title: INNOCUA_WT_STAT_37C_TAP

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
INNOCUA_WT_STAT_37C_TAP.align.txt: NC_003212

tag: strain

value: stationary


title: INNOCUA_WT__STAT_37C_NOTAP

status: Public on May 01 2012

type: SRA

city: Rehovot

first: Omri

last: Wurtzel

address: Hertzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
INNOCUA_WT_STAT_37C_NOTAP.align.txt: NC_003212

molecule: total RNA

organism: Listeria innocua Clip11262

growth_protocol: Strains used in this study were Listeria monocytogenes EGD-e (BUG1600), its isogenic mutants ∆prfA (BUG2214) and ∆sigB (Mandin et al, 2007) and Listeria innocua (CIP107775 CLIP11262BUG499) (Glaser et al, 2001). Bacteria were grown overnight in BHI medium at 37°C with shaking at 200 rpm. Cultures were subsequently diluted 1/500 into 100ml BHI and grown at either 37°C or 30°C until mid-exponential phase (OD600=1.0) or stationary phase (OD600=3.0 for L. monocytogenes and OD600=2.5 for L. innocua). For conditions of low oxygen (hypoxia), cultures were jar-sealed with CampyGen sachet (Oxoid). At the appropriate OD600, bacteria were pelleted by centrifugation at 10,000 X G for five minutes, flash frozen in liquid nitrogen and stored at -80°C until RNA was to be extracted.

extract_protocol: Each RNA sample was divided into two sub-samples (hereby TAP+ and TAP-) containing 2.5 μg of rRNA-depleted RNA. The RNA of TAP+ sub-sample was incubated with 2 U of TAP (Epicentre) for 1.5 h at 37°C to generate 5’ monophosphate RNAs. The other sub-sample (TAP-) was not treated with TAP. cDNA sequencing libraries were prepared as previously described (Wurtzel et al, 2010b), with an addition of a unique 4-base index sequence to the 5’ RNA adapter used for each sub-sample (Supplementary Figure S1A). cDNA libraries of every two sub-samples were mixed in equal amounts, and sent to Illumina sequencing. The resulting sequences were sorted to the correct sub-sample by their index. The TAP+ sub-samples include both primary RNAs and processed RNAs, in contrast to TAP- sub-samples, which contain only processed RNAs.

treatment_protocol: Bacterial pellets were resuspended in 400 ul solution A (½ vol Glucose 20% + ½ vol Tris 25mM pH7.6 + EDTA 10mM) to which an additional 60ul of 0.5M EDTA was added.  RNA was subsequently extracted using TRIzol reagent (Invitrogen) as described previously (Toledo-Arana et al, 2009).  RNA integrity was verified via analysis of intact ribosomal RNA bands via the Experion Automated Electrophoresis system (Biorad). Removal of 16S and 23S rRNA from total RNA was performed using MicrobExpress™ Bacterial mRNA Purification Kit (Ambion) according to the manufacturer's protocol (He et al, 2010). RNA concentrations and quality were determined by using the 2100 Bioanalzyer (Agilent).

tag: organism reference

value: Listeria innocua CIP107775 (Genbank NC_003212)

tag: growth phase

tag: growth temperature


title: INNOCUA_WT_37C_TAP

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
INNOCUA_WT_37C_TAP.align.txt: NC_003212

value: mid-log


title: WT_STAT_37C_NOTAP

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
WT_STAT_37C_NOTAP.align.txt: NC_003210

organism: Listeria monocytogenes EGD-e

value: Listeria monocytogenes EGD-e (Genbank NC_003210)

value: EGD-e


title: hypoxia_37C_NOTAP

description: For conditions of low oxygen (hypoxia), cultures were jar-sealed with CampyGen sachet (Oxoid)

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
hypoxia_37C_NOTAP.align.txt: NC_003210


title: WT_30C_NOTAP

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
WT_30C_NOTAP.align.txt: NC_003210


title: WT_30C_TAP

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
WT_30C_TAP.align.txt: NC_003210


title: hypoxia_37C_TAP

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
hypoxia_37C_TAP.align.txt: NC_003210


title: prfA_deletion_37C_NOTAP

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
prfA_deletion_37C_NOTAP.align.txt: NC_003210

value: Listeria monocytogenes EGD-e ΔprfA (BUG2214)


title: Dmel wildtype testis expression profiling 1

city: Cambridge

first: Sidi

last: Chen

state: MA

department: Biology

country: USA

institute: MIT

description: Trizol-chloroform-Qiagen

data_processing:
The sequences in fastq files were mapped back to whole genome sequences using Bowtie, allowing 2 mismatches; all the unmapped sequences were then mapped to all possbile exon-exon conjuction sequences as annotated by flybase using Bowtie, allowing 2 mismatches. The number of reads of a gene is then calculated as the total number of unique sequence read overlapping with annotated exonic regions of the gene and RPKM values are calculated as the number of reads per kilo base of annotated exon length per million total uniquely mapped reads.
Genome Build:
dmel_1_testis_RPKM_value.txt: dm3

organism: Drosophila melanogaster

source_name: Dmel wildtype

growth_protocol: standard cornmeal

extract_protocol: standard Illumina single-end mRNA-seq library prep Kit

tag: developmental stage

value: 1-7d adult

value: Oregon-R

tag: genotype/variation

value: wildtype

tag: tissue

value: dissected testis


title: prfA_deletion_37C_TAP

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
prfA_deletion_37C_TAP.align.txt: NC_003210


title: sigB_deletion_37C_TAP

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
sigB_deletion_37C_TAP.align.txt: NC_003210

value: Listeria monocytogenes EGD-e ΔsigB (Mandin et al, Nucleic Acids Research, 2007)


title: sigB_deletion_37C_NOTAP

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
sigB_deletion_37C_NOTAP.align.txt: NC_003210


title: WT_37C_NOTAP

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
WT_37C_NOTAP.align.txt: NC_003210


title: WT_37C_TAP

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
WT_37C_TAP.align.txt: NC_003210


title: PSU_ChipSeq_G1E-ER4_Pol2-4H8

status: Public on Apr 30 2012

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: lab

value: PSU-m

tag: lab description

value: Hardison - Penn State University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

tag: cell sex

value: M

tag: antibody

tag: antibody antibodydescription

value: Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target:POL24H8

tag: antibody targetdescription

value: This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: age

tag: age description

value: Embryonic day 0 (stem cell)

tag: control

value: Input

tag: control description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: controlid

tag: replicate

tag: strain description

value: Strain 129, has widely available embryonic stem cells


title: PSU_ChipSeq_G1E_GATA2_(SC-9008)

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: Gata1- erythroid progenitor

value: Rabbit polyclonal antibody raised against amino acids 120-235 of GATA-2 of human origin. Antibody Target:GATA2

value: The GATA family of transcription factors share a conserved zinc finger DNA-binding domain and are capable of binding the WGATAR consensus sequence. GATA1 is erythroid-specific and is essential for normal erythropeisis. By comparison, GATA2 is expressed at high levels in hematopoeitic progenitors, including early erythroid cells, but is strong repressed during erythroblast differentiaion.

value: Santa Cruz Biotech

tag: strain


title: WT_STAT_37C_TAP

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
WT_STAT_37C_TAP.align.txt: NC_003210

tag: organism reference

value: Listeria monocytogenes EGD-e (Genbank NC_003210)

value: EGD-e

tag: growth phase

value: stationary

tag: growth temperature


title: PSU_ChipSeq_Erythrobl_Input

source_name: Erythrobl

value: PSU-m

value: Hardison - Penn State University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: Erythrobl

tag: cell organism

value: mouse

tag: cell description

value: Erythroblast, ter119+ cells from liver

tag: cell sex

value: B

tag: antibody

tag: antibody description

value: Embryonic day 14.5

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


title: PSU_ChipSeq_G1E-ER4_GATA2_(SC-9008)

