title: H3K4me3_ChIPSeq

city: San Francisco

first: Abhinav

last: Nellore

address: 513 Parnassus Avenue

institute: UCSF

description: Sample 1

data_processing:
Reads aligned using Bowtie v1.1.2
Peaks called using MACs 1.0.1
Genome_build: mm9
Supplementary_files_format_and_content: .bed of called peaks

source_name: subventricular zone neural stem cells

growth_protocol: SVZ was accutely isolated and cells were cultured as neurospheres on low-attachment plates

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using standard Illumina protocols

tag: gender

value: male

value: H3K4me3 antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: DG Lane 1 [RNA-seq]

status: Public on Apr 11 2013

type: SRA

state: CA

country: USA

description: Mouse DG

library_source: transcriptomic

data_processing:
Illumina Casava basecalling
Reads aligned with Tophat v1.2.0
Transcripts assembled and quantified with Cufflinks v1.0.0
Genome_build: mm9
Supplementary_files_format_and_content: bed file of assembled lncRNA transcriptome, spreadsheet of coding and noncoding FPKM values from Cufflinks

molecule: polyA RNA

organism: Mus musculus

source_name: Microdissected mouse dentate gyrus

extract_protocol:
Brain regions were acutely microdissected from adult animals and snap-frozen. RNA was extracted by Trizol method, cleaned up, and DNAse treated on Rneasy columns (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype/variation

value: wild type

tag: age

value: adult

tag: tissue

value: microdissected dentate gyrus (DG)


title: OB Lane 1 [RNA-seq]

description: Mouse OB

source_name: Microdissected mouse olfactory bulb

value: microdissected olfactory bulb (OB)


title: STR  Lane 1 [RNA-seq]

description: Mouse STR

source_name: Microdissected mouse striatum

value: microdissected striatum (STR)


title: Pelvis FFPE

status: Public on Apr 15 2013

city: Columbus

first: wei

last: meng

state: Ohio

address: 400 W12 street

department: Radiation Oncology

institute: The Ohio State University

data_processing:
The linker sequences of small RNA libraries were removed using cutadapt software (http://code.google.com/p/cutadapt/) under default parameters.
After removing linker sequences and filtrating by different small RNA databases, reads were mapped with miRBase V16.
All reads of each sample were aligned against miRBase and the hg19 reference genome using SOLiD™ small RNA Analysis pipeline (http://solidsoftwaretools.com), and were normalized as reads per million (RPM).
Sequences with expression value below 5 RPMs were considered not detected.
Genome_build: miRBase version 16
Supplementary_files_format_and_content: txt file contained 250 microRNA expression information

molecule: total RNA

organism: Homo sapiens

source_name: Pelvis

extract_protocol:
RNA from FFPE samples were extracted using Recover All Total Nucleic Acid Isolation Kit (Life Technologies Corporation, Carlsbad, CA). The microRNA samples from the fresh frozen samples were extracted using PureLink™ miRNA Isolation Kit (Life Technologies Corporation, Carlsbad, CA).
Small RNAs from FFPE and fresh frozen samples were prepared for SOLiD sequencing as follows: the total RNA samples were processed by the flashPAGE fractionator (Ambion) and flashPAGE Clean-Up Kit (Ambion). The enriched small RNA was then processed according to the SOLiD Small RNA Expression Kit protocol (Applied Biosystems). The purified small RNAs were ligated with 5' and 3' adapter mix using RNA ligase. The ligated products (40–60 bases in length) were reverse transcribed and purified on Novex 10% TBE-Urea gel. Subsequently, 15–18 cycles of PCR were performed by amplifying the purified cDNA with barcoded PCR primer sets provided in the kit, which differed by a unique 6-nucleotide sequence. The amplified products were loaded on Novex 6% TBE gel (Invitrogen) and the gel bands containing 110 to 130bp fragments were excised. The amplified products were purfied from excised gel band, amplified by emulsion PCR, then loaded on Applied Biosystems SOLiD 4 next generation high throughput sequencing system for data acquisition.  The quality of the samples and libraries were verified on the Agilent Bioanalyzer.

treatment_protocol: Eight paired human malignant tissue samples were received.  Remnant surgical tissues were taken after diagnostic samples were secured from patients.Surgical specimens were transported from the operating rooms to Tissue Procurement, examined under a pathologist’s supervision and preserved within 5 to 57 recorded minutes. Paired tissue samples selected for research were either immediately snap frozen in liquid nitrogen and placed in a -80 °C freezer for monitored storage or fixed in 10% buffered formalin for up to 24 hours and then processed into a paraffin embedded block and stored at room temperature .

tag: tissue storage

value: FFPE

value: Pelvis

tag: histology

value: Metastatic Melanoma

tag: Sex

value: M


title: Atf4-/ Tm ChIP-seq

city: Ann Arbor

first: Maureen

middle: A

last: Sartor

state: MI

address: 2017 Palmer Commons Bldg., 100 Washtenaw Ave

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

description: ATF4 KO ChIP-Seq Replicates

library_source: genomic

data_processing:
ERANGE was used to create .rds database files and then bedgraph files with -raw option turned on.
ChIP-Seq peaks were identified using ERANG with default settings
Genome Build:
run48_s_2.bedgraph: mm9
run58_s_5.bedgraph: mm9
run58_s_7.bedgraph: mm9

molecule: genomic DNA

source_name: Mouse embronic fibroblast

growth_protocol: Mouse embryonic fibroblast cells were rountinely subcultured in high-glucose DMEM supplemented with 10% FBS, Pen/Strep, NEAA (all invitorgen) on cell culture dishes.

extract_protocol: unknown

treatment_protocol: MEFs were treated with tunicamycin for 10hr. After treatment, chromatin immunoprecipitation or RNA isolation were performed.

tag: cell type

value: Mouse embryonic fibroblast

tag: developmental stage

tag: antibody

tag: treatment

value: Tunicamycin


title: input DNA

description: Sample 3

value: WT

tag: chip antibody


title: Thigh, left posterior  Frozen

source_name: Thigh, left posterior

value: Frozen

value: Thigh, left posterior

value: Sarcoma


title: ddm1-2 F6 generation mutant total small RNA

first: Richard

middle: Keith

last: Slotkin

state: OH

address: 318 West 12th Ave.

department: Molecular Genetics

description: library strategy: small-RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads de-multiplexed and were trimmed for adaptor sequence
Sequences were masked for low-complexity or low-quality sequence, filtered for reads 18-28 nt in size, then mapped to the genome using bowtie with parameters --best --strata -M1
tRNA and rRNA-matching reads were removed
Genome_build: TAIR10
Supplementary_files_format_and_content: small RNA sequence and the number of times they were sequenced

organism: Arabidopsis thaliana

source_name: Inflorescence tissue

growth_protocol: Plants were grown on soil in 18 hour per day light at 23C. All plants used in this study were grown side-by-side.

extract_protocol:
Total RNA was extracted using Trizol reagent, and small RNAs were purified using mirVana microRNA isloation kit.
Cloning of small RNAs was performed using the Illumina TruSeq Small RNA Sample Preparation Kit

tag: background strain

value: unopened flower buds

tag: growth conditions

value: 18 hour light, 23C


title: wt Col total small RNA

description: library strategy: small-RNA-seq


title: SVZ Biological Replicate 2 [RNA-seq]

description: Mouse SVZ, second bioreplicate,

source_name: Microdissected mouse subventricular zone

tag: gender

value: male

value: wild type

value: microdissected subventricular zone (SVZ)


title: Chop -/- Tm ChIP-seq

description: CHOP KO ChIP-Seq

data_processing:
ERANGE was used to create .rds database files and then bedgraph files with -raw option turned on.
ChIP-Seq peaks were identified using ERANG with default settings
Genome Build:
CHOP_KO.bedgraph: mm9

value: anti-CHOP

value: Chop-/-


title: GBP14B

city: Copenhagen N

first: Morten

last: Rasmussen

address: Panum Building 6.6 Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: University of Copenhagen

data_processing:
Basecalls performed using CASAVA version 1.x
The raw fastq files were filtered using the FastX toolkit. Overrepresented adaptor sequences were clipped. Reads were 3' quality trimmed and 5' trimmed and only sequences longer than 15nts with at least 70% of the nts with quality >20 were kept.
The remaining sequences were aligned to hg19 using Bowtie 1 with alignment parameters "-m 1 -n 2 --best --strata".
The aligned files were converted to BED format using BedTools.
Genome_build: hg19
Supplementary_files_format_and_content: BED file with relevant gene promoters and tab-delimited expression matrix (extension exp.txt) of read counts within the relevant gene promoters. MACS called peaks (txt).

source_name: Vastus Lateralis immediately before gastric bypass (GBP)

extract_protocol:
Genomic DNA was extracted according the standard Dneasy protocol
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Male

value: Vastus Lateralis Muscle


title: GBP16A

source_name: Vastus Lateralis 6 months after gastric bypass (GBP)


title: GBP5B


title: SVZ Biological Replicate 1 [RNA-seq]

description: Mouse SVZ, first bio replicate

value: adult


title: SVZ Capture

description: RNA extracted from SVZ for capture-seq

data_processing:
library strategy: RNA CaptureSeq
Reads aligned using BLAT
Newbler 2.6 used for de novo assembly of transcriptome
FPKM values calculated using RSEM included in the Trinity package
Genome_build: mm9
Supplementary_files_format_and_content: Transcript structure and abundance calls for CaptureSeq-derived transcripts

source_name: Mouse subventricular zone

extract_protocol:
Total RNA was extracted using Trizol, and cleaned and DNAse-treated on an Rneasy column.
RNA CaptureSeq was performed according to standard Roche/Nimblegen protocols and as described in Mercer et al, Nature Biotechnology 2011

tag: molecule subtype

value: Capture-enriched cDNA


title: H3K27me3_ChIPSeq

description: Sample 2

value: H3K27me3 antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: GBP1B


title: GBP11B


title: GBP3B


title: GBP11A


title: GBP3A


title: GBP5A


title: GBP14A


title: Tfe3_shFlcn_ChIPSeq

status: Public on Apr 10 2013

city: Cambridge

first: Joerg

last: Betschinger

address: Tennis Court Road

country: United Kingdom

institute: Wellcome Trust and Medical Research Council Stem Cell Institute

data_processing:
Basecalls were performed using CASAVA version 1.4
36-nt reads were aligned with Bowtie (vs 0.12.8;  to the mouse reference genome (UCSC mm9/NCBI build 37) allowing no mismatches and excluding non-unique mappings. Potential PCR duplicates were removed.
Peaks were called over IgG and Tfe3 shRNA cells with MACS (vs 1.4.2). Processed data files are wig profiles calculated by MACS.
Genome_build: UCSC mm9/NCBI build 37

source_name: Flcn.4, 2i

growth_protocol: ES cells were cultured in N2B27 (NDiff N2B27 base medium, Stem Cell Sciences Ltd) supplemented with small-molecule inhibitors PD03 (1uM, PD0325901), CHIR (3uM, CHIR99021) on gelatin coated tissue culture flasks.

extract_protocol: ES cells were fixed for 10 min in 1.1% formaldehyde, neutralized with 1M glycine, collected in cold PBS and incubated for 10 min on ice in swelling buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40 and 0.25% Tx-100). Nuclei were pelleted, washed and resuspended in shearing buffer (50mM Tris pH 8.0, 10mM EDTA and 1% SDS). Lysates were sonicated using a Bioruptor (Diagenode). Lysates were diluted 1:10 in ChIP dilution buffer (50mM Tris pH 8.0, 167mM NaCl, 1.1% Tx-100 and 0.11% Na-Deoxycholate), pre-cleared for 2h over ProteinG sepharose beads (Amersham) and incubated overnight with 2g Tfe3 (Santa Cruz, sc-5958) or isotype IgG antibodies (Santa Cruz, sc-2025). Lysates were then incubated for 1h with blocked ProteinG sepharose beads, washed 6 times and eluted twice with elution buffer (1% SDS and 0.1M NaHCO3) for 15 min shaking at room temperature. Samples were incubated overnight at 65°C to reverse the cross-linking and purified using QIAquick PCR Cleanup kit (Qiagen). ChiP-Seq libraries were generated using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB) using 10 amplification cycles.

value: embryonic stem cell

tag: passage

tag: shRNA

value: shFlcn

value: Tfe3 (Santa Cruz, sc-5958)


title: IgG_ctrl_ChIPSeq

source_name: ctrl.2, 2i

value: control

value: IgG antibodies (Santa Cruz, sc-2025)


title: GBP1A

tag: tissue


title: Tfe3_shTfe3_ChIPSeq


title: Tfe3_ctrl_ChIPSeq


title: DicerWT_r1

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

description: Dicer WT MSCs with retrovirally expressed vector.

