitrogen). First-strand cDNA synthesis was performed on samples using SuperScript III RT and labeled using Alexa Fluor 555-aha-dUTP nucleotide with green fluorescent emission.

value: Female

value: Surface 0-30m


title: UCD 524 18h 1


title: 14BTon

source_name: oral sample


title: HKC CONTROL

city: Taichung City

first: Hong-Lin

last: Su

address: 250, Kuo-Kuang Rd

department: Department of Life Sciences

country: Taiwan

institute: National Chung Hsing University

description: Gene expression data from human keratinocytes with DMSO

hyb_protocol: Following fragmentation, 20 micrograms of mRNA from each sample was used in each array (Human Gene 2.0 ST Array, Affymetrix) by the Affymetrix Gene Expression Service Lab at Academic Sinica, Taiwan

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000.

data_processing: The data were analyzed with Expression Console RMA default settings.

source_name: human primary keratinocytes treated with DMSO

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: human primary keratincoytes were cultured with KSF medium with epithelical cell growth factor and bovine pituitary glad extracts

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.The quality of RNA was carefully evaluated by the electrophoresis and Bioanalyzer 2100

treatment_protocol: The cells were treated with 0.1 mcroM BIO for 6 days at a cell density of 5000 cells/ml

value: human primary keratiocytes

tag: treatment

value: DMSO

tag: passages


title: K562_rep2

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

institute: Memorial University of Newfoundland

description: Gene expression data from cell lines K562

hyb_protocol: A total of 2.5µg of labelled cDNA, along with GeneChip Hybridization Control reagents (Affymetrix), was injected into an Affymetrix GeneChip Human Gene 1.0 ST Array. The chips were incubated for 18 hours at 45oC and rotated at 60rpm to allow hybridization. The chips were then washed and stained using GeneChip Hybridization Wash and Stain Kit (Affymetrix) using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affimetrix GeneChip Scanner GCS 3000 with the GeneChip Operating software version 1.4.0.036

data_processing: CEL files were RMA normalized using R/bioconductor

source_name: K562 cell lines

label_protocol: Gene expression array analysis was performed using Affymetrix GeneChip Human Gene 1.0ST Array system (Affymetrix, Santa Clara, CA) according to manufacturer’s instructions. Briefly, for each sample, 200ng of total RNA in a volume of 5µl was amplified using the Applause WT Amp ST, RNA Amplification System (NuGen, San Carlos, CA) and labelled with Encore Biotin Module, Post–Amplification System (NuGen).

growth_protocol: Cells were grown in DMEM supplemented with 10%FBS, at 37 °C in a humidified atmosphere with 5% CO2

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

tag: cell line


title: hES_H1_rep2

description: Gene expression data from cell lines hES_H1

source_name: hES_H1 cell lines


title: K562_rep1


title: UCD 153 18h 1


title: hES_H1_rep1


title: Comparison B_Deep CV vs Surface female_rep4

tag: tissue


title: 14BS

tag: time of specimen collection

tag: sample type

value: saliva

tag: developed respiratory signs/symptoms (rss) or no rss


title: UCD 524 12h 1


title: Lips3_rep2

description: Gene expression data from cell lines Lips3

source_name: Lips3 cell lines


title: 14BP

value: plaque

value: No RSS


title: Lips3_rep1


title: Comparison B_Deep CV vs Surface female_rep3


title: Comparison B_Deep CV vs Surface female_rep2


title: 14ATon


title: 14AS


title: Comparison B_Deep CV vs Surface female_rep1


title: Lips1_rep2

description: Gene expression data from cell lines Lips1

source_name: Lips1 cell lines


title: Comparison A_Deep female vs Surface female_rep4

source_name: Adult deep females


title: Comparison A_Deep female vs Surface female_rep5


title: UCD 524 6h 1

value: patN-deletion


title: 14AP


title: 14ABuc


title: Comparison A_Deep female vs Surface female_rep3


title: 14BBuc

value: after transplant


title: UCD 153 6h 1

value: wild type


title: UCD 153 12h 1


title: UCD 524 3h 1


title: UCD 153 3h 1


title: 13CTon


title: UCD 524 1h 1


title: 13CS


title: Lips1_rep1


title: UCD 153 1h 1


title: HKC BIO

description: Gene expression data from human keratinocytes with BIO

source_name: human primary keratiocytes treated with BIO

tag: cell type

value: BIO


title: Dicer-null ES-WT-DICER1 R5

city: Vancouver

first: Michael

middle: S

last: Anglesio

state: BC

department: Obstetrics and Gynecology

institute: University of British Columbia

hyb_protocol: All samples were processed with the GeneChip WT terminal labeling and hybridization protocol in conjunction with the Ambion WT expression kit according the manufacturers instructions.

