title: Cflo.Minor.H3K9ac

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_minor_H3K9ac.Q.matrix.txt: C. floridanus v3.0


title: Cflo.Major.H3K9ac

status: Public on Nov 26 2012

type: SRA

city: Philadelphia

first: Daniel

middle: Francis

last: Simola

state: PA

address: 1041 BRB II/III

department: Cell and Developmental Biology

country: USA

institute: University of Pennsylvania

description: DNA fragments sequenced following chromatin immunoprecipitation

library_source: genomic

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_major_H3K9ac.Q.matrix.txt: C. floridanus v3.0

molecule: genomic DNA

organism: Camponotus floridanus

source_name: Head and thorax from adult ants

growth_protocol: Ants were grown and maintained as a single colony in the laboratory of Juergen Liebig (ASU) at constant temperature and fed regularly using meal worms

extract_protocol: Total RNA was isolated from ants using QIAzol lysis reagent (Qiagen). PolyA mRNA was purified from total RNA samples using PolyT beads (Invitrogen mRNA Direct Kit). Sequencing libraries were constructed using the NEBNext mRNA Library Prep Kit (New England Biolabs) according to manufacturer’s instruction.     For ChIP-seq, head and thorax sections, or dissected whole-brains, of C. floridanus major, minor, and male ants were collected and homogenized first on dry ice, then on ice in crosslinking buffer (60mM KCl, 15mM NaCl, 4mM MgCl2, 0.1% Triton X-100, 50mM HEPES, pH 7.5 with protease inhibitor) with 1.8% formaldehyde for 10 min. For CBP ChIP, additional long chain crosslinking was carried out first with 500mM EGS (Ethylene Glycol-bis Succinimidylsuccinate, fresh made in DMSO) for 10 min, followed by 1.8% formaldehyde crosslinking for 10 min87. Crosslinking was terminated by adding 2.5M glycine to a final concentration of 125mM for 5 min. Cuticles were discarded and homogenate was transferred to a new tube and centrifuged for 3 min, 4000g at 4°C. Pellet was washed once with lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5% Triton X-100, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine with protease inhibitors) and centrifuged again. The resulting pellet was resuspended in lysis buffer and sonicated using a Bioruptor (Diagenode) for 10 min with 30 sec on and 30sec off cycles. Samples were centrifuged for 10min, 20,000g at 4oC and supernatant collected as starting material for ChIP.    A 30ul protein A and protein G bead mixture (Invitrogen) was used to ChIP each sample. Beads were washed 3 times with blocking buffer (0.25% BSA in PBS), then incubated with 5µg antibodies in 500ul blocking buffer for 4h to allow antibody binding. Following binding, beads were washed 3 times with blocking buffer. 500µg chromatin was added to beads for each ChIP and incubated overnight at 4°C. Beads were washed sequentially with following buffers: twice with lysis buffer, once with FA-500mM buffer (50mM HEPES-KOH, pH7.5, 500mM NaCl, 1mM EDTA, 0.1% TritonX-100), twice with LiCl buffer (10mM Tris-HCl pH8.0, 0.25M LiCl, 1mM EDTA, 0.5% NP40), and once with TE pH 8.0. Beads were then eluted three times with 100µl TES buffer each (50mM Tris-HCl, pH8.0, 10mM EDTA, 1% SDS) at 65°C for 15 min. 12µl 5M NaCl was added to the pooled elute, which was then incubate at 65°C overnight to reverse the crosslinking. Samples were then treated with 5µl 20mg/ml protease K at 37°C for 1h and purified for DNA. ChIP samples (purified DNA) were used for qPCR application or high throughput sequencing. Sequencing libraries were constructed according to manufacturer’s instruction (Illumina).

treatment_protocol: Contrast of naturally occurring major, minor, and male ant castes (adults)

tag: colony

value: Colony C4 from Florida Keys, FL, USA

tag: dev. stage

value: Adult

tag: caste

value: Major

tag: modification

tag: antibody vendor

value: Abcam

tag: antibody catalog #


title: Cflo.Male.H3K9me3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_male_H3K9me3.Q.matrix.txt: C. floridanus v3.0

value: Male


title: Cflo.Minor.H3K9me3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_minor_H3K9me3.Q.matrix.txt: C. floridanus v3.0

value: Minor


title: tj-GAL4>RNAi tej rep2

city: Vienna

first: Grzegorz

last: Sienski

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

data_processing:
small RNA-seq libraries: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); fastq files were adapter 'AGATCGGAAGAGCACACGTCT' clipped using cutadapt, version 1.0, default settings; after adapter removal, the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini) from sequence as well using HomerTools, version 3.9.
small RNA-seq libraries: reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3) and BigWig files were created with Samtools v 0.1.16 and BedTools v2.16.1

GRO-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); fastq file was adapter' ATCGTATGCCGTCTTCTGCTTGT' clipped using cutadapt, version 1.0, default settings; after adapter removal, the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini) from sequence as well using HomerTools, version 3.9.
GRO-seq: reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3) and BigWig files were created with Samtools v 0.1.16 and BedTools v2.16.1

RNA-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); fastq files containing 2nd mate were reverse complemented and used together with fastq files containing 1st mate as single-end library; N-containing reads were discarded; reads were trimmed to high-quality bases 6-56 using HomerTools, version 3.9 and mapped to genome and transcriptome using in-house developed pipeline.

ChIP-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); reads were trimmed to bases 2-50 using HomerTools, version 3.9;  N-containing reads were discarded; smaller than 50nt-long reads were discarded.
ChIP-seq: reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3) and BigWig files were created with Samtools v 0.1.16 and BedTools v2.16.1

DNA-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); N-containing reads were discarded; smaller than 100nt-long reads were discarded; TEs insertions were called using in-house developed pipeline.
Supplementary_files_format_and_content: DNA-seq: file contains coordinates of TEs insertions called in OSC
Supplementary_files_format_and_content: RNA-seq, GRO-seq, ChIP-seq: file contains density coverage of uniquely mapped reads to dm3
Genome_build: dmel_release 5

organism: Drosophila melanogaster

source_name: tj-GAL4>RNAi tej

growth_protocol: flies were grown at 25 degrees; OSC were grown at 27 degrees on M3 medium

extract_protocol:
GRO-seq was done according to Core et al. 2008; ChIP-seq as described in Lee et al. 2006; RNA-seq as in Zhong et al. 2011
small-RNAs were cloned as described in Brennecke et al. 2007

treatment_protocol: OSC were transfected twice with siRNAs and analyzed after 4 days

tag: genotype/variation

value: tj-Gal4>RNAi tej

tag: Stage

value: from 5-6 days old flies

tag: tissue/cell type

value: ovaries

tag: molecule subtype

value: Rpb3-bound DNA

tag: chip antibody

tag: chip antibody information

value: gift of Karen Adelman; Adelman et al. Mol Cell 2005


title: small RNAs (18-29nt) from permissive

library_source: transcriptomic

molecule: total RNA

source_name: small RNAs_permissive

value: flamOR(P)

value: total RNA


title: tj-GAL4>RNAi armi rep2

source_name: tj-GAL4>RNAi armi

value: tj-Gal4>RNAi armi


title: tj-GAL4>RNAi tej rep1


title: Cflo.Major.H3K9me3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_major_H3K9me3.Q.matrix.txt: C. floridanus v3.0


title: Cflo.Male.H3K36me3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_male_H3K36me3.Q.matrix.txt: C. floridanus v3.0


title: Cflo.Minor.H3K36me3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_minor_H3K36me3.Q.matrix.txt: C. floridanus v3.0


title: DMSOtreated_p65_ChIPSeq

city: Singapore

first: Gaye

last: Saginc

address: 60 Biopolis Street

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

description: p65 ChIP-seq, with vehicle

data_processing:
35 bp long reads  were uniquely mapped to the Human Genome 19 (UCSC), using SOLID Bioscope 1.3.1 ChIP-Seq Module. For alignments, seed and extension approach was used. 30 bp seeds which aligned to the reference genome with at most 3 color mismatches were kept and extended up to 35 bp. Only reads with unique full length alignment (35 bp) allowing for 2 mismatches were used in the analysis.
Redundant reads (multiple reads aligning exactly to the same location) which are generally PCR-artefacts were filtered. Control-based ChIP-seq Analysis Tool version 3 (CCAT3) was performed for peak calling under default settings using reads which were mapped to unique regions in the genome.
Peaks with FDR superior than 0.2 are excluded from the analysis. For the downstream analysis, normalized fold enrichments reported by CCAT3 were used.
Genome_build: hg19 with random chr

