title: Kyoto_DGRC204406_het_input

description: ChIP input

data_processing:
The ChIP-seq libraries were sequenced on the Illumina HiSeq platform for 76 cycles in a pair-end run. The resulting reads were mapped with Bowtie 2 with the preset option --sensitive (Heinz et al., 2010). Only read pairs mapping concordantly were used for further analysis. For calling H3K9me3 peaks, annotation of called peaks and visualization, we used the HOMER software package (Breitkreutz et al., 2008). Enrichments of H3K9me3 signal were calculated using input libraries as a control signal. All peaks within 8kb distance from each other were merged into regions. We used annotatePeaks from Homer to then calculate the tag counts in heterozygous and homozygous libraries over those regions, normalizing each tag to reads per million genomic mappers.
Genome_build: dm3
Supplementary_files_format_and_content: H3K9me3 peaks in heterozygous 204406 flies identified with Homer are provided as BED files. Tag counts over these regions in heterozygous and homozygous 204406 flies calculated with Homer (annotatePeaks) are provided as text files.

extract_protocol:
Lysates from formaldehyde fixed ovaries were clarified after sonication and histone-DNA complexes were isolated with antibody.
ChIP was done as described in Ram et al. (2011) and Garber et al. (2012), with some modifications. Approximately fifty ovaries were dissected from heterozygous or homozygous flies into cold PBS and washed once with PBS. Ovaries were then fixed in 1.8% formaldehyde for 10 minutes, then quenched by adding glycine to 0.125M and immediately placed on ice. Tissue was then homogenized by douncing five times with pestle A (Kontes). Washed once with PBS supplemented with protease inhibitors (Roche) and pellet was flash frozen in liquid nitrogen. Pellets were then thawed on ice and resuspended in 1mL Lysis Buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and lysed for 10 minutes in ice. Chromatin was sheared to 200-800bp using a Branson sonifier (model S-450D). After clearing lysate by centrifugation, 9mLs of Dilution Buffer (0.01% SDS, 1.1%Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl) were added to the lysate and 5mLs of the lysate were incubated with a 50ul of an equal mixture of conjuagted protein A and G Dynabeads (Invitrogen). To conjugate beads, they first had been washed once in Blocking Buffer (1X PBS, 0.5% TWEEN 20, 0.5% BSA), then coupled for 1 hour at 4ºC with 5ug of H3K9me3 antibody (Abcam 8898) and finally washed twice with Blocking Buffer to remove excess antibody. Lysate and conjugated magnetic beads were rotated at 4ºC overnight. Beads were then resuspended in 200ul cold RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 14 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC) and transfer to a 96-well plate. All further separation steps were performed in the 96-well plate magnet. Beads were washed five times with 200ul cold RIPA, two times with RIPA buffer supplemented with 500 mM NaCl, two times with LiCl buffer (10 mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), and once with TE (10Mm Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted in 50 µl of 0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris HCl pH 8.0. The eluate was reverse cross-linked at 65ºC for 4 hours and then treated with 2ul of RNaseA (Roche, 11119915001) for 30 min followed by 2.5 µl of Proteinase K (NEB, P8102S) for two hours. Library preparation was done as indicated in Garber et al. (2012), but without automation. In brief, to purify DNA 120ul of Ampure XP beads (Agencourt) were added to the reverse cross-linked samples, mixed by pipetting and incubated for 2 minutes. Samples were then placed on the magnetic stand for 4 minutes to separate beads, followed by 2 washes with 70% ethanol and air dried for 4 minutes and eluted in 10mM Tris-HCl pH 8.0. Library was constructed by performing DNA end-repair, A-base addition, adaptor ligation and enrichment PCR. After each step DNA was purified by adding 20% PEG and 2.5 M NaCl to the reaction, to allow DNA to bind to Ampure XP beads already in the tube. Samples were not moved form their original well position, until after PCR enrichment. The libraries were sequenced on the Illumina HiSeq platform for 76 cycles in a pair-end run.

tag: antibody

value: ChIP input


title: Kyoto_DGRC204406_het_H3K9me3

status: Public on May 09 2013

type: SRA

city: Cold Spring Harbor

first: Felix

last: Muerdter

state: New York

address: 1 Bungtown Rd

country: USA

institute: Cold Spring Harbor Laboratories

description: ChIP H3K9me3

library_source: genomic

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Drosophila melanogaster ovary

growth_protocol: Flies were raised at 25°C on standard cornmeal-molasses agar medium.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP was done as described in Ram et al. (2011) and Garber et al. (2012), with some modifications. Approximately fifty ovaries were dissected from heterozygous or homozygous flies into cold PBS and washed once with PBS. Ovaries were then fixed in 1.8% formaldehyde for 10 minutes, then quenched by adding glycine to 0.125M and immediately placed on ice. Tissue was then homogenized by douncing five times with pestle A (Kontes). Washed once with PBS supplemented with protease inhibitors (Roche) and pellet was flash frozen in liquid nitrogen. Pellets were then thawed on ice and resuspended in 1mL Lysis Buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and lysed for 10 minutes in ice. Chromatin was sheared to 200-800bp using a Branson sonifier (model S-450D). After clearing lysate by centrifugation, 9mLs of Dilution Buffer (0.01% SDS, 1.1%Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl) were added to the lysate and 5mLs of the lysate were incubated with a 50ul of an equal mixture of conjuagted protein A and G Dynabeads (Invitrogen). To conjugate beads, they first had been washed once in Blocking Buffer (1X PBS, 0.5% TWEEN 20, 0.5% BSA), then coupled for 1 hour at 4ºC with 5ug of H3K9me3 antibody (Abcam 8898) and finally washed twice with Blocking Buffer to remove excess antibody. Lysate and conjugated magnetic beads were rotated at 4ºC overnight. Beads were then resuspended in 200ul cold RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 14 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC) and transfer to a 96-well plate. All further separation steps were performed in the 96-well plate magnet. Beads were washed five times with 200ul cold RIPA, two times with RIPA buffer supplemented with 500 mM NaCl, two times with LiCl buffer (10 mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), and once with TE (10Mm Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted in 50 µl of 0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris HCl pH 8.0. The eluate was reverse cross-linked at 65ºC for 4 hours and then treated with 2ul of RNaseA (Roche, 11119915001) for 30 min followed by 2.5 µl of Proteinase K (NEB, P8102S) for two hours. Library preparation was done as indicated in Garber et al. (2012), but without automation. In brief, to purify DNA 120ul of Ampure XP beads (Agencourt) were added to the reverse cross-linked samples, mixed by pipetting and incubated for 2 minutes. Samples were then placed on the magnetic stand for 4 minutes to separate beads, followed by 2 washes with 70% ethanol and air dried for 4 minutes and eluted in 10mM Tris-HCl pH 8.0. Library was constructed by performing DNA end-repair, A-base addition, adaptor ligation and enrichment PCR. After each step DNA was purified by adding 20% PEG and 2.5 M NaCl to the reaction, to allow DNA to bind to Ampure XP beads already in the tube. Samples were not moved form their original well position, until after PCR enrichment. The libraries were sequenced on the Illumina HiSeq platform for 76 cycles in a pair-end run.

treatment_protocol: Flies were fed with yeast paste.

tag: tissue

value: ovaries

tag: strain

value: DGRC 204406 heterozygous

tag: antibody vendor

value: Abcam 8898

tag: sample type

value: ChIP H3K9me3


title: sRNAseq_tj-uba2_KK110173

description: small RNA (2s rRNA depleted, no size selection)

library_source: transcriptomic

data_processing:
Small RNA -seq libraries were sequenced on  a Illumina HiSeq single-end 36 run, the TruSeq adapter (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC) was clipped from the 3’ end of the read and sequences shorter than 15 nt were discarded from further analysis. The remaining sequences were collapsed into a non-redundant list and mapped to Drosophila viral, tRNA and miscRNA (rRNA, snoRNA etc) sequences using the short read aligner Bowtie (Langmead et al., 2009). Clipping and collapsing was done using the FASTX Toolkit 0.0.14 by A. Gordon (gordon@cshl.edu). Only non-mapping reads were consequently mapped to the D. melanogaster genome (D. melanogaster Apr. 2006 [BDGP R5/dm3]). Up to two mismatches were allowed.
Genome_build: dm3
Supplementary_files_format_and_content: H3K9me3 peaks in heterozygous 204406 flies identified with Homer are provided as BED files. Tag counts over these regions in heterozygous and homozygous 204406 flies calculated with Homer (annotatePeaks) are provided as text files.

molecule: total RNA

extract_protocol:
Trizol extraction followed by isopropanol precipitation
TruSeq Small RNA Sample Preparation Kit after 2s rRNA depletion of 2.5ug total RNA

value: VDRC KK110173

value: tj driven knockdown of uba2


title: Kyoto_DGRC204406_hom_H3K9me3

description: ChIP H3K9me3

value: DGRC 204406 homozygous


title: Kyoto_DGRC204406_hom_input

description: ChIP input


title: el016_hf2_9

status: Public on May 08 2013

city: Cambridge

first: Dario

last: Beraldi

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute

description: G-quadruplex pull-down

data_processing:
Basecalls performed using CASAVA 1.7 and OLB 1.9.4
Sequence reads were aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.6, March 2008) using bwa 0.6.1 with default settings.
Reads mapped with MAPQ < 15 were filtered out. Reads overlapping regions producing aspecific binding were also removed (regions obtained from http://hgdownload-test.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeMapability/wgEncodeDukeRegionsExcluded.bed6.gz). Libraries were down-sampled to eight million reads using Picard/DownsampleSam (http://picard.sourceforge.net/command-line-overview.shtml#DownsampleSam).
Peak-calling was performed on the downsampled libraries using MACS 1.4 with default settings and the input library as control.
Genome_build: hg18
Supplementary_files_format_and_content: Text files produced by MACS reporting peak positons and statistics. Quoting the MACS manual (http://liulab.dfci.harvard.edu/MACS/00README.html):  NAME_peaks.txt is a tabular file which contains information about called peaks. You can open it in excel and sort/filter using excel functions. Information include: chromosome name, start position of peak, end position of peak, length of peak region, peak summit position related to the start position of peak region, number of tags in peak region, -10*log10(pvalue) for the peak region (e.g. pvalue =1e-10, then this value should be 100), fold enrichment for this region against random Poisson distribution with local lambda, FDR in percentage. Coordinates in XLS is 1-based which is different with BED format.

organism: Homo sapiens

source_name: MCF-7_G-quadruplex pull-down

growth_protocol: Human breast adenocarcinoma (MCF7) cells were obtained from the European Collection of Animal Cell Cultures and grown in Dulbecco’s Modified Eagle’s Media supplemented with 10% fetal calf serum (Sigma-Aldrich) at 37°C in 5% CO2.