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were aligned to the mouse genome  (genome build mm9). Read mapping was performed with Bowtie version 0.12.7 for uniquely mapping reads with 0 mismatches.  Peaks were called using MACS version 1.4.0beta.
Genome_build: mm9
Supplementary_files_format_and_content: BED files for peaks were generated using MACS version 1.4.0beta. Score column represents: -10log10(pvalue). For each replicate number (r1/r2) the corresponding bed file includes peaks called for Flag-HA-NR6A1 using vector-infected cells (Dicer_WT) as input control.

source_name: Dicer f/f murine MSC cell line

growth_protocol: Monoclonal immortalized Dicer WT MSCs were cultured in Alpha-MEM supplemented with pen/strep, 10% fetal bovine serum, and puromycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and bound DNA fragments were isolated with antibody.
Genomic DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Dicer WT cells were infected with pMMP-puro-vector or pMMP-puro-Flag-HA-NR6A1 and selected with puromycin.  After stably selected cultures were established, cells were crosslinked for 10 minutes at room temperature by the addition of one-tenth of the volume of 11% formaldehyde solution (11% formaldehyde, 50mM Hepes pH 7.3, 100mM NaCl, 1mM EDTA pH 8.0,  0.5mM EGTA pH 8.0) to the growth media. Cells were washed twice with PBS, supernatant was aspirated and the cell pellet was flash frozen in liquid nitrogen. Frozen crosslinked cells were stored at -80oC. 50ul of Dynal magnetic beads (Sigma) were blocked with 0.5% BSA (w/v) in PBS. Magnetic beads were bound with 5ug of the indicated antibody unless otherwise indicated.

value: murine MSC cell line

tag: genotype

value: Dicer f/f, retrovirally expressed vector

tag: strain


title: H3K4me3_DicerKO_R2

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were aligned to the mouse genome  (genome build mm9). Read mapping was performed with Bowtie version 0.12.7 for uniquely mapping reads with 0 mismatches.  Peaks were called using MACS version 1.4.0beta.
Genome_build: mm9
Supplementary_files_format_and_content: BED files for peaks were generated using MACS version 1.4.0beta. Score column represents: -10log10(pvalue). For each histone mark and replicate number (r1/r2) the *_WCE_r[12].bed files per sample are peaks called with the genotype-matched WCE (whole cell extract) sample as control input. For each histone mark and replicate number (r1/r2) the *_Diff_r[12].bed files per sample are peaks called using the opposite genotype as control input.

source_name: Dicer -/- murine MSC cell line

growth_protocol: Monoclonal immortalized Dicer WT and KO MSCs were cultured in Alpha-MEM supplemented with pen/strep and 10% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Genomic DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Dicer WT and KO cells were crosslinked for 10 minutes at room temperature by the addition of one-tenth of the volume of 11% formaldehyde solution (11% formaldehyde, 50mM Hepes pH 7.3, 100mM NaCl, 1mM EDTA pH 8.0,  0.5mM EGTA pH 8.0) to the growth media. Cells were washed twice with PBS, supernatant was aspirated and the cell pellet was flash frozen in liquid nitrogen. Frozen crosslinked cells were stored at -80oC. 50ul of Dynal magnetic beads (Sigma) were blocked with 0.5% BSA (w/v) in PBS. Magnetic beads were bound with 5ug of the indicated antibody unless otherwise indicated.

value: Dicer -/-

value: H3K4me3:Millipore 07-473, lot # DAM1731494 (7.5uL per ChIP)


title: NR6A1_r2

description: Dicer WT MSCs with retrovirally expressed Flag-HA-NR6A1.

value: Dicer f/f, retrovirally expressed Flag-HA-NR6A1


title: H3K56Q H2A.Z ChIP

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

description:
1. Liu CL, Schreiber SL, Bernstein BE (2003) Development and validation of a T7 based linear amplification for genomic DNA. BMC Genomics 4: 19.
2. Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Munster S, et al. (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature 457: 1033-1037.
H2A.Z ChIP in H3K56Q mutant

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling
reads were mapped to the yeast S288C genome using BLAT
genome wide cross correlation between the reads mapping to the Watson and Crick strands was determined and the length of the reads were extended by this value to count the number of reads present at each base pair
the average read count value was calculated and the data were normalized to one
S288C (S. cerevisiae)
Genome_build: SacCer_May2010
Supplementary_files_format_and_content: tab-delimited text files of the normalized read counts showing -500bp to end of gene coding sequence surrounding the transcription start site

organism: Saccharomyces cerevisiae W303

source_name: yeast with histone H3K56Q mutation

growth_protocol: WT and H3K56Q were grown to log phase in YPD media at 30°C and Hst 3,4 D was gorn at 23C in YPD

extract_protocol:
Cells were washed in water, cell walls were broken with bead beating and spheroplasts were treated with micrococcal nuclease.  Immunoprecipitations were performed with extract equivalent to 100 ml of cell culture in the following volume: 6μl anti-Htz1 (Active Motif). Immunoprecipitation, washing, protein degradation, and DNA isolation were performed as previously described [1].
ChIP DNA, was treated with calf intestinal phosphatase (NEB), was blunt-ended, A-tailed, and ligated (Epicentre) to Illumina genomic PE adaptors, and the final library was amplified via PCR and size selected by gel purification (BioRad)

treatment_protocol: Cells were fixed in 1% formaldehyde.

tag: ChIP

value: H3K56Q mutant


title: H3K4me3_DicerKO_R1

tag: cell type


title: H3K4me3_DicerWT_R1

value: Dicer f/f


title: H3K36me3_DicerWT_R2


title: H3K36me3_DicerKO_R2


title: H3K4me3_DicerWT_R2


title: WT_Ago2CLIP_Untagged

description: RNA fragments immunoprecipitated by tandem Flag/HA IP after UV crosslinking from immortalized clonal lines of Dicerf/f (Dicer WT) mesenchymal stem cells (MSCs) expressing an Untagged hAgo2 construct were cloned and sequenced.

data_processing:
Library strategy: CLIP-Seq
Sequenced reads were trimmed for adapter sequence and mapped to the UCSC mouse genome build mm9 using Bowtie1. Reads mapping to >1 location or with >2 mismatches were discarded.  Reads were collapsed  based on identical 5? and 3? end mapped coordinates. To include reads mapping across exon-exon junctions, we extracted splice junction coordinates from the isoforms produced by Tophat from RNA-seq data and used custom python scripts to generate a fasta file of the sequences +/- 45 nt of these splice junctions. We then mapped any previously unmapped iCLIP reads to these exon-exon junction sequences and added any splice junction mapping reads to the total mapped dataset. After initially calling putative Ago2 bound regions by identifying clusters of more overlapping reads than a null poisson distribution model with cut-off p value < 0.001, we filtered out any clusters that had the same mismatched nucleotide in >70% of its reads.  Finally, the remaining clusters were required to have significantly more tagged reads than untagged reads (binomial, p<0.05) after median-based normalization of the read counts in both libraries, using background regions found in both tagged and untagged datasets.  Annotation of genomic regions was taken from Ensembl NCBIM37 build annotation. Single nucleotide 5P end files that largely reflect crosslink sites are included as BigWig files for visualization.
Supplementary_files_format_and_content: Text file including processed CLIP-seq reads and corresponding number of observations in dataset.

source_name: Dicer f/f murine MSC TT-hAgo2 cell line

growth_protocol: Monoclonal immortalized Dicer WT MSCs were cultured in Alpha-MEM supplemented with pen/strep and 10% fetal bovine serum.

extract_protocol:
Sequencing was carried out on RNA fragments crosslinked to immunopurified hAgo2 that had undergone DNase digestion and limited RNase I digestion in lysate.
CLIP-seq RNA libraries were prepared for sequencing using a circulariaztion approach similar to Konig et al., 2011.

treatment_protocol: Tagged or Untagged hAgo2 expression was induced by doxycycline 48 hours prior to experiment, with 0.1 ug/ml dox at 0 hours and 1 ug/ml dox at 24 hours.

tag: rna type

value: Rnase I digested immunopurified RNA


title: NR6A1_r1


title: WT_Ago2CLIP_Tagged

description: RNA fragments immunoprecipitated by tandem Flag/HA IP after UV crosslinking from immortalized clonal lines of Dicerf/f (Dicer WT) mesenchymal stem cells (MSCs) expressing a FLAG-HA-tagged hAgo2 construct were cloned and sequenced.

source_name: Dicer f/f murine MSC TT-Flag-HA-hAgo2 cell line


title: H3K27me3_DicerWT_R1


title: H3K27me3_DicerKO_R2


title: H3K27me3_DicerWT_R2


title: H3K36me3_DicerKO_R1


title: WCE_DicerKO_R2


title: H3K27me3_DicerKO_R1


title: WCE_DicerWT_R2


title: Dicer_Null_2

description: Small RNAs (15-50 nts in length) from immortalized monoclonal lines of Dicer-/- (Dicer KO) mesenchymal stem cells (MSCs), a fibroblast cell type present in adult bone marrow, were analyzed.

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Raw reads were processed to remove traces of 3' linker (CTGTAGGCACCATCAAT) and summarized by sequence identity (observations).
Genome_build: mm9
Supplementary_files_format_and_content: Text file with sequence and count

growth_protocol: Monoclonal immortalized MSCs were cultured in Alpha-MEM supplemented with pen/strep and 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using Qiazol reagent according to manufacturer's instructions.  15-50 nt small RNAs were selected from a 15% polyacrylamide TBE-urea gel.
Libraries were cloned and sequenced using the Illumina small RNA-sequencing protocol.

treatment_protocol: Monoclonal immortalized Dicer WT and KO MSCs were cultured to near-confluence under normal growth conditions and then harvested for RNA isolation.

tag: rna

value: small RNA


title: WCE_DicerWT_R1


title: Dicer_WT

description: Small RNAs (15-50 nts in length) from immortalized monoclonal lines of Dicerf/f (Dicer WT) mesenchymal stem cells (MSCs), a fibroblast cell type present in adult bone marrow, were analyzed.


title: DicerWT_r2


title: GRO-seq_TNFa_30m_AC16_2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: GRO-seq in AC16 cells treated for 40 minutes with E2

data_processing:
Library strategy: GRO-Seq
Alignment: Short-reads were aligned to the human reference genome (hg19, 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: hg19
Supplementary_files_format_and_content: bed file

growth_protocol: AC16 human adult ventricular cardiomyocyte cells (Davidson et al., 2005) were purchased from the American Type Culture Collection.  The cells were maintained in DMEM F-12 supplemented with 12.5% fetal bovine serum, penicillin/streptomycin and gentamicin.

extract_protocol:
Nuclei extractions were preformed as described (Hah et. al. 2011).
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: The cells were grown to 75% confluence and switched to serum-free medium overnight prior to treatment with 25 ng/ml TNFα (Peprotech) for the indicated time.

tag: cell line

tag: treatment

value: TNFa

tag: time

tag: rna subtype

value: nascent RNA


title: Flag-HA-NR6A1_Clone12

description: mRNAs isolated from immortalized clonal lines of Dicerf/f (Dicer WT) mesenchymal stem cells (MSCs), a fibroblast cell type present in adult bone marrow, were infected with puromycin-resistant pMMP-puro retrovirus encoding Flag-HA-NR6A1.

