title: Yeast_Input_Other_ChIP-Seq

status: Public on Oct 24 2008

city: Palo Alto

first: Ghia

last: Euskirchen

address: 1501 S. California Ave.

department: Genetics

institute: Stanford University

description:
Barcoded input DNA samples from barcoded lane A (CATT) and lane B (ACGT) and non-barcoded not used in bioinformatics analyses.  Non-barcoded input DNA sample from lane I, which is also part of the input reference set.

fastq raw data files:
Sequence_barcoded_laneA_FC309DB_20080718_s_6.txt
Sequence_barcoded_laneB_FC302RW_20080603_s_3.txt
Sequence_Input_NB_laneI_FC301WV_20080419_s_1.txt

data_processing: Raw data from the Illumina Genome Analyzer and Illumina Genome Analyzer II were analyzed with Illumina’s Firecrest, Bustard and GERALD modules for image analysis, basecalling and run metrics respectively, and a PhiX174 control lane was used for matrix and phasing estimations, as per the manufacturer’s instructions. At this stage, a Perl script was used to partition the reads and remove the barcodes, i.e. the first four bases of each read. For barcoded samples, the next 26 bases of each read were aligned against the reference genome S288c Saccharomyces cerevisiae using Illumina’s ELAND program in standalone mode.  For non-barcoded samples, bases 5 to 30 were aligned against the S288c genome for consistency.  For each barcode from each flowcell lane of barcoded libraries, the numbers of total and mapped reads were determined.  Reads lacking a fully-intact barcode were discarded in a fifth bin called unclassified and were not used in individual barcode mapping analysis, although they are calculated in the global lane mapping analysis.  Uniquely-mapped reads from the same ChIP factor, with a similar barcoding scheme and from the same biologicial replicate were pooled to produce all the different data sets.  A full lane of non-barcoded input DNA comprising 2,455,181 mapped reads was used as a control when scoring barcoded input DNA (Input_Experiment).  For scoring ChIP DNA relative to input DNA, a reference set consisting of two full lanes of input DNA and two barcoded input DNA data sets were combined, adding up to 13,198,172 total reads (Input_Reference_Set).  Signal files were created using a 200 bp sliding window and scoring was performed with the PeakSeek program (J Rozowsky, G Euskirchen, Z Zhang, et al., Peak-Seek: Scoring ChIP-Seq Experiments Relative to Controls. Nature Biotechnology. Submitted.) using a mappability fraction of 1.0.  Significant “ChIP hits” were determined relative to the corresponding input DNA by PeakSeek and further filtered by requiring a hit length of at least 100 bp, a p-value of < 0.05, a ratio of at least 2.0 between ChIP DNA and input DNA read counts and a difference of at least 10 between the ChIP DNA and input DNA read counts.

organism: Saccharomyces cerevisiae

growth_protocol: CMY288-1B was grown in YPAD rich media to exponential mid-log phase (OD600=1.0, 500 mL culture).

extract_protocol: Chromatin immunoprecipitations were performed as described in Aparicio et al. 2004. All ChIP experiments were completed as biological triplicates for Cse4 and Ste12 and as biological quadruplicates for PolII.  After formaldehyde crosslinking, cells were lysed using a FastPrep24 (MP Biomedicals) and chromatin was sonicated using a Branson Digital Sonifier 450. For ChIP samples, clarified sonicated lysates were IPed in lysis/IP buffer containing protease inhibitors and PMSF.  For input DNA, clarified sonicated lysates from CMY288-1B were left without antibody but were otherwise processed as a ChIP sample.  For the immunoprecipitations of Ste12 and Cse4, anti-Myc EZiew affinity gel (Sigma) and anti-HA EZiew affinity gel (Sigma) were added to clarified lysates from Ste12 and Cse4 epitope-tagged strains respectively. For the immunoprecipitation of native RNA polymerase II from strain CMY288-1B, mouse ascites containing RNA polymerase II 8WG16 mouse monoclonal antibody (Covance, Cat. #MMS-126R) was added overnight and a pre-washed Protein G agarose slurry was used to precipitate antibody-PolII-DNA complexes.  For non-barcoded samples, Illumina genomic DNA libraries were prepared according to Illumina manufacturer's instructions with a few modifications based on experience gained from ChIP-Sequencing described in Robertson et al. 2007.  After end-repair and addition of a single adenosine nucleotide, non-barcoded Illumina genomic DNA adapters were ligated to the ChIP or input DNA sample.  Then DNA was PCR-amplified with Illumina genomic DNA primers 1.1 and 2.1 and DNA fragments of the library between 150 and 350 bp were gel-extracted.  The purified library was captured on one Illumina flowcell lane for cluster generation.  Libraries were sequenced on the Illumina Genome Analyzer or on the Illumina Genome Analyzer II following the manufacturer's protocols.  Here are our modifications to the library generation protocol in order to perform multiplex ChIP-Seq; other steps remained unchanged.  We first generated standard Illumina genomic DNA adapter sequences augmented with one of four barcodes (ACGT, CATT, GTAT and TGCT).  The first three bases uniquely tag or “barcode” a given sample preparation and are separated by a Hamming distance of three which will prevent one barcode being miscalled as another barcode when allowing for one- or two-base sequencing errors.  These barcodes also display a balanced base composition.  The final ‘T’ at the fourth base anneals with the ‘A’ overhang from the end-repaired DNA sample for ligation of ChIP or other DNA fragments. Illumina PCR primers for genomic DNA are used without any changes after adapter ligation to generate the barcoded sequencing libraries.  Four libraries are pooled together in equimolar ratios and sequenced simultaneously on the Illumina Genome Analyzer or Illumina Genome Analyzer II in a single Illumina flowcell lane.

tag: Yeast strain CMY288-1B, mid-log exponential growth, Christopher M. Yellman, unpublished

value: CMY288-1B (MATα his3delta1 leu2delta0 lys2delta0 ura3delta0) Parent strain:BY4741

value: CMY288-1B Genotype:MATα his3delta1 leu2delta0 lys2delta0 ura3delta0


title: Yeast_Input_Reference_Set_ChIP-Seq

type: SRA

state: CA

country: USA

description:
Input reference data set for scoring ChIP samples. For scoring ChIP DNA relative to input DNA, a reference set consisting of two full lanes of non-barcoded input DNA (lanes I and J) and two barcoded input DNA data sets (ACGT from barcoded lane B and CATT from barcoded K, same sequencing mix than barcoded lane A) were combined, adding up to 13,198,172 total reads.

fastq raw data files:
Sequence_Input_NB_laneI_FC301WV_20080419_s_1.txt
Sequence_Input_NB_laneJ_FC201WVA_20080307_s_1.txt
Sequence_barcoded_laneB_FC302RW_20080603_s_3.txt
Sequence_barcoded_laneK_FC302RW_20080603_s_2.txt

library_source: genomic

molecule: genomic DNA

tag: strain


title: Yeast_Ste12_ChIP-Seq

description:
Ste12 ChIP biological replicate 1 was made into an Illumina genomic DNA library using the TGCT barcoded adapter and was sequenced simultaneously with 3 other samples (PolII_Rep1_ACGT, Input_CATT and Cse4_Rep1_GTAT) in barcoded lane A.  Ste12 ChIP biological replicate 2 was made into an Illumina genomic DNA library using the GTAT barcoded adapter and was sequenced simultaneously with 3 other samples (Input_ACGT, Cse4_Rep2_CATT and PolII_Rep2_TGCT)  in barcoded lane B.  Ste12 ChIP biological replicate 3 was made into an Illumina genomic DNA library using non-barcoded Illumina genomic DNA adapter and was sequenced in non-barcoded lanes E and F.

fastq raw data files:
Sequence_barcoded_laneA_FC309DB_20080718_s_6.txt
Sequence_barcoded_laneB_FC302RW_20080603_s_3.txt
Sequence_Ste12_Rep3_laneE_FC301WV_20080419_s_3.txt
Sequence_Ste12_Rep3_laneF_FC202H2_20080204_s_2.txt

source_name: Yeast_Ste12_ChIP-Seq: 3 biological replicates

growth_protocol: CMY291 was grown overnight to mid-log phase to OD600=0.6 and then pseudohyphal growth was conducted in nitrogen-depleted SLAD for 4 h as described in Borneman et al. 2006 (500 mL culture). 3 biological replicates were grown.

tag: Yeast strain CMY291, pseudohyphal growth, Christopher M. Yellman, unpublished

value: CMY291 (MATa/α HO/HO STE12-13MYC-kanMX6/STE12-13MYC-kanMX6) Parent strain:YJM339

value: CMY291 Genotype:MATa/α HO/HO STE12-13MYC-kanMX6/STE12-13MYC-kanMX6 Antibody:anti-Myc EZview affinity gel (Sigma)


title: Yeast_Input_Experiment_ChIP-Seq

description:
An input DNA sample was divided into five aliquots to test whether our barcoded adapters generate similar results when added to the same population of DNA fragments.  Four of the samples were differentially barcoded and the libraries were mixed together in the same flow cell lane (barcoded lane L).  As a control, standard non-barcoded Illumina genomic DNA adapters were added to the fifth aliquot and this library was sequenced in another lane (lane J).  Each barcoded input DNA from lane L was scored against the non-barcoded input DNA (lane J) using PeakSeek.  Similar criteria were applied to filter barcoded input DNA hits as those described in the "data processing" section.

fastq raw data files:
Sequence_Input_exp_barcoded_laneL_FC201WVA_20080307_s_2.txt
Sequence_Input_NB_laneJ_FC201WVA_20080307_s_1.txt


title: Yeast_Cse4_ChIP-Seq

description:
Cse4 ChIP biological replicate 1 was made into an Illumina genomic DNA library using the GTAT barcoded adapter and was sequenced simultaneously with 3 other samples (PolII_Rep1_ACGT, Input_CATT and Ste12_Rep1_TGCT) in barcoded lane A.  Cse4 ChIP biological replicate 2 was made into an Illumina genomic DNA library using the CATT barcoded adapter and was sequenced simultaneously with 3 other samples (Input_ACGT, Ste12_Rep2_GTAT and PolII_Rep2_TGCT)  in barcoded lane B.  Cse4 ChIP biological replicate 3 was made into an Illumina genomic DNA library using non-barcoded Illumina genomic DNA adapter and was sequenced in non-barcoded lanes G and H.

fastq raw data files:
Sequence_barcoded_laneA_FC309DB_20080718_s_6.txt
Sequence_barcoded_laneB_FC302RW_20080603_s_3.txt
Sequence_Cse4_Rep3_laneG_FC301WV_20080419_s_2.txt
Sequence_Cse4_Rep3_laneH_FC202H2_20080204_s_1.txt

source_name: Yeast_Cse4_ChIP-Seq: 3 biological replicates

growth_protocol: CMY8082-20-3 was grown in YPAD rich media to exponential mid-log phase (OD600=1.0, 500 mL culture). 3 biological replicates were grown.

tag: Yeast strain CMY 8082-20-3, mid-log exponential growth, Meluh et al., 1998, Christopher M. Yellman, unpublished

value: CMY8082-20-3 (MATa ade2-1 bar1::loxP can1H cyh2H gal1H his3delta1 leu2-3,112 trp1-289 ura3-52 CSE4-3HA-URA3) Parent strain:A364a

value: CMY8082-20-3 Genotype:MATa ade2-1 bar1::loxP can1H cyh2H gal1H his3delta1 leu2-3,112 trp1-289 ura3-52 CSE4-3HA-URA3 Antibody:anti-HA EZview affinity gel (Sigma)


title: macIL-10tg Mtb d42 2

status: Public on Jan 08 2009

type: RNA

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

country: Germany

institute: University Hospital Erlangen

description: Gene expression data from lung of mice 42 days after M. tuberculosis infection

hyb_protocol: Biotinylated cRNA was hybridized on MOE430A 2.0 GeneChips, that were stained, washed and scanned following standard procedures.

