title: PIF5ox input

data_processing:
Reads were mapped to the Arabidopsis thaliana genome (TAIR8, www.arabidopsis.org) using bowtie (version 0.12.7) and filtered for uniquely mapping reads. Peak were detected with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
Genome Build:
PH2_m1.bam: TAIR8
PH2_m1_btb_chrom.bed: TAIR8

tag: age


title: FUS3_ChIP

status: Public on Jan 11 2013

type: genomic

city: Lexington

first: Sharyn

middle: E

last: Perry

state: KY

address: 1405 Veterans Dr.

department: Plant and Soil Sciences

country: USA

institute: University of Kentucky

description: rep 1-3

hyb_protocol: The UK Microarray core facility performed the hybridization and scan using the Affymetrix hybridization kit

scan_protocol: Affymetrix Scanner 3000 7G

data_processing:
Normalization was using quantile in CisGenome
additional results files: peakPM2.5left_all.bed
results file descriptions: results from analysis in CisGenome for all three biological replicates together

label: biotin

molecule: genomic DNA

organism: Arabidopsis thaliana

label_protocol: Samples (7.5 microgram of DNA) were processed following the Affymetrix protocol to fragment and biotin label

growth_protocol: An embryonic culture was derived from zygotic Arabidopsis embryos that constitutively express AGL15. The test culture also has proFUS3:FUS3-c-myc in the fus3-3 mutant background while the control expressed wild type FUS3 from the endogenous gene. The culture was grown on MS media supplemented with 10 g L-1 sucrose, 0.5 g L-1 MES and 7 g L-1 agar (pH 5.6-5.7) with kanamycin and/or hygromycin and maintained at 23°C to 24°C with a 23-h-light/1-h-dark regime.

extract_protocol: ChIP was performed as in Wang et al., 2013, Plant Physiology,  using c-myc antibody

treatment_protocol: Tissue was fixed in MC buffer (10 mM potassium phosphate pH 7, 50 mM NaCl, 0.1 M sucrose) with 1% formaldehyde for one hour on ice under vacuum. The reaction was quenched with addition of cold glycine to 0.125 M and incubation on ice continued 10-30 min, after which the tissue was washed with cold MC buffer and flash frozen.

tag: tissue

value: Embryonic culture expressing FUS3-10x-c-myc

tag: antibody

value: anti-c-myc

tag: antibody vendor/catalog

value: Cell Signaling Technology #2276S

source_name: Control immunoprecipitation

value: Embryonic culture expressing FUS3 (no c-myc tag)


title: P3M-ChIP-3

status: Public on Feb 01 2013

type: SRA

city: Albany

first: Yu

last: Zhang

state: California

address: 800 Buchanan Street

department: Plant and Microbial Biology

institute: UC Berkeley

library_source: genomic

data_processing:
Base-callling was performed using Illumina pipeline CASAVA-1.7.0.
Reads that have no unrecognized nucleotides (Ns) and passed quality filtering were aligned to the TAIR9 genome assembly using Bowtie-0.12.7 with the following settings: -v 2 --best --strata -m 1.
Only reads mapped uniquely to the nuclear genome with the lowest number of mismatches were retained for binding-peak identification.
The aligned reads from the two technical sequencing replicates of both libraries were combined and processed as single dataset in the 1st and 2nd biological replicates.
Peak-calling was performed using MACS-1.4.0rc2 with the following settings: gsize=1.1e8, bw=100, nomodel, shiftsize=50, slocal=1000, llocal=2000, and p=1e-5.
Genome_build: TAIR9
Supplementary_files_format_and_content: Tabular files generated by MACS containing peaks information, including chromosome name, start position of peak, end position of peak, length of peak region, peak summit position related to the start position of peak region, number of tags in peak region, -10*log10(pvalue) for the peak region, fold enrichment for this region against random Poisson distribution with local lambda, FDR in percentage.

source_name: whole seedlings

growth_protocol: Stratified seeds were irradiated with WL at 21 ºC for 3 h to induce germination, followed by a FR pulse for 15 min to suppress pseudo dark effects, and grown in darkness at 21 ºC for 2 d before harvest.

extract_protocol: The ChIP-seq library was constructed according to Illumina’s instruction with some modifications. Four ChIP samples from technical replicates of each biological replicate were pooled together and concentrated to increase the starting amount of DNA. The end repair of DNA fragments was performed using End-It DNA End-Repair Kit (Epicentre). The A-tailing was added to the end-repaired DNA fragments using Klenow Fragment (NEB), and then Illumina’s PE adapters were ligated by T4 DNA Ligase (Promega) at 16 ºC overnight. The adapter-ligated DNA fragments in the 200-300 bp size-range were selected by the gel purification, and then were amplified using Phusion High-Fidelity DNA Polymerase (NEB) with the Illumina PE PCR primer set. The library was purified using an Agencourt AMPure XP system (Beckman Coulter Genomics), and then validated by Bioanalyzer 2000 (Agilent).

treatment_protocol: Under green safelight, about 4 g of seedlings were cross-linked in 72 ml of 1% fresh formaldehyde solution for 5 plus 10 min by vacuum infiltration, and then were quenched by adding 5 ml of 2M of glycine with 5 min of vacuum infiltration. Seedlings were rinsed by sterile distilled water, dried by paper towels, and then frozen in liquid nitrogen.

tag: developmental satge

tag: growth conditions

value: true dark

tag: genotype

tag: chip antibody

value: anti-Myc (Abcam, ab9132)


title: input

status: Public on Sep 20 2012

city: Yokohama

first: Norihito

last: Nakamichi

address: Suehiro1-7-22, Tsurumi

department: Plant Science Center

country: Japan

institute: RIKEN

data_processing:
Basecalls was performed by Illumina Genome Analyzer Pipeline
ChIP-seq and input reads were aligned to the TAIR9 genome assembly using CLC bio genomic workbench.
Peaks were called using CLC bio genomic workbench
Genome_build: TAIR9

growth_protocol: Plants were grown on MS medium containing 2% sucrose and 0.3% gellan gum, under 12 h light / 12 h dark conditions for 18 days.