extract_protocol:
Genomic DNA was extracted from MCF7 cells using QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s protocol. The purified DNA was eluted from columns in 10 mM Tris pH 7.4. Genomic DNA was sheared by sonication sonicated with the Bioruptor™ UCD200 sonicator (Diagenode®) for 60 min at high power with a pulse of 30 s on/30 s off, to produce fragments of approximately 200 bp prior to pull-down experiment
50 μL of Protein A Dynabeads were washed three times with PBS then incubated with 2.5 μg of hf2 in 0.5 % BSA and 1 mg/mL yeast tRNA in PBS overnight rotating at 4 °C. Beads were washed three times with 0.5 % BSA then incubated with 400 μL of 300 ng/μL sonicated genomic DNA. Following overnight incubation rotating at 4°C, beads were washed 6 times with 10 mM Tris pH 7.4, 100 mM KCl, 0.1 % tween then once with 10 mM Tris pH 7.4, 100 mM KCl. Bound DNA was eluted in 50 μL of 1 % SDS, 0.1 M NaHCO3 at 30 °C for one hour then purified with Roche PCR purification columns. Recovered DNA was assessed for enrichment of telomeric sequences by qPCR with primers for telomeric repeats and a control genomic region in a regulatory region of the estrogen receptor gene without predicted G-quadruplex sequences. Recovered DNA was used to prepare libraries for Illumina sequencing using the TruSeq DNA library kit. Library quality was assessed using an Agilent Bioanalyzer 2100 before single end 36 base sequencing on the Illumina MiSeq, GAIIx or HiSeq 2000.

tag: cell line

tag: cell type

value: Breast adenocarcinoma

tag: enrichment method

value: G-quadruplex-specific probe

tag: molecule subtype

value: genomic DNA enriched in DNA G-quadruplex structures


title: SRSF2 HA tag ChIP-seq

city: La Jolla

first: Xiang-Dong

last: Fu

state: CA

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

data_processing:
All sequenced tags were trimmed and mapped to the mouse genome (mm9) by using Bowtie (version 0.12.2-0.12.7). Generally, two mismatches were allowed in the first 25nt region and only those tags with one unique hit in the mouse genome were kept. Multiple tags mapped to the same genomic position were collapsed into one or up to 4 tags to remove potential PCR amplicons.
Density files were generated by using bedItemOverlapCount and wigToBigWig programs from UCSC kent source package. Different density files in group of experiments such as WT and KO were normalized to same number of total mapped reads for comparision.
Genome_build: mm9

organism: Mus musculus

growth_protocol: DMEM plus 10% FBS

extract_protocol:
For genomic DNA extraction, we used QIAquick PCR purification kit. For RNA extraction, we used Trizol kit by following manufacturer's instructions.
For HA, SRSF1, SRSF2, RNAPII, CDK9, and HEXIM1 ChIP-seq, MEF cells were fixed with 1% Formaldehyde or 1% glutaraldehyde at room temperature for 10 min. After the treatment, cross linking was quenched with 0.125 M glycine for 5 min;10-50 million cells were used per ChIP. For GRO-Seq, ~20 million cell nuclei from wildtype or SR protein depleted cells were extracted and harvested, then We carried out the global nuclear run-on assay and then analyzed by deep sequencing using a published protocol (Wang et al., 2011). RNA-seq was performed after SR proteins depletion. Trizol-isolated RNA was enriched  for Poly(A+) RNA with paramagnetic oligo(dT), fragmented into ~200 nt in length, converted to cDNA with Superscript III (Invitrogen), and subjected to deep sequencing to detect counts at the 3’ end of individual transcripts (Fox-Walsh et al., 2011).

treatment_protocol: We treated SRSF1-MEFs with Dox for 4 days and SRSF2-MEFs with Dox for 2 days to deplete respective SR protein to ~90%. For DRB treated cells, treat MEFs with 100μM DRB for 3 hours

value: MEF cell line

tag: passages

tag: chip antibody

value: anti-HA (ab9110)

tag: molecule type

value: genomic DNA


title: SRSF1 HA tag ChIP-seq


title: Ago2 IP-seq (mitotic cells)

city: Basel

first: Andreas

middle: R

last: Gruber

address: Klingelbergstrasse 50-70

department: Biozentrum

country: Switzerland

institute: University of Basel

data_processing:
The raw reads were processed on the CLIPZ server (www.clipz.unibas.ch; Khorshid et al., Nucleic Acids Research 2011, 39:D245 (PMID 21087992)).
For subsequent analyses only uniquely mapped reads were considered.
Genome_build: hg19 Feb 2009
Supplementary_files_format_and_content: bed files with genomic coordinates of reads mapped; scores represent the number of reads

source_name: HeLa

growth_protocol: HEK293 and HeLa cells were routinely generated by replating every 3 d on T75 flasks (Falcon, 353133) in DMEM supplemented with 10% FCS.

extract_protocol:
PAR-CLIP samples were extracted following the PAR-CLIP method (Hafner et al. 2010; PMID: 20371350).
For HEK293 small RNA-seq samples total RNA was extracted with TRI Reagent, radiolabeled and size-selected on a PAA gel.
For HeLa Ago2-IP samples lysates were clarified and Ago2-RNA complexes isolated with an antibody, Ago2-associated RNA TRI Reagent-extracted, radiolabeled and size-selected on a PAA gel.
PAR-CLIP library preparation as described in (Hafner et al. 2010; PMID: 20371350).
Small RNA libraries for HEK293 cells were constructed as described in (Hafner et al. 2008; PMID: 18158127).
For HeLa Ago2 IP-seq samples Ago2-associated RNAs were extracted and used to prepare cDNA libraries as described in (Hafner et al. 2008; PMID: 18158127).

value: HeLa

value: monoclonal Ago2; 11A9

value: From Gunter Meister; PMID:18430891

tag: 3' adaptor

value: 5' TGGAATTCTCGGGTGCCAAGG 3'


title: Ago2 IP-seq (asynchronous cells)


title: sRNA-seq


title: FBL (MNase)

value: Fibrillarin; mouse monoclonal;  AFB01

value: Cytoskeleton, Inc.

tag: lot number


title: DCK1

value: Dyskerin; rabbit polyclonal IgG (C-15); sc-26982

value: Santa Cruz Biotechnology


title: sdRNA-seq


title: RNAseq_tj-armi_KK103589_rep1

description: total RNA (rRNA depleted with ribo-zero)

data_processing:
RNA-seq libraries were prepared using the Illumina Script Seq v2 RNA-Seq library preparation kit and were sequenced on an Illumina HiSeq platform for 36 cycles in a single end run. After collapsing all reads into a non-redundant list (cloning counts were preserved) using the FASTX Toolkit 0.0.14 by A. Gordon (gordon@cshl.edu), they were mapped to Drosophila viral, tRNA and miscRNA (rRNA, snoRNA etc) sequences using the short read aligner Bowtie (Langmead et al., 2009). Only sequences in each library that did not map to either of these contaminants were then mapped to the Drosophila genome with up to two mismatches. Additionally, only uniquely mapping sequences were considered for further analysis. The same reads were mapped to a custom index of transposon consensus sequences with up to 2 mismatches (Kaminker et al., 2002). Reads mapping to up to 2 locations were considered for further analysis. For differential expression analysis of transposons we aggregated read counts mapping to these consensus sequences in sense orientation. For differential expression analysis of genes, we used htseq-counts (Part of the 'HTSeq' framework, version 0.5.3p3) to assess read counts per gene. In both cases we used the R package DESeq to call differential expression at a FDR cutoff of 0.05 based on two biological replicates.
Genome_build: dm3
Supplementary_files_format_and_content: H3K9me3 peaks in heterozygous 204406 flies identified with Homer are provided as BED files. Tag counts over these regions in heterozygous and homozygous 204406 flies calculated with Homer (annotatePeaks) are provided as text files.

extract_protocol:
Trizol extraction followed by isopropanol precipitation
ScriptSeq v2 RNA-Seq Library Preparation Kit after rRNA depletion with Ribo-zero of 2.5-5 ug total RNA

value: ovaries

value: VDRC KK103589

value: tj driven knockdown of armi


title: NOP58 rep B

value: Nop58; goat polyclonal IgG; sc-23705


title: NOP56

value: ANTI-FLAG M2; mouse monoclonal

value: SIGMA


title: FBL


title: el018

description: G-quadruplex pull-down

value: Breast adenocarcinoma

value: G-quadruplex-specific probe

value: genomic DNA enriched in DNA G-quadruplex structures


title: Non-smoker female, NSCLC, MeDIP-Seq [P1N]

status: Public on May 10 2013

city: Daejeon

first: Sanghyuk

last: Lee

address: 125 Gwahak-ro

department: KOBIC

country: South Korea

institute: KRIBB

description: 44 years;  female; a non-smoker

data_processing:
Basecalls performed using Illumina Genome AnalyzerIIx
DNA methylation density is calculated by counting reads after binning with bin size 200bp
Genome_build: hg19
Supplementary_files_format_and_content: text

source_name: Non-smoker female, NSCLC

extract_protocol: Methylated CpG island-associated DNA was prepared using methylation specific antibody. This ChIPed DNA was processed for high throughput sequencing using Illumina ChIP-Seq Sample Prep Kit. For sequencing, 200bp insert sized library was selected from agarose gel. Sequencing was performed at Illumina Genome Analyzer IIx, single read sequencing.

treatment_protocol: Standard protocol by phenol extraction

tag: disease

value: Adenocarcinoma, NSCLC

tag: patient

tag: tissue type

value: normal

tag: Stage

value: IB

tag: gender

value: female

tag: age

value: 44 years

tag: smoker

value: non-smoker


title: NOP58 rep A

tag: antibody

tag: antibody vendor

value: 5' TGGAATTCTCGGGTGCCAAGG 3'


title: GRO-seq_E2_40m (Re-Sequenced GSM678540 to greater depth)

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
molecule: nascent RNA
library strategy: GRO-seq
library selection: bromo-UTP RNAs

data_processing:
Alignment: Short-reads were aligned to the human reference genome (hg18, NCBI36), including autosomes, X-chromosome, and one complete copy of an rDNA repeat (GenBank ID: U13369.1).  The SOAP2 software package (Li et al., 2009) was used to align reads with the following options: (1) all non-unique mappings were removed (-r 0), (2) three mismatches were allowed in each mapped read (-v 3), (3) low-quality reads with more than 10 ambiguous bases were removed (-N 10), and (4) for reads failing to align over the entire length of the read, the first 32 bp was used (-l 32).  SOAP2 output was processed using custom Perl scripts, and imported into R for most the analysis.
Genome_build: hg18
Supplementary_files_format_and_content: bed

growth_protocol: MCF-7 human breast adenocarcinoma cells were kindly provided by Dr. Benita Katzenellenbogen (University of Illinois, Urbana-Champaign).  The cells were maintained in minimal essential medium (MEM) with Hank’s salts (Sigma) supplemented with 5% calf serum (CS), sodium bicarbonate, penicillin/streptomycin and gentamicin.  Cells were plated for experiments in phenol red-free MEM (Sigma) supplemented with 5% charcoal-dextran treated calf serum (CDCS) prior to 17-b estradiol (E2) treatment.