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Sequence reads were trimmed to remove traces of adapter sequence (AGATCGGAAGAGCGGTTCAGCAGGAATG). Reads were first mapped to the mouse transcriptome (UCSC annotation, genome build mm9) and un-aligned reads were then mapped to the mouse genome where possible. Read mapping was performed with TopHat version 1.2.0 using default options. Abundance estimation and differential analysis were performed using Cufflinks version 1.0.3 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) value per gene for each sample

extract_protocol:
mRNA-sequencing was carried out with total RNA purified with the RNeasy reagent (Qiagen) and DNase-treated with TURBO Dnase.  (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two independent clones of immortalized Dicer WT MSCs (Clone 6 and Clone 12) were infected with puromycin-resistant pMMP-puro retrovirus encoding vector control or Flag-HA-NR6A1.


title: GRO-seq_TNFa_30m_AC16_1


title: GRO-seq_TNFa_10m_AC16_1

description: GRO-seq in AC16 cells treated for 10 minutes with E2


title: Flag-HA-NR6A1_Clone6


title: Vector_Clone6

description: mRNAs isolated from immortalized clonal lines of Dicerf/f (Dicer WT) mesenchymal stem cells (MSCs), a fibroblast cell type present in adult bone marrow, were infected with puromycin-resistant pMMP-puro retrovirus encoding vector control.


title: GRO-seq_Vehicle_AC16_2

description: GROseq in untreated AC16 cells


title: H3K36me3_DicerWT_R1

tag: chip antibody


title: Vector_Clone12


title: KO_siNr6a1_R1

description: mRNAs isolated from immortalized clonal lines of Dicer-/- (Dicer KO) mesenchymal stem cells (MSCs), a fibroblast cell type present in adult bone marrow, and transfected with siRNA against Nr6a1 (siNr6a1), were analyzed.

treatment_protocol: Monoclonal immortalized Dicer WT and KO MSCs were transfected with indicated siRNAs at 20 nM using Qiagen HiPerfect transfection reagent as per manufacturer's instructions.  48 hours after transfection, cells were harvested for RNA extraction.


title: KO_siNr6a1_R2


title: GRO-seq_E2_40m_MCF7_2

description: GRO-seq in MCF7 cells treated for 40 minutes with E2

data_processing:
Library strategy: GRO-Seq
The inclusion of the polyA tail in the adapter sequence lead us to devise a new pipeline for processing and mapping reads generated using the circular ligation approach.  First, we combined barcoded reads obtained from separate Illumina sequencing lanes, discarding all reads not passing Illumina quality filters.  We trimmed adapter sequences and polyA stretches allowing an error rate (-e) of up to 10% using the cutadapt package (Martin, 2011).  All reads longer than 32 bp after adapter trimming were aligned to hg18 chromosomes 1-22 and X  (the Y chromosome was not included, because MCF-7 cells are derived from a female) using the BWA software package (Li and Durbin, 2009).  After read alignment, we noted that one of the 25 minute time point replicates (replicate 2) showed a poor correlation with the other two replicates (the 10 and 40 minute replicates were unaffected).  Upon inspection we found a high proportion of reads mapping in ‘spikes’ near polyA sites, leading us to eliminate this replicate from further analysis at this stage.  Lastly, reads were converted to ‘wiggle’ tracks counting reads in non-overlapping 200 bp windows across the genome.  These tracks were used in subsequent analysis.
Genome_build: hg18
Supplementary_files_format_and_content: bed file

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:
Nuclei extractions were preformed as described (Hah et. al. 2011).
To reduce the ligation bias generated by the relatively low efficiency of single strand RNA ligation, MCF-7 libraries were prepared using a circular ligation based protocol, similar to one that has been described previously (Wang et al., 2011).  Briefly, global run-on and base hydrolysis were performed as previously described (Core et al., 2008).  Nascent RNA was treated with 5 l antarctic phosphatase (NEB) for 1 hour at 37C before immunopurification by using anti-BrdU antibody-conjugated beads.  Purified run-on RNA was subjected to polyA tailing by adding 0.8 l polyA polymerase buffer, 0.8 l 10 mM ATP, 0.5 l SuperRnaseIn and 0.75 l E. coli PolyA Polymerase (NEB) and incubating for 8 min. at 37ºC.  PolyA-tailed RNA was extracted by acid phenol-chloroform and subjected to another round of immunopurification by using anti-BrdU antibody conjugated beads to further avoid mRNA contamination.  Subsequently, purified polyA-tailed RNA was converted to cDNA by reverse transcription using SuperScript III reverse transcriptase (Invitrogen) and RT primer (pGATCGTCGGACTGTAGAACTCT/idSp/ CCTTGGCACCCGAGAATTCCATTTTTTTTTTTTTTTTTTTTVN) where p indicates phosphorylation, idSp indicates dSpacer Furan, and VN indicates degenerate nucleotides.  The RT primer incorporates the Illumina HiSeq 5’ and 3’ adaptors for later PCR amplification and sequencing.  Extra RT primers were eliminated by adding 4 l Exonuclease I (Fermentas) with incubation at 37C for 1 h and the RNA templates were eliminated by adding 1.8 l 1 N NaOH with incubation for 20 min. at 98C.  Reverse transcribed cDNAs were size selected (120 to 400 bp) by denaturing PAGE (8% acrylamide, 7 M urea, 1X TBE).  Purified cDNAs were circularized by adding 1 l CircLigase buffer, 0.5 l 1mM ATP and 0.5 l 50 mM MnCl2 and 0.5 l CircLigase (Epicentre), incubating at 60C for 1 h, and heat-inactivating at 80C for 20 min..  The circularized cDNAs were re-linearized by adding 3.8 l of 4X relinearization supplement (100 mM KCl, 2 mM DTT) and 1.5 l ApeI (NEB), with incubation at 37C for 1 h.  After phenol-chloroform extraction, the purified cDNAs were subjected to PCR amplification by using different Illumina TrueSeq small RNA sample barcoded primers from and Phusion high-fidelity polymerase (NEB).  PCR was performed by an initial 3 min. denaturation at 98C, subsequent 15 cycles of PCR amplification (80 seconds denaturation at 98C, 90 seconds annealing at 60C, and 30 seconds extension at 72C), and a final 10 min. extension at 65C.  PCR products were isolated by native PAGE (6% acrylamide, 1X TBE gel), excised (175 bp to 300 bp), eluted, and purified.  The final libraries were sequenced using an Illumina HiSeq per the manufacturer’s instructions.

treatment_protocol: MCF-7 cells were plated at a density of 1 x 10^6 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.


title: KO_siNr6a1_R0


title: GRO-seq_E2_25m_MCF7_2

description: GRO-seq in MCF7 cells treated for 25 minutes with E2


title: GRO-seq_E2_40m_MCF7_3


title: Nr15 Rotenone 5day rep3

status: Public on Apr 16 2013

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
Illumina Casava1.7 software used for extraction of FASTQ files
FASTQ files were mapped using TopHat (v1.4.1, parameters: --butterfly-search -g 1) vs. the C. elegans genome assembly WS220 (Ensembl release 66)
Gene counts were obtained using the Python package HTSeq and the respective Ensembl annotation GTF file (parameters: –stranded=no --idattr=gene_id --mode=union)
HTSeq result files were processed using the R programming language and RPKM values were calculated
Genome_build: WS220 (ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/sequence/genomic/c_elegans.WS220.genomic.fa.gz)/WBcel235
Supplementary_files_format_and_content: raw counts and RPKM values for each sample

organism: Caenorhabditis elegans

source_name: total RNA from whole animals

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at −80°C until use.
Total RNA was inspected for degradation using Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). For library preparation an amount of 2μg of total RNA per sample was processed using Illumina's TruSeq™ RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer's instruction. Each library includes its own index sequence.

treatment_protocol: Treatment of C. elegans was carried out on NGM agar plates containing respective complex I inhibitors. All agar plates were prepared from the same batch of NGM agar, whereas treatment plates were supplemented with the respective compound and control plates with the respective solvent

value: whole animal

tag: age

value: 5 days after L4

tag: developmental stage

value: Adult (5 days after L4)

value: 100nM rotenone


title: GRO-seq_E2_40m_MCF7_1


title: KO_let-7g_R2

description: mRNAs isolated from immortalized clonal lines of Dicer-/- (Dicer KO) mesenchymal stem cells (MSCs), a fibroblast cell type present in adult bone marrow, and transfected with a synthetic let-7g siRNA duplex, were analyzed.


title: GRO-seq_E2_25m_MCF7_1


title: GRO-seq_E2_10m_MCF7_3

description: GRO-seq in MCF7 cells treated for 10 minutes with E2


title: KO_let-7g_R0


title: WCE_DicerKO_R1


title: GRO-seq_E2_10m_MCF7_2


title: KO_siCtrl_R2

description: mRNAs isolated from immortalized clonal lines of Dicer-/- (Dicer KO) mesenchymal stem cells (MSCs), a fibroblast cell type present in adult bone marrow, and transfected with a nontargeting control siRNA (siCtrl), were analyzed.


title: KO_siCtrl_R1


title: GRO-seq_TNFa_10m_AC16_2


title: GRO-seq_E2_10m_MCF7_1


title: WT_siCtrl_R2

description: mRNAs isolated from immortalized clonal lines of Dicerf/f (Dicer WT) mesenchymal stem cells (MSCs), a fibroblast cell type present in adult bone marrow, and transfected with nontargeting control siRNA (siCtrl), were analyzed.