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: HeLa cells were grown to 70-80% confluence in Dulbecco’s modified eagle medium (DMEM) which was supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, 2 mM sodium pyruvate and 1 × PSF (penicillin, streptomycin and fungizone) at 37 °C with 5% CO2.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10min at room temperature, followed by 125mM glycine treatment to inactivate the crosslinking. Chromatin extracts were sonicated to 200- 500bp fragments, followed by overnight immunoprecipitation at 4˚C.Then, protein-DNA complexes were de-crosslinked with overnight incubation at 65°C and DNA extraction was performed using Qiagen PCR purification kit.
After the quality of the ChIP DNA was controlled by checking the concentration and the enrichment of known targets in ChIP DNA over input with Quant-iT PicoGreen assay (Invitrogen) and real time PCR respectively, libraries were constructed using SOLID ChIP-Seq Kit (Applied Biosystems) following manufacturer's protocol. For each sample, 10 ng of ChIP DNA was purified using AMPure XP Kit (Agencourt), end-repaired and ligated to SOLID adaptors. After ligation, samples were nick-translated and amplified using primers specific to adaptors for 15 cycles. Samples were purified multiple times between each steps. Following the final purification step, size distribution and quantity of libraries were checked by performing DNA 1000 assay (Agilent). Samples with expected size distribution (165-365 bp) and quantity (min 2ng/ul in 10 ul) were sequenced using SOLID4 sequencer following manufacturer's instructions for fragment sequencing. Each sample was loaded to a quarter SOLID slide.

treatment_protocol: HeLa cells were separated into 3 groups: "control", "TNFα-treated" and "TNFα & MST-312-treated" group. Cells in the "TNFα & MST-312" group were treated with 1 uM of MST-312 (Sigma) for 48 hours prior to the ChIP procedure. Then cells except the control group were treated with TNFα (Calbiochem)to a final concentration of 10 ng/ul for 45mins before the ChIP procedure.  The control cells were treated with an equal volume of DMSO (vehicle), for 45mins. For a ChIP experiment, approximately 2 x 10^8 cells from 5 of 150 mm diameter cell culture plates were used.

tag: treatment

value: DMSOtreated

tag: cell type

value: Cervical cancer cell line

value: p65 (Santa Cruz, C-20, Cat no. SC372)


title: Cflo.Major.H3K36me3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_major_H3K36me3.Q.matrix.txt: C. floridanus v3.0

value: Colony C4 from Florida Keys, FL, USA


title: Rpb3 ChIP-seq from Piwi-KD rep2

description: processed data file: Rpb3_siPiwi.bw

source_name: Rpb3 ChIP-seq_Piwi-KD

value: RNAi piwi

value: 96h after transfection

value: Ovarian Somatic Cells (OSC)


title: Cflo.Major.Brain.RNA.R2

description: DNA fragments sequenced following RNA isolation and polyA+ purification

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
CX.Major.brain.RNA.rep2.cufflinks.transcripts.gtf: C. floridanus v3.0

molecule: polyA RNA

source_name: Whole-brain dissection from adult ants

value: Colony from Florida Keys, FL, USA

value: Adult

value: Major

value: RNA (polyA+)


title: Rpb3 ChIP-seq from Mael-KD rep2

description: processed data file: Rpb3_siMael.bw

source_name: Rpb3 ChIP-seq_Mael-KD

value: RNAi mael


title: Cflo.Male.H3K27ac

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_male_H3K27ac.Q.matrix.txt: C. floridanus v3.0

value: Male

value: Abcam


title: Cflo.Minor.H3K27ac

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_minor_H3K27ac.Q.matrix.txt: C. floridanus v3.0

value: Minor


title: Rpb3 ChIP-seq from Piwi-KD rep1

description: processed data file: Rpb3_siPiwi.bw

value: Rpb3-bound DNA

value: gift of Karen Adelman; Adelman et al. Mol Cell 2005


title: Cflo.Major.H3K27ac

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_major_H3K27ac.Q.matrix.txt: C. floridanus v3.0


title: Rpb3 ChIP-seq from Mael-KD rep1

description: processed data file: Rpb3_siMael.bw


title: Cflo.Major.H3K27ac.rep

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4r2_major_H3K27ac.Q.matrix.txt: C. floridanus v3.0


title: Cflo.Male.H3K27me3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_male_H3K27me3.Q.matrix.txt: C. floridanus v3.0

value: Millipore


title: Rpb3 ChIP-seq from GFP-KD rep2

description: processed data file: Rpb3_siGFP.bw

source_name: Rpb3 ChIP-seq_GFP-KD

value: RNAi gfp


title: ZR751_input_r1

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

description:
Input DNA
JC21

data_processing:
Base calling: sequence reads were generated by the Illumina analysis pipeline version 1.3.4 and 1.4.0
Alignments: prior to peak calling, reads were aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.3, March 2008) using BWA version 0.5.5 (Li and Durbin, 2010). They were filtered by alignment quality score, removing all reads with a BWA score less than 15.
Peak calling: Enriched regions of the genome were identified by comparing the ChIP samples to input samples using MACS version 1.3.7.1
Genome_build: hg18
Supplementary_files_format_and_content: MACS peaks in .bed file format

growth_protocol: MCF7 cells were cultured in DMEM and ZR-75-1 cells in RPMI media (Invitrogen) at 10% FCS. For hormonal deprivation, cells were cultured for 3 days in phenol-redfree DMEM or RPMI respectively, supplemented with 5% charcoal-treated serum. E2 (Sigma) was added at a final concentration of 100nM for 3 hours.

extract_protocol: MCF7 cells were transfected with siRNA and cultured in hormone deprived conditions for a further 3 days. For every library, the starting material was four 15cm culture dishes. ChIP-Seq of histone marks were performed from three 15cm plates. For the libraries in siGATA3 conditions, a pool of the siRNAs was used at a 50nM final concentration.

treatment_protocol: Three different siRNAs were used against GATA3: ON-TARGET plus siRNA J-0033781-09 and two additional custom made targeting the 3'UTR of the RefSeq NM_002051. The sense sequences of the custom made ones are siGATA3-Custom-1: AAACUAGGUCUGAUAUUCAUU and siGATA3-Custom-2: CUUUAUUGCAUCUGGGUAGUU.  AllStars Negative Control siRNA (Cat nr:1027281, Qiagen) was used as a negative control. All siRNA experiments were at a final concentration of 50nM. Transfections were conducted using Lipofectamine 2000 (Invitrogen). A pool of three siRNAs against GATA3 was used to achieve better knockdown and eliminate potential non-specific effects by using a single siRNA.

tag: cell line

value: breast cancer cells

tag: stimulated with

value: Full Media


title: DNA input from Piwi-KD rep2

source_name: DNA input_Piwi-KD

value: RNAi piwi

value: total DNA


title: MCF-7_input_r3

description:
Input DNA
JC379


title: Rpb3 ChIP-seq from GFP-KD rep1

description: processed data file: Rpb3_siGFP.bw

value: 96h after transfection

value: Ovarian Somatic Cells (OSC)


title: Cflo.Minor.H3K27me3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_minor_H3K27me3.Q.matrix.txt: C. floridanus v3.0

value: Colony C4 from Florida Keys, FL, USA

value: Adult


title: DNA input from Mael-KD rep2

source_name: DNA input_Mael-KD


title: Cflo.Male.H3K4me1

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_male_H3K4me1.Q.matrix.txt: C. floridanus v3.0


title: ZR751_siGATA_ER_E2_r1

description:
Chromatin IP against ER
JC590

value: E2 at final conc. 100nM for 3 hrs

value: GATA knockdown

tag: tranfected with

value: ON-TARGET plus siRNA J-0033781-09, siGATA3-Custom-1, siGATA3-Custom-2

value: anti-ERa

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: ZR751_siNT_ER_E2_r1

description:
Chromatin IP against ER
JC589

value: negative control

value: AllStars Negative Control siRNA (Cat nr:1027281, Qiagen)


title: Cflo.Major.H3K27me3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_major_H3K27me3.Q.matrix.txt: C. floridanus v3.0

tag: colony

tag: dev. stage

tag: caste

value: Major

value: Millipore


title: siGATA_p300_Veh_r2

description:
Chromatin IP against p300
JC477

value: breast cancer cells

value: Vehicle


title: Cflo.Major.H3K4me1

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_major_H3K4me1.Q.matrix.txt: C. floridanus v3.0

tag: modification

tag: antibody vendor

value: Abcam

tag: antibody catalog #


title: Cflo.Minor.H3K4me1

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_minor_H3K4me1.Q.matrix.txt: C. floridanus v3.0

value: Minor


title: tj-GAL4>RNAi armi rep1

data_processing:
small RNA-seq libraries: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); fastq files were adapter 'AGATCGGAAGAGCACACGTCT' clipped using cutadapt, version 1.0, default settings; after adapter removal, the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini) from sequence as well using HomerTools, version 3.9.
small RNA-seq libraries: reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3) and BigWig files were created with Samtools v 0.1.16 and BedTools v2.16.1

GRO-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); fastq file was adapter' ATCGTATGCCGTCTTCTGCTTGT' clipped using cutadapt, version 1.0, default settings; after adapter removal, the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini) from sequence as well using HomerTools, version 3.9.
GRO-seq: reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3) and BigWig files were created with Samtools v 0.1.16 and BedTools v2.16.1

RNA-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); fastq files containing 2nd mate were reverse complemented and used together with fastq files containing 1st mate as single-end library; N-containing reads were discarded; reads were trimmed to high-quality bases 6-56 using HomerTools, version 3.9 and mapped to genome and transcriptome using in-house developed pipeline.

