title: WCE-309 ChIP-Seq

description: Input DNA for ELL-FL

data_processing: Sequencing reads were acquired through the primary Solexa image analysis pipeline, where bases were called and reads were filtered for quality, according to default Solexa standards. Filtered reads were then aligned to the fly genome (UCSC dm3) using the Bowtie (10) alignment tool, version 0.12.7. Only those sequences that matched uniquely to the genome with up to two mismatches were retained for subsequent analysis.Enriched regions of ChIP-seq signal were determined by the âMACSâ (11) peak-finding program, version 1.4.0rc2. Sequence reads for each ChIP-seq dataset and their associated whole-cell extract controls were used for the input and control file, respectively. The effective genome size was configured appropriately for the fly datasets, and the p-value cutoff was set to 1.00e-05 and a fold-change greater than five, or FDR < 1%. All other MACS parameters were left default.

growth_protocol: Drosophila chromatin immunoprecipitation was performed with S2 cells grown in Schneider's media with 10% FBS at room temperature.

extract_protocol: ChIP libraries were prepared with the Illumina DNA Sample Kit (Part# 0801-0303) according to Illumina's instructions and sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

treatment_protocol: Cells were fixed for 10 minutes in 1% formaldehyde, quenched with the addition of 1/10 volume of 2.5 M Glycine in PBS for 10 minutes, cells were washed twice in PBS, resuspended in hypotonic buffer and nutated for 10 minutes.3x10e7 cells were pelleted and resuspended in 1.3 ml RIPA buffer with 0.5% Sarkosyl.Cells were sonicated in polyethylene 15 ml tubes for 15 minutes, high output, in a Bioruptor Diagenode) at 4 degrees. Debris was pelleted 10 minutes at 20,000 x g 4Â° C. ChIP was performed with 200 Âµl of chromatin and 5 Âµg of antibodies, and scaled up 10 fold for ChIP-seq.

value: in house none


title: ELL-RNAi RNA-Seq rep2

status: Public on Dec 22 2011

type: SRA

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

country: USA

institute: Stowers Institute for Medical Research

description: RNAseq after ELL-RNAi; Replicate 2

library_source: transcriptomic

data_processing: RNA-seq analysis was done using TopHat v1.2.0 and Bowtie v0.12.7. Only uniquely mapping reads were used. Fly transcript annotations were from Ensembl 62. Differentially expressed genes after RNAi were called with an adjusted p-value < 0.001 and MA plots were determined by DEseq, v1.4.1. In order to avoid off-target RNAi, independent RNAi experiments, using two different dsRNA regions for each target, were treated as biological replicates for analysis of differential expression.

molecule: total RNA

organism: Drosophila melanogaster

source_name: Schneider's Drosophila Line 2

growth_protocol: S2 cells were grown in Schneider's media with 10% FBS at room temperature.

extract_protocol: Two micrograms of DNase-treated total RNA was depleted of Ribosomal RNA with the Ribo-Zero kit from Epicentre (catalog #RZH1046), followed by use of the TruSeq RNA Sample Prep Kit (catalog #FC-122-1001) following manufacturer instructions.

treatment_protocol: Drosophila RNAi was performed by feeding S2 cells with dsRNA prepared with the Megascript T7 dsRNA synthesis kit from Ambion (catalog #1626.) Cells at a density of 2e6 cells/ml were serum starved treated with 10 Âµg of dsRNA. Additional boosts of 10 Âµg dsRNA were added at 48 and 96 hours. Cells were harvested at 120 hours.

tag: cell type

value: S2; Schneider's Drosophila Line 2;  Marco Blanchette's Lab

tag: cell line

tag: knockdown

value: ELL


title: H3K36me3 IP 24 hpf

city: Cambridge

first: Igor

last: Ulitsky

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: ChIP-Seq was carried out as described in Guenther et al. 2010 (GSE22499)

library_source: genomic

data_processing: Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie, allowing for up to one mismatch and up to 4 genomic matches. Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS 1.4) algorithm (http://liulab.dfci.harvard.edu/MACS/), using the Input libraries to assess FDR

molecule: genomic DNA

organism: Danio rerio

source_name: whole embryo at 24 hours post fertilization, H3K36me3 ChIP

growth_protocol: Zebrafish embryos or adults grown under standard condition

treatment_protocol: Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS (137 mM NaCl, 2.7 mM KCl, 1.5 mM KH2PO4, 8 mM Na2HP04, pH 7.4) and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer, dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed, and pellets were rinsed twice with PBS, flash frozen in liquid nitrogen and stored at –80C.

tag: tissue

value: whole embryo

tag: developmental stage

value: 24 hours post fertilization

tag: genotype

value: wt

tag: antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog #


title: ELL-309 ChIP-Seq

description: Chromatin IP against ELL-FL

value: in house Rabbit anti-ELL-fl (aa 1-1079)


title: Input ChIP-Seq

description: Input DNA


title: 3P-Seq 24 hpf

description: 3P-Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html

data_processing: Reads were reverse complemented and aligned to the D. rerio genome (Zv9/danRer7) using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their 3' end within a terminal adenylate-run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. (GSE24924)

molecule: polyA RNA

source_name: whole embryo at 24 hours post fertilization


title: Lilli ChIP-Seq

description: Chromatin IP against Lilli

value: in house Guinea Pig anti-Lilli-CT (aa 1427-1673)


title: Bisulfite-seq in fcl, biological replicate 3

city: New Haven

first: Hang

last: He

state: CT

address: 165 Prospect St

department: MCDB

institute: Yale University

data_processing:
fcl_3.mapview; genome build: TAIR10
We selected multiple base read lengths during sequencing runs and observed that quality decreased rapidly upon sequencing longer reads. We therefore adopted a strategy combining MAQ v0.6.6 (Li et al., 2008) and custom Perl scripts to process mapped sequences. We ran MAQ using the “maq map –M c” option, allowing up to two mismatches per read.  We mapped less than 42-base reads as described above.  For longer-base reads, we added a step to insure that low-quality read tails would not influence mapping results.  We divided the these reads into the first 40 bases and others.  Each half of the reads was aligned independently using MAQ, allowing up to two mismatches.  The coordinates of the two halves were then checked with a Perl script and the second half was discarded if it did not match the first. After mapping, numbers of reads mapped to unique loci and of reads mapped to multiple loci were counted and then run separately in subsequent analyses.

organism: Arabidopsis thaliana

source_name: seedlings, F1 hybrids Fcl

growth_protocol: Plants were grown on Murashige and Skoog (MS) plates containing 1% sucrose at 22 0C under white light (100 μmolm-2s-1) conditions (16-h light/8-h dark).  The 15-d-old seedlings were used for various assays, unless otherwise indicated. Around 50 to 100 seedlings were pooled in each sample for genomic DNA and total RNA extractions.

extract_protocol: Libraries for high-throughput bisulfite sequencing were generated as described previously (Lister et al., 2008).  Briefly, 5 μg of purified genomic DNAs were first isolated, sonicated and ligated to Illumina methylated DNA adaptors, and then adaptor-ligated molecules of 50-500 bp were isolated by agarose gel electrophoresis, and subjected to two successive treatments of sodium bisulfite conversion to obtain a high conversion rate based on a recent report (Lister et al., 2008).  Five ng of bisulfite-converted, adapter-ligated DNA molecules were enriched by 15 cycles of PCR.  Finally the enriched libraries were purified with the PCR purification kit (Qiagen), and subjected to high-throughput Illumina sequencing.

tag: strain

value: F1 hybrids Fcl

value: seedlings

tag: development stage


title: Bisulfite-seq in fcl, biological replicate 2

data_processing:
fcl_2.mapview; genome build: TAIR10
We selected multiple base read lengths during sequencing runs and observed that quality decreased rapidly upon sequencing longer reads. We therefore adopted a strategy combining MAQ v0.6.6 (Li et al., 2008) and custom Perl scripts to process mapped sequences. We ran MAQ using the “maq map –M c” option, allowing up to two mismatches per read.  We mapped less than 42-base reads as described above.  For longer-base reads, we added a step to insure that low-quality read tails would not influence mapping results.  We divided the these reads into the first 40 bases and others.  Each half of the reads was aligned independently using MAQ, allowing up to two mismatches.  The coordinates of the two halves were then checked with a Perl script and the second half was discarded if it did not match the first. After mapping, numbers of reads mapped to unique loci and of reads mapped to multiple loci were counted and then run separately in subsequent analyses.


title: Ice1 ChIP-Seq

description: Chromatin IP against Ice1

value: in house Rabbit anti-Ice1 (CG13550, aa 1-192)


title: ELL ChIP-Seq

description: Chromatin IP against ELL

value: in house Rabbit anti-ELL-MR (aa 301-584)


title: Bisulfite-seq in flc, biological replicate 2

data_processing:
flc_2.mapview; genome build: TAIR10
We selected multiple base read lengths during sequencing runs and observed that quality decreased rapidly upon sequencing longer reads. We therefore adopted a strategy combining MAQ v0.6.6 (Li et al., 2008) and custom Perl scripts to process mapped sequences. We ran MAQ using the “maq map –M c” option, allowing up to two mismatches per read.  We mapped less than 42-base reads as described above.  For longer-base reads, we added a step to insure that low-quality read tails would not influence mapping results.  We divided the these reads into the first 40 bases and others.  Each half of the reads was aligned independently using MAQ, allowing up to two mismatches.  The coordinates of the two halves were then checked with a Perl script and the second half was discarded if it did not match the first. After mapping, numbers of reads mapped to unique loci and of reads mapped to multiple loci were counted and then run separately in subsequent analyses.

source_name: seedlings, F1 hybrids Flc

value: F1 hybrids Flc


title: Bisulfite-seq in fcl, biological replicate 1

data_processing:
fcl_1.mapview; genome build: TAIR10
We selected multiple base read lengths during sequencing runs and observed that quality decreased rapidly upon sequencing longer reads. We therefore adopted a strategy combining MAQ v0.6.6 (Li et al., 2008) and custom Perl scripts to process mapped sequences. We ran MAQ using the “maq map –M c” option, allowing up to two mismatches per read.  We mapped less than 42-base reads as described above.  For longer-base reads, we added a step to insure that low-quality read tails would not influence mapping results.  We divided the these reads into the first 40 bases and others.  Each half of the reads was aligned independently using MAQ, allowing up to two mismatches.  The coordinates of the two halves were then checked with a Perl script and the second half was discarded if it did not match the first. After mapping, numbers of reads mapped to unique loci and of reads mapped to multiple loci were counted and then run separately in subsequent analyses.