scan_protocol: Standard Affymetrix protocol

data_processing: CEL files were processed for global normalization and generation of expression values using the robust multi-array average algorithm (RMA) (ref.: Bolstad, B. M., Irizarry, R. A., Astrand, M. & Speed, T. P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-93 (2003)).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: lung RNA; day 42 after Mtb infection

label_protocol: Affymetrix GeneChips were used for genome-wide expression analysis of the impact of IL-10 overexpression during pulmonary Mtb infection. Tissue from individual mice was processed as biological duplicates (untreated controls and day 25 after infection) and triplicates (day 42 after infection). Per sample, 3 µg total lung RNA was processed using the GeneChip Expression 3’ Amplification One-Cycle Target Labeling Kit according to the manufacterer’s instruction.

growth_protocol: Transgenic mice (macIL-10tg mice) specifically expressing IL-10 in macrophages under control of the human CD68 promoter were bred under specific-pathogen-free conditions at the Technical University of Munich. macIL-10tg mice were on a FVB genetic background and transgene-negative littermates were used as controls (FVB).  For experiments, mice were maintained under barrier conditions in the BSL 3 facility at the Research Center Borstel in individually ventilated cages.

extract_protocol: Before and at different time points after aerosol infection with Mtb, weighed lung samples were homogenized in 5 ml of 4 M guanidinium-isothiocyanate buffer and total RNA was extracted by acid phenol extraction.

treatment_protocol: Mtb (H37Rv) were grown in Middlebrook 7H9 broth supplemented with Middlebrook OADC enrichment medium 0.002 % glycerol, and 0.05 % Tween 80. Midlog phase cultures were harvested, aliquoted, and frozen at –80°C. After thawing, viable cell counts were determined by plating serial dilutions of the cultures on Middlebrook 7H10 agar plates followed by incubation at 37°C. Before infection of experimental animals, stock solutions of Mtb were diluted in sterile distilled water and pulmonary infection was performed using an inhalation exposure system. To infect mice with a low dose of 100 CFU/lung, animals were exposed for 40 min to an aerosol generated by nebulizing approximately 5.5 ml of a suspension containing 10exp7 live bacteria. Inoculum size was checked 24 h after infection by determining the bacterial load in the lung of infected mice.

tag: Strain

value: macIL-10tg mice; tissue:lung; infected with M. tuberculosis for 42 days


title: Yeast_PolII_ChIP-Seq

description:
PolII ChIP biological replicate 1 was made into an Illumina genomic DNA library using the ACGT barcoded adapter and was sequenced simultaneously with 3 other samples (Input_CATT, Cse4_Rep1_GTAT and Ste12_Rep1_TGCT) in barcoded lane A.  PolII ChIP biological replicate 2 was made into an Illumina genomic DNA library using the TGCT barcoded adapter and was sequenced simultaneously with 3 other samples (Input_ACGT, Cse4_Rep2_CATT and Ste12_Rep2_GTAT)  in barcoded lane B.  PolII ChIP biological replicate 3 was made into an Illumina genomic DNA library using the ACGT barcoded adapter and was sequenced simultaneously in barcoded lane C with the 3 same libraries from barcoded lane A (Input_CATT, Cse4_Rep1_GTAT and Ste12_Rep1_TGCT).  PolII ChIP biological replicate 4 was made into an Illumina genomic DNA library using non-barcoded Illumina genomic DNA adapter and was sequenced in non-barcoded lane D.

fastq raw data files:
Sequence_barcoded_laneA_FC309DB_20080718_s_6.txt
Sequence_barcoded_laneB_FC302RW_20080603_s_3.txt
Sequence_barcoded_laneC_FC305DH_20080616_s_3.txt
Sequence_PolII_Rep4_laneD_FC301WV_20080419_s_5.txt

source_name: Yeast_PolII_ChIP-Seq: 4 biological replicates

growth_protocol: CMY288-1B was grown in YPAD rich media to exponential mid-log phase (OD600=1.0, 500 mL culture). 4 biological replicates were grown.

value: CMY288-1B Genotype:MATα his3delta1 leu2delta0 lys2delta0 ura3delta0 Antibody:RNA Polymerase II mouse monoclonal antibody, clone 8WG16 (Covance, MMS-126R)


title: FVB Mtb d42 3

value: wildtype FVB; tissue:lung; infected with M. tuberculosis for 42 days


title: FVB control 2

description: Gene expression data from lung of uninfected control mice

source_name: lung RNA; uninfected

value: wildtype FVB; tissue:lung; not infected


title: FVB Mtb d42 1


title: NRSF_ChIPSeq: Antibody: no antibody, mock

city: Hayward

first: Shujun

last: Luo

address: 25861 Industrial Blvd

institute: Illumina inc

description: Chromatin IP against NRSF

data_processing: not applicable

organism: Homo sapiens

source_name: Jurkat T cell line

growth_protocol: The Jurkat human T lymphoblast cell line was cultured according to standard protocols.

extract_protocol: NRSF mono antibody immunoprecipitated material was purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

tag: Jurkat T cell line


title: macIL-10tg Mtb d25 2

description: Gene expression data from lung of mice 25 days after M. tuberculosis infection

source_name: lung RNA; d25 after Mtb infection

value: macIL-10tg mice; tissue:lung; infected with M. tuberculosis for 25 days


title: macIL-10tg Mtb d42 1


title: FVB Mtb d25 2

value: wildtype FVB; tissue:lung; infected with M. tuberculosis for 25 days


title: FVB Mtb d42 2


title: macIL_10tg control 1

value: macIL-10tg mice; tissue:lung; not infected


title: FVB control 1


title: FVB Mtb d25 1


title: NRSF_ChIPSeq: Antibody: NRSF

description: Chromatin IP against NRSF


title: macIL-10tg Mtb d42 3


title: macIL_10tg control 2


title: macIL-10tg Mtb d25 1


title: CSV_1st454

status: Public on Sep 12 2008

city: Oxford

first: Thien

middle: Xuan

last: Ho

address: Mansfield road

country: United Kingdom

institute: CEH Oxford

description: siRNA

library_source: transcriptomic

data_processing: Cocksfoot grass (Dactylis glomerata) collected from Wytham, Oxford, UK, was tested for Cocksfoot streak virus infection. Small RNA of the grass was extracted and converted to DNA according to Ho, T., et al. (2008)  Biochem Biophys Res Commun. 368:433-7, with primers modified to contain 454 adapter nucleotide sequences. The DNA then passed quality control through Bioanalyzer and Nanodrop before sequenced by 454 Life Sciences.

organism: Cocksfoot streak virus

source_name: Cocksfoot grass total RNA

extract_protocol: Ho, T., et al. (2008)  Biochem Biophys Res Commun.368:433-7 with primer sequence modification

tag: Cocksfoot grass total RNA


title: Mouse_hippocampus_WT_3

status: Public on Oct 17 2008

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description: Sequence tag preparation was done with Illumina’s Digital Gene Expression Tag Profiling Kit according to the manufacturer’s protocol (version 2.1B). A schematic overview of the procedure is given in the figure at the end of this document.  One microgram of total RNA was incubated with oligo-dT beads to capture the polyadenlyated RNA fraction. First and second strand cDNA synthesis were performed while the RNA was bound to the beads. While on the beads, samples were digested with NlaIII to retain a cDNA fragment from the most 3’ CATG to the polyA-tail. Subsequently, the GEX adapter 1 was ligated to the free 5’ end of the RNA, and a digestion with MmeI was performed, which cuts 17 bp downstream of the CATG site. At this point, the fragments detach from the beads. After dephosphorylation and phenol extraction, the GEX adapter 2 was ligated to the 3’ end of the tag. A PCR amplifcation with 15 cycles using Phusion polymerase (Finnzymes) was performed with primers complementary to the adapter sequences to enrich the samples for the desired fragments. The resulting fragments of 85 bp were purified by excision from a 6% polyacrylamide TBE gel. The DNA was eluted from the gel debris with 1x NEBuffer 2 by gently rotation for 2h at room temperature. Gel debris were removed using Spin-X Cellulose Acetate Filter (2 ml, 0.45 µm) and the DNA was precipitated by adding 10 µl of 3M sodium acetate (pH 5.2) and 325 µl of ethanol (-20C), followed by  centrifugation at 14,000 rpm for 20 minutes. After washing the pellet with 70% ethanol, the DNA was resuspended in 10 µl of 10 mM Tris-HCl,. pH8.5 and quantified the DNA with a Nanodrop 1000 spectrophotometer.

data_processing: Cluster generation was performed after applying 4 pM of each sample to the individual lanes of the Illumina 1G flowcell. After hybridization of the sequencing primer to the single stranded products, 18 cycles of base incorporation were carried out on the 1G analyzer according to the manufacturer’s instructions. Image analysis and basecalling was performed using the Illumina Pipeline, where sequence tags were obtained after purity filtering. This was followed by sorting and counting the unique tags.

source_name: Hippocampus

extract_protocol: After transfer to ice-cold Trizol, hippocampi were homogenized using a tissue homogenizer (Salm&Kipp, Breukelen, The Netherlands) and total RNA was isolated according to the manufacturer’s protocol. After precipitation, RNA was purified with Qiagen’s RNeasy kit with on-column DNase digestion.

tag: wild-type. background


title: Drosophila erecta

status: Public on Apr 30 2009

city: New York

first: Colin

middle: Dean

last: Malone

state: NY

address: NYUMC, Skirball Institute, 540 1st Ave, 4-10

department: Skirball Institute - Developmental Genetics

institute: NYU Medical Center

description: small RNA sequencing

data_processing: The 36nt long Illumina reads were stripped of the 3’ linker and the resulting small RNA sequences were mapped to the Release 5 genome excluding the Uextra portion. Only reads matching the fly genome 100% were used for further analysis. For annotation, we used Flybase for protein coding genes, UCSC for non-coding RNAs and transposons/repeats (repeat masker tracks) and the most recent miRNA catalog. To control for sequencing depth, small RNA counts were normalized to the same total number after subtracting those matching abundant cellular RNAs such as rRNAs and tRNAs. For the piRNA analysis, we selected small RNAs, which exceeded 22 nt in length and were not annotated as miRNA, tRNA, rRNA, snoRNA, snRNA or smRNA.

organism: Drosophila erecta

source_name: ovaries

growth_protocol: 24 degrees C

extract_protocol: Trizol

treatment_protocol: Trizol/Phenol Cholorofom extractions

tag: tissue

value: ovaries


title: Mouse_hippocampus_DLCK-TG_1

tag: background

tag: Transgenic for the constitutively active form of the delta-double cortin-like kinase


title: TuMV_1st454

description: siRNA

data_processing: Mustard (Brassica juncea) was tested for Turnip mosaic virus infection. Small RNA of the plant was extracted and converted to DNA according to Ho, T., et al. (2006)  Journal of Virological Methods 136:217-223, with primers modified to contain 454 adapter nucleotide sequences. The DNA then passed quality control through Bioanalyzer and Nanodrop before sequenced by 454 Life Sciences.

organism: Turnip mosaic virus

source_name: Brassica juncea total RNA

extract_protocol: Ho, T., et al. (2006)  Journal of Virological Methods 136:217-223 with primer sequence modification

tag: Brassica juncea total RNA


title: Irf1-/-, no infection, mouse 1

status: Public on Sep 01 2008

description: Gene expression data from control lungs

hyb_protocol: Hybridization to MOE430A 2.0 according to Affymetrix protocol.