title: GRO-seq_Vehicle_MCF7_3

description: GROseq in untreated MCF7 cells


title: GRO-seq_Vehicle_MCF7_1

description: GROseq in untreated MCF7 cells


title: KO_siCtrl_R0


title: GRO-seq_Vehicle_AC16_1

description: GROseq in untreated AC16 cells


title: WT_siCtrl_R1


title: Histone mark #5-8: input (Nkx2-1-neg. tumor), rep. #2

status: Public on Apr 09 2013

first: Sebastian

last: Hoersch

address: 77 Massachusetts Avenue (E18-366)

department: David H. Koch Institute for Integrative Cancer Research at MIT

institute: Massachusetts Institute of Technology

data_processing:
Forty nucleotide of sequenced reads were mapped to reference mouse genome build 37 (mm9), using bowtie aligner.  Aligned reads for two biological replicates for each IP and input.were merged.
Sequencing reads from one Nkx2-1 IP were down-sampled to obtain equal contributions from each replicate.
Binding sites for Nkx2-1, and Foxa1/2 were identified using MACS (version 1.4.2) (Zhang et al. 2008 PMID:19505939), with a p-value cutoff of 10^-6 and with default values for other parameters.
H3K4me1, H3K4me3, H3K27Ac and H3K27me3 modified regions were detected using SICER (version 1.1) (Zang et al. 2009 PMID:19505939) with an effective genome fraction of 0.77, a FDR cutoff for calling peak regions (“islands”) of 0.01,  and a window size of 200. Following authors’ recommendations, a gap size of 200 (600) was used for H3K27ac and H3K4me3 (H3K27me3 and H3K4me1).
Genome_build: mm9
Supplementary_files_format_and_content: .wig: alignment wiggle files of paired replicates, rescaled to a target of 40 Mio // .bed: called peaks, based on paired replicates

source_name: lung adenocarcinoma

extract_protocol:
Lung tumors were pulverized, cross-linked with 1% formaldehyde in PBS for 10 min at RT, washed in 5mg/ml BSA in PBS and then in just cold PBS, re-suspended in lysis buffer [50mM Tris-HCl, pH 8.1, 10mM EDTA, 1% SDS, 1X complete protease inhibitors (Roche)], and sonicated with the Covaris E210 sonicator to obtain chromatin fragment lengths of 200-to-1500bp judged by Bioanalyzer DNA High sensitivity kit (Agilent). Fragmented chromatin was diluted in IP buffer [20mM Tris-HCl pH 8.1, 150mM NaCl, 2mM EDTA, 1% Triton X-100] and incubated overnight at 4C with Protein G magnetic beads (Dynabeads: Invitrogen) that had been pre-incubated with anti-NKX2-1 (Bethyl BL4000), anti-FOXA1/2 (Santa Cruz sc-6553), H3K4me1 (Abcam ab8895), H3K4me3 (Millipore 07-473), H3K27Ac (Abcam ab4729) or H3K27me3 (Millipore 07-449) antibodies. Immunoprecipitates were washed six times with wash buffer [50mM HEPES pH 7.6, 0.5M LiCl, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40] and twice with TE buffer. Immunoprecipitated (or no IP input) DNA was treated with RNase A and Proteinase K on the beads, recovered in 1% SDS plus 0.1M NaHCO3 over a period of 5 hours at 65C, column purified with QiaQuick columns (Qiagen) and quantified with use of a PicoGreen assay (Invitrogen). After a sonication to enrich DNA fragment lengths between 100-300bp, 5 to 50ng of DNA were used for the library construction.
After a sonication to enrich DNA fragment lengths between 100-300bp, 5 to 50ng of DNA were used for the library construction. DNA sequencing for Illumina cluster generation were prepared using the SPRI-works system (Beckman Coulter) with 200-400 bp size selection followed by enrichment with barcoded PCR primers for multiplexing at the MIT BioMicro Center. Sequencing was performed on a HiSeq2000 (HiSeq Flow Cell v3, TruSeq SBS Kit v3, RTAVersion 1.13.48) running HiSeq Control Software 1.5.15.1 for 40 to 50 nucleotides from a single end. Barcode-separated FASTQ files were generated from QSEQ files using a custom parsing script.

treatment_protocol: Mice were infected intratracheally with adenovirus (University of Iowa, Gene Transfer Vector Core) or lentivirus as described (DuPage et al., 2009). Tamoxifen (Sigma) was dissolved in corn oil (Sigma) and administered intraperitoneally at 56 micrograms (low dose) or 112 micrograms (high dose) per gram total body weight.

tag: tester-control pair

value: J

value: mixed 129/B6

value: lung

tag: tumor type

value: adenocarcinoma

tag: nkx2-1 status

value: deleted

tag: gender

value: female

value: 4 to 7 months

tag: chip antibody catalog number


title: Histone mark #8: H3K4me3 (Nkx2-1-neg. tumor), rep. #2

tag: strain

tag: tissue

value: Millipore


title: GRO-seq_Vehicle_MCF7_2

description: GROseq in untreated MCF7 cells


title: Histone mark #6: H3K27me3 (Nkx2-1-neg. tumor), rep. #2


title: Histone mark #7: H3K4me1 (Nkx2-1-neg. tumor), rep. #2

value: Abcam


title: Histone mark #5: H3K27ac (Nkx2-1-neg. tumor), rep. #2


title: Histone mark #5-8: input (Nkx2-1-neg. tumor), rep. #1

value: I

value: male


title: Histone mark #8: H3K4me3 (Nkx2-1-neg. tumor), rep. #1


title: KO_let-7g_R1

tag: cell type

value: murine MSC cell line

tag: genotype

value: Dicer -/-


title: Histone mark #6: H3K27me3 (Nkx2-1-neg. tumor), rep. #1


title: Histone mark #3: H3K4me1 (Nkx2-1-pos. tumor), rep. #2

value: H

value: positive


title: Histone mark #7: H3K4me1 (Nkx2-1-neg. tumor), rep. #1


title: Histone mark #1-4: input (Nkx2-1-pos. tumor), rep. #2


title: Histone mark #1: H3K27ac (Nkx2-1-pos. tumor), rep. #1

value: G


title: Histone mark #5: H3K27ac (Nkx2-1-neg. tumor), rep. #1


title: Histone mark #2: H3K27me3 (Nkx2-1-pos. tumor), rep. #1


title: Transcription factor #3: input, rep. #2

value: F


title: Histone mark #4: H3K4me3 (Nkx2-1-pos. tumor), rep. #2


title: Histone mark #4: H3K4me3 (Nkx2-1-pos. tumor), rep. #1


title: Histone mark #3: H3K4me1 (Nkx2-1-pos. tumor), rep. #1


title: Histone mark #2: H3K27me3 (Nkx2-1-pos. tumor), rep. #2


title: Histone mark #1: H3K27ac (Nkx2-1-pos. tumor), rep. #2


title: WT_siCtrl_R0

value: Dicer f/f


title: Transcription factor #3: input, rep. #1

value: E

value: mixed 129/B6


title: Transcription factor #2: input, rep. #2

value: D

value: lung

value: adenocarcinoma


title: Transcription factor #3: Foxa1/2 (Nkx2-1-neg. tumor), rep. #2

value: deleted

value: female

value: 4 to 7 months

value: Santa Cruz


title: Transcription factor #1: input, rep. #1

value: A

value: male


title: Transcription factor #2: input, rep. #1

value: C


title: Transcription factor #3: Foxa1/2 (Nkx2-1-neg. tumor), rep. #1


title: Transcription factor #2: Foxa1/2 (Nkx2-1-pos. tumor), rep. #1


title: Transcription factor #1: input, rep. #2 and Histone mark #1-4: input (Nkx2-1-pos. tumor), rep. #1

value: B and G


title: Transcription factor #2: Foxa1/2 (Nkx2-1-pos. tumor), rep. #2

value: positive


title: br-Y1

city: Jinan

first: Yuqi

last: Qin

address: 27 Shanda Nan Lu

country: China

institute: Shandong University

description: Penicillium decumbens brlA deletion strain  grown in liquid medium

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 21-nt long tags. Then low quality tags, one copy tags and tags which are not 21-nt long were removed to generate clean tags. Reference 21-nt tag databases were created from predicted P. decumbens transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed. The copy number of unambiguous tags (tags mapped to one single gene) for each gene was normalized to TPM (number of transcripts per million clean tags) for differential expression analysis.
Genome_build: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000

organism: Penicillium decumbens

source_name: Fungal mycelia

growth_protocol: The conidia of Penicillium decumbens were inoculated to 2% (wt/vol) glucose medium for 12 h as the pre-culture, and then mycelia were transferred and grown in the new medium for 48 h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was prepared from the mycelia by grinding under liquid nitrogen with a mortar and pestle, followed by extraction using the RNAisoTM reagent (TaKaRa, Japan) according to manufacturer  s protocol.
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 35bp.
3' adaptor sequences were first removed from the sequencing reads to produce 21-nt long tags. Then low quality tags, one copy tags and tags which are not 21-nt long were removed to generate clean tags. Reference 21-nt tag databases were created from predicted P. decumbens transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed. The copy number of unambiguous tags (tags mapped to one single gene) for each gene was normalized to TPM (number of transcripts per million clean tags) for differential expression analysis.

value: brlA deletion

tag: medium

value: Liquid

value: 48 h after transferring washed mycelia to the new medium


title: 114-Y1

description: Penicillium decumbens strain 114-2 grown in liquid medium

value: 114-2 (wild type)


title: Transcription factor #1: Nkx2-1, rep. #1

value: mixed 129/B6

value: Bethyl


title: Transcription factor #1: Nkx2-1, rep. #2

value: B

value: lung


title: 114-G1

description: Penicillium decumbens strain 114-2 grown on solid medium

value: Solid


title: Chicharo

city: MONTPELLIER

first: SEVERINE

last: CHAMBEYRON

address: 141, rue de la Cardonille

department: Institute of Human Genetics

description: small RNA

data_processing:
Base-calling performed by Fasteris SA (CASAVA pipeline v.1.8.)
Sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3’-end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila simulans (release 1.3) according to sequencing quality using Novoalign (www.novocraft.com). Only reads perfectly matching the fly genome were analyzed (one mismatch was nevertheless allowed on low-sequencing quality nucleotides, -e 20 option).
Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), micro RNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. rRNAs, tRNAs and snRNAs were retrieved from modEncode (http://www.modencode.org/ (Celniker et al. 2009)), miRNAs from miRBase (http://www.mirbase.org/ (Kozomara and Griffiths-Jones 2011)) and transcripts from Flybase (http://flybase.org/). As Drosophila simulans transposable elements have not yet been exhaustively sequenced, libraries are annotated according to Drosophila melanogaster transposable elements from Repbase (http://www.girinst.org/repbase/index.html (Jurka et al. 2005)).
After subtracting reads matching abundant cellular species such as rRNAs, tRNAs and snRNAs, the remainders, called bona fide reads, were split into siRNAs (21nt), miRNAs (22nt) and piRNAs (23-29nt). For the piRNA identification, we selected bona fide reads strictly exceeding 22 nt in length and not annotated as miRNAs.
Genome_build: ds1.3
Supplementary_files_format_and_content: Read counts (second column) for each bona fide sequence (first column)

organism: Drosophila simulans

source_name: Chicharo_3 day-old ovaries

growth_protocol: Flies were grown at 18 degrees C

extract_protocol: Extracted small RNAs were cloned by Fasteris SA (Switzerland) after being selected on acrylamide gel between 18 and 30 nucleotides

treatment_protocol: Small RNAs (18-30nt) were isolated using anion exchange chromatography extractions.

value: Chicharo (Portugal)

value: Ovaries

value: 3 day-old


title: NRT

description: small RNA

source_name: NRT_0-2 hours eggs

value: Cross between Chicharo female and Makindu male

value: Eggs

value: 0-2 hours


title: RT

description: small RNA

source_name: RT_0-2 hours eggs

value: Cross between Makindu female and Chicharo male


title: Makindu

description: small RNA

source_name: Makindu_3 day-old ovaries

value: Makindu (Kenya)


title: HSC KO rep 2

status: Public on Apr 07 2013

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

data_processing:
Image capture, analysis and base calling were performed using Illumina’s CASAVA 1.8 .
Read alignment and methylation calls at CpGs were performed using FAR software (Dodt, M, Ahmed R, Dieterich C. FAR – flexible adapter remover. FAR project website 2011, http://sourceforge.net/projects/theflexibleadap/) for adaptor filtering and  bismark was used for whole genome alignment.
Methylation level calls were performed on reads with a phred quality score of greater than thirty three and a 10-fold coverage.
Methlation calls with a minimum of 10 reads were retained, and differential methylation was analyzed using methylkit (http://code.google.com/p/methylkit/) using non-overlapping 1kb-sized differentially methylated regions (DMR) (>10% methylation difference, q<0.001). Differential methylation was assessed between WT and SATB1 KO HSC, and between WT HSC and WT MPP (2 independent replicates per population).
Overlap of DMR between WT HSC and MPP with DMR between WT and SATB1 KO HSC was assessed using 1kb non-overlapping DMR with a minimum coverage of 5 reads per DMC (q<0.001, >25%  methylation difference).
Genome_build: mm9
Supplementary_files_format_and_content: MethylCall files are tab delimited text files that contain the chromosomal locations of cytosines within CpGs covered in the data and their respective methylation levels.  Column headers are as follows: chrBase = cytosine location name ;  chr = chromosome on which the methylated base is located;  base = base location of methylated base on the chromosome; strand = F for forward strand and R for reverse strand; coverage = read coverage for the cytosine;  freqC = % methylated; freqT = % unmethylated

growth_protocol: Primary, uncultured cells.