title: Bisulfite-seq in flc, biological replicate 3

data_processing:
flc_3.mapview; genome build: TAIR10
We selected multiple base read lengths during sequencing runs and observed that quality decreased rapidly upon sequencing longer reads. We therefore adopted a strategy combining MAQ v0.6.6 (Li et al., 2008) and custom Perl scripts to process mapped sequences. We ran MAQ using the “maq map –M c” option, allowing up to two mismatches per read.  We mapped less than 42-base reads as described above.  For longer-base reads, we added a step to insure that low-quality read tails would not influence mapping results.  We divided the these reads into the first 40 bases and others.  Each half of the reads was aligned independently using MAQ, allowing up to two mismatches.  The coordinates of the two halves were then checked with a Perl script and the second half was discarded if it did not match the first. After mapping, numbers of reads mapped to unique loci and of reads mapped to multiple loci were counted and then run separately in subsequent analyses.


title: Bisulfite-seq in flc, biological replicate 1

data_processing:
flc_1.mapview; genome build: TAIR10
We selected multiple base read lengths during sequencing runs and observed that quality decreased rapidly upon sequencing longer reads. We therefore adopted a strategy combining MAQ v0.6.6 (Li et al., 2008) and custom Perl scripts to process mapped sequences. We ran MAQ using the “maq map –M c” option, allowing up to two mismatches per read.  We mapped less than 42-base reads as described above.  For longer-base reads, we added a step to insure that low-quality read tails would not influence mapping results.  We divided the these reads into the first 40 bases and others.  Each half of the reads was aligned independently using MAQ, allowing up to two mismatches.  The coordinates of the two halves were then checked with a Perl script and the second half was discarded if it did not match the first. After mapping, numbers of reads mapped to unique loci and of reads mapped to multiple loci were counted and then run separately in subsequent analyses.


title: Bisulfite-seq in C24, biological replicate 2

data_processing:
C24_2.mapview; genome build: TAIR10
We selected multiple base read lengths during sequencing runs and observed that quality decreased rapidly upon sequencing longer reads. We therefore adopted a strategy combining MAQ v0.6.6 (Li et al., 2008) and custom Perl scripts to process mapped sequences. We ran MAQ using the “maq map –M c” option, allowing up to two mismatches per read.  We mapped less than 42-base reads as described above.  For longer-base reads, we added a step to insure that low-quality read tails would not influence mapping results.  We divided the these reads into the first 40 bases and others.  Each half of the reads was aligned independently using MAQ, allowing up to two mismatches.  The coordinates of the two halves were then checked with a Perl script and the second half was discarded if it did not match the first. After mapping, numbers of reads mapped to unique loci and of reads mapped to multiple loci were counted and then run separately in subsequent analyses.

source_name: seedlings, C24 ecotype

value: C24 ecotype


title: H3K4me3 IP 72 hpf

source_name: whole embryo at 72 hours post fertilization, H3K4me3 ChIP

extract_protocol: ChIP-Seq was carried out as described in Guenther et al. 2010 (GSE22499)

value: 72 hours post fertilization


title: H3K4me3 IP 24 hpf

source_name: whole embryo at 24 hours post fertilization, H3K4me3 ChIP


title: Bisulfite-seq in Ler, biological replicate 2

data_processing:
Ler_2.mapview; genome build: TAIR10
We selected multiple base read lengths during sequencing runs and observed that quality decreased rapidly upon sequencing longer reads. We therefore adopted a strategy combining MAQ v0.6.6 (Li et al., 2008) and custom Perl scripts to process mapped sequences. We ran MAQ using the “maq map –M c” option, allowing up to two mismatches per read.  We mapped less than 42-base reads as described above.  For longer-base reads, we added a step to insure that low-quality read tails would not influence mapping results.  We divided the these reads into the first 40 bases and others.  Each half of the reads was aligned independently using MAQ, allowing up to two mismatches.  The coordinates of the two halves were then checked with a Perl script and the second half was discarded if it did not match the first. After mapping, numbers of reads mapped to unique loci and of reads mapped to multiple loci were counted and then run separately in subsequent analyses.

source_name: seedlings, Landsberg erecta ecotype

value: Landsberg erecta ecotype


title: smRNA-seq in fcl, biological replicate 3

data_processing:
fcl_3.bowtie; genome build: TAIR8
First, a custom Perl script was performed to remove the 3’ adapter sequences.  Next, we compared the trimmed sRNA reads with the NCBI plant tRNA and rRNA databases to remove potentially degraded rRNA and tRNA products from our datasets.  We then mapped the remaining trimmed reads to the Arabidopsis genome using Bowtie (Langmead et al., 2009), only accepting perfect matches.  After mapping, only reads mapped to unique loci were counted for subsequent analyses.

extract_protocol: Total RNAs were isolated from 15-d-old seedlings using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions and were treated with RNase-free DNase I (Promega) to remove contaminating genomic DNA. Small RNAs separated from total RNAs by polyacrylamide gel electrophoresis were extracted and used to create libraries for Illumina sequencing as described previously (Mi et al., 2008; Wang et al., 2009).


title: Bisulfite-seq in C24, biological replicate 1

data_processing:
C24_1.mapview; genome build: TAIR10
We selected multiple base read lengths during sequencing runs and observed that quality decreased rapidly upon sequencing longer reads. We therefore adopted a strategy combining MAQ v0.6.6 (Li et al., 2008) and custom Perl scripts to process mapped sequences. We ran MAQ using the “maq map –M c” option, allowing up to two mismatches per read.  We mapped less than 42-base reads as described above.  For longer-base reads, we added a step to insure that low-quality read tails would not influence mapping results.  We divided the these reads into the first 40 bases and others.  Each half of the reads was aligned independently using MAQ, allowing up to two mismatches.  The coordinates of the two halves were then checked with a Perl script and the second half was discarded if it did not match the first. After mapping, numbers of reads mapped to unique loci and of reads mapped to multiple loci were counted and then run separately in subsequent analyses.


title: Bisulfite-seq in Ler, biological replicate 3

data_processing:
Ler_3.mapview; genome build: TAIR10
We selected multiple base read lengths during sequencing runs and observed that quality decreased rapidly upon sequencing longer reads. We therefore adopted a strategy combining MAQ v0.6.6 (Li et al., 2008) and custom Perl scripts to process mapped sequences. We ran MAQ using the “maq map –M c” option, allowing up to two mismatches per read.  We mapped less than 42-base reads as described above.  For longer-base reads, we added a step to insure that low-quality read tails would not influence mapping results.  We divided the these reads into the first 40 bases and others.  Each half of the reads was aligned independently using MAQ, allowing up to two mismatches.  The coordinates of the two halves were then checked with a Perl script and the second half was discarded if it did not match the first. After mapping, numbers of reads mapped to unique loci and of reads mapped to multiple loci were counted and then run separately in subsequent analyses.


title: Bisulfite-seq in Ler, biological replicate 1

data_processing:
Ler_1.mapview; genome build: TAIR10
We selected multiple base read lengths during sequencing runs and observed that quality decreased rapidly upon sequencing longer reads. We therefore adopted a strategy combining MAQ v0.6.6 (Li et al., 2008) and custom Perl scripts to process mapped sequences. We ran MAQ using the “maq map –M c” option, allowing up to two mismatches per read.  We mapped less than 42-base reads as described above.  For longer-base reads, we added a step to insure that low-quality read tails would not influence mapping results.  We divided the these reads into the first 40 bases and others.  Each half of the reads was aligned independently using MAQ, allowing up to two mismatches.  The coordinates of the two halves were then checked with a Perl script and the second half was discarded if it did not match the first. After mapping, numbers of reads mapped to unique loci and of reads mapped to multiple loci were counted and then run separately in subsequent analyses.


title: H3K4me3 IP Adult

source_name: mixed gender adults, H3K4me3 ChIP

treatment_protocol: For adult fish, anesthetized fish were homogenized in the TissueRuptor (Qiagen). Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed, and pellets were rinsed twice with PBS, flash frozen in liquid nitrogen and stored at –80C.

value: whole adult

value: mixed gender adults


title: smRNA-seq in fcl, biological replicate 1

data_processing:
fcl_1.bowtie; genome build: TAIR8
First, a custom Perl script was performed to remove the 3’ adapter sequences.  Next, we compared the trimmed sRNA reads with the NCBI plant tRNA and rRNA databases to remove potentially degraded rRNA and tRNA products from our datasets.  We then mapped the remaining trimmed reads to the Arabidopsis genome using Bowtie (Langmead et al., 2009), only accepting perfect matches.  After mapping, only reads mapped to unique loci were counted for subsequent analyses.


title: smRNA-seq in C24, biological replicate 1

data_processing:
C24_1.bowtie; genome build: TAIR8
First, a custom Perl script was performed to remove the 3’ adapter sequences.  Next, we compared the trimmed sRNA reads with the NCBI plant tRNA and rRNA databases to remove potentially degraded rRNA and tRNA products from our datasets.  We then mapped the remaining trimmed reads to the Arabidopsis genome using Bowtie (Langmead et al., 2009), only accepting perfect matches.  After mapping, only reads mapped to unique loci were counted for subsequent analyses.


title: smRNA-seq in Ler, biological replicate 3

data_processing:
Ler_3.bowtie; genome build: TAIR8
First, a custom Perl script was performed to remove the 3’ adapter sequences.  Next, we compared the trimmed sRNA reads with the NCBI plant tRNA and rRNA databases to remove potentially degraded rRNA and tRNA products from our datasets.  We then mapped the remaining trimmed reads to the Arabidopsis genome using Bowtie (Langmead et al., 2009), only accepting perfect matches.  After mapping, only reads mapped to unique loci were counted for subsequent analyses.


title: smRNA-seq in flc, biological replicate 1

data_processing:
flc_1.bowtie; genome build: TAIR8
First, a custom Perl script was performed to remove the 3’ adapter sequences.  Next, we compared the trimmed sRNA reads with the NCBI plant tRNA and rRNA databases to remove potentially degraded rRNA and tRNA products from our datasets.  We then mapped the remaining trimmed reads to the Arabidopsis genome using Bowtie (Langmead et al., 2009), only accepting perfect matches.  After mapping, only reads mapped to unique loci were counted for subsequent analyses.


title: smRNA-seq in flc, biological replicate 2

data_processing:
flc_2.bowtie; genome build: TAIR8
First, a custom Perl script was performed to remove the 3’ adapter sequences.  Next, we compared the trimmed sRNA reads with the NCBI plant tRNA and rRNA databases to remove potentially degraded rRNA and tRNA products from our datasets.  We then mapped the remaining trimmed reads to the Arabidopsis genome using Bowtie (Langmead et al., 2009), only accepting perfect matches.  After mapping, only reads mapped to unique loci were counted for subsequent analyses.