scan_protocol: standard Affymetrix protocol

data_processing: RMA (Partek Genomics Suite v6.6)

source_name: Dicer-/- ES cells

growth_protocol: All cells were maintained in ES cell media (as described in Calabrese et al. Proc Natl Acad Sci U S A. 2007 Nov 13;104(46):18097-102.), 37C incubator with 5% CO2 and collected in log phase growth

extract_protocol: Qiagen miRNeasy kit

value: ES cell

tag: genotype

value: Dicer-/-

tag: vector

value: pLD-puro-PGKnvA

tag: group

value: wildtype DICER1

tag: transgene


title: Comparison A_Deep female vs Surface female_rep1

hyb_protocol: Printed slides were pre-hybridized following the manufacturer’s instructions (Pronto Microarray Hybridization Kit, Corning). After addition of the hybridization buffer (Pronto, Corning), the samples were loaded into slides and incubated in a MAUI Hybridization Chamber (BioMicro) overnight at 42ºC for  ~15 hours.

label_protocol: Fluorescently labeled cDNA was generated using SurperScriptTM Plus Direct cDNA Labeling System (Invitrogen). First-strand cDNA synthesis was performed on samples using SuperScript III RT and labeled using Alexa Fluor 555-aha-dUTP  nucleotide with green fluorescent emission.


title: UCD 524 0h 1

tag: genotype/variation


title: 13CP


title: Dicer-null ES-WT-DICER1 R6

label_protocol: All samples were processed with the GeneChip WT terminal labeling and hybridization protocol in conjunction with the Ambion WT expression kit according the manufacturers instructions.


title: Comparison A_Deep female vs Surface female_rep2


title: 13BTon

value: tongue brushing


title: Dicer-null ES-WT-DICER1 R4

value: pLD-puro-ENvA


title: Dicer-WT ES R1

source_name: Dicer+/+ ES cells

value: Dicer+/+

value: control (Dicer1-wildtype)


title: Dicer-WT ES R2


title: 13BS


title: 13BP


title: Dicer-null ES-WT-DICER1 R3


title: UCD 153 0h 1


title: 13ATon

value: before transplant


title: Dicer-null ES-WT-DICER1 R2


title: Dicer-null ES-DICER1-E1813Q R2

value: hotspot mutant

value: DICER1  E1813Q


title: Hypothalamus_non-heat stress_rep4

city: Beijing

first: hongyan

last: sun

address: Poultry genetic group, College of Animal Science and Technology, China Agricultural Univeristy, Yuanmingyuan West Rd. No. 2, Haidian District, Beijing, China

country: China

institute: Iowa State University

description: gene expression of non-infected spleens from controls

hyb_protocol: Arrays were incubated at 65C for 17h in Agilent’s microarray hybridization chambers and subsequently washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, US) and Stabilization and Drying Solution (Agilent Technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US) with default settings, Scan resolution=5μm, PMT 100%, 10%

data_processing: Raw data were normalized by Quantile algorithm by Gene Spring Software 11.0. The quality of features was also determined by Gene Spring Software 11.0 (Agilent Technologies, Santa Clara, CA, US). Features were deemed absent when not positive and significant or not above background. Features were deemed marginal when not uniform or if saturated or a population outlier. Features that were not absent or marginal were deemed present. P value and fold change in each comparison was calculated for each gene.

organism: Gallus gallus

source_name: non-heat stress hypothalamus from controls, replicate4

label_protocol: Two ug total RNA were reverse transcribed into cDNA. The synthesized cDNA was transcribed into cRNA labelled with cyanine 3-labelled nucleotide. Labelled cRNA was purified with QIAGEN RNeasy® Mini Kit (Qiagen, Valecia, CA), and the same amount (875 ng) of Cy3 labeled cRNA probes were hybridized on 44K chicken Agilent arrays

extract_protocol: Total RNA was isolated using TRIZOL Reagent according to manufacturer’s instruction (Life Technologies, Carlsbad, CA, US). The RNA quantity and purity were determined by NanoDrop ND-1000 spectrophotometer at 260/280 nm. The integrity of total RNA was assessed with an Agilent Bioanalyzer 2100. The RNA Integrity Numbers (RINs) for the samples were obtained. All the RNA samples showed 7.6 or higher RIN values and 28S/18S > 1.5, indicating sufficient quality to be used for microarray.