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

data_processing: Data were processed using the Bioconductor RMA algorithm.

source_name: Irf1-/-, no infection

label_protocol: RNA was processed with the Affymetrix One-Cycle Kit.

growth_protocol: Mice were infected by aerosol with 10^5 CFU M. avium TMC724 or left untreated.

extract_protocol: Lung RNA was extracted after homogenization of the tissue in Trifast Reagent.

treatment_protocol: After 14 weeks, mice were euthanised and the lungs removed.

tag: background C57Bl/6


title: Irf1+/+, infection with M. avium, mouse 3

description: Gene expression data 14 weeks after M. avium infection

source_name: Irf1+/+, infection with M. avium


title: Irf1+/+, infection with M. avium, mouse 1


title: Irf1-/-, infection with M. avium, mouse 2

source_name: Irf1-/-, infection with M. avium


title: Irf1-/-, no infection, mouse 2

description: Gene expression data from control lungs


title: Irf1-/-, no infection, mouse 3

description: Gene expression data from control lungs


title: Irf1-/-, infection with M. avium, mouse 3


title: Irf1+/+, no infection, mouse 3

description: Gene expression data from control lungs

source_name: Irf1+/+, no infection


title: Irf1+/+, infection with M. avium, mouse 2


title: Irf1+/+, no infection, mouse 2

description: Gene expression data from control lungs


title: Irf1+/+, no infection, mouse 1

description: Gene expression data from control lungs


title: small RNA from 1st instar larvae (2)

status: Public on Jan 21 2009

first: Nicolas

last: Robine

address: 1275 York Avenue, Box 252

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description: Small RNA data.

data_processing: raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt

organism: Drosophila melanogaster

source_name: Drosophila melanogaster 1st instar larvae

extract_protocol: total RNA from 1st instar larvae, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: 1st instar larvae


title: Mouse_hippocampus_DCLK-TG_3

tag: Transgenic for the constitutively active from of the delta-double cortin-like kinase


title: Mouse_hippocampus_WT_6


title: smRNASeq_root

status: Public on Apr 28 2009

city: New Haven

first: Xiangfeng

last: Wang

state: CT

address: 352 OML, 165 Prospect st

department: MCDB

institute: Yale University

description: siRNA and miRNA

data_processing: Sequencing reads were mapped to genome using MAQ software. ChIP-enriched regions were detected by MACS software. Further details found at http://www.plantcell.org/cgi/content/abstract/tpc.109.065714v1?papetoc

organism: Zea mays

source_name: seedling roots

growth_protocol: Maize inbred line B73 was obtained from the USDA-ARS North Central Regional Plant Introduction Station in Ames, IA. Seeds were planted in individual pots containing a mixture of three parts soil (Premier Pro-Mix Bx Professional, Premier Horticulture, Quakertown, PA) and two parts vermiculite (D3 Fine Graded Horticultural Vermiculite, Whittemore Co., Lawrence, MA). Plants were grown under controlled environmental conditions (15 hours light/25 ºC, 9 hours dark/20 ºC) in a growth chamber, and the soil mixture was kept moist by watering the pots with 0.7mM Ca(NO3)2. Seedlings were harvested after 14 days, separated into shoots and roots, frozen in liquid nitrogen and stored at –80 ºC or processed directly after harvesting for ChIP.

extract_protocol: Maize tissue from 10 different seedlings was ground in liquid nitrogen, and genomic DNA was extracted from 1 g pooled tissue using a Qiagen DNeasy plant maxi kit. To enrich for methylated genomic DNA, 20 mg genomic DNA were digested with 200 units McrBC (New England Biolabs) overnight, and fragments 500 nucleotides and smaller were gel purified and used for library construction following the manufacturer's instructions, but adding a final gel purification step. To enrich for histonemodified regions, ChIP was conducted using 5 g fresh maize tissue from 10 seedlings following a previously described procedure (Lee et al., 2007). The following antibodies were used: H3K9ac (Upstate; 07-352), H3K27me3 (Upstate; 07-449), H3K4me3 (Abcam; ab8580), and H3K36me3 (Abcam; ab9050). For each 1-mL ChIP reaction, 5 mL antibody were added. The ChIPed DNA from three reactions was pooled to construct Solexa libraries essentially following the manufacturer's standard protocol but running 18 PCR cycles before gel purification of the samples. Total RNA was isolated using TRIzol reagent (Invitrogen) following the manufacturer's instructions. mRNA was extracted from total RNA using Dynabeads Oligo(dT) (Invitrogen Dynal) following the manufacturer's directions. After elution from the beads, first- and secondstrand cDNA was generated using SuperscriptII reverse transcriptase (Invitrogen), and the standard Solexa protocol was followed thereafter to create mRNA libraries. smRNA was extracted by running total RNA on a 15% PAGE gel and cutting out bands in the ;19- to 24-nucleotide size range. Libraries for smRNAs were constructed following previously published procedures (Mi et al., 2008; see Supplemental Methods online for details). All samples were prepared for sequencing following the manufacturer's standard protocol.

value: B73 Strain

tag: age

value: 14 day-old

tag: tissue type

value: seedling roots


title: Mouse_hippocampus_DLCK-TG_4


title: Irf1-/-, infection with M. avium, mouse 1


title: Mouse_hippocampus_DCLK-TG_2


title: small RNA from 0-1 day old pupae

description: Small RNA data.

source_name: Drosophila melanogaster 0-1 day old pupae

extract_protocol: total RNA from 0-1 day old pupae, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: 0-1 day old pupae


title: Ifng+/+, infection with M. avium, mouse 2

source_name: Ifng+/+, infection with M. avium


title: Pho_ctrl_embryo_biorep1

status: Public on Aug 01 2008

type: genomic

city: Cambridge

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

institute: University of Cambridge

description: group2: ctrl ChIP using whole-embryo chromatin, pre-immune serum in wildtype, chromatin prep 1, hybridisation 1

hyb_protocol: Amplified ChIP DNA was fragmented to 50-100bp by treatment with DNAse I for 10min at 37 ºC and 10min at 99 ºC (0.02 U/ug, Epicentre; size distribution of fragmented DNA was verified on a 2% agarose gel). The fragmented DNA was then end-labeled with 70nM of bio-ddATP (Perkin Elmer) using 6-10U of terminal transferase (TdT, Roche) per 1 ug of fragmented DNA in 1x TdT buffer (Roche) and 5mM CoCl2 (Roche) for 2 hours at 37 ºC. The labeled DNA material was subsequently hybridized to the microarrays for 18 hours at 45 ºC in a 3M TMAC/1X MES-based solution.

scan_protocol: Chips were scanned on an Affymetrix GeneChip Scanner according to the manufacturer’s recommendations.

data_processing: Sample and control were analysed together in groups (1-4) using the TiMAT package. Affymetrix CEL files were converted into chromosomal enrichment profiles using the TiMAT2 package (http://bdtnp.lbl.gov/TiMAT/TiMAT2/). Probe mapping information (“bpmap”) to D. melanogaster genome release 4 was obtained from David Nix. Each CEL file was visualised for manual inspection and artefacts were masked using CelMasker. Normalisation was subsequently performed with CelProcessor using default parameters. Enrichment profiles were generated using ScanChip, outputting windowed enrichment signals and Wilcoxon Rank Sum scores.

label: TdT labeled

source_name: whole-embryo chromatin

label_protocol: 10-20 ng of ChIP and control DNA samples were amplified using a random-primed PCR method according to Affymetrix recommendations (Affymetrix Chromatin Immunoprecipitation Assay Protocol; http://www.affymetrix.com/support/technical/manuals.affx). Purified DNAs were then fragmented, TdT labeled, and hybridized to the Affymetrix Drosophila genome Tiling Array 1.0 (reverse part no. 520,054) as described previously (Manak et al. 2006).

growth_protocol: Embryo collections were performed at 25 ºC and L3 larvae were raised at 25 ºC.

extract_protocol: Chromatin was prepared from a minimum of 100 discs or 200mg embryos. Chromatin preparation and ChIP were performed as described previously (Birch-Machin et al. 2005; Adryan et al. 2007). For Pc target analysis the specific reaction used chromatin from the Pc-GFP fly line immunopurified using anti-GFP, and the control reaction used wild type chromatin immunopurified using anti-GFP. For Pho analysis wild type chromatin was used with anti-Pho for the specific reaction and pre-immune antiserum for the control.

treatment_protocol: Chromatin from embryos aged between 0 to 16 h after egg laying was purified as described previously (Birch-Machin et al 2005; Adryan et al. 2007). For the preparation of chromatin from T3 imaginal discs (haltere and third leg) late 3rd instar larvae were dissected in ice-cold Schneider's Medium. Dissected discs were washed with PBS, fixed in PBS/1.5% formaldehyde for 20 min and washed with PBS. Batches of material were snap-frozen in liquid N2 and stored at -80 ºC.

tag: 0-16h AEL embryo


title: Ifng+/+, no infection, mouse 1

description: Gene expression data from control lungs

source_name: Ifng+/+, no infection


title: Ifng+/+, no infection, mouse 3

description: Gene expression data from control lungs


title: Mouse_hippocampus_WT_4


title: Ifng+/+, infection with M. avium, mouse 3


title: small RNA from 1st instar larvae (1)

description: Small RNA data.


title: Mouse_hippocampus_WT_1


title: Ifng-/-, infection with M. avium, mouse 1

source_name: Ifng-/-, infection with M. avium


title: small RNA from 0-2 day old pupae

description: Small RNA data.

source_name: Drosophila melanogaster 0-2 day old pupae

extract_protocol: total RNA from 2-4 day old pupae, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: 0-2 day old pupae


title: smRNASeq_shoot

description: siRNA and miRNA

source_name: seedling shoots

tag: strain

value: seedling shoots


title: small RNAs from adult male head

status: Public on Sep 30 2008

description: Small RNA data.

source_name: Drosophila melanogaster adult male head

extract_protocol: total RNA from adult male head, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: adult male head


title: Ifng-/-, infection with M. avium, mouse 2


title: Ifng-/-, no infection, mouse 2

description: Gene expression data from control lungs

source_name: Ifng-/-, no infection


title: Ifng+/+, no infection, mouse 2

description: Gene expression data from control lungs


title: Monosiga

status: Public on Oct 01 2008

first: andrew

last: grimson

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description:
small RNA sequencing
15-30 nt size selection

data_processing: The processed files are collapsed to unique sequences (1 line per sequence); the second (numeric) value in each column is the number of times each unique sequence was sequenced.

organism: Monosiga brevicollis

source_name: whole organisms

extract_protocol: Trizol extracted whole RNA

treatment_protocol: Stored at -80

tag: whole organisms


title: Ifng-/-, no infection, mouse 1

description: Gene expression data from control lungs


title: MPI-590

status: Public on Jun 17 2008

city: Regensburg

first: Stefan

last: Bentink

state: Bayern

address: Josef Engertstr. 9

department: Institute of Functional Genomics

institute: University of Regensburg

description: Mature aggressive B-cell lymphoma

hyb_protocol: Affymetrix hybridization was carried with U133A GeneChips according to the manufacturer’s recommendations. In brief, 15 microgram of Biotin-labelled and fragmented cRNA were mixed with 20x GeneChip Eukaryotic Hybridization Control (Affymetrix) and supplemented with B2 control oligonucletide, salmon sperm DNA, acetylated bovine serum albumin and hybridization buffer and water making up a total volume of 300 microliter.

scan_protocol: After hybridization of night (16 hours, 45 C) the hybridization mixture was removed from the GeneChip and washing and staining of the GeneChips was performed in a fluidics station (Affymetrix). The detection of the Biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500).