title: Pol2 ChIP-Seq

description: Chromatin IP against Pol II

data_processing: Sequencing reads were acquired through the primary Solexa image analysis pipeline, where bases were called and reads were filtered for quality, according to default Solexa standards. Filtered reads were then aligned to the fly genome (UCSC dm3) using the Bowtie (10) alignment tool, version 0.12.7. Only those sequences that matched uniquely to the genome with up to two mismatches were retained for subsequent analysis.Enriched regions of ChIP-seq signal were determined by the âMACSâ (11) peak-finding program, version 1.4.0rc2. Sequence reads for each ChIP-seq dataset and their associated whole-cell extract controls were used for the input and control file, respectively. The effective genome size was configured appropriately for the fly datasets, and the p-value cutoff was set to 1.00e-05 and a fold-change greater than five, or FDR < 1%. All other MACS parameters were left default.

value: S2; Schneider's Drosophila Line 2;  Marco Blanchette's Lab

value: in house DrosophilaÂ Rpb1Â antibody was raised inÂ rabbitsÂ against the synthetic peptide ERLMKKVFTDDVIKEMTDSG(C) conjugated via cysteine to KLH


title: smRNA-seq in C24, biological replicate 3

data_processing:
C24_3.bowtie; genome build: TAIR8
First, a custom Perl script was performed to remove the 3’ adapter sequences.  Next, we compared the trimmed sRNA reads with the NCBI plant tRNA and rRNA databases to remove potentially degraded rRNA and tRNA products from our datasets.  We then mapped the remaining trimmed reads to the Arabidopsis genome using Bowtie (Langmead et al., 2009), only accepting perfect matches.  After mapping, only reads mapped to unique loci were counted for subsequent analyses.


title: smRNA-seq in Ler, biological replicate 2

data_processing:
Ler_2.bowtie; genome build: TAIR8
First, a custom Perl script was performed to remove the 3’ adapter sequences.  Next, we compared the trimmed sRNA reads with the NCBI plant tRNA and rRNA databases to remove potentially degraded rRNA and tRNA products from our datasets.  We then mapped the remaining trimmed reads to the Arabidopsis genome using Bowtie (Langmead et al., 2009), only accepting perfect matches.  After mapping, only reads mapped to unique loci were counted for subsequent analyses.


title: smRNA-seq in Ler, biological replicate 1

data_processing:
Ler_1.bowtie; genome build: TAIR8
First, a custom Perl script was performed to remove the 3’ adapter sequences.  Next, we compared the trimmed sRNA reads with the NCBI plant tRNA and rRNA databases to remove potentially degraded rRNA and tRNA products from our datasets.  We then mapped the remaining trimmed reads to the Arabidopsis genome using Bowtie (Langmead et al., 2009), only accepting perfect matches.  After mapping, only reads mapped to unique loci were counted for subsequent analyses.


title: mRNA-seq in fcl, technical replicate 2

data_processing:
fcl_2.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.

extract_protocol: Total RNAs were isolated from 15-d-old seedlings using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions and were treated with RNase-free DNase I (Promega) to remove contaminating genomic DNA.  Messenger RNAs were extracted from the total RNAs using Dynabeads oligo(dT) (Invitrogen Dynal) following the manufacturer’s instructions.  First- and second-strand cDNAs were generated using SuperScript II reverse transcriptase (Invitrogen) and random hexamer primers.  Double-stranded cDNAs were fragmented by nebulization and used for mRNA library construction following the standard Illumina protocol.


title: Bisulfite-seq in C24, biological replicate 3

data_processing:
C24_3.mapview; genome build: TAIR10
We selected multiple base read lengths during sequencing runs and observed that quality decreased rapidly upon sequencing longer reads. We therefore adopted a strategy combining MAQ v0.6.6 (Li et al., 2008) and custom Perl scripts to process mapped sequences. We ran MAQ using the “maq map –M c” option, allowing up to two mismatches per read.  We mapped less than 42-base reads as described above.  For longer-base reads, we added a step to insure that low-quality read tails would not influence mapping results.  We divided the these reads into the first 40 bases and others.  Each half of the reads was aligned independently using MAQ, allowing up to two mismatches.  The coordinates of the two halves were then checked with a Perl script and the second half was discarded if it did not match the first. After mapping, numbers of reads mapped to unique loci and of reads mapped to multiple loci were counted and then run separately in subsequent analyses.


title: mRNA-seq in flc, technical replicate 3

data_processing:
flc_3.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.


title: mRNA-seq in flc, technical replicate 4

data_processing:
flc_4.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.


title: mRNA-seq in flc, technical replicate 2

data_processing:
flc_2.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.


title: mRNA-seq in fcl, technical replicate 1

data_processing:
fcl_1.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.


title: mRNA-seq in C24, technical replicate 4

data_processing:
C24_4.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.


title: mRNA-seq in C24, technical replicate 3

data_processing:
C24_3.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.


title: mRNA-seq in C24, technical replicate 2

data_processing:
C24_2.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.


title: mRNA-seq in Ler, technical replicate 1

data_processing:
Ler_1.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.


title: mRNA-seq in flc, technical replicate 1

data_processing:
flc_1.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.


title: smRNA-seq in flc, biological replicate 3

data_processing:
flc_3.bowtie; genome build: TAIR8
First, a custom Perl script was performed to remove the 3’ adapter sequences.  Next, we compared the trimmed sRNA reads with the NCBI plant tRNA and rRNA databases to remove potentially degraded rRNA and tRNA products from our datasets.  We then mapped the remaining trimmed reads to the Arabidopsis genome using Bowtie (Langmead et al., 2009), only accepting perfect matches.  After mapping, only reads mapped to unique loci were counted for subsequent analyses.


title: mRNA-seq in fcl, technical replicate 4

data_processing:
fcl_4.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.


title: mRNA-seq in C24, technical replicate 1

data_processing:
C24_1.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.


title: mRNA-seq in Ler, technical replicate 4

data_processing:
Ler_4.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.


title: mRNA-seq in fcl, technical replicate 3

data_processing:
fcl_3.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.


title: smRNA-seq in C24, biological replicate 2

data_processing:
C24_2.bowtie; genome build: TAIR8
First, a custom Perl script was performed to remove the 3’ adapter sequences.  Next, we compared the trimmed sRNA reads with the NCBI plant tRNA and rRNA databases to remove potentially degraded rRNA and tRNA products from our datasets.  We then mapped the remaining trimmed reads to the Arabidopsis genome using Bowtie (Langmead et al., 2009), only accepting perfect matches.  After mapping, only reads mapped to unique loci were counted for subsequent analyses.


title: mRNA-seq in Ler, technical replicate 3

data_processing:
Ler_3.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.


title: smRNA-seq in fcl, biological replicate 2

data_processing:
fcl_2.bowtie; genome build: TAIR8
First, a custom Perl script was performed to remove the 3’ adapter sequences.  Next, we compared the trimmed sRNA reads with the NCBI plant tRNA and rRNA databases to remove potentially degraded rRNA and tRNA products from our datasets.  We then mapped the remaining trimmed reads to the Arabidopsis genome using Bowtie (Langmead et al., 2009), only accepting perfect matches.  After mapping, only reads mapped to unique loci were counted for subsequent analyses.


title: Early Maturation-stage Seed Coat Parenchyma compartment

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Seed lengths ~ 5.2 – 8.0 mm

data_processing:
Raw: Original unprocessed and unfiltered data file from the Illumina sequencing pipeline.  Each lane of sequencing is attached as an individual compressed file.  The sequence data are in the QSEQ format.
Count: Raw sequence reads were processed and filtered sequentially.  First, reads were trimmed to remove adapter sequences.  Sequences with length between 18 to 24 nucleotides after trimming were kept for further analysis.  Second, trimmed reads were mapped against  a reference containing soybean ribosomal RNA (rRNA) and transfer RNA (tRNA) using Bowtie [Langmead et al., Genome Research, (2009)] allowing for two mismatches.  Sequences that did not map were kept and processed further.  Third, the remaining filtered reads were mapped against the soybean reference genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net) using Bowtie allowing for two mismatches.  Sequences mapping exclusively to gene regions were removed.  The remaining sequences were collapsed and counted.  The final count for each unique remaining filtered sequence are reported in a text format.

organism: Glycine max

source_name: Laser captured seed coat parenchyma compartment from early maturation stage seed

growth_protocol: Soybean plants (Asgrow A3237) were grown under standard greenhouse conditions (Le et al., 2010). Seed stage was characterized by seed length as follows: early maturation stage (5.2-8 mm). For early maturation seed coat parenchyma compartment, seeds with length between 5.2 and 8.0 mm containing early maturation-stage embryos were harvested

extract_protocol: Harvested seeds were divided into two pools: one pool for whole seed enriched small RNA isolation and the other pool for laser-capture microdissection.  Enriched small RNA from whole seed was isolated using mirVANA miRNA isolation kit (Ambion/Invitrogen, Grand Island, NY). Seeds for laser capture microdissection were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al., Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from ten-micron sections using a Leica LMD6000.  Total RNA from captured compartment was extracted using the RNAqueous-Micro Kit (Ambion/Invitrogen, Grand Island, NY).  Then small RNA was enriched from total RNA using the mirVANA miRNA isolation kit (Ambion/Invitrogen, Grand Island, NY). Sequencing libraries were prepared using 50 nanograms of enriched small RNA following the Illumina Small RNA Library Preparation v1.5 Protocol (Part # 15002615 Rev. C). Briefly, enriched small RNA was ligated with 3’ and 5’ RNA adapter using T4 RNA ligase. Adapter-ligated small RNA was converted to complementary DNA (cDNA)  and amplified by PCR for 12 and 20 cycles. Amplified cDNA was size selected on an agarose gel for the desired size of ~ 100 bp. Quantification of purified size-selected cDNA libraries was carried out using a Nanodrop ND-3300 Fluoro-spectrophotometer (Thermo Scientific, Waltham, MA). Single-end 76-bp reads were generated for each library by the UCLA Genome Sequencing Center (http://gsc.ucla.edu/) using an Illumina Genome Analyzer IIx.

tag: cultivar

value: Asgrow A3237


title: mES ELL RNAi RNA-Seq

description: RNAseq after ELL-RNAi in mES cells

library_source: non-genomic

data_processing: RNA-seq analysis was done using TopHat v1.2.0 (Trapnell et al., 2009) and Bowtie v0.12.7. Only uniquely mapping reads were used.

organism: Mus musculus

source_name: V6.5 mES

growth_protocol: Mouse ES cells (V6.5) wre cultured under mouse ES complete medium on irradiated mouse embryonic fibroblasts (MEFs).

extract_protocol: Libraries were prepared with the Illumina DNA Sample Kit (Part# 0801-0303) according to Illumina's instructions and sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

treatment_protocol: RNAi in mouse ESCs (V6.5) was performed for 3 days by infecting cells with concentrated lentiviral particles with polybrene at a concentration of 4 mg/ml. ESCs were grown one passage off of feeder cells before harvesting.

