title: KO_NE_2_13290_AGTTCC

data_processing:
Sequencer: Illumina HiSeq 2500. Basecalling pipeline: HiSeq Control Software 2.2.58; Gerald version 1.8
Sequenced reads were mapped to the mouse genome (build GRCm38/mm10) using STAR (v2.5.0c). SAM/BAM files were further processed using SAMTOOLS v1.3
Read count quantifications were obtained using  HTSeq (v0.6.1). Normalization of read counts and differential expression analysis between genotypes was carried out using DESeq2 R package from Bioconductor (Release 2.13).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files include Ensembl gene identifiers (ENSMUSG) and raw counts.

source_name: brain hippocampal tissue from adult male mice

growth_protocol: The generation of Kdm5c-/y and Kdm5cf/f (Iwase et al., 2016) and CaMKIIα-creERT2 (Erdmann et al., 2007) mice have been previously described. Null mutant were maintained in a mixed genetic background (F1: C57/129), while ifKO mice were kept in a pure C57BL/6J background. Experiments were conducted in 2-4 months old animals, except when it is otherwise indicated. Mice were maintained and bred under standard conditions, consistent with Spanish and European regulations and approved by the Institutional Animal Care and Use Committee.

extract_protocol:
Total RNA from hippocampal cultures was extracted with TRI reagent (Sigma-Aldrich).
Conditional Paired-End stranded RNA libraries were prepared for sequencing using standard Illumina protocols (HiSeq Sequencing Kit Trueseq v4), with Read Length 75 and application RNAseq; and Conventional Single-End stranded RNA libraries were prepared for sequencing using standard Illumina protocols (HiSeq Sequencing v4 Chemistry), with Read Length 50 and application Truseq Stranded mRNA.  Service provided by crg

treatment_protocol: Exposure to novelty consisted of placing an individual animal in a white Plexiglas square box containing plastic tubing and small toys for 1h.

tag: tissue

value: brain hippocampal tissue

value: Kdm5c -/- (KO)

tag: read pair

tag: treatment

value: 1 h of novelty exploration

tag: flowcell

value: 2-4 months old animals


title: Kdm5C_wt

status: Public on Aug 18 2017

type: SRA

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

country: Spain

institute: Instituto de Neurociencias (UMH-CSIC)

library_source: genomic

data_processing:
Sequencer: Illumina HiSeq 2500. Basecalling pipeline: HiSeq Control Software 2.2.58.
Run: Mode HiSeq High-Output (HO) Version 4. Number of cycles: 1x50; Number of lanes: 1; Flow cell version: HiSeq Flow Cell v4; Kit version: TruSeq SBS Kit v4.Q30: >95%.
Sequenced reads were mapped to the mouse genome (Mus_musculus.GRCm.38.83) using bowtie 2 v2.2.9 (Langmead and Salzberg, 2012) . SAM/BAM files were further processed using SAMTOOLS v1.3.1 (Li et al., 2009).
Peak calling was performed using MACS2 (v2.1.0) (Zhang et al., 2008) with default parameters. Read counts on aligned bam files were performed using Rsubread (v1.22.3) (Liao et al., 2014). Differential peak methylation analysis was performed using DESeq2 (v1.10.0) (Love et al., 2014) of the bioconductor suite (Huber et al., 2015) in the R (v3.3) statistical computing platform. For consideration of differentially methylated regions between conditions, we used adjusted p-value < 0.05 as indicated in the manuscript.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: For H3K4me3: Tab-delimited text files include genomic positions of detected H3K4me3 peaks using MACS2 (2.1.0) in all samples in this study (36005) and raw counts at these regions using Rsubread (1.22.3). Peak calling was done in each sample. Subsequently, peak regions were merged using ChIPpeakAnno R package (Zhu et al., 2010) and non-overlapping peaks were included to have a full set of detetected peaks (36005). For Kdm5C and H3K4me1: Tab-delimited text files contain raw counts of reads at Kdm5C-bound genomic locations in wild-type mice. Peak calling for Kdm5c ChIP-seq in wild-type mice was run using MACS2 (v2.1.0) with the following parameters: -q 0.01 --nomodel --extsize 131 --broad --broad-cutoff 0.1. Read counts on aligned bam files were performed using featureCounts (Rsubread v1.22.3) (Liao et al., 2014).

molecule: genomic DNA

organism: Mus musculus

source_name: hipocampal tissue from adult mice

growth_protocol: Mice were group-housed in single-sex cages on a light:dark cycle (12/12 h) with food and water available ad limitum.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody against H3K4me3 (Millipore, #07-473), H3K4me1 (Abcam, #ab8895), or Kdm5C (Iwase et al., 2016).
Single-end DNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq V4 Sample Prep Kit). Service provided by CRG (Barcelona. Spain)

treatment_protocol: Exposure to novelty consisted of placing an individual animal in a white Plexiglas square box containing plastic tubing and small toys for 1h. ChIP assays were carried out in adult male mice and in all cases the mice used as control were littermates. The brains were removed and hippocampi rapidly dissected, minced in small pieces and crosslinked by addition of 1/10 volume of fresh 11% formaldehyde solution.

tag: genotype

value: Wild-type

tag: Sex

value: male

tag: age

value: Adult mice (2-4-month-old)

tag: strain

value: pure C57BL/6J background

tag: antibody

value: Kdm5C (Iwase et al., 2016)


title: Kdm5C_KO

value: mutant (KO Kdm5c)


title: KO_NE_1_13289_ATGTCA

library_source: transcriptomic

molecule: total RNA


title: H3K4me1_KO

value: H3K4me1 (Abcam, #ab8895)


title: wt_NE_3_13288_CCGTCC


title: KO_HC_2_13284_GTTTCG

value: Non-treated


title: wt_NE_1_13286_GTGAAA


title: KO_HC_3_13285_GTGGCC


title: wt_NE_2_13287_GTCCGC


title: KO_HC_1_13283_CGTACG


title: wt_HC_1_13280_ATTCCT


title: wt_HC_2_13281_ACTGAT


title: wt_HC_3_13282_GAGTGG


title: ifKO_3_12945_GTGGCC_read2

value: Kdm5c -/- (ifKO)


title: Glutamatergic neuron_1210B2

status: Public on Jul 10 2018

type: RNA

city: shinjuku-ku, Tokyo

first: Takaya

last: Ishii

department: School of medicine

country: Japan

institute: Keio university

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45℃ on GeneChip Clariom S array, human. GeneChips were washed and stained in the Genechip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene chip Scanner 3000 7G (Thermo Fisher Scientific)

data_processing: Data were processed using the Transcriptome Analysis Console (TAC) 4.0 Software (Thermo Fisher Scientific).

label: biotin

organism: Homo sapiens

source_name: Glutamatergic neuron induced from iPSC

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip™ WT PLUS Reagent Kit)

growth_protocol: neurons were induced from iPSCs and cultured in neuron culture medium

extract_protocol: Total RNA was extracted from induced neuron by Rneasy kit (QIAGEN)

tag: cell type

value: Glutamatergic neuron

tag: iPSc clone

tag: diagnosis

value: healthy


title: ifKO_2_12944_AGTCAA_read2


title: ifKO_3_12945_GTGGCC_read1


title: ifKO_1_12943_GGCTAC_read2


title: KO_NE_3_13291_AGTCAA


title: ifKO_2_12944_AGTCAA_read1


title: wt_3_12942_TAGCTT_read1

value: control mice


title: wt_2_12941_ACTTGA_read1


title: wt_1_12940_ATCACG_read1


title: wt_2_12941_ACTTGA_read2


title: wt_1_12940_ATCACG_read2


title: H3K4me3_ifKO_2

data_processing:
Sequencer: Illumina HiSeq 2500. Basecalling pipeline: HiSeq Control Software 2.2.58.
Run: Mode HiSeq High-Output (HO) Version 4. Number of cycles: 1x50; Number of lanes: 1; Flow cell version: HiSeq Flow Cell v4; Kit version: TruSeq SBS Kit v4.Q30: >95%.
Sequenced reads were mapped to the mouse genome (Mus_musculus.GRCm.38.83) using bowtie 2 v2.2.9 (Langmead and Salzberg, 2012) . SAM/BAM files were further processed using SAMTOOLS v1.3.1 (Li et al., 2009).
Peak calling was performed using MACS2 (v2.1.0) (Zhang et al., 2008) with default parameters. Read counts on aligned bam files were performed using Rsubread (v1.22.3) (Liao et al., 2014). Differential peak methylation analysis was performed using DESeq2 (v1.10.0) (Love et al., 2014) of the bioconductor suite (Huber et al., 2015) in the R (v3.3) statistical computing platform. For consideration of differentially methylated regions between conditions, we used adjusted p-value < 0.05 as indicated in the manuscript.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files include genomic positions of detected H3K4me3 peaks using MACS2 (2.1.0) in all samples in this study (36005) and raw counts at these regions using Rsubread (1.22.3). Peak calling was done in each sample. Subsequently, peak regions were merged using ChIPpeakAnno R package (Zhu et al., 2010) and non-overlapping peaks were included to have a full set of detetected peaks (36005).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody against H3K4me3 (Millipore, #07-473).
Single-end DNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq V4 Sample Prep Kit). Service provided by CRG (Barcelona. Spain)

value: mutant (ifKO Kdm5c)

value: anti-H3K4me3 (Millipore #07-473)


title: H3K4me3_ifKO_1


title: H3K4me3_KO_NE_2

value: novel environment exploration (1h)

value: mixed genetic background (F1:C57/129)


title: H3K4me3_wt_NE_2


title: H3K4me3_wt_NE_1


title: H3K4me3_ifwt_2

value: control


title: H3K4me3_KO_HC_2


title: H3K4me3_KO_NE_1


title: KELLY SNP Array

status: Public on Feb 07 2017

type: genomic

city: Philadelphia

first: Jo Lynne

last: Rokita

state: PA

address: 3501 Civic Center Blvd

country: USA

institute: Children's Hospital of Philadelphia

hyb_protocol: The resuspended DNA is heat-denatured and dispensed onto the BeadChip.  The DNA migrates under the gasket by capillary action and spreads over one entire region of the BeadChip.  Overnight, the DNA fragments anneal to their locus-specific 50-mer oligos, which are covalently linked to the beads.  Each bead represents one locus, though there are at least 20 replicates of each bead-type per sample. The unhybridized and non-specifically hybridized DNA is washed away with buffer and prepared for the X-Stain process.

scan_protocol: The BeadChips are then scanned by an Illumina iScan or BeadArray Reader.  A laser is used to excite the flurophores of the labeled and extended bases.  The scanner software then captures high-resolution images of the beads and saves the data onto the server.

data_processing: IDATS were imported into Illumina's Genome Studio, along with pertinent manifest and cluster files for array version humanomniexpress-24v1-0_a to generate various SNP values, and visualize in genome studio to detect breakpoints (*processed.txt).