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536).  Probe-set summarization was performed using the median polish method on the normalized data (Irrizary et al. Nucleic Acids Research 2003, PMID: 12582260).

label: Biotin

source_name: Frozen tissue

label_protocol: For Affymetrix GeneChip hybridization, 5 microgram of total RNA was employed to generate a double-stranded cDNA with the help of the INVITROGEN Superscript kit. After removal of small molecular components (Affymetrix Clean-up Module), Biotin-labelled cRNA was synthesized by application of the ENZO Labeling kit (T7 RNA polymerase). The concentration of the produced cRNA was determined photometrically (NanoDrop) and the size range of the labelled products was evaluated by BioAnalyzer (Agilent) measurement before and after fragmentation.

extract_protocol: RNA was isolated using RNeasy Mini Kit (both from QIAGEN).The concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed by analysis of an aliquot in the Agilent BioAnalyzer.

tag: Unique Identifier

tag: Age at diagnosis

tag: Sex of patient

value: male

tag: Consensus morphological diagnosis from expert hematopathologists

tag: Immunohistochemistry

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells CD10 (>1 => pos):0

value: Proportion of positive tumor cells BCL2 (>1 => pos):0

value: Signal intensity BCL2:NA

value: Percentage Ki-67 of positive tumor cells (proliferative index):95

value: Percentage of positive tumor cells CD5 (>1 => pos):0

value: Percentage of positive tumor cells BCL6 (>1 => pos):3

tag: Cytogenetics

value: Status of MYC translocation:IG-MYC

value: Breakpoint at BCL6-locus detected:neg

value: IgH-BCL2 Fusion:neg

tag: ArrayCGH

value: Complexity/relative number of genomic gains and losses:0

tag: Cytogenetics/arryCGH

value: MYC-break with simple or complex karyotype:MYC.simple

tag: Ann Arbour Stage

tag: Gene expression

value: Diagnosis according to mBL gene expression signature:mBL

tag: Germinal center like/ activated B-cell like signature

value: unclassified

tag: mBL index (>0.95 => mBL)


title: MPI-593

description: Mature aggressive B-cell lymphoma

value: BL

value: Proportion of positive tumor cells CD10 (>1 => pos):4

value: Proportion of positive tumor cells BCL2 (>1 => pos):NA

value: Complexity/relative number of genomic gains and losses:20

value: MYC-break with simple or complex karyotype:MYC.complex

value: Diagnosis according to mBL gene expression signature:intermediate

value: GCB


title: MPI-586

description: Mature aggressive B-cell lymphoma

value: male

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells BCL2 (>1 => pos):0

value: Signal intensity BCL2:NA

value: Percentage Ki-67 of positive tumor cells (proliferative index):100

value: Percentage of positive tumor cells BCL6 (>1 => pos):4

value: Complexity/relative number of genomic gains and losses:1


title: MPI-528

description: Mature aggressive B-cell lymphoma

value: Signal intensity BCL2:0

value: Percentage Ki-67 of positive tumor cells (proliferative index):95

value: Percentage of positive tumor cells CD5 (>1 => pos):0

value: Status of MYC translocation:IG-MYC

value: Breakpoint at BCL6-locus detected:neg

value: IgH-BCL2 Fusion:neg

value: Complexity/relative number of genomic gains and losses:5

value: MYC-break with simple or complex karyotype:MYC.simple


title: MPI-589

description: Mature aggressive B-cell lymphoma

value: aggressive B-NHL.unclassifiable

value: Proportion of positive tumor cells CD10 (>1 => pos):4

value: Complexity/relative number of genomic gains and losses:3

value: IV

value: Diagnosis according to mBL gene expression signature:mBL


title: MPI-584

description: Mature aggressive B-cell lymphoma

value: male

value: DLBCL

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells BCL2 (>1 => pos):1

value: Signal intensity BCL2:1

value: Percentage Ki-67 of positive tumor cells (proliferative index):80

value: Status of MYC translocation:neg

value: MYC-break with simple or complex karyotype:MYC.neg

value: Diagnosis according to mBL gene expression signature:non-mBL

value: GCB


title: Ifng-/-, infection with M. avium, mouse 3

tag: background C57Bl/6


title: Ifng+/+, infection with M. avium, mouse 1


title: S2cell (AGO1IP), Flock house virus

status: Public on Apr 30 2008

city: Cold Spring Harbor

first: Julius

last: Brennecke

address: 1 Bungtown Road

institute: Cold Spring Harbor Labs

description: small RNA from immunoprecipitate

data_processing: the 5'end of the Solexa read corresponds to the small RNA's 5'end. The 3' linker was computationally removed at the end of all reads if possible; only sequences matching the Drosophila genome with 100% identity are reported with the exception of the AGO1 and AGO2 IP libraries from Schneider cells, where also seqeunces matching NCBI deposited seqeunces for the Flock House Virus with up to 3 mismatches are included.

organism:
Drosophila melanogaster
Flock House virus

source_name: small RNA

growth_protocol: flies and Schneider cells were grown under standard conditions at 25 degrees.

extract_protocol: extraction of total RNA was with Trizol; extraction of small RNAs from immunoprecipitates was with Phenol/Chloroform; before adaptor ligation, small RNAs were PAGE isolated;

treatment_protocol: tissues and cells were harvested on ice

tag: from transfected Schneider cells


title: AML patient 4 Diagnosis

status: Public on May 01 2008

city: London

first: Manoj

last: Raghavan

address: Charterhouse Square

department: Centre for Medical Oncology, Institute of Cancer

institute: Barts and the London, Queen Mary's School of Medicine and Dentistry

description: SNP genotype data from AML patient at diagnosis

hyb_protocol: Affymetrix 10K mapping assay protocol

scan_protocol: Affymetrix GeneChip scanner 3000

data_processing: GCOS, GTYPE. Genotype calling algorithm MPAM

source_name: AML blood/marrow cells diagnosis

label_protocol: Affymetrix 10K mapping assay protocol

extract_protocol: Phenol chloroform

treatment_protocol: AML cells collected from blood or bone marrow. Ficoll separation, and cryopreserved in liquid nitrogen.

tag: FAB_type = M1


title: RPMI8402 DMSO control 24h rep1

status: Public on Apr 22 2008

first: Adolfo

middle: A

last: Ferrando

address: 1130 St Nicholas Ave Irving Cancer Research Center 5-505A

department: Institute for Cancer Genetics

institute: Columbia University

description: Standard Affymetrix procedure

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite Version 5 followed by  Dchip data normalization for adjustment of interarray intensity differences and calculation of  model based expression (VALUE).

source_name: RPMI8402 human T-cell lymphoblastic cell line vehicle only (DMSO) treatment control 24h

label_protocol: Approx. 10 micrograms of total RNA was processed to produce biotinylated cRNA targets

growth_protocol: Cells were cultured in RPMI1640 media supplemented with 10% fetal bovine serum plus antibiotics (pen/strep) in a humidified incubator with 5% CO2 atmosphere at 37C

extract_protocol: RNA was extracted with RNAqueous minikit (Ambion) following the manufacturer’s instructions

treatment_protocol: Vehicle treatment (DMSO) control for 24 h.

tag: T-cell acute lymphoblastic leukemia cell line


title: S2cell (AGO2IP), Flock house virus

description: small RNA from immunoprecipitate


title: HPB-ALL DMSO control 24h rep1

description: Standard Affymetrix procedure

source_name: HPB-ALL human T-cell lymphoblastic cell line vehicle only (DMSO) treatment control 24h


title: KOPTK1 DMSO control 24h rep1

description: Standard Affymetrix procedure


title: CUTLL1 DMSO control 24h rep1

description: Standard Affymetrix procedure

source_name: CUTLL1 human T-cell lymphoblastic cell line gamma-secretase inhibitor (CompE 500nM) treatment 24h

extract_protocol: RNA was extracted with Trizol reagent (Invitrogen) following the manufacturer’s instructions

tag: T-cell acute lymphoblastic lymphoma cell line


title: CUTLL1 DMSO control 24h rep2

description: Standard Affymetrix procedure

source_name: CUTLL1 human T-cell lymphoblastic cell line vehicle only (DMSO) treatment control 24h


title: RPMI8402 DMSO control 24h rep2

description: Standard Affymetrix procedure


title: DND41 DMSO control 24h rep2

description: Standard Affymetrix procedure

source_name: DND41 human T-cell lymphoblastic cell line vehicle only (DMSO) treatment control 24h


title: DND41 DMSO control 24h rep1

description: Standard Affymetrix procedure

source_name: DND41  human T-cell lymphoblastic cell line vehicle only (DMSO) treatment control 24h


title: HPB-ALL DMSO control 24h rep2

description: Standard Affymetrix procedure


title: CCRF-CEM DMSO control 24h rep1

description: Standard Affymetrix procedure

source_name: CCRF-CEM human T-cell lymphoblastic cell line vehicle only (DMSO) treatment control 24h

treatment_protocol: Vehicle control (DMSO) treatment for 24 h.


title: KOPTK1 DMSO control 24h rep2

description: Standard Affymetrix procedure

source_name: KOPTK1 human T-cell lymphoblastic cell line vehicle only (DMSO) treatment control 24h


title: CCRF-CEM DMSO control 24h rep2

description: Standard Affymetrix procedure

source_name: CCRF-CEM  human T-cell lymphoblastic cell line vehicle only (DMSO) treatment control 24h


title: ALLSIL DMSO control 24h rep1

description: Standard Affymetrix procedure

source_name: ALL-SIL human T-cell lymphoblastic cell line vehicle only(DMSO) treatment control 24h


title: whole animal, cochlea: ctr-noggin #3_e1_le1

status: Public on Apr 12 2008

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description:
sibs of six1-noggin #3; eggs collected from 2 females; un-injected; cultured in Noggin; 130 ACs in sample; stage16
Treatment, type=grow, description=un-injected; cultured in 200ng/ml Noggin

organism: Xenopus laevis

source_name: whole animal, cochlea


title: whole animal, cochlea: Six1-noggin#5_e1_le1

description:
Injected Six1 mRNA (400pg) into both cells at 2-cell stage.  ACs removed at stage 8-9 and cultured in 200ng/ml Noggin protein.  132 ACs in sample; st 15/16.
Treatment, type=genetic_modification, description=Six1 WT mRNA injected (400pg/cell); cultured in 200ng/ml Noggin


title: whole animal, cochlea: Biotin-cDNA

description:
Injected Six1 mRNA (400pg) into both cells at 2-cell stage.  ACs removed at stage 8-9 and cultured in 200ng/ml Noggin protein.  40 ACs in sample; st 15/16.
Treatment, type=genetic_modification, description=Six1 WT mRNA injected (400pg/cell); cultured in 200ng/ml Noggin


title: whole animal, cochlea: Six1-noggin#4_e1_le1


title: whole animal, cochlea: ctr-noggin #4_e1_le1

description:
sibs of six1-noggin #4; eggs collected from 1 female; un-injected; cultured in Noggin; 128 ACs in sample; stage 15/16
Treatment, type=grow, description=un-injected; cultured in 200ng/ml Noggin


title: whole animal, cochlea: Six1-noggin#2_e1_le1

description:
Injected Six1 mRNA (400pg) into both cells at 2-cell stage.  ACs removed at stage 8-9 and cultured in 200ng/ml Noggin protein.  110 ACs in sample; st 15/16.
Treatment, type=genetic_modification, description=Six1 WT mRNA injected (400pg/cell); cultured in 200ng/ml Noggin