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: M

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

tag: age

tag: age description

value: Embryonic day 0 (stem cell)

tag: control

value: Input

tag: control description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: controlid

value: Strain 129, has widely available embryonic stem cells


title: PSU_ChipSeq_G1E_Pol2-4H8

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: Gata1- erythroid progenitor

value: Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target:POL24H8

value: This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes

value: Abcam

tag: replicate

tag: strain

tag: strain description


title: PSU_ChipSeq_Megakaryo_Input

source_name: Megakaryo

value: PSU-m

value: Hardison - Penn State University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: Megakaryo

tag: cell organism

tag: cell description

value: Megakaryocyte

tag: cell sex

tag: antibody

tag: antibody description


title: PSU_ChipSeq_Erythrobl_TAL1_(SC-12984)

value: Erythrobl

value: mouse

value: Erythroblast, ter119+ cells from liver

value: B

tag: antibody antibodydescription

value: goat polyclonal antibody; epitope mapping at the C-terminus of TAL1 of human origin, recommended for detection of TAL1 of mouse, rat and human origin. Antibody Target:TAL1

tag: antibody targetdescription

value: TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: age

tag: age description

value: Embryonic day 14.5

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


title: PSU_ChipSeq_Megakaryo_GATA1_(SC-265)

tag: lab

tag: lab description

tag: datatype

value: rat monoclonal antibody raised against mouse recombinant GATA1; recommended for detection of GATA1 of mouse, rat and human origin. Antibody Target:GATA1

value: GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes.

tag: control

value: Input

tag: control description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: controlid


title: PSU_ChipSeq_G1E_GATA1_(SC-265)

value: PSU-m

value: Hardison - Penn State University

value: ChipSeq

tag: datatype description

tag: cell

tag: cell organism

value: Gata1- erythroid progenitor

value: M

value: Embryonic day 0 (stem cell)

tag: replicate

tag: strain

tag: strain description

value: Strain 129, has widely available embryonic stem cells


title: PSU_ChipSeq_G1E_Input

value: Chromatin IP Sequencing

value: mouse

tag: cell description

tag: cell sex

tag: antibody

tag: antibody description


title: PSU_ChipSeq_MEL_TAL1_(SC-12984)

source_name: MEL

value: MEL

value: Leukemia (K562 analog)

value: U

tag: antibody antibodydescription

value: goat polyclonal antibody; epitope mapping at the C-terminus of TAL1 of human origin, recommended for detection of TAL1 of mouse, rat and human origin. Antibody Target:TAL1

tag: antibody targetdescription

value: TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis.

tag: antibody vendorname

tag: antibody vendorid

tag: age

value: immortalized

tag: age description

value: Immortal cells

value: C57 black 6, the most common inbred strain of laboratory mouse


title: PSU_ChipSeq_MEL_Pol2-4H8

tag: lab

value: PSU-m

tag: lab description

tag: datatype

value: Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target:POL24H8

value: This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes

value: Abcam

tag: control

value: Input

tag: control description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: controlid


title: PSU_ChipSeq_G1E-ER4_TAL1_(SC-12984)

value: Hardison - Penn State University

value: ChipSeq

tag: datatype description

tag: cell

tag: cell organism

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: M

value: Santa Cruz Biotech

value: Embryonic day 0 (stem cell)

tag: replicate

tag: strain

tag: strain description

value: Strain 129, has widely available embryonic stem cells


title: PSU_ChipSeq_G1E_TAL1_(SC-12984)

value: Chromatin IP Sequencing

value: mouse

tag: cell description

value: Gata1- erythroid progenitor

tag: cell sex

tag: antibody

tag: antibody antibodydescription

value: goat polyclonal antibody; epitope mapping at the C-terminus of TAL1 of human origin, recommended for detection of TAL1 of mouse, rat and human origin. Antibody Target:TAL1

tag: antibody targetdescription

value: TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis.


title: PSU_ChipSeq_MEL_Input

tag: lab

value: PSU-m

value: MEL

value: Leukemia (K562 analog)

value: U

tag: antibody description

tag: age

value: immortalized

tag: age description

value: Immortal cells

value: C57 black 6, the most common inbred strain of laboratory mouse


title: PSU_ChipSeq_G1E-ER4_GATA1_(SC-265)

tag: lab description

value: Hardison - Penn State University

tag: datatype

value: ChipSeq

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: rat monoclonal antibody raised against mouse recombinant GATA1; recommended for detection of GATA1 of mouse, rat and human origin. Antibody Target:GATA1

value: GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes.

tag: antibody vendorname

tag: antibody vendorid

tag: control

value: Input

tag: control description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.


title: PSU_ChipSeq_G1E_CTCF

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: mouse

value: Gata1- erythroid progenitor

value: M

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

value: Embryonic day 0 (stem cell)

tag: controlid

tag: replicate

tag: strain

value: Strain 129, has widely available embryonic stem cells


title: PSU_ChipSeq_G1E-ER4_CTCF

value: PSU-m

value: Hardison - Penn State University

tag: cell description

tag: cell sex

tag: antibody

tag: antibody antibodydescription

tag: antibody targetdescription

tag: labversion

tag: strain description


title: PSU_ChipSeq_Erythrobl_GATA1_(SC-265)

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

value: Erythrobl

value: Erythroblast, ter119+ cells from liver

value: B

tag: antibody vendorname

value: Santa Cruz Biotech

tag: age

tag: age description

value: Embryonic day 14.5

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


title: PSU_ChipSeq_CH12_CTCF

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: mouse

value: B-cell lymphoma (GM12878 analog)

value: F

tag: antibody vendorid

value: immortalized

value: Immortal cells

tag: control

value: Input

tag: control description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: PSU_ChipSeq_G1E-ER4_Input

value: PSU-m

value: Hardison - Penn State University

tag: cell description

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

tag: cell sex

value: M

tag: antibody

tag: antibody description

value: Embryonic day 0 (stem cell)

tag: controlid

tag: replicate

tag: strain

value: Strain 129, has widely available embryonic stem cells


title: PSU_ChipSeq_CH12_PAX5_(N-15)

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

tag: antibody antibodydescription

value: rabbit polyclonal antibody; epitope is a synthetic peptide:MDLEKNYPTPRTSRT, corresponding to amino acids 1-15 of Human PAX5, cross-reacts with human and mouse PAX5. Antibody Target:PAX5

tag: antibody targetdescription

value: The PAX5 gene is a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA binding motif, known as the paired box. The PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. The PAX5 gene encodes the B cell lineage specific activator protein (BSAP) that is expressed at early, but not late stages of B cell differentiation.

value: Abcam

tag: strain description


title: E14-2i_H3K9me3

status: Public on Apr 27 2012

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

data_processing: ChIP DNA or ds-cDNA samples were prepared for sequencing by end repair of 20 ng DNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, which were subsequently size selected (~300bp). The adapter-modified DNA fragments were subjected to limited PCR amplification (14 cycles). Quality control was made by qPCR and by running the products on a Bioanalyzer (BioRad). Finally, cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina Genome Analyzer IIx (GAIIx) platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the mouse MM9 reference genome using the Illumina Analysis Pipeline allowing one mismatch. Samples were sequenced to a depth of approximately 10-20 million mapped tags per sample (Table S1). Unless specified otherwise, only the tags uniquely aligning to the genome were considered for further analysis. For RNA-Seq, further analysis was performed using the 36 bp sequence reads. For ChIP-Seq, the 36 bp sequence reads were directionally extended to 300 bp, corresponding to the length of the original fragments used for sequencing, and tags mapping on exact the same genomic locus were discarded to obtain a non-redundant set. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All ChIP-Seq and RNA-Seq sequence analyses were conducted based on the Mus musculus NCBI m37 genome assembly (MM9) accessed from the Ensembl (release 54; May 2009) or the UCSC (assembly July 2007) Genome Browsers.

