title: methylC-Seq in WT, day 3 differentiation, biological rep 2

first: Gary

middle: Chung

last: Hon

state: TX

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern

data_processing:
methylC-Seq: Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome_build: mm9
Supplementary_files_format_and_content: methylC-Seq: chromosome[tab]CpG location[tab]#mCG,depth,%mCG

source_name: ES cells

extract_protocol:
Genomic DNA extraction
Purified genomic DNA was fragmented to an average size of 300bp with a Biorupter 300 (high power, 15s on, 15s off, 40 cycles). Spike in unmethylated lambda DNA control was added prior to sonication at 0.5% of total genomic DNA. DNA was end-repaired, adenylated, and ligated to methylated (5mC) adapters (Illumina) according to standard Illumina protocols for genomic DNA library construction, maintaining the proper molar ratios of adapter to insert. Adapter ligated fragments of size 200-650bp were gel purified by 2% agarose gel electrophoresis and sodium-bisulfite treated using the MethylCode kit (Invitrogen). Bisulfite treated adapter-ligated DNA was amplified by PCR with the following conditions in a 50uL final reaction volume:  2.5U PfuTurbo Cx Hotstart DNA polymerase, 5uL 10X PfuTurbo Cx reaction buffer, 0.75uL 20mM dNTPs, 5uL Illumina PCR Primers. Cycling parameters: 95ºC 5min, 98ºC 30 sec, followed by 8-11 cycles of 98ºC 15 sec, 60ºC 30 sec, 72ºC 4 min, and ending with 72ºC 10 min. The number of PCR cycles used was determined by quantification of bisulfite treated adapter-ligated DNA by qPCR (KAPABiosystems library quant kit for Illumina libraries) such that the final library concentration obtained was approximately 20nM. Final sequencing libraries were purified by 2% agarose gel electrophoresis and quantified by qPCR (KAPABiosystems library quant kit for Illumina libraries).

tag: mutant

value: wild-type, differentiation day 3


title: methylC-Seq in tet2-/-, day 3 differentiation, biological rep 2

status: Public on Sep 25 2014

type: SRA

city: Dallas

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

value: tet2-/-, differentiation day 3


title: methylC-Seq in tet2-/-, day 3 differentiation, biological rep 1


title: Monocytes_Day6_RPMI_CD3depleted_Buffy11_80U

status: Public on Sep 26 2014

city: Nijmegen

first: Hindrik

last: Kerstens

address: Geert Grooteplein Zuid 26

department: Molecular Biology

country: Netherlands

institute: Radboud University

description:
DNAseI-seq
raw file: C3JYVACXX_7_5396.sorted.bam
BAM file for this sample used to derive:
RPMIall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed

data_processing:
Cluster generation and sequencing were performed using the Illumina HiSeq2000 genome analyzer. The image files were processed to extract DNA sequence data using CASAVA-1.8.2. The 42 bp sequence tags were mapped to the reference human genome hg19 (NCBI build37), using the BWA allowing one mismatch. Only uniquely mapped-reads were used for data analysis and visualization. The output data were converted to bam files for downstream analysis. Details about aligner version and parameters used are stored in the headers of the BAM files. PCR duplicates were removed, therefore the final BAM files only contain uniquely mapped reads. Wig files were generated by counting the number of sequence reads (directionally extended to a final 300 bp) per 10-bp genomic window and can be used for viewing the data in the UCSC Genome Browser.
DNAseI bam files were merged per source-treatment (Monocytes RPMI, Macrophages RPMI, Macrophages LPS, Macrophage BG), and DNaseI hotspots were called on the merged bam using the published “Hotspots” pipeline (Neph et al 2012).
Peak calling was performed using MACS2-2.0.10.09132012 using Blueprint C000S5H2 Input Monocytes as a reference input.
For archiving RNA-seq 42-bp reads were aligned to hg19 using GSNAP release 2012-07-20 using parameters -N 1 -n 1  -m 1 -Q.
Gene expression quantification was performed by first aligning RNA-Seq tags to the Ensembl GRCh37 version 68 transcriptome using bowtie with parameters "-a --best --strata -S -m 100 --chunkmbs 256". Name sorted bamfiles were converted using bam2hits and gene expression was quantitated using mmseq (doi: 10.1186/gb-2011-12-2-r13). Results are given in log (base e) RPKM.
Genome_build: hg19
Supplementary_files_format_and_content: Bed.gz files are the peak regions called by MACS2, wig.gz files visualizes the mapped data in the UCSC genome browser. RNA-Seq results are reported as log (base e) RPKM.

organism: Homo sapiens

extract_protocol: Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using HiSeq 2000 as recommended by the manufacturer. DNaseI treatment was done on isolated nuclei for 3 minutes and reaction was stopped with stop buffer ( 50mM Tris-HCl, pH 8, 100mM NaCl, 0.10% SDS, 100mM EDTA, pH 8.0, 1mM Spermidine, 0.3mM Spermine), sample was further fractionated on 9% Sucrose gradient for  24hrs/25000rpm at 16ºC . Further sequenced using HiSeq as recommended by the manufacturer.

treatment_protocol: Monocytes were pre-incubated either with cell culture medium (RPMI), β-glucan (5µg/mL) or with LPS (100ng/mL), for 24 hours in a total volume of 10 mL. After a wash-out, cells were cultured in RPMI supplemented with 10% human pool serum. Monocytes were collected at different time points (0 h and 6 d after treatment) and counted before further treatment for chromatin immunoprecipitation or DNaseI treatment.

tag: cell type


title: H1993_PPARG_ChIP

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Image scanning and basecalls were performed using BioScope (v. 1.2.1)
ChIP-seq reads were aligned to hg19 geneome assembly using BioScope (v. 1.2.1)
Mapped reads were filtered to remove low quality, ambiguous and redundant reads
Peaks were called using the MACS (v. 1.4.2)
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files contains SOX2 peak coordinates in BED format

source_name: NCI-H1993 cell line

growth_protocol: We generated PPARG-LAP BAC transgenic NCI-H2347 and NCI-H1993 cell lines using the BAC-transgenesis approach, cells were cultured in RPMI-1640 with 5% FBS.

extract_protocol:
Cells at 80% confluency (~1-1.5x107) were cross-linked with 1% formaldehyde for 10 minutes at 37°C, and quenched with 125 mM glycine at room temperature for 5 minutes. The fixed cells were washed twice with cold PBS, scraped, and transferred into 1 ml PBS containing protease inhibitors (Roche). After centrifugation at 700 g for 4 minutes at 4°C, the cell pellets were resuspended in 100 μl ChIP lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl [pH 8.1] with protease inhibitors) and sonicated at 4°C with a Bioruptor (Diagenode) (30 seconds ON and 30 seconds OFF at highest power for 12 minutes). The sheared chromatin with a fragment length of ~200 – 600 bp) was centrifuged at 10,000 g for 10 minutes at 4°C). 100 μl of the supernatant was used for ChIP or as input. A 1:10 dilution of the solubilized chromatin in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl 16.7 mM Tris-HCl [pH 8.1]) was incubated at 4°C overnight with 6 μg/ml of a goat anti-GFP (raised against His-tagged full-length eGFP and affinity-purified with GST-tagged full-length eGFP). Immunoprecipitations were carried out by incubating with 40 μl pre-cleared Protein G Sepharose beads (Amersham Bioscience) for 1 hour at 4°C, followed by five washes for 10 minutes with 1ml of the following buffers: Buffer I: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 150 mM NaCl; Buffer II: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 500 mM NaCl; Buffer III: 0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl [pH 8.1]; twice with TE buffer [pH 8.0]. Elution from the beads was performed twice with 100 μl ChIP elution buffer (1% SDS, 0.1 M NaHCO3) at room temperature (RT) for 15 minutes. Protein-DNA complexes were de-crosslinked by heating at 65°C in 192 mM NaCl for 16 hours. DNA fragments were purified using QiaQuick PCR Purification kit (Qiagen) and eluted into 30 μl H2O according to the manufacturer’s protocol after treatment with RNase A and Proteinase K.
Libraries were prepared according to SOLiD 5500 instructions accompanying the ChIP-seq kit with barcoding beta protocol. AMPure® XP beads were used in this protocol. Briefly, DNA was end-repaired using a combination of 5X reaction buffer, dNTP mix (10mM), end polishing enzyme 1 and 2, and nuclease free water included in the kit. Binding and washing of end-paired DNA was performed using AMPure® XP beads and 70% ethanol respectively. Then, the end-paired DNA was eluted with elution buffer included in the kit. Then,  the 5500 barcoded adaptors were liagted to the DNA and purified using 70% ethanol. Purified adaptor ligated DNA was PCR amplified for 10-15cycles. Amplified DNA was purified and ~1μL of purified amplified product was run on a 2% E-Gel® EX Gel to confirm the removal of any primer dimers.This product was quantified using qPCR. Following qPCR quantitation, the SOLiD™ ChIP-Seq fragment library was subjected to templated bead preparation.

treatment_protocol: Not applicable

tag: tag

value: EGFP

tag: chip antibody

value: Polyclonal (goat) against full length His-EGFP

tag: cell line


title: H1993_INPUT


title: H3K4me1 ChIP-Seq in tet2-/-, differentiation day 3, biological rep 2

data_processing:
ChIP-Seq: We mapped ChIP-Seq reads using the Bowtie program, keeping only those reads that mapped uniquely to mm9 with at most 3 mismatches. Specifically, the parameters used were: "--solexa1.3-quals -v 3 -m 1 --best --strata -S ". PCR duplicates for each library were removed with the Picard program(Picard 2011).
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq:bigwig density

extract_protocol:
To isolate chromatin, formaldehyde-cross-linked nuclei were sonicated using a Branson 450 Sonifier (Branson, Danbury, CT).
Following ChIP performed with Dynal beads (Invitrogen, Carlsbad, CA), ChIP DNA was subjected to end repair, A-tailing, adaptor ligation, and gel purification. Following PCR amplification, the final library underwent gel purification.


title: H3K27ac ChIP-Seq in tet2-/-, differentiation day 3, biological rep 1

value: H3K27ac (Active, Motif, lot 39133)


title: H3K27ac ChIP-Seq in tet2-/-, differentiation day 3, biological rep 2


title: H3K4me1 ChIP-Seq in WT, differentiation day 3, biological rep 1


title: H3K4me1 ChIP-Seq in tet2-/-, differentiation day 3, biological rep 1


title: H3K27ac ChIP-Seq in WT, differentiation day 3, biological rep 2


title: input ChIP-Seq in tet2-/-, differentiation day 3, biological rep 1

value: none (input)


title: methylC-Seq in WT, day 3 differentiation, biological rep 1


title: input ChIP-Seq in WT, differentiation day 3, biological rep 2


title: H3K4me1 ChIP-Seq in WT, differentiation day 3, biological rep 2


title: Blueprint_S00BYTH1_H3K4me1

description:
chromatin IP
raw file: C2N9FACXX_2_4716.sorted.bam

growth_protocol: Monocytes were pre-incubated either with cell culture medium (RPMI), β-glucan (5µg/mL) or with LPS (100ng/mL), for 24 hours in a total volume of 10 mL. After a wash-out, cells were cultured in RPMI supplemented with 10% human pool serum.


title: H2347_PPARG_ChIP

source_name: NCI-H2347 cell line


title: miR-155_1

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

country: United Kingdom

institute: The Babraham Institute

library_source: transcriptomic

data_processing:
Raw sequence reads were trimmed to remove both barcodes and adapters using Trim Galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (v0.3.3, default parameters).
Remaining sequences were mapped to the mouse NCBIM37 genome using Tophat (Bioinformatics. 2009 May 1;25(9):1105-11. and http://ccb.jhu.edu/software/tophat/index.shtml).
Quantitation was performed with the SeqMonk RNA-Seq quantitation pipeline to generate RPKM values (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab delimited text file containing RPKM values

molecule: polyA RNA

source_name: Splenic B cells, miR-155 KO

growth_protocol: After isolation, cells were purified using the negative selection B-cell isolation kit (Miltenyi Biotec). Cells were cultured in RPMI-1640 containing 10% FCS, 2mM L-Glutamine, 2-mercaptoethanol and 1% penicillin/streptomycin.

extract_protocol:
RNA extraction using TriZol (life Technologies)
Illumina TruSeq mRNA sample prep kit (Barcodes used for sample multiplexing: TGACCA, ACAGTG, GCCAAT, CAGATC, ACAGTG, GCCAAT, CAGATC, CTTGTA, CGATGT, TGACCA, ACAGTG, GCCAAT, CAGATC, CTTGTA)

treatment_protocol: Cultured B cells were stimulated for 4 days with LPS (5 ug/ml) and IL-4 (10 ng.ml).