title: whole animal, cochlea: ctr-noggin #2_e1_le1

description:
sibs of six1-noggin #2; eggs collected from 2 females; un-injected; cultured in Noggin; 130 ACs in sample; stage15/16
Treatment, type=grow, description=un-injected; cultured in 200ng/ml Noggin


title: 0-1hr embryo

status: Public on Jun 02 2008

first: Wei-Jen

last: Chung

address: 430 E 67th St

institute: Sloan-Kettering Institute

description: small RNAs

source_name: Drosophila melanogaster 0-1hr embryo

extract_protocol: total RNA from 0-1hr embryo, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: Drosophila melanogaster 0-1hr embryo


title: whole animal, cochlea: ctr-noggin #5_e1_le1

description:
sibs of six1-noggin #5; eggs collected from 1 female; un-injected; cultured in Noggin; 128 ACs in sample; stage 15/16
Treatment, type=grow, description=un-injected; cultured in 200ng/ml Noggin


title: whole animal, cochlea: Six1-noggin#3_e1_le1

description:
Injected Six1 mRNA (400pg) into both cells at 2-cell stage.  ACs removed at stage 8-9 and cultured in 200ng/ml Noggin protein.  140 ACs in sample; st 16.
Treatment, type=genetic_modification, description=Six1 WT mRNA injected (400pg/cell); cultured in 200ng/ml Noggin


title: whole animal, cochlea: foxD5-noggin #3_e1_le1

description:
foxD5-injected mRNA (100pg per cell) at 2CS; caps created at stage 8-9; cultured in 200ng/ml Noggin until st 12.0-12.5. 129 caps in sample.
Treatment, type=genetic_modification, description=injected 100 pg foxD5 mRNA per cell; cultured in 200ng/ml Noggin


title: whole animal, cochlea: ctl-noggin #4_e1_le1

description:
siblings of foxD5-noggin #4; un-injected; cultured in 200ng/ml Noggin. 110  small caps in sample; stage 12.0-12.5
Treatment, type=grow, description=uninjected, culturd in 200ng/ml Noggin


title: whole animal, cochlea: ctl-noggin #2_e1_le1

description:
siblings of foxD5-noggin #2; un-injected; cultured in 200ng/ml Noggin. 136 caps in sample; stage 11.5-12.0
Treatment, type=grow, description=uninjected, culturd in 200ng/ml Noggin


title: whole animal, cochlea: foxD5-noggin #4_e1_le1

description:
foxD5-injected mRNA (100pg per cell) at 2CS; caps created at stage 8-9; cultured in 200ng/ml Noggin until st 12.5. 100 small caps in sample.
Treatment, type=genetic_modification, description=injected 100 pg foxD5 mRNA per cell; cultured in 200ng/ml Noggin


title: whole animal, cochlea: ctr-noggin #1_e1_le1

description:
sibs of six1-noggin #1; eggs collected from 2 females; un-injected; cultured in Noggin; 97 ACs in sample; stage15/16
Treatment, type=grow, description=un-injected; cultured in 200ng/ml Noggin


title: whole animal, cochlea: ctl-noggin #3_e1_le1

description:
siblings of foxD5-noggin #3; un-injected; cultured in 200ng/ml Noggin. 135 caps in sample; stage 11.5-12.0
Treatment, type=grow, description=uninjected, culturd in 200ng/ml Noggin


title: whole animal, cochlea: ctl-noggin #1_e1_le1

description:
siblings of foxD5-noggin #1; un-injected; cultured in 200ng/ml Noggin. 128 caps in sample; stage 11.5-12.5
Treatment, type=grow, description=uninjected, culturd in 200ng/ml Noggin


title: whole animal, cochlea: foxD5 #4_e1_le1

description:
foxD5-injected mRNA (100pg per cell) at 2CS; caps created at stage 8-9; cultured until st 11.5-12.5. 142 caps in sample.
Treatment, type=genetic_modification, description=injected 100 pg foxD5 mRNA per cell


title: whole animal, cochlea: ctr #1_e1_le1

description:
siblings of foxD5 #1; un-injected . 45 caps in sample
Treatment, type=grow, description=no mRNA injection


title: whole animal, cochlea: foxD5-noggin_e1_le1

description:
foxD5-injected mRNA (100pg per cell) at 2CS; caps created at stage 8-9; cultured in 200ng/ml Noggin until st 11.5-12.5. 121 caps in sample.
Treatment, type=genetic_modification, description=injected 100 pg foxD5 mRNA per cell; cultured in 200ng/ml Noggin


title: whole animal, cochlea: foxD5-noggin #2_e1_le1

description:
foxD5-injected mRNA (100pg per cell) at 2CS; caps created at stage 8-9; cultured in 200ng/ml Noggin until st 11.5-12.5. 136 caps in sample.
Treatment, type=genetic_modification, description=injected 100 pg foxD5 mRNA per cell; cultured in 200ng/ml Noggin


title: whole animal, cochlea: ctr #4_e1_le1

description:
siblings of foxD5 #4; un-injected. 142 caps in sample.
Treatment, type=grow, description=no mRNA injection


title: whole animal, cochlea: cDNA labeling

description:
foxD5-injected mRNA (100pg per cell) at 2CS; caps created at stage 8-9; cultured until st 11.5-13.0. 171 caps in sample.
Treatment, type=genetic_modification, description=injected 100 pg foxD5 mRNA per cell


title: whole animal, cochlea: ctr #2_e1_le1

description:
siblings of foxD5 #2; un-injected . 169 caps in sample
Treatment, type=grow, description=no mRNA injection


title: whole animal, cochlea: ctr #3_e1_le1

description:
siblings of foxD5 #3; un-injected . 124 caps in sample
Treatment, type=grow, description=no mRNA injection


title: whole animal, cochlea: foxD5 #3_e1_le1

description:
foxD5-injected mRNA (100pg per cell) at 2CS; caps created at stage 8-9; cultured until st 12.5-13.0. 118 caps in sample.
Treatment, type=genetic_modification, description=injected 100 pg foxD5 mRNA per cell


title: whole animal, cochlea: foxD5 #2_e1_le1

description:
foxD5-injected mRNA (100pg per cell) at 2CS; caps created at stage 8-9; cultured until st 12.5-13.0. 135 caps in sample.
Treatment, type=genetic_modification, description=injected 100 pg foxD5 mRNA per cell


title: ALLSIL DMSO control 24h rep2

description: Standard Affymetrix procedure

source_name: ALL-SIL human T-cell lymphoblastic cell line vehicle only (DMSO) treatment control 24h


title: ATH-AGO2

status: Public on Apr 06 2008

city: Beijing

first: Tao

last: Cai

address: No. 7 Science Park Road, Zhongguancun Life Science Park

country: China

institute: National Institute Of Biological Sciences, Beijing (NIBS)

description: Small RNAs were prepared from Arabidopsis AGO1, AGO2, AGO4 and AGO4 complexes, ligated to a 3' adaptor and a 5' acceptor sequentially, and then RT-PCR amplified. PCR products were reamplified using a pair of solexa cloning primers and then provided for sequencing.

data_processing: The adaptor sequences were removed using “vectorstrip” in EMBOSS package. The sRNA reads with length of 19-27 nt were mapped to the Arabidopsis nuclear, chloroplast and mitochondrial genomes (http://www.arabidopsis.org/). The sRNAs with perfect genomic matches are used for further analysis

organism: Arabidopsis thaliana

source_name: Immunopurified Arabidopsis AGO2 complex

extract_protocol: Small RNAs were extracted from immunopurified AGO complexes using Trizol reagent

tag: Small RNAs that are associated with Arabidopsis AGO2 complex


title: ZM_4d_SG200_3inf_I

status: Public on Mar 01 2008

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

description:
3. leaf of maize seedlings 4 days post Ustilago maydis infection. Infection was performed 7 days post sowing. Dissected leaf tissue from 30 plants was pooled. Samples were harvested in the evening.
ZM_4d_SG200 I

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Maize Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (Expression Analysis Technical Manual, 2001, Affymetrix)

scan_protocol: Microarrays were scanned on an Affymetrix GSC3000.

data_processing: Data were analyzed with Microarray Suite version 5.1 (MAS 5.1) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.

source_name: leaf tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Maize plants of the cultivar Early Golden Bantam were grown in a phytochamber in a 15 h / 9 h light-dark cycle; light period started with a  continuous increase from 0% to 100% light for 1h, and ended 13h later with a continuous decrease from 100% to 0% light for 1 h. Temperature was 28°C and 20°C, relative humidity 40% and 60% during light and dark periods, respectively, with a 1 h ramping for both values. Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) to avoid shading of the plants.

extract_protocol: For RNA isolation, material from 30 plants was pooled and subsequently ground in liquid nitrogen by mortar and pestle. RNA was extracted from the powder with Trizol (Invitrogen) and purified using the Qiagen RNeasy kit, according to the manufacturer’s instructions, respectively.

treatment_protocol: U. maydis strain SG200 (Nature 444:97-101) was grown in liquid culture overnight to an OD600 of 1.0, harvested by centrifugation, and resuspended in water to an OD600 of 3.0; compatible strains were mixed in equal amounts immediately before infection; 0.2 ml of cell suspension mixes were injected into the leaf whorl of 6–7-day-old corn plants (as described in Mol Microbiology 42:1047-1063). Plants were infected 7 days after sowing 1 h before end of the light period with the exception of the 12 hpi samples were plants were infected during the beginning of the light period.

tag: tissue

value: leaf


title: ATH-AGO1

source_name: Immunopurified Arabidopsis AGO1 complex

tag: Small RNAs that are associated with Arabidopsis AGO1 complex


title: ATH-AGO5

source_name: Immunopurified Arabidopsis AGO5 complex

tag: Small RNAs that are associated with Arabidopsis AGO5 complex


title: 2-6hr embryo

description: small RNAs

source_name: Drosophila melanogaster 2-6hr embryo

extract_protocol: total RNA from 2-6hr embryo, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: Drosophila melanogaster 2-6hr embryo


title: ZM_4d_Mock_3inf_I

description:
3. leaf of maize seedlings 4 days post mock infection. Infection was performed 7 days post sowing. Dissected leaf tissue from 30 plants was pooled. Samples were harvested in the evening.
ZM_4d_Mock I


title: ZM_4d_SG200_3inf_II

description:
3. leaf of maize seedlings 4 days post Ustilago maydis infection. Infection was performed 7 days post sowing. Dissected leaf tissue from 30 plants was pooled. Samples were harvested in the evening.
ZM_4d_SG200 II


title: ZM_4d_Mock_3inf_III

description:
3. leaf of maize seedlings 4 days post mock infection. Infection was performed 7 days post sowing. Dissected leaf tissue from 30 plants was pooled. Samples were harvested in the evening.
ZM_4d_Mock III


title: ZM_4d_SG200_3inf_III

description:
3. leaf of maize seedlings 4 days post Ustilago maydis infection. Infection was performed 7 days post sowing. Dissected leaf tissue from 30 plants was pooled. Samples were harvested in the evening.
ZM_4d_SG200 III


title: ms1 series sample 4 vs wt - set 2

status: Public on Aug 31 2007

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

country: Spain

institute: Center for Research in Agricultural Genomics

description:
Plants were grown on a soil:vermiculite:perlite mixture under constant illumination at 20°C. For the analysis of temporal gene expression in ms1 and wild-type flowers, a total of seven tissue samples were generated for each genotype containing floral buds of different developmental stages. To this end, we first removed all flowers in an inflorescence that had progressed beyond stage 13 (the stage when flowers reach maturity). We then collected stage 13 flowers resulting in sample No. 1.  For the following five samples (No. 2 to 6), we collected the next oldest floral buds, pooling two consecutive flowers per sample. The last tissue sample (No. 7) was comprised of the remaining, early-stage floral buds and the inflorescence meristem. For each sample, tissue from 50 plants was collected using jewelry forceps. Tissue collection for the different biologically independent sets of samples was done on different days but at the same time of day to minimize any diurnal effects on gene expression.
The dyes used for labeling RNA from the individual samples were switched in the replicate experiments to reduce dye-related artifacts.