source_name: Embryonic Stem cells

growth_protocol: Embryonic stem cells were cultured without feeders in the presence of leukaemia inhibitory factor (LIF) either in medium containing 10% foetal calf serum or in serum-free medium containing the MEK inhibitor PD0325901 (1μM) and the Gsk3 inhibitor CH99021 (3μM), together known as 2i. TNGA female ES cells on a mixed strain 129 and C57BL/6 background and female and male NOD ES cells from the non-obese diabetic strain were derived in 2i. TNGA cells are heterozygous for knock-in of eGFP to the Nanog gene. The female XT67E1 line originates from a mixed 129 and PGK/C3H background, and contains a monoallelic deletion in the Xist gene. E14Tg2a, RGD2, Rex-GFP and HM1 cells are male ES cells of 129 background, established and grown in serum without feeders according to standard protocols. Rex-GFP cells contain a monoallelic GFP knock-in substitution at the endogenous Rex1 locus.

extract_protocol: ChIP experiments were performed using 3.3x106 cells and 3µg antibody per ChIP according to standard protocols as described with two minor modifications. Crosslinking of the cells was performed on the culture plates for 20 minutes, while ChIP’ed DNA was purified by Qiaquick PCR purification Kit (Qiagen). ChIP enrichment levels were analyzed by qPCR for quality control. Total RNA was isolated using Trizol (Invitrogen) and subjected to chloroform extraction, isopropanol precipitation and ethanol washing according to the manufacturer's recommendations. 100µg total RNA was subjected to two rounds of poly(A) selection using the Oligotex mRNA Mini Kit (Qiagen), followed by DNaseI treatment (Qiagen). 100-200ng mRNA was fragmented by hydrolysis (5x fragmentation buffer: 200mM Tris acetate, pH8.2, 500mM potassium acetate and 150mM magnesium acetate) at 94°C for 90 seconds and purified using the RNAeasy Minelute Kit (Qiagen). The fragmented mRNA was used as template for cDNA synthesis using 5µg random hexamers using Superscript III Reverse Transcriptase (Invitrogen) according to the manufacturer's recommendations. Ds-cDNA was synthesized in second strand buffer (Invitrogen) according to the manufacturer's recommendations and purified using the Minelute Reaction Cleanup Kit (Qiagen). Strand specific rRNA depleted ds_cDNA profiling was performed using the ScriptSeq kit (cat. no. SS10924) from Illumina, according to the instructions of the manufacturer. rRNA depletion was performed using the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat; cat. no. RZH110424). Quality control was performed by qPCR.

treatment_protocol: No specific treatments

tag: cell type

value: ES-cells

tag: source

value: Chromatin IP against H3K9me3

value: Antibody H3K9me3 (Abcam ab8898-100, lot. 733953)


title: TNGA-serum_H3K9me3


title: E14-serum_H3K9me3


title: TNGA-2i_H3K9me3


title: E14-serum_strand-specific-rRNA-depleted-RNA-Seq

value: rRNA depleted strand specific ds_cDNA

tag: rna subtype

value: rRNA depleted total RNA


title: TNGA-2i_strand-specific-rRNA-depleted-RNA-Seq


title: Rex-GFP-serum-GFP_positive_RNA-Seq

value: fragmentented two times Poly(A) selected ds_cDNA

value: Poly(A) RNA


title: PSU_ChipSeq_MEL_CTCF

value: PSU-m

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: MEL

tag: cell organism

value: mouse

value: Leukemia (K562 analog)

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: control

value: Input

tag: control description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: C57 black 6, the most common inbred strain of laboratory mouse


title: Rex-GFP-serum-GFP_positive_H3K27me3

tag: strain

value: ES-cells

value: Chromatin IP against H3K27me3

tag: antibody

value: Antibody H3K27me3 (Millipore 07-449, DAM-1588246)


title: Rex-GFP-serum-GFP_negative_RNA-Seq

value: fragmentented two times Poly(A) selected ds_cDNA

value: Poly(A) RNA


title: TNGA-serum_RNA-Pol-II

description: Chromatin IP against RNA Pol II

growth_protocol: Embryonic stem cells were cultured without feeders in the presence of leukaemia inhibitory factor (LIF) either in medium containing 10% foetal calf serum or in serum-free medium containing the MEK inhibitor PD0325901 (1uM) and the Gsk3 inhibitor CH99021 (3uM), together known as 2i. TNGA female ES cells on a mixed strain 129 and C57BL/6 background and female and male NOD ES cells from the non-obese diabetic strain were derived in 2i. TNGA cells are heterozygous for knock-in of eGFP to the Nanog gene. The female XT67E1 line originates from a mixed 129 and PGK/C3H background, and contains a monoallelic deletion in the Xist gene. E14Tg2a, RGD2 and HM1 cells are male ES cells of 129 background, established and grown in serum without feeders according to standard protocols.

extract_protocol: ChIP experiments were performed using 3.3x106 cells and 3µg antibody per ChIP according to standard protocols as described with two minor modifications. Crosslinking of the cells was performed on the culture plates for 20 minutes, while ChIPed DNA was purified by Qiaquick PCR purification Kit (Qiagen). ChIP enrichment levels were analyzed by qPCR for quality control. Total RNA was isolated using Trizol (Invitrogen) and subjected to chloroform extraction, isopropanol precipitation and ethanol washing according to the manufacturer's recommendations. 100µg total RNA was subjected to two rounds of poly(A) selection using the Oligotex mRNA Mini Kit (Qiagen), followed by DNaseI treatment (Qiagen). 100-200ng mRNA was fragmented by hydrolysis (5x fragmentation buffer: 200mM Tris acetate, pH8.2, 500mM potassium acetate and 150mM magnesium acetate) at 94°C for 90 seconds and purified using the RNAeasy Minelute Kit (Qiagen). The fragmented mRNA was used as template for cDNA synthesis using 5µg random hexamers using Superscript III Reverse Transcriptase (Invitrogen) according to the manufacturer's recommendations. Ds-cDNA was synthesized in second strand buffer (Invitrogen) according to the manufacturer's recommendations and purified using the Minelute Reaction Cleanup Kit (Qiagen). Quality control was performed by qPCR.

tag: chip antibody

value: RNA Pol II

tag: chip antibody vendor

value: Diagenode

tag: chip antibody catalog#

tag: chip antibody batch/lot#


title: E14-2i_strand-specific-rRNA-depleted-RNA-Seq

tag: cell type

tag: source

value: rRNA depleted strand specific ds_cDNA

value: rRNA depleted total RNA


title: RGD2-serum_RNA-Seq

description:
ds_cDNA
fragmentented two times Poly(A) selected ds_cDNA
library source: synthetic

molecule: polyA RNA


title: TNGA-2i_RNA-Pol-II

description: Chromatin IP against RNA Pol II


title: PSU_ChipSeq_CH12_Input

tag: lab

value: PSU-m

tag: lab description

value: Hardison - Penn State University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: mouse

tag: cell description

value: B-cell lymphoma (GM12878 analog)

tag: cell sex

value: F

tag: antibody description

tag: controlid

tag: replicate

tag: strain description

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: XT67E1-serum_RNA-Seq

tag: strain

value: ES-cells


title: TNGA-2i_Ezh2

description: Chromatin IP against Ezh2

tag: chip antibody

value: Active Motif


title: TNGA-serum_Ezh2

description: Chromatin IP against Ezh2

tag: chip antibody vendor


title: E14-2i_Ezh2

description: Chromatin IP against Ezh2

tag: chip antibody catalog#


title: TNGA-serum_strand-specific-rRNA-depleted-RNA-Seq

tag: antibody

tag: rna subtype


title: TNGA-2i_Genomic_DNA

description:
Genomic DNA from decrosslinked total chromatin.
No variables, sequencing of sonicated genomic DNA

tag: cell type

tag: chip antibody batch/lot#


title: Rex-GFP-serum-GFP_negative_H3K27me3

tag: source

value: Chromatin IP against H3K27me3

value: Antibody H3K27me3 (Millipore 07-449, DAM-1588246)