extract_protocol: Nuclei isolated from fixed plants, were sonicated and immunoprecipitated with anti-GFP antibody. Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq Sample Prep Kit (Part# IP-102-1001)

value: Whole plant

tag: time

value: 10 hr after light on

value: input


title: TOC1_ChIPSeq

status: Public on Mar 08 2012

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

country: Spain

institute: Center for Research in Agricultural Genomics

data_processing:
Sequence Reads: Read length was 38 nucleotides. The raw sequence data were processed using the Illumina sequence data analysis pipeline (GAPipeline1.5.0). Sequence reads were trimmed to the first 25 nucleotides and mapped to the Arabidopsis genome sequence (TAIR9 Genome Release; ftp://ftp.arabidopsis.org/) using ELAND (Illumina).
Peaks: Peak detection and identification of genomic regions that were enriched through the immunoprecipitation of TOC1 was performed using ERANGE v3.1 (Pepke, S., Wold, B. & Mortazavi, A. Computation for ChIP-seq and RNA-seq studies. Nat Meth 6, S22-S32 (2009)). Peaks were identified with a minimum fourfold enrichment relative to the corresponding site in the input control and a p-value≤0.001
Genome Build:
TOC1_ChIP_eland25_multi_TAIR9.txt: TAIR9
TOC1_regions.txt: TAIR9
TOC1_TAIR9_ChIP.bed: TAIR9

source_name: seedlings

growth_protocol: ChIP-Seq analyses were performed with TMG-YFP/toc1- 2 seedlings grown under LD cycles (12h light:12h dark) for two weeks. Samples were collected at Zeitgeber Time 15 (ZT15), the peak-time of TOC1 expression in TMG plants. Arabidopsis thaliana seedlings were stratified at 4ºC in the dark for 3 days on Murashige and Skoog (MS) agar medium supplemented with 3% sucrose and then transferred to Light:Dark conditions (LD, 12h light:12h dark) with 60 μmol m−2s−1 of cool white fluorescent light at 22°C.

extract_protocol: Lysates were clarified from sonicated nuclei and TOC1-DNA complexes were isolated with sepharose beads conjugated with an anti-GFP antibody. Following the ChIP procedure, libraries were constructed with the immunoprecipitated DNA using the ChIP-Seq DNA Sample Prep Kit (Illumina, Cat. No. IP-102-1001), following the manufacturer's recommendations. ChIP libraries were sequenced using an Illumina Genome Analyzer II kit, a Single Read Cluster Generation Kit v2 and a 36 Cycle Sequencing Kit v3.

tag: genetic background

value: anti-GFP


title: input DNA

data_processing:
Sequence Reads: Read length was 38 nucleotides. The raw sequence data were processed using the Illumina sequence data analysis pipeline (GAPipeline1.5.0). Sequence reads were trimmed to the first 25 nucleotides and mapped to the Arabidopsis genome sequence (TAIR9 Genome Release; ftp://ftp.arabidopsis.org/) using ELAND (Illumina).
Peaks: Peak detection and identification of genomic regions that were enriched through the immunoprecipitation of TOC1 was performed using ERANGE v3.1 (Pepke, S., Wold, B. & Mortazavi, A. Computation for ChIP-seq and RNA-seq studies. Nat Meth 6, S22-S32 (2009)). Peaks were identified with a minimum fourfold enrichment relative to the corresponding site in the input control and a p-value≤0.001
Genome Build:
TOC1_Input_eland25_multi_TAIR9.txt: TAIR9
TOC1_TAIR9_Input.bed: TAIR9


title: 35S:SVP_rep3

status: Public on Feb 01 2012

city: Singapore

first: Zhen

last: Tao

address: S1A 07-01, 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

description: SVP ChIP from 35S:SVP biological replicate 3

hyb_protocol: The hybridization cocktail was prepared for each fragmented and labeled DNA target according to Affymetrix® Chromatin Immunoprecipitation Assay Protocol. The sample solution was injected into the Affymetrix® Arabidopsis Tiling 1.0R Array and incubated in 45℃ hybridization oven at 60 rpm rotating overnight.

scan_protocol: After hybridization, washing and staining was performed using the fluidics protocol FS450_0001 on the GeneChip® Fluidics Station 450 controlled by GeneChip® Operating Software (GCOS). The probe array was then scanned by the GeneChip® Scanner 3000 7G.

data_processing:
The raw .CEL and .DAT files were exported by the Data Transfer Tool. The ChIP-on-chip tiling array data was analyzed using the CisGenome suite. All the probes were mapped to the TAIR 9 genome. Briefly, raw .CEL files were quantile normalized and probe intensity was computed by perfect match-mismatch (PM-MM). Peaks were called using TileMapv2. Only peaks detected at FDR < 0.05 were used for further analyses.
additional results files: At35b_MR_v04-2_TAIR9.bpmap
results file descriptionsL .BAR are generated by CisGenome software after quantile normalization

source_name: SVP ChIP DNA from 35S:SVP

label_protocol: 5 µg of DNA from each sample was fragmentated and terminally labelled with the GeneChip® WT (Whole Transcript) Double-Stranded DNA Terminal Labeling Kit following the manufacturer’s protocol

growth_protocol: Arabidopsis thaliana plants of different genotypes (Col-0) were grown on soil under long days (16-hour light/8-hour dark) at 23°C ± 2°C.

extract_protocol: The ChIP-chip experiments were performed in biological triplicates using the aerial part of 9-day-old whole seedlings of soc1-101D (Lee et al., 2000) or 35S:SVP (Li et al., 2008) against soc1-2 (Lee et al., 2000) or svp-41 (Hartmann et al., 2000) as a negative control, respectively. 9-day-old whole seedlings were fixed for 45 min in cold MC buffer (10 mM potassium phosphate, pH 7.0, 50 mM NaCl and 0.1 M sucrose) with 1% formaldehyde under vacuum. Fixed tissues were ground and homogenized. Chromatin was isolated and sonicated to produce DNA fragments below 500 bp. Endogenous SOC1 and SVP protein were immunoprecipitated by anti-SOC1 and anti-SVP antibody (Shen et al., 2011) bound to Protein A-agarose beads, respectively. Genomic DNA was purified after reverse cross-link the chromtain complex eluted from the beads.

tag: genotype/variation

value: 9-day-old whole seedlings

value: SVP rabbit polyclonal

tag: ecotype


title: 35S:SVP_rep2

description: SVP ChIP from 35S:SVP biological replicate 2


title: svp-41_rep1

description: SVP ChIP from svp-41 biological replicate 1 (negative control)

source_name: SVP ChIP DNA from svp-41


title: svp-41_rep2

description: SVP ChIP from svp-41 biological replicate 2 (negative control)


title: AML_patient_3

status: Public on Feb 07 2013

type: RNA

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

country: Germany

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner

data_processing: Normalization was performed using the Robust Multichip Average (RMA) method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set  summarization.

molecule: total RNA

organism: Homo sapiens

source_name: bone marrow mononuclear cells

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

extract_protocol: Mononuclear cells from bone marrow (BM) or peripheral blood (PB) were enriched by Ficoll gradient centrifugation. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany). cDNA preparation and  in vitro transcription were performed according to standard Affymetrix protocols.