label: Cy3, Cy5

source_name: neuroblastoma-derived cell line

label_protocol: Labeled single-bases (corresponding to the locus of interest) are extended from the oligos bound to the beads.  C and G nucleotides are biotin-labeled and A and T nucleotides are dinitrophenyl labeled.  The BeadChip then undergoes a series of staining steps to enable the beads to fluoresce and is washed and coated for imaging.

extract_protocol: DNA was extracted using Qiagen Dneasy blood & tissue kit

tag: cell line

value: KELLY

value: neuroblastoma-derived cell line

tag: growth media

value: RPMI 1640, 10% FBS, 1% Penicillin/Streptomycin, 2mM L-Glutamine


title: wt_3_12942_TAGCTT_read2

value: brain hippocampal tissue

value: 2-4 months old animals


title: CHP-212 SNP Array


title: SK-N-BE(2)-C SNP Array


title: IMR-05 SNP Array


title: NB-1691 SNP Array


title: ifKO_1_12943_GGCTAC_read1


title: SK-N-FI SNP Array

value: SK-N-FI


title: H3K3me3_ifwt_1

value: male

value: Adult mice (2-4-month-old)

value: pure C57BL/6J background


title: NB-69 SNP Array


title: H3K4me3_wt_HC_2

value: Wild-type


title: NB-1 SNP Array


title: SK-N-AS SNP Array

value: SK-N-AS


title: NB-EBc1 SNP Array


title: CHP-134 SNP Array


title: SK-N-BE(2) SNP Array


title: SMS-SAN SNP Array

value: SMS-SAN


title: NB-1643 SNP Array

value: IMDM, 20% FBS, 1% Penicillin/Streptomycin, 2mM L-Glutamine


title: H3K4me3_wt_HC_1

value: anti-H3K4me3 (Millipore #07-473)


title: H3K4me3_KO_HC_1

value: mutant (KO Kdm5c)


title: LA-N-6 SNP Array


title: NLF SNP Array

value: NLF


title: SMS-KAN SNP Array

value: SMS-KAN


title: NB-SD SNP Array

value: NB-SD


title: NGP SNP Array

value: NGP

value: neuroblastoma-derived cell line


title: SK-N-DZ SNP Array

value: SK-N-DZ

value: RPMI 1640, 10% FBS, 1% Penicillin/Streptomycin, 2mM L-Glutamine


title: NMB SNP Array

value: NMB


title: RD SNP Array

value: RD


title: LA-N-5 SNP Array


title: SH-SY5Y SNP Array


title: IMR-32 SNP Array


title: SK-N-SH SNP Array

value: SK-N-SH


title: SK-N-FI RNA-Seq

data_processing:
Sequences were aligned to the full hg19 transcriptome and gene counts generated using STAR 2.4.2_a
FPKM was calculated using a custom R script
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt file of gene FPKMs

growth_protocol: Cells were thawed and grown in 150mm plates to 60-80% confluency before being detached and pelleted for RNA extraction.

extract_protocol:
RNA was extracted using the Qiagen miRNeasy Mini kit (Cat 217004) following the manufacturer's protocol.
Libraries were constructed using Illumina's TruSeq Stranded Total RNA Library Prep kit with RiboZero


title: Human Fetal Brain RNA-Seq

source_name: Human fetal brain


title: SMS-KAN RNA-Seq


title: SMS-SAN RNA-Seq


title: SK-N-BE(2)-C RNA-Seq


title: NBLS SNP Array

value: NBLS


title: SK-N-SH RNA-Seq


title: SK-N-DZ RNA-Seq


title: RPE-1 RNA-Seq

source_name: retinal pigmented epithelial hTERT-immortalized cell line


title: SK-N-AS RNA-Seq


title: NLF RNA-Seq


title: NGP RNA-Seq


title: SH-SY5Y RNA-Seq


title: NMB RNA-Seq


title: NBL-S RNA-Seq


title: NB-SD RNA-Seq


title: SK-N-BE(2) RNA-Seq


title: NB-EBc1 RNA-Seq


title: IMR-05 RNA-Seq


title: NB-1691 RNA-Seq


title: NB-69 RNA-Seq


title: LA-N-6 RNA-Seq


title: IMR-32 RNA-Seq


title: KELLY RNA-Seq


title: NB-1 RNA-Seq


title: LA-N-5 RNA-Seq


title: RD RNA-Seq


title: COG-N-573 RNA-Seq

value: IMDM, 20% FBS, 1% Penicillin/Streptomycin, 2mM L-glutamine, 1:1000 ITS Premix Supplement


title: Felix RNA-Seq


title: COG-N-561 RNA-Seq


title: COG-N-496 RNA-Seq


title: COG-N-519 RNA-Seq


title: COG-N-534 RNA-Seq


title: COG-N-549 RNA-Seq


title: COG-N-453 RNA-Seq


title: CHP-134 RNA-Seq


title: CHP-212 RNA-Seq


title: COG-N-471nb RNA-Seq

value: Neurobasal-A plus EGE, FGF, 2mM L-glutamine, B27, and N2


title: COG-N-415 RNA-Seq


title: Col-0 4 hour air RNAseq, rep2

status: Public on Oct 04 2016

city: Austin

first: Hong

last: Qiao

state: TEXAS

address: 2506 speedway, NMS5.324

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

description: air treated for 4 hours

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome usingTopHat version 2.0.8 with default parameters
Differential expressed genes were calculated by Cuffdiff version 2.1.1
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, generated by Cuffdiff version 2.1.1

organism: Arabidopsis thaliana

source_name: whole COL-0 seedling after air treatment

growth_protocol: Arabidopsis seeds were  dark-grown at 24 ºC for 3 days

extract_protocol:
RNA was harvested using Trizol reagent from seedlings.
Libraries were prepared according to NEB instructions of the RNA Library Kit (NEB #E7420S/L)

treatment_protocol: Treated with air (hydrocarbon-free air (Zero grade air, AirGas)) or ethylene (hydrocarbon-free air with 10 parts per million  (ppm) ethylene) for 4 hours

tag: developmental stage

value: whole seedling


title: Col-0 4 hour air RNAseq, rep1

description: air treated for 4 hours


title: NB-1643 RNA-Seq

value: IMDM, 20% FBS, 1% Penicillin/Streptomycin, 2mM L-glutamine


title: P5 back skin_Mc_2

status: Public on Mar 17 2016

city: New York

first: Michael

last: Rendl

state: NY

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

data_processing:
All raw RNA sequencing reads were mapped to the mouse genome (mm10) with TopHat v2.0.3 coupled with the Bowtie2 aligner with default parameters.
Transcriptomes were assembled and fragments per kilo-base per million reads (FPKM) for each gene were computed with Cufflinks v2.1.1 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: P5 back skin_Mc

extract_protocol:
Total RNA obtained from FACS-sorted cells was purified with the Absolutely RNA Nanoprep kit (Agilent), quantified with the NanoDrop spectrophotometer (Thermo Scientific) and measured for quality control by the Agilent Bioanalyzer. Samples with RIN (RNA integrity number) scores 8.8 and higher were further processed. 6ng starting material was reverse transcribed and amplified to 5-7µg cDNA with the RNA Ovation RNA-seq System V2 (NuGEN).
From 100ng amplified cDNA sequencing libraries were generated with 28 unique barcoded adapters (14 samples x 2 replicates) using the Ovation Ultralow DR Library System (NuGEN).

tag: strain background

value: mixture of FVB/N, C57BI/6J and CD1

tag: genotype/variation

value: postnatal day 5

value: back skin

value: Melanocytes

tag: cell fraction/population

value: Lef1-RFP+/CD117+ from dermal preparation of K14-H2BGFP


title: P5 back skin_Mx_2

source_name: P5 back skin_Mx

tag: tissue

value: Matrix progenitor cells

value: K14-H2BGFPLo from dermal preparation of K14-H2BGFP


title: P5 back skin_ORS_2

source_name: P5 back skin_ORS

value: Outer Root Sheath cells

value: K14-H2BGFPHi from dermal preparation of K14-H2BGFP


title: COG-N-557nb RNA-Seq


title: P5 back skin_Mc_1


title: COG-N-440 RNA-Seq


title: P5 back skin_ORS_1


title: HD82Q_H3K4me3_GBD27

status: Public on Dec 31 2015

description: ChIP-Transgenic HD

data_processing:
Basecalls performed using: CASAVA version 1.8.2 (HiSeq 2500) (Read size: 50 bp. Single End)
ChIP-seq reads were aligned to the NCBIM37/mm9 genome assembly using BWA version 0.5.9 (Li and Durbin, 2010). BWA was used to map reads with a maximun of 2 mismatches in the first 32 bases of the sequences, and a maximun of n mismatches in total.
SAMTools (Li et al., 2009) was used to generate Binary of SAM files and also to mapping quality based filtering of the datasets. BAM files containing mapped reads with Mapping Quality > 0 were used to signal quantification.
Genome_build: NCBIM37/mm9
Supplementary_files_format_and_content: Tag density (wig) and enriched peaks (bed) are provided as processed data files.

source_name: mouse hippocampus

growth_protocol: Mice were C57/DBA F1 hybrid males. Mice were group-housed in single-sex cages on a light:dark cycle (12/12 h) with food and water available ad limitum.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody against H3K4me3 Millipore, #07-473).
Libraries were prepared according to standard Illumina's protocols and sequenced on HiSeq 2500 platform following the manufacturer's protocols.

treatment_protocol: ChIP assays were carried out in adult male mice and in all cases the mice used as control were littermates. The brains were removed and hippocampi rapidly dissected, minced in small pieces and crosslinked by addition of 1/10 volume of fresh 11% formaldehyde solution.

value: C57/DBA F1 hybrid

value: hippocampus

value: adult

value: male

tag: chip antibody

value: H3K4me3 (millipore  #07-473)


title: P5 back skin_Mx_1


title: Input_GBD11

description:
Input DNA
same raw data as GSM1062441

value: wild type


title: WT_H3K4me3_GBD26

description:
ChIP-Wild-type
same raw data as GSM1062440


title: DICER1-ifKO smallRNA rep2

status: Public on Feb 04 2015

data_processing:
Sequencer: Illumina HiSeq 2500. Basecalling pipeline: HiSeq Control Software 2.0.12.0; RTA 1.17.21.3; CASAVA 1.8.2.
Run: Mode HiSeq High-Output (HO). Number of cycles: 1x50+7; Number of lines: 1; Flow cell version: HiSeq Flow Cell v3; Kit version: TruSeq SBS Kit v3. Yield (Gb): 7.5; Error rate: 0.5%; Q30: 85%.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then filtered by length (insert size retained: 18-50bp) and mapped to the mouse genome (build GRCm38/mm10) using Burrows-Wheeler Alignment Tool (BWA) v.0.5.9. SAM/BAM files were further processed using SAMTOOLS v0.1.18.
Read count quantitations were obtained using Seqmonk (0.26.0). We get counts that mapped to annotated features of the genome (miRNAs, 2035; miscRNA, 491; mRNA 76938; rRNA, 341; snoRNA, 1602; snRNA, 1431; tRNAs, 26248; tRNA, 22). Normalization of read counts and differential expression analysis between genotypes was carried out using DESeq2 R package from Bioconductor (Release 2.13).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts and size factor normalized counts (DESeq2).