title: NOD_female_2i_RNA-Seq

description:
ds_cDNA
fragmentented two times Poly(A) selected ds_cDNA

value: NOD


title: TNGA-serum_RNA-Seq


title: E14-serum_RNA-Seq


title: TNGA-serum_Suz12

description: Chromatin IP against Suz12

value: Abcam


title: TNGA-2i_RNA-Seq


title: E14-2i_RNA-Seq


title: TNGA-2i_Suz12

description: Chromatin IP against Suz12


title: E14-serum_H3K27me3

description: Chromatin IP against H3K27me3

value: Millipore


title: E14-2i_H3K27me3

description: Chromatin IP against H3K27me3


title: TNGA-2i_H3K36me3

description: Chromatin IP against H3K36me3

value: Diagenode


title: E14-2i_H3K36me3

description: Chromatin IP against H3K36me3


title: E14-serum_H3K4me3

description: Chromatin IP against H3K4me3


title: TNGA-serum_H3K36me3

description: Chromatin IP against H3K36me3


title: E14-serum_Ezh2

description: Chromatin IP against Ezh2


title: E14-serum_H3K36me3

description: Chromatin IP against H3K36me3


title: TNGA-serum_H3K4me3

description: Chromatin IP against H3K4me3


title: NOD_male_2i_RNA-Seq


title: E14-2i_H3K4me3

description: Chromatin IP against H3K4me3


title: TNGA-serum_H3K27me3

description: Chromatin IP against H3K27me3


title: TNGA-2i_H3K4me3

description: Chromatin IP against H3K4me3


title: HudsonAlpha_RnaSeq_T-47D_Genistein_100nM_4hr_longPolyA (superseded by GSE93444)

description:
****************************
GSM923436 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93444
****************************

organism: Homo sapiens

tag: datatype

value: RnaSeq

value: Sequencing analysis of RNA expression

tag: treatment description

value: 4 h with 100 nM Genistein (Myers)

tag: rnaextract

value: longPolyA

tag: rnaextract description

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

tag: labexpid

tag: labversion

tag: mapalgorithm

tag: mapalgorithm description

value: bowtie v0.12.5

tag: readtype

tag: readtype description

value: Single 36 nt reads


title: HudsonAlpha_RnaSeq_A549_DEX_5nM_longPolyA (superseded by GSE93447)

description:
****************************
GSM923435 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93447
****************************

tag: datatype description

value: 1 h with 5 nM Dexamethasone (Myers)

tag: replicate


title: HudsonAlpha_RnaSeq_A549_DEX_1nM_longPolyA (superseded by GSE93445)

description:
****************************
GSM923433 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93445
****************************

value: 1 h with 1 nM Dexamethasone (Myers)


title: HudsonAlpha_RnaSeq_BE2_C_longPolyA (superseded by GSE93448)

description:
****************************
GSM923434 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93448
****************************

value: No special treatment or protocol applies


title: HudsonAlpha_RnaSeq_A549_DEX_500pM_longPolyA (superseded by GSE93446)

description:
****************************
GSM923432 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93446
****************************

value: 1 h with 500 pM Dexamethasone (Myers)


title: HudsonAlpha_RnaSeq_PFSK-1_longPolyA (superseded by GSE93451)

description:
****************************
GSM923430 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93451
****************************


title: HudsonAlpha_RnaSeq_T-47D_Estradiol_10nM_4hr_longPolyA (superseded by GSE93443)

description:
****************************
GSM923431 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93443
****************************


title: UW_RepliSeq_BG02ES

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: RepliSeq

value: Assessment of DNA Replication Timing

tag: cell

tag: cell organism

value: human

tag: cell description

value: embryonic stem cell (hESC), BG02, treatment:H9 conditioned medium

tag: cell karyotype

value: normal

tag: cell lineage

value: inner cell mass

tag: cell sex

value: M

tag: phase

tag: phase description

value: Flow sorted, G1b phase corresponds to the second half of the first DNA content window


title: HudsonAlpha_RnaSeq_ECC-1_Estradiol_10nM_4hr_longPolyA (superseded by GSE93439)

description:
****************************
GSM923427 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93439
****************************

tag: datatype

value: RnaSeq

value: Sequencing analysis of RNA expression

value: endoderm

tag: rnaextract

value: longPolyA

tag: rnaextract description

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

tag: labexpid

tag: labversion


title: HudsonAlpha_RnaSeq_T-47D_BPA_100nM_4hr_longPolyA (superseded by GSE93441)

description:
****************************
GSM923429 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93441
****************************

tag: datatype description

tag: mapalgorithm

tag: mapalgorithm description

value: bowtie v0.12.5

tag: readtype

tag: readtype description

value: Single 36 nt reads


title: UW_RepliSeq_HUVEC

source_name: HUVEC

tag: lab

value: UW

tag: lab description

tag: cell

value: HUVEC

tag: cell organism

value: umbilical vein endothelial cells

value: mesoderm

value: U

tag: replicate


title: UW_RepliSeq_GM12878

value: Stamatoyannopoulous - University of Washington

value: RepliSeq

value: Assessment of DNA Replication Timing

value: human

tag: cell description

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

tag: cell karyotype

tag: cell lineage

tag: cell sex

value: F

tag: phase


title: HudsonAlpha_RnaSeq_T-47D_DMSO_4hr_longPolyA (superseded by GSE93442)

description:
****************************
GSM923428 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93442
****************************

tag: datatype

value: RnaSeq

value: Sequencing analysis of RNA expression

tag: rnaextract

tag: rnaextract description

tag: labexpid


title: UW_RepliSeq_GM12813

tag: datatype description

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment:Epstein-Barr Virus transformed

value: normal

tag: phase description

value: Flow sorted, G1b phase corresponds to the second half of the first DNA content window


title: HudsonAlpha_RnaSeq_ECC-1_Genistein_100nM_4hr_longPolyA (superseded by GSE93440)

description:
****************************
GSM923426 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93440
****************************

value: endoderm

tag: treatment description

value: 4 h with 100 nM Genistein (Myers)

value: longPolyA

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

tag: labversion

tag: mapalgorithm

tag: mapalgorithm description

value: bowtie v0.12.5

tag: readtype

tag: readtype description

value: Single 36 nt reads


title: TNGA-2i_H3K27me3

description: Chromatin IP against H3K27me3

tag: strain

tag: cell type

value: ES-cells

tag: chip antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody catalog#

tag: chip antibody batch/lot#


title: HudsonAlpha_RnaSeq_U87_longPolyA (superseded by GSE90176)

description:
****************************
GSM923437 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90176
****************************

tag: datatype

tag: rnaextract

tag: replicate

value: No special treatment or protocol applies


title: HudsonAlpha_RnaSeq_ECC-1_BPA_100nM_4hr_longPolyA (superseded by GSE93437)

description:
****************************
GSM923422 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93437
****************************

tag: datatype description

tag: cell lineage

tag: rnaextract description

tag: labexpid


title: HudsonAlpha_RnaSeq_PANC-1_longPolyA (superseded by GSE93450)

description:
****************************
GSM923421 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93450
****************************

tag: labversion

tag: mapalgorithm

tag: treatment description


title: HudsonAlpha_RnaSeq_A549_EtOH_0.02pct_longPolyA

tag: mapalgorithm description

tag: readtype

tag: readtype description

value: 1 h with 0.02% Ethanol (Myers)


title: HudsonAlpha_RnaSeq_SK-N-SH_longPolyA (superseded by GSE93449)

description:
****************************
GSM923419 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93449
****************************

source_name: SK-N-SH


title: UW_RepliSeq_HeLa-S3

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: RepliSeq

value: Assessment of DNA Replication Timing

tag: cell

tag: cell organism

value: human

tag: cell description

value: cervical carcinoma

tag: cell karyotype

value: cancer

value: ectoderm

tag: cell sex

tag: phase

tag: phase description


title: HudsonAlpha_RnaSeq_A549_DEX_100nM_longPolyA

value: immortalized cell line

tag: line

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

value: 1 h with 100 nM Dexamethasone (Myers)

tag: rnaextract

tag: rnaextract description

tag: replicate


title: HudsonAlpha_RnaSeq_ECC-1_DMSO_4hr_longPolyA (superseded by GSE93438)

description:
****************************
GSM923423 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93438
****************************

tag: cell lineage

value: endoderm

value: longPolyA

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

tag: labexpid

tag: labversion

tag: mapalgorithm

tag: mapalgorithm description

value: bowtie v0.12.5

tag: readtype

value: Single 36 nt reads


title: UW_RepliSeq_K562

tag: lab

value: UW

tag: lab description

tag: cell

tag: cell organism

tag: cell description

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: mesoderm

value: F

value: Flow sorted, G1 phase corresponds to the first DNA content window


title: UW_RepliSeq_HepG2

value: Stamatoyannopoulous - University of Washington

value: RepliSeq

value: Assessment of DNA Replication Timing

value: human

value: liver carcinoma

tag: cell karyotype

tag: cell sex

value: M

tag: phase

tag: phase description

value: Flow sorted, G1b phase corresponds to the second half of the first DNA content window


title: HudsonAlpha_RnaSeq_A549_DEX_100pM_longPolyA (superseded by GSE93436)

description:
****************************
GSM923418 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93436
****************************