hyb_protocol: Dye-labeled antisense RNA was hybridized to microarrays using a MAUI hybridization system (BioMicro Systems, Salt Lake City, UT, USA) as previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). Specifically, hybridizations were done as follows: dye-labeled antisense RNA preparations were dried down and the resulting pellets were re-suspended in 5 ul 10 mM EDTA and 45 ul SlideHyb Buffer #1 (Ambion, Austin, Texas, United States) and hybridized for 14 h to microarrays at 48C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah, United States) according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned and the data acquired with an Axon GenePix 4200A scanner using GenePix v5.0 analysis software.

data_processing: Data were processed with the Resolver data analysis system (Rosetta Biosoftware, Seattle, WA). VALUE column reports log10 (mutant/wt) ratio data.

source_name: wt sample 4

label_protocol: Dye-labeled antisense RNA was generated from the total RNA preparation as previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). In brief, first and second strand cDNA was synthesized from 3 ug of total RNA using a poly(A)-primer with a T7 promoter sequence. Then, in vitro transcription was performed using the Megascript T7 kit (Ambion, Austin, TX). For the oligonucleotide array, dye molecules were coupled to the amplified RNA, and the dye-labeled RNA was fragmented before hybridization.

extract_protocol: Total RNA was isolated from all tissue samples using the RNeasy RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.

tag: Material was derived from inflorescences of wt plants.

source_name: ms1 sample 4

label_protocol: same as for channel 1

tag: Material was derived from inflorescences of ms1-1 plants.


title: 2-6hr embryo #1

description: small RNAs


title: ms1 series sample 7 vs wt - set 2

source_name: wt sample 7

source_name: ms1 sample 7


title: ms1 series sample 3 vs wt - set 2

source_name: wt sample 3

source_name: ms1 sample 3


title: ms1 series sample 1 vs wt - set 2

source_name: wt sample 1

source_name: ms1 sample 1


title: ms1 series sample 5 vs wt - set 2

source_name: wt sample 5

source_name: ms1 sample 5


title: ms1 series sample 6 vs wt - set 2

source_name: wt sample 6

source_name: ms1 sample 6


title: ATH-AGO4

source_name: Immunopurified Arabidopsis AGO4 complex

tag: Small RNAs that are associated with Arabidopsis AGO4 complex


title: loqs-/- ovaries (18-29nt)

source_name: adult ovaries from loqs mutant flies

tag: from 2-4 day old flies


title: dcr-2-/- ovaries (18-29nt)

source_name: adult ovaries from dcr-2 mutant flies


title: S2cell (AGO1IP)

description: small RNA from immunoprecipitate

source_name: small RNAs isolated from AGO1 immunoprecipitate from S2 cells


title: ms1 series sample 7 vs wt - set 3


title: WT testes (18-24nt)

source_name: adult testes from OreR flies


title: S2cell (AGO2IP)

description: small RNA from immunoprecipitate

source_name: small RNAs isolated from AGO2 immunoprecipitate from S2 cells


title: ms1 series sample 2 vs wt - set 2

source_name: wt sample 2

source_name: ms1 sample 2


title: Wild type inflorescence PARE

status: Public on Jun 10 2008

city: Newark

first: Marcelo

middle: Ariel

last: German

state: DE

address: 15 Innovation Way

institute: Delaware Biotechnology Institute

description: raw data requested but not provided

data_processing: Raw abundances were normilazed according to the formula: normalized abundance (TP10M)= raw/(total genome match - (t/r/sn/snoRNA)*10,000,000.

molecule: polyA RNA

source_name: inflorescence whole

extract_protocol: A conventional Trizol extraction was used for total RNA extraction, followed by oligo (dT) columns for polyA RNA extraction.

tag: floral tissue (up to stage 11/12)


title: ms1 series sample 1 vs wt - set 3


title: WT ovaries (18-29nt)

source_name: adult ovaries from Celera sequencing strain


title: ms1 series sample 3 vs wt - set 3

source_name: ms1 sample 3

source_name: wt sample 3


title: ms1 series sample 7 vs wt - set 1

source_name: ms1 sample 7

source_name: wt sample 7


title: ms1 series sample 5 vs wt - set 3

source_name: ms1 sample 5

source_name: wt sample 5


title: ms1 series sample 4 vs wt - set 3

source_name: ms1 sample 4

source_name: wt sample 4


title: ms1 series sample 6 vs wt - set 1

source_name: ms1 sample 6

source_name: wt sample 6


title: ms1 series sample 5 vs wt - set 1


title: ms1 series sample 4 vs wt - set 1


title: ms1 series sample 2 vs wt - set 3


title: xrn4 inflorescence PARE

description: raw data requested but not provided


title: ms1 series sample 2 vs wt - set 1


title: ms1 series sample 6 vs wt - set 3


title: nzz vs wt - replicate 1

description:
Plants were grown on a soil:vermiculite:perlite mixture under constant illumination at 20°C.  For each sample, tissue from 50 plants was collected using jewelry forceps. Tissue samples containing the inflorescence meristem and floral buds up to stage 13 were collected for analysis. Tissue collection for the different biologically independent sets of samples was done on different days but at the same time of day to minimize any diurnal effects on gene expression.
The dyes used for labeling RNA from the individual samples were switched in the replicate experiments to reduce dye-related artifacts.

source_name: wt

source_name: nzz

tag: Material was derived from inflorescences of nzz-1 plants.


title: nzz vs wt - replicate 2


title: ms1 series sample 3 vs wt - set 1


title: nzz vs wt - replicate 3


title: ms1 vs wt - replicate 4

extract_protocol: Total RNA was isolated from using the RNeasy RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.


title: ms1 vs wt - replicate 1


title: nzz vs wt - replicate 4


title: ms1 vs wt - replicate 3


title: WT ovaries (AGO2IP)

description: small RNA from immunoprecipitate

source_name: small RNAs isolated from AGO2 immunoprecipitate from ovaries


title: ms1 series sample 1 vs wt - set 1

source_name: ms1 sample 1

source_name: wt sample 1


title: ms1 vs wt - replicate 2


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, custom chip, replicate 4, Cy3

status: Public on Sep 13 2006

city: Durham

first: Amanda

middle: J.

last: Moehring

state: NC

department: DCMB/Biology

institute: Duke University

scan_protocol: Fluorescent array images were collected at the Duke Microarray Core Facility.

data_processing: The median pixel feature intensity after background subtraction (EXPRESSION column) was log2 transformed, and normalized on Actin5C (giving the VALUE column) to obtain the values given in the data table.

organism: Drosophila sechellia x Drosophila simulans

source_name: Drosophila simulans/D. sechellia F1 hybrid males, 4 days old

label_protocol: The labelling was done at the Duke Microarray Core Facility.

extract_protocol: RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (10 µg) was annealed at the Duke Microarray Core Facility.

tag: Drosophila simulans/D. sechellia F1 hybrids


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, custom chip, replicate 3, Cy3

organism: Drosophila sechellia

source_name: Drosophila sechellia males, 4 days old

tag: Drosophila sechellia


title: D. simulans pure-species adults, D. simulans pure-species adults, custom chip for sim-sec, replicate 1, Cy3

organism: Drosophila simulans

source_name: Drosophila simulans males, 4 days old

tag: Drosophila simulans


title: D. sechellia pure-species adults, D. sechellia pure-species adults, custom chip, replicate 1, Cy3


title: D. simulans/D. sechellia hybrid adults, D. simulans/D. sechellia hybrid adults, custom chip, replicate 1, Cy3


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, custom chip, replicate 4, Cy3


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, custom chip, replicate 2, Cy3


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, custom chip, replicate 4, Cy3

organism: Drosophila simulans x Drosophila mauritiana

source_name: Drosophila simulans/D. mauritiana F1 hybrid males, 4 days old

tag: Drosophila simulans/D. mauritiana F1 hybrids


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, custom chip, replicate 2, Cy3


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, custom chip, replicate 1, Cy3

data_processing: The median pixel feature intensity after background subtraction (VALUE column) was log2 transformed, and normalized on Actin5C (giving the VALUE column) to obtain the values given in the data table.


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, custom chip, replicate 1, Cy3


title: Small RNAs from Chlamydomonas reinhardtii whole extracts

status: Public on May 16 2007

first: Yijun

last: Qi

address: No.7 Science Park Road,Zhongguancun Life Science Park

institute: National Institute of Biological Sciences, Beijing

description: Total small RNAs from Chlamydomonas reinhardtii

data_processing: The small RNA sequences were mapped to the Chlamydomonas reinhardtii  genome by using Perl scripts

organism: Chlamydomonas reinhardtii

source_name: whole extracts, Chlamydomonas reinhardtii

extract_protocol: Small RNAs were extracted by Trizol reagent and further purified by denaturing polyacrylamide gel


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, custom chip, replicate 3, Cy3


title: ap3 early stages vs wt - replicate 3

description:
Plants were grown on a soil:vermiculite:perlite mixture under constant illumination at 20°C.  For each sample, tissue from 50 plants was collected using jewelry forceps. We dissected older flowers from the inflorescences, and then collected the inflorescence meristem and floral buds up to early stage 10 for analysis. Tissue collection for the different biologically independent sets of samples was done on different days but at the same time of day to minimize any diurnal effects on gene expression.
The dyes used for labeling RNA from the individual samples were switched in the replicate experiments to reduce dye-related artifacts.

source_name: wt early stages

source_name: ap3 early stages

tag: Material was derived from inflorescences of ap3-3 plants.


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, custom chip, replicate 2, Cy3


title: Hubrecht/NIOB Ketting zebrafish testis piRNAs

status: Public on Apr 05 2007

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

institute: University Medical Center Groningen

description: small RNA

data_processing: adapter sequences were trimmed and inserts mapped to the zebrafish genome (Zv6 assembly).

organism: Danio rerio

source_name: freshly dissected zebrafish testes

extract_protocol: total RNA, ~25-30 nt RNAs isolated using PAGE

tag: Strain

value: TL, male, average age - 6 months


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, custom chip, replicate 3, Cy3

organism: Drosophila mauritiana

source_name: Drosophila mauritiana males, 4 days old

tag: Drosophila mauritiana


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, custom chip, replicate 1, Cy3


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, custom chip, replicate 2, Cy3


title: D. simulans/D. mauritiana hybrid adults, D. simulans/D. mauritiana hybrid adults, custom chip, replicate 1, Cy3


title: ap3 early stages vs wt - replicate 4


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, custom chip, replicate 3, Cy3


title: D. mauritiana pure-species adults, D. mauritiana pure-species adults, custom chip, replicate 1, Cy3


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, custom chip, replicate 4, Cy3


title: D. simulans pure-species adults, D. simulans pure-species adults, custom chip, replicate 1, Cy3


title: Hubrecht/NIOB Ketting zebrafish ovary piRNAs

description: small RNA

source_name: freshly dissected zebrafish ovaries

tag: strain

value: TL, females, average age - 6 month


title: ap3 early stages vs wt - replicate 1


title: ap3 early stages vs wt - replicate 2


title: MIT/WI Bartel C.elegans 454 2006

status: Public on Oct 15 2006

first: James

middle: Graham

last: Ruby

department: Biology

institute: Whitehead Institute for Biomedical Research and MIT

description: small RNAs

data_processing: extraction of sequences flanked by perfect 9mer matches to the expected adjacent adapter sequences

organism:
Escherichia coli
Caenorhabditis elegans

source_name: mixed-stage Caenorhabditis elegans with contaminating Escherichia coli

extract_protocol: total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: mixed-stage, wild-type, N2, 20 deg C