tag: genotype

tag: cell isolation

value: Splenic B cells

tag: condition

value: Ex-vivo


title: miR-155_2


title: miR-155_3


title: miR-155_4


title: PU.1_5

source_name: Splenic B cells, PU.1_KI


title: PU.1_3


title: PU.1_4


title: PU.1_1

source_name: Splenic B cells, PU.1 KI


title: PU.1_2


title: WT_2

source_name: Splenic B cells, Wild type

value: Wild type


title: WT_1


title: input ChIP-Seq in tet2-/-, differentiation day 3, biological rep 2


title: miR-155-inducible Torin-treated 3T3 12 h RPF

first: Stephen

last: Eichhorn

state: MA

address: 9 Cambridge Center

department: Biology

institute: Whitehead Institute for Biomedical Research

description:
miR-155_translational_state_analysis.txt
miR-155_torin_3T3_12h.txt
cytoplasmically-enriched RNA

data_processing:
Raw read files were stripped of adaptor and mapped to the appropriate species' genome and transcriptome (for smallRNA-seq, reads were mapped to mature mouse miRNA sequences).
RNA-seq and ribosome profiling reads mapping within the coding sequence of an annotated gene, excluding the first 50 nucleotides of the coding sequence, were assigned to that gene and used to calculate its RPKM value. SmallRNA-seq reads were mapped to annotated mature miRNAs.
Genome_build: Human: hg19; Mouse: mm9
Supplementary_files_format_and_content: One set of processed data files contains abundance measurements for each gene. Another set contains the fold change (log2) for a given miRNA experiment.

molecule: total RNA

source_name: 3T3 cell line

growth_protocol: Each sample was grown or maintained according to standard protocols

extract_protocol:
RNA-seq and RPF libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809) except for B cell and U2OS samples, which were constructed as described in Guo et al., 2010 (GSE22004). SmallRNA-seq libraries were constructed as described in Chiang et al., 2010 (GSE20384).
RNA-seq or SmallRNA-seq

treatment_protocol: RNA-seq: For most samples, cytoplasmically-enriched RNA was extracted, poly(A)-selected, randomly fragmented by partial alkaline hydrolysis and then size-selected RNA fragments were used for library preparation In the case of B cells total RNA was extracted and then poly(A)-selected. In the case of U2OS cells, three different isolation methods were performed, two of them are the aforementioned isolation methods, the third total RNA was depleted of tRNA and rRNA. Ribosome profiling: In most cases, cell extracts were processed as described in Subtelny et al., 2014 (GSE52809). For U2OS and B cell samples, cell extracts were processed as described in Guo et al., 2010 (GSE22004). SmallRNA-seq: Total RNA was extracted as described in Chiang et al., 2010 (GSE20384)

tag: time

value: 3T3 cell line

tag: growth condition

value: contact inhibited

tag: treatment

value: doxycycline, Torin1


title: miR-155-inducible Torin-treated 3T3 0 h RPF

description:
miR-155_translational_state_analysis.txt
miR-155_torin_3T3_0h.txt
cytoplasmically-enriched RNA

value: 0 h


title: miR-155_5


title: miR-155-inducible Torin-treated 3T3 12 h RNA


title: miR-1-inducible Torin-treated 3T3 0 h RPF

description:
miR-1_translational_state_analysis.txt
miR-1_torin_3T3_0h.txt
cytoplasmically-enriched RNA


title: miR-155-inducible actively dividing 3T3 12 h RPF

description:
miR-155_translational_state_analysis.txt
miR-155_actively_dividing_3T3_12h.txt
cytoplasmically-enriched RNA

value: actively dividing

value: doxycycline


title: miR-155-inducible actively dividing 3T3 12 h RNA


title: miR-155-inducible actively dividing 3T3 0 h RNA

description:
miR-155_translational_state_analysis.txt
miR-155_actively_dividing_3T3_0h.txt
cytoplasmically-enriched RNA


title: miR-1-inducible Torin-treated 3T3 12 h RNA

description:
miR-1_translational_state_analysis.txt
miR-1_torin_3T3_12h.txt
cytoplasmically-enriched RNA


title: miR-155-inducible actively dividing 3T3 0 h RPF


title: miR-1-inducible Torin-treated 3T3 0 h RNA


title: input ChIP-Seq in WT, differentiation day 3, biological rep 1


title: miR-1-inducible actively dividing 3T3 12 h RPF

description:
miR-1_translational_state_analysis.txt
miR-1_actively_dividing_3T3_12h.txt
cytoplasmically-enriched RNA


title: miR-124-inducible contact-inhibited 3T3 12 h RPF

description:
miR-124_contact_inhibited_3T3_changes.txt
miR-124_contact_inhibited_3T3_12h.txt
cytoplasmically-enriched RNA


title: miR-1-inducible actively dividing 3T3 12 h RNA


title: miR-124-inducible contact-inhibited 3T3 10 h RPF

description:
miR-124_contact_inhibited_3T3_changes.txt
miR-124_contact_inhibited_3T3_10h.txt
cytoplasmically-enriched RNA


title: miR-1-inducible actively dividing 3T3 0 h RPF

description:
miR-1_translational_state_analysis.txt
miR-1_actively_dividing_3T3_0h.txt
cytoplasmically-enriched RNA


title: WT_4


title: miR-1-inducible actively dividing 3T3 0 h RNA


title: WT_3


title: miR-124-inducible contact-inhibited 3T3 4 h RPF

description:
miR-124_contact_inhibited_3T3_changes.txt
miR-124_contact_inhibited_3T3_4h.txt
cytoplasmically-enriched RNA

value: 4 h


title: miR-124-inducible contact-inhibited 3T3 6 h RPF

description:
miR-124_contact_inhibited_3T3_changes.txt
miR-124_contact_inhibited_3T3_6h.txt
cytoplasmically-enriched RNA

value: 6 h


title: miR-124-inducible contact-inhibited 3T3 0 h RPF

description:
miR-124_contact_inhibited_3T3_changes.txt
miR-124_contact_inhibited_3T3_0h.txt
cytoplasmically-enriched RNA


title: miR-124-inducible contact-inhibited 3T3 10 h RNA


title: miR-124-inducible contact-inhibited 3T3 12 h RNA


title: miR-155-inducible Torin-treated 3T3 0 h RNA


title: miR-124-inducible contact-inhibited 3T3 8 h RNA

description:
miR-124_contact_inhibited_3T3_changes.txt
miR-124_contact_inhibited_3T3_8h.txt
cytoplasmically-enriched RNA

value: 8 h


title: miR-1-inducible Torin-treated 3T3 12 h RPF


title: miR-124-inducible contact-inhibited 3T3 6 h RNA


title: miR-124-inducible contact-inhibited 3T3 4 h RNA


title: miR-155-inducible contact-inhibited 3T3 8 h RPF

description:
miR-155_contact_inhibited_3T3_changes.txt
miR-155_contact_inhibited_3T3_8h.txt
cytoplasmically-enriched RNA


title: miR-155-inducible contact-inhibited 3T3 12 h RPF

description:
miR-155_contact_inhibited_3T3_changes.txt
miR-155_contact_inhibited_3T3_12h.txt
cytoplasmically-enriched RNA


title: miR-124-inducible contact-inhibited 3T3 0 h RNA


title: miR-155-inducible contact-inhibited 3T3 0 h RPF

description:
miR-155_contact_inhibited_3T3_changes.txt
miR-155_contact_inhibited_3T3_0h.txt
cytoplasmically-enriched RNA


title: miR-155-inducible contact-inhibited 3T3 4 h RPF

description:
miR-155_contact_inhibited_3T3_changes.txt
miR-155_contact_inhibited_3T3_4h.txt
cytoplasmically-enriched RNA


title: miR-155-inducible contact-inhibited 3T3 8 h RNA


title: miR-155-inducible contact-inhibited 3T3 12 h RNA


title: miR-155-inducible contact-inhibited 3T3 4 h RNA


title: miR-124-inducible contact-inhibited 3T3 8 h RPF


title: miR-155-inducible contact-inhibited 3T3 0 h RNA


title: miR-1-inducible contact-inhibited 3T3 4 h RPF

description:
miR-1_contact_inhibited_3T3_changes.txt
miR-1_contact_inhibited_3T3_4h.txt
cytoplasmically-enriched RNA


title: miR-1-inducible contact-inhibited 3T3 48 h RPF

description:
miR-1_contact_inhibited_3T3_changes.txt
miR-1_contact_inhibited_3T3_48h.txt
cytoplasmically-enriched RNA


title: miR-1-inducible contact-inhibited 3T3 12 h RNA

description:
miR-1_contact_inhibited_3T3_changes.txt
miR-1_contact_inhibited_3T3_12h.txt
cytoplasmically-enriched RNA


title: miR-1-inducible contact-inhibited 3T3 0 h RPF

description:
miR-1_contact_inhibited_3T3_changes.txt
miR-1_contact_inhibited_3T3_0h.txt
cytoplasmically-enriched RNA


title: miR-122 knockout mouse liver RPF

description:
miR-122_liver_changes.txt
miR-122_ko_liver.txt
cytoplasmically-enriched RNA

source_name: primary liver tissue

tag: tissue

value: primary liver tissue

tag: strain

tag: age

value: 6 weeks

tag: Sex

value: male


title: miR-1-inducible contact-inhibited 3T3 8 h RPF

description:
miR-1_contact_inhibited_3T3_changes.txt
miR-1_contact_inhibited_3T3_8h.txt
cytoplasmically-enriched RNA


title: miR-1-inducible contact-inhibited 3T3 4 h RNA


title: miR-1-inducible contact-inhibited 3T3 12 h RPF


title: Input.Taf4.wt.ChIP.Seq

city: Illkirch

first: Irwin

last: Davidson

address: 1 rue Laurent Fries

department: Functional Genomics

country: France

institute: IGBMC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie v0.12.7 with the following parameters -m 1 --strata --best.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)

extract_protocol:
Mouse livers were homogenized by douncing and fixed with 1% PFA for 10 minutes and fixing was stopped by adding glycine. Chromatin was fragment by sonication or Mnase I digestion and immunoprecipitation was performed using specific antobodies.
ChIP-seq libraries were prepared using ChIP-Seq Sample Prep Kit (#IP-102-1001, Illumina) following the manufacturer's protocol with some modifications. Briefly, 10 ng of ChIP enriched DNA or control DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 14 cycles; 5 min at 72°C) and then purified using Agencourt AMPure XP beads (#A63881, Beckman). DNA library size selection was performed by excising the 250-350 bp fragments from a 2% agarose gel followed by purification using a QIAquick Gel Extraction Kit (#28906, Qiagen).

value: liver

value: post natal day 54

value: wild type


title: Hnf4.e18.5.liver.wt.ChIP.Seq

value: embryonic day 18.5

value: HNF4A (Santa Cruz sc-8987 X)


title: miR-1-inducible contact-inhibited 3T3 0 h RNA

value: 3T3 cell line


title: wild-type mouse liver RPF

description:
miR-122_liver_changes.txt
miR-122_wt_liver.txt
cytoplasmically-enriched RNA


title: wild-type mouse liver RNA


title: Ctcf.Taf4hep-.ChIP.Seq

value: post natal day 12

value: CTCF ((Millipore 07-729)


title: miR-122 knockout mouse liver RNA


title: miR-1-inducible contact-inhibited 3T3 8 h RNA

value: contact inhibited


title: H3K27ac ChIP-Seq in WT, differentiation day 3, biological rep 1

value: wild-type, differentiation day 3

value: H3K27ac (Active, Motif, lot 39133)


title: Ctcf.Taf4.wt.ChIP.Seq


title: Hnf4a.Taf4.wt.ChIP.Seq


title: H3k4m3.Taf4hep-.ChIP.Seq

value: H3K4me3 ((Millipore 04-745)


title: Hnf4a.Taf4hep-.ChIP.Seq


title: Taf3.Taf4hep-.ChIP.Seq

value: TAF3 (IGBMC)


title: H3k4m3.Taf4.wt.ChIP.Seq

value: H3K4me3 (Millipore 04-745)


title: miR-1-inducible contact-inhibited 3T3 48 h RNA

value: doxycycline


title: Taf3.Taf4.wt.ChIP.Seq


title: Tf2e.Taf4hep-.ChIP.Seq

value: TFIIE (Santa Cruz sc-6935X)


title: Tf2b.Taf4.wt.ChIP.Seq

value: TFIIB (Santa Cruz sc-225 X)


title: Rnap2.Taf4hep-.ChIP.Seq

value: liver

value: Pol II (Santa Cruz sc-9001X)


title: Tbp.Taf4hep-.ChIP.Seq

value: TBP (Abcam ab28175)


title: Rnap2.Taf4.wt.ChIP.Seq

value: wild type


title: Tf2e.Taf4.wt.ChIP.Seq


title: Tbp.Taf4.wt.ChIP.Seq


title: RNA-seq.liver.Taf4hep-/-

data_processing:
Both libraries (WT and KO) were sequenced twice. Illumina Casava v1.7 (1st sequencing) and v1.8 (2nd sequencing) software were used for basecalling.
Sequence reads mapped to reference genome mm9/NCBI37 using Tophat (Trapnell et al., 2009) v1.0.12 (1st sequencing) and v1.4.1 (2nd sequencing).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using the Wiggles program supplied by Tophat.