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: treatment description

value: 1 h with 100 pM Dexamethasone (Myers)

tag: rnaextract

tag: rnaextract description

tag: readtype description


title: UW_RepliSeq_IMR90

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

value: normal

tag: cell lineage

value: endoderm

tag: labexpid

tag: replicate


title: UW_RepliSeq_NHEK

source_name: NHEK

tag: lab

value: UW

tag: lab description

value: NHEK

value: epidermal keratinocytes

value: ectoderm


title: UW_RepliSeq_MCF-7

value: Stamatoyannopoulous - University of Washington

tag: cell

tag: cell organism

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: cancer

value: F


title: UW_RepliSeq_SK-N-SH

value: RepliSeq

value: Assessment of DNA Replication Timing

value: SK-N-SH

value: human

tag: cell description

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

tag: cell karyotype


title: UW_RepliSeq_GM06990

value: lymphoblastoid, International HapMap Project, CEPH/Utah, treatment:Epstein-Barr Virus transformed

value: mesoderm

tag: cell sex

tag: phase

value: Flow sorted, G1b phase corresponds to the second half of the first DNA content window


title: HudsonAlpha_RnaSeq_Jurkat_longPolyA (superseded by GSE93435)

description:
****************************
GSM923424 record metadata submitted on Apr 27 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93435
****************************

source_name: Jurkat

tag: datatype

value: RnaSeq

value: Sequencing analysis of RNA expression

value: longPolyA

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

tag: labversion

tag: mapalgorithm

tag: mapalgorithm description

value: bowtie v0.12.5

tag: readtype

value: Single 36 nt reads

value: No special treatment or protocol applies


title: HDAC2 ChIP sequencing in 2hr 100nM DHT treated VCaP cells

city: Singapore

first: Kern Rei

last: Chng

address: 60 Biopolis Street #02-01 Genome

department: Cancer Biology and Pharmacology 3

country: Singapore

institute: GIS

description: HDAC2 DHT

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer II Pipeline. In-house (Genome Institute of Singapore) BATMAN program was used for mapping the sequence tags to the reference genome hg18. In order to avoid potential PCR amplification bias, tags that shared the same mapping location on the same strand were removed. The uniquely-mapped reads with at most 2-mismatches were kept for further processing.
Peak calling: Binding peaks were determined using in-house Control based ChIPSeq Analysis Tools (CCAT) program with reference to a set of input reads as negative control. Peaks with a cut-off of FDR 0.2 were considered.
CCAT file format: chromosome, peakcenter, regionstart, regionend, tagcount, bgcount, zscore, fdr

source_name: VCaP prostate cancer cells, 2hr DHT treated, HDAC2 ChIP DNA

growth_protocol: The human prostate cancer VCaP cells (American Type Culture Collection) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution at 37C under 5% CO2. For experiments requiring androgen/vehicle (DHT (Tokyo Chemical Industry) /EtOH) treatment, VCaP cells were grown in phenol red free DMEM supplemented with 10% charcoal stripped fetal bovine serum (CDFBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution for 24 hours prior stimulation unless otherwise stated.

extract_protocol: All DNA samples were processed as per the Illumina Solexa ChIP-seq sample processing methods. VCaP cells were harvested, pelleted down, crosslinked and lysed with SDS (with protease inhibitor) before sonication was done. The sonicated chromatin was first decrosslinked and then purified by the QIAquick spin PCR purification kit (Qiagen, California) to obtain the genomic VCaP DNA for ChIP-Seq. 5 to 10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments followed by the QIAquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification with Pfx DNA polymerase (Invitrogen) and Illumina primers. 200-300 bp size fractions were selectively isolated from the 2% ultra low range agarose gel and eluted by Qiagen gel extraction kit. The extracted DNA was quantified using Agilent bioanalyzer and subjected to Solexa sequencing according to the manufacturer's instructions.

treatment_protocol: Hormone-depleted cells were treated with DHT to a final concentration of 100 nM.  Cells treated with an equal volume vehicle, ETOH (ethanol) are used as controls

tag: cell line

value: VCaP

tag: cell type

value: prostate cancer cells

tag: treatment

value: dihydrotestosterone (DHT)

tag: treatment duration

tag: chip antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog number

tag: antibody lot#


title: UW_RepliSeq_GM12801

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: RepliSeq

tag: datatype description

value: Assessment of DNA Replication Timing

tag: cell

tag: cell organism

tag: cell description

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

tag: cell lineage

value: M

tag: labexpid

tag: phase description

tag: replicate


title: EZH2 ChIP sequencing in 2hr ETOH treated VCaP cells

description: EZH2 ETOH

source_name: VCaP prostate cancer cells, 2hr ETOH treated, EZH2 ChIP DNA

tag: cell line

tag: cell type

value: ETOH

value: Active Motif


title: UW_RepliSeq_GM12812

tag: datatype

value: human

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment:Epstein-Barr Virus transformed

tag: cell karyotype

value: normal

value: mesoderm

tag: cell sex

tag: phase

value: Flow sorted, G1b phase corresponds to the second half of the first DNA content window


title: HDAC3 ChIP sequencing in 2hr 100nM DHT treated VCaP cells

description: HDAC3 DHT

source_name: VCaP prostate cancer cells, 2hr DHT treated, HDAC3 ChIP DNA

value: VCaP

tag: treatment

tag: treatment duration

tag: chip antibody

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog number

tag: antibody lot#


title: EZH2 ChIP sequencing in 2hr 100nM DHT treated VCaP cells

description: EZH2 DHT

source_name: VCaP prostate cancer cells, 2hr DHT treated, EZH2 ChIP DNA

value: prostate cancer cells

value: dihydrotestosterone (DHT)


title: HDAC1 ChIP sequencing in 2hr ETOH treated VCaP cells

description: HDAC1 ETOH

source_name: VCaP prostate cancer cells, 2hr ETOH treated, HDAC1 ChIP DNA

value: Abcam


title: HDAC1 ChIP sequencing in 2hr 100nM DHT treated VCaP cells

description: HDAC1 DHT

source_name: VCaP prostate cancer cells, 2hr DHT treated, HDAC1 ChIP DNA


title: ERG ChIP sequencing in 18hr 100nM DHT treated VCaP cells

description: ERG 18 hr

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer II Pipeline. In-house (Genome Institute of Singapore) BATMAN program was used for mapping the sequence tags to the reference genome hg18. In order to avoid potential PCR amplification bias, tags that shared the same mapping location on the same strand were removed. The uniquely-mapped reads with at most 2-mismatches were kept for further processing.
Peak calling: Binding peaks were determined using in-house Control based ChIPSeq Analysis Tools (CCAT) program with reference to a set of input reads as negative control. Peaks with a cut-off of FDR 0.05 were considered.
CCAT file format: chromosome, peakcenter, regionstart, regionend, tagcount, bgcount, zscore, fdr