treatment_protocol: Pretreatment bone marrow or peripheral blood mononuclear cells from patients with newly diagnosed acute myeloid leukemia (AML)

value: bone marrow mononuclear cells

tag: fab


title: AML_patient_423

value: No

tag: overall survival (days)

tag: life status

value: dead


title: soc1-2_rep1

description: SOC1 ChIP from soc1-2 biological replicate 1 (negative control)

source_name: SOC1 ChIP DNA from soc1-2

value: SOC1 rabbit polyclonal


title: soc1-2_rep2

description: SOC1 ChIP from soc1-2 biological replicate 2 (negative control)


title: soc1-101D_rep1

description: SOC1 ChIP from soc1-101D biological replicate 1

source_name: SOC1 ChIP DNA from soc1-101D


title: soc1-101D_rep3

description: SOC1 ChIP from soc1-101D biological replicate 3


title: soc1-2_rep3

description: SOC1 ChIP from soc1-2 biological replicate 3 (negative control)


title: svp-41_rep3

description: SVP ChIP from svp-41 biological replicate 3 (negative control)


title: 35S:SVP_rep1

description: SVP ChIP from 35S:SVP biological replicate 1


title: FHY3_Far-Red

status: Public on Aug 02 2011

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

country: China

institute: SUSTC (current, may different with previous institution )

data_processing: Sequencing reads from D and FR libraries were mapped to TAIR9 genome release of Arabidopsis thaliana using the MAQ software, allowing for up to two mismatching nucleotides and no gaps. Only uniquely mapped reads were retained for further analyses. The output of the analysis pipeline was converted to browser extensible data (BED) files for viewing the data in the Integrative Genomics Viewer (IGV) genome browser. Numerous peak detection algorithms have been proposed recently for analyzing the ChIP-seq datasets, and they provide more or less similar results. In this study, MACS software with default parameters (bandwidth, 300 bp; mfold, 32; p-value of 1.00e-05) was used to call peaks representing enriched binding sites.

growth_protocol: The homozygous 35S:3FLAG-FHY3-3HA fhy3-4 seedlings grown in D or continuous FR light for 4 d were used for ChIP assays following the procedure described previously

extract_protocol: 5 g of seedlings were first cross-linked with 1% formaldehyde under vacuum, and then the samples were ground to powder in liquid nitrogen. The chromatin complexes were isolated and sonicated and then incubated with monoclonal FLAG antibodies (Sigma-Aldrich). The precipitated DNA was recovered and used to generate Illumina sequencing libraries according to the manufacturerâs instructions.

tag: developmental stage

value: seedling

value: 4 days

value: FLAG (Sigma-Aldrich)

value: 35S:3FLAG-FHY3-3HA fhy3-4 transgenic line


title: soc1-101D_rep2

description: SOC1 ChIP from soc1-101D biological replicate 2


title: FHY3_Dark


title: cbp+/- Env Enrichment Rep1

status: Public on Aug 30 2011

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

institute: Instituto de Neurociencias (UMH-CSIC)

description:
CBP_EE_1
Gene expression data from hippocampal tissue

hyb_protocol: Following Affymetrix instructions

scan_protocol: Following Affymetrix instructions

data_processing: GeneSpring GX software (Agilent Technologies Inc) was used. RMA algorithm was uset to background correction, data normalization and probe sumarization.

organism: Mus musculus

source_name: hippocampal tissue from cbp+/- mice (2 weeks Env Enrichment)

label_protocol: Following Affymetrix instructions

growth_protocol: CBP deficient heterozygous mice were maintained in a mixed background (F2 of C57BL/6J and DBA) (Alarcon et al., 2004). Mice were group-housed in single-sex cages on a light:dark cycle (12/12 h) with food and water available ad limitum. The wild type mice used as control were, in all cases, littermates of the mutant mice.

extract_protocol: Total RNA was extracted separately from individual hippocampi using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) per manufacturers instructions followed by DNaseI treatment (Qiagen, Valencia, CA, USA) and a clean-up step using RNeasy RNA purification columns (Qiagen, Valencia, CA, USA). Equal amounts of total RNA from four animals were pooled, processed, and hybridized to GeneChIP Mouse Gene 1.0 ST Arrays (Affymetrix, Santa Clara, CA) according to the manufacture's protocol. Three to five independent biological replicates were prepared for each genotype and condtition (wild-type and crebbp deficient mice (cbp+/-; standar housing and environmental enrichment). GeneChIP® Mouse Gene 1.0 ST Arrays were hybridized, stained, washed and screened for quality according to the manufacturer's protocol. Microarray data were processed, normalized and statistically analyzed using GeneSpring GX (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Experiments were performed in 2-3 month old animals and in all cases the mice used as control were littermates of the mutant mice. Standard housing consisted of 30x15x11 cm clear cages occupied by up to 5 mice. The environmental enrichment boxes were large white plexiglass boxes (>1m2) and were occupied by a maximum of 20 mice. We used natural materials, plastic tubing, running wheels and toys to create an enriched environment whose configuration was modified every 48h shortly before the start of the dark cycle. The samples were obtained at least 16 h afther the last modification in the enviromental enrichment box to prevent any interference between the response to novelty and to environmental enrichment. The brains were immediately removed, and hippocampi rapidly dissected and placed in RNAlater solution (Qiagen, Venlo, The Netherlands) until total RNA extraction.

tag: strain background

value: F2 of C57BL/6J and DBA

tag: gender

value: female

value: cbp+/-  (CBP deficient, heterozygous)

value: 3 months

value: hippocampus


title: cbp+/- standard cage Rep5

description:
CBP_SC_5
Gene expression data from hippocampal tissue

source_name: hippocampal tissue from cbp+/- mice (standard cage)

tag: age

tag: tissue


title: AML_patient_459

value: alive


title: cbp+/- standard cage Rep3

description:
CBP_SC_3
Gene expression data from hippocampal tissue


title: Wild-type Env Enrichment Rep1

description:
WT_EE_1
Gene expression data from hippocampal tissue

source_name: hippocampal tissue from wild-type mice (2 weeks Env Enrichment)