extract_protocol:
DNA was extracted using the Allprep DNA/RNA purification Kit (Qiagen) and analyzed using a Bioanalyzer (Agilent Technologies).
10ng of DNA was digested with the MspI restriction enzyme. End repair and ligation of paired end Illumina sequencing adaptors was followed by size selection for 150-400 bp library fragments by gel extraction (Qiagen gel extraction kit). Bisulfite conversion using the EZ DNA Methylation Kit (Zymo Research) was followed by PCR amplification using Illumina PCR PE1.0 and 2.0 primers. Library products were purified using AMPure XP beads per manufacturer’s recommended protocol (Agencort). Quality control was performed using quantitation on a Qubit 2.0 fluorometer (Invitrogen) and library visualization using a Quant-iT dsDNA HS Assay Kit (Agilent 2100 Bioanalyzer).
Enhanced Reduced Represantation Bisulfite Sequencing (ERRBS): Amplified libraries were sequenced using a 50bp single end read run on a HiSeq2000 per manufacturer’s recommended protocol.

treatment_protocol: Satb1 wild type or knock out CD45.2+ fetal liver cells transplanted into lethally irradiated congenic (CD45.1+) recipient animals. Purification of donor-derived (CD45.2+) HSC and MPP from a pool of three animals.

value: Satb1 -/-

value: Hematopoietic stem cells


title: br-G1

description: Penicillium decumbens brlA deletion strain  grown on solid medium

value: brlA deletion

value: 48 h after transferring washed mycelia to the new medium


title: MPP WT rep2

value: Satb1 +/+

value: Hematopoietic multipotent progenitor cells


title: MPP WT rep1


title: HSC WT rep2


title: FAIRE_MO_Indiv-D-E

status: Public on Apr 08 2013

city: Hinxton

first: Dirk

middle: Stefan

last: Paul

address: Wellcome Trust Genome Campus

department: Human Genetics

institute: Wellcome Trust Sanger Institute

description: This sample includes bed files from two different standard deviation thresholds (T=6.0 and T=8.0) from two individuals and a bed file from the individuals combined.

data_processing:
We obtained the raw sequence files from two independent FAIRE experiments in K562 erythroblastoid cells from the ENCODE Project (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/) and remapped the data as described below. For the K562 single-end sequencing data set, we adjusted the mode of the peak width distribution to the mean of the modes across all non-K562 cell types.
Raw sequence reads were aligned to the human reference sequence (NCBI build 37, hg19) using the read mapper Stampy.
Reads were realigned around known insertions and deletions, followed by base quality recalibration using the Genome Analysis Toolkit (GATK). Duplicates were flagged using the software Picard and excluded from subsequent analyses.
Regions of enrichment (peaks) were determined using the software F-Seq v1.84. We applied a feature length of L=600 bp and two different standard deviation thresholds of T=6.0 (‘moderate’) and T=8.0 (‘stringent’) over the mean across a local background.
In order to reduce false-positive peak calls, we removed regions of collapsed repeats, applying a threshold of 0.1% (http://eqtl.uchicago.edu/Masking).
For comparison of cell type-specific chromatin profiles, we merged all read fragments into one data set for each cell type and the called peaks as described.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files in bed format, with the following columns: chromosome, peak start, peak end, name, F-Seq score.

source_name: Peripheral blood

growth_protocol: Cord blood-derived CD34+ hematopoietic progenitor cells from two unrelated individuals were differentiated in vitro into either megakaryocytes in the presence of thrombopoietin (TPO) and interleukin-1β (IL-1β), or erythroblasts in the presence of erythropoietin (EPO), interleukin-3 (IL-3) and stem cell factor (SCF). Monocytes were purified from peripheral blood from another two individuals. CHRF-288-11 cells were cultured as previously described (D.S. Paul et al, 2011, PLoS Genet 7(6), e1002139).

extract_protocol: FAIRE DNA was processed following the Illumina paired-end library generation protocol.

value: Monocytes

tag: individual/replicate

value: Indiv-D + Indiv-E

tag: f-seq parameter


title: FAIRE_MK_Indiv-B-C

source_name: Umbilical cord blood

value: Megakaryocytes

value: Indiv-B + Indiv-C


title: FAIRE_CHRF_1_2

description: This sample includes bed files from two different standard deviation thresholds (T=6.0 and T=8.0) from two biological replicates and a bed file from the replicates combined.

source_name: Cell culture

value: Repl-1 + Repl-2


title: FAIRE_EB_Indiv-A-B

value: Erythroblasts

value: Indiv-A + Indiv-B


title: FAIRE_K562_1_2


title: HSC WT rep1


title: M82.Sun.stem

status: Public on Apr 05 2013

city: Tuebingen

first: Daniel

last: Koenig

address: Spemmannstr 30

department: Molecular Biology

institute: Max Planck Institute for Developmental Biology

description: SRX252003 SRX252004

data_processing:
Basecalls performed using CASAVA version 1.4 and trimmed for quality
Reads were mapped to pseudoITAG sequences generated from alignement of cDNAs from S. lycopersicum and S, pennellii
Alignments of the first paired end only used BWA version 0.5.7 7 with parameters -k 1 -l 25 -n 0.02 -e 15 -i 10
Read counts for each ITAG were then summed and RPKM were calculated
genome build: S. lycopersicum var. Heinz v2.4
supplementary files format and content: space-delimited text files include RPKM values for each Sample ...

organism: Solanum lycopersicum

source_name: stem

growth_protocol: 22C in conviron growth chamber. Seedling samples were harvested from plates

extract_protocol:
Trizol extractions were used for the mixed tissue experiments and Qiagen plant mRNA easy for seedling tissues
Illumina mRNA-seq sample prerparation kit

treatment_protocol: Shade and Sun treatments applied with light intensity averaged 95 µE with a red to far-red ratio of 0.48 or 3.1

tag: light

value: Artificial sun

value: stem


title: M82.Sun.sdling

description: SRX252001 SRX252002

source_name: Seedling

value: Seedling


title: M82.Sh.stem

description: SRX252019 SRX252020

value: Artificial shade


title: M82.Sun.floral

description: SRX251992 SRX251993

source_name: Inflorescence

value: Inflorescence


title: M82.Sh.veg

description: SRX252021 SRX252022 SRX252023

source_name: vegetative meristem

value: vegetative meristem


title: FAIRE_Islet

data_processing:
We retrieved FAIRE sequencing data for the erythroblastoid cell line K562 (GSM864361) and pancreatic islets ('sample 3'; GSM491290), and reanalyzed these data sets using the same methodology as described below.
Raw sequence reads were aligned to the human reference sequence (NCBI build 37, hg19) using the read mapper Stampy.
Reads were realigned around known insertions and deletions, followed by base quality recalibration using the Genome Analysis Toolkit (GATK). Duplicates were flagged using the software Picard and excluded from subsequent analyses.
Regions of enrichment (peaks) were determined using the software F-Seq v1.84. We applied a feature length of L=600 bp and two different standard deviation thresholds of T=6.0 (‘moderate’) and T=8.0 (‘stringent’) over the mean across a local background. For the K562 and pancreatic islets single-end sequencing data sets, we adjusted the mode of the peak width distribution to the mean of the modes across all non-K562 cells/pancreatic islets.
In order to reduce false-positive peak calls, we removed regions of collapsed repeats, applying a threshold of 0.1% (http://eqtl.uchicago.edu/Masking).
For comparison of cell type-specific chromatin profiles, we merged all read fragments into one data set for each cell type and then called peaks as described.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files in bed format, with the following columns: chromosome, peak start, peak end, name, F-Seq score.

source_name: Pancreatic islets

value: Pancreatic islets

value: Sample 3


title: SLY_6

value: Standard


title: M82.Sh.leaf

description: SRX252012 SRX252013 SRX252014

source_name: leaf

value: leaf


title: M82.Sh.root

description: SRX252015 SRX252016

source_name: root

value: root


title: HSC KO rep 1

value: Satb1 -/-

value: Hematopoietic stem cells


title: SLY_4


title: M82.Sh.floral

description: SRX252007 SRX252008 SRX252009


title: SLY_5


title: M82.Sun.veg

description: SRX252005 SRX252006


title: M82.Sh.sdling

description: SRX252017 SRX252018


title: SLY_1


title: SLY_2


title: M82.Sun.leaf

description: SRX251996 SRX251997


title: SRSF1 CLIP siSRSF2

city: La Jolla

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

data_processing:
Density files on two different strands were generated by using bedItemOverlapCount and wigToBigWig programs from UCSC kent source package.
genome build: mm9

source_name: MEF cells

growth_protocol: Previously generated SRSF1 and SRSF2 tet-repressible MEFs were maintained in DMEM plus 10% FBS without tetracycline (Clontech 631106).

extract_protocol:
CLIP-seq was carried out as previously described (Xue et al., 2009; Yeo et al., 2009) using anti-HA antibody (Abcam ab9110).
Library was constructed as previously described (Xue et al., 2009) for Illumina GA2 or Hi-seq 2000.

treatment_protocol: For surveying SR protein binding in the absence of another SR protein, we treated SRSF1-HA MEFs with siRNA against SRSF2 (Dharmacon onTargetplus J-044306-05).

value: MEF

tag: sr protein

value: SRSF1 (SF2/ASF)

tag: sirna

tag: sample description

value: SRSF1 tet-repressible MEFs

tag: antibody

value: anti-HA antibody (Abcam ab9110)


title: M82.Sun.root

description: SRX251998 SRX251999 SRX252000

value: Artificial sun


title: SRSF1 CLIP


title: SLY_7


title: SRSF1 CLIP siControl

value: control


title: penn.Sun.stem

description: SRX252034 SRX252035

organism: Solanum pennellii

value: stem


title: penn.Sun.veg

description: SRX252036 SRX252037


title: penn.Sh.root

description: SRX252044 SRX252045

value: Artificial shade


title: penn.Sh.stem

description: SRX252048 SRX252049


title: SPE_28

value: Seedling


title: SPE_25


title: SPE_23


title: SPE_22


title: SHA_21

organism: Solanum habrochaites


title: SHA_19


title: SRSF2 CLIP

value: SRSF2 (SC35)

value: SRSF2 tet-repressible MEFs


title: SHA_16


title: SHA_15


title: penn.Sun.sdling

description: SRX252032 SRX252033


title: AC MG

city: Wageningen

first: Ruud

last: de Maagd

address: PO Box 619

country: Netherlands

institute: Plant Resarch International

data_processing:
Image analysis, base-calling, and quality check was performed with the Illumina data analysis pipeline RTA v1.12.4.2 and/or OLB v1.9, and CASAVA v1.8.0
5' and 3' adapter sequences were removed and filtered for quality, oligo-A reads up to 15A's, tomato chloroplast DNA and for small non-coding RNAs as present in the Rfam 10.1 database. This was performed using parts of the FASTX Toolkit v.0.0.13 and Vmatch v2.0
Remaining reads were mapped on the sense strand strand of the ITAG release 3 predicted cDNAs (SL2.4) using SHRiMP v2.0 allowing 1 mismatch and retaining only the best scoring hit or hits in the event of of equally scoring his
Mapped reads were matched to potential miRNA target sites in tomato cDNAs, identified using the TargetFinder v1.6 script (Allen et al., 2005; Fahlgren et al., 2007), using an updated version of the CleaveLand pipeline (Addo-Quaye et al., 2009), Cleaveland v3.0.1 (kindly provided by Dr. M. Axtell), according to the instructions of the author. In order to allow for inaccurate target cleavage or variations in miRNA 5’ ends, the pipeline was modified to recognize targets cleaved at the 9th or 11th position of the miRNA, as well as the at the 10th position.
Tag numbers for any position were normalized for library size by using the formula TP10M (tags per 10 million)=(raw abundance/total filtered tags-cDNA matches)*10,000,000.
Genome_build: SL2.40
Supplementary_files_format_and_content: cDNAp9.txt; cDNAp10.txt, cDNAp11.txt are tab-delimited table files reporting miRNA, iTAG2.3 cDNA number, cDNA annotation, target finder penalty, peak category, total read number, peak read number, p-value and q-value for each of the four libraries at miRNA position 9, 10, and 11, respectively.