source_name: VCaP prostate cancer cells, 18hr DHT treated, ERG ChIP DNA

value: anti-ERG


title: AR ChIP sequencing in 18hr 100nM DHT treated VCaP cells

description: AR 18 hr

source_name: VCaP prostate cancer cells, 18hr DHT treated, AR ChIP DNA

value: anti-AR


title: ERG ChIP sequencing in 2hr 100nM DHT treated VCaP cells

description: ERG 2 hr

source_name: VCaP prostate cancer cells, 2hr DHT treated, ERG ChIP DNA


title: T47D_PR_ChIP_Replicate3

status: Public on Apr 26 2012

city: Westmead

first: J

middle: Dinny

last: Graham

state: NSW

address: 176 Hawkesbury Rd

department: Westmead Institute for Medical Research

country: Australia

institute: University of Sydney

data_processing: All sequences were at 36bp read length except for one ChIP (T47D_PR_ChIP1.fq) and one matched input control sample from T-47D cells. These samples were processed with a 64bp read length, but were trimmed to 36bp during data processing to avoid bias in the downstream analysis.Sequences were aligned to repeat masked human genome hg18 (NCBI build 36) using Bowtie 0.12.0.1 (bowtie-bio.sourceforge.net). Up to 2 mismatches were allowed in the aligned sequences. Multiple alignments were permitted up to a multiplicity of 10, but only the best ranked alignment was reported.

source_name: T-47D breast cancer cell line

growth_protocol: Cells were grown in standard recommended media in monolayer cultures at 37C and 5% CO2 to 80-90% confluent prior to treatment

extract_protocol: Sonicated lysates were cleared by centrifugation and PR-bound DNA fragments were isolated using anti-PR mouse monoclonal antibody and magnetic bead secondary.

treatment_protocol: Cells were treated with 10nM ORG2058 for 45 minutes, then fixed in culture by addition of formaldehyde to 1% v/v for 10 minutes, followed by cold PBS wash and harvesting by scraping. Pellets were lysed and sonnicated to achieve genomic DNA fragments with average size 300-500bp.

tag: tissue

value: Breast

tag: malignant status

value: adenocarcinoma


title: T47D_input_DNA_Replicate2


title: AR ChIP sequencing in 2hr 100nM DHT treated VCaP cells

description: AR 2 hr

source_name: VCaP prostate cancer cells, 2hr DHT treated, AR ChIP DNA


title: ERG ChIP sequencing in 0hr treated VCaP cells

description: ERG 0 hr

source_name: VCaP prostate cancer cells, 0hr treated, ERG ChIP DNA


title: T47D_PR_ChIP_Replicate2


title: AR ChIP sequencing in 0hr treated VCaP cells

description: AR 0 hr

source_name: VCaP prostate cancer cells, 0hr treated, AR ChIP DNA


title: VCaP Genomic Input sequencing

description: VCaP Input

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer II Pipeline. In-house (Genome Institute of Singapore) BATMAN program was used for mapping the sequence tags to the reference genome hg18. In order to avoid potential PCR amplification bias, tags that shared the same mapping location on the same strand were removed. The uniquely-mapped reads with at most 2-mismatches were kept for further processing.
Peak calling: Binding peaks were determined using in-house Control based ChIPSeq Analysis Tools (CCAT) program with reference to a set of input reads as negative control. Peaks with a stringent cut-off of FDR 0.005 were considered.
CCAT file format: chromosome, peakcenter, regionstart, regionend, tagcount, bgcount, zscore, fdr

source_name: VCaP prostate cancer cells, input


title: AB32_PR_ChIP_Replicate2

source_name: AB32 PR positive transformed normal breast cell line

value: normal transformed


title: AB32_input_DNA_Replicate1


title: AB32_input_DNA_Replicate2


title: T47D_input_DNA_Replicate1


title: T47D_PR_ChIP_Replicate1


title: HDAC3 ChIP sequencing in 2hr ETOH treated VCaP cells

description: HDAC3 ETOH

source_name: VCaP prostate cancer cells, 2hr ETOH treated, HDAC3 ChIP DNA

value: ETOH


title: AB32_PR_ChIP_Replicate1


title: HDAC2 ChIP sequencing in 2hr ETOH treated VCaP cells

description: HDAC2 ETOH

source_name: VCaP prostate cancer cells, 2hr ETOH treated, HDAC2 ChIP DNA


title: DG75-eGFP, 60 min untagged RNA,  Rep.1

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

description:
AY60U
w/o rRNA depletion

data_processing: Reads were mapped in a 3-step process using the Bowtie alignment program (Langmead, et al., 2009). First, reads were aligned to pre-rRNA sequences (18S, 5.8S, 28S and spacer regions). The remaining unmapped reads were aligned to all Ensembl transcripts (Ensembl version 60) excluding pseudo-genes and haplotypes to identify exonic and exon-exon junction reads (aligned reads overlapping an exon-exon junction by at least 1 nt). Reads that remained unmapped after step two were aligned to the human reference genome (GRCh37/hg19) to identify intron and exon-intron junction reads (overlapping an exon-intron junction by at least 1 nt). For each read the best alignment location was used. Reads mapping equally well to two different locations were discarded. The following Bowtie settings were used: seed region = first 20 nt, 3 mismatches allowed in the seed, 5 in the whole alignment.

source_name: DG75-eGFP, 60 min untagged RNA

growth_protocol: RPMI 1640 medium, 10% fetal calf serum, 100 IU/ml Penicillin, 100 ug/ml Streptomycin and 2 mM L-Glutamin

extract_protocol: whole-transcriptome analysis (WTAK) protocol

treatment_protocol: 500 uM 4sU added for 5 to 60 min, isolation of total cellular RNA using Trizol (Invitrogen), separation of total cellular RNA into nascent and untagged pre-existing RNA as described in Dolken et al., RNA 2008.

value: B-cells

tag: plasmid

value: eGFP

tag: celluar rna type

value: untagged RNA


title: hj20_b

city: Kansas City

first: Huan

last: Yang

state: MO

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

description: small RNA

data_processing:
The quality of the raw sequence data was analyzed to check if any alteration of the data needed to be done before continuing with downstream analysis. Fastqc was used for a more in-depth look at the quality of the sequence data. All samples were run on the same lane, using TruSeq indexes to distinguish between samples. Overall, sequence quality looks very good for all samples. Clipping is still performed on these samples due to the presence of adapter sequence in the reads as described in the Methods section.
Due to the short read lengths of the small RNA’s, adapter sequence was present at the 5’ end of the reads. Fastx_clipper (v0.0.13) was used to remove this adapter sequence. As the valid portion of the reads are of variable length (the small RNAs range in size), a subset of the adapter sequence was used that looked to be matched in the vast majority of reads. Then, remaining portions of the read smaller than 8 bases long were removed from the resulting clipped sequence file. In this way, reads that contained more of the adapter sequence than what was clipped would still have the rest of the adapter removed, as the length of the remaining adapter was less than 8bp.
Tophat (v1.4.0) was used to perform the alignment of the clipped reads. The UCSC reference genome ce6 was used for alignment and gene annotations. These reference files were downloaded from Illumina’s igenome ftp site. Samtools was used to sort and index the resulting bam files.
Genome_build: ce6

organism: Caenorhabditis elegans

growth_protocol: Synchronized L1 worms were grown on RNAi plates seeded with HT115 E. coli expressing a sel-1 RNAi trigger as previously described (Pak and Fire 2007). After 48hrs at 20oC, 40000 worms were washed 5 times with 10ml M9, and then homogenized in Tri-reagent. Samples were kept at -80oC.