value: C57BL/6 (female)  x 129/S (male)

tag: passage

value: passage 10-18


title: mES control RNAi RNA-Seq rep2

description: RNAseq after non-targetting-RNAi in mES cells; replicate 2


title: mES control RNAi RNA-Seq rep1

description: RNAseq after non-targetting-RNAi in mES cells; replicate 1


title: mES input ChIP-Seq

description: WCE Chromatin IP

data_processing: Sequencing reads were acquired through the primary Solexa image analysis pipeline, where bases were called and reads were filtered for quality, according to default Solexa standards. Filtered reads were then aligned to the fly genome (UCSC dm3) using the Bowtie (10) alignment tool, version 0.12.7. Only those sequences that matched uniquely to the genome with up to two mismatches were retained for subsequent analysis

source_name: KH2 mES

growth_protocol: Mouse embryonic stem cells (KH2) were cultured under feeder-free medium ESGRO (Millipore).

extract_protocol: The ChIP Libraries were prepared with the Illumina DNA Sample Kit (Part# 0801-0303) according to Illumina's instructions and sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

treatment_protocol: Chromatin immunoprecipitation (ChIP) was performed according to previously described protocols (Wang et al. 2009 [MCB]).  Briefly,  ES cells were cross-linked by 1% formaldehyde and sonicated. 10 ug of antibodies were used in the ChIP assays.

value: input


title: mES ELL ChIP-Seq

description: Chromatin IP against ELL

value: custom ELL, see Lin et al. 2010 (Mol. Cell)


title: Breast milk exosomes rep4

status: Public on Dec 21 2011

city: Ya'an

first: Mingzhou

last: Li

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

data_processing: The reads that passed through a series of additional filters are called mappable reads which are sequences satisfy the following criteria from the statistics of mammalian miRNAs in miRBbase 17.0: (1) not sequencing adapters; (2) containing no more than 80% A, C, G, or T; (3) containing no more than two N (undermined bases); (4) containing not only A and C or G and T, (5) containing no stretches of A7, C8, G6, or T7; (6) being longer than 14 nt and shorter than 27 nt; (7) not containing more than nine repeats of any dimer, more than five repeats of any trimer, or more than four repeats of any tetramer; (8) been observed more than two times; and (9) not originating from porcine known classes of RNAs (i.e., mRNA in NCBI database; rRNA, tRNA, snRNA and snoRNA in Rfam database; and repetitive sequence elements in Repbase database). All identical reads were counted and combined into one kind. The mappable readsthen were mapped to the 1,424 human pre-miRNAs registered in miRBase 17.0.

organism: Homo sapiens

source_name: Breast milk exosomes

extract_protocol: Human breast milk samples (20-50 ml) were separately collected from four healthy women (30 +/-0.9 years old, primiparity) when the infant were aged at 60 days using a manual breast pump in sterile tubes. The exosomes in the breast milk are enriched using ExoQuick Exosome Precipitation Solution (SBI, CA, USA) following manufacturer's instruction. Total RNA of exosomes was extracted using TRIzol-LS (Invitrogen, CA, USA) following manufacturer's instruction. Small RNAs were analyzed with the Agilent Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA). The small RNA fraction between 10-40 nt was isolated by polyacrylamide gel electrophoresis (PAGE) and ligated with proprietary adaptors (Illumina). The short RNAs were then converted to cDNA by RT-PCR and each small RNA library was sequenced individually using Illumina Genome Analyzer II according to manufacturer instructions.

tag: sample type

value: Breast milk exosomes

tag: gender

value: female

value: Healthy women (30 +/-0.9 years old, primiparity) when the infant were aged at 60 days


title: Breast milk exosomes rep3


title: macrophage_Bcl6_ChIPSeq replicate

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description: Chromatin IP against Bcl6

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (July, 2007) mm9 genome using Eland. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Peaks: Peak detection was performed with the HOMER software suite (http://biowhat.ucsd.edu/homer/).

source_name: wild-type primary bone marrow-derived macrophages

growth_protocol: Bone marrow was purified and differentiated in DMEM containing 20% fetal bovine serum, 30% L929 conditioned media, and antibiotics for 5 days, then re-plated in macrophage serum free media (Invitrogen) overnight.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the ChIP seq sample prep kit (IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200-400 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 following the manufacturer's protocols.

treatment_protocol: Cells were fixed with 2 mM disuccinimidyl glutarate for 30 minutes, then with 1% formaldehyde for 10 minutes, then glycine-quenched and harvested.

tag: treatment

value: unstimulated macrophages

tag: chip antibody

value: primary bone marrow-derived macrophages

tag: donor age

value: 10 month old male


title: Breast milk exosomes rep1


title: mRNA-seq in Ler, technical replicate 2

data_processing:
Ler_2.chromosomes.mapview; genome build: TAIR10
For each of the 3 technical replicates, all 35-base reads were aligned to both Arabidopsis genomic and cDNA scaffolds using MAQ, allowing up to two mismatches.  After normalizing the numbers of mapped reads in different samples to the same level, a score was assigned to each cDNA model as the number of mapped reads per 1000 bp of sequence.

value: seedlings


title: Early Maturation Stage Whole Seed

description: Seed lengths ~ 5.2 – 8.0 mm

source_name: Soybean seeds containing early maturation stage embryos


title: Berlin_C1674_F1_hybrid_heads_R3

city: Gainesville

first: Martin

last: McCrory

state: FL

address: 2033 Mowry Road

institute: University of Florida

data_processing:
rna_3_updated_compare.csv; genome build: Custom Strain Specific References
Hybrid RNA and DNA reads were mapped to each of two custom strain specific references for exonic regions only (details can be found in Graze et al. 2012 and references are available at http://bioinformatics.ufl.edu/McIntyre_Lab/Interspecific_AI). Reads were categorized based on how well they mapped to each fusion, and each category was counted on a per-fusion basis and output in csv format.     Reads had leading and trailing Ns stripped before alignment. This can result in "orphaned" reads -- reads that were initially paired but whose mate has been filtered out because of high N content (i.e. the length after N trimming is less than 25bp). Orphans were stripped out and each lane was aligned with paired and then unpaired reads with the following  Bowtie flags: --solexa1.3-quals --tryhard --chunkmbs 256 -m 1 --best --strata --sam. Reads that were unaligned or ambiguous in the paired alignment were given a second chance to align in the unpaired alignment, along with reads that were orphaned in the N-trimming step.     The two resulting .sam files are stripped of unaligned reads and merged. A counts table was created with a custum script  (sam-compare custom.pl available at http://bioinformatics.ufl.edu/McIntyre_Lab/Interspecific_AI). The script assigns reads to alleles and outputs a counts table for each each exon region with read counts for each allele split into categories based on the quality of the alignment to each of the two references.

organism: Drosophila melanogaster x Drosophila simulans

source_name: RNA from interspecific hybrid heads

growth_protocol: Flies were reared in incubators (25°C, 12:12 hour light/dark cycle) on banana medium with added yeast paste. A high male to female ratio of 20 D. melanogaster females to 60 D. simulans males was used to overcome behavioral isolation. Flies were housed in vials to provide high density mating conditions for three days and then transferred to bottles. Females were collected as virgins (under CO2) and aged 1-1.5 days before snap freezing in liquid nitrogen (without anesthesia). All flies were frozen from 4:00-6:30 PM on consecutive days. Progeny from two bottles (100 flies each) were pooled (200 individuals) to create one replicate for head collections and RNA extractions.  This process was repeated three times for three independent replicates. Heads were separated from bodies using a series of differentially sized mesh sieves (Graze et al. 2009) and stored at -80°C prior to nucleic acid extraction.  DNA was extracted from a single pool of 20 individuals (adult bodies).

extract_protocol:
Nucleic acid extractions: For each RNA extraction, heads were homogenized in 1 ml of Trizol (Invitrogen) and isolations done according to manufacturer’s protocol. RNA was purified from total RNA using oligo dT Dynabeads (Invitrogen). In brief, 200 μl of Dynabeads were washed and resuspended into 200 μl of 2X binding buffer.  mRNA (75 μg total RNA in 100 μl DEPC H2O) was diluted with 100 μl binding buffer and was heated at 65°C for 2 minutes and then placed on ice immediately. The RNA was then added to 100 μl (1mg) Dynabeads and incubated at RT for 30 minutes. The solution was mixed and annealed by pipetting every 5 minutes during this incubation period. The protocol was then completed following manufacturer’s instructions (using option 9.B.). gDNA was extracted from the control sample using the MasterPure DNA purification kit (Epicentre), with the following exceptions. Frozen flies were homogenized in cell lysis solution after addition of Proteinase K (Qiagen).  The homogenate was incubated at 55°C for 30 minutes.  After the homogenate was cooled to room temperature, proteins were precipitated following the manufacturer’s protocol. The supernatant was retained and the Genomic DNA Clean and Concentrator kit (Zymo Research) was used to isolate only high molecular weight DNA, following the manufacturer’s protocol.  RNA and DNA concentrations were quantified by Qubit (Invitrogen). Library construction: For each RNA sample, 100 ng of purified mRNA was fragmented using RNA fragmentation reagents (Ambion) and concentrated to 10 μl (DEPC H2O) using an RNA concentrator kit (Zymo Research). First and second strand cDNA syntheses were carried out using Random Hexamer Primers (3μg/ μl, Invitrogen) following a standard protocol.  Double-stranded cDNA was then purified and concentrated to 10 μl (Zymo Research DNA Concentrator kit). Library construction was completed using reagents from the Epicentre End-IT Repair kit, Fast-Link DNA Ligation Kit (Epicenter) and Illumina Genomic DNA Sample Prep Kit (part # 1000181). A clean-up and concentration step (10 μl, DEPC H2O) was repeated following each step in library preparation (Zymo Research DNA Concentrator kit). In brief, samples were processed to produce 5´-phosphorylated, blunt-ended DNA using the End-It DNA End-Repair kit.  3’ A overhangs were added by treatment with Klenow Fragment (3´→5´ exo–; NEB) and dATP (50 μl rxn, 37°C, 30 minutes).  Illumina genomic DNA adaptors (1 μl adaptor oligo mix 10 mM) were then ligated to cDNA fragments using the Fast-Link DNA Ligation kit and processed cDNA was size selected (200-500 bp) by gel purification. Cleaned, concentrated, size selected templates were enriched for adaptor modified cDNA by PCR following the Illumina Genomic DNA Sample Prep protocol. For each gDNA sample, approximately 1 μg of gDNA was fragmented with a standard probe sonicator (Duty Cycle 80%, Output 2, sets of 20 pulses for 5 rounds), placing DNA on ice between rounds of sonication. Fragmented gDNA was concentrated using the Zymo Research DNA Concentrator kit (10 μl) and library construction was completed as described for cDNA libraries (2 μl adaptor oligo mix was used for gDNA samples).
RNA and DNA derived libraries were quantified by Qubit. cDNA libraries were sequenced on 3 lanes (1 lane per biological replicate) with 54 bp paired end chemistry with the Illumina technology. The gDNA library was sequenced on 3 lanes using 36 bp paired end chemistry.