source_name: whole fruit

growth_protocol: Tomato plants were grown in a greenhouse on rockwool with liquied nutrient solution

extract_protocol:
Total RNA was extracted using an InviTrap Spin Plant RNA mini kit (Stratec, Berlin); PolyA RNA was purified using oligo-dT Dynabeads
cDNA was synthesized according to the PARE protocol described by German et al. (Nature protocols 4(3),2009). Libraries were prepared with a SOLEXA GEX1 adapter on the 5' end and the Illumina 3' TruSeq adapter with barcode was ligated on the 3' end after MmeI digestion. Products were amplified and sequenced on a HiSeq 2000. Samples were pooled with 4 other bar-coded samples, and each pool was sequenced in two lanes.

treatment_protocol: Fruits kept at -80C untill further use, and ground in liquied nitrogen before RNA extraction

tag: variety

value: Ailsa Craig

tag: developmental stage

value: mature green


title: AC 5DAP

value: 5 days after pollination


title: SPI_13

organism: Solanum pimpinellifolium

value: Standard


title: SPE_27


title: SPI_14


title: penn.Sun.leaf

description: SRX252028 SRX252029

value: leaf


title: penn.Sun.root

description: SRX252030 SRX252031

value: root


title: SPI_12


title: penn.Sun.floral

description: SRX252024 SRX252025

value: Inflorescence


title: SPI_11


title: penn.Sh.veg

description: SRX252050 SRX252051 SRX252052

value: vegetative meristem


title: SLY_3


title: AC Br

value: breaker


title: SPE_26


title: penn.Sh.leaf

description: SRX252042 SRX252043


title: penn.Sh.sdling

description: SRX252046 SRX252047


title: SHA_20


title: SPE_24


title: SHA_17


title: SPI_8


title: penn.Sh.floral

description: SRX252038 SRX252039


title: SHA_18


title: ESG1A-04

status: Public on Apr 04 2013

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

data_processing:
Basecalls performed using CASAVA version 1.8.2
All raw sequencing reads were trimmed sequencing primer and WTA primer using by Trimmomatic.
After trimmed sequencing primer and WTA primer, all reads were aligned to the mm9 genome assembly using tophat version 2.0.1
The FPKM (Fragments Per Kilobase of exon per Million mapped fragments) were calculated by Cufflinks 2.0.1 with transcriptome reference (Ensembl Mouse Transcript)
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: ES_Technical replicate for LIMprep

growth_protocol: We used EB5 ES cells for preparation of total RNA. This cell line is derived from E14tg2a ES cells, in which one endogenous Pou5f1 allele is disrupted by a blasticidin resistance gene. We used 5G6GR ES cells for single-cell Quartz-Seq. The cell line is generated by random integration of the linearized Gata6-GR-IRES-Puro vector into EB5 ES cells. These cells were cultured on gelatin-coated dishes in the absence of feeder cells in Glasgow minimal essential medium (GMEM, Sigma) supplemented with 10 % fetal calf serum, 1000 U/ml Leukemia Inhibitory Factor (ESGRO, Invitrogen), 100 uM 2-mercaptoethanol (nacalai tesque), 1x non-essential amino acids (Invitrogen), 1 mM sodium pyruvate (Invitrogen), 2 mM L-glutamine (nacalai tesque), 0.5x Penicillin/Streptomycin (Invitrogen), and 10 ug/ml blasticidin (Invivogen). For the culture of 5G6GR ES cells, 0.5 ug/ml puromycin (Sigma)  was additionally supplemented to the culture.

extract_protocol:
Cultured cells were dissected out using trypsin-EDTA at 37°C for 3 min. Subsequently, resulted cells were washed with PBS buffer. 0.5x10^6 cell was stained with 1 ml of PBS buffer with Hoechst 33342 10 ug/ml at 37°C for 15 min. Stained cells were sorted by reference to information of Hoechst 33342 area. To increase the success rate of amplification, we added several bubbles to single-cell lysis buffer using micropipette. We collected single-cell to 0.4 ul lysis buffer with bubble, which prechilled on 4C IsoFreeze rack. Subsequently, we performed whole-transcript amplification with single-cell lysis sample. For a decrement of RNase contamination risk, working bench environment and all experimental equipments were kept clean using RNase removal reagent RNase Out (Molecular Bio Products). We used low retention single-PCR-tube or 8-linked-PCR-tube for single-cell amplification (TaKaRa). Cells and 10 pg total RNA was dissolved in 0.4 ul single-cell lysis buffer (0.5 % NP40) on 0°C aluminum PCR-rack, which put on ice. These solutions were mixed by bench-top mixer Mixmate (Eppendorf ) at 2500 rpm under 4°C for 15 sec. Immediately, After 3000 G centrifugation for 10 sec under 4°C, 0.8 ul of priming buffer (1.5x PCR-buffer with MgCl2 Takara, 41.67 pM RT primer (HPLC purified, TATAGAATTCGCGGCCGCTCGCGATAATACGACTCACTATAGGGCGTTTTTTTTTTTTTTTTTTTTTTTT),  4 u/ul RNasin-plus (Promega), 50uM dNTPs) was added to each tubes. Solution was mixed at 2500 rpm for 15 sec under 4°C. Denature and priming was performed at 70°C for 90 sec, 35°C for 15 sec using thermal cycler (C1000 and S1000 BioRad) and the reaction-tubes were put on 0°C aluminum PCR-rack . 0.8 ul of RT buffer (1x PCR-buffer, 25 u/ul SuperScript III (Life technologies), 12.5mM DTT) was added to each tubes. Reverse-transcription was performed at 35°C for 5 min, 45°C 20 min and heat-inactivated at 70°C for 10 min. After that, the reaction-tubes were put on 0°C aluminum PCR-rack. We always used latest lots of SuperScript III for single-cell amplification. After 3000 G centrifugation for 10 sec under 4°C, 1 ul of exonuclease solution (1x Exonuclease-buffer(Takara), 1.5 u/ul exonuclease I (Takara)) was added to each tubes. Primer digestion was performed at 37°C for 30 min and heat-inactivated at 80°C for 10 min. The reaction-tubes were put on 0°C aluminum PCR-rack. After 3000 G centrifugation for 30 sec under 4°C, 2.5 ul of poly-A tailing buffer (1x PCR-buffer, 33.6 u/ul Terminal transferase (Roche), 0.048 u RNase H (Invitrogen)) was added to each tubes at 0°C aluminum PCR-rack. The reaction-tubes were mixed at 2500 rpm under 4°C for 15 sec. Immediately, after 3000 G centrifugation for 10 sec under 0°C, the reaction-tubes were put on 0°C  pre-chilled thermal cycler block. Subsequently, poly-A tailing reaction was performed at 37°C for 50 sec and heat-inactivated at 65°C for 10 min. The reaction-tubes were put on 0°C aluminum PCR-rack. After 3000 G centrifugation for 30 sec under 4°C, the reaction-tubes were put on 0°C aluminum PCR-rack.  23 ul of second strand buffer (1.09x MightyAmp Buffer v2, 70 pM tagging primer (HPLC purified, TATAGAATTCGCGGCCGCTCGCGATTTTTTTTTTTTTTTTTTTTTTTT), 0.054 u/ul MighyAmp DNA polymerase). The reaction-tubes were mixed at 2500 rpm under 4°C for 15 sec. After 3000 G centrifugation for 10 sec under 4°C, Second strand synthesis was performed at 98°C for 2 min, 10 sec, 40°C for 1 min and 68°C for 5 min. Immediately, the reaction-tubes were put on 0°C aluminum PCR-rack.  Add 25 ul of PCR buffer (1x MightyAmp Buffer v2, 1.9 uM sPCR primer (HPLC purified, (NH2)-GTATAGAATTCGCGGCCGCTCGCGAT)). The reaction-tubes were mixed at 2500 rpm under 4°C for 15 sec. After 3000 G centrifugation for 10 sec under 4°C, PCR enrichment was performed following condition (98°C for 10 sec, 65°C for 15 sec and 68°C for 5 min per cycle). PCR cycle number is under 21 cycle. After that, the reaction-tubes were incubated at 68°C for 5 min. The reaction-tubes were put on 25°C aluminum PCR-rack. The amplified cDNA was purified using MinElute PCR purification column (Qiagen) or Agencourt Ampure XP (Beckman). To detect in each platform, amplified cDNA was used for each subsequent process. The cost of our amplification method was about ￥500 per single-cell.   For Smart-Seq analysis, we amplified cDNA from ES 10 pg total RNA using SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech). After 19 cycle PCR enrichment with ES 10 pg total RNA, we got about 2 ng amplified cDNA.
For library preparation of conventional RNA-Seq (without WTA), we used TruSeq RNA sample kit (Illumina). Library preparation was performed according to Illumina protocol except PCR enrichment. For PCR enrichment, we used KAPA HiFi DNA polymerase (KAPA BIOSYSTEMS).   For library preparation of Quartz-Seq (with WTA) and Smart-Seq (with WTA), we prepared sequencing library DNA using our optimized library preparation method, named LIMprep (Ligation-based Illumina Multiplex library PREParation). In LIMprep, we used KAPA library preparation kit (KAPA Biosystems), self-produced TruSeq adaptors and PCR primers. For Quartz-Seq, 20 ng of Amplified cDNA was diluted into 130 ul TE buffer. The solutions were transferred into snap cap microTUBEs (Covaris). Amplified cDNA in microTUBEs was fragmented by S220 Focused-ultrasonicators (Covaris). Process configuration was as follow, Duty Factor 10 %, Peak Incident Power 175, Cycles per Burst 100, Time 600 second. Fragmented cDNA was purified into 10 ul of nuclease free water by using DNA Clean & Concentrator 5 (Zymo research). 40 ul of end repair reaction mix (1.25x End Repair Buffer, 1.25 x End Repair Enzyme Mix ) was added to 10 ul of fragmented cDNA solution. End repair reaction was performed at 20°C for 30 min. After that, end-repaired DNA was purified into 12.5 ul of EB1/10 buffer (1 mM TrisHCl pH8.0) using DNA Clean & Concentrator 5. 12.5 ul of A-tailing mix (2x A-tailing Buffer, 2x A-tailing Enzyme) was added to 12.5 ul of end-repaired DNA solution. A-tailing reaction was performed at 30°C for 30 min. After that, A-tailing DNA was purified into 12.5 ul of EB1/10 buffer using DNA Clean & Concentrator 5. 12.5 ul of adaptor ligation mix (2x Ligation Buffer, 2x DNA Ligase, 10 pmol of each self-produced adaptor) was added to 12.5 ul of A-tailed DNA solution under 4°C. Adaptor ligation was performed at 20°C for 15 min. For adaptor ligation, we used 10 pmol of self-produced TruSeq adaptor per sample. Each Self-produced TruSeq adaptor was prepared using following HPLC-purified primers (Hokkaido System Science);
TRSU: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T
TRSI-2: (5'-phosphate)GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTT*G
TRSI-4: (5'-phosphate)GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTT*G
TRSI-5: (5'-phosphate)GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTT*G
TRSI-6: (5'-phosphate)GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTT*G
TRSI-7: (5'-phosphate)GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTT*G
TRSI-12: (5'-phosphate)GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTT*G
Asterisks indicate phosphorothioate bond. Each primers are dissolved with Adaptor Buffer (10 mM Tris-HCl pH 7.8, 0.1 mM EDTA pH8.0, 50 mM NaCl) to 100 uM concentration. We equally mixed 100uM TRSU and 100 uM each TRSI primer on PCR tubes, respectively. After mixing, these primers were incubated at 95°C for 2 min. After that,  primer annealing was performed following condition (95°C for 2 min and temperature drop of -0.5°C per cycle for 170 cycles). After that, the reaction-tubes were incubated at 4°C for 5 min. Resulted adaptors were diluted with adaptor buffer to 10 uM concentration. We dispensed 1 ul of 10 uM each adaptors at -80 °C before use.  Removal of adaptor dimer was performed as follows. 25 ul of binding support buffer (1 M NaCl, 20 mM MgCl2, 20 mM TrisHCl pH7.8) and 60 ul Agencort Ampure XP bead solution were added to 25 ul of adaptor-ligated DNA solution. After 15 min incubation at 25 °C, the beads were separated using magnetic stand for over 10 min. The beads were washed with 80 % EtOH for 1 min twice.  Adaptor-ligated DNA was eluted with 25 ul of EB1/10. The purification for removal of adaptor dimer was repeated again. Finally, adaptor-ligated DNA was eluted to 20 ul of EB1/10. 30 ul of PCR solution (1.666x KAPA HiFi DNA polymerase ready mix, 17.5 pmol TPC1 primer, 17.5 pmol TPC2 primer) was added to 20 ul of adaptor-ligated DNA. Primer sequences were as follows. TPC1 : AATGATACGGCGACCACCGA*G  TPC2 : CAAGCAGAAGACGGCATACGA*G  Asterisks indicate phosphorothioate bond. Each primers are dissolved with Adaptor Buffer (10 mM Tris-HCl pH7.8, 0.1 mM EDTA pH8.0, 50 mM NaCl) to 100 uM concentration. Before PCR enrichment, reaction tubes were incubated at 98°C for 45 sec. PCR enrichment was performed following condition (98°C for 15 sec, 60°C for 30 sec and 72°C for 30 sec per cycle). Typical PCR cycle number is 10-12 cycle. After PCR enrichment, sequencing library DNA was purified using Ampure XP beads. Accurate concentration of sequencing library DNA including TruSeq Index sequence was estimated by KAPA library quantification kit (KAPA). The Pearson correlation coefficient of three technical replications of LIMprep were 0.9976  ±  0.0005.