extract_protocol: Purified total RNA were processed with MirVana kit (Invitrogen) for small RNA enrichment. Equal amount of small RNAs (20~30ug) were resolved on 15% TBE-Urea Acrylamide gels. Gels containing small RNAs of 21-24nt were cut out and purified with a small-RNA PAGE Recovery Kit (Zymo Research, R1070). Each small RNA sample was split into two (one for TAP treatment and another untreated) and processed with the ScriptMiner Small RNA-Seq Library Preparation Kit (Epicentre, SMMP1012). Libraries from different samples were indexed with RNA-Seq Barcode Primers (Epicentre, RSBC10948). Two biological samples of each condition (wild type, wild type + TAP, rde-10 mutant, rde-10 mutant + TAP, rde-11 mutant and rde-11 mutant + TAP) were used for library preparation.

value: whole animal

tag: genotype/variation

value: rde-10 mutant

tag: Stage

value: 48hrs after L1

tag: tap treatment

value: No


title: hj37_b

description: small RNA

value: rde-11 mutant


title: hj20+TAP_b

description: small RNA

value: Yes


title: N2_b

description: small RNA

value: wild type


title: hj37+TAP_a

description: small RNA


title: N2+TAP_b

description: small RNA


title: DG75-eGFP, 20 min nascent RNA,  Rep.1

description:
AY20E
w/o rRNA depletion

source_name: DG75-eGFP, 20 min nascent RNA

tag: cell line

tag: cell type

value: nascent RNA


title: hj37+TAP_b

description: small RNA


title: hj20+TAP_a

description: small RNA


title: DG75-eGFP, 60 min nascent RNA,  Rep.1

description:
AY60E
w/o rRNA depletion

source_name: DG75-eGFP, 60 min nascent RNA


title: DG75-eGFP, 15 min nascent RNA, Rep.1

description:
AY15E
w/o rRNA depletion

source_name: DG75-eGFP, 15 min nascent RNA


title: DG75-eGFP, 10 min nascent RNA,  Rep.1

description:
AY10E
w/o rRNA depletion

source_name: DG75-eGFP, 10 min nascent RNA


title: hj37_a

description: small RNA


title: DG75-eGFP, 5 min nascent RNA, Rep.1

description:
AY5E
w/o rRNA depletion

source_name: DG75-eGFP, 5 min nascent RNA


title: N2+TAP_a

description: small RNA


title: ICF patient

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

data_processing:
Illumina Casava1.7 software was used for basecalling.
Read mapping: Two reference sequences were prepared based on the hg19 human reference; referenceC2T had the C residues replaced by T's, and referenceG2A had the G’s replaced by A's. Two sets of reads were generated in the same way; setC2T with the C’s replaced by T's, and setG2A with the G's replaced by A's. Both sets of reads were aligned to each of the two references, producing four sets of mappings. This mapping strategy allowed reads to be aligned irrespective of the methylation status of any C residues.
The alignment was performed using the GEM alignment software allowing up to 4 mismatches in high quality bases (bases with quality scores > 25). Uniquely mapping read pairs were used to generate an empirical distribution of insert sizes of each of the libraries, and this information was used to select read pairs with unique compatible mappings.
The bisulfite conversion followed by a PCR step generates 4 different strands; the original + and - strands along with their complements. Reads derived from the original + strand (and its complement) will align to referenceC2T, while reads from the original - strand (and complement) will align to referenceG2A. Both members of a read pair are derived from the same original strand, and >99% of mapped reads could have the original strand assigned unambiguously. By keeping the information on the original strand origin of each read pair, the methylation status of C residues on either of the two original strands can be inferred along with the underlying genotypes, because any conversion due to the bisulphite treatment will only be seen on read pairs deriving from one of the two original strands.
Genome_build: hg19
Supplementary_files_format_and_content: Methylation calls files for C's in the bsmap alignment files were generated using methratio.py.

source_name: Blood, ICF patient

extract_protocol:
DNA were extracted using phenol:chloroform:isoamylalcohol (Sigma).
For normal BS-seq library construction, 10μg genomic DNA was fragmented using a Covaris sonication system (Covaris S2). Following fragmentation, libraries were constructed using the Illumina Paired-End protocol consisting of end repair, <A> base addition and methylated-adaptor ligation. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different insert sizes were excised from the same lane of a 2% TAE agarose gel. Normally, three bands are excised corresponding to DNA insert sizes of 80-100 bp, 100-120 bp to 120-150bp. Products were purified by using the QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. PCR was carried out in a final reaction volume of 50μl consisting of 20μl purified DNA, 4μl 2.5 mM dNTP, 5 μl 10X buffer, 0.5 μl JumpStart™ Taq DNA polymerase, 2μl 10uM PCR primers and 37.5 μl ΜltraPure TM Water and the following thermal cycling program: 94ºC 30 s, 10 cycles of 94ºC 30 s, 60ºC 30 s, 72ºC 30 s then prolong with 1 min at 72ºC. PCR products were sequenced with a HiSeq 2000. The alignment was performed using GEM.

treatment_protocol: B cells of a healthy donor and ICF patient were immortalized by Epstein-Barr-Virus (EBV).

value: blood

value: EBV immortalized B cells

tag: disease status

value: immunodeficiency, centromere instability and facial anomalies (ICF) syndrome


title: Healthy control

source_name: Blood, healthy control

value: healthy


title: N2_a

description: small RNA


title: hj20_a

description: small RNA


title: DG75-eGFP, 60 min total RNA,  Rep.1

description:
AY60T
w/o rRNA depletion

source_name: DG75-eGFP, 60 min total RNA

value: total RNA


title: SNEB3

status: Public on Apr 25 2012

city: Dunsany

first: Chris

last: Creevey

state: Co. Meath

address: Grange

department: Animal & Bioscience Research Department

country: Ireland

institute: Teagasc

description: experimental:14d post-caliving with restricted diet

data_processing:
Basecalls performed using CASAVA version 1.4
RNAseq reads were aligned to Btau4.0 genome using Bowtie (settings:  -S -m 1 -n 2 --solexa1.3-quals), sorted and possible PCR duplicates were removed using Samtools.
Raw counts were enumerated using HTSEQ-count (settings: mode = union)
Genome_build: Btau_4.0
Supplementary_files_format_and_content: Tab delimited txt files: First row contains the ENSEMBL gene IDs and second row the raw number of reads that map to each gene.

organism: Bos taurus

source_name: experimental:14d post-calving with restricted diet

extract_protocol: Total RNA was extracted from frozen liver tissue by homogenisation in Trizol. RNA was then DNAse treated and purified using Qiagen RNeasy spin columns. Standard Illumina single read mRNA-seq libraries were constructed from cDNA which was made from mRNA which had been purified from total RNA by two rounds of polyA tail selection using oligo dT beads.

tag: energy balance

value: severe negative

value: liver


title: MNEB4

description: control:14d post-calving with adlibitum diet

value: mild negative


title: SNEB2


title: SNEB6


title: SNEB1


title: SNEB5


title: MNEB5

source_name: control:14d post-calving with adlibitum diet


title: SNEB4


title: MNEB3


title: MNEB1


title: [E-MTAB-935] polyA+_testis_7060321, Batch_7_testis

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

description: Performer: University of Lausanne, Switzerland

data_processing: processed data not provided

extract_protocol:
nucleic_acid_extraction | RNA from tissues was isolated by a modified guanidium thiocynate methods followed by polyA+ RNA selection with two rounds of oligo(dT)-cellulose columns. Selected targets were then amplified by RT-PCR
sequencing | Aliquots of up to 5000 RT-PCRs reactions were pooled together and the sequencing library was prepared with no fragmentation using the TruSeq DNA protocol. DNA fragments were sequenced on a Illumina HiSeq2000 sequencer and 2 multiplexed libraries were loaded per lane. The sequencing was performed at the University of Lausanne, Lausanne, Switzerland.
bioassay_data_transformation |

tag: material type

tag: organismpart

value: testis

tag: Sex

value: male

tag: biosourcetype

tag: biosourceprovider

value: Clontech


title: 6hr_Recovery BC7

city: Durham

first: Colin

last: Maxwell

state: NC

address: 4314 FFSC

institute: Duke

description:
Reads mapping to genome and transcriptome and eads mapping to genome after 22 bp stripped from 5' end of read when the 22 bp is either SL1 or SL2
mRNA-seq: single-stranded RNA adapter ligation 5' sequencing