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
Total RNA-seq libraries were prepared following the Illumina protocol with some modifications. Briefly, 2 µg of total RNA was hybridized with rRNA sequence-specific 5’biotin labeled oligonucleotide probes to selectively deplete ribosomal RNA. The rRNA/5’biotin labeled probe was removed from the sample with streptavidin-coated magnetic beads. (Ribominus Eukaryote kit for RNA-seq, #A10837-08, Invitrogen Corporation). The rRNA depleted RNAs were then fragmented using divalent cations at 95°C for 5 minutes and used to generate a reverse transcribed cDNA library. 100 ng of each DNA library was then denatured at 98°C for 2 minutes, incubated at 68°C for 5 hours and then incubated in the presence Duplex-Specific thermostable Nuclease enzyme (DSN, #EA001, Evrogen) for DSN normalization following the Illumina protocol. DSN treated libraries were purified using Agencourt AMPure XP beads, enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 6 cycles; 5 min at 72°C) and purified again using Agencourt AMPure XP beads.


title: RNA-seq.liver.wt


title: Murine activated T cells (Replicate 2)

city: Basel

first: Andreas

middle: R

last: Gruber

address: Klingelbergstrasse 50-70

department: Biozentrum

country: Switzerland

institute: University of Basel

description: 3' end sequencing of murine activated Tcells

data_processing:
For the murine A-seq libraries, reads were pre-processed to remove the six diagnostic adenosines derived from the poly(A) tail as well as the 3' adaptor sequence and then were mapped to the mouse genome (mm9) and annotated using the CLIPZ server. For the human A-seq libraries, only reads that contained three T residues at positions 5-7 (indicating the beginning of the poly(A) tail) were selected for further use. From these, randomized nucleotides at positions 1-4 at the 5’ end of the reads (needed for cluster coordination in Illumina sequencing) were trimmed together with the three Ts, thus removing seven nucleotides. The reverse complement of the remaining sequences, presumably representing mRNA 3’ ends, were then mapped to the human genome (hg19). For the construction of the set of 3' end cleavage sites, we only used reads that had the adaptor removed, mapped uniquely to genomic regions. Based on the precise mapping of the 3' ends of these reads we computed putative cleavage sites with their associated abundance. To minimize the frequency of internal priming sites in our data set, we discarded those that in the eight-nucleotide-region immediately downstream of the putative cleavage site had at least seven A nucleotides. The raw reads were processed on the CLIPZ server (http://http://www.clipz.unibas.ch; Khorshid et al., Nucleic Acids Research 2011, 39:D245).
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: gzipped BED files with inferred 3' ends of Pol II transcripts; column 5 represents the number of reads

source_name: T cells

extract_protocol:
Selection for poly(A)+ RNA (for details see A-seq protocol)
A-seq protocol (see Martin G, Gruber AR, Keller W, Zavolan M (2012) Genome-wide analysis of pre-mRNA 3’ end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length. Cell Rep 1: 753–763.)

treatment_protocol: For mouse T cells, spleen and lymph nodes were dissected from 8-10 week old female C57BL/6 mice and total, untouched T cells were isolated by MACS purification (Pan T cell isolation kit; Miltenyi) according to the manufacturer's protocol. T cells were activated for 72 hrs with mouse T-Activator CD3/CD28 Dynabeads (Gibco/Life Technologies) and 30 Units of recombinant IL-2 (Peprotech). Corresponding naive cells were from the same T cell preparations. Human T cells from single donor human blood samples were isolated with the Pan T cell isolation kit from Miltenyi and either left untreated or were stimulated with human T-Activator CD3/CD28 Dynabeads (Life Technologies) and 30 Units of recombinant IL-2 from Peprotech.

value: T cells


title: Murine naive T cells (Replicate 2)

description: 3' end sequencing of murine naïve Tcells


title: RNA-Seq in tet1-/-T, biological rep 2, differentiation day 6

data_processing:
mRNA-Seq reads were mapped with the TopHat program with the following non-default parameters: -g 1 --library-type=fr-firststrand . We then counted the number of RNA-Seq reads in each gene, represented by the union of all exons with the same (common gene name, chromosome, strand) tuple. Counts were stratified by whether they were in exons or introns, and whether they were on the same or opposite strand relative to the gene. RPKM was calculated from these counts, with a pseudocount of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: common name[tab]chromosome[tab]strand[tab]gene left end[tab]gene right end[tab]#sense exonic[tab]#antisense exonic[tab]#sense intronic[tab]#antisense intronic[tab]RPKM sense exonic[tab]RPKM antisense exonic[tab]RPKM sense intronic[tab]RPKM antisense intronic

extract_protocol:
Total RNA from 2 million cells was extracted with TRIZOL (Invitrogen, Carlsbad, CA) using manufacturer's instructions
Total RNA was subjected to mRNA purification with Dynabeads Oligo (dT)25 (Invitrogen, Carlsbad, CA). First strand synthesis was performed with SuperScript® III First-Strand Synthesis System (Invitrogen, Carlsbad, CA), followed by purification with Sephadex G50 beads (medium) (GE Healthcare, UK) and second strand synthesis with dUNTPs. cDNA was sonicated with a Bioruptor (Diagenode, Woburn, MA) followed by end repair, addition of a 3' base, and ligation of adaptors. Fragments were purified on a 2% agarose gel and the second strand was degraded with AmpErase UNG (Applied Biosystems, Foster City, CA). Samples were amplified with between 7 and 10 cycles of PCR, followed by gel purification.

value: embryonic stem cells

tag: differentiation

value: differentiation day 6


title: Murine naive T cells (Replicate 1)


title: Murine activated T cells (Replicate 1)


title: RNA-Seq in tet1-/-, biological rep 1, differentiation day 3

value: differentiation day 3


title: RNA-Seq in WT, biological rep 1, differentiation day 6

value: wild-type


title: RNA-Seq in WT, biological rep 2, differentiation day 6


title: RNA-Seq in tet1-/-, biological rep 1, differentiation day 6


title: RNA-Seq in WT, biological rep 2, differentiation day 3


title: Tf2b.Taf4hep-.ChIP.Seq

value: post natal day 12


title: RNA-Seq in tet2-/-, biological rep 1, differentiation day 3


title: RNA-Seq in tet2-/-, biological rep 1, differentiation day 6


title: RNA-Seq in tet2-/-, biological rep 2, differentiation day 3


title: RNA-Seq in tet2-/-T, biological rep 2, differentiation day 6


title: methylC-Seq in tet2-/-, biological rep 2, technical rep 1

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome_build: mm9
Supplementary_files_format_and_content: chromosome[tab]CpG location[tab]#mCG,depth,%mCG


title: methylC-Seq in tet2-/-, biological rep 1, technical rep 1


title: methylC-Seq in tet1-/-, biological rep 2, technical rep1


title: methylC-Seq in WT, biological rep 2, technical rep 1


title: methylC-Seq in tet1-/-, biological rep 1, technical rep 2


title: TAB-Seq in tet2-/-, biological rep 2, technical rep 1

data_processing:
Reads were trimmed for adapter sequences and mapped with bowtie to the computationally bisulfite-converted mm9 genome as in Lister et al, Nature, 2009. After PCR duplicate removal with Picard, basecalls of cytosines in CpG context were tabulated as methylated or unmethylated (Phred score >= 20). The processed tables indicate the number of methylated cytosines, total sequencing depth, and %mCG for each CpG dinucleotide, combined over both Watson and Crick strands.
Genome_build: mm9
Supplementary_files_format_and_content: chromosome[tab]CpG location[tab]#hmCG,depth,%hmCG

extract_protocol:
Genomic DNA extraction
Purified genomic DNA was fragmented to an average size of 300bp with a Biorupter 300 (high power, 15s on, 15s off, 40 cycles). Spike in DNA control was added prior to sonication at 0.5% of total genomic DNA. DNA was end-repaired, adenylated, and ligated to methylated (5mC) adapters (Illumina) according to standard Illumina protocols for genomic DNA library construction, maintaining the proper molar ratios of adapter to insert. Adapter ligated fragments of size 200-650bp were gel purified by 2% agarose gel electrophoresis and sodium-bisulfite treated using the MethylCode kit (Invitrogen). Bisulfite treated adapter-ligated DNA was amplified by PCR with the following conditions in a 50uL final reaction volume:  2.5U PfuTurbo Cx Hotstart DNA polymerase, 5uL 10X PfuTurbo Cx reaction buffer, 0.75uL 20mM dNTPs, 5uL Illumina PCR Primers. Cycling parameters: 95ºC 5min, 98ºC 30 sec, followed by 8-11 cycles of 98ºC 15 sec, 60ºC 30 sec, 72ºC 4 min, and ending with 72ºC 10 min. The number of PCR cycles used was determined by quantification of bisulfite treated adapter-ligated DNA by qPCR (KAPABiosystems library quant kit for Illumina libraries) such that the final library concentration obtained was approximately 20nM. Final sequencing libraries were purified by 2% agarose gel electrophoresis and quantified by qPCR (KAPABiosystems library quant kit for Illumina libraries).


title: TAB-Seq in tet2-/-, biological rep 1, technical rep 1


title: methylC-Seq in WT, biological rep 1, technical rep 1


title: methylC-Seq in WT, biological rep 1, technical rep 2


title: TAB-Seq in tet2-/-, biological rep 1, technical rep 2


title: TAB-Seq in tet1-/-, biological rep 2, technical rep1


title: RNA-Seq in tet1-/-, biological rep 2, differentiation day 3


title: TAB-Seq in tet1-/-, biological rep 1, technical rep 1


title: TAB-Seq in WT, biological rep 1, technical rep 1


title: RNA-Seq in tet2-/-, biological rep 1, technical rep 1


title: TAB-Seq in WT, biological rep 2, technical rep 1


title: RNA-Seq in tet2-/-, biological rep 2, technical rep 1


title: TAB-Seq in WT, biological rep 1, technical rep 2


title: RNA-Seq in WT, biological rep 1, differentiation day 3


title: RNA-Seq in WT, biological rep 2, technical rep 1


title: RNA-Seq in tet1-/-, biological rep 1, technical rep 1


title: RNA-Seq in WT, biological rep 1, technical rep 1


title: methylC-Seq in tet1-/-, biological rep 1, technical rep 1


title: H3K36me3 ChIP-Seq in tet2-/-, biological rep 2

data_processing:
We mapped ChIP-Seq reads using the Bowtie program, keeping only those reads that mapped uniquely to mm9 with at most 3 mismatches. Specifically, the parameters used were: "--solexa1.3-quals -v 3 -m 1 --best --strata -S ". PCR duplicates for each library were removed with the Picard program(Picard 2011).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig density


title: input ChIP-Seq in tet2-/-, biological rep 2

value: none (input)


title: H3K4me1 ChIP-Seq in tet2-/-, biological rep 2


title: miR-155-transfected U2OS tRNA and rRNA depleted RNA

description:
miR-155_U2OS_changes.txt
miR-155_U2OS_dep_RNA.txt
cytoplasmically-enriched RNA

source_name: U2OS cell line

value: U2OS cell line

value: miR-155 transfection


title: miR-155-transfected U2OS RPF

description:
miR-155_U2OS_changes.txt
miR-155_U2OS_paRNA.txt
miR-155_U2OS_cytoRNA.txt
miR-155_U2OS_dep_RNA.txt
cytoplasmically-enriched RNA


title: H3K27me3 ChIP-Seq in tet2-/-, biological rep 2

value: H3K27me3 (Active, Motif, lot AM)


title: H3K27ac ChIP-Seq in tet2-/-, biological rep 2

value: H3K27ac (Active, Motif, lot AM)


title: miR-155-transfected U2OS poly(A)-selected cytoplasmic RNA

description:
miR-155_U2OS_changes.txt
miR-155_U2OS_cytoRNA.txt
cytoplasmically-enriched RNA


title: H3K36me3 ChIP-Seq in tet2-/-, biological rep 1


title: H3K9me3 ChIP-Seq in tet2-/-, biological rep 2


title: miR-155-transfected U2OS poly(A)-selected total RNA

description:
miR-155_U2OS_changes.txt
miR-155_U2OS_paRNA.txt
cytoplasmically-enriched RNA


title: input ChIP-Seq in tet2-/-, biological rep 1


title: H3K4me3 ChIP-Seq in tet2-/-, biological rep 2

value: H3K4me3 (Active, Motif, lot 39159)


title: H3K27ac ChIP-Seq in tet2-/-, biological rep 1

value: H3K27ac (Active, Motif, lot 39133)


title: H3K27me3 ChIP-Seq in tet2-/-, biological rep 1

value: H3K27me3 (Active, Motif, lot 39155)


title: H3K4me3 ChIP-Seq in tet2-/-, biological rep 1


title: TAB-Seq in tet1-/-, biological rep 1, technical rep 2


title: mock-transfected U2OS tRNA and rRNA depleted RNA

description:
miR-1_U2OS_changes.txt
Mock_U2OS_dep_RNA.txt
miR-155_U2OS_changes.txt
cytoplasmically-enriched RNA