extract_protocol:
Nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of NTPs and 0.5% Sarkosyl in run-on buffer to allow a run-on of ~100 nucleotides.  The reaction was stopped by incubation with DNase I, followed by incubation with proteinase K.  Newly synthesized nascent RNAs were isolated by acid phenol-chloroform extraction, followed by ethanol precipitation.  After re-dissolving, the isolated RNAs were base-hydrolyzed with 0.2 N NaOH and the reaction was neutralized by the addition of 500 mM Tris×HCl, pH 6.8.  The base-hydrolyzed RNAs were subjected to BioRad P-30 chromatography for buffer exchange.  The isolated and base hydrolyzed RNAs were subjected to three bead binding steps where the bromo-UTP incorporated nascent RNAs (BrU-RNAs) were enriched using anti-bromo-deoxy-U antibody conjugated beads.  After each binding step, the BrU-RNAs were eluted, acid phenol-chloroform extracted, and precipitated.  Each of the three bead binding steps also contained additional manipulations.  After the first binding step, the BrU-RNAs were treated with tobacco acid pyrophosphatase to remove 5’-methyl guanosine caps, then with T4 polynucelotide kiase to remove 3’-phosphate group at low pH.  The BrU-RNAs were treated with T4 PNK again at high pH in the presence of ATP to add 5’-phosphate group.  5’-adaptors were added to the end-repaired BrU-RNAs by T4 RNA ligase.  After the addition of the 5’-adaptors, the BrU-RNAs were subjected to the second bead binding step to remove excessive adaptors and further enrich the BrU-RNAs.  After the second bead binding step, 3’ adaptors were ligated by T4 RNA ligase, followed by the third bead binding.  The affinity purified 5’- and 3’-adaptor-ligated BrU-RNAs were reverse transcribed into cDNAs usining annealed RT-oligo and Super Scripts III reverse transcriptase.  The RNAs were then degraded by incubation with RNase cocktail.  The cDNAs were then subjected to PCR-amplification using Phusion DNA Polymerase with small RNA PCR primers.  Samples of the amplified cDNAs were analyzed on a 2% agarose gel to assess yield and size.  The remaining samples were extracted by phenol:chloroform:isoamyl alcohol (25:24:1).  The purified cDNAs were run on a 6% native PAGE gel for further purification. The gel was stained with SYBRE gold and the cDNAs were visualized using a Dark Reader transilluminator.  The bands between size 100 bp to 250 bp were cut out and the cDNAs were eluted from the gel by incubating overnight in elution buffer.  The eluted cDNA were extracted again with phenol-chloroform, resuspended in water, and quantified using a Nanodrop.  The final libraries were then sequenced using an Illumina Genome Analyzer.
Nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of NTPs and 0.5% Sarkosyl in run-on buffer to allow a run-on of ~100 nucleotides.  The reaction was stopped by incubation with DNase I, followed by incubation with proteinase K.  Newly synthesized nascent RNAs were isolated by acid phenol-chloroform extraction, followed by ethanol precipitation.  After re-dissolving, the isolated RNAs were base-hydrolyzed with 0.2 N NaOH and the reaction was neutralized by the addition of 500 mM Tris×HCl, pH 6.8.  The base-hydrolyzed RNAs were subjected to BioRad P-30 chromatography for buffer exchange.  The isolated and base hydrolyzed RNAs were subjected to three bead binding steps where the bromo-UTP incorporated nascent RNAs (BrU-RNAs) were enriched using anti-bromo-deoxy-U antibody conjugated beads.  After each binding step, the BrU-RNAs were eluted, acid phenol-chloroform extracted, and precipitated.  Each of the three bead binding steps also contained additional manipulations.  After the first binding step, the BrU-RNAs were treated with tobacco acid pyrophosphatase to remove 5’-methyl guanosine caps, then with T4 polynucelotide kiase to remove 3’-phosphate group at low pH.  The BrU-RNAs were treated with T4 PNK again at high pH in the presence of ATP to add 5’-phosphate group.  5’-adaptors were added to the end-repaired BrU-RNAs by T4 RNA ligase.  After the addition of the 5’-adaptors, the BrU-RNAs were subjected to the second bead binding step to remove excessive adaptors and further enrich the BrU-RNAs.  After the second bead binding step, 3’ adaptors were ligated by T4 RNA ligase, followed by the third bead binding.  The affinity purified 5’- and 3’-adaptor-ligated BrU-RNAs were reverse transcribed into cDNAs usining annealed RT-oligo and Super Scripts III reverse transcriptase.  The RNAs were then degraded by incubation with RNase cocktail.  The cDNAs were then subjected to PCR-amplification using Phusion DNA Polymerase with small RNA PCR primers.  Samples of the amplified cDNAs were analyzed on a 2% agarose gel to assess yield and size.  The remaining samples were extracted by phenol:chloroform:isoamyl alcohol (25:24:1).  The purified cDNAs were run on a 6% native PAGE gel for further purification. The gel was stained with SYBRE gold and the cDNAs were visualized using a Dark Reader transilluminator.  The bands between size 100 bp to 250 bp were cut out and the cDNAs were eluted from the gel by incubating overnight in elution buffer.  The eluted cDNA were extracted again with phenol-chloroform, resuspended in water, and quantified using a Nanodrop.  The final libraries were then sequenced using an Illumina Genome Analyzer.

treatment_protocol: MCF-7 cells were plated at a density of 1 x 106 cells per 15 cm diameter dish in phenol-red free MEM + 5% CDCS, using one dish per experimental condition.  After three days, the cells were treated with 100 nM E2 as indicated and washed three times with ice cold PBS.

tag: cell line

tag: treatement time

tag: treatment

value: treated for 40 minutes with E2


title: el007

description: Input control

tag: cell type

tag: molecule subtype

value: input DNA


title: GRO-seq_E2_40m (Re-Sequenced GSM678539 to greater depth)


title: el004_8

description: G-quadruplex pull-down

tag: enrichment method


title: el001_6

description: G-quadruplex pull-down


title: GRO-seq_Vehicle  (Re-Sequenced GSM678536 to greater depth)

value: untreated


title: GRO-seq_E2_10m (Re-Sequenced GSM678537 to greater depth)

value: treated for 10 minutes with E2


title: Wildtype 3 weeks (RNA-Seq)

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

description: Sample 13

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to mm9 using TopHat with default parameters
RNAseq: FPKM were obtained using CuffLinks with upper-quartile and GC normalization
RRBS: Sequence reads were aligned to bisulfite converted mm9 genome using Bismark
RRBS: methylation calls were obtained using methylKit
Genome_build: mm9
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.
Supplementary_files_format_and_content: RRBS: methylation values for each CpG with >=10X coverage.

source_name: Wildtype tail fibroblasts reprogrammed for three weeks

extract_protocol:
RNA was harvested using Trizol treatment. DNA was extracted using standard phenol chloroform method
Illumina TruSeq, SR51 (RRBS) and PE 75x2 (RNA-seq)

value: fibroblast (reprogrammed for 3 weeks)

tag: genotype/variation

value: Wildtype


title: AID-null clone 3 (RRBS)

description: Sample 10

source_name: AID-null tail clones reprogrammed for three weeks

value: clone (after 3 weeks of reprogramming (picked at 2 weeks))

value: AID-null


title: AID-null clone 2 (RRBS)

description: Sample 9


title: RNAseq nos::KD-U2A

first: Benjamin

last: Czech

institute: Cold Spring Harbor Laboratory

description: mRNA seq

data_processing:
Basecalling with Illumina CASAVA version 1.3+.  Pooled libraries were de-multiplexed according to the barcode sequence used during ScriptSeq library generation.
Sequenced reads were trimmed for adaptor sequence and iteratively mapped to the genome of Drosophila melanogaster (dm3) using Bowtie. Reads were mapped allowing 0 mismatches, and remaining reads were remapped with 1 and 2 mismatches in subsequent steps to produce a total pool of 0-, 1-, and 2- mismatch mapped reads.
Unmapped reads were mapped to annotated Drosophila melanogaster transcripts (dm3) in the refSeq database (release 48 [September 13, 2011]) using Tophat to detect reads overlapping known splice junctions using the parameters --no-novel-juncs -g 1
Bowtie and Tophat outputs were catenated and processed by Cufflinks to produce mRNAs quantified in fragments per kilobase per million reads (FPKM)
In parallel, all trimmed reads were mapped using the same bowtie parametsr to the consensus sequences of Drosophila transposons, using Flybase transposon sequences version 9.42.
Genome_build: dm3
Supplementary_files_format_and_content: For gene expression profiling of Drosophila tissues: tab-delimted text file in the standard Cufflinks FPKM Tracking Format
Supplementary_files_format_and_content: For quantification of transposable element expression in nos-driven knockdown ovaries:  tab-delimited text file with column listing transposable element name and column 2 displaying reads_per_million_genomic_mappers rounded to the nearest integer.  The first row contains the total number of genomic mappers in that library.

growth_protocol: OSS cells were grown in M3 media supplemented with 10% FBS, 5% Fly extract, 1X insulin and 1X glutathione and kept in a 25C incubator.  Flies were raised at 25°C on standard cornmeal-molasses agar medium.

extract_protocol: RNA was extracted from cells or tissues using TRIzol reagent (Invitrogen).  RNA-seq libraries were prepared using the ScriptSeq V2 kit from Epicentre.  5ug total RNA was depleted of ribosomal RNA using the RiboZero Gold (Human/Mouse/Rat) kit from Epicentre and used as input for the ScriptSeq protocol, as per the manufacturer's instructions.

value: Whole dissected ovaries


title: GRO-seq_Vehicle  (Re-Sequenced GSM678535 to greater depth)


title: Wildtype clone 3 (RRBS)

description: Sample 7

source_name: Wildtype tail clones reprogrammed for three weeks


title: Wildtype clone 1 (RRBS)

description: Sample 5


title: AID-null clone 1 (RRBS)

description: Sample 8


title: Wildtype 3 weeks (RRBS)

description: Sample 3


title: AID-null 3 weeks (RRBS)

description: Sample 4

source_name: AID-null tail fibroblasts reprogrammed for three weeks


title: AID-null fibroblast (RRBS)

description: Sample 2

source_name: AID-null tail fibroblasts

value: fibroblast (tail)


title: Wildtype fibroblast (RRBS)

description: Sample 1

source_name: Wildtype tail fibroblasts


title: Wildtype clone 2 (RRBS)

description: Sample 6


title: C_44_GRHL2_Input

status: Public on May 07 2013

city: Durham

first: Timothy

middle: E

last: Reddy

state: NC

address: 2347 CIEMAS, 101 Science Drive

department: Department of Biostatistics & Bioinformatics

institute: Duke University

description: Input control sample

data_processing:
Base-calling was performed on instrument using CASAVA software
Reads were aligned to the human genome (version hg19) using Bowtie version 0.12.8.
GRHL2 binding sites were called using the MACS peak caller with a bandwidth of 300 bp, an model fold parameter of 15, and a p-value threshold of 1E-10.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files of genome-wide sequenced tag density.

source_name: Bronchial Epithelial Cells

growth_protocol: Cells were seeded into plastic dishes coated with bovine collagen (PureCol, Advanced BioMatrix, 5005-B) in bronchial epithelial cell growth medium (BEGM) containing 0.11mM Ca++ and 25 ng/ml EGF. Confluent cultures were passaged to P2 in dishes without collagen, and grown to confluence.

extract_protocol:
20 million cells were crosslinked for 10 minutes in 1% formaldehyde followed by 5 minutes of quenching in 0.125 M glycine. Cells were then washed with cold PBS pH7.4, and collected in the presence of cold cell lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, and Roche Complete Protease Inhibitor Cocktail Cat #11836145001). Nuclei were pelleted by centrifugation at 2,000 rpm for 5 minutes at 4C, and the supertanant discarded.  Sheared chromatin was then prepared by sonicating the nuclei in the presence of RIPA buffer (1 x PBS pH 7.4, 1% NP-40, 0.5% NaDOC, Roche Protease Inhibitor Cocktail), followed by centrifugation to remove cell debris. To collected GRHL2-bound DNA, the chromatin was immunoprecipitated with an anti-GRHL2 antibody (Sigma HPA004820), the formaldehyde crosslinks were reversed by heating overnight at 65C, and the DNA was collected using Qiagen PCR cleanup columns.  For input control samples, reverse-crosslinked DNA was isolated from an aliquot of the sonicated but not immunoprecipitated chromatin.
DNA ends were blunted using a mixture of Klenow DNA polymerase, T4 DNA polymerase, and T4 polynucleotide kinase (PNK). Three-prime adenine was then added using 3'-5' exo- Klenow fragment, Illumina Y-adapters were ligated using T4 DNA ligase.  The ligated DNA was gel size selected for 150-300 bp fragments, and PCR-amplified to make the final sequencing library. Samples were sequenced on an Illumina HiSeq 2000.