source_name: Hippocampus

extract_protocol:
Total hippocampal RNA was extracted with TRI reagent (Sigma). Total RNA extracted was treated with DNaseI (Qiagen) and precipitated using potassium acetate. All samples were tested by qRT-PCR for recombination. To prepare each sample equal amounts of purified total RNA from 3 mice were pooled together. 3 samples (biological replicates) per genotype were sequenced in HiSeq 2500 apparatus (Illumina). Service provided by Fasteris S.A.
RNA libraries were prepared for sequencing using standard Illumina protocols (Small RNA TruSeq Protocol). Service provided by Fasteris S.A.

tag: genotype 1

value: Dicer1 flox/flox

tag: genotype 2

tag: treatment

value: Tamoxifen (TMX)

value: Adult mice (3-month-old)

tag: sacrifice

value: 3 weeks upon TMX administration


title: DICER1-ifKO smallRNA rep3

tag: strain

tag: age


title: WT smallRNA rep3

value: wild-type


title: DICER1-ifKO smallRNA rep1


title: WT smallRNA rep1


title: WT smallRNA rep2


title: WT RNAseq rep3

data_processing:
Sequencer: Illumina HiSeq 2500. Basecalling pipeline: HiSeq Control Software 2.0.12.0; RTA 1.17.21.3; CASAVA 1.8.2.
Run: Mode HiSeq High-Output (HO). Number of cycles: 1x50+7; Number of lines: 1; Flow cell version: HiSeq Flow Cell v3; Kit version: TruSeq SBS Kit v3. Yield (Gb): 7.5; Error rate: 0.5%; Q30: 85%.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mouse genome (build GRCm38/mm10) using bowtie 2 v2.0.5 and TopHAT v2.0.6. SAM/BAM files were further processed using SAMTOOLS v0.1.18.
Read count quantitations were obtained using Seqmonk (0.26.0). Normalization of read counts and differential expression analysis between genotypes was carried out using DESeq2 R package from Bioconductor (Release 2.13).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts and size factor normalized counts (DESeq2).

extract_protocol:
Total hippocampal RNA was extracted with TRI reagent (Sigma). Total RNA extracted was treated with DNaseI (Qiagen) and precipitated using potassium acetate. All samples were tested by qRT-PCR for recombination. To prepare each sample equal amounts of purified total RNA from 3 mice were pooled together. 3 samples (biological replicates) per genotype were sequenced in HiSeq 2500 apparatus (Illumina). Service provided by Fasteris S.A.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Sample Prep Kit). Service provided by Fasteris S.A.


title: WT RNAseq rep2


title: WT RNAseq rep1


title: DICER1-ifKO RNAseq rep1


title: DICER1-ifKO RNAseq rep2


title: DICER1-ifKO RNAseq rep3


title: PTC BRAF mut 3

status: Public on Feb 16 2015

city: Jeddah

first: Hans-Juergen

last: Schulten

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

description:
Sample name: TM-155-12R
Gene expression data from PTC with a BRAF mutation

hyb_protocol: Following fragmentation, 6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip HuGene-1.0-st arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data were generated using the Affymetrix Expression Console Software using Affymetrix default analysis settings. Data were RMA normalized and analyzed with Partek Genomics Suite 6.5.

source_name: PTC histology

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

extract_protocol: Total RNA from biospecimens was extracted using the Quagen RNeasy mini kit according to the manufacturer's instructions and integrity of RNA was checked using the Agilent Bioanalyzer.

tag: braf status

value: BRAFmutant

value: PTC with a BRAF mutation


title: PTC BRAF wt 8

description:
Sample name: TM-919-12R
Gene expression data from PTC without a BRAF mutation

value: BRAF wild type

value: PTC without a BRAF mutation


title: PTC BRAF mut 13

description:
Sample name: TM-1064-11R
Gene expression data from PTC with a BRAF mutation


title: PTC BRAF wt 11

description:
Sample name: TM-1098-11R
Gene expression data from PTC without a BRAF mutation


title: PTC BRAF wt 7

description:
Sample name: TM-908-12R
Gene expression data from PTC without a BRAF mutation


title: PTC BRAF wt 5

description:
Sample name: TM-509-11R
Gene expression data from PTC without a BRAF mutation


title: PTC BRAF mut 1

description:
Sample name: TM-98-10R
Gene expression data from PTC with a BRAF mutation


title: PTC BRAF wt 3

description:
Sample name: TM-158-13R
Gene expression data from PTC without a BRAF mutation


title: PTC BRAF wt 9

description:
Sample name: TM-993-11R
Gene expression data from PTC without a BRAF mutation


title: PTC BRAF mut 2

description:
Sample name: TM-131-10R
Gene expression data from PTC with a BRAF mutation


title: PTC BRAF mut 14

description:
Sample name: TM-1152-12R
Gene expression data from PTC with a BRAF mutation


title: PTC BRAF mut 5

description:
Sample name: TM-197-12R
Gene expression data from PTC with a BRAF mutation


title: PTC BRAF mut 8

description:
Sample name: TM-681-11R
Gene expression data from PTC with a BRAF mutation


title: PTC BRAF wt 2

description:
Sample name: TM-37-13R
Gene expression data from PTC without a BRAF mutation


title: PTC BRAF wt 6

description:
Sample name: TM-556-10R
Gene expression data from PTC without a BRAF mutation


title: PIF4-peaks-3

status: Public on Oct 02 2014

city: Albany

first: james

middle: m

last: tepperman

state: CA

address: 800 Buchanan St.

department: Plant and Microbial Biology

institute: Plant Gene Expression Center/UC Berkeley

data_processing:
Base-callling was performed using Illumina pipeline CASAVA-1.8.0.
Reads passed quality filtering were aligned to the chromosomes 1-5 of the TAIR10 genome assembly using Bowtie-0.12.7 with the following settings: -v 2 --best --strata -m 1 -5 3
Peak-calling was performed using MACS-1.4.1 with the following settings: -g 150000000 --off-auto --nomodel --shiftsize=60 -w -S.
Genome_build: TAIR10
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: 0.2 g stratified seeds were irradiated with WL at 21 ºC for 3 h to induce germination and grown in darkness at 21 ºC for 3 d before harvest.

extract_protocol: For each PIF-ChIP and each WT control ChIP three independent libraries were generated pooling DNA of four ChIP assays of two biological replicates each using the NEXTflex ChIP-seq kit and 6 NEXTflex ChIP-Seq Barcodes (Bioo Scientific) according to the manufacturer’s instructions. Adapter-ligated DNA-fragments of 200-300 bp were gel-purified, validated by Bioanalyzer 2000 (Agilent) and quantified by the KAPA Library Quantification Kit  (KAPABiosystems). Six libraries were pooled on a single lane and sequenced by 50-cycle single-end sequencing on the Illumina HiSeq platform.

treatment_protocol: Under green safelight, 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: dark-grown

value: anti-Myc (Abcam, ab9132)


title: PTC BRAF wt 4

description:
Sample name: TM-164-13R
Gene expression data from PTC without a BRAF mutation


title: PIF4-peaks-2


title: WT-ChIP-2A


title: PIF4-peaks-1


title: PTC BRAF mut 10

description:
Sample name: TM-827-12R
Gene expression data from PTC with a BRAF mutation


title: WT-ChIP-3


title: PIF1-peaks-2


title: PIF1-peaks-3


title: WT-ChIP-1


title: PIF1-peaks-1


title: H3K27me3_GBD40_140319

status: Public on Jul 18 2014

data_processing:
Basecalls performed using: CASAVA version 1.8.2 (HiSeq 2500) (Read size: 50 bp. Single End)
ChIP-seq reads were aligned to the NCBIM37/mm9 genome assembly using BWA version 0.5.9 (Li and Durbin, 2010). BWA was used to map reads with a maximun of 2 mismatches in the first 32 bases of the sequences, and a maximun of n mismatches in total.
SAMTools (Li et al., 2009) was used to generate Binary of SAM files and also to mapping quality based filtering of the datasets. BAM files containing mapped reads with Mapping Quality > 0 were used to signal cuantification.
BAM files containing uniquely mapped reads for each sequencing replicate were merged to generate a single mapping file per condition. Normalized read counts (read per million mapped reads) sourounding RefSeq TSSs (28015) (10 kb window around TSS) was obtained using SeqMINER (Ye et al., 2011)
Genome_build: NCBIM37/mm9
Supplementary_files_format_and_content: NormalizedReadDensityTSSs.txt: Tab delimited text file including read count collected within a window of 10 kb around RefSeq TSSs (28015) per dataset. Read count is presented as total read count per window and as read density (per base pair normalized read count (reads per million mapped reads)). Tab delimited text file has the format: Chr: Chromosome; Start: Gene Start; Stop: Gene End; RefSeq: RefSeq Accession Number; MIGI_Symbol: Gene Symbol; Strand: Gene Strand; Input: Raw counts in 10 kbp region surounding TSS in input dataset; WT: Raw counts in 10 kbp region surounding TSS in wild-type mice dataset; H2BGFP: Raw counts in 10 kbp region surounding TSS in CaMKII-tTA/tetO-H2BGFP bitransgenic mice dataset; Input (rpm): Normalized read density (read per million mapped reads) in 10 kbp region surounding TSS in input dataset); WT (rpm): Normalized read density (read per million mapped reads) in 10 kbp region surounding TSS in wild-type mice dataset; H2BGFP (rpm): Normalized read density (read per million mapped reads) in 10 kbp region surounding TSS in in CaMKII-tTA/tetO-H2BGFP bitransgenic mice dataset.

growth_protocol: pCaMKII-tTA/line B and tetO-HIST1H2BJ/GFP mice were crossed to produce CaMKII-tTA/tetO-H2BGFP bitransgenic mice (H2BGFP mice). Both parental strains are available at Jackson laboratories (stock number 7004 and 5104, respectively) and are maintained on a C57BL/6J genetic background (the second one after backcrossing to this background). H2BGFP mice were raised without doxycycline (dox). In all our experiments, we used as control littermates mice carrying either no transgene or the tTA or tetO transgene alone. Mice were group-housed in single-sex cages on a light:dark cycle (12/12 h) with food and water available ad limitum.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody against H3K27me3 (abcam, #ab6002).
Libraries were prepared according to standard Illumina's protocols and sequenced on HiSeq 2500 apparatus following the manufacturer's protocols.

treatment_protocol: ChIP assays were carried out in 2.5 month old male mice and in all cases the mice used as control were littermates. The brains were removed and hippocampi rapidly dissected, minced in small pieces and crosslinked by addition of 1/10 volume of fresh 11% formaldehyde solution.