ChIP-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); reads were trimmed to bases 2-50 using HomerTools, version 3.9;  N-containing reads were discarded; smaller than 50nt-long reads were discarded.
ChIP-seq: reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3) and BigWig files were created with Samtools v 0.1.16 and BedTools v2.16.1

DNA-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); N-containing reads were discarded; smaller than 100nt-long reads were discarded; TEs insertions were called using in-house developed pipeline.
Supplementary_files_format_and_content: DNA-seq: file contains coordinates of TEs insertions called in OSC
Supplementary_files_format_and_content: RNA-seq, GRO-seq, ChIP-seq: file contains density coverage of uniquely mapped reads to dm3
Genome_build: dmel_release 5

tag: genotype/variation

value: tj-Gal4>RNAi armi

tag: Stage

value: from 5-6 days old flies

tag: tissue/cell type

value: ovaries

value: Rpb3-bound DNA

value: gift of Karen Adelman; Adelman et al. Mol Cell 2005


title: DNA input from Piwi-KD rep1

value: RNAi piwi

value: 96h after transfection

value: Ovarian Somatic Cells (OSC)

tag: molecule subtype

value: total DNA


title: DNA input from GFP-KD rep2

source_name: DNA input_GFP-KD

value: RNAi gfp


title: DNA input from Mael-KD rep1

value: RNAi mael


title: Cflo.Male.H3K4me3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_male_H3K4me3.Q.matrix.txt: C. floridanus v3.0

value: Colony C4 from Florida Keys, FL, USA

value: Adult

value: Male

value: Active Motif


title: siGATA_p300_E2_r2

description:
Chromatin IP against p300
JC478

value: breast cancer cells

value: E2 at final conc. 100nM for 3 hrs

value: GATA knockdown

value: ON-TARGET plus siRNA J-0033781-09, siGATA3-Custom-1, siGATA3-Custom-2

tag: chip antibody

value: Santa Cruz


title: siNT_p300_E2_r2

description:
Chromatin IP against p300
JC476

tag: cell type

value: negative control

value: AllStars Negative Control siRNA (Cat nr:1027281, Qiagen)


title: DNA input from GFP-KD rep1


title: Cflo.Major.H3K4me3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_major_H3K4me3.Q.matrix.txt: C. floridanus v3.0

value: Major


title: siNT_p300_Veh_r2

description:
Chromatin IP against p300
JC475

tag: cell line

value: Vehicle


title: Cflo.Minor.H3K4me3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_minor_H3K4me3.Q.matrix.txt: C. floridanus v3.0

value: Minor


title: H3K9m3 ChIP-seq from Piwi-KD rep2

description: processed data file: H3K9m3_siPiwi.bw

source_name: H3K9m3 ChIP-seq_Piwi-KD

value: RNAi piwi

value: 96h after transfection

value: Ovarian Somatic Cells (OSC)

value: H3K9m3-bound DNA

value: abcam

tag: chip antibody lot/batch #


title: siGATA_H3K4me1_Veh_r1

description:
Chromatin IP against H3K4me1
JC619

tag: stimulated with

tag: tranfected with

value: Abcam


title: siGATA_H3K4me1_E2_r1

description:
Chromatin IP against H3K4me1
JC620

tag: chip antibody vendor

tag: chip antibody cat. #


title: H3K9m3 ChIP-seq from GFP-KD rep2

description: processed data file: H3K9m3_siGFP.bw

source_name: H3K9m3 ChIP-seq_GFP-KD

value: RNAi gfp


title: Cflo.Minor.H3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_minor_H3.Q.matrix.txt: C. floridanus v3.0

tag: colony

value: Colony C4 from Florida Keys, FL, USA

tag: dev. stage

value: Adult


title: Cflo.Major.H3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_major_H3.Q.matrix.txt: C. floridanus v3.0

tag: caste

tag: modification


title: siNT_H3K4me1_Veh_r1

description:
Chromatin IP against H3K4me1
JC617

value: breast cancer cells


title: siNT_H3K4me1_E2_r1

description:
Chromatin IP against H3K4me1
JC618

value: E2 at final conc. 100nM for 3 hrs


title: Cflo.Male.H3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_male_H3.Q.matrix.txt: C. floridanus v3.0

value: Male

tag: antibody vendor

tag: antibody catalog #


title: siGATA_H3K27ac_Veh_r1

description:
Chromatin IP against H3K27ac
JC623

tag: genotype/variation

value: GATA knockdown

value: ON-TARGET plus siRNA J-0033781-09, siGATA3-Custom-1, siGATA3-Custom-2


title: H3K9m3 ChIP-seq from GFP-KD rep1

description: processed data file: H3K9m3_siGFP.bw

tag: Stage

tag: tissue/cell type


title: H3K9m3 ChIP-seq from Piwi-KD rep1

description: processed data file: H3K9m3_siPiwi.bw

tag: molecule subtype

tag: chip antibody


title: H3K9m3 ChIP-seq from Mael-KD rep1

description: processed data file: H3K9m3_siMael.bw

source_name: H3K9m3 ChIP-seq_Mael-KD

value: RNAi mael


title: ribosomal RNA-depleted total RNA from Mael-KD

source_name: ribosomal RNA-depleted total RNA_Mael-KD

value: total RNA


title: siGATA_H3K27ac_E2_r1

description:
Chromatin IP against H3K27ac
JC624

tag: cell line

tag: cell type


title: GATA3_Veh_r5

description:
Chromatin IP against GATA3
JC632

tag: stimulated with

value: Vehicle

value: Santa Cruz


title: siNT_H3K27ac_Veh_r1

description:
Chromatin IP against H3K27ac
JC621

value: negative control

tag: tranfected with

value: AllStars Negative Control siRNA (Cat nr:1027281, Qiagen)


title: siNT_H3K27ac_E2_r1

description:
Chromatin IP against H3K27ac
JC622

tag: chip antibody vendor


title: Cflo.Major.Brain.RNA.R1

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4C31.Major.brain.RNA.rep1.cufflinks.transcripts.gtf: C. floridanus v3.0

value: Colonies C4+C31 from Florida Keys, FL, USA

value: Major

value: RNA (polyA+)


title: ribosomal RNA-depleted total RNA from Piwi-KD

source_name: ribosomal RNA-depleted total RNA_Piwi-KD

value: RNAi piwi

value: 96h after transfection

value: Ovarian Somatic Cells (OSC)


title: GATA3_E2_r5

description:
Chromatin IP against GATA3
JC633

value: breast cancer cells

tag: chip antibody cat. #


title: ribosomal RNA-depleted total RNA from Armi-KD

source_name: ribosomal RNA-depleted total RNA_Armi-KD

value: RNAi armi


title: ribosomal RNA-depleted total RNA from GFP-KD

source_name: ribosomal RNA-depleted total RNA_GFP-KD

value: RNAi gfp


title: total nascent RNA from Piwi-KD ovarian somatic cells

source_name: total nascent RNA_Piwi-KD OSCs

value: total nascent RNA


title: Cflo.Minor.Brain.RNA.R1

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4C31.Minor.brain.RNA.rep1.cufflinks.transcripts.gtf: C. floridanus v3.0

tag: colony

value: Adult

value: Minor


title: GATA3_E2_r4

description:
Chromatin IP against GATA3
JC556

value: E2 at final conc. 100nM for 3 hrs


title: total nascent RNA from wild-type ovarian somatic cells

source_name: total nascent RNA_wild-type OSCs

value: wild-type


title: Cflo.Minor.RNA

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
CX.Minor.HT.RNA.cufflinks.transcripts.gtf: C. floridanus v3.0

source_name: Head and thorax from adult ants

value: Colony from Florida Keys, FL, USA

tag: dev. stage


title: H3K9m3 ChIP-seq from Mael-KD rep2

description: processed data file: H3K9m3_siMael.bw

value: RNAi mael

value: H3K9m3-bound DNA

value: abcam

tag: chip antibody lot/batch #


title: GATA3_Veh_r3

description:
Chromatin IP against GATA3
JC484

value: Vehicle

value: Santa Cruz


title: Cflo.Major.RNA

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
CX.Major.HT.RNA.cufflinks.transcripts.gtf: C. floridanus v3.0