value: mock transfection


title: RNA-Seq in tet1-/-, biological rep 2, technical rep1


title: mock-transfected U2OS RPF

description:
miR-1_U2OS_changes.txt
Mock_U2OS_paRNA.txt
Mock_U2OS_cytoRNA.txt
Mock_U2OS_dep_RNA.txt
miR-155_U2OS_changes.txt
cytoplasmically-enriched RNA


title: mock-transfected U2OS poly(A)-selected cytoplasmic RNA

description:
miR-1_U2OS_changes.txt
Mock_U2OS_cytoRNA.txt
miR-155_U2OS_changes.txt
cytoplasmically-enriched RNA


title: miR-1-transfected U2OS poly(A)-selected total RNA

description:
miR-1_U2OS_changes.txt
miR-1_U2OS_paRNA.txt
cytoplasmically-enriched RNA

value: miR-1 transfection


title: input ChIP-Seq in tet1-/-, biological rep 2


title: H3K4me1 ChIP-Seq in tet2-/-, biological rep 1


title: H3K27me3 ChIP-Seq in tet1-/-, biological rep 2

value: H3K27Me3 (Active, Motif, lot 39155)


title: mock-transfected U2OS poly(A)-selected total RNA

description:
miR-1_U2OS_changes.txt
Mock_U2OS_paRNA.txt
miR-155_U2OS_changes.txt
cytoplasmically-enriched RNA


title: H3K9me3 ChIP-Seq in tet1-/-, biological rep 2


title: H3K27ac ChIP-Seq in tet1-/-, biological rep 2

value: H3K27Ac (Active, Motif, lot 39133)


title: H3K4me3 ChIP-Seq in tet1-/-, biological rep 2

value: embryonic stem cells


title: miR-1-transfected U2OS poly(A)-selected cytoplasmic RNA

description:
miR-1_U2OS_changes.txt
miR-1_U2OS_cytoRNA.txt
cytoplasmically-enriched RNA


title: H3K4me1 ChIP-Seq in tet1-/-, biological rep 2


title: Virilizer siRNA

city: Kawasaki

first: Horiuchi

last: Keiko

state: Kanagawa

address: 1-396 Kosugi-cho, Nakahara-ku,

department: Protein-Protein Interaction

country: Japan

institute: Institute for Advanced Medical Sciences, Nippon Medical School

description: Sample 3

data_processing:
Illumina CASAVA_v1.7.0 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using ELAND software (Illumina).
Reads per kilobase of open reading frame per million reads (RPKM) were calculated using the random sampling model in the DEGseq v1.10.0 program.
For splice junction detection, MapSpclice 1.15.2 software was used with parameters k=25, h=8 and ek=1.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

source_name: HUVEC_Virilizer siRNA

extract_protocol:
2 ug Trizol-extracted total RNA from cotrol, WTAP or Virilizer siRNA-treated HUVECs was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human umbilical vein endothelial cells

tag: genotype/variation

value: Virilizer knockdown


title: Control siRNA

description: Sample 1

source_name: HUVEC_Control siRNA

value: wild type


title: Neutrophil smallRNA

description: total RNA

source_name: primary Neutrophil

value: primary Neutrophil

value: 3 months

value: male


title: H3K36me3 ChIP-Seq in tet1-/-, biological rep 1


title: WTAP siRNA

description: Sample 2

source_name: HUVEC_WTAP siRNA

value: WTAP knockdown


title: miR-155 knockout B cell 8h RPF

description:
miR-155_Bcell_changes.txt
miR-155_ko_Bcell_8h.txt
cytoplasmically-enriched RNA

source_name: primary B cell

value: primary B cell

value: LPS, IL-4, and anti-CD-40 antibody


title: Macrophage smallRNA

description: total RNA

source_name: primary Macrophage

value: primary Macrophage


title: input ChIP-Seq in tet1-/-, biological rep 1

source_name: ES cells

value: none (input)


title: H3K27me3 ChIP-Seq in tet1-/-, biological rep 1

value: H3K27me3 (Active, Motif, lot AM)


title: lovHK_2

city: Chicago

first: Sean

last: Crosson

state: IL

address: 929 E 57th St. GCIS-W125

department: Biochemistry and Molecular Biology

institute: University of Chicago

data_processing:
CASAVA-1.8.2 basecalling
The obtained RNA-seq reads were aligned to the genome sequence of B. abortus 2308 (RefSeq AM040265) using the short-read aligner Bowtie 2.
mRNA abundance were determined by Cufflinks in FPKM (Fragments Per Kilobase of transcript per Million mapped reads)
Differential gene expression was measured by Cuffdiff. Geometric library normalization and pooled dispersion estimation methods were employed with a 0.05 false discovery rate and a minimum alignment count of 10.
Genome_build: RefSeq AM040265
Supplementary_files_format_and_content: Tab-delimited text files include FPKM

organism: Brucella melitensis

source_name: Bacterial cells

growth_protocol: Brucella cells were grown in 50 ml of brucella broth until OD600 ~0.15 at 37°C, 5mM H2O2 was added and incubated for 10 min.

extract_protocol:
Total RNAs were extracted with a modified hot phenol-SDS extraction method (Chuang et al., 1993) and the RNeasy kit (Qiagen).
rRNAs were depleted using (Gram-negative bacteria) Ribo-Zero Magnetic Kit (Epicentre). Libraries were prepared with Illumina TruSeq RNA kit according to manufacturer’s instructions and were then quantified using a 2100 Bioanalyzer (Agilent) and sequenced on a HiSeq2500 (Illumina).

treatment_protocol: For oxidative stress, 5 mM of hydrogen peroxide was added.

tag: growth

value: Exponentially growing lovHK mutant

value: lovHK mutant

tag: biovar

value: Abortus 2308

tag: cdna type

value: total fragmented mRNA


title: miR-155 knockout B cell 48h RPF

description:
miR-155_Bcell_changes.txt
miR-155_ko_Bcell_48h.txt
cytoplasmically-enriched RNA

tag: cell type


title: lovHK_1


title: H3K27ac ChIP-Seq in tet1-/-, biological rep 1

tag: chip antibody

value: H3K27ac (Active, Motif, lot 39133)

value: embryonic stem cells


title: H3K9me3 ChIP-Seq in tet1-/-, biological rep 1

tag: genotype


title: rpoE1_1

value: Exponentially growing rpoE1 mutant

value: rpoE1 mutant


title: rpoE1_2


title: H3K4me3 ChIP-Seq in tet1-/-, biological rep 1

value: H3K4me3 (Active, Motif, lot 39159)


title: miR-155 knockout B cell 2h RPF

description:
miR-155_Bcell_changes.txt
miR-155_ko_Bcell_2h.txt
cytoplasmically-enriched RNA

value: 3 months


title: miR-155 knockout B cell 48h RNA

description:
miR-155_Bcell_changes.txt
miR-155_ko_Bcell_48h.txt
total RNA

value: male


title: miR-155 knockout B cell 8h RNA

description:
miR-155_Bcell_changes.txt
miR-155_ko_Bcell_8h.txt
total RNA


title: H3K36me3 ChIP-Seq in tet1-/-, biological rep 2


title: H3K4me1 ChIP-Seq in tet1-/-, biological rep 1


title: WT_2

value: Exponentially growing wild type

value: wild type


title: H3K36me3 ChIP-Seq in WT, biological rep 2

value: wild-type


title: miR-155 knockout B cell 4h RNA

description:
miR-155_Bcell_changes.txt
miR-155_ko_Bcell_4h.txt
total RNA

value: primary B cell

value: LPS, IL-4, and anti-CD-40 antibody


title: miR-155 knockout B cell 4h RPF

description:
miR-155_Bcell_changes.txt
miR-155_ko_Bcell_4h.txt
cytoplasmically-enriched RNA


title: input ChIP-Seq in WT, biological rep 2

value: none (input)


title: WT_1


title: H3K27ac ChIP-Seq in WT, biological rep 2

value: H3K27Ac (Active, Motif, lot 39133)


title: wild-type B cell 2 h RPF

description:
miR-155_Bcell_changes.txt
miR-155_wt_Bcell_2h.txt
cytoplasmically-enriched RNA

value: 2 h


title: Bcell smallRNA

description: total RNA


title: wild-type B cell 48 h RPF

description:
miR-155_Bcell_changes.txt
miR-155_wt_Bcell_48h.txt
cytoplasmically-enriched RNA


title: wild-type B cell 4 h RPF

description:
miR-155_Bcell_changes.txt
miR-155_wt_Bcell_4h.txt
cytoplasmically-enriched RNA

value: 4 h


title: H3K27me3 ChIP-Seq in WT, biological rep 2

value: H3K27Me3 (Active, Motif, lot 39155)


title: H3K4me3 ChIP-Seq in WT, biological rep 2

value: H3K4Me3 (Active, Motif, lot 39159)


title: wild-type B cell 48 h RNA

description:
miR-155_Bcell_changes.txt
miR-155_wt_Bcell_48h.txt
total RNA


title: miR-155 knockout B cell 2h RNA

description:
miR-155_Bcell_changes.txt
miR-155_ko_Bcell_2h.txt
total RNA


title: wild-type B cell 8 h RNA

description:
miR-155_Bcell_changes.txt
miR-155_wt_Bcell_8h.txt
total RNA

value: 8 h


title: wild-type B cell 8 h RPF

description:
miR-155_Bcell_changes.txt
miR-155_wt_Bcell_8h.txt
cytoplasmically-enriched RNA


title: H3K9me3 ChIP-Seq in WT, biological rep 2

value: embryonic stem cells


title: wild-type B cell 4 h RNA

description:
miR-155_Bcell_changes.txt
miR-155_wt_Bcell_4h.txt
total RNA


title: input ChIP-Seq in WT, biological rep 1


title: H3K27me3 ChIP-Seq in WT, biological rep 1

value: H3K27me3 (Active, Motif, lot 39155)


title: wild-type B cell 2 h RNA

description:
miR-155_Bcell_changes.txt
miR-155_wt_Bcell_2h.txt
total RNA


title: H3K4me1 ChIP-Seq in WT, biological rep 2


title: H3K27ac ChIP-Seq in WT, biological rep 1

value: H3K27ac (Active, Motif, lot 39133)


title: ES cells, d6, rep3

city: Lausanne

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

institute: Swiss Institute of Bioinformatics

description:
TODO
Ebs5

data_processing:
Base calling was with Illumina GAP Pipeline Software v1.90
Sequences were aligned to mm9 reference genome using Tophat 2.0.8 with option -g with mm9 reference GTF
Novel transcripts were predicted with Cufflinks 2.1.1
Novel transcripts predictions were merged with mm9 reference genome using Cuffmerge 2.1.1 with option -G with mm9 reference GTF
Counts were generated using htseq-count v0.5.4p3
Genome_build: mm9
Supplementary_files_format_and_content: Raw count data for genes were normalized to the relative size of each library using R/Bioconductor package DESeq, estimateSizeFactors function. Count data are provided in tab-delimited format

source_name: ES cells, d6

growth_protocol: Nkx2.5-EmGFP BAC reporter ES cell line (129/OlaHsd strain, subline E14Tg2A.4) were were cultured on mouse embryonic fibroblasts feeders or on gelatinized plates in standard ES cell medium supplemented with 1000U/ml of LIF

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen). RNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 Bioanalyzer.
Sequencing libraries were prepared according to Illumina long RNA Seq library kit instructions with Poly(A) selection. Libraries were sequenced with the Illumina HiSeq2000 (2x100bp).

treatment_protocol: Cardiac differentiation of ES cells was induced by aggregating aliquots containing 1000 cells in hanging drops to form embryoid bodies. Differntiating cells were harvest 6 days following induction of differentiation.