treatment_protocol: Twelve 56 day full-sib or half-sib female broilers Anak_40, were randomly divided into three groups including control group (CL), heat treated group (HS) and temperature recovery group (TR) with  four birds in each group. All the chickens were initially reared in an artificial climate chamber (humidity 40%-60%) with free access to food and water at 25C. Both the heat treated group and temperature recovery group were subjected to 34C for 24h when the chickens were at age of 56 day. After heat stress, four heat treated hens were dissected for hypothalamus. The four chickens in temperature recovery group were further provided the normal temperature at 25C for 24h after exposed to heat, and then the hypothalamus was collected.

value: spleen

tag: gender

value: male

tag: age

tag: infection/resistance status

value: non-infected spleens from controls


title: Dicer-null ES-WT-DICER1 R1


title: Hypothalamus_non-heat stress_rep3

source_name: non-heat stress hypothalamus from controls, replicate3


title: 13AS

value: saliva

value: No RSS


title: Dicer-null ES-DICER1-E1813Q R1


title: severe_Cp, biological rep2

city: Ghent

first: Stefanie

last: De Bodt

address: Technologiepark 927

country: Belgium

institute: VIB/UGent

description: Gene expression data of a developing Brachypodium leaf grown in soil under severe drought stress regimen

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on a custom Affymetrix Brachypodium Tiling array followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: apt-probeset-summarize

organism: Brachypodium distachyon

source_name: Brachypodium leaf 3, proliferation zone, severe drought stress

label_protocol: Samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.

growth_protocol: After harvest, Bd21 seeds were air-dried and stored at room temperature for two weeks. Then they were transferred to 4°C for at least two weeks, before being used for experiments. After manual removal of palea and lemma, the seeds were placed loosely on wet soil. Sealed with micropore tape the plates were incubated at 4°C for two days, in darkness. Subsequently, the plates were transferred to a growth room, with 16 hours of light (120µmol-2 s-1 photosynthetically active radiation), at 24°C and 55% relative humidity.  When the first leaf was about 3 cm in length, individual plantlets were carefully transferred to small plastic pots (5.5 cm diameter, 5 cm high), which contained an equal amount of soil (Beroepspotgrond, Saniflor), to which a controlled volume of water had been added. At the time of plantlet transfer all pots contained 2.27 g water per g dry soil. Plants were harvested at a fixed time point in the afternoon, about 24 hours after the emergence of leaf 3. The growing leaf 3 – between 1.5 and 2 cm in size at that point – was carefully removed from the leaf sheath of the older two leaves, without damaging the fragile meristem at its base.

extract_protocol: Samples were immediately stored in RNA-Later solution (Ambion, Austin, Texas). After overnight incubation at 4°C the leaves were dissected into three distinct developmental zones with a sharp razor blade. Based on microscopic observations we defined the proliferation zone as the first 2 mm from the leaf base, the expansion zone as the next 4 mm, and the mature zone as the remaining distal part of the leaf. The leaf zones were immediately frozen at -80°C, and stored until RNA isolation could be performed. Total RNA was isolated using the RNeasy Plant Mini Kit protocol (Qiagen, Hilden, Germany). RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA.

treatment_protocol: Pots containing control plants were dried down to 1.82 g g-1, while pots containing plants that would be subjected to drought stress were dried down to 0.73 g g-1 (moderate drought) or 0.45 g g-1 (severe drought). Pot weight was monitored on a daily basis to compensate for evaporation, and water was added only after the target weight had been reached. Two to three days later the second leaf emerged in a highly reproductive manner, and another three days later the third leaf appeared.

value: leaf

tag: developmental zone

value: proliferation

tag: stress

value: severe drought stress


title: Hypothalamus_non-heat stress_rep2

source_name: non-heat stress hypothalamus from controls, replicate2


title: severe_Cp, biological rep1


title: Hypothalamus_non-heat stress_rep1

source_name: non-heat stress hypothalamus from controls, replicate1


title: 13AP

value: plaque


title: 13ABuc

value: buccal brushings


title: 12CTon

value: after transplant

value: tongue brushing


title: Hypothalamus_temperature recovery_rep4

description: gene expression of resistant spleens from MDV-infected chickens

source_name: temperature recovery hypothalamus from temperature recovery chickens, replicate4


