title: Control: Seed from C24A9 X C24 rep1 single

description: Control: Seed from C24A9 X C24

data_processing:
All sequence preprocessing was done with custom python scripts available at the Comai lab wiki (http://comailab.genomecenter.ucdavis.edu/index.php/Barcoded_data_preparation_tools). We chose to process forward reads only so as not to inflate count scores. Sequences were trimmed using 4 separate scripts to remove adaptors, remove barcodes, convert Illumina 1.5+ fastq to sanger, and remove ambiguous bases. Reads that were shorter than 34-35 bp were discarded along with base quality score lower than Phred 20.
To assess gene expression, each biological replicate was aligned separately to both TAIR10 cDNA (available for download at ftp://ftp.arabidopsis.org//home/tair/Sequences//blast_datasets/TAIR10_blastsets/TAIR10_cdna_20101214) using Burrows-Wheeler Aligner (BWA) version 0.5.8c (Li and Durbin, 2009).
After alignment, read counts were generated using a custom python script.Sequences that mapped to more than one gene model of the same gene were saved and counted as one read count while sequences that mapped to more than one gene were excluded.
Genome_build: TAIR10 cDNA (all gene models)
Supplementary_files_format_and_content: .txt (read count per locus file generated from the .sam files)

organism: Arabidopsis thaliana

source_name: Arabidopsis seeds

growth_protocol: All plants were grown under long day conditions (16hrs light at 21°C and 8hrs dark at 18°C) in a controlled environment facility at Davis, CA. For expression analysis, the female Col-0 (seed stock ID CS6673) and C24 (seed stock ID CS22620) diploid ecotypes of A. thaliana were hemizygous for a male sterility construct (Paul et al., 1992) and were gifts from Dr. Rod Scott (University of Bath, United Kingdom). These male sterile lines were selected to reduce contamination. Diploid Arabidopsis arenosa var. Strecno was given to the lab by Dr. M. Lysak. The male-sterile A. thaliana lines were used as seed parent and A. arenosa was used as the pollen donor for all interspecific crosses. One A. arenosa plant was used for all crosses in these experiments to reduce genetic variation due to heterozygosity in A. arenosa lines. Crosses were performed by pollinating fully developed stigmas by hand at 10am to reduce circadian biases; no emasculation was necessary because of the male sterility construct.

treatment_protocol: Seeds were harvested fresh from ColA9 X A. arenosa, C24A9 X A. arenosa, ColA9 x Col-0 and C24A9 x C24 and frozen on dry ice. Total RNA was obtained using Plant RNA Reagent (Invitrogen, Carlsbad, California). Frozen tissue was placed in a 1mL Dounce Tissue Grinder (Omni International, Kennesaw, GA) with 200 μL Plant RNA Reagent. The tissue was ground for approximately 30 seconds and then the extract was transferred to a clean tube. The grinder was washed with 300 μL of Plant RNA Reagent, which was combined with the tissue extract. RNA extraction proceeded with the manufacturer’s protocol and followed by a DNAse I (Invitrogen) digest at room temperature for 60 minutes according to manufacturer’s recommendation to remove any DNA contamination. RNA was eluted in 20 μL DNAse-free water and concentration was determined using a NanoDrop 1000 Spectophotometer. RNA was stored at -80°C for downstream applications.