treatment_protocol: For differentiation of 5G6GR ES cells into PrE cells, cells were seeded in the medium supplemented with 100 mM dexamethasone instead of blasticidin, and cultured for 72 h. After culture for 72 h, 5G6GR cells completely differentiated into PrE cells.

value: Embryonic stem (PE) cell

tag: sample type

value: Technical replicate for LIMprep

tag: starting amount

value: Averaged amplified cDNA from averaged single cell lysis

tag: cell cycle phase

tag: method subtype

value: Quartz-Seq


title: ESG1A-05


title: PrEG1A-04

source_name: PE_Averaged single cell lysis from 12 cells

value: Primitive endoderm (PE) cell

value: 6 pg


title: AC RR

value: 7 days after breaker


title: PrEG1A-01

value: Averaged single cell lysis from 12 cells


title: SPI_10

tag: strain

tag: tissue

value: Seedling


title: ESG1A-02

source_name: ES_Averaged single cell lysis from 12 cells

tag: cell type

value: Embryonic stem (ES) cell


title: SPI_9


title: ESM-04

source_name: ES_single cell

value: single cell

value: 14 pg


title: ESM-07


title: ESG1A-06


title: PrEG1A-06


title: ESM-02


title: ESM-03


title: ESS-07

value: S


title: ESS-03


title: PrEG1A-03


title: PrEG1A-05


title: PrEG1A-02


title: ESG1A-03


title: ESM-05


title: ESM-08


title: ESG1A-01


title: ESG1-05


title: ESG1-04


title: ESG1-07


title: ESS-05


title: ESS-04


title: ESS-06


title: PE-11

source_name: PE_single cell


title: ESS-02


title: PE-10


title: ESM-06


title: ESS-01


title: ESM-01


title: ESG1-06


title: ESG1-08


title: PE-04


title: ESG1-02


title: PE-07


title: Dauer sRNA library

city: BOSTON

first: NELSON

middle: C

last: LAU

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

data_processing: Data tables include the reads and counts after barcode removal and trimming of adaptor sequences.

source_name: N2 wildtype dauer stage

growth_protocol: Adult control and postdauer animals were collected as previously described (Hall, Beverly, et al 2010). Dauer animals were collected 24 hours after SDS treatment, following the postdauer growth strategy. L3 animals were grown according to the control adult strategy, but collected at the L3 stage.

extract_protocol: Total RNA was extracted with Trizol reagent (Sigma) from flash-frozen staged worms, and 25 ug was subjected to 5'-triphosphate removal treatment with Tobacco Acid Phosphatase (TAP; Epicentre). This treatment left a 5’-monophosphate on siRNAs. Small RNAs between 18-32 nt were size selected and subjected to linker ligation reactions and amplification as described previously (Lau et al 2001 Science). Two biological replicates were sequenced for adult libraries, one biological replicate for L3 larvae and dauer libraries. sRNA libraries were sequenced on an Illumina GAII machine, yielding between 4 and 14 million reads per library that matched to the C. elegans genome.

value: N2 wildtype

tag: Stage

value: dauer

tag: barcode

value: CCAA


title: PE50-02

source_name: PE_50 cells

value: 50 cells


title: PE50-01


title: PE-02


title: PE-12


title: ESG1-01


title: PE-06


title: ESG1-03


title: PE-09


title: PE-01


title: PE-08


title: PE-05


title: PE-03


title: ES-07


title: ESSP1-05

source_name: ES_dilution total RNA

value: dilution total RNA

value: 10 pg

value: All phase


title: ES-06

value: Quartz-Seq


title: ESSP1-03


title: ES50-01

source_name: ES_50 cells


title: ES-12


title: ESSP1-04


title: ES-09


title: ES-08


title: ES-10


title: ES-11


title: EB5K-02

source_name: ES_purified total RNA

value: purified total RNA

value: 1 ug

value: TruSeqRNA with KAPA DNA polymerase


title: ES-01


title: ES50-02


title: EB5K-01


title: Smart-Seq_04

source_name: ES_dilution Total RNA

value: dilution Total RNA

value: Smart-Seq


title: ES-05

value: Embryonic stem (ES) cell


title: Smart-Seq_03


title: Smart-Seq_02


title: ES-04

value: single cell


title: Quartz-Seq_03


title: ES-03


title: Quartz-Seq_02


title: ES-02


title: Quartz-Seq_01


title: EB5T-01

value: TruSeqRNA with TruSeq DNA polymerase


title: Smart-Seq_01


title: Quartz-Seq_04


title: M0 stage, repeat 1

first: Jeffrey

last: Parvin

address: 904 Biomedical Research Tower

department: Biomedical Informatics

institute: the Ohio State University

description:
Cells were either arrested by a thymidine-nocodazole block and released for 0 hour,
ChAP-Seq

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg18 genome assembly using ELAND
peaks were called using FindPeaks version 4.0.10  with the following setting: subpeaks 0.5, trim 0.2, dist_type 1 200, minimum 5-12, aligner bed, min_ht_process 5-12
Genome_build: hg18
Supplementary_files_format_and_content: txt file, contain peakcalling results generated by FindPeaks4.0.10

source_name: HeLa cell

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% BS, glutamax, penicillin/streptomycin and sodium pyruvate (Invitrogen). HeLa cells expressing the HBT tagged Ubiquitin (HeLa-Ub) (23)were grown in DMEM containing biotin (0.5 µM, Sigma Aldrich) and puromycin (1.5 ug/ml, Invitrogen).

extract_protocol:
Chromatin affinity purification (ChAP) samples for sequencing by Illumina GA II were prepared as follows. Chromatin affinity purification was based on a standard ChIP method (27) with modification of a two-step affinity purification. HeLa-Ub cells were cross-linked with 1% formaldehyde (Sigma) and the reaction stopped by adding 1/20 volume of 2.5 M glycine. The cross-linked material was then washed with PBS, lysed as for the ChIP protocol and sonicated to an average DNA fragment size of 200 bp. All buffers were freshly supplemented with 10 mM N-Ethylmaleimide (Sigma), 1 mM PMSF (Sigma), 1X Protease inhibitor cocktail (Sigma). The sheared chromatin was incubated with 375 µl Ni-NTA beads (Qiagen) for 16h at 4°C.An aliquot of the input DNA was saved prior to immunoprecipitation as reference sample. After washing in 6 ml of wash buffer I (50 mM Tris pH 8; 0.01% SDS; 1.1% Triton X-100; 150 mM NaCl), chromatin fragments were eluted in 3 cycles of 2 ml elution buffer I (50 mM Tris pH 8; 0.01% SDS; 1.1% Triton X-100; 150 mM NaCl; 300 mM Imidazole). The nickel eluate was incubated with 375 µl of avidin beads (Thermo Scientific) for 6h at 4°C. After washing in 1 ml of wash buffer II (50 mM Tris pH 8; 1% SDS; 1.1% Triton X-100; 1M NaCl) followed by two washes in low salt buffer (50 mM Tris pH 8; 1% SDS; 1.1% Triton X-100; 0.5 M NaCl), then two washes with 1 ml TE buffer (100 mM Tris pH 8; 10 mM EDTA; 50 mM NaCl). Crosslinks were reversed by adding 2 ml of elution buffer (50 mM Tris pH 8; 10 mM EDTA; 1% SDS; 200 mM NaCl) to the beads and incubating at 65°C for 15h. The supernatant was collected and diluted 1:2 with TE buffer. The eluate was treated with RNase (0.2 mg/ml final concentration; Sigma) for 2h at 37°C, followed by adding Proteinase K (0.2 µg/ml final concentration; Sigma) for 2h at 55°C, and DNA was extracted in phenol/chloroform/isomyl alcohol, and the DNA was precipitated in 200 mM NaCl (final concentration), 30 µg of glycogen (Ambion), 2x of the volume of ice cold 100% ethanol and incubation at -20°C for 1h followed by centrifugation. The pellet was washed in 500 µl of 70% ethanol, then the DNA was finally recovered, and its concentration was quantified by Picogreen assay (Invitrogen).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).
modified version of ChIP-seq using affinity tag (called ChAP-seq), so there is no antibody involved, we used His6-Biotin labeled ubiquitin for all ChAP-seq samples

treatment_protocol: Cells were either arrested by a thymidine-nocodazole block and released for 0 (mitosis), 4 or 7 (G1) hours or with a double thymidine block and released for 0, 2, 4, 6, 8, 10 or 12h.   For transcription inhibition, HeLa-Ub cells were treated with flavopiridol (1µM) or α-amanitin (50µg/ml) for 3 and 5 hours respectively before crosslinking for ChAP.