tag: caste

value: Major

tag: modification

value: RNA (polyA+)


title: DNA-seq from OSC

value: Ovarian Somatic Cells (OSC)

value: DNA


title: GATA3_E2_r3

description:
Chromatin IP against GATA3
JC485

data_processing:
Base calling: sequence reads were generated by the Illumina analysis pipeline version 1.3.4 and 1.4.0
Alignments: prior to peak calling, reads were aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.3, March 2008) using BWA version 0.5.5 (Li and Durbin, 2010). They were filtered by alignment quality score, removing all reads with a BWA score less than 15.
Peak calling: Enriched regions of the genome were identified by comparing the ChIP samples to input samples using MACS version 1.3.7.1
Genome_build: hg18
Supplementary_files_format_and_content: MACS peaks in .bed file format

value: breast cancer cells


title: Cflo.Minor.Brain.H3K27ac

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4C31_minor_H3K27ac.Q.matrix.txt: C. floridanus v3.0

value: Colonies C4+C31 from Florida Keys, FL, USA

tag: antibody vendor

value: Abcam

tag: antibody catalog #


title: GATA3_Veh_r2

description:
Chromatin IP against GATA3
JC426


title: Cflo.Minor.Brain.H3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4C31_minor_H3.Q.matrix.txt: C. floridanus v3.0

value: Adult


title: Cflo.Major.Brain.H3K27ac

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4C31_major_H3K27ac.Q.matrix.txt: C. floridanus v3.0


title: Rrp6 -/+

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

data_processing:
base calls were performed using CASAVA, or ELAND, or BUSTARD for files sequenced on MiSeq, Ilumina Genome Analyser IIx, and HiSeq2000 respectively
The sequence reads were trimmed for adapters and aligned to the S. pombe genome version released on April 2007 using novoalign program.
The parameters for novoalign were as follows: "-m" to treat the data as small RNA and "-a" to automatically trim the adapters
We used custom Python scripts to count number of times each location in the genome was seen in the data on the + and the - strand.
The processed data is uploaded as SGR file.  This file is similar to a wig file, first column denotes 'chromosome", second column denotes "position" on the chromosome, and the last column denotes number of times the position was seen in the data.
A negative value on 3rd column denotes the number of times the position was seen when reads mapped to the "-" (minus) strand, and a positive value denotes the number of times the given position was seen when the reads mapped to the "+" (plus) strand.
The counts were nomalized to million mapped reads.
Genome Build: NCBI release 5_30, May 30, 2011. The short reads from the D. melanogaster were aligned to NCBI genome release 5_30, May 30, 2011, using novoalign.  The aligned reads were processed with custom scripts to produce the SGR files that were visualized in a Genome Browser.
Supplementary_files_format_and_content: The data is uploaded as SGR file where first column denotes the chromosome, second column denotes the position on the chromosome counted from the 5' end on the + strand, and the 3rd column denotes the count (normalized to million mapped reads).

source_name: Rrp6 heterozygous deletion

extract_protocol:
Yeast total RNAs are extracted by using MasterPure Yeast RNA purification kit (epicentre). Fly total RNAs are extracted by using specific buffer(0.5M NaCl, 0.2M Tris-HCl(pH 7.5), 0.01M EDTA, 1% SDS), glass beads, and phenol chloroform.
The protocol is described in [RNA. 2010 Dec;16(12):2537-52].

tag: genotype

tag: tissue

value: whole organism


title: GATA3_E2_r2

description:
Chromatin IP against GATA3
JC427

value: E2 at final conc. 100nM for 3 hrs


title: GATA3_E2_r1

description:
Chromatin IP against GATA3
JC315


title: siGATA_FOXA1_Veh_r1

description:
Chromatin IP against FoxA1
JC732

tag: genotype/variation

value: GATA knockdown

value: ON-TARGET plus siRNA J-0033781-09, siGATA3-Custom-1, siGATA3-Custom-2


title: Cflo.Major.Brain.Input

data_processing: Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.

source_name: Whole-brain dissection from adult ants

value: Input


title: GATA3_Veh_r1

description:
Chromatin IP against GATA3
JC314

tag: chip antibody


title: Cflo.Major.Brain.H3

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4C31_major_H3.Q.matrix.txt: C. floridanus v3.0


title: Cflo.Minor.CBP

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_minor_CBP.Q.matrix.txt: C. floridanus v3.0

value: Colony C4 from Florida Keys, FL, USA

value: Minor

value: CREB binding protein

value: Custom recombinant


title: Cflo.Minor.Brain.Input


title: GATA3_Veh_r4

description:
Chromatin IP against GATA3
JC555

tag: cell line

value: Vehicle

value: Santa Cruz


title: siGATA_ER_E2_r3

description:
Chromatin IP against ER
JC472

tag: cell type

value: anti-ERa


title: siNT_ER_E2_r3

description:
Chromatin IP against ER
JC471

tag: stimulated with

value: negative control

value: AllStars Negative Control siRNA (Cat nr:1027281, Qiagen)


title: siNT_FOXA1_Veh_r1

description:
Chromatin IP against FoxA1
JC731

value: breast cancer cells

tag: tranfected with


title: Cflo.Minor.Input


title: siGATA_ER_E2_r2

description:
Chromatin IP against ER
JC407

tag: chip antibody vendor


title: siGATA_ER_E2_r1

description:
Chromatin IP against ER
JC350

tag: chip antibody cat. #


title: Cflo.Major.Input

tag: colony

value: Major


title: Cflo.Major.CBP

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_major_CBP.Q.matrix.txt: C. floridanus v3.0

tag: dev. stage

value: Adult


title: siNT_ER_E2_r2

description:
Chromatin IP against ER
JC406


title: siNT_ER_E2_r1

description:
Chromatin IP against ER
JC349


title: Cflo.Male.Input

value: Male


title: Rrp6 -/-

source_name: Rrp6 homozygous deletion

value: whole organism


title: RNAseq_TbetKO

status: Public on Nov 24 2012

first: Golnaz

last: Vahedi

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

description: RNA-seq

data_processing:
For H3K4me1: the unique tags were mapped into non-overlapping 200 bp windows of the mouse genome. Significant islands were identified based on window tag-count threshold determined from a p-value=0.05 defined by Poisson background model using SICER, a method appropriate for broad peaks
For p300 and STATs CisGenome v2.0, an extension of the earlier version (Ji et al., 2008), was utilized based on the normal rabbit serum as the control IP. The parameters used for seq-peak command were c=2 or 3, b=100, and e=0.
RNA-seq: tophat and cufflinks. Sequence reads from each cDNA library were mapped onto the mouse genome build mm9 using tophat and the mappable data were then processed by Cufflinks (Trapnell et al.). The obtained data were normalized based on RPKM (reads per kilobase exon model per million mapped reads).
Genome_build: mm9

organism: Mus musculus

source_name: primary CD4+ T cells from spleen and lymph nodes

extract_protocol: Total RNA was prepared from 2-5 million cells using mirVana miRNA Isolation kit (#AM1560, ABI). One microgram of total RNA was subsequently used to prepare RNA-seq library using TruSeq SRRNA sample prep kit (FC-122-1001,Illumina)  by following manufacturer's protocol. The libraries were sequenced for 100 cycles (single read) with HiSeq 2000 (Illumina).

tag: strain

value: Tbet<tm1> (TbetKO)

value: in vitro polarized T helper1 cells for 7 days

tag: passages

value: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th1 condition and restimulated with plate-bound CD3/28 +IL12 for 2 hrs


title: p300S1KO_2

description: Chromatin IP against p300

extract_protocol: Cell lysates were made by sonication and protein-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase 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 was PCR amplified with Illumina primers for 16 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIX following the manufacturer's protocols.

value: STAT1<tm1> (STAT1KO)

tag: antibody vendor/catalog#

value: sc-585, Santa Cruz Biotechnology


title: p300WTTh2_2

description: Chromatin IP against p300

value: wild type

value: in vitro polarized T helper2 cells for 7 days

value: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th2 condition and restimulated with plate-bound CD3/28 +IL4 for 2 hrs


title: p300TbetKO_2

description: Chromatin IP against p300


title: p300WTTh1_2

description: Chromatin IP against p300


title: p300WTTh2_controlV

description: Chromatin IP against p300

treatment_protocol: To perform retroviral transduction of CD4+ T cells, sorted naïve CD4+ T cells from WT or Stat6-/- mice were cultured in the presence of plate-bound anti-CD3 and anti-CD28 (10 μg/mL each) with anti-IFNG (10 μg/mL) for 16 h. Culture medium was replaced with retroviral soup and 4 μg/ml polybrene, followed by centrifugation at 2500 rpm for 2 hours. After 4-hour incubation at 37 C, viral supernatant was replaced with Th2 cell culture medium containing IL-4 (10 ng/mL) and anti-IFNG for 2 days. After that, cells were released from TCR stimulation and were cultured further in IL-2 (50 U/mL) and IL-4 and grown an additional 3 days.