tag: genotype

value: C57BL/6J genetic background

value: mouse hippocampus

tag: Sex

value: adult 2.5 month old


title: WT-ChIP-1A


title: Input_GBD36_140319

description: Input DNA_R2

value: control

value: input

value: male


title: H3K27me3_GBD40_140228


title: H3K27me3_GBD39_140319

value: wild type


title: H3K27me3_GBD39_140228


title: Input_GBD36_140228

description: Input DNA_R1


title: gFLM control 3 (DP34)

status: Public on Sep 19 2013

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

country: Germany

institute: Max Planck Institute for Developmental Biology

data_processing:
Base calling: Illumina SCS/RTA version 2.8
Read filtering and trimming: SHORE import version 0.8 (shore.sf.net). Filtering parameters: “-n 10% -c -k 32”
Read mapping: SHORE mapflowcell version 0.8 (shore.sf.net) utilizing GenomeMapper version 0.4.4 (http://1001genomes.org/software/genomemapper.html). mapflowcell alignment parameters “-n 4 --select=10,11,12,13 --restrict=on”
Peak calling: SHORE peak version 0.8 (shore.sf.net). Peak calling on each set of replicates using default peak calling parameters, TAIR10 genome annotation file provided via “-a”.
Genome_build: TAIR10
Supplementary_files_format_and_content: Peak region lists generated by SHORE peak, see README.txt

source_name: gFLM control 3 (DP34)

growth_protocol: 15 days LD 16ºC (gFLM) and 10 days LD 23ºC (iFLMbeta and iFLMdelta)

extract_protocol:
Material collection: ZT8. ChIP protocol using anti-GFP Ab (Abcam #ab290)
Libraries were prepared according to manufacture's instructions of the ChIP-seq sample prep kit from Illumina. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA from 150-400 bp was band isolated from an agarose gel. The purified DNA was PCR amplified with Illumina primers for 18 cycles and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

tag: ecotype

value: Seedlings

tag: antibody

value: IP with untagged FLM protein


title: mock PSB-d ChIP output

status: Public on Nov 04 2013

city: Gent

first: Ken

last: Heyndrickx

address: Technologiepark 927

department: Department of Plant Biotechnology and Bioinformatics

country: Belgium

institute: Ghent University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Overrepresented sequences were clipped from the reads using fastx-clipper (fastx toolkit v 0.0.13)
ChIP-Seq reads were aligned to the TAIR10 genome assembly using BWA 0.5.9 with the quality threshold for trimming set at 20 (-q 20)
Peaks not mapping uniquely at one position in the genome were removed using samtools 0.1.18 (-q 1)
Redundant reads were removed using Picard Tools
Peaks were called using MACS v 1.4.2 with following adapted settings: mfold 5,40; genome size 1.0e8
Genome_build: TAIR10
Supplementary_files_format_and_content: BED files were generated by MACS

source_name: Plant cell suspension cells

growth_protocol: The cell suspension culture PSB-D is maintained by weekly subculturing 7 mL of a 7-day-old culture into 45 mL of fresh MSMO containing NAA and kinetin, in a 100-mL Erlenmeyer flask. Growth conditions are always shaking on an orbital shaker at 130 rpm at 25°C in the dark.

extract_protocol:
Cells were grinded in N2(l), mixed with extraction buffer and incubated with detergents for 30 minutes. After sonication, the extract was clarified by centrifugation.  ERF115-DNA complexes were isolated through a Tandem Chromatin Affinity Purification procedure (TChAP) with Ni2+-NTA and Streptavidin-sepharose beads based on the HBH tag.
Standard Illmuna Protocol

treatment_protocol: Cells were treated with 0.75% formaldehyde for 10 minutes. After crosslinking, formaldehyde was quenched with 250mM glycine and cells were washed with PBS

tag: cell type

value: PSB-d dark growing cell suspension cells

value: Landsberg erecta

value: cells were crosslinked and harvested 2 days after subculturing


title: gFLM-GFP replicate 1 (DP28)

source_name: gFLM-GFP replicate 1 (DP28)

value: anti-GFP Ab (Abcam #ab290)


title: ERF115-HBH ChIP output


title: gFLM control 2 (DP34)

source_name: gFLM control 2 (DP34)


title: gFLM-GFP replicate 3 (DP28)

source_name: gFLM-GFP replicate 3 (DP28)


title: gFLM control 1 (DP34)

source_name: gFLM control 1 (DP34)


title: gFLM-GFP replicate 2 (DP28)

source_name: gFLM-GFP replicate 2 (DP28)


title: WT-ChIP-2

tag: genotype/variation

value: wild-type


title: WT-ChIP-3A


title: prr7-3 PRR7::HA-PRR7 #151 IP (ExpI)

status: Public on Jul 27 2013

city: East Lansing

first: Tiffany

middle: L

last: Liu

state: Michigan

address: 3260 Molecular Plant Sciences Building

department: Plant Biology

institute: Michigan State University

description: IP using anti-HA antibody

data_processing:
FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) to filter out adapter sequences (fastx_clipper) and low quality reads (fastq_quality_trimmer) with minimum read length set at 30bp and minimum quality threshold at 20
Bowtie alignment to Arabidopsis TAIR10 genome with -m to exclude reads that can align more than once to the genome
QuEST to identify binding sites and determine false discovery rates, with the type of experiment specified as a transcription factor, calling parameter set to relaxed, and peak shift lower threshold set to 10
Python scripts to define common binding sites as those located within 500bp
In Experiment II, python scripts were used to randomly discard immunoprecipitated reads until their total number closely matched the total number of negative control reads in order for QuEST to estimate FDR values
The binding sites determined by QuEST were compared to TAIR10 genes to associate binding sites to putative target genes using a python script (genes were associated to binding sites located 1000bp upstream of the transcriptional start site to 1000bp downstream of the transcriptional stop)
Flanking sequences around each binding site were acquired using a publicly available script (http://www.stanford.edu/%7evalouev/QuEST/output_genomic_regions_from_calls.pl.gz) for input into MEME and Weeder
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: <file name>_peak_caller.ChIP.out.accepted was used to determine corresponding genes in reference to the TAIR10 genome.  Binding sites were visualized from the <file name>_normalized.profile.wig file.

growth_protocol: Plants were grown on Murashige and Skoog medium with 0.8% agar and 2% sucrose under 70 µmol m-2s-1 and a 12 h light/12 h dark regime for two weeks before analysis.

extract_protocol:
Nuclei were extracted from cross-linked cells, sonicated, and immunoprecipitated with antibodies.
Libraries were contructed for Illumina sequencing.

value: prr7-3 PRR7::HA-PRR7

value: anti-HA

value: 15 days

tag: experiment

value: Experiment 1 (ExpI)

tag: tissue

value: whole seedlings


title: prr7-3 IP (ExpII)

description: IP using anti-HA antibody

value: prr7-3 IP

tag: chip antibody

value: Experiment 2 (ExpII)


title: prr7-3 PRR7::HA-PRR7 #151 IP (ExpII)

description: IP using anti-HA antibody


title: GTL1 ChIP-chip

status: Public on Aug 01 2013

city: Columbus

first: Kengo

last: Morohashi

state: OH

address: 1060 Carmack Rd

department: Molecular Genetics

institute: The Ohio State University

description:
GTL1 ChIP from two independent ChIP experiments:
IP: GTL1_GFP_1_Grotewold_110609.CEL
IP: GTL1_GFP_2_Grotewold_110609.CEL
Input: GTL1_I_1_Grotewold_110609.CEL
Input: GTL1_I_2_Grotewold_110609.CEL

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: MAT (Model-based analysis of tiling array)

source_name: ChIPed DNA from GTL1p:GTL1-GFP transgenic Arabidopsis

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

growth_protocol: 1/2 MS with 1% sucrose under continuous light

extract_protocol: Samples were prepared by ChIP using an antibody against GFP

value: anti-GFP

source_name: Input DNA from GTL1p:GTL1-GFP transgenic Arabidopsis


title: prr7-3 IP (ExpI)

description: IP using anti-HA antibody


title: prr7-3 Input (ExpI)

description: IP using anti-HA antibody

value: input


title: H2BGFP Rep3

description: Gene expression data from hippocampal tissue

hyb_protocol: Following Affymetrix instructions

scan_protocol: Following Affymetrix instructions

data_processing: Microarray data were analyzed using arrayQualityMetrics, oligo, genefilter and limma Bioconductor R packages (Gentleman et al., 2004). Expression data were preprocessed with RMA (Irizarry et al., 2003). Probe-set summarization was performed using the median polish method. Control probes were removed and intensity filtering was applied to eliminate non-expressed probe-sets (intensity value below 20% percentile in all arrays). Then, differential expression analysis was performed by using the limma package (Smyth, 2004).

source_name: hippocampal tissue from H2BGFP mice

label_protocol: Following Affymetrix instructions

growth_protocol: pCaMKII-tTA/line B (Mayford et al., 1996) and tetO-HIST1H2BJ/GFP (Tumbar et al., 2004) mice were used to produce CaMKII-tTA/tetO-H2BGFP bitransgenic mice (referred to as “H2BGFP mice”). pCaMKII-tTA/line B mice (Jackson laboratories stock #7004) are in a pure C57BL/6J background. TetO-HIST1H2BJ/GFP mice (Jackson laboratories stock #5104) were backcrossed 6 times to C57BL/6J prior to the production of H2BGFP bitransgenics. We used as control littermates mice carrying either no transgene or the tTA or tetO transgene alone. Mice were group-housed in single-sex cages (30x15x11 cm clear cages occupied by up to 5 mice and raised on a light:dark cycle (12/12 h) with food and water available ad limitum. Mice were maintained according to animal care standards established by the European Union and all the protocols were approved by the Institutional Animal Care and Use Committee.

extract_protocol: Total RNA from the hippocampus of age, gender and genotype-matched mice was extracted with TRI reagent (Sigma). Equal amounts of purified total RNA from two genotype-matched mice were subsequently pooled, treated with DNaseI (Qiagen) and cleaned up using the RNeasy mini kit (Qiagen). To balance gender factor, each pooled sample contained total RNA from one male and one female. Three independent pooled samples per genotype were hybridized to Mouse Gene 1.0ST expression arrays (Affymetrix).

treatment_protocol: Experiments were performed in three-month old animals and in all cases the mice used as control were littermates of the transgenic mice. Mice were sacrificed by decapitation. The brains were immediately removed, and hippocampi rapidly dissected and placed in RNAlater solution (Qiagen, Venlo, The Netherlands) until total RNA extraction.

value: hippocampus


title: H2BGFP Rep1


title: H2BGFP Rep2


title: Wild-type Rep2

source_name: hippocampal tissue from wild-type mice


title: prr7-3 PRR7::HA-PRR7 #151 Input (ExpI)

description: IP using anti-HA antibody


title: Wild-type Rep3


title: Wild-type Rep1


title: cbp+/- Novelty Vehicle Rep1

status: Public on Jul 09 2013

data_processing: GeneSpring GX 11 software (Agilent Technologies Inc) was used. RMA algorithm was uset to background correction, data normalization and probe sumarization.

source_name: hippocampal tissue from cbp+/- mice treated with vehicle and exposed to Novelty

growth_protocol: Mice were cbp+/- or wild-type littermates C57/DBA F1 hybrid females. Mice were group-housed in single-sex cages on a light:dark cycle (12/12 h) with food and water available ad limitum.