tag: stage of differentiation

value: at day 6 after induction of differentiation


title: ES cells, d6, rep2

description:
TODO
Ebs4


title: H3K9me3 ChIP-Seq in WT, biological rep 1


title: ES cells, d6, rep1

description:
TODO
Ebs2


title: ES cells, d0, rep3

description:
TODO
4LL2

source_name: ES cells, d0

value: undifferntiated state


title: H3K4me3 ChIP-Seq in WT, biological rep 1

value: H3K4me3 (Active, Motif, lot 39159)


title: ES cells, d0, rep2

description:
TODO
3LL2


title: H3K4me1 ChIP-Seq in WT, biological rep 1


title: ES cells, d0, rep1

description:
TODO
1LL2


title: GM12878 2x262 bp

first: Hyunghoon

last: Cho

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

description: The cell line was obtained from The Coriell Institute (Camden, NJ) (Cat# XC01463)

data_processing:
Reads were aligned to hg19 using GSNAP (version 2012-07-20) with default settings, using splice junction annotations from GENCODE 15. For L262, we identified and merged read pairs coming from fragments shorter than the read length by searching for adapter sequences. Only uniquely aligned reads were used for further analysis.
To assign each read to a genomic feature (gene or mRNA isoform), we constructed a feature set based on GENCODE 15 for each locus in the reference genome representing the features that contain the corresponding nucleotide. Then, for each aligned read, we took the intersection of all nonempty feature sets associated with the bases covered by the read. If the resulting set of features (which we refer to as "consistent" features) only has a single element, it implies that the read pair is unambiguously mapped to a feature. For mRNA isoforms, we only considered the set of isoforms whose splicing patterns agree with the read.
The VCF file containing positions genotyped for NA12878 was obtained from the 1000 Genomes Project (http://www.1000genomes.org). Phased genotypes were inferred by family relationships using Ped-IBD, while discarding sites with Mendelian inconsistencies. For each aligned read, we examined all heterozygous sites that appear in the read and assigned the read to either paternal or maternal haplotype only if all heterozygous sites have the corresponding alleles.
Given the reads we classified as either paternal or maternal, we flipped the bases at heterozygous sites so that the maternal alleles are substituted with paternal alleles and vice versa. We then remapped the modified reads and calculated, for each gene, the proportion of reads that mapped to the same location as before, which we refer to as "mapping retention rate". When we tested the significance of allele effects, we disregarded genes with mapping retention rate lower than 0.9 for each library to avoid artifacts due to mapping errors.
To detect allele-specific alternative splicing, the exonic regions of each gene were divided into "exon blocks" such that each block does not contain any of the exon boundaries of known mRNA isoforms. Then we counted the number of reads that overlap with each exon block (included as processed data) and performed a chi-square test on a 2-by-2 contingency table where the rows indicate whether a read is maternal or paternal and the columns indicate whether a read overlaps with the exon block of interest (only considering reads assigned to the corresponding gene).
For some of our analyses, L75 was randomly subsampled to match either the number of sequenced bases (L75B) or the number of reads (L75R) with L262.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with a header line describing the content of each column. "gene_read_counts.txt" contains the number of reads unambiguously assigned to each gene. "consistent_isoform_counts_L75.txt" and "consistent_isoform_counts_L262.txt" contain the number of consistent mRNA isoforms for each aligned read. "allele_specific_expression.txt" contains the number of maternal or paternal reads unambiguously assigned to each gene for L262 and ten datasets of each subsampling scheme (L75B and L75R). "allele_specific_alternative_splicng.txt" contains the number of maternal or paternal reads overlapping with each exon block for each dataset. "mapping_retention_rate.txt" contains the per-gene mapping retention rate calculated for each dataset.

source_name: B lymphocyte cell line

growth_protocol: The cells were grown in RPMI 1640 supplemented with 10% FCS and penicillin/streptomycin in humidified 5% CO2 at a concentration of approximately 1x106 cells/ml.

extract_protocol:
Total RNA was isolated from 1 x107 GM12878 cells using Trizol.
RNA quality was assessed with the Agilent Bioanalyzer 2100 and RIN scores above 9 were used for cDNA production.  One microgram poly A purified mRNA was used for cDNA library construction using the Illumina TruSeq RNA Preparation Kit.

value: Blood

tag: transformant

value: Epstein-Barr Virus

tag: cell line


title: miR-1-transfected HEK293T RPF

description:
miR-1_HEK293T_changes.txt
miR-1_HEK293T.txt
cytoplasmically-enriched RNA

source_name: HEK293T cell line

value: HEK293T cell line

value: miR-1 transfection


title: PAR-CLIP WDR33

description: PAR-CLIP of WDR33 in HEK293 cells

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

growth_protocol: 0.1 mM 4-thiouridine was added to 2x 10^8 HEK293 cells for 16 hrs in DMEM before UV crosslink and harvest

extract_protocol:
Immunoprecipitation with anti WDR33 antibody, Bethyl A301-152A
PAR-CLIP with modifications [PMID: 22813749]

treatment_protocol: UV croslinking with 365 nm light, 150 mJ/cm2 in Stratalinker 2400

tag: rip antibody

value: WDR33 antibody

tag: rip antibody vendor

value: Bethyl

tag: rip antibody cat. #


title: H3K36me3 ChIP-Seq in WT, biological rep 1

value: wild-type


title: European_males_1

city: Planegg

first: John

last: Parsch

state: BY

address: Grosshaderner Str. 2

department: Biology II

country: Germany

institute: University of Munich (LMU)

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina sequence reads were mapped to the reference D. melanogaster transcriptome (FlyBase release 5.54) using NextGenMap (version 0.4.11) with default parameters
Expression was quantified on a “per gene” basis. For this, if a sequence read mapped to one or more transcripts of the same gene, it was counted as one “hit” for that gene. For calculations of RPKM, the length of the longest transcript of each gene was used
Genome_build: dmel_r5.54
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Drosophila melanogaster

source_name: Malpighian tubule

growth_protocol: All flies were maintained on standard cornmeal-molasses medium at 22° with a 14 h light:10 h dark cycle

extract_protocol:
Total RNA extraction was performed using the MasterPure RNA Purification Kit (Epicentre)
Poly-A mRNA was purified and fragmented by sonication. First strand single end cDNA was synthesized using random primers. Eight tagged libraries were generated, pooled and run on one lane of a HiSeq 2000 sequencer (Illumina) to generate single reads of 50 bases

treatment_protocol: Adult flies aged 2–4 days were anesthetized on ice and tubules were dissected in 1xPBS (phosphate buffered saline) and stored in RNAlater (Qiagen) to prevent RNA degradation

value: male

tag: population

value: Europe (The Netherlands)

value: 2-4 days


title: SpnIIID variant strain replicate 2

city: Leicester

first: Marco Rinaldo

last: Oggioni

address: University Road

department: Genetics

institute: University of Leicester

data_processing:
Fastq file QC performed by ERNE
RNA-seq reads were aligned to the Streptococcus pneumoniae D39 genome assembly using Tophat
Transcript abundance and differential expression analyses were carried out using Cufflinks and cummeRbund
Genome_build: D39 (NC_008533.1)
Supplementary_files_format_and_content: FPKM

organism: Streptococcus pneumoniae

source_name: bacterial cells

growth_protocol: growth of Strpetococcus pneumoniae D39 derivatives in liquid medium at 37 C to exponential phase (OD 0.15) in Brain Heart Infusion (Oxoid

extract_protocol:
2 mL of cells were centrifuged at 10.000 rpm for 15 min, re-suspended in 90 ul of TE with 10ul of lysozime and then the RNA extraction was made following the protocol of the kit NucleoSpinRNA II kit from Macherey-Nagel.
'Ovation Prokaryotic RNA-Seq System (Nugen)

tag: strain

value: strain expressing stabely SpnIIID


title: SpnIIIB variant strain replicate 3

value: strain expressing stabely SpnIIIB


title: SpnIIIC variant strain replicate 1

value: strain expressing stabely SpnIIIC


title: SpnIIIC variant strain replicate 2


title: SpnIIIB variant strain replicate 2


title: SpnIIIC variant strain replicate 3


title: European_females_2

tag: Sex

value: female

tag: age


title: European_females_1


title: African_males_2

value: Africa (Zimbabwe)


title: mock-transfected HEK293T RPF

description:
miR-1_HEK293T_changes.txt
Mock_HEK293T.txt
cytoplasmically-enriched RNA

tag: treatment

value: mock transfection


title: SpnIIIB variant strain replicate 1


title: SpnIIID variant strain replicate 3


title: mock-transfected HEK293T RNA


title: African_males_1


title: miR-1-transfected U2OS RPF

description:
miR-1_U2OS_changes.txt
miR-1_U2OS_paRNA.txt
miR-1_U2OS_cytoRNA.txt
miR-1_U2OS_dep_RNA.txt
cytoplasmically-enriched RNA

value: U2OS cell line


title: SpnIIIA variant strain replicate 3

value: strain expressing stabely SpnIIIA


title: African_females_2


title: SpnIIID variant strain replicate 1


title: miR-1-transfected U2OS tRNA and rRNA depleted RNA

description:
miR-1_U2OS_changes.txt
miR-1_U2OS_dep_RNA.txt
cytoplasmically-enriched RNA


title: European_males_2


title: GM12878 2x75 bp

tag: tissue

value: Blood

value: Epstein-Barr Virus


title: African_females_1


title: S8114-A

city: Tianjin

first: Pengli

last: Cai

address: Xiqi Dao 32, Tianjin Airport Economic Area

country: China

institute: Tianjin Institute of Industrial Biotechnology, CAS

data_processing:
Illumina HiSeq™ 2000 used for sequencing
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.
The alignment results were stored in SAM format files for subsequent analysis.
The counts of reads counts uniquely mapped to only one gene for each gene were calculated by HTseq-count using SAM files and genome annotation as input.
The normalized expression values for each gene were calculated by the number of uniquely mapped reads per kilobase of exon region per million mapped reads (RPKM).
N. crassa WT and Δcdt-2
Genome_build:   ASM18292v1
Supplementary_files_format_and_content: GeneID, gene_length, reads, RPKM values for each Sample

organism: Neurospora crassa

growth_protocol: All the strains were innoculated at 106 conidia/mL and grown 16 hours in sucrose media.

extract_protocol:
Total RNA was isolated from frozen mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA). Total RNA was then treated with DNase I (Turbo DNA-free kit; Ambion).
Double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays

treatment_protocol: Mycelia were Washed and transferred to fresh media with cellulose (Avicel PH101), or Xylan (birch wood) for 4 hours inducing cultivation.

value: cdt-2 null

tag: induce condition

value: 4 hours on Avicel

value: mycelia

value: Avicel


title: Human naive T cells (Replicate 1)

description: 3' end sequencing of human naïve Tcells

value: T cells


title: WT-XN

source_name: WT

value: FGSC 2489

value: wild type

value: 4 hours on Xylan

value: Xylan


title: miR-1-transfected HEK293T RNA

value: HEK293T cell line

value: miR-1 transfection


title: Human activated T cells (Replicate 1)

description: 3' end sequencing of human activated Tcells

source_name: T cells


title: miR-155_mix

data_processing:
Raw sequence reads were trimmed to remove both barcodes and adapters using Trim Galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (v0.3.3, default parameters).
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie.
Peaks were called using MACS peak caller software (version 1.3.6.1) with defualt parameters using Input_DNA sample as input.
Genome_build: MGSCv37
Supplementary_files_format_and_content: BED files containing the called peaks

source_name: Splenic B cells, miR-155 KO, PU.1 IP

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Genome Analyzer Iix following the manufacturer's protocols.

treatment_protocol: Cultured B cells were stimulated for 4 days with LPS (5 ug/ml) and IL-4 (10 ng.ml) and treated with 2% formaldehyde to cross-link the DNA and protein. Glycine was then used to quench the reaction, before cells were permeabilised. Following permeabilisation, a Diagenode Bioraptor UCD-200 sonicator was used to fragment the chromatin, before PU.1 or control antibodies were used for precipitation.

tag: cell isolation

value: Splenic B cells

tag: condition

value: Ex-vivo


title: HSPC DMSO FAIRE Replicate 2

city: Duarte

first: Dustin

middle: E

last: Schones

state: CA

address: 1500 E Duarte Rd.

institute: City of Hope

description: FAIRE library DMSO replicate 2

data_processing:
FAIRE-seq: FAIRE was performed as previously described (Giresi et al., 2007). Isolated DNAs were barcoded and sequenced on the Illumina HiSeq 2500 to produced 100bp x 100bp paired-end reads. Reads were aligned to the human genome (version hg19, from the UCSC Genome Browser) using Bowtie2 with  local alignment.
Peak calling was performed with F-seq using default parameters and a 200bp feature length. Irreproducible Discovery Rate (IDR) analysis was performed to identify reproducible peaks.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak format, as described here: http://genome.ucsc.edu/FAQ/FAQformat.html#format12

source_name: CD34+ HSPCs

growth_protocol: CD34+ cells were obtained as described previously (Chen et al., 2012  Genes Dev 26:2499-2511). Cells were maintained in either serum-containing or serum-free media.