value: in vitro polarized T helper2 cells for 5 days with control vector.

value: Gata3 overexpression vector was made in Th2 cells.


title: RNAseq_WTTh1_2

description: RNA-seq


title: Rrp6D Red1D

data_processing:
base calls were performed using CASAVA, or ELAND, or BUSTARD for files sequenced on MiSeq, Ilumina Genome Analyser IIx, and HiSeq2000 respectively
The sequence reads were trimmed for adapters and aligned to the S. pombe genome version released on April 2007 using novoalign program.
The parameters for novoalign were as follows: "-m" to treat the data as small RNA and "-a" to automatically trim the adapters
We used custom Python scripts to count number of times each location in the genome was seen in the data on the + and the - strand.
The processed data is uploaded as SGR file.  This file is similar to a wig file, first column denotes 'chromosome", second column denotes "position" on the chromosome, and the last column denotes number of times the position was seen in the data.
A negative value on 3rd column denotes the number of times the position was seen when reads mapped to the "-" (minus) strand, and a positive value denotes the number of times the given position was seen when the reads mapped to the "+" (plus) strand.
The counts were nomalized to million mapped reads.
Genome_build: Spombe Genome Released in April 2007
Supplementary_files_format_and_content: The data is uploaded as SGR file where first column denotes the chromosome, second column denotes the position on the chromosome counted from the 5' end on the + strand, and the 3rd column denotes the count (normalized to million mapped reads).

organism: Schizosaccharomyces pombe

source_name: Rrp6 and Red1 double deletion

value: Rrp6D Red1D


title: p300WTTh2_Gata3V

description: Chromatin IP against p300

value: in vitro polarized T helper2 cells for 5 days with Gata3 overexpression


title: STAT1WTTh1

description: Chromatin IP against STAT1

value: sc-592, Santa Cruz Biotechnology


title: p300S6KO_controlV

description: Chromatin IP against p300

value: Stat6<tm1> (Stat6KO)


title: p300S4KO_controlV

description: Chromatin IP against p300

treatment_protocol: To over-express T-bet, we first made pMY-IRES-hNGFR vector as a control vector by replacing EGFP of pMYs-IRES-GFP vector (Cell Biolabs) with hNGFR lacking intracellular domain. Then T-bet cDNA was appropriately subcloned into pMY-IRES-hNGFR vector to generate pMY-T-bet-IRES-hNGFR vector (RV-T-bet) for T-bet over-expression. Retroviral vector was transfected into PlatE cells (Cell Biolabs) to generate recombinant retrovirus. To perform retroviral transduction of CD4+ T cells, sorted naïve CD4+ T cells from WT or Stat4-/- mice were cultured in the presence of plate-bound anti-CD3 and anti-CD28 (10 μg/mL each) with anti-IL-4 (10 μg/mL) for 16 h. Culture medium was replaced with retroviral soup and 4 μg/ml polybrene, followed by centrifugation at 2500 rpm for 2 hours. After 4-hour incubation at 37 C, viral supernatant was replaced with Th1 cell culture medium containing IL-12 (10 ng/mL) and anti-IL-4 for 2 days. After that, cells were released from TCR stimulation and were cultured further in IL-2 (50 U/mL) and IL-12 and grown an additional 3 days.

value: STAT4<tm1> (STAT4KO)

value: in vitro polarized T helper1 cells for 5 days with control vector

value: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th1 condition and restimulated with plate-bound CD3/28 +IL12 for 2 hrs.


title: K4me1S6KO

description: Chromatin IP against K4me1

value: ab8895, AbCam


title: K4me1WTTh2

description: Chromatin IP against K4me1


title: p300WTTh2

description: Chromatin IP against p300


title: RNAseq_S6KO_Gata3V

description: RNA-seq


title: K4me1S4KO

description: Chromatin IP against K4me1

value: in vitro polarized T helper1 cells for 7 days


title: p300S4KO_TbetV

description: Chromatin IP against p300

value: in vitro polarized T helper1 cells for 5 days with T-bet overexpression.


title: p300S6KO

description: Chromatin IP against p300


title: K4me1TbetKO

description: Chromatin IP against K4me1

value: Tbet<tm1> (TbetKO)

value: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th1 condition and restimulated with plate-bound CD3/28 +IL12 for 2 hrs


title: K4me1S1KO

description: Chromatin IP against K4me1

value: STAT1<tm1> (STAT1KO)


title: p300S6KO_2

description: Chromatin IP against p300

value: in vitro polarized T helper2 cells for 7 days

value: sc-585, Santa Cruz Biotechnology


title: RNAseq_S6KO_controlV

description: RNA-seq

value: in vitro polarized T helper2 cells for 5 days with control vector.


title: RNAseq_WTTh2_Gata3V

description: RNA-seq

value: wild type

value: Gata3 overexpression vector was made in Th2 cells.


title: p300S4KO _2

description: Chromatin IP against p300


title: p300S6KO_Gata3V

description: Chromatin IP against p300

value: in vitro polarized T helper2 cells for 5 days with Gata3 overexpression


title: p300WTTh1_TbetV

description: Chromatin IP against p300

value: in vitro polarized T helper1 cells for 5 days with T-bet overexpression


title: p300WTTh1_controlV

description: Chromatin IP against p300


title: p300TbetKO

description: Chromatin IP against p300


title: p300S4KO

description: Chromatin IP against p300


title: 24h

city: Rio de Janeiro

first: Paulo

last: Ferreira

address: Rua Rodolpho Paulo Rocco s/nº, CCS, Bl.L, Cidade Universitária

country: Brazil

institute: Universidade Federal do Rio de Janeiro

data_processing:
Quality of the sequences was evaluated by measuring the quality of the reads according to the percentage of bases having a base quality greater or equal than 30 (Q30)
3’ Illumina adapters (CTGTAGGCACCATCAAT) and “N” bases were trimmed
Using the UEA sRNA toolkit-Plant version filter pipeline (http://srna-tools.cmp.uea.ac.uk/) and  three different databases -  all plant t/rRNAs from Rfam, all Arabidopsis tRNAs from The Genomic tRNA Database and all plant t/rRNA sequences from EMBL release - reads with low-complexity (less than 3 different bases) and both sense and antisense matches with t/rRNAs were removed
Detection of conserved miRNAs with UEA sRNA toolkit-Plant version miRProf pipeline was done allowing three mismatches with mature miRNAs from miRBase (v17.0). Only reads with match to Sorghum bicolor were included in the analysis.
The output of the miRProf contains information about unique sequences counts. Counts were normalized in reads per 1 million (RPM) and total reads counts after the final trimming and filtering steps were used for normalization
Genome_build: Sorghum bicolor v1.0
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

organism: Saccharum hybrid cultivar SP70-1143

source_name: leaf

growth_protocol: Saccharum sp Cv. SP70-1143 plantlets were grown in vitro for approximately 1 month in Murashige and Skoog media supplemented with kinetin (0,1mg/ml), Indol butyric acid (I-BA- 0,2mg/ml) and citric acid (150mg/ml). Next, these plantlets were transferred to a hydroponic system supplied with 1x Hoagland’s solution and grown for 2 months

extract_protocol:
Total RNA was isolated from whole plants using Trizol (Invitrogen, CA, USA) as described by the manufacturer.
TruSeq Small RNA Sample Prep Kit

treatment_protocol: After the acclimation period, salinity stress was induced with a concentration of 170mM (mild) in plantlets by adding the salt to the Hoagland solution. The time-course established was (0, 1, 6 and 24hs). For each time point, a group of three plants was submitted to stress, and other three plants used as controls. Individual plants were used for the analysis. All experiments were carried in a greenhouse at 28ºC, 16 hours/light and 8 hours/dark.

tag: treatment

value: 24h after salt treatment with 170mM NaCl

value: leaf


title: p300WTTh1

description: Chromatin IP against p300


title: 1h

value: 6h after salt treatment with 170mM NaCl


title: RNAseq_WTTh1_TbetV

description: RNA-seq

value: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th1 condition and restimulated with plate-bound CD3/28 +IL12 for 2 hrs.


title: 0h

value: 1h after salt treatment with 170mM NaCl


title: RNAseq_S4KO_controlV

description: RNA-seq

value: STAT4<tm1> (STAT4KO)

value: in vitro polarized T helper1 cells for 5 days with control vector.