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 condtition (standard housing and novelty; vehicle and TSA treatment). 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 11 (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Experiments were performed in 3 month old animals and in all cases the mice used as control were littermates of the treated mice. Standard housing consisted of 30x15x11 cm clear cages occupied by up to 5 mice. Exposure to novelty consisted of placing an individual animal in a white plexiglas square box containin plastic tubing and small toys for 1h. The brains were immediately removed, and hippocampi rapidly dissected and placed in RNAlater solution (Qiagen, Venlo, The Netherlands) until total RNA extraction.

value: C57/DBA F1 hybrid

value: cbp+/-


title: cbp+/- Novelty TSA Rep2

source_name: hippocampal tissue from cbp+/- mice treated with TSA and exposed to Novelty


title: cbp+/- Novelty Vehicle Rep3


title: cbp+/- Standard Cage Vehicle Rep3

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


title: cbp+/- Novelty TSA Rep3


title: cbp+/- Standard Cage Naïve Rep1

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


title: cbp+/- Standard Cage Vehicle Rep5


title: cbp+/- Standard Cage Naïve Rep2


title: cbp+/- Standard Cage TSA Rep2

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


title: cbp+/- Standard Cage TSA Rep1


title: cbp+/- Novelty TSA Rep1


title: cbp+/- Standard Cage TSA Rep3


title: cbp+/- Standard Cage Vehicle Rep4


title: Wild-type Novelty TSA Rep3

source_name: hippocampal tissue from wild-type mice treated with TSA and exposed to Novelty

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 condtition (standar housing and novelty; vehicle and TSA treatment). 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 11 (Agilent Technologies, Santa Clara, CA).


title: Wild-type Novelty Vehicle Rep3

source_name: hippocampal tissue from wild-type mice treated with vehicle and exposed to Novelty


title: Wild-type Standard Cage Vehicle Rep4

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


title: Wild-type Standard Cage TSA Rep3

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


title: Wild-type Novelty TSA Rep2


title: Wild-type Novelty Vehicle Rep1


title: Wild-type Standard Cage TSA Rep2


title: Wild-type Standard Cage Vehicle Rep5


title: Wild-type Standard Cage TSA Rep1


title: Wild-type Novelty Vehicle Rep2


title: Wild-type Novelty TSA Rep1


title: cbp+/- Novelty Vehicle Rep2


title: GBD3_Veh_AcH2B_ChIPseq

description:
processed data file:
gbd1_3_X_SICER-W200-G600-E10-islandfiltered.wig.normalized.wig
Sample 2

data_processing:
Basecalls performed using: GAPipeline-1.0rc4 (GA-II) (samples 1-3) (Read size: 32 bp), CASAVA version 1.8.2 (HiSeq2000) (Samples 4-15) (Read size: 50 bp)
ChIP-seq reads were aligned to the mm9 genome assembly using BWA version 0.5.9. BWA was used to map reads with a maximun of 2 mismatches in the first 32 bases of the sequences, and a maximun of n mismatches in total.
To subset uniquelly mapped reads, the produced BAM files where then parsed using the SAMTOOLS and all mapped with a mapping quality greater than 0 were exported.
Peaks were called using SICER version 1.1 (program settings are described in the methods sections of the manuscript).
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using IGV tools and normalized by using Wigreader library (https://github.com/rgejman/wigreader). Scores represent normalized (RPM) read density.

growth_protocol: Mice were C57/DBA F1 hybrid. Mice were group-housed in single-sex cages on a light:dark cycle (12/12 h) with food and water available ad limitum.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to standard Illumina's protocols and sequenced on the Genome Analyzer II or HiSeq2000 following the manufacturer's protocols.

treatment_protocol: Experiments were performed in 3 month old animals and in all cases the mice used as control were littermates of the treated mice. Trichostatin A (TSA) 2.4 mg/kg in DMSO/Saline solution (1:4) was administered by intraperitoneal injection. The brains were removed 30 min after treatment, and hippocampi rapidly dissected, minced in small pieces and crosslinked by addition of 1/10 volume of fresh 11% formaldehyde solution.

tag: gender

value: female

value: 3 month

tag: treatment group

value: vehicle; DMSO/Saline solution (1:4)

value: AcH2B (in-house made rabbit whole antiserum)


title: GBD24_IgG_naïve

description: Sample 15

source_name: naïve

value: male

value: Naïve

value: whole serum from normal nonimmunized rabbits


title: GBD1_Veh_AcH2B_ChIPseq

description:
processed data file:
gbd1_3_X_SICER-W200-G600-E10-islandfiltered.wig.normalized.wig
Sample 1


title: GBD20_Veh_AcH4K12_ChIPseq

description: Sample 11

value: AcH4K12; Anti-Histone H4 (acetylated) (acetyl K12) antibody

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. #


title: GBD26_naïve_H3K4me3_ChIPseq

description: Sample 13

tag: strain

tag: age

value: H3K4me3; Anti-trimethyl-Histone H3 (Lys4) Antibody

value: millipore


title: Wild-type Standard Cage Naïve Rep2

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

value: wild-type


title: GBD11_Input_Veh

description: Sample 14

source_name: Veh


title: GBD5_TSA_AcH2B_ChIPseq

description:
processed data file: gbd5_X_SICER-W200-G600-E10-islandfiltered.wig.normalized.wig
Sample 3

value: Trichostatin A (TSA) 2.4 mg/kg


title: GBD30_naïve_AcH4K12_ChIPseq

description: Sample 10


title: Wild-type Standard Cage Naïve Rep1


title: Wild-type Standard Cage Vehicle Rep3


title: GBD18_Veh_AcH3K9,14_ChIPseq

description: Sample 8

value: AcH3K9,14; Anti-acetyl-Histone H3 Antibody


title: GBD19_TSA_AcH3K9,14_ChIPseq

description: Sample 9

value: hippocampus


title: GBD12_naïve_AcH3K9,14_ChIPseq

description: Sample 6

value: C57/DBA F1 hybrid


title: GBD28_naïve_AcH3K9,14_ChIPseq

description: Sample 7


title: GBD9_naïve_AcH2B_ChIPseq

description: Sample 4


title: GBD11_Input_Veh

status: Public on Jun 20 2013

description: Sample 5

data_processing:
Basecalls performed using: CASAVA version 1.8.2 (HiSeq2000) (Read size: 50 bp)
ChIP-seq reads were aligned to the mm9 genome assembly using BWA version 0.5.9. BWA was used to map reads with a maximun of 2 mismatches in the first 32 bases of the sequences, and a maximun of n mismatches in total.
To subset uniquelly mapped reads, the produced BAM files where then parsed using the SAMTOOLS and all mapped with a mapping quality greater than 0 were exported.
Peaks were called using SICER version 1.1 (program settings are described in the methods sections of the manuscript).
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using IGV tools and normalized by using Wigreader library (https://github.com/rgejman/wigreader). Scores represent normalized (RPM) read density.

treatment_protocol: Experiments were performed in 10 week old animals and in all cases the mice used as control were littermates of the HD-82Q mice. The brains were removed 30 min after treatment, and hippocampi rapidly dissected, minced in small pieces and crosslinked by addition of 1/10 volume of fresh 11% formaldehyde solution.

tag: strain background

value: Vehicle

value: 10 wks


title: GBD29_AcH3K9,14_ChIPseq

description: Sample 2

value: Millipore


title: GBD31_AcH4K12_ChIPseq

description: Sample 4

value: Abcam


title: GBD22_naïve_AcH2B_ChIPseq

description: Sample 5

value: female

value: 3 month

value: AcH2B (in-house made rabbit whole antiserum)


title: MethylC-Seq_mm_fc_male_7wk_neun_neg

status: Public on Jul 03 2013

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: Bisulfite-Seq

data_processing:
Data were mapped to the Homo sapiens reference genome (hg18) or the Mus musculus reference genome (mm9).
MethylC-Seq, TAB-Seq, CMS-IP and hmC-gluc-IP-Seq analyses were performed as described in Lister, Mukamel et al. Global epigenomic reconfiguration during mammalian brain development. Science (2013).
RNA-Seq RPKM data were generated using Bowtie2 and Tophat2. Gene expression values were calculated using Cufflinks2.
genome build: mm9
Supplementary_files_format_and_content: The processed data for the allC.MethylC-Seq_<sample>.<chr>.txt files contain a row of headers indicating the chromosome, position, strand, methylation class, methylation count, and total coverage. This is a tab-delimited file.

source_name: NeuN- nuclei isolated from frontal cortex from 7 week old male mouse brain

growth_protocol: The mouse lines C57Bl/6 and S100b-eGFP (B6;D2-Tg(S100B-EGFP)1Wjt/J), both from Jackson Laboratories, ME were bred and maintained in our animal facility in 12 h light/dark cycles with food ad libitum. To produce the S100b-eGFP animals used for FACS, animals were crossed to C57BL/6 to produce heterozygotes for eGFP expression. Tet2-/- mice were produced by targeted disruption of the Tet2 gene. Animals were weaned in groups of 3-4 per cage, and used at the postnatal time-points indicated. Three animals obtained from separate litters were processed together for DNA and RNA isolations.

extract_protocol: Genomic DNA was purified from tissue, sorted cells or nuclei using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. MethylC-Seq libraries were constructed as descibed previously [Lister R. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells, Nature 471, 68-73 (2011)], except library amplification was performed with either PfuTurboCx Hotstart DNA polymerase (Agilent Technologies, Santa Clara, CA, USA) or KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA, USA).

value: wild type

value: brain (frontal cortex)

tag: cell type(s)

value: non-neurons (NeuN-, predominantly glia)

value: 7 weeks (P49)

value: male


title: GBD28_AcH3K9,14_ChIPseq

description: Sample 1

value: Wild-type


title: GBD24_IgG_naïve

description: Sample 6

value: Naive

value: whole serum from normal nonimmunized rabbits


title: MethylC-Seq_mm_fc_fetal

description: Bisulfite-Seq

source_name: Frontal cortex from fetal mouse brain

tag: genotype

value: all

value: male/female


title: GBD30_AcH4K12_ChIPseq

description: Sample 3

value: C57/DBA F1 hybrid

value: hippocampus


title: MethylC-Seq_mm_fc_male_7wk_neun_pos

description: Bisulfite-Seq

source_name: NeuN+ nuclei isolated from frontal cortex from 7 week old male mouse brain

value: neurons (NeuN+)


title: gSOC1-GFP replicate 3

status: Public on Apr 09 2013

description:
mGFP6
Sample 6

data_processing:
Base calling: Illumina SCS/RTA version 2.8
Read filtering and trimming: SHORE import version 0.8 (shore.sf.net). Filtering parameters: “-n 10% -c -k 32”
Read mapping: SHORE mapflowcell version 0.8 (shore.sf.net) utilizing GenomeMapper version 0.4.4 (http://1001genomes.org/software/genomemapper.html). mapflowcell alignment parameters “-n 4 --select=10,11,12,13 --restrict=on”
Peak calling: SHORE peak version 0.8 (shore.sf.net). Peak calling on all 3 replicates using default peak calling parameters, TAIR10 genome annotation file provided via “-a”.
Genome_build: TAIR10
Supplementary_files_format_and_content: Peak region list generated by SHORE peak (SOC1_SUMMARY.txt), see README.txt for format description.