value: Bronchial Epithelial Cells

tag: donor

tag: chip antibody


title: C_36_GRHL2_ChIPseq

description: GRHL2 ChIP-seq

tag: chip antibody manufacturer

value: Sigma

tag: chip antibody catalog #


title: C_36_GRHL2_Input

description: Input control sample


title: C_29_GRHL2_ChIPseq

description: GRHL2 ChIP-seq


title: GRO-seq_E2_10m (Re-Sequenced GSM678538 to greater depth)


title: Wildtype fibroblast (RNA-Seq)

description: Sample 14


title: C44_DN

data_processing:
Base-calling was performed on instrument using CASAVA software
Reads were aligned to known RefSeq transcripts from hg19 using Bowtie version 0.12.8 and allowing up to 2 kb between paired reads.
Read counts were normalized and differential expression was called using Deseq (v. 1.10.1) by usiong a chi-squared test to compare fits to a model that contained donor and count (i.e. count ~ donor + condition) to a model that only contained donor information (i.e. count ~ donor).
P-values were converted to a False Discovery Rate using the method of Benjamini and Hochberg (1995)
Genome_build: hg19
Supplementary_files_format_and_content: Counts of the number of reads aligned to each RefSeq transcript.

growth_protocol: Cells were seeded into plastic dishes coated with bovine collagen (PureCol, Advanced BioMatrix, 5005-B) in bronchial epithelial cell growth medium (BEGM) containing 0.11mM Ca++ and 25 ng/ml EGF. Confluent cultures were passaged to P2 in dishes without collagen.P2 cells at 40% confluence were infected with H2B-GFP or DN-GRHL2 lentivirus and 1 mg/ml puromycin added 48 h later.

extract_protocol:
Between 0.5-1 million cells were trypsinized, washed with PBS, pelleted and snap frozen. Total RNA was extracted using Qiagen RNeasy mini-columns with 1% β-mercaptoethanol in RLT buffer and a 15 min on column DNase digestion. mRNA was isolated using the Dynabeads mRNA Direct Kit (Invitrogen).
First strand cDNA was generated using SuperScript Vilo cDNA synthesis master mix (Invitrogen), and second strand cDNA was synthesized using E. coli DNA Polymerase I (New England Biolabs) with random hexamer primers. Double stranded cDNA was purified using 1.8X Agentcourt SPRI beads (Beckman Coulter). Double stranded cDNA was fragmented and sequencing adaptors added using Nextera transposase (Illumina) and indexed for sequencing by PCR as described previously. Samples were pooled in equimolar ratios and sequenced on an Illumina HiSeq 2000.

treatment_protocol: At confluence, Doxycycline 0.5 mg/ml was added for 24 h.


title: C29_DN


title: C36_DN


title: C36_Ctl


title: AID-null 3 weeks (RNA-Seq)

description: Sample 11


title: C_44_GRHL2_ChIPseq

description: GRHL2 ChIP-seq


title: C29_Ctl


title: C44_Ctl


title: skinEC

city: Montreal

first: Charles

last: St-Pierre

state: Quebec

address: 2950, Chemin de Polytechnique

department: Institute for Research in Immunology and Cancer

country: Canada

institute: Montreal University

data_processing:
ELANDv2 alignment tool from the CASAVA 1.8.2 software
Paired-end (2 x 100bp) sequencing was performed using the Illumina HiSeq2000 machine running TruSeq v3 chemistry. Cluster density was targeted at around 600-800k clusters/mm2. Two RNA-Seq librairies were sequenced per lane (8 lanes per slide).
Samples were prepared into 250bp paired-end libraries and sequenced on the Illumina HiSeq 2000 to obtain an average of 10.2 giga base pair of transcript sequences. Sequencing adapters were masked from the end of both sets of 100bp reads prior to alignment. Data was mapped to the Mus musculus (mm9) reference genome using the ELANDv2 alignment tool from the CASAVA 1.8.2 software (http://www.illumina.com/software/genome_analyzer_software.ilmn). We quantified transcript levels in reads per kilobase of exon model per million mapped reads (RPKM). The RPKM measure of read density reflects the molar concentration of a transcript in the starting sample by normalizing for RNA length and for the total read number in the measurement
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for cTEC, mTEC and skinEC

source_name: Skin epithelial cells

extract_protocol:
Thymi from fourteen 7-days old C57BL/6 mice were isolated and stromal cell enrichment was performed. Thymic stromal cells were stained with biotinylated Ulex Europaeus Lectin 1 (UEA1; Vector Laboratories), PE-Texas Red conjugated streptavidin (BD Biosciences) and the following antibodies from BD Biosciences: Alexa700 anti-CD45, APC-Cy7 anti-EpCAM and Alexa647 anti-Ly51. Both cTEC (CD45 EpCAM+Ly51+UEA1 ) and mTEC (CD45 EpCAM+Ly51 UEA1+) populations were sorted on a three laser FACSAria (BD Biosciences). Epidermal cells were harvested from the trunk and dorsum of seven newborn mice, and stained with the following antibodies (BD Biosciences): APC-Cy7 anti-EpCAM and FITC anti-CD11c. Keratinocytes (EpCAM+CD11c ) were sorted on a three laser FACSAria. Total RNA was isolated using Trizol reagent as recommended by the manufacturer (Invitrogen), and then further purifed using RNeasy columns (Qiagen). Transcriptome libraries were generated from 1 μg of total RNA using the TruSeq RNA Sample Prep Kit (v2) (Illumina).
RNA libraries were prepared for sequencing following recommended Illumina protocols

tag: strain

tag: tissue

value: Epidermis

value: newborn


title: cTEC

source_name: Cortical thymic epithelial cells

value: Thymus

tag: age

value: post natal day 7


title: C36_WT

value: Untreated control


title: AID-null fibroblast (RNA-Seq)

description: Sample 12


title: C_29_GRHL2_Input

description: Input control sample


title: Treatment Rat 5

city: West Lafayette

first: Amy

last: Lossie

state: IN

address: 125 S. Russell St.

institute: Purdue University

data_processing:
Reads were analyzed and mapped using CLCbio Genomics Workbench 4.9 software (Cambridge).
Reads were first normalized by reads per kilobase per million mapped reads (RPKM, Mortazavi et al. 2008 Nature Methods). Values were transformed by square root to stabilize variances, and then renormalized (a second time) by quantile normalization to adjust for among sample variation. A standard t-test with pooled error term was applied to determine p values, which were then corrected for a false discovery rate (FDR) of 5%.
Genome_build: RGSC_v3.4.63

organism: Rattus norvegicus

source_name: Liver from ethanol-treated group

growth_protocol: All rats had ad libitum access to food and tap water throughout the experiment (23 weeks).

extract_protocol:
Livers were snap frozen using a dry ice and isopentane bath. Total RNA was extracted using RNA Stat-60 (Amsbio) following manufacturer's directions.
We used the Illumina TruSeq RNA kit for library preparation with some modifications to the manufacturer’s directions (detailed below). Poly-A RNA was isolated by annealing biotinylated oligo-dT to total RNA and purifying using streptavidin-conjugated beads. RNA was fragmented for 4 minutes at 94°C to increase the population of 200-600 nt fragments. cDNA synthesis was accomplished using random hexamers. Fragment ends were repaired and 3’ ends were adenylated for adaptor ligation. Adaptor ligated fragments were enriched following 10 cycles of PCR. 320-600 bp molecules were size selected from the resulting amplicon pool using a PippinPrep (Sage Science). The final cDNA library was titrated by qRT-PCR and sequenced in 101 nt paired-end reads.

treatment_protocol: We took advantage of the fact iP10a rats will voluntarily consume pharmacologically relevant levels of alcohol daily. Ethanol exposure was achieved by ad libitum access to bottles containing 10, 20, and 30% ethanol (v/v) for 23 weeks.

value: Inbred alcohol-preferring (iP10a)

tag: Sex

value: Female

tag: age at collection

value: 38 weeks

value: Liver


title: Treatment Rat 3


title: Control Rat 5

source_name: Liver from water control group


title: Treatment Rat 6

value: 39 weeks


title: Treatment Rat 2


title: Treatment Rat 1


title: Control Rat 6


title: Control Rat 3


title: Treatment Rat 4


title: Control Rat 1


title: Control Rat 2


title: Sman

status: Public on May 06 2013

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
BS-mapping: bsmap 2.0
computation of methylation ratios: methratio.py (part of bsmap package)
Genome_build: sma_v5.0
Supplementary_files_format_and_content: Bedgraph-format containing the genomic methylation ratios of the respective sample

organism: Schistosoma mansoni

source_name: male worms

extract_protocol: Adult male worms from the S. mansoni Puerto Rican strain were homogenized and DNA was isolated using the Qiagen DNeasy Blood & Tissue Kit, according to the manufacturer's instructions.  5 µg of high molecular weight DNA were used for fragmentation using the Covaris S2 AFA System in a total volume of 100 µl. Fragmentation-run parameters: Duty cycle 10%; Intensity: 5; Cycles/burst: 200; Time: 3 min; number of cycles: 3, resulting in a total fragmentation-time of 180 s. Fragmentation was confirmed with a 2100 Bioanalyzer (Agilent Technologies) using a DNA1000 chip. The fragmented DNAs were concentrated to a final volume of 75 µl using a DNA Speed Vac. End repair of fragmented DNA was carried out in a total volume of 100 µl using the Paired End DNA Sample Prep Kit (Illumina) as recommended by the manufacturer. For the ligation of the adaptors, the Illumina Early Access Methylation Adaptor Oligo Kit and the Paired End DNA Sample Prep Kit (Illumina) were used, as recommended by the manufacturer. For the size selection of the adaptor-ligated fragments, we used the E-Gel Electrophoresis System (Invitrogen) and a Size Select 2% precast agarose gel (Invitrogen). Each fragmented DNA was loaded on two lanes of the E-gel. Electrophoresis was carried out using the “Size Select” program for 16 min. According to the standard loaded (50 bp DNA Ladder, Invitrogen), 240 bp fragments were extracted from the gel, pooled, and directly transferred to bisulfite treatment without further purification. For the bisulfite treatment we used the EZ-DNA Methylation Kit (Zymo) as recommended by the manufacturer with the exception of a modified thermal profile for the bisulfite conversion reaction. The conversion was carried out in a thermal cycler using the following thermal profile: 95°C for 15 s, 50°C for 1 h, repeat from step 1, 15×, 4°C for at least 10 min. The libraries were subsequently amplified, using the Fast Start High Fidelity PCR System (Roche) with buffer 2, and Illuminas PE1.1 and PE2.1 amplification primers. PCR thermal profile: 95°C for 2 min, 95°C for 30 s, 65°C for 20 s, 72°C for 30 s, then repeat from step 2, 11×, 72°C for 7min, hold at 4°C. PCR reactions were purified on PCR purification columns (MinElute, Qiagen) and eluted in 20 µl elution buffer (Qiagen).