extract_protocol: Libraries were prepard according to Illumina instructions for DNA samples

treatment_protocol: Cells were treated with 2uM UNC0638 for 48 hours, as described previously (Chen et al., 2012 Genes Dev 26:2499-2511)

tag: cell type

value: CD34+ HSPCs

value: DMSO Control


title: PU.1_mix

source_name: Splenic B cells, PU.1 KI, PU.1 IP

tag: genotype


title: HSPC UNC FAIRE Replicate 1

description: FAIRE library UNC0638 treatment replicate 1


title: WT_mix

source_name: Splenic B cells, Wild type, PU.1 IP

value: willd type


title: BB18_tomato_bot

status: Public on Sep 24 2014

city: Berkeley

first: Abraham

last: Morales-Cruz

state: California

address: 1 Cyclotron Road

institute: Joint Genome Institute

description: Detach fruits inoculated under laboratory conditions

data_processing:
Quality trimming of raw reads was done with Sickle v.1.210 with a threshold of 20 (Q>20).
Quality filtering was done with Scythe v.0.991 with a prior of 0.4
Predicted non-ribosomal transcriptomes of B. cinerea (strain B05.10 v.1) and tomato (ITAG2.3) were combined and used as a reference for mapping Botrytis-infected grape reads.
Bowtie2 v.2.1.0  was used to map the processed reads to the combined references with the following options: -q --end-to-end --sensitive --no-unal -p20.
Read counts were extracted from the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Combination of B. cinerea (Genbank ID AAID00000000.2) (strain B05.10 v.1, http://www.broadinstitute.org/annotation/genome/botrytis_cinerea) and tomato (ITAG2.3, ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG2.3_release/) transcriptomes
Supplementary_files_format_and_content: Botrytis_tomato_raw_reads.txt : tab delimited text file, raw read counts determined by mapping the sequencing reads

organism: Botrytis cinerea B05.10

source_name: Botrytis cinerea B05.10 on Solanum lycopersicum host

extract_protocol:
Total RNA was extracted using a CTAB based protocol with a chloroform denaturation step. RNA was cleaned with RNeasy kit (Qiagen, US) including the Dnase treatment on column.
Illumina TruSeq RNA Sample Prep Kit v2 protocol

tag: host species

value: Solanum lycopersicum cv Ailsa Craig

tag: host organ

value: fruit

tag: host organ stage

value: ripe


title: Dolce-rnaseq-2-1

description: Berries naturally infected with B. cinerea, samples could include other environmental organisms.

data_processing:
Quality trimming of raw reads was done with Sickle v.1.210 with a threshold of 20 (Q>20).
Quality filtering was done with Scythe v.0.991 with a prior of 0.4
Predicted non-ribosomal transcriptomes of B. cinerea (strain B05.10 v.1) and V. vinifera (GCA_000003745.2) were combined and used as a reference for mapping Botrytis-infected grape reads.
Bowtie2 v.2.1.0  was used to map the processed reads to the combined references with the following options: -q --end-to-end --sensitive --no-unal -p20.
Read counts were extracted from the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Combination of B. cinerea strain B05.10 v.1, (Genbank ID AAID00000000.2) ( http://www.broadinstitute.org/annotation/genome/botrytis_cinerea) and V. vinifera (GenBank Assembly ID: GCA_000003745.2) transcriptomes
Supplementary_files_format_and_content: Botrytis_grapes_raw_reads.txt : tab delimited text file, raw read counts determined by mapping the sequencing reads

organism:
Vitis vinifera
Botrytis cinerea

source_name: Vitis vinifera cv. Semillon berries infected with Botrytis cinerea

value: grape berries

value: post-véraison (ripe)

tag: environmental conditions

value: field


title: Dolce-rnaseq-2-3


title: HSPC UNC FAIRE Replicate 2

description: FAIRE library UNC0638 treatment replicate 2


title: BB17_tomato_bot


title: SpnIIIA variant strain replicate 2

value: strain expressing stabely SpnIIIA


title: HSPC DMSO FAIRE Replicate 1

description: FAIRE library DMSO replicate 1


title: Dolce-rnaseq-2-2


title: BB16_tomato_bot


title: Input_DNA

source_name: Splenic B cells, Input


title: SpnIIIA variant strain replicate 1


title: phm4_del, no Pi, 195 min

city: rehovot

first: Noam

last: Vardi

address: herzel 235

department: molecular genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
RNA reads were aligned to the yeast strain S288C R64 reference genome using BOWTIE. Each read contains an unique molecular identidier (UMI) of 4 basepairs. Identical mRNA reads with the same UMI were discarded from the analysis to neutrilize  PCR amplification biases,
50 base pares single reads are in the R1.fastq.gz files. UMI reads are in the matching R2.fastq.gz.files. Fastq.gz.10Indices files are combined R1 and R2 files as produced by the illumina machine
Number of reads for each gene was normalized by the total number of reads and multiplied by 10^6.  Genes that obtained below ten reads were discarded from the analysis.
After alignment to the genome read number per sample was calculated samples that had less than 5*10^5 reads were discarded from the analysis in order to prevent an artificial enrichment for highly expressed genes. The expression at those time points was calculated as the mean between the 2 closest time points in the time course.
Genome_build: S288C R64; GCF_000146045.2
Supplementary_files_format_and_content: excel files containing the log2 number of reads in each time point.

organism: Saccharomyces cerevisiae

source_name: phm4_del, no Pi, 195 min

growth_protocol: Δphm4 cells were grown at high Phosphate medium, washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 3.75 hours

extract_protocol:
RNA was extracted using nucleospin® 96 RNA kit Cells lysis was done in a 96 well plate by adding 450 µl of lysis buffer containing 1M sorbitol (SIGMA-ALDRICH), 100mM EDTA and 0.45µl lyticase (10IU/µl). The plate was incubated in 30°C of 30' in order to break the cell wall, then centrifuged for 10' at 2500rpm, and the soup was transfer to a new 96 well plate, that provided by the nucleospin® 96 RNA kit. From that stage on the extraction continued using this kit
cDNA was made for each sample. The cDNA of each samples were run in the Illumina highsec 2500

treatment_protocol: cells were harevested and frozen in liquid nitrogen

tag: strain background

tag: genotype/variation

value: pho84pr-YFP, delta-phm4

tag: time after transfer to no-phosphate medium

value: 195 min


title: phm4_del, no Pi, 180 min

source_name: phm4_del, no Pi, 180 min

value: 180 min


title: phm4_del, no Pi, 210 min

source_name: phm4_del, no Pi, 210 min

value: 210 min


title: S8114-XN

tag: strain

value: cdt-2 null

value: 4 hours on Xylan

value: mycelia

value: Xylan


title: phm4_del, no Pi, 225 min

source_name: phm4_del, no Pi, 225 min

value: 225 min


title: phm4_del, no Pi, 165 min

source_name: phm4_del, no Pi, 165 min

value: 165 min


title: Dolce-rnaseq-2-5


title: phm4_del, no Pi, 150 min

source_name: phm4_del, no Pi, 150 min

value: 150 min


title: phm4_del, no Pi, 135 min

source_name: phm4_del, no Pi, 135 min

value: 135 min


title: phm4_del, no Pi, 120 min

source_name: phm4_del, no Pi, 120 min

value: 120 min


title: phm4_del, no Pi, 75 min

source_name: phm4_del, no Pi, 75 min

value: 75 min


title: phm4_del, no Pi, 105 min

source_name: phm4_del, no Pi, 105 min

value: 105 min


title: phm4_del, no Pi, 60 min

source_name: phm4_del, no Pi, 60 min

value: 60 min


title: phm4_del, no Pi, 15 min

source_name: phm4_del, no Pi, 15 min

value: 15 min


title: phm4_del, no Pi, 30min

source_name: phm4_del, no Pi, 30min

value: pho84pr-YFP, delta-phm4


title: phm4_del, high Pi, 0 min

source_name: phm4_del, high Pi, 0 min

value: 0 min


title: phm3_DaMP, no Pi, 360 min

source_name: phm3_DaMP, no Pi, 360 min

growth_protocol: phm3 damp cells were grown at high Phosphate medium, washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 6 hours

value: pho84pr-YFP, phm3 damp

value: 360 min


title: phm4_del, no Pi, 45 min

source_name: phm4_del, no Pi, 45 min

value: 45 min


title: phm3_DaMP, no Pi, 330 min

source_name: phm3_DaMP, no Pi, 330 min

value: 330 min


title: phm3_DaMP, no Pi, 315 min

source_name: phm3_DaMP, no Pi, 315 min

value: 315 min


title: phm3_DaMP, no Pi, 285 min

source_name: phm3_DaMP, no Pi, 285 min

value: 285 min


title: phm3_DaMP, no Pi, 300 min

source_name: phm3_DaMP, no Pi, 300 min

value: 300 min


title: phm3_DaMP, no Pi, 255 min

source_name: phm3_DaMP, no Pi, 255 min

value: 255 min


title: phm3_DaMP, no Pi, 270 min

source_name: phm3_DaMP, no Pi, 270 min

value: 270 min


title: phm3_DaMP, no Pi, 225 min

source_name: phm3_DaMP, no Pi, 225 min

value: 225 min


title: phm3_DaMP, no Pi, 345 min

source_name: phm3_DaMP, no Pi, 345 min

value: 345 min


title: phm3_DaMP, no Pi, 240 min

source_name: phm3_DaMP, no Pi, 240 min

value: 240 min


title: phm3_DaMP, no Pi, 195 min

source_name: phm3_DaMP, no Pi, 195 min

value: 195 min


title: phm3_DaMP, no Pi, 210 min

source_name: phm3_DaMP, no Pi, 210 min

value: 210 min


title: phm3_DaMP, no Pi, 150 min

source_name: phm3_DaMP, no Pi, 150 min

value: 150 min


title: phm3_DaMP, no Pi, 180 min

source_name: phm3_DaMP, no Pi, 180 min

value: 180 min


title: phm3_DaMP, no Pi, 135 min

source_name: phm3_DaMP, no Pi, 135 min

value: 135 min


title: phm3_DaMP, no Pi, 105 min

source_name: phm3_DaMP, no Pi, 105 min

value: pho84pr-YFP, phm3 damp

value: 105 min


title: phm3_DaMP, no Pi, 120 min

source_name: phm3_DaMP, no Pi, 120 min

value: 120 min


title: phm3_DaMP, no Pi, 165 min

source_name: phm3_DaMP, no Pi, 165 min

value: 165 min


title: phm3_DaMP, no Pi, 75 min

source_name: phm3_DaMP, no Pi, 75 min

value: 75 min


title: phm4_del, no Pi, 90 min

source_name: phm4_del, no Pi, 90 min

value: pho84pr-YFP, delta-phm4

value: 90 min


title: phm3_DaMP, no Pi, 30min

source_name: phm3_DaMP, no Pi, 30min


title: phm3_DaMP, no Pi, 45 min

source_name: phm3_DaMP, no Pi, 45 min

value: 45 min


title: phm3_DaMP, no Pi, 15 min

source_name: phm3_DaMP, no Pi, 15 min

value: 15 min


title: phm3_DaMP, high Pi, 0 min

source_name: phm3_DaMP, high Pi, 0 min

value: 0 min (high phosphate medium)


title: phm3_DaMP, no Pi, 60 min

source_name: phm3_DaMP, no Pi, 60 min

value: 60 min


title: pho90_OX, no Pi, 345 min

source_name: pho90_OX, no Pi, 345 min

growth_protocol: pho90_OX cells were grown at high Phosphate medium, washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 6 hours

value: pho84pr-YFP, pho90_OX

value: 345 min


title: pho90_OX, no Pi, 360 min

source_name: pho90_OX, no Pi, 360 min

value: 360 min


title: pho90_OX, no Pi, 330 min

source_name: pho90_OX, no Pi, 330 min

value: 330 min


title: pho90_OX, no Pi, 315 min

source_name: pho90_OX, no Pi, 315 min

value: 315 min


title: pho90_OX, no Pi, 300 min

source_name: pho90_OX, no Pi, 300 min

value: 300 min


title: pho90_OX, no Pi, 270 min

source_name: pho90_OX, no Pi, 270 min

value: 270 min


title: pho90_OX, no Pi, 255 min

source_name: pho90_OX, no Pi, 255 min

value: 255 min


title: pho90_OX, no Pi, 240 min

source_name: pho90_OX, no Pi, 240 min

value: 240 min


title: pho90_OX, no Pi, 210 min

source_name: pho90_OX, no Pi, 210 min

value: 210 min


title: pho90_OX, no Pi, 225 min

source_name: pho90_OX, no Pi, 225 min

value: 225 min


title: pho90_OX, no Pi, 180 min

source_name: pho90_OX, no Pi, 180 min

value: 180 min


title: pho90_OX, no Pi, 195 min

source_name: pho90_OX, no Pi, 195 min

value: 195 min


title: phm3_DaMP, no Pi, 90 min

source_name: phm3_DaMP, no Pi, 90 min

value: pho84pr-YFP, phm3 damp

value: 90 min


title: pho90_OX, no Pi, 120 min

source_name: pho90_OX, no Pi, 120 min

value: 120 min


title: pho90_OX, no Pi, 150 min

source_name: pho90_OX, no Pi, 150 min

value: 150 min


title: pho90_OX, no Pi, 135 min

source_name: pho90_OX, no Pi, 135 min

value: pho84pr-YFP, pho90_OX

value: 135 min


title: pho90_OX, no Pi, 105 min

source_name: pho90_OX, no Pi, 105 min

value: 105 min


title: pho90_OX, no Pi, 165 min

source_name: pho90_OX, no Pi, 165 min

value: 165 min


title: pho90_OX, no Pi, 90 min

source_name: pho90_OX, no Pi, 90 min


title: pho90_OX, no Pi, 75 min

source_name: pho90_OX, no Pi, 75 min

value: 75 min


title: pho90_OX, no Pi, 45 min

source_name: pho90_OX, no Pi, 45 min

value: 45 min


title: pho90_OX, no Pi, 30min

source_name: pho90_OX, no Pi, 30min


title: vip1_del, no Pi, 345 min

source_name: vip1_del, no Pi, 345 min

growth_protocol: Δvip1 cells were grown at high Phosphate medium, washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 6 hours