title: severe_Cm, biological rep3

source_name: Brachypodium leaf 3, mature zone, severe drought stress

value: mature


title: severe_Cp, biological rep3


title: Dicer-null ES-DICER1-D1810Y R2

value: ES cell

value: Dicer-/-

value: pLD-puro-ENvA

value: DICER1 D1810Y


title: Hypothalamus_temperature recovery_rep2

source_name: temperature recovery hypothalamus from temperature recovery chickens, replicate2

value: spleen

value: resistant spleens from MDV-infected chickens


title: 12CS

source_name: oral sample


title: 12CP


title: Hypothalamus_temperature recovery_rep1

source_name: temperature recovery hypothalamus from temperature recovery chickens, replicate1

value: male


title: Dicer-null ES-DICER1-E1705K R2

value: hotspot mutant

value: DICER1 E1705K


title: severe_Ce, biological rep3

source_name: Brachypodium leaf 3, expansion zone, severe drought stress

value: leaf

value: expansion


title: Hypothalamus_temperature recovery_rep3

source_name: temperature recovery hypothalamus from temperature recovery chickens, replicate3


title: severe_Ce, biological rep2

value: severe drought stress


title: severe_Cm, biological rep1


title: 12CBuc

value: No RSS


title: Dicer-null ES-DICER1-E1705K R1


title: Dicer-null ES-DICER1-D1810Y R1


title: Hypothalamus_heat stress_rep4

description: gene expression of susceptible spleens from MDV-infected chickens

source_name: heat stress hypothalamus from heat stress chickens, replicate4


title: Dicer-null ES-DICER1-E1705K R3


title: severe_Cm, biological rep2


title: Dicer-null ES-DICER1-D1810Y R3


title: Hypothalamus_heat stress_rep2

source_name: heat stress hypothalamus from heat stress chickens, replicate2

value: susceptible spleens from MDV-infected chickens


title: 12BTon

description: 16S rRNA genes are PCR amplified from DNA extracts using 16S rRNA universal forward and reverse primers and labeled via incorporation of Cy3-dCTP in a second nested PCR.

value: after transplant


title: Dicer-null ES-DICER1-D1709N R2

value: pLD-puro-PGKnvA

value: DICER1 D1709N


title: severe_Ce, biological rep1


title: Dicer-null ES-DICER1-D1709N R1

value: ES cell


title: mild_Bp,biological rep2

description: Gene expression data of a developing Brachypodium leaf grown in soil under mild drought stress regimen

source_name: Brachypodium leaf 3, proliferation zone, mild drought stress

value: proliferation

value: mild drought stress


title: 12BS

value: saliva


title: 12BP

value: plaque


title: Hypothalamus_heat stress_rep1

source_name: heat stress hypothalamus from heat stress chickens, replicate1

value: spleen


title: mild_Bm, biological rep2

source_name: Brachypodium leaf 3, mature zone, mild drought stress

value: mature


title: Hypothalamus_heat stress_rep3

source_name: heat stress hypothalamus from heat stress chickens, replicate3

value: male


title: Dicer-null ES-DICER1-D1709A R4

source_name: Dicer-/- ES cells

value: Dicer-/-

value: pLD-puro-ENvA

value: hotspot mutant

value: DICER1 D1709A


title: 12BBuc

value: buccal brushings

value: No RSS


title: 12ATon

value: before transplant

value: tongue brushing


title: 12AS


title: mild_Be, biological rep2

source_name: Brachypodium leaf 3, expansion zone, mild drought stress

value: leaf

value: expansion


title: Dicer-null ES-DICER1-D1709A R3

value: ES cell


title: mild_Bm, biological rep1

value: mild drought stress


title: SOIV_Animal_1027_D3_LM

city: Minato

first: Yoshihiro

last: Kawaoka

state: Tokyo

address: Shirokanedai 4-6-1

department: ERATO Influenza-induced Host Responses Project

country: Japan

institute: Japanese Science and Technology Agency

hyb_protocol: Using Agilents Gene Expression Hybridizatoin kit #4 and Gene Expression wash pack #5, Cy3-labeled cRNA preparations were hybridized with rhesus macaque arrays (Agilent Microarray Design Identification Number 015421) for 17 h at 65°C.

scan_protocol: Immediately after washing, Feature Extraction Software, version 7 (Agilent Technologies) was used for image analysis and data extraction.

data_processing: Per chip and per gene normalization was performed using GeneSpring GX version 11.0.2. Expression values were baselined to the mean of the uninfected samples

organism: Macaca mulatta

source_name: Lung

label_protocol: Using the Quick Amp Labeling Kit, T7 RNA polymerase was used to simultaneously amplify target material and incorporate cyanine 3-labeled CTP to prepare Cy3-labeled cRNA.