value: puerto rico

tag: developmental stage

value: adult


title: PGT45

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
BS-mapping: bsmap 2.0
computation of methylation ratios: methratio.py (part of bsmap package)
Genome_build: dm3
Supplementary_files_format_and_content: Bedgraph-format containing the genomic methylation ratios of the respective sample

source_name: embryos

growth_protocol: Drosophila embryos were collected by placing 1-3 day old flies in a large embryo collection cages, with a 10cm grape agar dish. After females had been in the cage overnight (to synchronize egglaying) embryos were collected every 2 hours. Embryos were brushed off agar plates using PBS, dechorionized for 2 minutes in 100% bleach and flash frozen in liquid nitrogen until genomic DNA extraction.

extract_protocol: To extract genomic DNA, embryos were homogenized in 2X PK Buffer (200 mM Tris-HCl, pH 7.5, 25 mM EDTA, pH 8, 300 mM NaCl, 2% SDS) followed by phenol choloroform extraction and ethanol precipitation. Samples were then trated with RNAseA and purified again by phenol-chloroform and ethanol precipitation. To make bisulfite converted libraries, 1 ug of genomic DNA was sonicated with a Bioruptor using 3 cycles of 7 minutes (30 seconds on and 30 seconds off on high). Ice water was replaced after each cycle. Sonicated DNA was incubated with  a mixture of T4 DNA polymerase (NEB), T4 Polynucleotide kinase (NEB) and standard Taq Polymerase (Roche) in 1X T4 DNA ligase buffer with 10mm ATP (NEB). Methylated illumina Paired End adaptors were ligated using Rapid T4 DNA Ligase (Roche). Adaptors and ligase were added directly to the previous reaction. Ligated fragments were purified using Zymo Clean and Concentrator -5. Bisulfite conversion was performed using the EZ DNA Methylation kit (Zymo), following the manufacturer's instructions. Library was PCR amplified using Roche HIgh Fidelity Plus enzyme, and 2ul bisulfite converted DNA template. 2 PCR reactions were done in parallel and pooled. Final library was purified using Zymo clean and concentrate -25.

value: 0-2 hour embryos

tag: note


title: mTEC

source_name: Medullary thymic epithelial cells


title: ypgal_bio3_lib3

first: Wu

last: Wei

address: EMBL Heidelberg,Meyerhofstraße 1

department: Genome Biology Unit

institute: EMBL Heidelberg

description:
Sample 19
B.subtillis capped IVT  spike-ins added

data_processing:
Library strategy: TIF-Seq
Base-calling was performed using Illumina CASAVA pipeline and standard parameters.
5' and 3' sequences were extracted from paired-end sequences
5' and 3' sequences were aligned to the S288c reference R64 genome assembly using novoalign V2.07.10 with default parameters
Transcript isoforms (TIFs) were identified by exact identical 5' and 3' positions
Genome_build: Saccharomyces cerevisiae S288C reference genome R64 downloaded from SGD (http://www.yeastgenome.org/)
Supplementary_files_format_and_content: tab-delimited text files include number of TIFs of each sample (abundance measurements)

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown to mid-log phase (OD1) using either YPAD (1% yeast extract, 2% peptone, 1% glucose) or YPGal (1% yeast extract, 2% peptone, 1% galactose).

extract_protocol: Total RNA was isolated by a standard hot phenol method and contaminant DNA was removed by DNase I treatment. The sample was subject to TIF-Seq protocol (Transcript IsoForm Sequencing) for the unambiguous identification of overlapping transcripts by sequencing both 5’ and 3’ ends of the each mRNA molecule. Briefly, full-length cDNA molecules for capped and polyadenylated mRNAs is produced. After that, they are subject to intramolecular ligation, fragmentation and capture of the 5’-3’ junctions. Finally paired end sequencing of those tags give information to reconstruct the transcriptome architecture.

value: SLS045 (diploid, S288c background)

tag: media

value: YPGal media

value: mid-log phase cells, OD 1

value: WT


title: ypd_bio1_lib4

description:
Sample 21
enriched for long mRNAs

value: YPAD media


title: ypgal_bio4_lib3

description:
Sample 20
B.subtillis capped IVT  spike-ins added


title: ypgal_bio1_lib4

description:
Sample 23
enriched for long mRNAs


title: ypgal_bio4_lib4

description:
Sample 24
enriched for long mRNAs


title: PGT44

description: In this sample 10ng of human sperm DNA was spiked in


title: ypgal_bio4_lib2

description: Sample 10


title: ypd_bio2_lib3

description:
Sample 18
B.subtillis capped IVT  spike-ins added


title: Control Rat 4


title: ypd_bio2_lib2

description: Sample 8


title: ypgal_bio3_lib2

description: Sample 9


title: ypd_bio1_lib1

description: Sample 1


title: nypd_bio2_lib1

description:
Sample 13
non-capped molecules


title: ypd_bio1_lib2

description: Sample 7


title: Sample_9_180

city: Excelsior

first: Rod

middle: A.

last: Staggs

state: MN

address: 20040 Cottagewood Ave

institute: Minnesota Informatics

data_processing:
Libraries were sequenced to 100 nucleotide lengths on Illumina HiSeq2000 using RTA (real-time analysis) for image analysis, base calling, and data filtering.
Casava 1.8.0 was used to demultiplex and generate fastq files for each patient index.
Image analysis, base calling, and base call quality calibration were done using the Real Time Analysis software (Illumina).
Alignment and transcript abundance estimates generated with Tophat and Cufflinks software suite.
Genome_build: Ensembl GRCh37.66
Supplementary_files_format_and_content: bed file format of Tophat alignments

extract_protocol:
RNA extraction from whole blood was carried out per the manufacturer’s instructions using the PreAnalytiX PAXgene Blood RNA Kit, Version 2 from Qiagen.
Libraries were created using the Illumina TruSeq RNA Sample Preparation kit.

tag: time

value: 180 days post LVAD

value: whole blood


title: ypgal_bio2_lib1

description: Sample 4

tag: cell type


title: Sample_9_0

value: pre-LVAD


title: Sample_8_180


title: ypd_bio2_lib4

description:
Sample 22
enriched for long mRNAs


title: ypd_bio1_lib3

description:
Sample 17
B.subtillis capped IVT  spike-ins added


title: Sample_9_7

value: 7 days post LVAD


title: ypgal_bio1_lib1

description: Sample 3


title: Sample_8_7


title: Sample_8_0


title: nypgal_bio3_lib1

description:
Sample 14
non-capped molecules


title: C29_WT

value: Untreated control


title: Sample_7_0


title: Sample_6_180


title: Sample_6_0


title: Sample_5_0


title: Sample_7_7


title: Sample_5_180


title: Sample_6_7


title: Sample_4_180


title: Sample_5_7


title: ypd_bio2_lib1

description: Sample 2


title: Sample_3_180


title: Sample_4_7


title: Sample_3_7


title: Sample_4_0


title: Sample_2_0


title: Sample_2_7


title: CC_6

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

description:
Bisulfite treated, MspI digestion
The cell line used in our study in a chromaffin cell (cc) line that was generated from a mouse harboring a knock-in at the Sdhb endogenous gene locus, with LoxP sites flanking Sdhb exon 2 (Sdhb lox/lox). These cells were infected with an adenovirus expressing Cre recombinase, to induce exon 2 excision, and thus Sdhb gene knock-out (Sdhb-/-). Two different Sdhb-/- pure clones were isolated by limited dilution (Clones 8 and 6). Wild-type cells correspond to two different DNA extraction of the same population of Sdhb lox/lox chromaffin cells.

data_processing:
Illumina Casava1.8.2 software used for basecalling.
We used Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to filter out the adapter sequences.
Bisulfite mapping and methylation calling were performed in a single step using the bismark software (Krueger and Andrews, 2011).
Genome_build: mm9
Supplementary_files_format_and_content: A bed file is provided for each sample. Each line describes a CpG site with the following information: chromosome, cytosine position (start), cytosine position (end), methylation rate, number of methylated reads, number of unmethylated reads.

source_name: Mouse chromaffin cells

growth_protocol: DMEM Glutamax + 10% FBS

extract_protocol:
AllPrep kit (Qiagen)
RRBS was performed by Integragen SA (Evry, France), as described elsewhere (Gu et al., 2011; Smallwood et al., 2012). In brief, 300 ng of mouse genomic DNA was digested with 14 units of MspI (NEB). After end-repair, A-tailing and ligation to methylated Illumina adapters, the library fragments of 40-220 bp were gel isolated, subjected to a double bisulfite conversion with the EpiTect Bisulfite kit from Qiagen, PCR amplified and sequenced on an Illumina HiSeq2000 sequencer as paired-end 75-bp reads.

tag: sdhb

value: knock-out

tag: clone

value: chromaffin cell line


title: Sample_3_0


title: CC_WT2

value: wild-type


title: CC_8


title: Sample_1_7


title: pu1-D1-2

status: Public on May 04 2013

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: anti-PU.1 ChIP, Day 1, rep1

data_processing:
0) genome alignment: Data provided from University of Chicago sequencing center aligned to mm9.
1) peak calling: QuEST 2.4, using threshold of 15 against input (input.extended).
2) post-processing on peaks: threshold was raised from 15 to obtain a FDR (# input peaks/# ChIP peaks) of 1%.
3) peak comparison: final lists of peaks were obtained from replicates: for PU.1, took the coincident peaks between 2 replicates. For IRF-4, took peaks that were found in at least 2 of 3 replicates. Peak coincidence determined by peak positions within 200 bp.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Outputs from steps 2 and 3 are provided as processed data files.
Supplementary_files_format_and_content: GSM1133*.bed (linked to Sample records): Sequence enrichment processed by QuEST at a fixed 1% FDR.
Supplementary_files_format_and_content: GSE46607_*.bed (linked to Series record): QuEST output was merged to create a master peak list by identifying overlapping peaks within 200bp.

source_name: purified primary B cells from Bi-8i mice; stimulated for 1 Days; anti-PU.1 ChIP

growth_protocol: RPMI medium + 10% FCS and supplements (Hepes, 2-Me, glutamine, NEAA, Na-Pyruvate, Pen/Strep); isolated primary cells stimulated as indicated at a density of 0.5million/mL.

extract_protocol:
Lysates were clarified from sonicated nuclei, and transcription factor-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation, DNA was PCR amplified with Illumina primers for 12-14 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer 2 following the manufacturer's protocols.

treatment_protocol: NP-Ficoll (0.01 ng/mL) + CD40L + IL-2 + IL-4 + IL-5.