title: sensitive 0h (root)

organism: Saccharum hybrid cultivar (mixed)

source_name: root

growth_protocol: Stalks of sugarcane cultivars, with different drought sensitivities, were provided by the Centro de Tecnologia Canavieira (CTC). Based on chlorophyll and water content measurements, cultivars CTC15, CTC6, SP83-2847 and SP83-5073, and CTC9, CTC13, SP90-1638 and SP90-3414 were considered as drought tolerant and sensitive, respectively. Stalks were planted germinated and grown in 5L pots with a mixture of soil and sand (2:1) in a greenhouse at 28ºC, and irrigated by dripping.

treatment_protocol: After three months, the plants were exposed to drought stress by withholding water for 24hrs. Treated and control roots and shoots were harvested at 0 and 24 hours of treatment, respectively.

value: pool of four genotypes (CTC9, CTC13, SP90-1638 and SP90-3414)

value: control

value: root


title: sensitive 24h (root)

value: drought stress by withholding water for 24hrs


title: tolerant 24h (leaf)

value: pool of four genotypes (CTC15, CTC6, SP83-2847 and SP83-5073)


title: control


title: RNAseq_WTTh1

description: RNA-seq

value: in vitro polarized T helper1 cells for 7 days

value: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th1 condition and restimulated with plate-bound CD3/28 +IL12 for 2 hrs


title: Rrp6D Pab2D

source_name: Rrp6 and Pab2 double deletion

value: Rrp6D Pab2D


title: RNAseq_S6KO

description: RNA-seq

value: Stat6<tm1> (Stat6KO)

value: in vitro polarized T helper2 cells for 7 days

value: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th2 condition and restimulated with plate-bound CD3/28 +IL4 for 2 hrs


title: RNAseq_S4KO

description: RNA-seq


title: tolerant 24h (root)


title: tolerant 0h (leaf)

value: leaf


title: sensitive 0h (leaf)


title: RNAseq_WTTh1_controlV

description: RNA-seq

value: wild type


title: Input M

status: Public on Nov 23 2012

first: Rohan

last: Williams

address: Medical Drive

institute: SCELSE-NUS

data_processing:
Adapter clipping: fastx_clipper, Trimmomatic (CTCF study)
Quality trimming: fastx_quality trimmer -t 3 -l 19, Trimmomatic (CTCF study)
Alignment: BWA v0.5.8, Bowtie2 (CTCF study)
Keep unique mapped only: Grep “XT:A:U”
BAM to BED conversion: Bamtools
Genome_build: mm9
Supplementary_files_format_and_content: BED, BEDgraph (CTCF study)

source_name: TS cells_Input M

growth_protocol: Mouse Trophoblast Stem (TS) cells  were cultured in TS cell specific media with FGF4 and heparin

extract_protocol:
ChIP and sequential ChIP assays.  Chromatin immunoprecipitations were performed with the following modifications. Anti-H2A.Z antibodies (5 µg), Anti-H3 antibodies (5 µg), anti-CTCF antibodies (7 µg) were added to 40 µl of Dynabeads Protein A or Protein G (Dynal Biotech ASA, Oslo, Norway) and incubated for 1 hr at room temperature, followed by two washes with 200 µl PBS, 0.01% (v/v) Tween 20. 100 µg of chromatin was combined with 1ml of RIPA buffer (140mM NaCl, 10mM Tris-HCl -HCl pH 8.0, 1mM EDTA, 1% (v/v) Triton X100, 0.1% (w/v) SDS, 0.1% (w/v) sodium deoxycholate, 1mM PMSF), mixed with antibodies and incubated overnight at 4°C. Bound chromatin was subsequently washed (10 min per wash) three times with RIPA buffer, three times with RIPA buffer plus 0.36M NaCl, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH 7.6, 1mM EDTA, 0.5% (v/v) NP-40, 0.5% (w/v) sodium deoxycholate, and finally twice with TE buffer (10mM Tris-HCl pH 7.6, 1mM EDTA). Washed beads were re-suspended in 90 µl of cold TE buffer and treated with 1 µl (0.5mg/ml) RNAse A (Roche) for 30 min and then with 0.5mg per ml Proteinase K (Invitrogen) for 4 hr at 65°C followed by 1 hr at 72ºC to reverse cross-linking. An aliquot of the original input chromatin was processed in parallel. DNA from the samples was recovered using AMPure XP beads (Agencourt) according to the manufacturer's protocol. Sequential H2A.Z ChIP-H2A reChIP was carried out as described previously with minor modifications 1; following the final ChIP wash, chromatin complexes were eluted twice in 100 μl of 10mM DTT at 37°C for 30 minutes and diluted 20 times with RIPA buffer. Eluates were re-immunoprecipitated with the second primary antibody against H2A (5 µg), as described above. Rference: 1. Soutoglou, E. & Talianidis, I. Coordination of PIC assembly and chromatin remodeling during differentiation-induced gene activation. Science 295, 1901-4 (2002)
Chromatin preparation from TS cells arrested at the G1;S and M stages. Cells were grown in 150 mm dishes, containing 2-5 x 107 cells per dish. Cells were fixed for 15 min at room temperature in 10 ml of fresh DMEM medium with 10% (v/v) FBS in the presence of 1.5% (v/v) formaldehyde. Cross-linking was stopped by adding glycine solution to a final concentration of 0.125M. Fixed cells were washed 3 times with ice-cold PBS (20 ml). Cells were then scraped into ice-cold PBS (15 ml), containing 0.05% (v/v) Triton X–100. Cells were then pelleted at 900 g for 5 min at 40C. The cell pellet was re-suspended with 2 ml of Buffer I (25mM Hepes pH-7.6, 15mM NaCl, 10mM KCL, 2mM MgCl2, 0.2% (v/v) NP-40, 1mM EDTA, 0.5mM EGTA, 0.5mM DTT, 0.2mM PMSF, Roche EDTA-free protein inhibitor cocktail) and incubated on ice for 10 min. 2 ml of Buffer II (0.6M Sucrose, 15mM Hepes pH-7.6, 120mM KCL, 15mM NaCl, 2mM MgCl2, 0.2% (v/v) NP-40, 1mM EDTA, 0.5mM EGTA, 0.5mM DTT, 0.2mM PMSF, Roche EDTA-free protein inhibitor cocktail) was added and the suspension was incubated for a further 10 min. Nuclei were released by 20 strokes with a Dounce homogeniser type B and pelleted by centrifugation (40 min at 5000 g) through a 8 ml sucrose cushion containing Buffer III (1.2 M Sucrose, 60mM KCL, 15mM Hepes pH-7.6, 15mM NaCl, 2mM MgCl2, 1mM EDTA, 0.5mM EGTA, 0.5mM DTT, 0.2mM PMSF, Roche EDTA-free protein inhibitor cocktail). The supernatant was carefully removed and the nuclei pellet was re-suspended in 1ml of micrococcal digestion buffer (50mM Tris-HCl  pH-7.6, 3mM CaCl2) and passed 10 times through a size 29-gauge needle. The nuclear extract was digested for 30 min at 37°C with micrococcal nuclease (New England Biolabs; 2 units per 330 μl of extract) to obtain chromatin comprising mostly of mononucleosomes. The reaction was stopped by adding 15 μl of 100mM EDTA. The digested nuclear extract was centrifuged at 10,000 g for 5 min. The supernatant containing mononucleosomes (S1) and the pellet (which was re-suspended in 500 μl of dialysis buffer (10mM Tris-HCl  pH-7.6, 1mM EDTA, 0.5mM EGTA) were dialysed independently overnight at 40C. The dialysed re-suspended pellet was centrifuged at 10,000 g for 10 min and the supernatant (S2), containing short chromatin fragments primarily mono-nucleosomes, was mixed with S1. The combined S1 and S2 supernatants were dialysed against 10mM Tris-HCl  pH-7.6, 1mM EDTA, 0.5mM EGTA, 4% (v/v) glycerol, aliquoted and stored at -80°C. Antibodies: anti-H2A (ab18255; Abcam) ; anti-H3 (ab1791; Abcam); anti-CTCF (ab70303; Abcam); for H2A.Z antibodies were produced in-house, please see Rangasamy, D., Berven, L., Ridgway, P. & Tremethick, D.J. Pericentric heterochromatin becomes enriched with H2A.Z during early mammalian development. EMBO J 22, 1599-607 (2003)
Libraries for ChIP Sequencing of DNA were prepared using ChIP-Seq Sample Prep Kit (Illumina) according to the manufacturer's protocol. Quality and concentration of the libraries were assessed on Agilent Technologies 2100 Bioanalyzer and using quantative PCR with adaptor specific primers (ABI Prism 7900HT) according to Illumina's recommendations. DNA from input nucleosomes, H2A.Z ChIP and H2A.ZchIP-H2A reChIP was sequenced employing the Genome Analyser 2X (Illumina) using 75 base pair single end reads. For H3 ChIP-seq we used 100 bp single end reads on Illumina Hi-Seq 2000. For CTCF ChIP-seq we used 100 bp paired-end reads on Illumina Hi-Seq 2000.