value: wild type


title: lfy-ctrl-rep1

status: Public on May 13 2011

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

institute: Max Planck Institute for Developmental Biology

data_processing: Standard Illumina base calling software was used to base call the 40-42 nucleotide sequence reads. We used SHORE (http://shore.sourceforge.net) as a platform for further analysis. The obtained reads were quality filtered and low quality bases at the 3’ end were pruned as described. GenomeMapper (http://1001genomes.org/software/) was used for mapping to the TAIR9 genome, allowing for up to four mismatching nucleotides and no gaps. To proceed, the mapped data were subjected to a heuristic for removal of duplicate sequence reads which were assumed to be uninformative for the detection of enriched loci. A threshold was applied limiting the number of 5’ ends mapping to the same position on the same strand. To retain the power to discriminate between multiple strongly enriched regions, the threshold for any particular position was varied depending on the coverage in close vicinity, such that the variance of the number of reads per position would roughly equal its mean in a 30 bp sliding window. We further applied a two-step procedure to identify regions significantly enriched in the positive sample when compared to the control. First, potentially enriched regions were identified based on the positive samples only. These sites were then directly compared to the corresponding control sample regions to assess statistical significance. For estimation of the depth of coverage for each position in the genome, all positive sample reads mapping to unique positions were extended in 3’ direction to 130 bp, corresponding to half the experimentally observed approximate DNA fragment size, while discarding all other reads. To detect possible peak sites, a 2 kb wide sliding window was applied to the coverage graph in single base steps. In each step a p-value was assigned to the coverage value at the central base using a one-sided Poisson test, with the distribution parameter set to the average coverage within the sliding window. Only positions with coverage greater than zero were included in the calculation of the average, assuming all other positions to be inaccessible to the experiment. Finally, any consecutive stretch of positions with p-value <0.05 and length >130 bp was retained as a potentially enriched site. To further reduce the number of regions to be considered, each was checked for unwarranted high average coverage in the control sample. A potential peak in the positive sample was discarded if the coverage mean in the control sample in the corresponding region was larger than the median average control coverage plus a tolerance of three standard deviations in all peak regions. For assignment of final p-values to each candidate region, in each replicate a one-sided binomial test was applied to the number of reads mapping to the region in the positive sample, with the distribution parameter N set to the joint read count for the site for the positive and the corresponding control sample. To estimate the probability parameter for the test, from now on called r, we computed a scaling factor s for the control sample and the chromosome containing the considered region. The complete chromosome sequence was subdivided into 400 base pair bins, and for each bin the positive sample as well as the control sample read counts were recorded. Then s was chosen such that the median ChIP sample read count for all bins equaled the median control sample read count multiplied by s. From this the binomial test parameter r was calculated as r=s/(s+1). Finally, false discovery rates were obtained through the Benjamini-Hochberg correction method. To establish a ranking of peak regions across replicates, the rank product over the per-replicate fdr ranks was used. To define the bound DNA set, we used all peaks with fdr > 0.1 in both ChIP experiments, resulting in a set of 1564 peaks.

source_name: complete seedlings

growth_protocol: 15 day-old 35S::LFY and Col-0 (control) seedlings (complete seedlings, including aerial part+roots) grown under long day photoperiods at 23 °C on MS plates

extract_protocol: The entire experiment from seed sowing through deep sequencing was performed twice to produce independent biological replicates. ChIP-seq was performed with an antibody raised in rabbit (#4028) against the LFY C-terminal amino acids 223-424 (BioGenes, Berlin, Germany). Briefly, 15 day-old 35S::LFY and Col-0 (control) seedlings grown under long day photoperiods at 23 °C on MS plates were harvested and fixed as described previously [38]. Frozen tissue was ground, filtered three times through Miracloth (Calibrochem), and washed as described previously thorough buffers M1, M2, and M3. Nuclear pellets were resuspended in sonic buffer as described (1 mM PEFA BLOC SC (Roche Diagnostics) was substituted for PMSF), split into technical duplicate samples, and sonicated with a Branson sonifier at continuous pulse (output level 3) for 8 rounds of 2 x 6 seconds and allowed to cool on ice between rounds. IP reactions were performed by incubating chromatin with 2.5 μl anti- LFY serum overnight at 4 °C as described. The immunoprotein–chromatin complexes were captured by incubating with protein A-agarose beads (Santa Cruz Biotechnology), followed by consecutive washes in IP buffer and then elution as described. Immunoprotein-DNA was then incubated consecutively in RNase A/T1 mix (Fermentas) and Proteinase K (Roche Diagnostics) as described after which DNA was purified using Minelute columns (Qiagen). ChIP samples were tested for enrichment by QPCR and then deep sequencing libraries were produced by standard Illumina protocols.

tag: strain


title: lfy-ctrl-rep2

value: rabbit (#4028) against the LFY C-terminal amino acids 223-424 (BioGenes, Berlin, Germany)


title: Wild-type Env Enrichment Rep3

description:
WT_EE_3
Gene expression data from hippocampal tissue


title: lfy-samp-rep2

value: Col-0 35S::LFY


title: cbp+/- Env Enrichment Rep2

description:
CBP_EE_2
Gene expression data from hippocampal tissue


title: lfy-samp-rep1


title: cbp+/- standard cage Rep4

description:
CBP_SC_4
Gene expression data from hippocampal tissue


title: Wild-type standard cage Rep3

description:
WT_SC_3
Gene expression data from hippocampal tissue

source_name: hippocampal tissue from wild-type mice (standard cage)


title: Wild-type standard cage Rep2

description:
WT_SC_2
Gene expression data from hippocampal tissue


title: Rep6-GFP

status: Public on Jan 02 2011

city: Ames

first: Xiaofei

last: Yu

state: IA

address: 1035D Roy J Carver Co-Lab

institute: Iowa state Univeristy

description: ChIP with anti-GFP antibody from biological replicate 3

hyb_protocol: 7.5μg of DNA was hybridzed per array using the Affymetrix hybridization kit.Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000

data_processing: Log2-transformed signal intensity data was quantile normalized with the cisgenome software and stored in BAR files (combined in "BES1_ChIP_normalization.txt" for all samples).

source_name: ChIP DNA with anti-GFP antibody from bes1-D seedlings

label_protocol: 7.5ug of DNA from each sample was fragmentated and terminally labelled with the GeneChip® WT (Whole Transcript) Double-Stranded DNA Terminal Labeling Kit following the product manual

growth_protocol: bes1-D Arabidopsis plants were grown in MS plates or soil under long day (16h light/8h dark) conditions at 22oC

extract_protocol: Chromatin immunoprecipitation was performed with 14-day-old bes1-D seedlings. Briefly, plant tissues were cross-linked with 1% formaldehyde for 15mins and nuclei were isolated using sucrose gradients. Chromatin was sonicated to generate fragments with the average size of 500bp and precipitated using BES1 antibody or GFP antibody (Molecular Probe) as negative control. Immunocomplexes were harvested by protein A beads, washed and reverse cross-linked by boiling in the presence of Chelex resin (Bio-Rad).