tag: cell line

value: HeLa cell

tag: cell stage

value: M0 stage

tag: molecule type

value: genomic DNA after ChAP pull-down


title: M0 stage, repeat 3


title: S0 stage, treated with Amanitin repeat 1

description:
Cells were arrested by double thymidine block and released for 0 hours, amanitin treated
ChAP-Seq

value: S0 stage, treated with Amanitin


title: S4 stage, repeat 1

description:
Cells were arrested by double thymidine block and released for 4 hours.
ChAP-Seq

value: S4 stage


title: Postdauer adult#2 sRNA library

source_name: N2 wildtype postdauer adults

value: N2 wildtype

value: postdauer adults

value: CCAA


title: S2 stage, repeat 2

description:
Cells were arrested by double thymidine block and released for 2 hours.
ChAP-Seq

value: S2 stage


title: Larval L3 sRNA library

source_name: N2 wildtype Larval L3 stage

value: larval L3

value: AAAA


title: S2 stage, repeat 3


title: M0 stage, repeat 2


title: G1 stage, repeat 1

description:
Cells were arrested by a thymidine-nocodazole block and released for 4 or 7 (G1) hours or with a double thymidine block and released for 12h
ChAP-Seq

value: G1 stage


title: G1 stage, repeat 3


title: S0 stage, repeat 3

description:
Cells were arrested by double thymidine block and released for 0 hours.
ChAP-Seq

value: S0 stage


title: G1 stage, repeat 2


title: S2 stage, repeat 1


title: S0 stage, repeat 1


title: S0 stage, repeat 2


title: S0 stage, treated with Amanitin repeat 2


title: S4 stage, repeat 3


title: CHIP-seq:Ti

status: Public on Apr 03 2013

city: Lausanne

first: Adamandia

last: Kapopoulou

address: Station 15

department: Sciences de la Vie

country: Switzerland

institute: EPFL

description:
Sorted cells from bone marrow of 8- to 12-wk-old Kap-flox/stopfloxYFP
The Ti correspond to sonicated chromatin that is directly de-crosslinked without any IP.
Processed data file:
Chipseq_KAP1_BMsortedTer119CD71_no_repeats_peaks.bed

data_processing:
Raw reads were mapped to the mouse genome and human transcriptome using Bowtie
Peaks were called using MACS
RPKM values were calculated using R/Bioconductor
Genome_build: mm9 (mouse)
Supplementary_files_format_and_content: .bed file contains the peaks called (linked as supplementary file on Series record)

source_name: CD71+Ter119+ cells facs sorted cells

growth_protocol: no growth protocol for CD71+Ter119+ cells. HEL are cultured in RPMI 10%

extract_protocol:
Cells were crosslinked by 1% formaldehyde and sonicated, and chromatin was immunoprecipitated by using an affinity-purified rabbit polyclonal antibody raised against KAP1 aa 20-418, RBCC (F. R. Santoni de Sio et al.,. Blood 119, 4675 (2012)). Detailed protocols for ChIP are described in D. C. Schultz,. Genes Dev 15, 428 (2001).
Reverse cross-linking was performed overnight in the presence of proteinase K and RNase, followed by DNA extraction using the MinElute PCR purification kit (Quiagen) according to manufacturer protocol.
10 ng were used to prepare libraries for sequencing, following the ChIP Seq library preparation protocol (including End Repair for blunted end fragments, addition of "A" base to the 3' end and ligation of adapters to DNA fragments (kit IP-102-1001). Ligation products were then purified on 2% E Gels Size Select (Invitrogen, fragments of 200 bp recovered), followed by enrichment of DNA fragments by PCR (18 cycles).

treatment_protocol: HEL were activated  in presence of hemin at a final concentration of 50 micromolar during five days

value: bone marrow

value: CD71+Ter119+ cells (facs sorted)

tag: age

value: 8- to 12-wk-old

tag: genotype/variation

value: KAP1 WT

value: mix strain

tag: chip antibody

value: none (total input control)


title: S4 stage, repeat 2

city: Columbus

value: HeLa cell

value: genomic DNA after ChAP pull-down


title: CHIP-seq:IgG control

description:
Sorted cells from bone marrow of 8- to 12-wk-old Kap-flox/stopfloxYFP
Processed data file:
Chipseq_KAP1_BMsortedTer119CD71_no_repeats_peaks.bed

value: IgG (control IP)


title: ChIP-seq:KAP1

value: KAP1 [affinity-purified rabbit polyclonal antibody raised against KAP1 aa 20–418, RBCC (F. R. Santoni de Sio et al.,. Blood 119, 4675 (2012))]


title: RNA-seq:KAP1 WT  activated

description:
Cells were activated  (or not) in presence of hemin at a final concentration of 50 micromolar during five days. RNA was extracted using TZrizol according to Manufacturer protocol.
Processed data file: HELKAP1KDvsCtrl_RNAseq.txt

data_processing:
Raw reads were mapped to the mouse genome and human transcriptome using Bowtie
Peaks were called using MACS
RPKM values were calculated using R/Bioconductor
Genome_build: hg19 (human)
Supplementary_files_format_and_content: .txt file include RPKM values for each Sample (linked as supplementary file on Series record)

source_name: HEL cells

extract_protocol:
RNA was extracted using TZrizol according to Manufacturer protocol.
The library was generated from 250 ng total RNA using the TruSeq RNA Sample Preparation Kit v2

value: human erythroleukemia cell line, HEL

tag: activation

value: hemin


title: RNA-seq:KAP1 KD  activated

value: KAP1 KD


title: RNA-seq:KAP1 KD not activated

value: not activated


title: H3K79me2_MOLM-13

city: Boston

first: Amit

last: Sinha

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: ChIP-Seq Multiplexing using Illumina adapters

data_processing:
Sequence reads were aligned to human genome assembly hg19 using BWA with default parameters.
Wiggle files were generated using a using a custom pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: wig

source_name: leukemia cell line

growth_protocol: All cell lines were grown in RPMI 10%FBS supplemented with 2mM L-glutamine and penicillin/streptomycin and used directly for fixing/crosslinking for ChIP-seq

extract_protocol:
DNA was sheared from the fixed leukemia cell lines using sonication. Histone-DNA complexes enriched for H3K79me2 were isolated by immunoprecipitation with the Abcam anti-H3K79me2 specific antibody (Ab 3594)
ChIP DNA libraries were made following the Illumina ChIP-seq library preparation kit.

treatment_protocol: Frozen leukemia bone marrow cells were thawed using standard conditions and  1 million cells were used for fixing and subsequent ChIP seq steps.

tag: disease state

value: MLL-AF9 positive human AML

tag: cell  line

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody cataolog #


title: RNA-seq:KAP1 WT not activated


title: ERRα mouse liver ChIP-seq

city: Montréal

first: Vincent

last: Giguère

state: Québec

address: 1160 Pine Avenue West, room 710A

department: Biochemistry, Medicine and Oncology

country: Canada

institute: McGill University

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using BWA v0.5.9
Peaks were called using MACS version 1.4.1 with the following setting: mfold=10,30, bandwith=300, p-value cutoff=1E-5.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: BED files

source_name: liver

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies.
Libraries were prepared according to Illumina's instructions using the TruSeq DNA sample preparation kit. The ChIP-seq DNA libraries were sequenced as single 50bp reads using an Illumina Hiseq 2000 sequencer.

tag: age/gender

value: 2-3 month old males

value: Epitomics ERRα (2131-1)


title: FRDA19.UTB

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina CASAVA 1.8.2 software was used for basecalling. The reads were demultiplexed, allowing no mismatches in the index sequence.
Sequence reads were aligned to hg19 version of human genome with Tophat 1.4.1 software with parameters -p 8 and transcript annotation file supplied.
Gene based counts were obtained using HTSeq count module (version 0.5.3p9) using parameters -m intersection-nonempty  --stranded=no
Differential expression analysis was then performed using DESeq Bioconductor package with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Count files were obtained using HTSeq count module (version 0.5.3p9) using parameters -m intersection-nonempty  --stranded=no

source_name: primary cultured lymphocytes

growth_protocol: Primary lymphocytes from FRDA patients were isolated from the blood samples using Ficoll-Hypaque TM gradient (Sigma) by following the manufacturer’s protocol. Human blood samples were obtained from patients in accordance with UK Human Tissue Authority ethical guidelines. Cells were grown in RPMI 1640 (PAA) medium with 2 mM L-glutamine and 10% fetal calf serum (PAA) and supplemented with 1x penicillin/streptomycin solution (GIBCO) at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. TruSeq DNA Sample Prep Kits v2 - Illumina (Cat#FC-121-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary lymphocytes at cell density of 1x10^7cells/ml were treated with 10mM nicotinamide for 3 days. Culture medium with or without (untreated as control) nicotinamide was changed every 24 hours incubation.

value: PBMC

tag: treatment

value: Un-treated control


title: H3K79me2_HL60

value: MLL wildtype human AML


title: Control adult#2 sRNA library

source_name: N2 wildtype control adults

tag: strain

value: N2 wildtype

value: control adults

value: AAAA


title: H3K79me2_MLL-AF6 rep1

data_processing:
Sequence reads were aligned to human genome assembly mm9 using BWA with default parameters.
Wiggle files were generated using a using a custom pipeline.
Genome_build: mm9
Supplementary_files_format_and_content: wig

source_name: Leukemic bone marrow cells, primary

growth_protocol: Cells were not grown prior to the ChIP-seq

extract_protocol:
DNA was sheared from the fixed MLL-AF6 leukemia cells using sonication. Histone-DNA complexes enriched for H3K79me2 were isolated by immunoprecipitation with the Abcam anti-H3K79me2 specific antibody (Ab 3594)
ChIP DNA libraries were made following the Illumina ChIP-seq library preparation kit.

tag: background strain

value: B6/129 (Taconic)

tag: cell type

value: Leukemic bone marrow cells, primary

value: MLL-AF6 positive leukemia


title: Rabbit IgG mouse liver ChIP-seq

value: Santa Cruz Tech. rIgG (sc-2027)


title: FRDA19.NB

tag: tissue

value: 10mM nicotinamide


title: mTOR mouse liver ChIP-seq

value: Abcam mTOR ChIP grade (ab32028)


title: H3K79me2_MLL-AF6 rep3


title: H3K79me2_ML2

value: MLL-AF6 positive human AML


title: H3K79me2_MLL-AF6 rep2


title: Empty_ChIP-seq

city: Heidelberg

first: Lukas

last: Chavez

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

data_processing:
Basecalls performed using 'HiSeq Control Software' version 1.5.15.1
Sequencing reads were mapped against hg19 using bowti (bowtie-0.12.7 -n 2 -l 28 -m 3 -k 1 --best --chunkmbs 512 -p 8 -S -q)
Peaks were called using MACS (1.4.1) using default parameter settings for human (hs)
Enrichment profiles along selected annotations were calculated using custom scripts inside of the R/Bioconductor environment.
Genome_build: hg19
Supplementary_files_format_and_content: wiggle files were generated as follows: i) reads are extended to the length of estimated average fragment length. ii) coverage is calculated in the single nucleotide-level and its normalised by the number of million mapped reads (RPM)

growth_protocol: Stable HEK293T cells were generated by transfecting empty vector, wild-type Myc-Idax or DNA-binding mutant of Myc-Idax (Myc-IdaxDBM).

extract_protocol:
Nuclei were isolated and chromatin was sheared using Covaris S2 instrument and protein-DNA complexes were isolated by antibody.
ChIP-seq library was constructed using TruSeq Sample Prep kit (Illumina) and Illumina HiSeq sequencing was performed as per manufacturer's instructions.

tag: cell line

tag: transfection

value: empty vector

tag: antibody

value: Anti-c-Myc; Sigma, Cat#:A7470-1ML (Agarose Affinity Gel)