data_processing: We first mapped reads to the WormBase 210 version of the genome (WS210) using Bowtie (v. 0.12.7)  (Langmead et al. 2009). Reads that did not map in this step were aligned to the Wormbase 220 predicted transcriptome, whose coordinates had been mapped back to the WS210 coordinate system. We used Bowtie to map to the transcriptome as opposed to TopHat because we found that many reads mapped to transcriptome-derived splice junctions with Bowtie were not mapped with TopHat (data not shown). ~70% of genes in C. elegans are spliced to a 22 nt sequence donated by a snRNA called a ‘trans-splice leader’ (T Blumenthal 2005). The vast majority of trans-splice leaders come from two different sequences: either splice leader 1 or 2 (SL1 or SL2) (T Blumenthal 2005). We were interested in quantifying the overall levels of trans-splicing.  Therefore, reads that did not map to either the genome or the transcriptome were stripped of the first (5’) 22 nt of sequence and remapped to determine if these reads came from the 5’ end of trans-spliced mRNAs. We determined whether the stripped 22 nt sequence corresponded to SL1 or SL2 for the reads that mapped after stripping. We created alignment files of reads mapping to the genome and transcriptome along with an index linking the IDs of reads containing splice leaders to the type of splice leader contained in the read (ie, SL1 or SL2). Langmead B, Trapnell C, Pop M, and Salzberg S. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25. doi:10.1186/gb-2009-10-3-r25 Blumenthal, T. 2005. Trans-splicing and operons. In Wormbook (ed. The C. Elegans Research Community). http://www.wormbook.org.

source_name: L1 larvae

growth_protocol: Wild-type C. elegans strain N2 was used for RNA-seq.  The N2 stock used was from the Sternberg collection at the California Institute of Technology; this strain was obtained from the Caenorhabditis Genetics Center in 1987, expanded and frozen.  Nematodes were maintained on standard NGM plates with E. coli OP50 as food (Lewis, 1995), but liquid culture was used to prepare RNA-seq samples.

extract_protocol: RNA was prepared using TRIzol (Invitrogen) according to the manufacturer’s protocol with minor modifications.  1 mL TRIzol was used per sample, and homogenization was supplemented with 100 mL of acid washed sand.  Poly-adenylated mRNA was isolated from total RNA using Dynal oligo-(dT) magnetic beads (Invitrogen) according to the manufacturer’s protocol.  200 ng poly-adenylated RNA was used in a Tobacco Acid Pyrophosphatase reaction (Epicentre) according to the manufacturer’s protocol in order to remove 5’ caps.  The product was purified with phenol/chloroform extraction and ethanol precipitation using GlycoBlue as a coprecipitant (Ambion).  This purified product was then used in the RNAse III fragmentation reaction at the beginning of the Solid Total RNA-Seq Kit Whole Transcriptome protocol (Applied Biosystems).  The manufacturer’s instructions were followed for the remainder of the library preparation process.  Fragmentation efficiency was analyzed with the BioAnalyzer (Agilent), and one-half of each sample (corresponding to approximately 100 ng RNA) was used for adapter ligation.  cDNA was gel purified to capture inserts of RNA fragment size 100 – 200 nt.  12 PCR cycles were used to amplify the libraries.  Libraries were processed and sequenced on the Solid 4 system according to the manufacturer’s protocols.

treatment_protocol: A starved 5 cm plate was used to inoculate 25 mL of liquid culture (S-complete plus 40 mg/mL E. coli HB101)(Lewis, 1995).  The culture was incubated at 20°C and 180 rpm for 65 hr and then bleached to produce a clean preparation of embryos.  Embryos were suspended in S-complete at 5 eggs/mL and incubated at 20°C and 180 rpm for 24 hr so that they hatch and enter L1 arrest.  After 24 hr, cultures were fed with 40 mg/mL HB101 to initiate synchronous development and they were incubated at 20°C and 180 rpm for 57 hr.  After 57 hr the cultures were bleached, and the eggs were suspended in S-complete at 10 eggs/mL.  In these conditions, the first eggs are fertilized at about 53 hr, and when bleached at 57 hr the yield is typically about 10 eggs per worm.  Animals were incubated at 20°C and 180 rpm for 24 hr so that they hatch and enter L1 arrest.  The 0 hr time point was collected 24 hr after bleaching, corresponding to approximately 12 hr L1 arrest.  The remainder of the culture was fed with 25 mg/mL HB101 and incubated at 20°C and 180 rpm with collections at 1, 3 and 6 hr after feeding .  Larvae were collected by centrifugation and washed 3 times in S-basal before being flash frozen. Lewis, J.A., and Fleming, John T. 1995. Basic Culture Methods. In Caenorhabditis elegans: Modern biological analysis of an organism (eds. H.F. Epstein, and Shakes, D. C.), pp. 4-27. Academic Press, San Diego, California.

tag: hours of recovery

tag: develomental stage

value: L1 larvae


title: 3hr_Recovery BC6


title: 6hr_Recovery BC4


title: 12hr_Starved BC5


title: 6hr_Recovery BC16


title: 1hr_Recovery BC8


title: [E-MTAB-935] polyA+_spleen_6090097, Batch_7_spleen

value: spleen


title: 12hr_Starved BC13


title: [E-MTAB-935] polyA+_muscle_7040106, Batch_7_muscle

value: muscle


title: [E-MTAB-935] polyA+_lung_1100350, Batch_7_lung

value: lung


title: 1hr_Recovery BC3


title: [E-MTAB-935] polyA+_kidney_7110096, Batch_7_kidney

value: kidney


title: MNEB2

tag: tissue


title: [E-MTAB-935] polyA+_heart_7082801A, Batch_7_heart

value: heart


title: 3hr_Recovery BC1


title: [E-MTAB-935] polyA+_brain_6120217, Batch_7_brain

value: brain


title: Mouse_Liver_Input

city: Tel-Hashomer

first: Sharon

last: Moshitch-Moshkovitz

address: Laboratory wing

department: Cancer Research Center

institute: Sheba Medical Center

data_processing: Supplementary_files_format_and_content: Supplementary data human brain' and 'Supplementary data mouse liver' files are provided in .txt format. They contain a dataset of all identified m6A peaks in normal human brain and nornal mouse liver, respectively. Corresponding legends are:  id – KnownCanonical identification; chr – chromosome; txStart – transcription start position on chromosome; txEnd – Transcription end position on chromosome; strand - +/- chromosome strand;  geneSymbol – official symbol of gene; desc – description;  Factor_iscoding– either coding or noncoding, depending on the annotation of the gene in the UCSC table; Meanexpquant – expression quantile of the gene based on reads in input experiment; Peaksnum – number of peaks identified in gene; Peakspos – position of peaks relative to beginning of transcript (after removing introns); Peaksexonnum – ordinal number of exons in which the peaks were identified; Peaksexlengths – lengths of the exons in which the peaks were found; Peakscores – the peakscore of the identified peaks; Annotpeakpos – segment along the gene in which the peaks.

source_name: Mouse liver

extract_protocol: Total RNA was purified from whole mouse liver using 5PRIME PerfectPure RNA Cultured Cell kit (cat#2302340). PolyA RNA was selected by one round of Sigma GenElute mRNA Miniprep Kit (cat#MRN70-1KT).Total RNA of normal human brain was purchased from Biochain, CA, USA. RNA was fragmented chemically to ~100 nt long fragments and subjected to IP using anti-m6A antibodies. 1st strand cDNA was synthesized using Illumina random primers and Invitrogen SuperScript II Reverse Transcriptase (Cat# 18044-014) then 2strand cDNA was synthesized by Illumina's mRNA Sample preparation Kit (Part# 1004814). 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 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  ~200 bp DNA fragments (insert plus adaptor and PCR primer sequences)  were isolated from 2% agarose gel. Purified DNA fragments were PCR amplified with Illumina primers for 15 cycles and 10pM DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

value: Normal mouse liver

tag: antibody