value: 2-week old seedlings

tag: antibody

value: rabbit anti-GFP polyclonal antibody


title: cbp+/- Env Enrichment Rep3

description:
CBP_EE_3
Gene expression data from hippocampal tissue


title: cbp+/- standard cage Rep2

description:
CBP_SC_2
Gene expression data from hippocampal tissue


title: Wild-type Env Enrichment Rep2

description:
WT_EE_2
Gene expression data from hippocampal tissue


title: Wild-type standard cage Rep4

description:
WT_SC_4
Gene expression data from hippocampal tissue


title: Rep4-BES1

description: ChIP with anti-BES1 antibody from biological replicate 2

source_name: ChIP DNA with anti-BES1 antibody from bes1-D seedlings

value: rabbit anti-BES1 polyclonal antibody


title: Wild-type standard cage Rep5

description:
WT_SC_5
Gene expression data from hippocampal tissue


title: Rep6-BES1

description: ChIP with anti-BES1 antibody from biological replicate 3


title: cbp+/- standard cage Rep1

description:
CBP_SC_1
Gene expression data from hippocampal tissue


title: Rep1-GFP

description: ChIP with anti-GFP antibody from biological replicate 1


title: WT_IPvsInput (negative control)

status: Public on May 11 2011

city: Philadelphia

first: Cara

middle: Michele

last: Winter

address: 421 Curie Blvd.

institute: University of Pennsylvania

description:
WT 9-day-old seedlings, IP vs. Input, 3 biological reps
No bed files, as no significant regions identified.

hyb_protocol: Hybridization was performed at the University of Pennsylvania Microarray Core Facility using standard Affymetrix protocols.

scan_protocol: Scanning was performed at the University of Pennsylvania Microarray Core Facility using standard Affymetrix protocols.

data_processing:
Data were quantile normalized and analyzed with CisGenome. Log2(IP/Input) fold changes (fc) and CisGenome moving average (ma) statistics were reported in BAR files. Significantly bound regions are reported in the .bed file.
Results file descriptions: fc.bar and ma.bar are generated by CisGenome software (previously TileMap). fc.bar contains log2(IP/Input) fold changes for each probe. ma.bar contains a moving average statistic (i.e. the MA statistic in TileMap) for each probe. File LFYGR_IP_Input.bed contains all 1588 reported significantly bound regions.

source_name: WT ChIP DNA from 9-day-old seedlings

label_protocol: Biotin labeling was performed using the Affymetrix GeneChIP WT Double-Stranded DNA Terminal Labeling Kit.

growth_protocol: Seeds cold-treated for 7 days at 4°C were grown in inductive conditions (continuous light or 16 hour long-day light conditions) at 23°C at a fluence rate of 45 μmol/m2 sec on 0.5x Murashige and Skoog plates

extract_protocol: ChIP was performed with an anti-LFY antibody (Wagner et al., 1999; PMID 10417387) essentially as described (Kwon et al., 2005) except that DNA was sonicated to an average size range of 300-500bp.

treatment_protocol: 35S::LFY-GR and WT seedlings were treated with 10uM dexamethasone, 0.1% ethanol, for 4 hours by submersion prior to ChIP.

value: seedlings

value: LFY

source_name: WT Input DNA from 9-day-old seedlings


title: lfy6_IPvsInput (negative control)

description: lfy6 19-day-old inflorescences IP vs. Input, no replicates

data_processing:
Data were quantile normalized and analyzed with CisGenome. Log2(IP/Input) fold changes (fc) and CisGenome moving average (ma) statistics were reported in BAR files. Significantly bound regions are reported in the .bed file.
Results file descriptions: fc.bar and ma.bar are generated by CisGenome software (previously TileMap). fc.bar contains log2(IP/Input) fold changes for each probe. ma.bar contains a moving average statistic (i.e. the MA statistic in TileMap) for each probe. File WT_IP_Input.bed contains all 867 reported significantly bound regions. lfy6_IP.CEL.bar and lfy6_Input.CEL.bar contain processed probe-level signal intensities.

source_name: ChIP DNA from 19-day-old lfy6 inflorescences using LFY antibody

value: inflorescences

source_name: lfy6 Input DNA from 19-day-old inflorescences


title: LFYGR_IPvsInput

description: 35S::LFY-GR 9-day-old seedlings, IP vs. Input, 3 biological reps

source_name: LFY-GR ChIP DNA from 9-day-old seedlings

source_name: LFY-GR Input DNA from 9-day-old seedlings


title: WT_IPvsInput

description: WT 19-day-old inflorescences IP vs. Input, 5 biological reps

source_name: ChIP DNA from 19-day-old WT inflorescences using LFY antibody

source_name: WT Input DNA from 19-day-old inflorescences


title: WF_Grotewold_020907

status: Public on Sep 01 2010

city: Columbus

first: Zidian

last: Xie

state: OH

address: 1060 Carmack Rd.

department: Dept. of Plant Cellular and Molecular Biology

institute: The Ohio State University

hyb_protocol: Whole Genome Tiling Array was hybridized for 16 hrs, washed, and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned on Affymetrix scanner G7

data_processing: R Bioconductor was used to quantile normalize our ChIP-chip data

source_name: FLP/MYB88 ChIP DNA from wild type (Col) shoots (rep 2)

label_protocol: The sample was 3'-end-labelled with dd-UTP (Roche) by the terminal transferase (TdT, Roche) reaction for 1.5 h at 37 degrees C.

growth_protocol: Ten-days old plants were grown under 16 h light on 1/2 MS plates

extract_protocol: sample was prepared by ChIP using an antibody against FLP/MYB88 proteins

value: Ten-day old Green tissue

value: Shoots

value: FLP/MYB88 rabbit polyclonal


title: Wild-type standard cage Rep1

description:
WT_SC_1
Gene expression data from hippocampal tissue

value: F2 of C57BL/6J and DBA

value: female


title: Rep1-BES1

description: ChIP with anti-BES1 antibody from biological replicate 1


title: WI_Grotewold_120806

source_name: Input DNA from wild type (Col) shoots (rep 1)

extract_protocol: sonicated Arabidopsis genomic DNA


title: WI_Grotewold_020907

source_name: Input DNA from wild type (Col) shoots (rep 2)


title: DI_Grotewold_091907

source_name: Input DNA from flp-1 myb88 mutant shoots (rep 3)


title: WF_Grotewold_120806

source_name: FLP/MYB88 ChIP DNA from wild type (Col) shoots (rep 1)


title: WI_Grotewold_091907

source_name: Input DNA from wild type (Col) shoots (rep 3)


title: WF_Grotewold_091907

source_name: FLP/MYB88 ChIP DNA from wild type (Col) shoots (rep 3)