value: Berlin (BDSC 8522) and C167.4 (BDSC 4736)

value: heads

tag: replicate


title: Brugia pahangi L3

status: Public on Dec 20 2011

city: Glasgow

first: Alan

middle: Derek

last: Winter

address: Garscube Estate, Bearsden Road

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

description: Aedes aegypti mosquitoes (refm strain) were infected with B. pahangi by membrane feeding on rabbit blood containing first stage larvae (microfilariae). L3 were isolated from mosquitoes after 10 days at 27°C.

data_processing:
3978_3_WA_unique.txt; genome build: Ghedin et al Science 2007, 317:1756-1760. File "Brugia_assembly.ghedin.fasta" from "ftp://ftp.sanger.ac.uk/pub/pathogens/Brugia/malayi/REF".
Processed files were produced from the raw data by trimming reads of adapter sequence, identifying identical reads and converting these to unique sequences with associated read counts, mapping sequences to the genome and retaining only those with perfect alignment.

organism: Brugia pahangi

source_name: Whole organism

extract_protocol: Total RNA was extracted with Trizol (Invitrogen) and small RNA libraries were prepared using an Illumina Small RNA Sample Prep kit and the Alternative v1.5 Protocol.

value: Strain derived from the original isolate reported by Buckley and Edeson, 1956.

value: Larval stage 3


title: Berlin_C1674_F1_hybrid_heads_R1

data_processing:
rna_1_updated_compare.csv; genome build: Custom Strain Specific References
Hybrid RNA and DNA reads were mapped to each of two custom strain specific references for exonic regions only (details can be found in Graze et al. 2012 and references are available at http://bioinformatics.ufl.edu/McIntyre_Lab/Interspecific_AI). Reads were categorized based on how well they mapped to each fusion, and each category was counted on a per-fusion basis and output in csv format.     Reads had leading and trailing Ns stripped before alignment. This can result in "orphaned" reads -- reads that were initially paired but whose mate has been filtered out because of high N content (i.e. the length after N trimming is less than 25bp). Orphans were stripped out and each lane was aligned with paired and then unpaired reads with the following  Bowtie flags: --solexa1.3-quals --tryhard --chunkmbs 256 -m 1 --best --strata --sam. Reads that were unaligned or ambiguous in the paired alignment were given a second chance to align in the unpaired alignment, along with reads that were orphaned in the N-trimming step.     The two resulting .sam files are stripped of unaligned reads and merged. A counts table was created with a custum script  (sam-compare custom.pl available at http://bioinformatics.ufl.edu/McIntyre_Lab/Interspecific_AI). The script assigns reads to alleles and outputs a counts table for each each exon region with read counts for each allele split into categories based on the quality of the alignment to each of the two references.


title: Berlin_C1674_F1_hybrid_heads_R2

data_processing:
rna_2_updated_compare.csv; genome build: Custom Strain Specific References
Hybrid RNA and DNA reads were mapped to each of two custom strain specific references for exonic regions only (details can be found in Graze et al. 2012 and references are available at http://bioinformatics.ufl.edu/McIntyre_Lab/Interspecific_AI). Reads were categorized based on how well they mapped to each fusion, and each category was counted on a per-fusion basis and output in csv format.     Reads had leading and trailing Ns stripped before alignment. This can result in "orphaned" reads -- reads that were initially paired but whose mate has been filtered out because of high N content (i.e. the length after N trimming is less than 25bp). Orphans were stripped out and each lane was aligned with paired and then unpaired reads with the following  Bowtie flags: --solexa1.3-quals --tryhard --chunkmbs 256 -m 1 --best --strata --sam. Reads that were unaligned or ambiguous in the paired alignment were given a second chance to align in the unpaired alignment, along with reads that were orphaned in the N-trimming step.     The two resulting .sam files are stripped of unaligned reads and merged. A counts table was created with a custum script  (sam-compare custom.pl available at http://bioinformatics.ufl.edu/McIntyre_Lab/Interspecific_AI). The script assigns reads to alleles and outputs a counts table for each each exon region with read counts for each allele split into categories based on the quality of the alignment to each of the two references.


title: Brugia pahangi adult

description: L3 were used to infect the laboratory host, the jird (Meriones unguiculatus) and mixed sex adult B. pahangi worms were isolated after 3-4 months.

data_processing:
3984_3_WA_unique.txt; genome build: Ghedin et al Science 2007, 317:1756-1760. File "Brugia_assembly.ghedin.fasta" from "ftp://ftp.sanger.ac.uk/pub/pathogens/Brugia/malayi/REF".
Processed files were produced from the raw data by trimming reads of adapter sequence, identifying identical reads and converting these to unique sequences with associated read counts, mapping sequences to the genome and retaining only those with perfect alignment.

value: Mixed sex adult


title: Caulonema

city: Beijing

first: Lihong

last: Xiao

address: No.105 North Road of West 3rd-ring Road.Haidian District

institute: Capital Normal University

data_processing: Adaptor tags, low quality tags and tags of copy number=1 were filtered,then the distinct clean tags were aligned to the reference P.patens database by bowtie.

organism: Physcomitrium patens

source_name: Caulonema

growth_protocol: samples taken from P. patens protonema at 3, 14 and 24 days, and also from or leafy shoot tissues l at 30 days after protoplastes isolated, and from 14-day-old caulonemal and chloronemal tissues.

extract_protocol: RNA extracted from P. patens protonema at 3, 14 and 24 days, and also from or leafy shoot tissues l at 30 days after protoplastes isolated, and from 14-day-old caulonemal and chloronemal tissues.

value: protonema

value: Caulonema


title: 30d

value: leafy shoot


title: Haemonchus contortus L3

description: Ensheathed L3 stage larvae were harvested from faecal cultures.

data_processing:
3984_1_WA_unique.txt; genome build: File "combined_worms_supercontigs200808.fasta" from ftp://ftp.sanger.ac.uk/pub/pathogens/Haemonchus/contortus/genome/contigs.
Processed files were produced from the raw data by trimming reads of adapter sequence, identifying identical reads and converting these to unique sequences with associated read counts, mapping sequences to the genome and retaining only those with perfect alignment.

organism: Haemonchus contortus


title: 24d


title: Cyt mRNA

city: Durham

first: David

last: Reid

state: NC

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

institute: Duke University

description: total RNA

data_processing: Mapped to Refseq genes using Bowtie; mRNAs >10 RPKM were considered.

growth_protocol: Clutured in DMEM + 10% FBS at 37C, 5% CO2

extract_protocol: Ribosome footprints were generated by nuclease treatment of polyribosomes. The mRNA footprints were purified by centrifugation. In parallel, mRNAs were enriched by treatment of total RNA with RiboMinus, then treated with Rnase III. Each library was generated according to standard SOLiD library preparation. Briefly, primers were ligated onto RNAs and then cDNA was generated by reverse transcription. cDNA was purified by gel electrophoresis, amplified, then emusified to beads and sequenced.

treatment_protocol: Detergent fractionation of cytosol and ER

tag: cell line

tag: sample fraction

value: Purified cytoplasm


title: Chloronema

source_name: Chloronema

tag: tissue

tag: developmental stage

value: Chloronema


title: 14d


title: ER footprints

description: small RNA

value: Purified endoplasmic reticulum


title: Cyt footprints

description: small RNA


title: MeDIP-Seq-1

city: Delhi

first: Shantanu

middle: Sen

last: Gupta

state: New Delhi

address: Mall Road, Delhi University Campus

department: Genomics and Molecular Medicine Unit

country: India

institute: Institute of Genomics & Integrative Biology

description: DNA IP against anti-5-methylcytidine

data_processing: Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) [Processed data not provided]

organism: Rattus norvegicus

extract_protocol: DNA was fragmented and single read adaptors were ligated to them. Followed by immunoprecipitation, library PCR with adaptor specific primers and the  sequenced in Illumina GAIIx.

treatment_protocol: Control

value: WNIN

tag: age

value: Adult

value: liver

tag: antibody

tag: antibody vendor

value: Eurogentec

tag: antibody cat.number

tag: antibody batch number


title: ER mRNA

description: total RNA


title: IgG_control

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description: negative control ChIP

data_processing:
***fastq*** Image analysis, base calling, quality filtering:  Standard settings of GAPipeline 1.3+ using PhiX control; Fastq files contain full length reads (36nts) that passed the chastity filter. If necessary, quality scales were adjusted to phred64.
***bam format alignment***  Illumina reads in fastq format were aligned against the mouse mm9 genome with bowtie 0.12.5 using parameters '--phred64-quals --chunkmbs 128 --all -m 1 --best --strata -l 36 -p8 --sam'. Sam files were converted to bam, unmapped reads were removed, and bam files were sorted with samtools 0.1.12.

source_name: B cells

growth_protocol: Resting splenic B cells were isolated from 6- to 8-week-old mice with anti-CD43 Microbeads (anti-Ly48; Miltenyi Biotech) and were cultured for 60 h with LPS (50 μg/ml; Sigma) and IL-4 (5 ng/ml; Sigma).