source_name: SOC1p:gSOC1-GFP;soc1-2 #7 apices

growth_protocol: 15 days SD + 3 days LD

extract_protocol:
Material collection: ZT4. ChIP protocol using anti-GFP Ab (Abcam #ab290)
Libraries were prepared according to manufacture's instructions of the ChIP-seq sample prep kit from Illumina. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA from 150-400 bp was band isolated from an agarose gel. The purified DNA was PCR amplified with Illumina primers for 18 cycles and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

value: anti-GFP

value: Abcam


title: gSOC1 negative 3

description: Sample 5

source_name: SOC1p:gSOC1;soc1-2 #9 apices


title: gSOC1 negative 1

description: Sample 1


title: gSOC1-GFP replicate 1

description:
mGFP6
Sample 2


title: gSOC1 negative 2

description: Sample 3


title: wt (10 weeks), cerebellum, biological rep3

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Microarray data were background corrected, normalized, summarized, and statistically analyzed using R (http://www.r-project.org/; The R Development Core Team) and Bioconductor (Gentleman et al, 2004). Mouse Gene 1.0 ST arrays were read using oligo package, using RMA algorithm as normalization method.

source_name: Cerebellum 10 weeks wt

label_protocol: standard Affymetrix protocol

growth_protocol: The transgenic strain PrP-htt-N171-82Q (Schilling et al, 1999) (http://www.informatics.jax.org/reference/allele/MGI:2670626) was acquired from Jackson Laboratories (Sacramento, CA, USA) and maintained in a DBA and C57BL/6J mixed background (50:50) because the viability of the strain is severely compromised in a pure C57BL/6J background. Experimental protocols were consistent with European regulations and approved by the Institutional Animal Care and Use Committee.

extract_protocol: Total RNA was extracted separately from individual hippocampi using TRI reagent (Sigma-Aldrich) following manufacturers' instructions.  Equal amounts of total RNA from 3-4 animals were pooled and treated with RNAse-free DNaseI (Qiagen) treatment and a cleaned up using RNeasy RNA purification columns (Qiagen).

treatment_protocol: Animals were sacrificed by cervical dislocation and brains were immediately removed. Cerebella and hippocampi were dissected and placed into RNAlater solution (Qiagen) until RNA purification.

value: Cerebellum

value: 10 weeks

value: wt

tag: genetic background

value: DBA and C57BL/6J


title: N171-HD82Q (20 weeks), hippocampus, biological rep2

source_name: Hippocampus 20 weeks transgenic

value: Hippocampus

value: 20 weeks

value: female


title: N171-HD82Q (10 weeks), cerebellum, biological rep1

source_name: Cerebellum 10 weeks transgenic

value: male


title: N171-HD82Q (10 weeks), cerebellum, biological rep3


title: N171-HD82Q (20 weeks), hippocampus, biological rep3


title: wt (20 weeks), hippocampus, biological rep1

source_name: Hippocampus 20 weeks wt


title: gSOC1-GFP replicate 2

description:
mGFP6
Sample 4


title: N171-HD82Q (20 weeks), hippocampus, biological rep1


title: wt (10 weeks), cerebellum, biological rep2


title: N171-HD82Q (10 weeks), cerebellum, biological rep2


title: wt (10 weeks), hippocampus, biological rep3

source_name: Hippocampus 10 weeks wt


title: wt (10 weeks), cerebellum, biological rep1


title: wt (20 weeks), hippocampus, biological rep3


title: N171-HD82Q (10 weeks), hippocampus, biological rep2

source_name: Hippocampus 10 weeks transgenic


title: wt (10 weeks), hippocampus, biological rep2


title: wt (20 weeks), hippocampus, biological rep2


title: AML_patient_419

status: Public on Feb 07 2013

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

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.

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

value: No

tag: overall survival (days)