title: DF_Grotewold_020907

source_name: FLP/MYB88 ChIP DNA from flp-1 myb88 mutant shoots (rep 2)


title: DI_Grotewold_020907

source_name: Input DNA from flp-1 myb88 mutant shoots (rep 2)


title: DF_Grotewold_091907

source_name: FLP/MYB88 ChIP DNA from flp-1 myb88 mutant shoots (rep 3)


title: DI_Grotewold_120806

source_name: Input DNA from flp-1 myb88 mutant shoots (rep 1)


title: DF_Grotewold_120806

source_name: FLP/MYB88 ChIP DNA from flp-1 myb88 mutant shoots (rep1)


title: AP1-GR_2h_induced_sample_2

status: Public on Apr 02 2010

city: Wageningen

first: Gerco

last: Angenent

address: Bornsesteeg 65

country: Netherlands

institute: Plant Research International

description: Chromatin IP against AP1 transcription factor

data_processing: Alignment: Sequence reads were obtained and mapped to the Arabidopsis thaliana genome using the SOAP mapping software (soap.genomics.org.cn/). All reads mapping with two or fewer mismatches at unique positions were retained. Iteratively, one base was discarded form the 3`end of the nonmapped reads until the reads were uniquelly mapped or fell bellow a minimum length of 30 bp

source_name: AP1-GR ap1 cal apical meristematic tissue; 2 h induced with DEX

growth_protocol: Plants were grown on a soil:vermiculite:perlite (2:1:1) mixture at 20ºC under constant illumination with cool white fluorescent light, unless indicated otherwise

extract_protocol: Libraries were prepared using the Illumina protocol for preparation of ChIP-SEQ libraries with modifications described in Kaufmann et al., Nature Protocols 2010

treatment_protocol: For the ChIP experiments, we treated inflorescences with a solution containing 1 mM dexamethasone, 0.01% (v/v) ethanol, and 0.015% (v/v) Silwett L-77, and harvested the inflorescences after 2h induction

value: AP1 antibody, affinity-purified against IKC-domains


title: AP1-GR_uninduced_control_1

source_name: AP1-GR ap1 cal apical meristematic tissue; uninduced


title: AP1-GR_2h_induced_sample_1

value: AP1-GR ap1 cal apical meristematic tissue


title: AP1-GR_uninduced_control_2


title: ap2_chip_rep1

status: Public on Apr 13 2010

data_processing: Standard Illumina base calling software was used to base call the 42 nucleotide sequence reads. We used SHORE (http://1001genomes.org/downloads/shore.html) for read mapping and coverage analysis. The raw reads were pruned of low quality bases at their 3’ end before mapping them to the TAIR9 genome, allowing for up to four mismatching nucleotides and no gaps.

source_name: influorescence

extract_protocol: The entire experiment from harvest through deep sequencing was repeated twice to produce independent biological replicates. ChIP-seq was performed with an antibody raised against the C-terminus of AP2 amino acids 289-432 (right after the second AP2 DNA binding domain until the stop codon). Col-0 plants were used to determine binding sites in the fully native context and ap2-12 (SALK_071140) plants were used as negative controls for any non-specific background antibody binding and pulldown. To maximize AP2 levels, we harvested clusters of young influorescences at the beginning of bolting, but before flowers opened, when AP2 expression is high. Briefly, clusters of just-bolting inflorescences were harvested and fixed as described previously {Gómez-Mena et al., 2005, Development, 132, 429-38}. Frozen tissue was ground, filtered three times through Miracloth (Calibrochem), and washed as described previously thorough buffers M1, M2, and M3 {Gómez-Mena et al., 2005, Development, 132, 429-38}. Nuclear pellets were resuspended in sonic buffer as described (1 mM PEFA BLOC SC (Roche Diagnostics) was substituted for PMSF), split into technical duplicate samples, and sonicated with a Branson sonifier at continuous pulse (output level 3) for 8 rounds of 2 x 6 seconds and allowed to cool on ice between rounds. IP reactions were performed by incubating chromatin with 2.5 microliters anti-rabbit AP2 antiserum overnight at 4C as described {Gómez-Mena et al., 2005, Development, 132, 429-38}. The immunoprotein–chromatin complexes were captured by incubating with protein A-agarose beads (Santa Cruz Biotechnology), followed by consecutive washes in IP buffer and then elution as described {Gómez-Mena et al., 2005, Development, 132, 429-38}. Immunoprotein-DNA was then incubated consecutively in RNase A/T1 mix (Fermentas) and Proteinase K (Roche Diagnostics) as described after which DNA was purified using Minelute columns (Qiagen) {Gómez-Mena et al., 2005, Development, 132, 429-38}. ChIP samples we tested for enrichment by QPCR and then deep sequencing libraries were produced by standard Illumina protocols.

tag: cell type

value: influorescence

value: AP2 custom antibody raised against the C-terminus of AP2 amino acids 289-432 (right after the second AP2 DNA binding domain until the stop codon) produced in the lab of Prof. Xuemei Chen, UC Riverside.


title: ap2_chip_rep2


title: Control littermate for VP16-CREB 1 week-induction sample 2

status: Public on Apr 20 2010

description:
Total RNA was extracted from hippocampi of 3 to 4 mice with the same age, sex and genotype to produce one pooled sample.
Mice were raised with dox, and 1 week before experimentation dox was removed

hyb_protocol: Following Affymetrix recommendations

scan_protocol: Following Affymetrix recommendations

label: Biotin

source_name: Hippocampus

label_protocol: Following Affymetrix recommendations

extract_protocol: TRI reagent (Invitrogen) followed by RNase Mini column (Qiagen) following manufacturers' instructions

tag: genotype variation

value: WT

value: 3 week old


title: VP16-CREB 1 week-induced sample 2

value: tetO-VP16-CREB C57BL/6J


title: A-CREB 6 weeks-old sample 2

description:
Total RNA was extracted from hippocampi of 3 to 4 mice with the same age, sex and genotype to produce one pooled sample.
Mice were raised without dox

value: TetO-A-CREB-95 C57BL6 F1/J

value: 6 weeks-old


title: Control littermate for VP16-CREB 1 week-induction sample 1


title: A-CREB 6 weeks-old sample 3


title: VP16-CREB 1 week-induced sample 1


title: ap2_ctrl_rep1

tag: chip antibody


title: ap2_ctrl_rep2


title: VP16-CREB 3 weeks-induced sample 3

description:
Total RNA was extracted from hippocampi of 3 to 4 mice with the same age, sex and genotype to produce one pooled sample.
Mice were raised with dox, and 3 weeks before experimentation dox was removed