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37°C for 10 minutes followed by quenching with 0.125 M glycine (final concentration). Chromatin was sheared by sonication to a size of 200-500bp which was then precleared with 40 μl protein A or protein G magnetic beads, followed by incubation overnight at 4 °C in RIPA buffer (10 mM Tris, pH 7.6, 1 mM EDTA, 0.1% (wt/vol) SDS, 0.1% (wt/vol) sodium deoxycholate and 1% (vol/vol) Triton X-100). Beads were washed twice with RIPA buffer alone, then twice with RIPA buffer plus 0.3 M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% (vol/vol) Igepal CA630 and 0.5% (wt/vol) sodium deoxycholate), once with Tris-EDTA buffer (Tris 10 mM, pH 8.0, and 1 mM EDTA) plus 0.2% (vol/vol) Triton X-100, and once with Tris-EDTA buffer alone. ChIP DNA was extracted for 4 h at 65 °C in Tris-EDTA buffer with 0.3% (wt/vol) SDS and proteinase K (1 mg/ml) before processing with standard Illumina library preparation protocols.

tag: strain

tag: cell type

value: B cells

tag: chip target

value: Mixture of various non-specific antibodies


title: 3d


title: MeDIP-Seq-2

description: DNA IP against anti-5-methylcytidine


title: ActivatedBCell_AID_rep2

description: AID ChIP from in vitro activated B cells with a second antibody.  Cells were isolated from a mouse strain expressing an AID-GFP fusion protein in addition to normal AID as a transgene under the native AID promoter control.

source_name: Activated B cells

growth_protocol:
CD43- resting B cells were isolated from mouse spleens by negative selection with magnetic beads (Miltenyi Biotech).  Following isolation, resting B cells were stimulated with LPS (50 mcg/ml) and IL-4 (2.5 ng/ml) for 72 hrs.
Resting splenic B cells were isolated from 6- to 8-week-old mice with anti-CD43 Microbeads (anti-Ly48; Miltenyi Biotech) and were cultured for 60 h with LPS (50 μg/ml; Sigma) and IL-4 (5 ng/ml; Sigma).

value: C57BL/6 AID-GFP

value: in vitro activated B cells

value: AID

value: Santa Cruz rabbit polyclonal anti-AID antibody (Catalog No. sc-25620)


title: DGE_TALL_4

city: Uppsala

first: Jessica

last: Nordlund

address: Academic Hospital, Entrance 70, 3rd floor

department: Medical Sciences

country: Sweden

institute: Uppsala University

data_processing: Image analysis and base calling were performed with Illumina pipeline v1.4. The processed data (see data table below and supplementary file on the Series record) contains the trimmed, quality filtered, unique 17bp reads (column 1) and the frequency of each tag in transcripts per million (TPM) for each sample. Custom perl scripts were used to generate the processed data file.

source_name: Peripheral blood

extract_protocol: DGE-Tag Profiling NlaIII sample prep kit from Illumina

tag: disease state

value: acute lymphoblastic leukemia (ALL)

tag: all lineage

value: T-cell lineage ALL (T-ALL)

value: Peripheral blood


title: DGE_TALL_1

source_name: Bone marrow

value: Bone marrow


title: DGE_TALL_2


title: DGE_TALL_3


title: Breast milk exosomes rep2

tag: sample type

value: Breast milk exosomes

tag: gender

value: female

value: Healthy women (30 +/-0.9 years old, primiparity) when the infant were aged at 60 days


title: Haemonchus contortus adult

description: Mixed sex adult worms were collected at necropsy (day 28) from Suffolk lambs (5-9 months old) infected with 5,000 L3 larvae and maintained indoors to eliminate risk of other nematode infections.

data_processing:
3984_2_WA_unique.txt; genome build: File "combined_worms_supercontigs200808.fasta" from ftp://ftp.sanger.ac.uk/pub/pathogens/Haemonchus/contortus/genome/contigs.
Processed files were produced from the raw data by trimming reads of adapter sequence, identifying identical reads and converting these to unique sequences with associated read counts, mapping sequences to the genome and retaining only those with perfect alignment.

value: Mixed sex adult


title: DGE_t9-22_3

value: B-cell precursor (BCP) ALL

tag: bcp all subtype


title: DGE_t9-22_1


title: DGE_t9-22_2


title: DGE_t12-21_3


title: DGE_t12-21_2


title: DGE_t12-21_1


title: DGE_HeH_8

value: High Hyperploidy (HeH)


title: DGE_HeH_5


title: DGE_HeH_7


title: DGE_HeH_4


title: DGE_HeH_3


title: DGE_HeH_6


title: DGE_HeH_2b


title: DGE_HeH_2a


title: DGE_dic9-20_1


title: DGE_HeH_1


title: DGE_dic9-20_3


title: DGE_dic9-20_2


title: KO IgG

status: Public on Dec 19 2011

city: Berlin

first: Jonas

last: Maaskola

address: Robert-Roessle Str. 10

department: Systems Biology of Gene Regulatory Elements

country: Germany

institute: Max-Delbrueck Centrum Berlin-Buch

data_processing:
Alignment:Solexa reads were base called using the manufacturer's software SCS 2.5 / RTA 1.5. Subsequently, 3' ligation adapter sequences were identified and removed from the reads. Reads were clipped to 25 bases, and reads shorter than 17 bases were discarded. The remaining reads were mapped against the mouse genome (NCBI37/mm9) allowing up to edit distance 1 per read using a custom read mapping pipeline. Only reads mapping uniquely to the genome were considered. The mapped reads were reduced to non-redundant tag position sets.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).

source_name: MEF

growth_protocol: MEFs were cultured in DMEM (Dulbecco's modified Eagle's Medium) with 4.5 g/L glucose (Gibco) supplemented with 10% inactivated fetal calf serum (Gibco) and 1% penicillin/streptomycin (Gibco).

extract_protocol: 100 million WT or E2f3-/- cells were lyzed and 10µg of antibody or µg IgG used (I5006; Sigma). The DNA was purified with a MinElute PCR Purification column (Qiagen) and eluted in 11 µl. All reagents used were supplied with the Genomic Sample Prep Kits (Illumina). Blunt ends were created to repair the ends of the ChIP-DNA and the DNA was cleaned with the aid of a PCR purification column (Qiagen) according to the manufacturers suggestion. Again, DNA was purified with the MinElute PCR Purification column (Qiagen). Next, adapters (Sample Prep Kit) were ligated to the ChIP-DNA. The adapter-ligated ChIP-DNA was amplified using Kit-derived oligonucleotides (Sample Prep Kit) with a 22 cycles PCR-run. The size selection of the chip library was attained by separation on a 2%-Agarose gel. The PCR amplified DNA between 200-300 bp was cut out and cleaned with the help of a MinElute gel extraction kit (Qiagen). The size distribution and quantity of the DNA was analyzed through a Bioanalyzer chip (Agilent) before the DNA was used for cluster generation. Single-end sequencing of 36 nucleotides was performed using a Genome Analyzer IIx.

tag: genotype/variation

value: mouse embryonic fibroblasts (MEF)

tag: chip antibody

value: IgG


title: KO HELLS

value: HELLS


title: KO H3K27me3


title: WT H3K27me3

value: wild type


title: WT HELLS


title: IgG_control

status: Public on Dec 18 2011

city: Boston

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: Chromatin IP against IgG

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 (July 2007) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: liver tissue

growth_protocol: Male and female CD-1 mice (Charles River Laboratories), 7-8 weeks old, were killed and their livers extracted.

extract_protocol: Multiplexed samples were prepared for Illumina sequencing using standard Illumina methods.

treatment_protocol: Mouse livers were excised from individual male and female mice killed at either a peak of STAT5 binding activity, or during the interpulse interval, when STAT5 activity is either low (females) or essentially undetectable (males).  Sonicated, cross-linked liver nuclear chromatin was then used to identify STAT5 binding sites by ChIP-Seq.

tag: Sex

value: male

value: 7-8 weeks old

value: normal rabbit IgG

tag: chip antibody vendor

value: Santa Cruz Biotechnology, Inc

tag: chip antibody cat./batch #


title: F_Bcl6_ChIPSeq_rep2_G65-M1

description: Chromatin IP against Bcl-6

tag: age

value: Bcl6 antibody N-3


title: F_Bcl6_ChIPSeq_rep4_G65-M3

description: Chromatin IP against Bcl-6


title: F_Bcl6_ChIPSeq_rep3_G65-M2

description: Chromatin IP against Bcl-6


title: KO E2F3

tag: developmental stage


title: M_Bcl6_ChIPSeq_rep2_G50

description: Chromatin IP against Bcl-6


title: M_Bcl6_ChIPSeq_rep1_G49

description: Chromatin IP against Bcl-6


title: M_Bcl6_ChIPSeq_rep3_G71-M2

description: Chromatin IP against Bcl-6


title: F_Bcl6_ChIPSeq_rep1_G51

description: Chromatin IP against Bcl-6


title: FH_STAT5_ChIPSeq_rep3_G66-M3

description: Chromatin IP against STAT5

value: STAT5 antibody C-17


title: ML_STAT5_ChIPSeq_rep1_G35

description: Chromatin IP against STAT5


title: ML_STAT5_ChIPSeq_rep2_G40

description: Chromatin IP against STAT5


title: FL_STAT5_ChIPSeq_rep1_G52

description: Chromatin IP against STAT5


title: FH_STAT5_ChIPSeq_rep1_G66-M1

description: Chromatin IP against STAT5


title: WT IgG


title: FL_STAT5_ChIPSeq_rep2_G70-M3

description: Chromatin IP against STAT5


title: MH_STAT5_ChIPSeq_rep1_G36

description: Chromatin IP against STAT5


title: TN_DMSO_JNK13 [ChIP-Seq]

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing: 2007 M. musculus genome assembly (mm9) was used as a basis for all analyses. Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.

source_name: Terminally differentiated neurons (TN)

growth_protocol: Wild-type embryonic stem cells (129Sv-C57Bl/6) were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007))

extract_protocol: ChIP experiments were performed as described before (F. Mohn et al., Mol Cell 30, 755 (Jun 20, 2008)), starting with 70 Âµg of chromatin and 5 Âµg of the JNK1.3 antibody (proprietary) was used. The ChIP libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illuminaâs instructions and sequenced on the Genome Analyzer 2 following the manufacturerâs protocols. ChIP-real time PCR was performed using SYBR Green chemistry (ABI) and 1/40 of ChIP or 1:100 diluted Input DNA per PCR reaction. Primers sequences are available upon request.

tag: treatment

value: DMSO (control)

value: Terminally differentiated Neurons (TN)


title: MH_STAT5_ChIPSeq_rep3_G42

description: Chromatin IP against STAT5


title: WT E2F3


title: TN_JNKi_JNK1/3 [ChIP-Seq]

value: JNKi


title: MH_STAT5_ChIPSeq_rep2_G41

description: Chromatin IP against STAT5


title: TN_PolII [ChIP-Seq]

source_name: Terminally differentiated Neurons (TN)

extract_protocol: ChIP experiments were performed as described before (F. Mohn et al., Mol Cell 30, 755 (Jun 20, 2008)), starting with 70 µg of chromatin and 5 µg of the following (proprietary) antibodies: anti-JNK1/3, anti-phospho-JNK, anti-NF-YA, anti-RNA Pol II, anti-H3K4me2, and anti-H3K27me3. The ChIP libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illumina’s instructions and sequenced on the Genome Analyzer 2 following the manufacturer’s protocols. ChIP-real time PCR was performed using SYBR Green chemistry (ABI) and 1/40 of ChIP or 1:100 diluted Input DNA per PCR reaction. Primers sequences are available upon request.