tag: life status

value: alive


title: wt (10 weeks), hippocampus, biological rep1


title: AML_patient_418

value: Yes

value: dead


title: AML_patient_422


title: AML_patient_421


title: AML_patient_416


title: AML_patient_420


title: N171-HD82Q (10 weeks), hippocampus, biological rep1


title: N171-HD82Q (10 weeks), hippocampus, biological rep3


title: AML_patient_415


title: AML_patient_417


title: AML_patient_413


title: AML_patient_412


title: AML_patient_408


title: AML_patient_411


title: AML_patient_410


title: AML_patient_409


title: AML_patient_406


title: AML_patient_407


title: AML_patient_414


title: AML_patient_403


title: AML_patient_405


title: AML_patient_402


title: AML_patient_404


title: AML_patient_400


title: AML_patient_401


title: AML_patient_399


title: AML_patient_398


title: AML_patient_396


title: AML_patient_395


title: AML_patient_397


title: AML_patient_390


title: AML_patient_394


title: AML_patient_388


title: AML_patient_393


title: AML_patient_392


title: AML_patient_391


title: AML_patient_387


title: AML_patient_389


title: AML_patient_386


title: AML_patient_383


title: AML_patient_381


title: AML_patient_382


title: AML_patient_385


title: AML_patient_379


title: AML_patient_375


title: AML_patient_376


title: AML_patient_378


title: AML_patient_384


title: AML_patient_377


title: AML_patient_380


title: AML_patient_373


title: AML_patient_370


title: AML_patient_372


title: AML_patient_371


title: AML_patient_367


title: AML_patient_368


title: AML_patient_369


title: AML_patient_366


title: AML_patient_364


title: AML_patient_361


title: AML_patient_363


title: AML_patient_360


title: AML_patient_365


title: GBD21_TSA_AcH4K12_ChIPseq

description: Sample 12

value: C57/DBA F1 hybrid

value: 3 month

value: Trichostatin A (TSA) 2.4 mg/kg

value: hippocampus

value: AcH4K12; Anti-Histone H4 (acetylated) (acetyl K12) antibody

value: abcam


title: AML_patient_362


title: AML_patient_374


title: AML_patient_358


title: AML_patient_356


title: AML_patient_357


title: AML_patient_354


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title: AML_patient_353


title: AML_patient_350


title: AML_patient_345


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title: AML_patient_359


title: AML_patient_343


title: AML_patient_346


title: AML_patient_344


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title: AML_patient_320


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title: AML_patient_270


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title: AML_patient_262


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title: AML_patient_261


title: AML_patient_269


title: AML_patient_256


title: AML_patient_258


title: AML_patient_260


title: AML_patient_257


title: AML_patient_259


title: AML_patient_417


title: AML_patient_418


title: AML_patient_422


title: AML_patient_421


title: AML_patient_251


title: AML_patient_250


title: AML_patient_419


title: AML_patient_415


title: AML_patient_252


title: AML_patient_414


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title: AML_patient_420


title: AML_patient_253


title: AML_patient_413


title: AML_patient_410


title: AML_patient_249


title: AML_patient_416


title: AML_patient_255


title: AML_patient_254


title: AML_patient_411


title: AML_patient_409


title: AML_patient_248


title: AML_patient_408


title: AML_patient_247


title: AML_patient_407


title: AML_patient_246


title: AML_patient_405


title: AML_patient_406


title: AML_patient_245


title: AML_patient_244


title: AML_patient_403


title: AML_patient_243


title: AML_patient_241


title: AML_patient_402


title: AML_patient_238


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title: AML_patient_237


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title: AML_patient_233


title: AML_patient_400


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title: AML_patient_393


title: AML_patient_396


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title: AML_patient_232


title: AML_patient_404


title: AML_patient_236


title: AML_patient_401


title: AML_patient_395


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title: AML_patient_392


title: AML_patient_231


title: AML_patient_235


title: AML_patient_394


title: AML_patient_391


title: AML_patient_228


title: AML_patient_229


title: AML_patient_230


title: AML_patient_389


title: AML_patient_390


title: AML_patient_225


title: AML_patient_226


title: AML_patient_388


title: AML_patient_222


title: AML_patient_387


title: AML_patient_386


title: AML_patient_227


title: AML_patient_223


title: AML_patient_385


title: AML_patient_384


title: AML_patient_379


title: AML_patient_380


title: AML_patient_383


title: AML_patient_381


title: AML_patient_378


title: AML_patient_221


title: AML_patient_220


title: AML_patient_377


title: AML_patient_224


title: AML_patient_382


title: AML_patient_218


title: AML_patient_219


title: AML_patient_376


title: AML_patient_215


title: AML_patient_375


title: AML_patient_373


title: AML_patient_216


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title: AML_patient_208


title: AML_patient_209


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title: AML_patient_213


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title: AML_patient_368


title: AML_patient_363


title: AML_patient_365


title: AML_patient_207


title: AML_patient_364


title: AML_patient_201


title: AML_patient_202


title: AML_patient_362


title: AML_patient_206


title: AML_patient_200


title: AML_patient_204


title: AML_patient_199


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title: AML_patient_197


title: AML_patient_196


title: AML_patient_198


title: AML_patient_360


title: AML_patient_359


title: AML_patient_355


title: AML_patient_195


title: AML_patient_356


title: AML_patient_358


title: AML_patient_361


title: AML_patient_354


title: AML_patient_353


title: AML_patient_192


title: AML_patient_189


title: AML_patient_357


title: AML_patient_352


title: AML_patient_193


title: AML_patient_351


title: AML_patient_190


title: AML_patient_350


title: AML_patient_188


title: AML_patient_194


title: AML_patient_185


title: AML_patient_186


title: AML_patient_345


title: AML_patient_346


title: AML_patient_191


title: AML_patient_187


title: AML_patient_184


title: AML_patient_349


title: AML_patient_183


title: AML_patient_343


title: AML_patient_347


title: AML_patient_341


title: AML_patient_180


title: AML_patient_178


title: AML_patient_181


title: AML_patient_344


title: AML_patient_342


title: AML_patient_177


title: AML_patient_338


title: AML_patient_339


title: AML_patient_348


title: AML_patient_179


title: AML_patient_182


title: AML_patient_176


title: AML_patient_175


title: AML_patient_335


title: AML_patient_334


title: AML_patient_337


title: AML_patient_336


title: AML_patient_340


title: AML_patient_174


title: AML_patient_173


title: AML_patient_172


title: AML_patient_333


title: AML_patient_170


title: AML_patient_332


title: AML_patient_171


title: AML_patient_331


title: AML_patient_169


title: AML_patient_330


title: AML_patient_328


title: AML_patient_165


title: AML_patient_327


title: AML_patient_167


title: AML_patient_324


title: AML_patient_325


title: AML_patient_326


title: AML_patient_164


title: AML_patient_323


title: AML_patient_329


title: AML_patient_166


title: AML_patient_162


title: AML_patient_163


title: AML_patient_159


title: AML_patient_157


title: AML_patient_322


title: AML_patient_158


title: AML_patient_321


title: AML_patient_156


title: AML_patient_161


title: AML_patient_317


title: AML_patient_168


title: AML_patient_319


title: AML_patient_320


title: AML_patient_160


title: AML_patient_154


title: AML_patient_316


title: AML_patient_155


title: AML_patient_314


title: AML_patient_318


title: AML_patient_313


title: AML_patient_152


title: AML_patient_153


title: AML_patient_312


title: AML_patient_151


title: AML_patient_311


title: AML_patient_315


title: AML_patient_150


title: AML_patient_149


title: AML_patient_310


title: AML_patient_309


title: AML_patient_308


title: AML_patient_307


title: AML_patient_145


title: AML_patient_143


title: AML_patient_305


title: AML_patient_142


title: AML_patient_144


title: AML_patient_306


title: AML_patient_302


title: AML_patient_303


title: AML_patient_304


title: AML_patient_141


title: AML_patient_301


title: AML_patient_299


title: AML_patient_300


title: AML_patient_139


title: AML_patient_147


title: AML_patient_140


title: AML_patient_148


title: AML_patient_138


title: AML_patient_298


title: AML_patient_146


title: AML_patient_136


title: AML_patient_295


title: AML_patient_296


title: AML_patient_297


title: AML_patient_134


title: AML_patient_135


title: AML_patient_294


title: AML_patient_137


title: AML_patient_133


title: AML_patient_293


title: AML_patient_132


title: AML_patient_130


title: AML_patient_292


title: AML_patient_288


title: AML_patient_290


title: AML_patient_291


title: AML_patient_131


title: AML_patient_289


title: AML_patient_124


title: AML_patient_286


title: AML_patient_125


title: AML_patient_285


title: AML_patient_283


title: AML_patient_122


title: AML_patient_121


title: AML_patient_282


title: AML_patient_281


title: AML_patient_123


title: AML_patient_280


title: AML_patient_128


title: AML_patient_129


title: AML_patient_127


title: AML_patient_126


title: AML_patient_118


title: AML_patient_287


title: AML_patient_119


title: AML_patient_117


title: AML_patient_120


title: AML_patient_284


title: AML_patient_279


title: AML_patient_116


title: AML_patient_115


title: AML_patient_277


title: AML_patient_274


title: AML_patient_276


title: AML_patient_114


title: AML_patient_113


title: AML_patient_275


title: AML_patient_278


title: AML_patient_111


title: AML_patient_273


title: AML_patient_112


title: AML_patient_271


title: AML_patient_109


title: AML_patient_269


title: AML_patient_270


title: AML_patient_108


title: AML_patient_267


title: AML_patient_105


title: AML_patient_110


title: AML_patient_263


title: AML_patient_264


title: AML_patient_265


title: AML_patient_104


title: AML_patient_106


title: AML_patient_272


title: AML_patient_107


title: AML_patient_103


title: AML_patient_262


title: AML_patient_268


title: AML_patient_261


title: AML_patient_258


title: AML_patient_257


title: AML_patient_96


title: AML_patient_101


title: AML_patient_259


title: AML_patient_98


title: AML_patient_97


title: AML_patient_95


title: AML_patient_254


title: AML_patient_99


title: AML_patient_253


title: AML_patient_256


title: AML_patient_255


title: AML_patient_260


title: AML_patient_100


title: AML_patient_102


title: AML_patient_92


title: AML_patient_91


title: AML_patient_93


title: AML_patient_250


title: AML_patient_89


title: AML_patient_251


title: AML_patient_249


title: AML_patient_90


title: AML_patient_252


title: AML_patient_88


title: AML_patient_248


title: AML_patient_94


title: AML_patient_247


title: AML_patient_84


title: AML_patient_246


title: AML_patient_244


title: AML_patient_87


title: AML_patient_86


title: AML_patient_245


title: AML_patient_241


title: AML_patient_83


title: AML_patient_240


title: AML_patient_82


title: AML_patient_81


title: AML_patient_242


title: AML_patient_80


title: AML_patient_85


title: AML_patient_79


title: AML_patient_243


title: AML_patient_239


title: AML_patient_76


title: AML_patient_77


title: AML_patient_237


title: AML_patient_78


title: AML_patient_75


title: AML_patient_238


title: AML_patient_236


title: AML_patient_234


title: AML_patient_233


title: AML_patient_73


title: AML_patient_72


title: AML_patient_74


title: AML_patient_232


title: AML_patient_66


title: AML_patient_70


title: AML_patient_71


title: AML_patient_231


title: AML_patient_229


title: AML_patient_228


title: AML_patient_65


title: AML_patient_227


title: AML_patient_225


title: AML_patient_67


title: AML_patient_222


title: AML_patient_69


title: AML_patient_64


title: AML_patient_61


title: AML_patient_63


title: AML_patient_62


title: AML_patient_221


title: AML_patient_224


title: AML_patient_223


title: AML_patient_230


title: AML_patient_59


title: AML_patient_60


title: AML_patient_220


title: AML_patient_226


title: AML_patient_217


title: AML_patient_56


title: AML_patient_216


title: AML_patient_57


title: AML_patient_58


title: AML_patient_219


title: AML_patient_214


title: AML_patient_212


title: AML_patient_54


title: AML_patient_213


title: AML_patient_215


title: AML_patient_53


title: AML_patient_52


title: AML_patient_218


title: AML_patient_51


title: AML_patient_48


title: AML_patient_49


title: AML_patient_210


title: AML_patient_55


title: AML_patient_211


title: AML_patient_208


title: AML_patient_50


title: AML_patient_47


title: AML_patient_266


title: AML_patient_206


title: AML_patient_46


title: AML_patient_209


title: AML_patient_207


title: AML_patient_45


title: AML_patient_205


title: AML_patient_203


title: AML_patient_42


title: AML_patient_204


title: AML_patient_235


title: AML_patient_41


title: AML_patient_202


title: AML_patient_39


title: AML_patient_40


title: AML_patient_199


title: AML_patient_198


title: AML_patient_43


title: AML_patient_35


title: AML_patient_44


title: AML_patient_68


title: AML_patient_37


title: AML_patient_34


title: AML_patient_38


title: AML_patient_36


title: AML_patient_196


title: AML_patient_197


title: AML_patient_193


title: AML_patient_192


title: AML_patient_194


title: AML_patient_33


title: AML_patient_32


title: AML_patient_195


title: AML_patient_200


title: AML_patient_31


title: AML_patient_30


title: AML_patient_191


title: AML_patient_201


title: AML_patient_190


title: AML_patient_28


title: AML_patient_189


title: AML_patient_187


title: AML_patient_26


title: AML_patient_24


title: AML_patient_184


title: AML_patient_186


title: AML_patient_27


title: AML_patient_185


title: AML_patient_25


title: AML_patient_183


title: AML_patient_20


title: AML_patient_188


title: AML_patient_19


title: AML_patient_29


title: AML_patient_17


title: AML_patient_179


title: AML_patient_18


title: AML_patient_22


title: AML_patient_21


title: AML_patient_182


title: AML_patient_23


title: AML_patient_180


title: AML_patient_178


title: AML_patient_176


title: AML_patient_15


title: AML_patient_16


title: AML_patient_181


title: AML_patient_175


title: AML_patient_14


title: AML_patient_13


title: AML_patient_174


title: AML_patient_177