value: whole seeds

value: 3 days after pollination


title: Control: Seed from ColA9 X Col-0 rep1 single

status: Public on Jun 05 2013

type: SRA

city: Davis

first: Luca

last: Comai

state: Calif

address: 451 Health Sciences Dr

department: Genome Center

country: USA

institute: UC Davis

description: Control: Seed from ColA9 X Col-0

library_source: transcriptomic

molecule: total RNA

extract_protocol: Approximately 10μg of total RNA was processed in preparation for Illumina Sequencing using a homemade kit. All enzymatic reactions followed manufacture’s protocol unless otherwise noted. Messenger RNA was purified from total RNA using Dynabeads (Invitrogen, Carlsbad, California), which purify poly-A containing transcripts. Then, cDNA was synthesized with random priming using SuperscriptIII (Invitrogen) followed by heat inactivation for 5 minutes at 85°C. Second strand cDNA was then synthesized as follows: We combined 5x second strand buffer [200 mM Tris-HCl, pH 7; 22 mM MgCl2; 425 mM KCl], water, and 10mM dNTPs with the first strand mix. The reaction was incubated on ice for 5 minutes and then DNA polymerase I (NEB, Ipswich, Massachusetts) and RNAseH (NEB, Ipswich, Massachusetts) were added and the reaction was incubated at 16°C for 2.5 hours. The double stranded cDNA was cleaned using Agencourt AMPure XP (Beckman Coulter Genomics, Danvers, Massachusetts) with a 1.8:1 (v/v), AMPure to library ratio. After cDNA synthesis, each library was chemically fragmented using 1 μl of NEB’s dsDNA Fragmentase for 30 minutes at 37°C and cleaned with AMPure. Fragmentation was followed by end repair with NEB’s End Repair Module Enzyme Mix and A-base overhangs, which are needed for adaptor ligation, were added with Klenow (NEB). End repair and A-base addition were both followed by AMPure cleanup. Barcoded Illumina adaptors for controls and regular Illumina adaptors for controls were ligated at room temperature using NEB Quick Ligase. To remove adapter contamination in library sequencing, we size selected our libraries using AMPure. Changing the amount of AMPure buffer changes bead size selection. We used 0.1:1 (v/v), AMPure: library to obtain fragments (library + adaptor) greater than 300 bp and eluted in 20 μl Qiagen Elution Buffer . 10 μl of each library was enriched using 15 μl Phusion 2x HF master mix (NEB), 3 μl water, and 2 μl 5 μM premixed PE primers with the following reaction conditions: 30 sec at 98°C; 14 cycles of 10 sec at 98°C, 30 sec at 65°C, and 30 sec at 72°C; final extension with 5 min at 72°C. Enriched libraries were purified with AMPure (0.8:1 v/v; AMPure: library) and quality and quantity was assessed using Agilent BioAnalyzer. Libraries were sequenced according to manufacture’s instructions. The hybrids were sequenced using Illumina’s HiSeq 2000 (100-bp paired-end reads) and the controls were sequenced using Illumina’s HiSeq 2000 (Illumina, San Diego) (100-bp paired-end reads) or Illumina’s Genome Analyzer IIx (40-bp single-end reads).

tag: ecotype

value: ColA9 X Col-0

tag: tissue

tag: time


title: Control: Seed from C24A9 X C24 rep2 single

description: Control: Seed from C24A9 X C24


title: 1395-ORSI-22Apr2011

city: Corvallis

first: Richard

last: Cronn

state: OR

address: 3200 SW Jefferson Way

department: PNW Research Station

institute: USDA Forest Service

data_processing:
Basecalls performed using CASAVA version 1.8.  Sequences were filtered for quality and adaptor contamination using default CASAVA settings.
Reads from the 3/25/2011, 4/7/2011, and 5/25/2011 samples were de novo assembled using the software Trinity version r2011-11-26.  The final transcriptome reference was created by clustering of the Trinity assembly with two other data sources.
Reads from the 3/10/2011, 4/22/2011, 5/6/2011, and 6/17/2011 collection dates were mapped to the transcriptome reference using bowtie2.0.0-beta7 (Langmead and Salzberg, 2012) using the following calls: bowtie2 --end-to-end -D 15 -R 2 -L 22 -i S,1,1.15 \ -x <index_basename> -U <fastq_input_files> -S <outfile.sam>.
processed data files format and content: Text file in csv format.  Expression counts for each gene across 47 samples (4 dates).  Samples are identified by sample_id, as listed in characteristics.

organism: Pseudotsuga menziesii

source_name: needle tissue from prior year growth

growth_protocol: Seeds from the various seed sources were planted in a common garden in the J. Herbert Stone Nursery in southern Oregon, USA (42.3° N, -122.9° W)

extract_protocol:
Needle tissue was collected from one year old needles (previous season’s growth).  Needles were flash frozen in liquid nitrogen on site and subsequently stored at -80°C until RNA extraction.  Frozen needles (~ 8 – 12) were mechanically homogenized on dry ice in a FastPrep-24 bead mill (MP, Solon, OH) with two ceramic beads and crushed garnet. To the ground tissue, we added 1.5 ml of ice-cold extraction buffer (3M LiCl/8M urea; 1% PVP K-60; 0.1M dithiothreitol(Tai et al., Plant Molecular Biology Reporter 22(1): 93, 2004), homogenized the tissue again to suspend the ground tissue in buffer, and then pelleted cellular debris at 200×g for 10 minutes at 4°C. The supernatant was transferred to an RNase-free tube and incubated overnight at 4°C. RNA was pelleted by centrifugation (20,000×g for 30 minutes, 4°C), rinsed with 70% EtOH (200 µl), and repelleted at 20,000×g for 5 minutes at 4°C. After removal of the supernatant, RNA pellets were air dried for 5 minutes and given a final clean-up using the ZR Plant RNA MiniPrep kit (Zymo Research, Irvine, CA).
Illumina RNA-Seq library preparation used 2 µg total RNA and followed the standard TruSeq protocol (Part #15026498 Rev. A), modified for strand-specific sequencing by the dUTP method (Parkhomchuk et al., Nucleic Acids Res 37(18):e123, 2009). The product of first-strand cDNA synthesis is desalted to remove unincorporated dNTPs using Sephadex G-50, and the second strand synthesis used a dUTP/dNTP mixture (Fermentas #R0251) in place of the standard dNTPs to incorporate dUTP into the second strand. All subsequent steps follow the Illumina protocol, except that the PCR cocktail is prepared with an additional uracil-specific excision reagent (New England Biolabs #M5505S), and the PCR cocktail was heated to 37°C for 15 minutes prior to PCR to degrade the uracil-containing strand.