value: anti-RNA Pol II


title: NP_NFYA_biological_replicate_a [ChIP-Seq]

source_name: Neuronal Progenitor (NP) Cells

value: Neuronal Progenitors (NP)

value: anti-NFYA


title: TN_NFYA_biological_replicate_a [ChIP-Seq]


title: TN_H3K4me2 [ChIP-Seq]


title: TN_H3K27me3_technical_replicate_a1 [ChIP-Seq]


title: TN_JNK13_biological_replicate_a [ChIP-Seq]


title: NP_NFYA_biological_replicate_b [ChIP-Seq]


title: TN_H3K27me3_biological_replicate_b1 [ChIP-Seq]


title: NP_PolII [ChIP-Seq]


title: NP_JNK13_biological_replicate_a [ChIP-Seq]


title: FL_STAT5_ChIPSeq_rep3_G72-M1

description: Chromatin IP against STAT5

value: female


title: NP_JNK13_biological_replicate_b [ChIP-Seq]


title: TN_H3K27me3_technical _replicate_a2 [ChIP-Seq]


title: FH_STAT5_ChIPSeq_rep2_G66-M2

description: Chromatin IP against STAT5


title: NP_H3K4me2 [ChIP-Seq]


title: NP_H3K27me3_technical _replicate_a2 [ChIP-Seq]


title: NP_H3K27me3_technical_replicate_a1 [ChIP-Seq]


title: TN_NFYA_biological_replicate_b [ChIP-Seq]


title: NP_H3K27me3_biological_replicate_b1 [ChIP-Seq]


title: ES_PolII [ChIP-Seq]

source_name: Embryonic Stem Cells (ESCs)

value: Embryonic Stem Cells (ESCs)


title: ES_NFYA_biological_replicate_a [ChIP-Seq]


title: Input [ChIP-Seq]

description: Input

value: none (input)


title: TN_JNK13_biological_replicate_b [ChIP-Seq]


title: ES_JNK13_biological_replicate_a [ChIP-Seq]


title: ES_H3K27me3_technical _replicate_a2 [ChIP-Seq]


title: ES_H3K27me3_biological_replicate_b1 [ChIP-Seq]


title: ES_H3K27me3_technical_replicate_a1 [ChIP-Seq]


title: ES_JNK13_biological_replicate_b [ChIP-Seq]


title: ES_NFYA_biological_replicate_b [ChIP-Seq]


title: Arabidopsis thaliana leaf mRNA 24 hr after Botrytis cinerea infection Rep 1

city: Coventry

first: Nigel

middle: Paul

last: Dyer

address: Gibbet Hill Road

institute: University of Warwick

data_processing:
aligned_24hRep1_cdna.txt; genome build: TAIR10
aligned_24hRep1_repcdna.txt; genome build: TAIR10
For 24hRep2 Illumina Pipeline software Casava version 1.7.0 was used using default parameters. For 24hRep1 Illumina Pipeline software Casava version 1.5.1 was used using default parameters.
Alignment: The first 34 base-pairs of the paired end illumina sequences were aligned to the full TAIR10 cDNA sequence files using bowtie using -m 1 to reject non-unique mappings and the default -n 2 to allow up to two mismatches.  The sequences were first matched to the TAIR10 cDNA sequences TAIR10_cdna_20101214, and those that did not match were matched to the TAIR10_cdna_20110103_representative_gene_model cDNA sequences

source_name: Infected leaves

growth_protocol: Plants were grown under a 16:8 hr light:dark cycle at 20°C, 60% humidity and light intensity of 100 μmol photons.m-2.s-1. Arabidopsis seed was stratified for three days in 0.1% agar at 4°C before sowing onto Arabidopsis soil mix (Scotts Levingtons F2 compost:sand:fine grade vermiculite in a ratio of 6:1:1)

extract_protocol: Total RNA was extracted from 10 pooled infected Arabidopsis leaves using Invitrogen TRIzol reagent according to the manufacturer's procedure. The total RNA was purified using Qiagen RNeasy columns according to the manufacturer's procedure. Libraries were constructed using the Illumina mRNA-seq Library Prep Kit (Illumina part number RS-100-0801) according to the manufacturer’s procedure

treatment_protocol: Leaves from 4 week old plants were detached and infected with Botrytis cinerea as described in Denby et al. (2004) Plant Journal 38(3):473-86, with 5 droplets per leaf.

value: Columbia-0 wild type

tag: tissue

value: leaf

tag: infection

value: Botrytis cinerea


title: NP [RNA_Seq]

source_name: Neuronal Progenitors (NP)

growth_protocol: Wild-type embryonic stem cells (129Sv-C57Bl/6) were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007)) and differentiated to Neuronal  Progenitors and further to Terminally diffentiated Neurons (TN)

extract_protocol: RNA was isolated using RNeasy Mini Kit   (Invitrogen) following the manufacturer’s instructions. Libraries for sequencing were prepared with the Illumina mRNA-Seq 8-Sample Prep Kit (Cat# RS-100-0801) according to Illumina's instructions. After adapter ligation library fragments of ~250 bp were band isolated from an agarose gel. The cDNA was PCR amplified with Illumina primers for 15 cycles, purified and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

tag: strain

value: wild type

tag: cell type


title: ES [RNA_Seq]


title: Arabidopsis thaliana leaf mRNA 24 hr after Botrytis cinerea infection Rep 2

data_processing:
aligned_24hRep2_cdna.txt; genome build: TAIR10
aligned_24hRep2_repcdna.txt; genome build: TAIR10
For 24hRep2 Illumina Pipeline software Casava version 1.7.0 was used using default parameters. For 24hRep1 Illumina Pipeline software Casava version 1.5.1 was used using default parameters.
Alignment: The first 34 base-pairs of the paired end illumina sequences were aligned to the full TAIR10 cDNA sequence files using bowtie using -m 1 to reject non-unique mappings and the default -n 2 to allow up to two mismatches.  The sequences were first matched to the TAIR10 cDNA sequences TAIR10_cdna_20101214, and those that did not match were matched to the TAIR10_cdna_20110103_representative_gene_model cDNA sequences


title: WPP_INPUT_1

status: Public on Dec 16 2011

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

source_name: WPP

growth_protocol: 1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.

extract_protocol: After chromatin immuno-precipitation, the DNA is purified in 30ul of water.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 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 following the manufacturer's protocols.

treatment_protocol: No Treatment

value: iso1 (y; bw cn sp)

value: WPP


title: TN [RNA_Seq]


title: WPP_psq_INPUT_1


title: WPP_Stat92E_ChIPSeq_1 and 2

tag: antibody name

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: RIKEN_Cage_NHEK_cytosol_longPolyA

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

source_name: NHEK

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage

tag: datatype

value: Cage

tag: datatype description

value: CAGE 5' RNA Tags

tag: rnaextract

value: longPolyA

tag: rnaextract description

value: Poly(A)+ RNA longer than 200 nt

tag: biorep

tag: labexpid

tag: labversion

value: IDR

tag: replicate

tag: cell lineage

value: ectoderm

tag: cell sex

value: U

tag: localization

value: cytosol

tag: localization description

value: The fluid between the cells outer membrane and the nucleus

tag: replicate description

value: tier 3


title: RIKEN_Cage_K562_cell_longPolyA

value: mesoderm

value: F

value: cell

value: Whole cell

value: tier 1


title: WPP_psq_ChIPSeq_1 and 2

tag: strain

value: iso1 (y; bw cn sp)

tag: developmental stage

value: WPP

tag: antibody name

value: psq


title: en_INPUT_1


title: RIKEN_Cage_NHEK_cell_longPolyA

value: Cage

value: CAGE 5' RNA Tags


title: ES_H3K4me2 [ChIP-Seq]

tag: genotype/variation

value: wild type

tag: cell type

value: Embryonic Stem Cells (ESCs)

tag: chip antibody


title: RIKEN_Cage_SK-N-SH_RA_cell_longPolyA

tag: datatype

tag: datatype description

tag: rnaextract

value: longPolyA

value: Poly(A)+ RNA longer than 200 nt

value: IDR

value: ectoderm


title: RIKEN_Cage_MCF-7_cell_longPolyA

tag: rnaextract description

tag: biorep

tag: labexpid


title: RIKEN_Cage_NHEK_nucleus_longPolyA

tag: labversion

tag: readtype

tag: readtype description

value: Single 36 nt reads

tag: replicate

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA

value: tier 3


title: en_ChIPSeq_1

value: en

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: psq_ChIPSeq_1 and 2

tag: strain

tag: developmental stage

tag: antibody name


title: RIKEN_Cage_A549_cell_longPolyA

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: localization

value: cell

tag: localization description

value: Whole cell

tag: replicate description

value: tier 1


title: RIKEN_Cage_AG04450_cell_longPolyA

tag: datatype

value: Cage

tag: datatype description

value: CAGE 5' RNA Tags

tag: rnaextract

tag: rnaextract description

tag: biorep


title: RIKEN_Cage_H1-hESC_cell_longPolyA

growth_protocol: missing

tag: labexpid

tag: labversion

tag: replicate

value: inner cell mass


title: Kr_ChIPSeq_1 and 2

value: iso1 (y; bw cn sp)

value: Kr

tag: manufacturer

tag: lot/batch#

tag: catalog


title: Kc167_INPUT_1

tag: strain

tag: developmental stage


title: RIKEN_Cage_H1-hESC_cytosol_longPolyA

value: longPolyA

value: Poly(A)+ RNA longer than 200 nt

tag: readtype

tag: readtype description

tag: cell lineage

tag: cell sex

value: cytosol

value: The fluid between the cells outer membrane and the nucleus

value: tier 2


title: RIKEN_Cage_GM12878_cytosol_longPolyA

tag: datatype

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: IDR

value: F

tag: localization

tag: localization description

tag: replicate description


title: RIKEN_Cage_GM12878_nucleus_longPolyA

tag: datatype description

tag: rnaextract

tag: rnaextract description

tag: biorep

tag: labexpid

value: nucleus

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: Kc167_Sin3A_ChIPSeq_1 and 2

tag: antibody name

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: E8-16_sr_INPUT_1

tag: strain

tag: developmental stage


title: E8-16_sr_ChIPSeq_1 and 2

value: sr


title: Kc167_dCTBP_ChIPSeq_1

value: dCTBP


title: E8-16_SuH_ChIPSeq_1 and 2

value: SuH


title: Hth_INPUT_1


title: jim_INPUT_1


title: Hth_ChIPSeq_1 and 2

value: Hth


title: jim_ChIPSeq_1 and 2

value: iso1 (y; bw cn sp)