value: pho84pr-YFP, delta-vip1

value: 345 min


title: vip1_del, no Pi, 360 min

source_name: vip1_del, no Pi, 360 min

value: 360 min


title: pho90_OX, no Pi, 285 min

source_name: pho90_OX, no Pi, 285 min

value: 285 min


title: pho90_OX, high Pi, 0 min

source_name: pho90_OX, high Pi, 0 min

value: 0 min (high phosphate medium)


title: pho90_OX, no Pi, 15 min

source_name: pho90_OX, no Pi, 15 min

value: 15 min


title: vip1_del, no Pi, 300 min

source_name: vip1_del, no Pi, 300 min

value: 300 min


title: vip1_del, no Pi, 315 min

source_name: vip1_del, no Pi, 315 min

value: 315 min


title: vip1_del, no Pi, 330 min

source_name: vip1_del, no Pi, 330 min

value: 330 min


title: vip1_del, no Pi, 270 min

source_name: vip1_del, no Pi, 270 min

value: 270 min


title: vip1_del, no Pi, 240 min

source_name: vip1_del, no Pi, 240 min

value: 240 min


title: vip1_del, no Pi, 225 min

source_name: vip1_del, no Pi, 225 min

value: 225 min


title: pho90_OX, no Pi, 60 min

source_name: pho90_OX, no Pi, 60 min

value: pho84pr-YFP, pho90_OX

value: 60 min


title: vip1_del, no Pi, 150 min

source_name: vip1_del, no Pi, 150 min

value: 150 min


title: vip1_del, no Pi, 165 min

source_name: vip1_del, no Pi, 165 min

value: 165 min


title: vip1_del, no Pi, 195 min

source_name: vip1_del, no Pi, 195 min

value: 195 min


title: vip1_del, no Pi, 180 min

source_name: vip1_del, no Pi, 180 min

value: pho84pr-YFP, delta-vip1

value: 180 min


title: vip1_del, no Pi, 120 min

source_name: vip1_del, no Pi, 120 min

value: 120 min


title: vip1_del, no Pi, 105 min

source_name: vip1_del, no Pi, 105 min

value: 105 min


title: vip1_del, no Pi, 60 min

source_name: vip1_del, no Pi, 60 min


title: vip1_del, no Pi, 90 min

source_name: vip1_del, no Pi, 90 min

value: 90 min


title: vip1_del, no Pi, 15 min

source_name: vip1_del, no Pi, 15 min

value: 15 min


title: vip1_del, no Pi, 30min

source_name: vip1_del, no Pi, 30min


title: pho85_DaMP, no Pi, 360 min

source_name: pho85_DaMP, no Pi, 360 min

growth_protocol: 25 samples were taken during the time course. Expression data was normalized to the first time point (cells grown at high phosphate medium)

value: pho84pr-YFP, pho85 damp

value: 360 min


title: vip1_del, high Pi, 0 min

source_name: vip1_del, high Pi, 0 min

value: 0 min (high phosphate medium)


title: pho85_DaMP, no Pi, 345 min

source_name: pho85_DaMP, no Pi, 345 min

value: 345 min


title: vip1_del, no Pi, 285 min

source_name: vip1_del, no Pi, 285 min

value: 285 min


title: pho85_DaMP, no Pi, 330 min

source_name: pho85_DaMP, no Pi, 330 min

value: 330 min


title: pho85_DaMP, no Pi, 315 min

source_name: pho85_DaMP, no Pi, 315 min

value: 315 min


title: vip1_del, no Pi, 255 min

source_name: vip1_del, no Pi, 255 min

value: 255 min


title: pho85_DaMP, no Pi, 300 min

source_name: pho85_DaMP, no Pi, 300 min

value: 300 min


title: pho85_DaMP, no Pi, 285 min

source_name: pho85_DaMP, no Pi, 285 min


title: pho85_DaMP, no Pi, 270 min

source_name: pho85_DaMP, no Pi, 270 min

value: 270 min


title: vip1_del, no Pi, 210 min

source_name: vip1_del, no Pi, 210 min

value: 210 min


title: pho85_DaMP, no Pi, 240 min

source_name: pho85_DaMP, no Pi, 240 min

value: 240 min


title: pho85_DaMP, no Pi, 225 min

source_name: pho85_DaMP, no Pi, 225 min

value: 225 min


title: pho85_DaMP, no Pi, 210 min

source_name: pho85_DaMP, no Pi, 210 min


title: vip1_del, no Pi, 45 min

source_name: vip1_del, no Pi, 45 min

value: pho84pr-YFP, delta-vip1

value: 45 min


title: pho85_DaMP, no Pi, 150 min

source_name: pho85_DaMP, no Pi, 150 min

value: 150 min


title: pho85_DaMP, no Pi, 195 min

source_name: pho85_DaMP, no Pi, 195 min

value: 195 min


title: pho85_DaMP, no Pi, 120 min

source_name: pho85_DaMP, no Pi, 120 min

value: pho84pr-YFP, pho85 damp

value: 120 min


title: pho85_DaMP, no Pi, 135 min

source_name: pho85_DaMP, no Pi, 135 min

value: 135 min


title: vip1_del, no Pi, 135 min

source_name: vip1_del, no Pi, 135 min


title: pho85_DaMP, no Pi, 180 min

source_name: pho85_DaMP, no Pi, 180 min

value: 180 min


title: vip1_del, no Pi, 75 min

source_name: vip1_del, no Pi, 75 min

value: 75 min


title: pho85_DaMP, no Pi, 90 min

source_name: pho85_DaMP, no Pi, 90 min

value: 90 min


title: pho85_DaMP, no Pi, 60 min

source_name: pho85_DaMP, no Pi, 60 min

value: 60 min


title: pho85_DaMP, no Pi, 105 min

source_name: pho85_DaMP, no Pi, 105 min

value: 105 min


title: pho85_DaMP, no Pi, 75 min

source_name: pho85_DaMP, no Pi, 75 min


title: pho85_DaMP, no Pi, 15 min

source_name: pho85_DaMP, no Pi, 15 min

value: 15 min


title: pho85_DaMP, high Pi, 0 min

source_name: pho85_DaMP, high Pi, 0 min

value: 0 min (high phosphate medium)


title: pho85_DaMP, no Pi, 45 min

source_name: pho85_DaMP, no Pi, 45 min


title: phm3_del, no Pi, 345 min

source_name: phm3_del, no Pi, 345 min

growth_protocol: Δphm3 cells were grown at high Phosphate medium, washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 6 hours

value: pho84pr-YFP, delta-phm3

value: 345 min


title: phm3_del, no Pi, 360 min

source_name: phm3_del, no Pi, 360 min

value: 360 min


title: phm3_del, no Pi, 330 min

source_name: phm3_del, no Pi, 330 min

value: 330 min


title: pho85_DaMP, no Pi, 30min

source_name: pho85_DaMP, no Pi, 30min


title: phm3_del, no Pi, 300 min

source_name: phm3_del, no Pi, 300 min

value: 300 min


title: pho85_DaMP, no Pi, 255 min

source_name: pho85_DaMP, no Pi, 255 min

value: 255 min


title: phm3_del, no Pi, 285 min

source_name: phm3_del, no Pi, 285 min

value: 285 min


title: phm3_del, no Pi, 315 min

source_name: phm3_del, no Pi, 315 min

value: 315 min


title: phm3_del, no Pi, 270 min

source_name: phm3_del, no Pi, 270 min

value: 270 min


title: phm3_del, no Pi, 255 min

source_name: phm3_del, no Pi, 255 min


title: phm3_del, no Pi, 240 min

source_name: phm3_del, no Pi, 240 min

value: 240 min


title: phm3_del, no Pi, 225 min

source_name: phm3_del, no Pi, 225 min

value: 225 min


title: phm3_del, no Pi, 210 min

source_name: phm3_del, no Pi, 210 min

value: 210 min


title: phm3_del, no Pi, 195 min

source_name: phm3_del, no Pi, 195 min

value: 195 min


title: phm3_del, no Pi, 180 min

source_name: phm3_del, no Pi, 180 min

value: 180 min


title: phm3_del, no Pi, 150 min

source_name: phm3_del, no Pi, 150 min

value: 150 min


title: pho85_DaMP, no Pi, 165 min

source_name: pho85_DaMP, no Pi, 165 min

value: pho84pr-YFP, pho85 damp

value: 165 min


title: phm3_del, no Pi, 135 min

source_name: phm3_del, no Pi, 135 min

value: pho84pr-YFP, delta-phm3

value: 135 min


title: phm3_del, no Pi, 165 min

source_name: phm3_del, no Pi, 165 min


title: phm3_del, no Pi, 90 min

source_name: phm3_del, no Pi, 90 min

value: 90 min


title: phm3_del, no Pi, 75 min

source_name: phm3_del, no Pi, 75 min

value: 75 min


title: phm3_del, no Pi, 105 min

source_name: phm3_del, no Pi, 105 min

value: 105 min


title: phm3_del, no Pi, 30min

source_name: phm3_del, no Pi, 30min


title: phm3_del, no Pi, 60 min

source_name: phm3_del, no Pi, 60 min

value: 60 min


title: phm3_del, no Pi, 45 min

source_name: phm3_del, no Pi, 45 min

value: 45 min


title: phm3_del, no Pi, 15 min

source_name: phm3_del, no Pi, 15 min

value: 15 min


title: phm3_del, high Pi, 0 min

source_name: phm3_del, high Pi, 0 min

value: 0 min (high phosphate medium)


title: Wt, no Pi, 360 min

data_processing:
RNA reads were aligned to the yeast strain S288C R64 reference genome using BOWTIE. Each read contains an unique molecular identidier (UMI) of 4 basepairs. Identical mRNA reads with the same UMI were discarded from the analysis to neutrilize  PCR amplification biases,
50 base pares single reads are in the R1.fastq.gz files. UMI reads are in the matching R2.fastq.gz.files. Fastq.gz.10Indices files are combined R1 and R2 files as produced by the illumina machine
Number of reads for each gene was normalized by the total number of reads and multiplied by 10^6.  Genes that obtained below ten reads were discarded from the analysis.
After alignment to the genome read number per sample was calculated samples that had less than 5*10^5 reads were discarded from the analysis in order to prevent an artificial enrichment for highly expressed genes. The expression at those time points was calculated as the mean between the 2 closest time points in the time course.
Genome_build: S288C R64
Supplementary_files_format_and_content: excel files containing the log2 number of reads in each time point.

source_name: Wt_no Pi_360 min

growth_protocol: Wild type cells were grown over night at high Phosphate medium , washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 6 hours

extract_protocol:
RNA was extracted using nucleospin® 96 RNA kit Cells lysis was done in a 96 well plate by adding 450 µl of lysis buffer containing 1M sorbitol (SIGMA-ALDRICH), 100mM EDTA and 0.45µl lyticase (10IU/µl). The plate was incubated in 30°C of 30' in order to break the cell wall, then centrifuged for 10' at 2500rpm, and the soup was transfer to a new 96 well plate, that provided by the nucleospin® 96 RNA kit. From that stage on the extraction continued using this kit
cDNA was made for each sample. The cDNA of each samples were run in the Illumina HiSeq 2500

value: wild type

value: 360 min


title: Wt, no Pi, 345 min

source_name: Wt_no Pi_345 min

value: 345 min


title: Wt, no Pi, 330 min

source_name: Wt_no Pi_330 min

value: 330 min


title: Wt, no Pi, 315 min

source_name: Wt_no Pi_315 min

value: 315 min


title: Wt, no Pi, 270 min

source_name: Wt_no Pi_270 min

value: 270 min


title: Wt, no Pi, 285 min

source_name: Wt_no Pi_285 min

value: 285 min


title: Wt, no Pi, 255 min

source_name: Wt_no Pi_255 min

value: 255 min


title: Wt, no Pi, 195 min

source_name: Wt_no Pi_195 min

value: 195 min


title: Wt, no Pi, 210 min

source_name: Wt_no Pi_210 min

value: 210 min


title: Wt, no Pi, 240 min

source_name: Wt_no Pi_240 min

value: 240 min


title: Wt, no Pi, 225 min

source_name: Wt_no Pi_225 min

value: 225 min


title: Wt, no Pi, 180 min

source_name: Wt_no Pi_180 min

value: 180 min


title: Wt, no Pi, 150 min

source_name: Wt_no Pi_150 min

value: 150 min


title: Wt, no Pi, 165 min

source_name: Wt_no Pi_165 min

value: 165 min


title: phm3_del, no Pi, 120 min

source_name: phm3_del, no Pi, 120 min

value: pho84pr-YFP, delta-phm3

value: 120 min


title: Wt, no Pi, 90 min

source_name: Wt_no Pi_90 min

value: wild type

value: 90 min


title: Wt, no Pi, 75 min

source_name: Wt_no Pi_75 min

value: 75 min


title: Wt, no Pi, 105 min

source_name: Wt_no Pi_105 min

value: 105 min


title: Wt, no Pi, 60 min

source_name: Wt_no Pi_60 min

value: 60 min


title: Wt, no Pi, 120 min

source_name: Wt_no Pi_120 min


title: Wt, no Pi, 15 min

source_name: Wt_no Pi_15 min

value: 15 min


title: RtcB-null_Tm

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

data_processing:
Aligned to ce10 assembly using tophat2
Differential expression calculated using cuffdiff
Genome_build: ce10
Supplementary_files_format_and_content: Cuffdiff output of differential RNA-Seq signal between sample conditions