value: 6 week old


title: A-CREB 6 weeks-old sample 1


title: Control littermate for A-CREB 6 weeks-old sample 2


title: VP16-CREB 3 weeks-induced sample 1


title: Control littermate for A-CREB 6 weeks-old sample 1

description:
Total RNA was extracted from hippocampi of 3 to 4 mice with the same age, sex and genotype to produce one pooled sample.
Mice were raise without dox


title: VP16-CREB 3 weeks-induced sample 2


title: Control littermate for A-CREB 6 weeks-old sample 3


title: Rep4-GFP

description: ChIP with anti-GFP antibody from biological replicate 2

source_name: ChIP DNA with anti-GFP antibody from bes1-D seedlings

value: 2-week old seedlings

tag: genotype

value: rabbit anti-GFP polyclonal antibody


title: Control littermate for VP16-CREB 3 weeks-induction sample 1


title: AGL15_ChIP_experiment 1

status: Public on Sep 18 2009

description: AGL15ChIP Biological Rep 1-3, Affymetrix GeneChip® Arabidopsis Tiling 1.0R array

hyb_protocol: Approximately 7.5μg of DNA was hybridzed per array using the Affymetrix hybridization kit for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned using an Affymetrix Scanner 3000 7G.

data_processing:
Data was quantile normalized and analyzed with TileMap. Log2(IP/Preimmune) fold changes (fc) and TileMap moving average (ma) statistics were reported in BAR files.

fc.bar and ma.bar are generated by CisGenome software (previously TileMap). fc.bar contains log2(IP/Input) fold changes for each probe. ma.bar contains a moving average statistic (i.e. the MA statistic in TileMap) for each probe.

source_name: ChIP DNA (I) from 35S:AGL15 Arabidopsis embryonic culture tissue

label_protocol: Samples (7.5 μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments.

growth_protocol: An embryonic culture was derived from zygotic Arabidopsis embryos that constitutively express AGL15, cultured in 10 g L-1 Suc, 0.5 g L-1, MES, and 7 g L-1  agar (pH 5.6–5.7), with 50 -g  mL-1  kanamycin, maintained at 23°C to 24°C, with a 23-h-light/1-h-dark regimen.

extract_protocol: ChIP experiment was performed as in Wang et al., 2002 using anti-AGL15 specific antiserum or preimmune serum.

treatment_protocol: Tissue was fixed in MC buffer (10 mM potassium phosphate pH 7, 50 mM NaCl, 0.1 M sucrose) with 1% formaldehyde for one hour on ice under vacuum. The reaction was quenched with addition of cold glycine to 0.125 M and incubation on ice 10-30 min, after which the tissue was washed with cold MC buffer and flash frozen.

value: embryonic culture tissue

value: AGL15 antiserum rabbit polyclonal terminal bleed

tag: genome/variation

source_name: Preimmune ChIP DNA (PI) from 35S:AGL15 Arabidopsis embryonic culture tissue

value: AGL15 antiserum rabbit polyclonal preimmune bleed


title: Control littermate for VP16-CREB 3 weeks-induction sample 3


title: Control littermate for VP16-CREB 3 weeks-induction sample 2


title: SEP3_ChIPSeq_ag_3

status: Public on Apr 21 2009

description: Chromatin IP against SEP3

data_processing: Reads were mapped to the unmasked Arabidopsis reference genome (ATH1.1con.01222004; ftp://ftp.arabidopsis.org/) using the SOAP software.Only uniquely mapped reads were retained. Reads were extended directionally to 300 nt. For each nucleotide position enrichment was tested using a Poisson model.

source_name: Primary and secondary inflorescences of 5-7 weeks old plants

growth_protocol: Arabidopsis thaliana, wild-type (Col-0), sep3-1 (Col-0) and ag-1 (Ler) mutant plants were grown under standard greenhouse conditions (20°C, long day light regime: 16 h light, 8 hours dark cycle). Flower material was harvested from primary and secondary inflorescences of 5-7 weeks old plants

extract_protocol: ChIP experiments were performed as described in Gomez-Mena et al. 2005 (PMID: 15634696) with modifications in de Folter et al. 2007 (PMID: 17868439)

treatment_protocol: Inflorescences were harvested and fixed using FAA following a protocol published in Gomez-Mena et al. 2005 (PMID: 15634696) with modifications in de Folter et al. 2007 (PMID: 17868439)

tag: variable


title: SEP3_ChIPSeq_wt_3

description: Chromatin IP against SEP3

value: wild-type


title: SEP3_ChIPSeq_wt_1

description: Chromatin IP against SEP3

data_processing: Reads were mapped to the unmasked Arabidopsis reference genome (ATH1.1con.01222004; ftp://ftp.arabidopsis.org/) using the SOAP software.Only uniquely mapped reads were retained. Reads were extended directionally to 300 nt. For each nucleotide position enrichment was tested using a Poisson model. We have processed "SEP3_ChIPSeq_wt_1" and "SEP3_ChIPSeq_wt_2" sample records together on the file "wkk1b_aligned.txt"


title: SEP3_ChIPSeq_wt_2

description: Chromatin IP against SEP3


title: Wild-type Rep3

status: Public on Oct 03 2009

description: Gene expression data from hippocampal tissue

data_processing: GeneSpring GX software (Agilent Technologies Inc) was used. Data were extracting using RMA16 algorithm and values were normalized by the median of all samples. Data are represented as log2.

source_name: hippocampal tissue from wild-type mice

growth_protocol: P300 deficient heterozygous mice were maintained in a C57BL/6J pure background. Mice were group-housed in single-sex cages on a light:dark cycle (12/12 h) with food and water available ad limitum. The wild type mice used as control were, in all cases, littermates of the mutant mice.

extract_protocol: Total RNA was extracted separately from individual hippocampi using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) per manufacturers instructions followed by a cleanup step using RNeasy RNA purification columns (Qiagen, Valencia, CA, USA). Equal amounts of total RNA from four animals were pooled, processed, and hybridized to Mouse Genome 430 2.0 genechips (Affymetrix, Santa Clara, CA). Three independent biological replicates were prepared for each genotype (wild-type and p300 deficient mice (p300+/-)). Mouse Genome 430 2.0 genechips were hybridized, stained, washed and screened for quality according to the manufacturer's protocol. Microarray data were processed, normalized and statistically analyzed using GeneSpring GX (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The brains were immediately removed, and hippocampi rapidly dissected and placed in RNAlater solution (Qiagen, Venlo, The Netherlands) until total RNA extraction.