tag: strain/background

value: resting mature peripheral primary B cells

tag: stimulation duration

value: 1 days

tag: antibody

value: anti-PU.1 (Santa Cruz; sc-352)


title: CC_WT1


title: pu1-D3-3

description: anti-PU.1 ChIP, Day 3, rep2

source_name: purified primary B cells from Bi-8i mice; stimulated for 3 Days; anti-PU.1 ChIP

value: 3 days


title: pu1-D1-3

description: anti-PU.1 ChIP, Day 1, rep2


title: irf4-D3-4,5

description: anti-Irf4 ChIP, Day 3, rep3

source_name: purified primary B cells from Bi-8i mice; stimulated for 3 Days; anti-Irf4 ChIP

value: anti-Irf4 (Santa Cruz; sc-6059)


title: irf4-D3-3

description: anti-Irf4 ChIP, Day 3, rep2


title: TKO

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
BS-mapping: bsmap 2.0
computation of methylation ratios: methratio.py (part of bsmap package)
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph-format containing the genomic methylation ratios of the respective sample

source_name: ES cells

extract_protocol:
For mouse TKO ES DNA, cells derived from the Dnmt1-/-, Dnmt3a-/- and Dnmt3b-/- clone #19, gift from M.Okano (Tsumura et al., 2006), were grown on gelatine (no fibroblast feeder cells) in complete ES medium (as in Ficz et al., 2010 ). Before harvesting, the cells were stained by immunofluorescence against 5-methylcytosine and Dnmt1 for potential parental line contaminants (results not shown). Genomic DNA was prepared using the Qiagen DNEasy Blood & Tissue Kit, according to the manufacturer’s instructions.
For the TKO ES bisulfite sequencing library, genomic DNA spiked in with a 2kb PCR fragment from M13mp18 (1:10,000 ratio) were fragmented via sonication with a Covaris E220 instrument in a total volume of 70 µl. Methylated adapters (Illumina) were ligated to 250ng of the fragmented DNA with the NEB Next DNA Library Prep Master Mix Set for Illumina, according to the manufacturer‘s instructions, and subsequently BS-converted using Imprint DNA Modification kit (Sigma). The ligated fragments were amplified (15 cycles) using Pfu Turbo Cx Hotstart DNA Polymerase (Agilent) and indexed adapter-specific primers for Illumina – iPCRtagT5 (Quail et al., 2012 ), followed by purification and size-selection using AMPure XP beads (Agencourt). Paired end 100 bp sequencing was performed on an Illumina HiSeq.

tag: genotype/variation

value: Dnmt1-/-, Dnmt3a-/- and Dnmt3b-/-


title: irf4-D1-3

description: anti-Irf4 ChIP, Day 1, rep3

source_name: purified primary B cells from Bi-8i mice; stimulated for 1 Days; anti-Irf4 ChIP


title: input

description: Input DNA; pooled from different 2 independent preps of peripheral or immature B cells

source_name: Input DNA

extract_protocol:
Lysates were clarified from sonicated nuclei.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation, DNA was PCR amplified with Illumina primers for 12-14 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer 2 following the manufacturer's protocols.

value: peripheral and immature B cells


title: irf4-D1-1

description: anti-Irf4 ChIP, Day 1, rep1


title: Input DNA [IMS13q cell line]

city: Philadelphia

first: Ben

last: Black

address: 422 Curie Blvd.

institute: University of Pennsylvania

data_processing:
Basecalling performed by CASAVA pipeline
For alignments to higher order repeats, ChIP-seq reads were aligned to the ChrX or ChrY higher order repeat using Bowtie2 v2.0.0, reporting only single best alignment. Parameters: Mismatches = 0, Seed length = 50
For all other aligments, ChIP-seq reads were aligned to human genome hg19 using Bowtie2 v2.0.0, reporting only single best alignment: Parameters: Mismatches = up to 2, Seed length = 50
BED.txt and bedGraph (BDG) files were generated from SAM files using SAMtools and BAMtools
Genome_build: hg19

source_name: IMS13q cell line

growth_protocol: PDNC4 fibroblasts were grown in DMEM + 10% FBS 1% P/S.  Lyphoblast lines were cultured in RPMI-1640 + 10% FBS 1% P/S, 5% L-Glutamine.

extract_protocol:
Histone-DNA complexes were immunopurified from clarified Mnase-digested chromatin.
Sequencing libraries were generated and barcoded for multiplexing according to Illumina recommendations with minor modifications.  Briefly, 2-15 ng Input or ChIP DNA was end-repaired and A-tailed.  Illumina Truseq adaptors were ligated, libraries were size-selected to exclude polynucleosomes, and the libraries were PCR-amplied using Phusion polymerase.  All steps in library preparation were carried out using NEB enzymes. Resulting libraries were submitted for 100 bp, paired-end Illumina sequencing on a HiSeq 2000 instrument.

value: Lymphoblast

tag: chip antibody

tag: cell line


title: Input DNA [MS4221 cell line]

source_name: MS4221 cell line


title: Sample_1_180

tag: tissue


title: CENP-A ChIP-seq [IMS13q cell line]

value: CENP-A (Abcam, ab13939)


title: CENP-A ChIP-seq [MS4221 cell line]


title: Input DNA [PDNC4 cell line]

source_name: PDNC4 cell line

value: Fibroblast


title: CENP-A ChIP-seq [PDNC4 cell line]


title: Brain_Locust

status: Public on May 03 2013

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
BS-mapping: bsmap 2.0
computation of methylation ratios: methratio.py (part of bsmap package)
Genome_build: Locust2 EST project (http://titan.biotec.uiuc.edu/locust)
Supplementary_files_format_and_content: Bedgraph-format containing the genomic methylation ratios of the respective sample

organism: Schistocerca gregaria

source_name: brain

growth_protocol: Schistocerca gregaria were reared under crowded conditions to induce features typical for the gregarious phase. All animals were raised under a controlled temperature of 32°C, a photoperiod of 13 hours and a relative humidity between 40 and 60%. Animals were fed daily with fresh cabbage and dried oats. The crowded adult locusts were kept in cages of 38 x 38 x 38 cm with 100-200 individuals per cage. For both the cDNA sequencing and methylome analysis, 20 day-old adult animals (10 males and females) were sacrificed.

extract_protocol: Nucleic acids were extracted from 20 brains and 20 metathoracic ganglia of adult S. gregaria. Tissues were dissected with great care under a binocular microscope in insect saline buffer (ISB: 150 mM NaCl, 10 mM KCl, 4 mM CaCl2, 2 mM MgCl2, 10 mM Hepes, pH 7.0) and collected in tubes containing MagNA Lyser Green Beads (Roche). All samples were snap frozen in liquid nitrogen and stored at -80°C until homogenisation using the MagNA Lyser instrument (Roche). Genomic DNA was isolated using the DNeasy Blood & Tissue Kit (Qiagen). 5 µg of high molecular weight DNA were used for fragmentation using the Covaris S2 AFA System in a total volume of 100 µl. Fragmentation-run parameters: Duty cycle 10%; Intensity: 5; Cycles/burst: 200; Time: 3 min; number of cycles: 3, resulting in a total fragmentation-time of 180 s. Fragmentation was confirmed with a 2100 Bioanalyzer (Agilent Technologies) using a DNA1000 chip. The fragmented DNAs were concentrated to a final volume of 75 µl using a DNA Speed Vac. End repair of fragmented DNA was carried out in a total volume of 100 µl using the Paired End DNA Sample Prep Kit (Illumina) as recommended by the manufacturer. For the ligation of the adaptors, the Illumina Early Access Methylation Adaptor Oligo Kit and the Paired End DNA Sample Prep Kit (Illumina) were used, as recommended by the manufacturer. For the size selection of the adaptor-ligated fragments, we used the E-Gel Electrophoresis System (Invitrogen) and a Size Select 2% precast agarose gel (Invitrogen). Each fragmented DNA was loaded on two lanes of the E-gel. Electrophoresis was carried out using the “Size Select” program for 16 min. According to the standard loaded (50 bp DNA Ladder, Invitrogen), 240 bp fragments were extracted from the gel, pooled, and directly transferred to bisulfite treatment without further purification. For the bisulfite treatment we used the EZ-DNA Methylation Kit (Zymo) as recommended by the manufacturer with the exception of a modified thermal profile for the bisulfite conversion reaction. The conversion was carried out in a thermal cycler using the following thermal profile: 95°C for 15 s, 50°C for 1 h, repeat from step 1, 15×, 4°C for at least 10 min. The libraries were subsequently amplified, using the Fast Start High Fidelity PCR System (Roche) with buffer 2, and Illuminas PE1.1 and PE2.1 amplification primers. PCR thermal profile: 95°C for 2 min, 95°C for 30 s, 65°C for 20 s, 72°C for 30 s, then repeat from step 2, 11×, 72°C for 7min, hold at 4°C. PCR reactions were purified on PCR purification columns (MinElute, Qiagen) and eluted in 20 µl elution buffer (Qiagen).

tag: strain

value: leuven

value: adult

value: brain


title: MTG_Locust

source_name: mtg

value: metathoracic ganglia (mtg)


title: M. kandleri sRNAs + Tris-HCl pH8.8

city: Marburg

first: Lennart

last: Randau

address: Karl-von-Frisch Strasse 10

institute: MPI for terrestrial microbiology

description:
total small RNA (<200 bases)
Sample 5
10 µg of M. kandleri sRNA was incubated in a buffer containing 170 mM Tris-HCl pH 8.8 37° C for 3 hours to facilitate deacetylation of tRNA molecules

data_processing:
Illumina Software CASAVA1.8 was used for basecalling and removal of adaptor sequences
Sequencing reads were trimmed ((i) removal poly-A tails, (ii) removal of sequences using a quality score limit of 0.05)) and mapped to the reference genome (GenBank: NC_003551) with CLC Genomics Workbench 6.0 (CLC Bio, Aarhus, Denmark). A total of 83338855 reads with an average length of 61 nt were obtained after trimming. The following mapping parameters were employed (mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.5, similarity: 0.8). Reads below 15 nt were removed.
CLC Genomics Workbench 6.0 was utilized to determine the coverage for the individual RNA molecules.
GenBank: NC_003551
Genome_build: ASM718v1
Supplementary_files_format_and_content: tab-delimited text file including the coverage of mapped sequence reads at single nucleotide resolution for the M. kandleri genome.

organism: Methanopyrus kandleri AV19

source_name: Cultured organism

growth_protocol: Methanopyrus kandleri was grown in the Archaeenzentrum Regensburg (H. Huber, M. Thomm, K. Stetter) in a  300 l fermenter as described (Slesarev AI, Mezhevaya KV, Makarova KS, Polushin NN, Shcherbinina OV, Shakhova VV, Belova GI, Aravind L, Natale DA, Rogozin IB et al. 2002. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proceedings of the National Academy of Sciences of the United States of America 99(7): 4644-4649.)

extract_protocol: Total RNA was isolated by SDS-lysis of the cell pellet and phenol/chloroform extraction and small RNAs were purified from total RNA using the MirVana RNA extraction kit (Ambion). Specific sample treatment protocols were followed as described in the samples section. The RNAs were treated with poly(A) polymerase to add a poly-A tail that was used for cDNA synthesis and were prepared with an Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001). Libary preparation and sequencing on an Illumina HiSeq2000 sequencer was performed at the Max-Planck Genomecentre Cologne.

tag: protocol

value: sRNAs + Tris-HCl pH8.8


title: Sample_1_0

value: pre-LVAD

value: whole blood


title: M. kandleri sRNAs + H2O2

description:
total small RNA (<200 bases)
Sample 6
10 µg of M. kandleri sRNA was incubated in a buffer containing 50 mM sodium phosphate, 1 mM EDTA and 0,36% H2O2 at 20°C for 3 hours to facilitate dethiolation of RNA

value: sRNAs + H2O2


title: Chlamydomonas reinhardtii 2137 - TAP supplemented with a revised trace element recipe

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

description: Illumina's RNA-Seq whole transcriptome analysis

data_processing:
Illumina's proprietary software was used for basecalling.
The reads were aligned using bowtie  in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome.
Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates.
Genome_build: version 4.0 assembly of the Chlamydomonas genome
Supplementary_files_format_and_content: Processed files correpond to expression estimates per lane, in units of RPKMs, including those for the control samples (GEO record GSE25622)