extract_protocol: Total RNA was extracted from homogenized lung tissues with the RNeasy Mini Kit (Qiagen, Hilden, Germany)  following the manufacturer's recommendation.

treatment_protocol: Excised lung tissues were placed in the RNA stabilization reagent RNAlater (Ambion, CA) and stored at -80°C. All tissues were thawed together and homogenized (2 minutes at 30Hz) by using a TissueLyser (Qiagen, Hilden, Germany), following the manufacturer’s instructions.

value: Lung

tag: monkey

tag: influenza a virus titer

value: Yes

tag: strains

value: SOIV

tag: day

tag: lung lobe

value: Left Middle


title: mild_Bp,biological rep1

tag: tissue

value: proliferation


title: SOIV_Animal_1028_D7_LM


title: KUTK4_Animal_1026_D3_RL

value: Right Lower


title: mild_Be, biological rep1


title: SOIV_Animal_1028_D7_RL


title: Dicer-null ES-eGFP R3

tag: cell type

value: Dicer-/-

value: pLD-puro-ENvA

value: vector

value: Vector (eGFP)


title: control_Ap, biological rep3

description: Gene expression data of a developing Brachypodium leaf grown in soil under control drought regimen

source_name: Brachypodium leaf 3, proliferation zone, control

value: control


title: Dicer-null ES-eGFP R2

tag: genotype


title: Dicer-null ES-DICER1-D1709A R2

tag: vector

value: hotspot mutant

value: DICER1 D1709A


title: Dicer-null ES-DICER1-D1709A R1

tag: group


title: control_Ap, biological rep2

value: leaf


title: KUTK4_Animal_1026_D3_LM


title: SOIV_Animal_1027_D3_RL


title: 12AP

tag: time of specimen collection

value: before transplant

tag: sample type

value: plaque

tag: developed respiratory signs/symptoms (rss) or no rss

value: No RSS


title: Dicer-null ES-eGFP R1

value: ES cell

tag: transgene


title: control_Ap, biological rep1


title: 11CTon

value: after transplant

value: tongue brushing


title: SOIV_Animal_1021_D7_RL

value: Lung

value: SOIV


title: SOIV_Animal_1021_D7_LM

value: Left Middle


title: 12ABuc

value: buccal brushings


title: 11CP


title: SOIV_Animal_1019_D7_LM


title: control_Am, biological rep3

source_name: Brachypodium leaf 3, mature zone, control

value: mature


title: Dicer-null ES R3

value: Dicer-/-

value: control (Dicer1-null)


title: 11BTon


title: 11BS

value: saliva


title: 11BP


title: Dicer-null ES R2


title: 11ATon


title: KUTK4_Animal_1016_D7_RM

value: Right Middle


title: control_Am, biological rep2

value: control


title: 11AS


title: control_Ae, biological rep3

source_name: Brachypodium leaf 3, expansion zone, control

value: leaf

value: expansion


title: control_Am, biological rep1


title: KUTK4_Animal_1015_D7_LM


title: KUTK4_Animal_1015_D7_RL

value: Right Lower


title: control_Ae, biological rep2


title: 11AP

value: before transplant

value: plaque

value: No RSS


title: control_Ae, biological rep1


title: KS02c

city: Houston

first: Govindarajan

last: Kunde Ramamoorthy

state: Texas

address: 1100 Bates Street

institute: Baylor College of Medicine

description: Male Small litter P180 biol-rep1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation and log2 transformation with LUMI package in R

source_name: Male Small litter P180

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNA was extracted using the Rneasy Mini Kit (Qiagen). Quality control was performed by spectrophotometry (NanoDrop-1000 Spectrophotometer, Thermo Fisher Scientific).

tag: strain

value: FVB/NJ-Jax

tag: Sex

value: Male

tag: age

value: Small litter


title: KS18d

description: Male Small litter P180 biol-rep3


title: Dicer-null ES R1

value: ES cell


title: 10DTon

source_name: oral sample

value: after transplant

value: tongue brushing

value: RSS


title: SOIV_Animal_1014_D3_LM

value: Lung

tag: monkey

value: Yes

value: SOIV

value: Left Middle


title: SOIV_Animal_1014_D3_LL

tag: influenza a virus titer

value: Lung LL


title: KUTK4_Animal_1016_D7_RL

tag: strains


title: KC21h

description: Male Control P180 biol-rep3

source_name: Male Control P180

value: Control