treatment_protocol: To synchronize TS cells at the G2/M boundary, cells were treated with nocodazole (40ng/ml) for 7 hr before harvesting. This concentration was chosen after an extensive analysis to determine the minimum concentration required to synchronize cells without any adverse effects to the cell cycle or subsequent differentiation. In order to synchronize TS cells in S phase, TS cells were washed following treatment with nocodazole (40ng/ml) an allowed to grow for an additional 7 hr in drug free fresh TS medium. To synchronize TS cells at the G1/S boundary following nocodazole treatment, TS cells were washed and grown for 3 hr in fresh medium. Hydroxyurea (5mM) was then added and the cells were grown for an additional 5 hr before they were harvested.

tag: developmental stage

value: blastocysts

value: trophoblast stem (TS) cells

tag: cell cycle stage

value: M

tag: molecule subtype

value: Input DNA


title: Input G1

source_name: TS cells_Input G1


title: Input S

source_name: TS cells_Input S

value: S


title: K4me1WTTh1

description: Chromatin IP against K4me1

tag: genotype/variation

value: ab8895, AbCam


title: RNAseq_WTTh2_controlV

description: RNA-seq

value: in vitro polarized T helper2 cells for 5 days with control vector.

value: Gata3 overexpression vector was made in Th2 cells.


title: p300S1KO

description: Chromatin IP against p300

value: STAT1<tm1> (STAT1KO)

tag: chip antibody

value: sc-585, Santa Cruz Biotechnology


title: RNAseq_S4KO_TbetV

description: RNA-seq

value: STAT4<tm1> (STAT4KO)

value: in vitro polarized T helper1 cells for 5 days with T-bet vector.

value: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th1 condition and restimulated with plate-bound CD3/28 +IL12 for 2 hrs.


title: H3 G1

source_name: TS cells_H3 G1

value: Abcam

value: ChIP DNA


title: reChIP H2A G1

source_name: TS cells_reChIP H2A G1

value: ChIPreChIP DNA


title: reChIP H2A S

source_name: TS cells_reChIP H2A S


title: H3 S

source_name: TS cells_H3 S


title: reChIP H2A M

source_name: TS cells_reChIP H2A M


title: CTCF M

source_name: TS cells_CTCF M

value: anti-CTCF


title: tolerant 0h (root)

tag: genotype

value: pool of four genotypes (CTC15, CTC6, SP83-2847 and SP83-5073)

value: control

tag: tissue

value: root


title: sensitive 24h (leaf)

value: pool of four genotypes (CTC9, CTC13, SP90-1638 and SP90-3414)

value: drought stress by withholding water for 24hrs

value: leaf


title: RNAseq_WTTh2

description: RNA-seq

value: wild type

tag: cell type

value: in vitro polarized T helper2 cells for 7 days

value: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th2 condition and restimulated with plate-bound CD3/28 +IL4 for 2 hrs


title: H2A.Z S

source_name: TS cells_H2A.Z S

value: blastocysts

value: trophoblast stem (TS) cells

value: S

value: H2A.Z antibodies produced in-house [PMID:12660166]


title: CTCF G1

source_name: TS cells_CTCF G1

value: Abcam


title: CTCF S

source_name: TS cells_CTCF S

value: ChIP DNA


title: H2A.Z G1

source_name: TS cells_H2A.Z G1


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh K1 isolate at 24hpi, replicate 1

status: Public on Nov 22 2012

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

country: Germany

institute: Max Planck Institute

description:
pps_K1_24hpi_1
PolyA-enriched RNA

data_processing:
Illumina Casava 1.8 software was used for basecalling.
Sequenced reads were mapped to the TAIR10 whole genome using tophat v1.3.2 with parameters -p 12 -a 10 -g 5 --library-type fr-unstranded -G TAIR10_GFF3_genes.gff
Read counts per gene per sample were obtained using the bedTools suite v2.13.2 (function coverageBed).
Genome_build: TAIR10
Supplementary_files_format_and_content: CompleteCountTable_At.txt: Tab-delimited text file including raw read counts per gene for each sample. This file is linked to the Series record as a supplementary file.

organism: Arabidopsis thaliana

source_name: Bgh K1-infected pps leaves, 24hpi

growth_protocol: Growth of plants and pathogens was performed as described in V. Lipka, et al., Science 310, 1180 (2005) (PMID 16293760).

extract_protocol: Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen). RNA-seq libraries were prepared from an input of 4 ug total RNA according to recommendations of the supplier (TruSeq RNA sample preparation v2 guide, Illumina). Libraries were quantified by fluorometry, immobilized and processed onto a flow cell with a cBot (Illumina) followed by sequencing-by-synthesis with TruSeq v3 chemistry on a HiSeq 2000. Library construction and sequencing were performed by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de).

treatment_protocol: Inoculation of the pathogens was perfomed as described in V. Lipka, et al., Science 310, 1180 (2005) (PMID 16293760).

tag: plant strain

value: Columbia-0 pen2-1 pad4-1 sag101-2 mutant

value: leaves

tag: fungal isolate

value: Blumeria graminis f. sp. hordei isolate K1

tag: virulence

value: virulent

tag: time

tag: virulence_time (as used for model)


title: H3 M

source_name: TS cells_H3 M

tag: strain

value: M

tag: chip antibody vendor

tag: chip antibody cat. #


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh K1 isolate at 18hpi, replicate 3

description:
pps_K1_18hpi_3
PolyA-enriched RNA

source_name: Bgh K1-infected pps leaves, 18hpi


title: H2A.Z M

source_name: TS cells_H2A.Z M


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh K1 isolate at 24hpi, replicate 2

description:
pps_K1_24hpi_2
PolyA-enriched RNA


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh A6 isolate at 24hpi, replicate 2

description:
pps_A6_24hpi_2
PolyA-enriched RNA

source_name: Bgh A6-infected pps leaves, 24hpi

value: Blumeria graminis f. sp. hordei isolate A6


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh A6 isolate at 24hpi, replicate 3

description:
pps_A6_24hpi_3
PolyA-enriched RNA


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh A6 isolate at 24hpi, replicate 1

description:
pps_A6_24hpi_1
PolyA-enriched RNA


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh K1 isolate at 24hpi, replicate 3

description:
pps_K1_24hpi_3
PolyA-enriched RNA


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh K1 isolate at 18hpi, replicate 2

description:
pps_K1_18hpi_2
PolyA-enriched RNA


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh A6 isolate at 18hpi, replicate 3

description:
pps_A6_18hpi_3
PolyA-enriched RNA

source_name: Bgh A6-infected pps leaves, 18hpi


title: InputDNATh0

description: Input DNA

source_name: primary CD4+ T cells from spleen and lymph nodes

tag: passages

value: FACS sorted naive CD4+T cells with plate-bound CD3/28


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh K1 isolate at 12hpi, replicate 1

description:
pps_K1_12hpi_1
PolyA-enriched RNA

source_name: Bgh K1-infected pps leaves, 12hpi


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh A6 isolate at 6hpi, replicate 2

description:
pps_A6_6hpi_2
PolyA-enriched RNA

source_name: Bgh A6-infected pps leaves, 6hpi


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh K1 isolate at 12hpi, replicate 2

description:
pps_K1_12hpi_2
PolyA-enriched RNA


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh A6 isolate at 12hpi, replicate 1

description:
pps_A6_12hpi_1
PolyA-enriched RNA

source_name: Bgh A6-infected pps leaves, 12hpi


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh A6 isolate at 12hpi, replicate 3

description:
pps_A6_12hpi_3
PolyA-enriched RNA


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh A6 isolate at 6hpi, replicate 3

description:
pps_A6_6hpi_3
PolyA-enriched RNA


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh A6 isolate at 18hpi, replicate 2

description:
pps_A6_18hpi_2
PolyA-enriched RNA


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh A6 isolate at 6hpi, replicate 1

description:
pps_A6_6hpi_1
PolyA-enriched RNA


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh K1 isolate at 6hpi, replicate 3

description:
pps_K1_6hpi_3
PolyA-enriched RNA

source_name: Bgh K1-infected pps leaves, 6hpi


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh A6 isolate at 12hpi, replicate 2

description:
pps_A6_12hpi_2
PolyA-enriched RNA


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh A6 isolate at 18hpi, replicate 1