organism: Caenorhabditis elegans

source_name: 2000 L4 worms

growth_protocol: L4 worms

extract_protocol:
Worms were washed twice with M9 buffer, resuspended in TRIzol (Invitrogen), frozen in liquid nitrogen, thawed at 37°C, vortexed briefly, then freeze-thaw repeated five additional times, and then incubated at room temperature for 10 min. RNA was isolated from the aqueous phase following manufacturer’s instructions.
RNA was polyA selected and pair-end sequencing was performed on the Illumina HiSeq 2000 platform using 75bp reads

treatment_protocol: +/- tunicamycin 50ug/mL on NGM plates, 4 hours

value: RtcB-null, pre-spliced tRNAs

value: tunicamycin


title: WT, high Pi

source_name: WT_high Pi

value: 0 min (high phosphate medium)


title: RtcB-null


title: Wt, no Pi, 300 min

source_name: Wt_no Pi_300 min

value: 300 min


title: Wt, no Pi, 45 min

source_name: Wt_no Pi_45 min

value: 45 min


title: Control_Tm

value: control. pre-spliced tRNAs


title: PU1_siMM_Kasumi1_ChIPSeq

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

data_processing:
The raw sequence reads in fastq format returned by the Illumina Pipeline was aligned to the hg19 human genome build using BWA (Li and Durbin, 2010).
The reads in the resulting alignment files were used to generate density maps using bed-tools (Quinlan and Hall, 2010)
Regions of enrichment (peaks) of ChIP and DNAse1 sequencing data were identified using MACS (Zhang et al., 2008) and cisGenome (Ji et al., 2008) software. The resulting peaks common for the two peak calling methods were considered for further analysis
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: PU.1 from Kasumi1 cells

extract_protocol:
Libraries of DNA fragments from chromatin immunoprecipitation or DNase I treatment were prepared from approximately 10 ng of DNA. Firstly, overhangs were repaired by treatment of sample material with T4 DNA polymerase, T4 PNK and Klenow DNA polymerase (all enzymes obtained from New England Biolabs UK) in a reaction also containing 50 mM Tris-HCl,10 mM MgCl2, 10 mM Dithiothreitol, 0.4 mM dNTPs and 1 mM ATP. Samples were purified after each step using Qiagen MinElute columns (according to the manufacturer’s guidelines). Adenosine bases were added to 3’ ends of fragments using Klenow Fragment (3´- 5´ exo-minus), allowing for subsequent ligation of adapter oligonucleotides (Illumina part #1000521) using Quick T4 DNA ligase. After a further column clean up to remove excess adaptors, fragments were amplified in an 18 cycle PCR reaction using adapter-specific primers (sequences 5’- CAAGCAGAAGACGGCATACGAGCTCTTCCGATC*T and 5’-AATGATACGGCGACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T).
The libraries were purified and adapter dimers removed by running PCR products on 2% agarose gels and excising gel slices corresponding to fragments approximately 200-300 bp in size, which were then extracted using the Qiagen gel extraction kit. Libraries were validated using quantitative PCR for known targets, and quality assessed by running 1 μl each sample on an Agilent Technologies 2100 Bioanalyser. Once prepared, DNA libraries were subject to massively parallel DNA sequencing on an Illumina Genome Analyzer. ETO, RUNX1, C/EBPα, PU.1, LMO2 ChIP and Kasumi-1 DNase I libraries were sequenced employing the Illumina Genome Analyzer GAIIx, by using 36 base pair single end reads. For Patient ♯1 and ♯2 DNase I and control Patient libraries we used 50 bp single end reads on Illumina Hi-Seq.

tag: chip antibody

value: PU.1 (Santa Cruz, sc-352x)

tag: target

tag: transfection

value: scrambled siRNA


title: Control

tag: treatment


title: LMO2_siRE_Kasumi1_ChIPSeq

source_name: LMO2 after RUNX1/ETO knockdown from Kasumi1 cells

value: RUNX1-ETO siRNA


title: CEBPA_siMM_Kasumi1_ChIPSeq

source_name: CEBPA from Kasumi1 cells

value: sc-61X lot C1510

value: C/EBPa


title: LMO2_siMM_Kasumi1_ChIPSeq

source_name: LMO2 from Kasumi1 cells


title: CEBPA_siRE_Kasumi1_ChIPSeq

source_name: CEBPA after RUNX1/ETO knockdown from Kasumi1 cells


title: Wt, no Pi, 135 min

source_name: Wt_no Pi_135 min

value: wild type

value: 135 min


title: DHS_siRE_Kasumi1_DNAseSeq

description:
transfection with RUNX1-ETO siRNA
DNase-Seq

data_processing:
The raw sequence reads in fastq format returned by the Illumina Pipeline was aligned to the hg19 human genome build using BWA (Li and Durbin, 2010).
The reads in the resulting alignment files were used to generate density maps using bed-tools (Quinlan and Hall, 2010)
Regions of enrichment (peaks) of ChIP and DNAse1 sequencing data were identified using MACS (Zhang et al., 2008) and cisGenome (Ji et al., 2008) software. The resulting peaks common for the two peak calling methods were considered for further analysis
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files containing peak coordinates

source_name: DNAse1 after RUNX1/ETO Knockdown from Kasumi1 cells


title: RUNX1_AMLblast_CD34_ChIPSeq

source_name: RUNX1 CD34+ AML blast J282 apheresis

value: AML blast


title: EP300_siMM_Kasumi1_ChIPSeq

description: transfection with scrambled siRNA

source_name: EP300 from Kasumi1 cells


title: DHS_CD34_normal_DNAseSeq

description:
Normal' CD34+ - donor with Ewing's Sarcoma
DNase-Seq

source_name: DNAse1 from human peripheral blood stem cells (CD34+) cells

value: Human peripheral blood stem cells (CD34+)


title: DHS_siMM_Kasumi1_DNAseSeq

description:
transfection with scrambled siRNA
DNase-Seq

source_name: DNAse1 from Kasumi1 cells


title: wild-type DLS

city: Martinsried

first: Cemil

last: Kerimoglu

address: Grosshaderner Strasse 2

institute: Ludwig-Maximilians University Munich

data_processing:
Basecalls were performed using Ibis.
Sequenced reads were mapped to mm9 whole genome using TopHat 1.4.1.
Mapped reads were counted by Bedtools.
Differential gene expression was analyzed by multifactor model of DESeq package (Anders and Huber, 2010).
Genome_build: mm9
Supplementary_files_format_and_content: The Excel file includes normalized reads computed by DESeq for each detected gene in every sample used.

source_name: Dorsolateral striatum (DLS)

extract_protocol:
Brains from 8-week old mice were isolated and flash-frozen in isopentane (-20°C). Samples from dorsomedial and dorsolateral striatum were collected with laser capture microdissection. RNA was isolated with RNeasy Micro kit from Qiagen.
Enrichment for mRNA, RNA fragmentation and cDNA synthesis were performed using an in-house protocol modified from Illumina TruSeq protocol in order to be suitable for small RNA amounts (15 ng of total RNA/sample).

tag: tissue

value: dorsolateral striatum

tag: age

value: 8 weeks

value: wild-type


title: Reh DNAse-Seq

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

data_processing:
Base-calling (Illumina)
DNAse-seq reads were aligned to the hg18 genome assembly using Bowtie 1.00 to SAM output using standard parameters
Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. 2011.
Fixed-step 10bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. 2011
Peaks were called using CoCAS
Genome_build: hg18
Supplementary_files_format_and_content: Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. 2011. Fixed-step 10bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. 2011. Peaks were called using CoCAS

source_name: Pro-B lymphoblastic leukemia cell line

growth_protocol: Cells lines from Hodgkin's lymphoma (L1236, L428 and L519), Pro-B lymphoblastic leukemia (Reh) and Burkitt's lymphoma (Namalwa) were grown in IMDM medium containint 10% FCS, penicillin 100 U/mL, and streptomycin 50 pg/mL and incubated at 37C in a humidified atmosphere containing 5% CO2, with cell densities kept under 5x105 per ml

extract_protocol: DNaseI-Seq samples were generated from a size selection of DNaseI-digested DNA fragments comprised within a range of 100 to 600 bp and subjected to library preparation as per manufacturer´s instruction (Illumina)

treatment_protocol: To perform DNaseI accessibility assays with HRS and NH cell lines, the optimal cell number and DNaseI (DPFF DNaseI, Worthington Biochemical Corporation) concentration was titrated for each cell line. The DNA digestion extent was comparable in all the generated samples as measured by RT-PCR (5). Briefly, nuclei were isolated from 1-5 x 106 cells by detergent lysis and immediately digested for 3 min at 33 °C with DNaseI at 1-10 U/ml in a 1 mM CaCl2 supplemented buffer. The nuclei were lysed, the nuclear proteins digested with 1 mg/ml Proteinase K overnight at 37 °C

tag: cell line

value: Reh

tag: lymphoma type

value: non-Hodgkin's Lymphoma cell line

tag: passages

tag: dnasei origin

value: Worthington

tag: dnasei units (u/ml)


title: L1236 DNAse-Seq

source_name: Hodgkin's Lymphoma cell line

value: Hodgkin's Lymphoma cell line


title: DHS_patient_I_J168_HiSeq

description:
Patient: H18901/09. J168. Mutations:t(8;21), WT FLT & WT NPM1
DNase-Seq

source_name: DNAse1 from AML bone marrow CD34 purified cells

tag: cell type

value: AML bone marrow CD34 purified


title: DHS_patient_II_J171_HiSeq

description:
Patient: H12812/09. J171. Mutations:t(8;21), WT FLT& WT NPM1
DNase-Seq

value: AML  bone marrow CD34 purified


title: wild-type DMS

source_name: Dorsomedial striatum (DMS)

value: dorsomedial striatum

tag: genotype


title: EP300_siRE_Kasumi1_ChIPSeq

description: transfection with RUNX1-ETO siRNA

source_name: EP300 after RUNX1/ETO knockdown from Kasumi1 cells


title: L591 DNAse-Seq


title: PU1_siRE_Kasumi1_ChIPSeq

source_name: PU.1 after RUNX1/ETO knockdown from Kasumi1 cells

value: PU.1 (Santa Cruz, sc-352x)

value: RUNX1-ETO siRNA


title: L428 DNAse-Seq


title: Input_ChIPSeq_Control

address: 1500 Duarte Rd

department: Cancer Biology

data_processing:
basecalling have been done by CASAVA-1.8.2
Histone modification ChIP-seq data have been aligned to human hg19 by bowtie ( version 1.0.0 "–strata –best –n 1 –m 1 -3 10" for sequence by Illumina HiSeq 2500 because Fastqc checked last 10 bases are not good in quality, otherwise "–strata –best –n 1 –m 1"). CTCF ChIP-seq data have been aligned to human hg19 by bowtie ( version 1.0.0 –strata –best –n 1 –m 1 )
H3K4me3, H3K9ac, CTCF peaks have been called by MACS (1.4.2 version 20120305, default parameters) take correspond input sequence as control.
H3K9me2 and H3K27me3 domains have been called by RSEG (version 0.4.8-rc) with binsize 10kb and 5kb respectively
Genome_build: hg19

source_name: BEAS-2B cells

growth_protocol: Immortalized human Bronchial Epithelial Cells (Beas-2B) were cultured in Dulbecco’s Modified Eagle’s Medium (Cellgro) supplemented with 1% Penicillin Streptomycin and 10% Fetal Bovine Serum (Atlanta Biologicals) at 37° C and 5 % CO2.

extract_protocol:
For ChIP, untreated and NiCl2 exposed BEAS-2B cells were crosslinked with 1% formaldehyde for 10 minutes at 25°C and sonicated to obtain 200-500 base pair fragments. ChIP was performed using ChIP grade antibodies against H3K9me2 (Abcam, ab1220), H3K27me3 (Millipore, 07-449), H3K4me3 (Millipore, 07-473), H3K9ac (Abcam, ab4441) and CTCF (Active Motif, 61311).
ChIP-Seq libraries were prepared using Illumina TruSeq ChIP sample preparation Kit (IP-202-1024), according to manufacturer’s protocol.

treatment_protocol: For exposing cells to nickel, NiCl2  (Sigma N6136) was added to the media at a concentration of 500 mM and the cells were cultured for 72 hours.

tag: time point (hours)


title: Input_ChIPSeq_Nickel