value: Wild-type

tag: replicate

value: female

value: adult

value: hippocampus


title: SEP3_ChIPSeq_sep3_3

description: Chromatin IP against SEP3


title: p300+/- Rep3

source_name: hippocampal tissue from heterozygous p300 mice


title: GL1_1st2nd

status: Public on Mar 02 2009

first: Kengo

last: Morohashi

address: 1060 Carmack Rd

department: Molecular Genetics

description:
GL1 ChIP biological replicate 1-2
results file description: Enriched DNA associated with GL1 or GL3

data_processing: MAT (Model-based analysis of tiling array)

source_name: ChIPed DNA with anti-GFP antibody from three-week old GL1-YFP-MYC plants

growth_protocol: Plants were grown under 16 h light on soil

extract_protocol: sample was prepared by ChIP using an antibody against GFP

treatment_protocol: no treatment

tag: AGE

value: Three-week old Green tissue

tag: Amplification method

value: LMPCR

tag: Antibody

value: GFP rabbit polyclonal

source_name: Input DNA from three-week old GL1-YFP-MYC plants


title: GL3_2B6th

description:
GL3 ChIP biological replicate 1-2
results file description: Enriched DNA associated with GL1 or GL3

source_name: ChIPed DNA with anti-GFP antibody from three-week old GL3-YFP plants

source_name: Input DNA from three-week old GL3-YFP plants


title: Saline Rep 2

status: Public on Aug 22 2009

description: Gene expression data from striatal tissue

data_processing: GeneSpring GX software (Agilent Technologies Inc) was used. Data were extracting using RMA16 algorithm and values were normalized by the median of controls. Data are represented as log2

source_name: Induction: vehicle-vehicle. Challenge: saline

growth_protocol: Two months-old Swiss-Albino male mice maintained in housing standard conditions.

extract_protocol: Mice striatal tissue was rapidly dissected from anterior 6mm coronal sections using a chilled acrylic mouse brain slicer matrix (Zivic Instruments) with 2 mm coronal section slice intervals, in RNAlater solution until further RNA extraction (Qiagen, Venlo, The Netherlands). Equal amounts of total RNA from four animals were pooled, processed and hybridized to Mouse Gene 1.0 ST genechips (Affymetrix, Santa Clara, CA). Three to six biological replicates of the microarray were prepared for each experimental group (saline-saline, N=6; saline-morphine, N=3; butyrate-morphine, N=3)..

treatment_protocol: Behavioural sensitization: Locomotor sensitization induced by morphine was evaluated using a protocol divided into two phases: induction and challenge. The induction phase involved six trials on alternate days, one trial per day. On each one of these trials, mice received and injection of saline or sodium butyrate (300 mg/kg) immediatedly followed by a second injection of morphine (20 mg/kg). The challenge phases consisted of a single trial conducted 7 days after the last test of the induction phase. In this case, all animals received a single injection of morphine (20 mg/kg). Striatal RNA was extracted 1h after the morphine challenge in groups of four animals that received either saline (N=6) or morphine (N=3), or the sodium butyrate-morphine (N=3) co-treatment during the sensitization induction phase.

value: Striatum

value: 2 months

value: male


title: Saline Rep 4


title: SEP3_replicate 1_ChIP_sample

description: sample of chromatin immunoprecipitation using SEP3 antibody

hyb_protocol: The samples are delivered in 60µl. The hybridization mixture is made according to the Affymetrix Genechip Whole Transcript Double-stranded Target Assay protocol. The Arabidopsis Tiling arrays are hybridized at 45°C for 16 hours

scan_protocol: The Command Console software form Affymetrix is used of the whole process of washing, staining, scanning of the chips and primary data extraction. The Genechip Scanner 3000 7G was used

data_processing: The data were analyzed with Tiling Analysis Software version 1.1 (TAS 1.1) using Affymetrix default analysis settings except the bandwidth parameter set to 250

source_name: wildtype inflorescences

label_protocol: Labelling of sheared amplified ChIP material and unamplified input DNA was performed as described in Katou et al. 2006 (PMID: 16793414)

growth_protocol: Arabidopsis thaliana, wild-type (Col-0) plants were grown under standard greenhouse conditions (20°C, long day light regime: 16 h light, 8 hours dark cycle). Flower material was harvested from primary and secondary inflorescences of 5-7 weeks old plants.


title: p300+/- Rep2


title: SEP3_replicate 2_Input

description: sheared input chromatin (replicate 2)

tag: sheared input chromatin


title: ButMorphine Rep 3

source_name: Induction: butyrate-morphine. Challenge: morphine


title: Saline Rep 1


title: Wild-type Rep2


title: Saline Rep 5


title: Wild-type Rep1


title: Saline Rep 6


title: SEP3_replicate 2_ChIP_sample

tag: sample of chromatin immunoprecipitation using SEP3 antibody


title: SEP3_replicate 1_Input

description: sheared input chromatin (replicate 1)


title: SalMorphine Rep 3

source_name: Induction: vehicle-morphine. Challenge: morphine

tag: gender


title: SalMorphine Rep 2

tag: age


title: SalMorphine Rep 1

tag: tissue


title: ButMorphine Rep 1


title: Saline Rep 3


title: p300+/- Rep1

tag: strain


title: WT_saline_rep2

status: Public on Jan 12 2009

description: Effect of A-CREB on basal and kainate-induced gene expression

hyb_protocol: Fragmented labeled cRNA was hybridized according to the manufacturer's instructions as described in the GeneChip Expression Analysis Technical Manual (Affymetrix)

scan_protocol: Scanning was performed according to the manufacturer's instructions as described in the GeneChip Expression Analysis Technical Manual (Affymetrix)

data_processing: The data was generated with MAS5 algorithm (GCOS, Affymetrix)

label_protocol: Labeling was performed according to the manufacturer's instructions as described in the GeneChip Expression Analysis Technical Manual (Affymetrix)

extract_protocol: TRI reagent (Sigma) accordingly to manufacturer's instructions. 3-4 hippocampi were pooled and RNA was cleaned up using RNeasy Mini column (Qiagen) accordingly to manufacturer's instructions.

tag: C57BL6 F1/J

tag: Age

value: 3 weeks old

tag: Treatment

value: saline


title: ACREB_saline_rep2

tag: Strain

value: TetO-A-CREB-95 C57BL6 F1/J


title: ACREB_kainate_18mg/Kg_rep2

value: 18 mg/Kg kainate


title: WT_kainate_14mg/Kg_rep1

value: 14 mg/Kg kainate


title: WT_saline_rep1

value: C57BL6 F1/J


title: WT_kainate_14mg/Kg_rep2


title: ACREB_kainate_14mg/Kg_rep2

tag: train


title: ACREB_kainate_18mg/Kg_rep1


title: ACREB_saline_rep1


title: ACREB_kainate_14mg/Kg_rep1


title: ButMorphine Rep 2