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells

growth_protocol: Cells were cultured under continuous light of ~50-90 μmol photon m-2s-1 at 23ºC in liquid and on solid Tris-Acetate-Phosphate (TAP) medium supplemented with a revised trace element recipe.

extract_protocol: RNA was extracted by Cell lysis by SDS / proteinase K, Purification by phenol / chloroform extraction, and EtOH precipitation.  Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina by whole transcriptome analysis.

treatment_protocol: Cells grown on TAP agar plates supplemented with Hutner's trace elements were grown to mid to late log phase (10e6-10e7 cells/ml) in TAP supplemented with a revised trace element recipe and diluted 1/100 into fresh medium.

tag: treatment

value: Zn deprivation


title: M. kandleri sRNAs +T4PNK/ATP

description:
total small RNA (<200 bases)
Sample 4
10 μg of small RNA was incubated at 37°C for 6 hours with 20 units T4 PNK and 10 μl 5× T4 PNK buffer in a total volume of 50 μl. Subsequently, 2 mM ATP was added and the reaction mixture was incubated for 1 hour at 37°C to generate monophosphorylated 5’ termini.

value: sRNAs +T4PNK/ATP


title: CCL30 AZ8010 2

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

description: Sample 20

data_processing:
Basecalls performed using CASAVA
shRNA read were mapped to the SBI shRNA library using Bowtie version 0.12.5
Supplementary_files_format_and_content: read count table (text file) - each shRNA has its mapped read counts

growth_protocol: Cells were maintained in Dulbecco's modified Eagle medium (UMSCC25 and CCL30) or RPMI-1640 (584-A2) supplemented with 10% Fetal Bovine Serum and 1% penicillin-streptomycin at 37°C in a 5% CO2 humidified incubator.

extract_protocol: 4x10^6 cells from each of the cells lines UMSCC25, 584-A2, and CCL30 were plated and transduced 24 hrs later with the SBI shRNA library (Mountain View, CA) and 8 μg/mL polybrene (Sigma-Aldrich) at a multiplicity of infection of ~0.2. After 72 hrs, transfected cells were selected with puromycin (1 μg/mL) for 5 days. Library expressing cells were divided into six groups of 5x106 cells per T-75 flask where three were treated with vehicle (DMSO) and the remaining three groups were treated with AZD12908010 (1.0 μM for UMSCC25, 0.125 μM for 584-A2 and 0.5 μM for CCL30). After 72 hrs, the cells were placed in fresh media without drug for an additional 72 hrs. Total RNA was collected from each replicate using a RNeasy Mini Kit (Qiagen, Germantown, MD) and reverse transcribed using vector specific primers and MMLV reverse transcriptase (Invitrogen, Carlsbad, CA). The cDNA was amplified using nested PCR to isolate the shRNA sequences and to add Illumina adapter sequences. The samples were then sequenced on an Illumina Genome Analyzer IIx (Illumina, San Diego, CA), and shRNA sequences were identified and quantified.

treatment_protocol: Cells were treated with 0.5 μM AZ8010 for a period of 72 hrs and allowed to recover in media for 72 hrs. RNA was isolated at 144 hrs.

value: Head and Neck Squamous Cell Carcinoma cells

tag: agent


title: CCL30 AZ8010 3

description: Sample 21


title: Mash1_ChIPseq

city: Singapore

first: Wenjie

last: SUN

address: 60 Biopolis Street, #02-01, Genome

country: Singapore

institute: Genome Institute of Singapore

description: Sample 1

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq raw tags were aligned to the assembly mm8 using Eland which allows maximum two mismatches
peaks were called using MACS2.0 with default settings.
Genome_build: mm8
Supplementary_files_format_and_content: bedGraph files were generated using MACS2.0

source_name: spinal cord at embryonic day 12.5

extract_protocol:
chromatin was extracted from the dorsal domain of the dissected spinal cords of the embryonic day 12.5 mouse embryos
Libraries were prepared for sequencing using standard illumina protocols

tag: age

value: embryonic day 12.5

value: spinal cord

tag: chip antibody vendor

value: Pharmingen


title: M. kandleri sRNAs +T4PNK +ATP

description:
total small RNA (<200 bases)
Sample 3
The protocol for sample 4 was followed but 2 mM ATP was added from the beginning.

value: sRNAs +T4PNK +ATP


title: CCL30 AZ8010 1

description: Sample 19


title: M. kandleri sRNAs +T4PNK -ATP

description:
total small RNA (<200 bases)
Sample 2
The protocol for sample 4 was followed but the final addition of 2 mM ATP was omitted.

value: sRNAs +T4PNK -ATP


title: irf4-D3-2

description: anti-Irf4 ChIP, Day 3, rep1

value: resting mature peripheral primary B cells

value: 3 days

value: anti-Irf4 (Santa Cruz; sc-6059)


title: M. kandleri sRNAs control

description:
total small RNA (<200 bases)
Sample 1
no additional treatment

value: sRNAs control


title: irf4-D1-2

description: anti-Irf4 ChIP, Day 1, rep2

value: 1 days


title: CCL30 untreated

description: Sample 15

treatment_protocol: Untreated, RNA isolated at 0 hrs

value: Untreated


title: CCL30 DMSO 3

description: Sample 18

treatment_protocol: Cells were treated with DMSO for a period of 72 hrs and allowed to recover in media for 72 hrs. RNA was isolated at 144 hrs.

value: DMSO


title: 584-A2 AZ8010 3

description: Sample 14

treatment_protocol: Cells were treated with 0.125 μM AZ8010 for a period of 72 hrs and allowed to recover in media for 72 hrs. RNA was isolated at 144 hrs.


title: 584-A2 AZ8010 2

description: Sample 13


title: 584-A2 AZ8010 1

description: Sample 12


title: 584-A2 DMSO 2

description: Sample 10


title: 584-A2 untreated

description: Sample 8


title: 584-A2 DMSO 1

description: Sample 9


title: UMSCC25 AZ8010 1

description: Sample 5

treatment_protocol: Cells were treated with 1.0 μM AZ8010 for a period of 72 hrs and allowed to recover in media for 72 hrs. RNA was isolated at 144 hrs.


title: UMSCC25 AZ8010 2

description: Sample 6


title: UMSCC25 DMSO 3

description: Sample 4


title: UMSCC25 DMSO 2

description: Sample 3


title: UMSCC25 untreated

description: Sample 1


title: CCL30 DMSO 2

description: Sample 17


title: Small RNAs in pepper (Fruit3 samples) by high-throughput sequencing

city: SEOUL

first: Chanseok

last: Shin

address: Gwanak-gu Daehak-dong

institute: Seoul National University

data_processing:
Removed adaptors. Sequences without adapters were discarded. Small RNA sequences that did not match tRNA and rRNA sequences were selected.
Adaptor trimming: Fastx toolkit
rRNA, tRNA, snRNA/snoRNA masking: Blast  Data processing: Python script

organism: Capsicum annuum

extract_protocol: A small RNA sequencing library was constructed using the TruSeq Small RNA Sample Preparation Kit v2 (Illumina, CA, US), according to the manufacturer's instructions. Briefly, 5μg of total RNAs from each smaples were ligated to a 3’ adaptor and a 5’ adaptor sequentially and then converted to cDNA by RT-PCR. The resulting cDNAs were then amplified by PCR, gel-purified and submitted for sequencing.  Illumina GA single read sequencing, 38 cycle.

value: fruit

tag: development stage

value: 3rd stage

tag: molecule subtype

value: small RNA


title: SHX treated interactions S2

status: Public on May 02 2013

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description:
proximity ligation (Genome conformation capture) library
S2 sample lane 7

data_processing:
Sequences were intercalated
Network assembly was performed using the Topography suite v1.19. GCC networks were constructed from 100bp (E. coli) paired end Illumina Genome Analyser sequence reads. Topography uses the SOAP algorithm to position PE tags and single ends which contain a HhaI (E. coli) restriction site onto the E. coli (NC_000913). pUC19 (SYNPUC19CV), pRS426 plasmid, and Lambda phage ligation control sequences were also included in the genome reference file. No mismatches or unassigned bases (N) were allowed during positioning.
Except where indicated, bioinformatics and statistical analyses were performed on interactions in which the sequence reads were able to be mapped uniquely onto the reference genome and were above the FDR cut-off value (5).
Genome_build: ASM584v1
Supplementary_files_format_and_content: combined_L1_L2.txt includes LB grown (exponential) interactions. combined_S1_S2.txt includes serine hydroxamate treated (SHX) interactions.
Supplementary_files_format_and_content: The data in the columns is ordered in the following way: First interacting fragment (FIF) number/Second interacting fragment (SIF) number/Number of interactions between FIF and SIF/FIF Chromosome/ FIF Chromosome start/ FIF Chromosome stop/SIF Chromosome/SIF Chromosome Start/ SIF Chromosome Stop/FIF annotation/SIF annotation

organism: Escherichia coli

source_name: Escherichia coli MG1655

growth_protocol: For Genome Conformation Capture (GCC)(1) analyses, E. coli strains were recovered from -80°C on LB agar (2%) plates for 24 hours. LB medium (3ml) starter cultures were inoculated and grown (37°C, 220rpm, 16h). The Optical Density (OD600) of cultures was measured and used to inoculate LB test cultures to an OD600 of ~0.02. The test cultures were grown (37°C, 220rpm) until the OD600 reached ~0.25 and then harvested.

extract_protocol:
E. coli chromatin was prepared according to Rodley et al. (2009)(1) with the following modifications. A total of 5*109 cells were cross-linked with formaldehyde (1% final v/v, 20min, RT) and then quenched with glycine (125mM final, 10min). Cells were collected by centrifugation (4000rpm, 15min, 4°C), washed twice (1% PBS, 1% TritonX-100, 5ml/50ml culture) and pelleted (4000rpm, 15min, 4°C). Cell pellets were suspended in 800μl of B1 lysis buffer (10mM Tris pH 8.0, 50mM NaCl, 10mM EDTA, 20% (w/v) sucrose, 1mg/ml lysozyme) and incubated (37°C, 30min). 800μl of B2 lysis buffer (200mM Tris pH 8.0, 600mM NaCl, 4% TritonX-100, 1 protease inhibitor tablet (Roche) per 10ml of buffer added just before use) was gently added, mixed by inversion 3-4 times and incubated (37°C, 10min). The cell lysate was centrifuged (21,500g, 20min, 4°C) and the supernatant decanted. The chromatin was washed once with 1ml of chromatin digestion buffer (10mM Tris-HCl pH 8.0, 5mM MgCl2, 0.1% TritonX-100) by inverting the tube 3-4 times and centrifuged (21,500g, 20min, 4°C). The supernatant was decanted and the chromatin pellet was suspended in 500μl chromatin digestion buffer. Chromatin samples were aliquoted into 10 sets of 5*108 cells. Samples were digested with HhaI (100U, New England Biolabs). Following digestion a ligation control was added (see below and Table 2) and the samples were ligated with T4 DNA ligase (20U, Invitrogen). Following ligation, cross-links were removed in the presence of proteinase K (0.45U, Fermentas). RNA was removed and pUC19 plasmid (27.4pg/2ml) was added as a sequencing control prior to three extractions with 1:1 Phenol:Chloroform. DNA was column purified (Zymo, DNA clean and concentratorTM-5 kit) according to the manufacturer’s instructions and eluted in milliQ H2O before combining for sequencing. 3μg of purified DNA was sent for paired-end sequencing at the ATC sequencing facility (Rockville, MD, USA) on an Illumina Hi-Seq.
Sequences were fragmented to 200 bp fragments. End filled and primers ligated on, following standard Illumina protocols.