description:
pps_A6_18hpi_1
PolyA-enriched RNA


title: OCT1_ChIPSeq

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

description:
Antibodies references :PMID 1495986, PMID 8628262
OCT1

data_processing:
Basecalls performed using Bustard from the Illumina Genome Analyzer II
Alignment : The sequenced tags were mapped onto the unmasked genome build hg18 using the fetchGWI software and allowing 1000 repeats on the genome. The tags mapping more than once onto the genome were then attributed a weight corresponding to the number of times the tag was sequenced divided by the number of genomic matches . The files with these weighted repeated tags as well as the unique tags were then used for peak detection
Peak detection : peaks were determined with the sissrs software (www.rajajothi.com/sissrs/). Peaks mapping in satellite and micro-satellite repeats and peaks mapping in 18 and 28S rRNA sequences, were eliminated from the analysis. This first analysis resulted in the identification of peaks.
For the SNAP subunits, we divided the genome into 200 nucleotide bins, counted tags obtained for each of the four SNAPc subunits analyzed, and and retained only bins displaying an enrichment for at least two of the SNAPc subunits. Bins were considered positive only if the tag number in bin reached at least the minimum tag count determined by sissrs for enriched regions with a 0.001 false discovery rate as the one used in sissrs set at the default parameters. Only the genomic regions containing POLR2B and GTF2B, or POLR3D and BRF2, sissrs peaks as well as a bin positive for two SNAPc subunits within 100 nucleotides of the polymerase sissrs peak were retained.
The obtained genomic loci were then quantified using the protocol described in PMID:20413673.
Genome_build: hg18
Supplementary_files_format_and_content: The Processed files include the weighted tags counts per nucleotide calculated in a window of minus 150 to plus 150 nucleotides around each SNAPc gene. For the polymerase III and polymerase II (RPC4 and RPB2) files, tags were neither centered nor extended. For the transcription factors (all other files), tags were extended to the insert length given by the bioanalyzer (minus the adapters length), and tags count per nucleotide was calculated on the whole insert length. In both cases, the nucleotide position score is the sum of the tags scores at that position, where the score for each tag is given by the ratio between the number of times the tag has been sequenced and the number of times the tag matches on the genome. For RPB2, the additional file called “RPB2_perfect_matches_on_SNAPc_genes.bedGraph” contains only the tags with one unique and perfect match on the genome.

growth_protocol: The chromatin immunoprecipitations (ChIPs) were performed with exponentially growing IMR90HTert or HeLa cells. IMR90HTert cells are diploid fibroblast-like cells established from fetal female lung tissue and transfected with the gene coding for human Telomerase reverse Transcriptase. HeLa cells were grown as spinners in a flask.

extract_protocol: At least 10 ng was used to prepare sequencing libraries with the Illumina ChIP-Seq Sample Preparation Kit according to the protocol supplied with the reagents. Aliquots of the sequencing libraries were then loaded into Genome Analyzer flow cells and sequenced with the Genome Analyzer or Genome Analyzer II (Illumina) using the 36 Cycle Sequencing Kit v2 (Catalog number FC-204-2036). As controls, aliquots of the input DNA (collected after the crosslinking and sonication steps) were also subjected to ultra high throughput sequencing.

treatment_protocol: Both IMR90HTert and HeLa cells were cross-linked for seven minutes in 1% formaldehyde.  Following cell and nuclear lysis as described, extracted chromatin was sonicated to an average size of 200-600 base pairs and used for immunoprecipitations.  The sonicated chromatin was mixed with various antibodies and incubated on a rotating wheel overnight at 4˚C.  Immunoprecipitated material was recovered by addition of 10 ul of protein A agarose beads (pre-blocked with 10ug/ml of BSA and salmon sperm DNA) and incubation for 1 h at room temperature on a rotating wheel.  The beads were then washed with dialysis and wash buffer [PMID 17140114]

tag: cell line

value: HeLa

value: mix of monoclonal antibodies YL8 and YL15

tag: chip antibody reference


title: SNAP43_ChIPSeq

description:
Chromatin IP against SNAP43, followed by high-througput sequencing
SNAP43

value: diploid fibroblast-like cells

tag: tissue origin

value: fetal female lung

tag: transfected with

value: human Telomerase reverse Transcriptase gene

value: polyclonal rabbit antibody CS47 #7,8

value: Rabbit anti-peptide antibody raised against SNAPC1 peptide lehqqwhkdrknpslksk, Faresse, N., et al., PLoS Genetics, submitted.


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh K1 isolate at 6hpi, replicate 2

description:
pps_K1_6hpi_2
PolyA-enriched RNA


title: SNAP19_ChIPSeq

description:
Chromatin IP against SNAP19, followed by high-througput sequencing
SNAP19

tag: chip antibody

value: polyclonal rabbit antibody CS539 #7,8

value: Rabbit anti-peptide antibody raised against SNAPC5 peptide mlsrlqelrkeeet, Faresse, N., et al., PLoS Genetics, submitted.


title: SNAP45_ChIPSeq_225-275

description:
MR90HTert stable cell line expressing the human SNAP45 fused to the Tobacco etch virus (TEV), the Flag epitope, and the biotin acceptor domain (BAD) growing DMEM, 10% FBS, and 0,1% of non essential amino acids, were cross-linked for 7 min by addition of 1% of Formaldehyde (Sigma, Cat. No. F-1635). Crosslinking was stopped by addition of glycine to a final concentration of 0.125 M, followed by 5-min incubation at room temperature. Fixed cells were washed twice with cold PBS and harvested in cold PBS containing protease inhibitors. Cells were pelleted by centrifugation, suspended in 1mL of Cell lysis buffer (5mM Pipes at pH 8.0, 0.5% NP40, 85mM KCl, 1mM DTT and protease inhibitors (sigma N° 8340)), and incubated for 10 min on ice. Cells were then pelleted by centrifugation, resuspended in 200 µL of Nuclear lysis buffer (50mM Tris-Cl pH 8.0, 10mM EDTA, 1% SDS, 1mM PMSF, 1mM DTT and protease inhibitors) and incubated for 30min at room temperature. Nuclear extraction was diluted 1:5 with salty buffer (250mM NaCl, 25mM Hepes pH 7.9, 2mM DTT, 0,5 mM PMSF). DNA was disrupted by sonication, yielding genomic DNA fragments  of a size of 200–600 bp. Crude chromatin was cleared by centrifugation at 16’000xg for 20 minutes. 500µl of cleared chromatin was next incubated overnight with 30µl of Dynabeads M280-streptavidin (Invitrogen N° 112.05D). Beads were then washed twice with SDS buffer (20mM Hepes pH 7.9, 200mM NaCl, 0.5mM EDTA, 10% glycerol 1mM DTT, 10.5mM PMSF, 2% SDS) followed by two washes with IP wash buffer (100mM Tris at pH 8.0, 500mM LiCl, 1% NP-40, 1% deoxycholic acid), and two washes with TEV-buffer (20mM Hepes pH 7.9, 200mM NaCl, 0.5mM EDTA, 10% glycerol 1mM DTT, 0.5mM PMSF).  Samples were then resuspended in 100µl TEV-buffer containing 1unit of TEV enzyme; incubated for 3 hours at room temperature. Beads were concentrate with a magnet and supernatant was collected as first elution. 100µl of TEV-buffer was added to beads and supernatant was pooled with the first elution, then 2µl of DNase-free RNase-A (10mg/ml) was added and samples were decrosslinked by an overnight incubation at 65 °C. Proteinase K and 5X Proteinase K buffer (50mM Tris at pH 7.5, 25mM EDTA, 1.25% SDS) were then added to the samples and incubate at 37°C for 2 hours. DNA from the samples was purified using Gene PCR cleanup columns (Sigma, NA-1020). Purified DNA was recovered in 50µl of elution buffer.
SNAP45_76_r41_l3_225-275
The processed data 'SNAP45_on_SNAPc_genes.bedGraph' available on Series records


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh K1 isolate at 6hpi, replicate 1

description:
pps_K1_6hpi_1
PolyA-enriched RNA


title: MLA1 expressing plants challenged with Bgh K1 isolate at 24hpi, replicate 3

description:
B12_K1_24hpi_3
PolyA-enriched RNA

source_name: Bgh K1-infected B12 leaves, 24hpi

value: Columbia-0 pen2-1 pad4-1 sag101-2 mutant expressing MLA1-HA

value: avirulent


title: SNAP190_ChIPSeq

description:
Chromatin IP against SNAP190, followed by high-througput sequencing
SNAP190

value: polyclonal rabbit antibody CS696 #4,5

value: Mittal, V., Ma, B., and Hernandez, N. (1999).  Genes and Development 13, 1807-1821.