title: AML_patient_10


title: AML_patient_173


title: AML_patient_170


title: AML_patient_5


title: AML_patient_12


title: AML_patient_7


title: AML_patient_164


title: AML_patient_172


title: AML_patient_165


title: AML_patient_6


title: AML_patient_9


title: AML_patient_8


title: AML_patient_4


title: AML_patient_11


title: AML_patient_169


title: AML_patient_171


title: AML_patient_168


title: AML_patient_163


title: AML_patient_1


title: AML_patient_3


title: AML_patient_166


title: AML_patient_161


title: AML_patient_167


title: AML_patient_162


title: AML_patient_157


title: AML_patient_158


title: AML_patient_156


title: AML_patient_2


title: AML_patient_160


title: AML_patient_159


title: AML_patient_150


title: AML_patient_152


title: AML_patient_144


title: AML_patient_148


title: AML_patient_155


title: AML_patient_149


title: AML_patient_133


title: AML_patient_151


title: AML_patient_147


title: AML_patient_143


title: AML_patient_142


title: AML_patient_153


title: AML_patient_134


title: AML_patient_140


title: AML_patient_145


title: AML_patient_139


title: AML_patient_137


title: AML_patient_154


title: AML_patient_138


title: AML_patient_146


title: AML_patient_132


title: AML_patient_135


title: AML_patient_136


title: AML_patient_127


title: AML_patient_141


title: AML_patient_131


title: AML_patient_126


title: AML_patient_129


title: AML_patient_130


title: AML_patient_128


title: AML_patient_123


title: AML_patient_122


title: AML_patient_116


title: AML_patient_125


title: AML_patient_114


title: AML_patient_113


title: AML_patient_119


title: AML_patient_118


title: AML_patient_120


title: AML_patient_117


title: AML_patient_112


title: AML_patient_115


title: AML_patient_121


title: AML_patient_124


title: AML_patient_109


title: AML_patient_111


title: AML_patient_108


title: AML_patient_104


title: AML_patient_105


title: AML_patient_106


title: AML_patient_103


title: AML_patient_99


title: AML_patient_98


title: AML_patient_102


title: AML_patient_100


title: AML_patient_97


title: AML_patient_94


title: AML_patient_101


title: AML_patient_96


title: AML_patient_95


title: AML_patient_93


title: AML_patient_92


title: AML_patient_89


title: AML_patient_560


title: AML_patient_88


title: AML_patient_559


title: AML_patient_90


title: AML_patient_555


title: AML_patient_550


title: AML_patient_562


title: AML_patient_552


title: AML_patient_551


title: AML_patient_553


title: AML_patient_91


title: AML_patient_549


title: AML_patient_85


title: AML_patient_557


title: AML_patient_86


title: AML_patient_558


title: AML_patient_546


title: AML_patient_548


title: AML_patient_547


title: AML_patient_554


title: AML_patient_544


title: AML_patient_556


title: AML_patient_545


title: AML_patient_561


title: AML_patient_543


title: AML_patient_84


title: AML_patient_83


title: AML_patient_82


title: AML_patient_540


title: AML_patient_539


title: AML_patient_542


title: AML_patient_81


title: AML_patient_110


title: AML_patient_541


title: AML_patient_80


title: AML_patient_537


title: AML_patient_535


title: AML_patient_534


title: AML_patient_536


title: AML_patient_79


title: AML_patient_532


title: AML_patient_87


title: AML_patient_533


title: AML_patient_531


title: AML_patient_529


title: AML_patient_527


title: AML_patient_76


title: AML_patient_526


title: AML_patient_528


title: AML_patient_530


title: AML_patient_538


title: AML_patient_75


title: AML_patient_525


title: AML_patient_78


title: AML_patient_73


title: AML_patient_74


title: AML_patient_522


title: AML_patient_524


title: AML_patient_519


title: AML_patient_72


title: AML_patient_71


title: AML_patient_521


title: AML_patient_520


title: AML_patient_516


title: AML_patient_70


title: AML_patient_523


title: AML_patient_69


title: AML_patient_518


title: AML_patient_513


title: AML_patient_514


title: AML_patient_515


title: AML_patient_509


title: AML_patient_512


title: AML_patient_67


title: AML_patient_68


title: AML_patient_508


title: AML_patient_510


title: AML_patient_511


title: AML_patient_77


title: AML_patient_66


title: AML_patient_507


title: AML_patient_517


title: AML_patient_506


title: AML_patient_505


title: AML_patient_65


title: AML_patient_64


title: AML_patient_504


title: AML_patient_503


title: AML_patient_63


title: AML_patient_62


title: AML_patient_501


title: AML_patient_502


title: AML_patient_499


title: AML_patient_498


title: AML_patient_61


title: AML_patient_500


title: AML_patient_497


title: AML_patient_495


title: AML_patient_60


title: AML_patient_496


title: AML_patient_494


title: AML_patient_493


title: AML_patient_59


title: AML_patient_107


title: AML_patient_492


title: AML_patient_490


title: AML_patient_491


title: AML_patient_58


title: AML_patient_56


title: AML_patient_55


title: AML_patient_487


title: AML_patient_489


title: AML_patient_54


title: AML_patient_57


title: AML_patient_53


title: AML_patient_52


title: AML_patient_51


title: AML_patient_485


title: AML_patient_484


title: AML_patient_50


title: AML_patient_480


title: AML_patient_482


title: AML_patient_486


title: AML_patient_481


title: AML_patient_488


title: AML_patient_477


title: AML_patient_478


title: AML_patient_49


title: AML_patient_475


title: AML_patient_476


title: AML_patient_474


title: AML_patient_48


title: AML_patient_483


title: AML_patient_471


title: AML_patient_472


title: AML_patient_473


title: AML_patient_47


title: AML_patient_479


title: AML_patient_469


title: AML_patient_468


title: AML_patient_470


title: AML_patient_464


title: AML_patient_44


title: AML_patient_43


title: AML_patient_42


title: AML_patient_466


title: AML_patient_465


title: AML_patient_467


title: AML_patient_463


title: AML_patient_461


title: AML_patient_46


title: AML_patient_457


title: AML_patient_458


title: AML_patient_462


title: AML_patient_45


title: AML_patient_38


title: AML_patient_40


title: AML_patient_453


title: AML_patient_451


title: AML_patient_454


title: AML_patient_456


title: AML_patient_39


title: AML_patient_460


title: AML_patient_452


title: AML_patient_37


title: AML_patient_450


title: AML_patient_448


title: AML_patient_455


title: AML_patient_41


title: AML_patient_35


title: AML_patient_447


title: AML_patient_443


title: AML_patient_33


title: AML_patient_444


title: AML_patient_440


title: AML_patient_446


title: AML_patient_441


title: AML_patient_445


title: AML_patient_36


title: AML_patient_31


title: AML_patient_34


title: AML_patient_32


title: AML_patient_29


title: AML_patient_437


title: AML_patient_28


title: AML_patient_30


title: AML_patient_436


title: AML_patient_433


title: AML_patient_435


title: AML_patient_442


title: AML_patient_434


title: AML_patient_431


title: AML_patient_429


title: AML_patient_439


title: AML_patient_27


title: AML_patient_430


title: AML_patient_438


title: AML_patient_426


title: AML_patient_25


title: AML_patient_428


title: AML_patient_427


title: AML_patient_425


title: AML_patient_424


title: AML_patient_22


title: AML_patient_23


title: AML_patient_24


title: AML_patient_21


title: AML_patient_16


title: AML_patient_20


title: AML_patient_15


title: AML_patient_449


title: AML_patient_17


title: AML_patient_19


title: AML_patient_13


title: AML_patient_14


title: AML_patient_11


title: AML_patient_12


title: AML_patient_432


title: AML_patient_26


title: AML_patient_7


title: AML_patient_10


title: AML_patient_9


title: AML_patient_8


title: AML_patient_5


title: WT-ChIP-4

status: Public on Feb 01 2013

first: Yu

last: Zhang

state: California

address: 800 Buchanan Street

institute: UC Berkeley

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

value: WT

value: anti-Myc (Abcam, ab9132)


title: WT-ChIP-2


title: AML_patient_6

tag: tissue


title: AML_patient_2


title: AML_patient_18


title: WT-ChIP-3

tag: chip antibody


title: AML_patient_4


title: AML_patient_1


title: WT-ChIP-1


title: P3M-ChIP-2


title: P3M-ChIP-1


title: P3M-ChIP-4


title: negative control (AP1-GR ap1 cal)

status: Public on Jun 01 2012

city: Zurich

first: Samuel

middle: Elias

last: Wuest

address: Winterthurerstrasse 190

department: Institute of Evolutionary Biology and Environmental Studies

country: Switzerland

institute: University of Zurich

description: generated on an Illumina GAIIx machine running data collection SCS2.9/RTA1.9 software

data_processing:
For each dataset, two independent alignment- and peak calling methods were performed. The main method was using the SOAPv2 short read alignment program and subsequent peak calling using the CSAR package as implemented in the Bioconductor project. These peak definitions were retained, but only if confirmed by an overlapping peak range as determined by the independent method as described below.
Main method: Arabidopsis genomic sequences were downloaded from TAIR (www.arabidopsis.org; files ‘TAIR10_chr1.fas’ - ‘TAIR10_chr5.fas’). Short read alignments were performed using the SOAP2 software with default settings. Data were read into R using the CSAR package. and functionality provided by various Bioconductor packages (including the IRanges v1.12.5 and GenomicRanges v1.6.4 packages) was used for data handling operations.
Peak calling was performed using the CSAR package that included a normalization and a test based on the Poisson distribution, and enriched regions were identified at a False Discovery Rate (FDR)<0.001 (with five rounds of permutations for each dataset, resulting in >600,000 permutations). Default parameters were used. Only peak regions with stretches of >50 bp were retained.
In order to validate peak regions detected by the CSAR software, the peak calling was repeated using independent short-read aligner and peak calling tools as follows: short-reads were aligned to the reference genome using BWA version 0.6.1, aligned reads were sorted and duplicated reads removed using samtools. and peak calling was performed using MACS Version 1.4.1 with default parameters. Peaks as determined by the CSAR software were then retained only if they had any overlap with peaks determined by the MACS software. In order to merge biological replicates from the PI-GFP ChIP-Seq experiments, peak definitions determined for PI-GFP replicate 2 were retained only if they showed any overlap with the PI-GFP replicate 1.
Peaks were associated with genes located in the vicinity using CSAR functionality, whereby a peak had to reside in a genomic region ranging from 3 kb upstream of a gene’s transcriptional start position to 1 kb downstream of its transcriptional end position. Gene range definitions were downloaded from TAIR (file TAIR10_GFF3_genes.gff).
Genome_build: TAIR10 Arabidopsis thaliana
Supplementary_files_format_and_content: csv formatted files, 1) file containing peak definitions (chromosome, peak start, peak end, peak position and maximal Poisson-based enrichment score) and putative direct target genes and 2) lists of putative direct target genes according to TAIR v10 genome build. The position of significantly enriched region(s) with respect to the corresponding gene is indicated by dividing the gene region into different segments (as indicated) and the maximum peak scores within these segments are shown. A value of 0 indicates that no significantly enriched peak region was detected within a given segment.

source_name: negative control (AP1-GR ap1 cal)

growth_protocol: Plants were grown on a soil:vermiculite:perlite (3:1:1) mixture at 20 degrees (16 degrees for plants used for temperature-sensitive perturbation experiments) under constant illumination with cool white fluorescent light

extract_protocol: ChIP was performed using a modified version of previously described protocols (Gomez-Mena C, de Folter S, Costa MM, Angenent GC, & Sablowski R (2005); Development 132(3):429-438 + Kaufmann K, et al. (2010), Nat Protoc 5(3):457-472.) Library preparation was performed as described in the instructions of the Illumina ChIP-Seq DNA Sample Prep Kit (IP-102-1001), whereby the adapter-oligo dilution used was 1:30 in water, the gel for DNA purification was run at low voltage (20V for > 6hrs) and gel-extraction step performed twice.

treatment_protocol: For all experiments,  ~4 week-old plants were used. For the experiments using the FIS (35S:AP1-GR ap1-1 cal-1 plants), flower development was induced using a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol and 0.015% (v/v) Silwet L-77 (De Sangosse) – as described in  Wellmer F, et al. (2006) Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development. PLoS Genetics 2(7):e117.

value: AP1-GR ap1 cal

value: flower

tag: developmental stage

value: 4 days after Dexamethasone treatment (early-intermediate floral stage ~ stage 4-5 flowers)

value: Anti-GFP

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #

value: Ler


title: AP3-GFP (AP1-GR ap1 cal) ChIPseq

source_name: AP3-GFP (AP1-GR ap1 cal) ChIPseq

value: AP3-GFP AP1-GR ap1 cal


title: PI-GFP (AP1-GR ap1 cal) ChIPseq

source_name: PI-GFP (AP1-GR ap1 cal) ChIPseq replicate 1

value: PI-GFP AP1-GR ap1 cal


title: PRR5-ChIP

status: Public on Sep 20 2012

city: Yokohama

first: Norihito

last: Nakamichi

address: Suehiro1-7-22, Tsurumi

department: Plant Science Center

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: anti-GFP


title: PIF5ox shade ChIPSeq

status: Public on May 03 2012

city: Lausanne

first: Markus

middle: Volker

last: Kohnen

state: Vaud

address: Genopode Building

department: Center for Integrative Genomics (CIG)

institute: Université de Lausanne

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:
PM1_m1.bam: TAIR8
PM1_m1_btb_chrom.bed: TAIR8

source_name: whole seedling

growth_protocol: Seeds were plated on half MS and kept in the dark for 3 days at 4°C. Seedlings were then transferred to white light with high R/FR ratio in 12:12 LD circles for 14 days.

extract_protocol: Seedlings were ground in cold mortar with protein extraction buffer (50 mM TrisHCl (pH 7.5); 100 mM NaCl; 10% glycerol; 0.1% NP-40; 1 mM DTT; 1 × protease inhibitors (Sigma); 50 μM MG132). Soluble proteins were incubated with 40 μl of EZview red anti FlagM2 affinity gel (Sigma) beads for 1 h and 30 min at 4°C. After four washes in the protein extraction buffer, specifically bound proteins were eluted with Laemmli buffer. HRP-conjugated anti-HA antibodies (Roche) were used to detect proteins.

treatment_protocol: After 2h high R/FR treatment in the morning, seedlings were transferred to low R/FR (supplemental FR) for additional 2h before protein extraction.

value: PIF5-HA overexpressor Flag tagged

value: 14 days

value: seedling

tag: treatment

value: low R/FR

tag: chip antibody manufactuer

value: Sigma