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species larvae, replicate 4, Cy3

source_name: Drosophila simulans/D. sechellia F1 hybrid males, third instar larvae


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species larvae, replicate 3, Cy3

source_name: Drosophila sechellia males, third instar larvae


title: D. simulans/D. sechellia hybrids, D. simulans pure-species larvae, replicate 1, Cy3

source_name: Drosophila simulans males, third instar larvae


title: D. simulans/D. sechellia hybrids, D. simulans pure-species larvae, replicate 2, Cy3


title: D. simulans/D. sechellia hybrids, D. simulans pure-species larvae, replicate 3, Cy3


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species larvae, replicate 2, Cy3


title: D. simulans/D. mauritiana hybrids, D. simulans/D. mauritiana hybrids, replicate 1, Cy3

source_name: Drosophila simulans/D. mauritiana F1 hybrid males, third instar larvae


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species larvae, replicate 1, Cy3


title: D. mauritiana pure-species, D. mauritiana pure-species, replicate 1, Cy3

source_name: Drosophila mauritiana males, third instar larvae


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species, replicate 2, Cy3


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species, replicate 4, Cy3


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species, replicate 4, Cy3


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species, replicate 3, Cy3


title: D. simulans/D. sechellia hybrids, D. simulans pure-species larvae, replicate 4, Cy3


title: D. sechellia pure-species larvae, D. sechellia pure-species larvae, replicate 1, Cy3


title: D. simulans/D. sechellia hybrid larvae, D. simulans/D. sechellia hybrid larvae, replicate 1, Cy3


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, custom chip, replicate 1, Cy3


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species, replicate 2, Cy3


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species, replicate 1, Cy3


title: D. simulans pure-species, D. simulans pure-species, replicate 1, Cy3


title: ZM_4d_Mock_3inf_II

description:
3. leaf of maize seedlings 4 days post mock infection. Infection was performed 7 days post sowing. Dissected leaf tissue from 30 plants was pooled. Samples were harvested in the evening.
ZM_4d_Mock II

source_name: leaf tissue

tag: tissue


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species, replicate 3, Cy3


title: D. sechellia pure-species adults, D. sechellia pure-species adults, custom chip, replicate 1, Cy5


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, custom chip, replicate 4, Cy5


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, custom chip, replicate 4, Cy5


title: D. simulans/D. sechellia hybrid adults, D. simulans/D. sechellia hybrid adults, custom chip, replicate 1, Cy5

source_name: Drosophila simulans/D. sechellia F1 hybrid males, 4 days old


title: D. simulans pure-species adults, D. simulans pure-species adults, custom chip for sim-sec, replicate 1, Cy5


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, custom chip, replicate 2, Cy5

source_name: Drosophila sechellia males, 4 days old


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, custom chip, replicate 3, Cy5


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, custom chip, replicate 4, Cy5

source_name: Drosophila simulans males, 4 days old


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, custom chip, replicate 3, Cy5


title: D. simulans pure-species adults, D. simulans pure-species adults, custom chip, replicate 1, Cy5


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, custom chip, replicate 1, Cy5


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, custom chip, replicate 1, Cy5


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, custom chip, replicate 2, Cy5


title: D. simulans/D. mauritiana hybrid adults, D. simulans/D. mauritiana hybrid adults, custom chip, replicate 1, Cy5

source_name: Drosophila simulans/D. mauritiana F1 hybrid males, 4 days old


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, custom chip, replicate 4, Cy5


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species, replicate 1, Cy3


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species larvae, replicate 4, Cy5


title: D. simulans/D. sechellia hybrid larvae, D. simulans/D. sechellia hybrid larvae, replicate 1, Cy5


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, custom chip, replicate 1, Cy5


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, custom chip, replicate 3, Cy5


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, custom chip, replicate 3, Cy5


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species larvae, replicate 3, Cy5


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, custom chip, replicate 2, Cy5


title: D. simulans/D. sechellia hybrids, D. simulans pure-species larvae, replicate 4, Cy5


title: D. mauritiana pure-species adults, D. mauritiana pure-species adults, custom chip, replicate 1, Cy5


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, custom chip, replicate 2, Cy5


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species larvae, replicate 1, Cy5


title: D. sechellia pure-species larvae, D. sechellia pure-species larvae, replicate 1, Cy5


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, custom chip, replicate 1, Cy5


title: D. simulans/D. sechellia hybrids, D. simulans pure-species larvae, replicate 2, Cy5


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species larvae, replicate 2, Cy5


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species, replicate 1, Cy5


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species, replicate 2, Cy5


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species, replicate 2, Cy5


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species, replicate 3, Cy5


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species, replicate 4, Cy5


title: D. simulans/D. mauritiana hybrids, D. simulans/D. mauritiana hybrids, replicate 1, Cy5


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species, replicate 3, Cy5


title: D. simulans pure-species, D. simulans pure-species, replicate 1, Cy5


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species, replicate 4, Cy5


title: D. simulans/D. sechellia hybrids, D. simulans pure-species larvae, replicate 1, Cy5


title: D. mauritiana pure-species, D. mauritiana pure-species, replicate 1, Cy5


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, genome chip, replicate 2, Cy3

data_processing: The median pixel feature intensity after background subtraction (EXPRESSION column) was log2 transformed, and normalized on the median for that hybridization (giving the VALUE column) to obtain the values given in the data table.


title: D. simulans/D. sechellia hybrids, D. simulans pure-species larvae, replicate 3, Cy5


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, genome chip, replicate 3, Cy3


title: D. simulans/D. sechellia hybrids, D. simulans/D. sechellia hybrid adults, genome chip, replicate 1, Cy3


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, genome chip, replicate 1, Cy3

data_processing: The median pixel feature intensity after background subtraction (VALUE column) was log2 transformed, and normalized on the median for that hybridization (giving the VALUE column) to obtain the values given in the data table.


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, genome chip, replicate 1, Cy5


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, genome chip, replicate 3, Cy3


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, genome chip, replicate 1, Cy3


title: D. mauritiana pure-species adults, D. mauritiana pure-species adults, genome chip, replicate 1, Cy5


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, genome chip, replicate 2, Cy5


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, genome chip, replicate 4, Cy3


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species, replicate 1, Cy5


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, genome chip, replicate 4, Cy3


title: D. sechellia pure-species, D. sechellia pure-species adults, genome chip, replicate 1, Cy3


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, genome chip, replicate 3, Cy3


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, genome chip, replicate 2, Cy3


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, genome chip, replicate 4, Cy3


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, genome chip, replicate 1, Cy3


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, genome chip, replicate 2, Cy3


title: D. mauritiana pure-species adults, D. mauritiana pure-species adults, genome chip, replicate 1, Cy3


title: D. simulans pure-species adults, D. simulans pure-species adults, genome chip, replicate 1, Cy3


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, genome chip, replicate 1, Cy5


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, genome chip, replicate 4, Cy5


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, genome chip, replicate 3, Cy5


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, genome chip, replicate 1, Cy3


title: D. simulans/D. sechellia hybrids, D. simulans/D. sechellia hybrid adults, genome chip, replicate 1, Cy5


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, genome chip, replicate 1, Cy5


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, genome chip, replicate 4, Cy5


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, genome chip, replicate 4, Cy5


title: D. simulans/D. sechellia hybrids, D. simulans pure-species adults, genome chip, replicate 2, Cy5


title: D. sechellia pure-species, D. sechellia pure-species adults, genome chip, replicate 1, Cy5


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, genome chip, replicate 3, Cy3


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, genome chip, replicate 2, Cy5


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, genome chip, replicate 3, Cy5


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, genome chip, replicate 2, Cy3


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, genome chip, replicate 2, Cy5


title: D. simulans/D. mauritiana hybrid adults, D. simulans/D. mauritiana hybrid adults, genome chip replicate 1, Cy5


title: D. simulans/D. mauritiana hybrids, D. simulans pure-species adults, genome chip, replicate 1, Cy5


title: D. simulans/D. sechellia hybrids, D. sechellia pure-species adults, genome chip, replicate 3, Cy5


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, genome chip, replicate 3, Cy5


title: D. simulans/D. mauritiana hybrid adults, D. simulans/D. mauritiana hybrid adults, genome chip replicate 1, Cy3


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, genome chip, replicate 4, Cy5


title: D. simulans pure-species adults, D. simulans pure-species adults, genome chip, replicate 1, Cy5


title: D. simulans/D. mauritiana hybrids, D. mauritiana pure-species adults, genome chip, replicate 4, Cy3


title: BF-MCF10A-A1(rep2)

status: Public on Sep 10 2006

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

description: HB4A was used as reference

hyb_protocol: Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 4 ug Cot1 DNA; 5X Denhardt´s ; 10 ug Esperma de salmão,  Formamida 25%. / Temperature:14 a 24 hs / Time:42 C / Touch Down: Washing - Round 1 - Solution: 0,1 X SSC / Temperature:sol 42C / Lavagem TA / Time:5 min / Washing Number: 1 Washing - Round 2 - Solution: 0,1 X SSC / Temperature:sol 42C / Lavagem TA / Time:10 min / Washing Number: 2 Washing - Round 3 - Solution: 0,1 X SSC / Temperature:sol 42C / Lavagem TA / Time:2,5 min / Washing Number: 2

scan_protocol: Hardware: Perkinelmer / Software: ScanArray

data_processing: Lowesss

organism: Homo sapiens

source_name: MCF10A cell line

tag: cell line

source_name: HB4A luminal mammary epithelial cell line


title: BF-MDA231b-A1(rep2)

description: HB4A was used as reference

source_name: MDA231b cell line


title: BF-MDA231b-3(rep1)

description: HB4A was used as reference


title: BF-MDA231b-2(rep2)

description: HB4A was used as reference


title: BF-MDA231b-3(rep2)

description: HB4A was used as reference


title: BF-MDA231b-A1(rep1)

description: HB4A was used as reference


title: BF-MDA231b-2(rep1)

description: HB4A was used as reference


title: BF-MCF10A-3(rep1)

description: HB4A was used as reference


title: BF-FT4c-c(rep2)

description: HB4A was used as reference

source_name: MCF10A cells cocultured with CAF4


title: BF-FT3d-d(rep2)

description: HB4A was used as reference

source_name: MDA-MB231 cells cocultured with CAF3


title: BF-MCF10A-2(rep1)

description: HB4A was used as reference


title: BF-FT4d-FT4(rep1)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF4 cocultured with MDA-MB231

tag: female


title: BF-FT3d-d(rep1)

description: HB4A was used as reference


title: BF-FT4a(rep2)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF4


title: BF-FT3c-c(rep1)

description: HB4A was used as reference

source_name: MCF10A cells cocultured with CAF3


title: BF-MCF10A-2(rep2)

description: HB4A was used as reference


title: BF-FT3c-FT3(rep2)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF3 cocultured with MCF10A cells


title: BF-FT3a(rep2)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF3


title: BF-MCF10A-3(rep2)

description: HB4A was used as reference


title: BF-FT3c-c(rep2)

description: HB4A was used as reference

tag: Cell line


title: BF-FT3d-FT3(rep1)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF3 cocultured with MDA-MB231


title: BF-FT3b(rep1)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF3 HAMF-12 medium


title: BF-FT4d-d(rep1)