treatment_protocol: For the serine hydroximate (SHX) treated samples the cultures were treated with SHX (500 µg/ml, 30 min) before harvesting.

tag: biological replicate


title: SHX treated interactions S1B

description:
sample S1 was split and tagged with three mids. These were then run across two lanes on the hiseq to determine the effect of tag and sequence lane on the results
proximity ligation (Genome conformation capture) library
S1 sample tag B lane 6


title: UMSCC25 DMSO 1

description: Sample 2

tag: cell type


title: SHX treated interactions S1C

description:
sample S1 was split and tagged with three mids. These were then run across two lanes on the hiseq to determine the effect of tag and sequence lane on the results
proximity ligation (Genome conformation capture) library
S1 sample tag C lane 6


title: SHX treated interactions S1A

description:
sample S1 was split and tagged with three mids. These were then run across two lanes on the hiseq to determine the effect of tag and sequence lane on the results
proximity ligation (Genome conformation capture) library
S1 sample tag A Lane 5


title: Exponential interactions L1B

description:
sample L1 was split and tagged with three mids. These were then run across two lanes on the hiseq to determine the effect of tag and sequence lane on the results
proximity ligation (Genome conformation capture) library
L1 sample tag B lane 6


title: Exponential interactions L1C

description:
sample L1 was split and tagged with three mids. These were then run across two lanes on the hiseq to determine the effect of tag and sequence lane on the results
proximity ligation (Genome conformation capture) library
L1 sample tag C lane 6


title: Exponential interactions L1A

description:
sample L1 was split and tagged with three mids. These were then run across two lanes on the hiseq to determine the effect of tag and sequence lane on the results
proximity ligation (Genome conformation capture) library
L1 sample tag A Lane 5


title: Exponential interactions L2

description:
proximity ligation (Genome conformation capture) library
L2 sample lane 7


title: BSSeq_Buccal_rep_2_14

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

description: Buccal rep 2 Sample 14

data_processing:
BS-Seq data was mapped using BIFast with parameters –n 1 and –l 50 to hg19 (https://bitbucket.org/xboxrob/bifast)
Clonal reads were filtered and tDMRs were called using BiFast (dmrcaller)
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated Chromsome/Position of CpG/methylation fraction/Methylated Reads/Total Reads

source_name: Normal Buccal Cells

extract_protocol:
DNA from Buccal cells was extracted using the Gentra Puregene Buccal cell kit, USA.
50 ng of buccal genomic DNA was sonicated using a Bioruptor (Diagenode) to fragments around 300 bp on average and ligated to methylated pair end adapters (Illumina). Samples were bisulphite converted using EZ DNA methylation kit (ZYMO research) and sequenced using Illumina HiSeq 2000.

tag: Sex

value: Male

tag: ethnicity

value: Caucasian


title: CCL30 DMSO 1

description: Sample 16

value: Head and Neck Squamous Cell Carcinoma cells


title: BSSeq_Buccal_rep_2_13

description: Buccal rep 2 Sample 13


title: BSSeq_Buccal_rep_2_12

description: Buccal rep 2 Sample 12


title: BSSeq_Buccal_rep_2_10

description: Buccal rep 2 Sample 10

value: Female


title: BSSeq_Buccal_rep_2_9

description: Buccal rep 2 Sample 9


title: BSSeq_Buccal_rep_2_11

description: Buccal rep 2 Sample 11


title: BSSeq_Buccal_rep_2_8

description: Buccal rep 2 Sample 8


title: BSSeq_Buccal_rep_2_7

description: Buccal rep 2 Sample 7


title: UMSCC25 AZ8010 3

description: Sample 7


title: BSSeq_Buccal_rep_2_5

description: Buccal rep 2 Sample 5


title: BSSeq_Buccal_rep_2_3

description: Buccal rep 2 Sample 3


title: BSSeq_Buccal_rep_2_6

description: Buccal rep 2 Sample 6


title: BSSeq_Buccal_rep_2_4

description: Buccal rep 2 Sample 4


title: BSSeq_Buccal_rep_2_2

description: Buccal rep 2 Sample 2


title: BSSeq_Buccal_rep_1_14

description: Buccal rep 1 Sample 14


title: BSSeq_Buccal_rep_2_1

description: Buccal rep 2 Sample 1


title: BSSeq_Buccal_rep_1_13

description: Buccal rep 1 Sample 13


title: BSSeq_Buccal_rep_1_11

description: Buccal rep 1 Sample 11


title: BSSeq_Buccal_rep_1_9

description: Buccal rep 1 Sample 9


title: BSSeq_Buccal_rep_1_12

description: Buccal rep 1 Sample 12


title: BSSeq_Buccal_rep_1_5

description: Buccal rep 1 Sample 5


title: BSSeq_Buccal_rep_1_6

description: Buccal rep 1 Sample 6


title: BSSeq_Buccal_rep_1_3

description: Buccal rep 1 Sample 3


title: BSSeq_Buccal_rep_1_10

description: Buccal rep 1 Sample 10


title: BSSeq_Buccal_rep_1_7

description: Buccal rep 1 Sample 7


title: BSSeq_Buccal_rep_1_2

description: Buccal rep 1 Sample 2


title: BSSeq_Buccal_rep_1_8

description: Buccal rep 1 Sample 8


title: 584-A2 DMSO 3

description: Sample 11


title: BSSeq_Buccal_rep_1_1

description: Buccal rep 1 Sample 1


title: LTED_INPUT_Raw

status: Public on May 01 2013

city: Lebanon

first: xiaoyang

last: zhang

address: 1 Medical Center Driver

institute: Dartmouth Medical School

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (Feburary, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome_build: Hg 19
Supplementary_files_format_and_content: Bed file (1st Column: chromosome; 2nd: Peak starting site; 3rd: Peak ending site)

source_name: Long-term estrogen deprived breast cancer cell line

growth_protocol: MCF7-LTED cells were developed by being maintained in Phenol-red free DMEM media for more than one year.

extract_protocol: DNA was fragmented in the  200-500 bp range and then purified using 3 consecutive extraction with Phenol/Chloroform. Next, DNA was purified using a Quiagen column. Library preparation for next-generation sequencing was performed according to manufacturer’s instruction starting with 5 ng of material (Illumina Inc.).

treatment_protocol: No treatment was applied to MCF7-LTED cells


title: FAIRE_H19_LTED_rep2


title: FAIRE_H19_LTED_rep1


title: H3K4me2_LTED

data_processing: Alignment: Sequence reads were obtained and mapped to the human (Feburary, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.

growth_protocol: MCF7 cells were maintained in DMEM (Invitrogen) supplemented with 10% FBS, MCF7-LTED cells were developed by being maintained in Phenol-red free DMEM media for more than one year.

extract_protocol: Library preparation for next-generation sequencing was performed according to manufacturer’s instruction starting with 5 ng of material (Illumina Inc.).

treatment_protocol: For MCF7 cells, 10-8M E2 treatment 45mins; No treatment was applied to LTED cells. Antibody was used as 4ug/ChIP.

tag: antibody

tag: vendor

value: Millipore

tag: catalog#


title: H3K36me3_E2 treated

source_name: Breast Cancer Cell Line

tag: cell line

value: E2 treated (45mins)

value: Abcam


title: H3K36me3_LTED


title: Input


title: BSSeq_Buccal_rep_1_4

description: Buccal rep 1 Sample 4


title: 3628Ago

city: Madison

first: Bill

last: Sugden

state: WI

address: 1111 Highland Ave

institute: University of Wisconsin-Madison

description: total RNA after RISC-IP

data_processing:
Primary analysis performed using RTA 1.12.4.2 followed by secondary analysis with CASAVA 1.8.1
Sequence analysis was conducted using CLC Genomics Workbench Version 4.9; reads were mapped to hg18 human genome build
Unique exon reads for each gene were then used to create expression values for each gene with the following formula: Expression Value = (unique exon reads)(10^9)/(exon length)(total unique exon reads)
A table was constructed consisting of genes with the respective associated expression values for each condition.
Genome_build: hg18
Supplementary_files_format_and_content: text file contains genes and associated enrichment values for each sample.  Fold change (Column 4) is the ratio of the respective values BJAB_3628/BJAB_3626 (Column_3/Column_2)

source_name: BJAB cells_BARTs_RISC-IP

growth_protocol: BJAB cells were grown in RPMI 1640 (Gibco) supplemented with 10% fetal bovine serum (R10F) and 200 U/mL penicillin and 200 µg/mL streptomycin at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol:
1×10^8 cells were washed with PBS and lysed with 500 µl of PLB buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 0.5% NP-40, 5 mM MgCl2, 200 U/ml RNase inhibitor (Ambion), 1 mM DTT, proteinase inhibitor cocktail) at 4°C for 30 min. Following centrifugation, the lysate was incubated with anti-human Ago2 (11A9) antibody (Provided by Dr. Gunter Meister [Rüdel S, et al. (2008) A multifunctional human Argonaute2-specific monoclonal antibody. RNA 6: 1244–2153.]) conjugated dynabeads (Invitrogen) in 500 µl of NET-2 buffer (20 mM EDTA, pH 8.0, 1 mM DTT, and 200 U/ml RNase inhibitor in NT-2 buffer (150 mM Tris-HCl, pH 7.0, 100 mM Tris-HCl, pH 8.0, 750 mM NaCl, 0.25% NP-40, 5 mM MgCl2)) at 4°C for overnight. The protein-dynabead complexes were washed 6 times with NT-2 buffer, once with NTmS buffer (150 mM Tris-HCl, pH 7.0, 100 mM Tris-HCl, pH 8.0, 0.25% NP-40, 5 mM MgCl2) and resuspended with 1× Turbo DNase buffer and 2 U of Turbo DNase (Ambion) at 37°C for 30 min. The activity of DNase was eliminated with 15 mM of EDTA followed by addition of same volume of proteinase K buffer (2.4 mg/ml of proteinase K and 2% SDS in NT-2 buffer) at 55°C for 30 min. The RNA was extracted with acid-phenol/chloroform (pH 4.5) once, chloroform once and precipitated and resuspended in RNAse-free water.
Libraries were generated using Illumina’s mRNA Seq kit (lot#5701543) Rev. D according to manufacturer's protocol.  Briefly, samples were fragmented then precipitated at -80°C, followed by first strand & second strand cDNA synthesis.  After end repair and adenylation of 3' ends, adapters were ligated to cDNA molecules.  Following ligation, cDNA was purified using E-gel Size Select 2% agarose gels.  Enrichment of purified cDNA was done via LMPCR (15 cycles) followed by purification using ZymoResearch DNA Clean & Concentrator columns (25ul elution volume). Libraries were validated on Agilent 1000 DNA chip and Quant-iT quantification.

treatment_protocol: Cell lines grown under the same conditions

value: BJAB

value: EBV-negative Burkitt's lymphoma cells

tag: ectopic barts

value: yes (expressing EBV's BART miRNAs)

tag: ip antibody

value: anti-human Ago2 (11A9) antibody

tag: ip antibody info


title: 3626Ago

description: total RNA after RISC-IP

source_name: BJAB cells_empty_RISC-IP

value: no (empty retroviral vector)