value: jim


title: E8-16_INPUT_1


title: RIKEN_Cage_K562_nucleus_longPolyA

value: Cage

value: CAGE 5' RNA Tags

value: longPolyA

tag: labversion

tag: replicate

tag: cell lineage

value: mesoderm

tag: cell sex

value: tier 1


title: RIKEN_Cage_HepG2_cell_longPolyA

tag: datatype

tag: cell description

value: hepatocellular carcinoma

value: Poly(A)+ RNA longer than 200 nt

value: M

tag: localization

value: cell

tag: localization description

value: Whole cell


title: RIKEN_Cage_HeLa-S3_cell_longPolyA

tag: datatype description

tag: rnaextract

tag: rnaextract description

value: IDR

value: ectoderm

value: F

tag: replicate description


title: RIKEN_Cage_HepG2_cytosol_longPolyA

tag: biorep

tag: labexpid

value: cytosol

value: The fluid between the cells outer membrane and the nucleus


title: RIKEN_Cage_K562_cytosol_longPolyA

value: bedtools v2.7.1,IDR

value: Delve version 0.9


title: E8-16_HP1_ChIPSeq_1 and 2

value: iso1 (y; bw cn sp)

tag: antibody name

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: RIKEN_Cage_HeLa-S3_nucleus_longPolyA

value: Cage

value: CAGE 5' RNA Tags

value: longPolyA

tag: labversion

tag: replicate

value: nucleus

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: RIKEN_Cage_HeLa-S3_cytosol_longPolyA

value: Poly(A)+ RNA longer than 200 nt

tag: cell lineage

tag: cell sex

value: tier 1


title: RIKEN_Cage_BJ_cell_longPolyA

source_name: BJ

tag: datatype

tag: cell description

value: skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID:9916803)

value: cell

value: Whole cell


title: SuH_ChIPSeq_1 and 2

tag: strain

tag: developmental stage

value: SuH


title: RIKEN_Cage_HUVEC_cell_longPolyA

source_name: HUVEC

tag: datatype description

tag: rnaextract

value: IDR

value: mesoderm

value: U

tag: localization

tag: localization description


title: RIKEN_Cage_H1-hESC_nucleus_longPolyA

tag: rnaextract description

tag: biorep

tag: labexpid

tag: readtype

tag: readtype description

value: Single 36 nt reads

value: inner cell mass

value: M

tag: replicate description

value: tier 2


title: sr_INPUT_1

value: iso1 (y; bw cn sp)


title: RIKEN_Cage_HUVEC_nucleus_longPolyA

value: Cage

value: CAGE 5' RNA Tags

value: longPolyA

tag: labversion

tag: replicate

value: tier 3


title: immunoprecipitating small RNA with an antibody againt H3K9me2 proteins from human senescent fibroblast WI-38

status: Public on Dec 17 2011

city: paris

first: Moussa

last: BENHAMED

address: Institut pasteur

country: France

institute: Institut Pasteur

description: small rna immunoprecipitated

data_processing:
Library strategy: RIP-Seq
Small RNA samples were prepared from RIPs or unfractionated, cellular RNA of senescent cells using small RNA-Seq sample Prep kit (Illumina) followed by the standard Illumina RNA sequencing protocol using the Genome Analyzer. Bioinformatic analysis of RNA Seq results was performed by GenomeQuest Inc. France (www.genomequest.com). Beginning with raw reads obtained from ILLUMINA G1 sequencing adaptor sequence was removed. All reads smaller than 18 nucleotides after removing the adaptor sequence were discarded allowing one mismatch within the adaptor sequence. Small RNA sequences were mapped to the complete, unmasked, version of the NCBI version of the human genome (Build 36). The alignment algorithm used aligns the entire read allowing one mismatch, insertion or deletion. Each sequence read was classified as (a) hit or (b) no hit and was annotated with the number of hits found. All reads mapping to a single contiguous position in the genome were then clustered. For each genomic cluster the genomic sequence was extracted and put into a separate sequence database (the genomic cluster database). The cluster database was mapped to mirBase (mirBase v12, http://www.mirbase.org/) resulting in a microRNA (miR) annotated cluster database. miR reads were normalized to one million small RNAs (cpm). All mappings used the Genomequest Kerr proprietary implementation. The KERR algorithm belongs to a class of approximate string matching algorithms. Given two sequences S1 and S2, KERR computes the minimal number of differences between S1 and S2, by trying to optimally fit the shorter sequence into the longer one (Myers). Differences in sequence alignments arise from mismatches or gaps. This strategy assures to find all the local alignments allowing a given number of mismatch, insertion or deletion. For all comparisons one error was allowed. For more information about the Genomequest Kerr implementation, please refer to: http://wiki.genomequest.com/index.php/LSPMUL_HELP#KERR_.28aka_GenePAST.29

source_name: human fibroblast

growth_protocol:
Culturing of cells of primary human diploid fibroblasts strain WI38 were performed at physiological oxygen concentration of 3%
Culturing of cells of primary human diploid fibroblasts strain WI38 were performed at physiological oxygen concentration of 3%

extract_protocol: Senescent cells induced by oncogenic RAS were crosslinked by UV at 100-400mJ/cm2 and immediately collected afterwards on ice.  Cell pellets were lysed in RIPA lysis buffer on ice, adjusted to a protein concentration of 10mg/ml and digested extensively with DNAse I for 15 minutes at 37ºC followed by digestion with RNAse T1 (1000U/ml) for 15 minutes at 23ºC. Lysates were cleared and incubated with pan-anti-AGO, anti-H3K9me2 antibodies or IgG-antibodies (Upstate). Immunoprecipitates were collected with protein A/G beads, washed extensively and incubated again with 5,000U/ml RNAse T1 at 23ºC to rid the precipitates of any unspecifically attached RNA molecules. Immuncomplexes were proteinase-K digested and purified RNA molecules ethanol-precipitated.

treatment_protocol: transformed by Retroviral vector pBABE-RASV12

tag: cell line

tag: antibody

tag: antibody vendor

value: Upstate


title: immunoprecipitating small RNA with an antibody againt AGO proteins from human senescent fibroblast WI-38

description: small rna immunoprecipitated

value: pan AGO


title: sr_ChIPSeq_1 and 2

tag: strain

tag: antibody name

value: sr

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: RIKEN_Cage_HepG2_nucleus_longPolyA

tag: datatype

tag: datatype description

tag: cell description

value: hepatocellular carcinoma

tag: rnaextract

value: Poly(A)+ RNA longer than 200 nt

tag: cell sex

tag: localization

value: nucleus

tag: localization description

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA

value: tier 1


title: input H3.3

city: Paris

first: Genevieve

last: Almouzni

state: Ille De France

address: 26 Rue D'Ulm

department: Nuclear Dynamics and Genome Plasticity

institute: Institut Curie

description: input DNA

data_processing:
Sequence reads were aligned to the human genome (Assembly hg18) using Bowtie allowing for a maximum of 3 mismatches and reporting only reads with a unique match in the genome.
Wig files were created from Bowtie alignment output using the FindPeaks4 program (http://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=FindPeaks#FindPeaks_4.0)

source_name: Hela S3 cells

growth_protocol: Hela S3 cells were cultured in spinners to the concentration of 106 per ml.

extract_protocol: Libraries were prepared and sequenced according to Illumina's instructions by Fasteris SA, Switzerland.

treatment_protocol: Mnase digestion, mononucleosome purification and IP was carried out as described in Loyola et al 2006.

tag: cell line specifics

value: Hela S3 stably expressing H3.3-FLAG-HA

tag: chip antibody


title: Fru_ChIPSeq_1 and 2

tag: developmental stage

value: Fru


title: SuH_INPUT_1


title: input H3.1

description: input DNA

value: Hela S3 stably expressing H3.1-FLAG-HA


title: E16-24_CNC_INPUT_1

value: iso1 (y; bw cn sp)


title: CG16778_INPUT_1


title: dm_INPUT_1


title: RIKEN_Cage_HUVEC_cytosol_longPolyA

value: Cage

tag: rnaextract description

tag: biorep

tag: labexpid

tag: labversion

value: IDR

tag: replicate

tag: cell lineage

value: mesoderm

value: U

value: cytosol

value: The fluid between the cells outer membrane and the nucleus

tag: replicate description


title: RIKEN_Cage_HeLa-S3_nucleolus_total

molecule: nuclear RNA

tag: datatype

value: CAGE 5' RNA Tags

value: total

value: Total RNA extract (longer than 200 nt)

value: cervical carcinoma

tag: cell karyotype

value: cancer

value: ectoderm

value: F

value: nucleolus

value: The part of the nucleus where ribosomal RNA is actively transcribed


title: RIKEN_Cage_HeLa-S3_cytosol_longNonPolyA

molecule: cytoplasmic RNA

tag: datatype description

value: longNonPolyA

value: Poly(A)- RNA longer than 200 nt


title: dm_ChIPSeq_1 and 2

tag: strain

value: iso1 (y; bw cn sp)

tag: antibody name

value: dm

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: H3.3 IP

description: Chromatin IP against stably expressed H3.3-FLAG-HA

tag: cell line specifics

value: Hela S3 stably expressing H3.3-FLAG-HA

tag: chip antibody

value: anti-FLAG [Sigma, Catalog #:A2220, Lot #:040M6007]


title: E16-24_CNC_ChIPSeq_1 and 2

tag: developmental stage

value: CNC


title: H3.1 IP

description: Chromatin IP against stably expressed H3.1-FLAG-HA

value: Hela S3 stably expressing H3.1-FLAG-HA


title: RIKEN_Cage_H1-hESC_cell_longNonPolyA

value: Cage

value: CAGE 5' RNA Tags

tag: rnaextract

tag: rnaextract description

tag: biorep

tag: softwareversion

value: bedtools v2.7.1

value: normal

value: inner cell mass

tag: cell sex

value: M

tag: localization

value: cell

tag: localization description

value: Whole cell

value: Delve version 0.9


title: Fru_INPUT_1


title: RIKEN_Cage_K562_polysome_longNonPolyA

tag: datatype

value: longNonPolyA

value: Poly(A)- RNA longer than 200 nt

tag: labexpid

tag: labversion

tag: cell karyotype

value: cancer

tag: cell lineage

value: mesoderm

value: F

value: polysome

value: Strand of mRNA with ribosomes attached


title: br-core_INPUT_1

tag: strain

value: iso1 (y; bw cn sp)


title: CG16778_ChIPSeq_1 and 2

tag: antibody name

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: RIKEN_Cage_K562_cytosol_longNonPolyA

extract_protocol: Instrument model unknown. ("AB SOLiD System" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage

value: Cage

tag: datatype description

value: CAGE 5' RNA Tags

tag: rnaextract

value: cytosol

value: The fluid between the cells outer membrane and the nucleus

value: bowtie version 0.12.5


title: RIKEN_Cage_GM12878_nucleolus_total

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: total

tag: rnaextract description

value: Total RNA extract (longer than 200 nt)

tag: biorep

value: normal

value: nucleolus

value: The part of the nucleus where ribosomal RNA is actively transcribed


title: br-core_ChIPSeq_1 and 2

tag: developmental stage

value: br-core