description: HB4A was used as reference

source_name: MDA-MB231 cells cocultured with CAF4


title: BF-FT4c-FT4(rep2)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF4 cocultured with MCF10A cells

tag: cell ine


title: BF-MCF10A-A1(rep1)

description: HB4A was used as reference


title: BF-FT4c-FT4(rep1)

description: HB4A was used as reference


title: BF-FT3b(rep2)

description: HB4A was used as reference


title: BF-FT3d-FT3(rep2)

description: HB4A was used as reference


title: BF-FT3c-FT3(rep1)

description: HB4A was used as reference


title: BF-FT4b(rep2)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF4 HAMF-12 medium


title: BF-FT4c-c(rep1)

description: HB4A was used as reference


title: BF-FT4b(rep1)

description: HB4A was used as reference


title: BF-FT2d-FT2(rep2)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF2 cocultured with MDA-MB231 cells

source_name: HB4A Luminal mammary epithelial cell line


title: BF-FT4d-FT4(rep2)

description: HB4A was used as reference


title: BF-FT3a(rep1)

description: HB4A was used as reference


title: BF-FT4d-d(rep2)

description: HB4A was used as reference


title: BF-FT2c-c (rep2)

description: HB4A was used as reference

source_name: MCF10A cells cocultured with carcinoma associated fibroblasts CAF2


title: BF-FT2d-d (rep1)

description: HB4A was used as reference

source_name: MDA-MB231 cells cocultured with carcinoma associated fibroblasts CAF2

label: c


title: BF-FT2d-d (rep2)

description: HB4A was used as reference


title: BF-FT2c-FT2(rep2)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF2 cocultured with MCF10A cells


title: BF-FT1d-d(rep2)

description: HB4A was used as reference

source_name: MDA-MB231 cells cocultured with CAF1

source_name: HB4A luminal mammary epithelial cell line


title: BF-FT2a (rep1)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF2


title: BF-FT2a (rep2)

description: HB4A was used as reference

source_name: HHB4A Luminal mammary epithelial cell line


title: BF-FT2c-c (rep1)

description: HB4A was used as reference


title: BF-FT1d-d(rep1)

description: HB4A was used as reference


title: BF-FT2d-FT2(rep1)

description: HB4A was used as reference


title: BF-FT2c-FT2(rep1)

description: HB4A was used as reference


title: BF-FT1c-c(rep1)

description: HB4A was used as reference

source_name: MCF10A cells cocultured with carcinoma associated fibroblasts CAF1


title: BF-FT2b (rep2)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF2 HAMF-12 medium


title: BF-FT1c-c(rep2)

description: HB4A was used as reference


title: BF-FT2b (rep1)

description: HB4A was used as reference


title: BF-FT1a(rep1)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF1


title: BF-FT1a(rep2)

description: HB4A was used as reference

tag: cell


title: BF-FT1c-FT1(rep2)

description: HB4A was used as reference

source_name: Carcinoma Associated Fibroblast CAF1 cocultured with MCF10A cells

tag: cell lineh


title: BF-FT1d-FT1(rep2)

description: HB4A was used as reference

source_name: Carcinoma Associated Fibroblast CAF1 cocultured with MDA-MB231 cells


title: BF-FN8d-d(rep1)

description: HB4A was used as reference

source_name: MDA-MB231 cell line cocultured with benign breast disease NAF8


title: BF-FN8d-FN8(rep1)

description: HB4A was used as reference

source_name: Benign Breast Disease cocultured with MDA-231MB NAF8


title: BF-FT1d-FT1(rep1)

description: HB4A was used as reference


title: BF-FT1b(rep2)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF1 HAMF-12 medium


title: BF-FN8c-FN8(rep2)

description: HB4A was used as reference

source_name: Breast Benign Disease cocultured with MCF10A cells


title: BF-FT1b(rep1)

description: HB4A was used as reference

source_name: Carcinoma Associated Fibroblast CAF1 HAMf-12 medium


title: BF-FN8d-FN8(rep2)

description: HB4A was used as reference


title: BF-FN8d-d(rep2)

description: HB4A was used as reference


title: BF-FT1c-FT1(rep1)

description: HB4A was used as reference


title: BF-FN8c-FN8(rep1)

description: HB4A was used as reference


title: BF-FN8c-c(rep1)

description: HB4A was used as reference

source_name: MCF10A cell line cocultured with benign breast disease NAF8


title: BF-FN8c-c(rep2)

description: HB4A was used as reference


title: BF-FN8a(rep1)

description: HB4A was used as reference

source_name: Benign Breast Disease NAF8


title: BF-FN8a(rep2)

description: HB4A was used as reference


title: BF-FN7c-c(rep2)

description: HB4A was used as reference

source_name: MCF10A cell line cocultured with benign breast disease NAF7


title: BF-FN8b(rep2)

description: HB4A was used as reference

source_name: Benign Breast Disease NAF8 HAMf-12 Medium


title: BF-FN7c-c(rep1)

description: HB4A was used as reference

source_name: HB4A luminal mammary epithelial cell line


title: BF-FN7a(rep1)

description: HB4A was used as reference

source_name: Benign Breast Disease NAF7


title: BF-FN8b(rep1)

description: HB4A was used as reference


title: BF-FN7c-FN7(rep2)

description: HB4A was used as reference


title: BF-FN6d-d(rep2)

description: HB4A was used as reference

source_name: MDA-MB231 cell line cocultured with benign breast disease NAF6


title: BF-FN6d-d(rep1)

description: HB4A was used as reference


title: BF-FN6d-FN6(rep2)

description: HB4A was used as reference

source_name: Benign Breast Disease cocultured with MDA-231MB


title: BF-FN5d-d (rep2)

description: HB4A was used as reference

source_name: MDA-MB231 cell line cocultured with benign breast disease


title: BF-FN5d-d (rep1)

description: HB4A was used as reference


title: BF-FN6c-c (rep2)

description: HB4A was used as reference

source_name: MCF10A cell line cocultured with benign breast disease NAF6

source_name: HB4A Luminal mammary epithelial cell line


title: BF-FN6c-c (rep1)

description: HB4A was used as reference


title: BF-FN6a (rep1)

description: HB4A was used as reference

source_name: Benign Breast Disease NAF6


title: BF-FN6a (rep2)

description: HB4A was used as reference


title: BF-FN7a(rep2)

description: HB4A was used as reference


title: BF-FN6c-FN6(rep2)

description: HB4A was used as reference


title: BF-FN7c-FN7(rep1)

description: HB4A was used as reference


title: BF-FN6b (rep1)

description: HB4A was used as reference

source_name: Benign Breast Disease NAF6 HAMf-12 Medium


title: BF-FN5c-c (rep2)

description: HB4A was used as reference

source_name: MCF10A cocultured with NAF5


title: BF-FN6d-FN6(rep1)

description: HB4A was used as reference


title: BF-FN6b (rep2)

description: HB4A was used as reference


title: BF-FN5d-FN5 (rep2)

description: HB4A was used as reference

source_name: Benign Breast Disease cocultured with MDA-MB231 cells

tag: Female


title: BF-FN5d-FN5 (rep1)

description: HB4A was used as reference


title: BF-FN6c-FN6(rep1)

description: HB4A was used as reference

source_name: Breast Benign Disease cocultured with MCF10A cells


title: BF-FT4a(rep1)

description: HB4A was used as reference

source_name: Carcinoma associated fibroblast CAF4


title: Bf-FN5c-FN5 (rep1)

description: HB4A was used as reference

source_name: Benign Breast Disease cocultured with MCF10A cells


title: Bf-FN5c-FN5 (rep2)

description: HB4A was used as reference


title: BF-FN5a (rep1)

description: HB4A was used as reference sample

source_name: Benign Breast Disease


title: BF-FN5a (rep2)

description: HB4A was used as reference sample


title: BF-FN5c-c (rep1)

description: HB4A was used as reference


title: BF-FN5b (rep2)

description: HB4A was used as reference

source_name: Benign Breast disease


title: Epithelial_Component_Wilms_Tumor_30_rep2

status: Public on Aug 01 2006

type: other

description: Patient had chemotherapy as first treatment. Epithelial component was scalpel microdissected / polyA RNA was amplified.

hyb_protocol: Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 4 ug Cot1 DNA; 5X Denhardt´s ; 10 ug Salmon sperm, Deyonized formamide 25%, 20 mg BSA / Temperature:42oC / Time:16-20hrs / Touch Down: 70oC-55oC-42oC Washing - Round 1 - Solution: SSC2X / Temperature:42ºC / Time:15' / Washing Number: 1 Washing - Round 2 - Solution: SSC0,1X-SDS0,1% / Temperature:42ºC / Time:15' / Washing Number: 2 Washing - Round 3 - Solution: SSC0,1X / Temperature:42ºC / Time:15' / Washing Number: 2

molecule: other

source_name: Reference

tag: Pool of 6 mature kidneys

source_name: Epithelial Component 30

tag: Gender male, Age

value: 11 months, Epithelial component from Wilms tumor triphasic, stage III


title: Epithelial_Component_Wilms_Tumor_22_rep1

description: Patient had chemotherapyas first treatment. Epithelial component was laser microdissected / polyA RNA was amplified.

source_name: Epithelial Component 22

tag: Gender female, Age

value: 86 months, Epithelial from Wilms tumor tripasic, stage I


title: Stromal_Component_Wilms_Tumor_28_rep1

description: Patient had surgery as first treatment. Stromal component was scalpel microdissected / polyA RNA was amplified.

source_name: Stromal Component 28

value: 7 months, Stromal component from Wilms tumor predominatly stromal, stage III


title: Epithelial_Component_Wilms_Tumor_10_rep1

description: Patient had surgery as first treatment. Epithelial component was scalpel microdissected / polyA RNA was amplified.

source_name: Epithelial Component 10

value: 15 months, Blastema component from Wilms tumor predominatly epithelial, stage I


title: Stromal_Component_Wilms_Tumor_28_rep2


title: Epithelial_Component_Wilms_Tumor_30_rep1


title: Epithelial_Component_Wilms_Tumor_26_rep2

source_name: Epithelial Component 26

value: 19 months, Epithelial component from Wilms tumor predominatly epithelial, stage I


title: Epithelial_Component_Wilms_Tumor_26_rep1


title: Epithelial_Component_Wilms_Tumor_18_rep2

description: Epithelial component was scalpel microdissected / polyA RNA was amplified.

source_name: Epithelial Component 18

tag: unknown


title: Epithelial_Component_Wilms_Tumor_17_rep1

description: Patient had chemotherapy as first treatment. Epithelial component was laser microdissected / polyA RNA was amplified.

source_name: Epithelial Component 17

value: 44 months, Epithelial component from Wilms tumor triphasic, stage I


title: Stromal_Component_Wilms_Tumor_20_rep2

description: Patient had chemotherapy as first treatment. Stromal component was scalpel microdissected / polyA RNA was amplified.

source_name: Stromal Component 20

value: 38 months, Stromal component from Wilms tumor predominatly stroma, stage IV


title: Epithelial_Component_Wilms_Tumor_10_rep2


title: Stromal_Component_Wilms_Tumor_7_rep2

source_name: Stromal Component 7

value: 29 months, Stromal component from Wilms tumor predominatly blastemal, stage


title: Stromal_Component_Wilms_Tumor_20_rep1


title: Blastemal_Component_Wilms_Tumor_7_rep2

description: Patient had chemotherapy as first treatment. Blastema component was scalpel microdissected / polyA RNA was amplified.

source_name: Blastemal Component 7

value: 29 months, Blastema component from Wilms tumor triphasic, stage III


title: Epithelial_Component_Wilms_Tumor_17_rep2


title: Blastemal_Component_Wilms_Tumor_7_rep1