tag: collection date

tag: dormancy state

value: post-budbreak

tag: source longitude_latitude_elev(m)

tag: flowcell

tag: index

value: CTTGTA

tag: purpose

value: Reference


title: 522-WACA-22Apr2011

value: pre-budbreak

value: TGACCA


title: 395-WACA-22Apr2011

value: CGATGT


title: BLRP-RevErbalpha, biotin ChIPseq

city: La Jolla

first: Michael

middle: T

last: Lam

state: CA

address: 9500 Gilman Drive, MC 0651

department: School of Medicine

institute: University of California, San Diego

library_source: genomic

data_processing:
For ChIP-Seq and GRO-Seq samples (single end reads), reads were aligned to the mm9 genome using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location.  Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, and perform other analyses in the study.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include BEDGRAPH (principle component values along the genome for Hi-C), text files (for all common, H3K4me1hi H3K4me3lo, and H3K4me1hi H3K4me3lo intergenic RevErb sites), and summary file (Signal for ChIPseq, GROseq, and 5'GROseq at RevErb bound peaks).  All genomic coordinates are relative to mm9 (NCBI 37) mouse assembly.

molecule: genomic DNA

organism: Mus musculus

source_name: RAW macrophages

growth_protocol: mouse bone marrow were differentiate to macrophages in RPMI medium containing 30% L-cell condition medium and 20% FBS.  After differentiation, bone marrow derived macrophages were grown in 10% RPMI supplement with 10ng/mL M-CSF.  RAW macrophages were cultured in RPMI with 10% FBS.

extract_protocol:
ChIP-seq: Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody or with streptavidin-magnetic beads for biotinylated protein. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina Genomic adaptors or with NEXTflex DNA barcodes adaptors for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size-selected (150-250bp) from a 2% agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a Genome Analyzer II (Illumina) or HiSeq 2000 (Illumina) following the manufacturer's protocols.
GRO-seq: GRO-Seq was performed as described (Core, L.J., Waterfall, J.J., and Lis, J.T., Science 322, 1845-1848 (2008)) with minor modifications.  Approximately 10 million nuclei per sample were extracted and used for run-on and BrU incorporation. BrU labeled nascent transcripts were immunoprecipiated with anti-BrU agarose beads (Santa Cruz Biotech), washed, eluted and precipitated in ethanol.  BrU precipitated RNA were subjected for first strand complementary DNA synthesis. First, polyA tailed was added using Poly(A)-polymerase (NEB). Reverse transcription was then performed using Scriptscript III Reverse Transcriptase (Invitrogen) with 5' phosphorylated primer containing  an abasic dSpacer furan with binucleotide barcode.  Excess primers were removed by Exonuclease I (Fermentas). First-strand cDNA products were fragment with basic hydrolysis and size-selected (105-400 nt) in a 10% polyacrylamide TBE-urea gel (Invitrogen). cDNA was subsequently circularlized using CircLigase (Epicentre), and relinearized at the abasic dSpacer furan with ApeI (NEB). The ssDNA template was amplified to generate DNA for sequencing by Phusion Hig-Fidelity DNA Polymerase (Thermo Science). PCR product was purified and size selected (140-225 bp) by gel electrophoresis on a non-denaturing 8% polyacrylamide TBE gel (Invitrogen). Purified DNA was then sequence on Illumina Genome Analyzer II according to the manuactuere’s instructions.
5'GRO-seq: For each RAW264.7 cell line, 20x106 nuclei were prepared from approximately 30x106 cells. Nuclear run-ons were performed in parallel on 100 μl aliquots containing 5x106 nuclei as for conventional GRO-Seq. Reactions were stopped and RNA was extracted with 450 μl TRIzol LS reagent (Invitrogen) each according to the manufacturer’s instructions. Following DNase treatment, the RNA was hydrolyzed in 20 μl total volume with 2 μl RNA fragmentation buffer (Ambion) for 10 minutes, and divalent cations were removed by gel filtration. Fragmented RNA was then 3’-dephosphorylated with polynucleotide kinase (Enzymatics), for 2 h at 37°C. The reaction was stopped with EDTA and PNK was inactivated and RNA denatured by heating the reaction to 75°C for 5 minutes, then cooled on ice for 2 minutes. BrdU-containing RNA fragments were precipitated using anti-BrdU agarose beads. The resulting RNA was dephosphorylated with calf intestinal phosphatase (NEB) and 5’-de-capped with tobacco acid pyrophosphatase (Epicentre). The reaction was stopped and RNA was extracted with Trizol LS, and libraries were prepared by ligating Illumina TruSeq-compatible adapters to the RNA 3’ and 5’ ends with truncated mutant RNA ligase 2 (K227Q) and RNA ligase 1 (NEB), respectively, followed by reverse transcription, cDNA isolation, and PCR amplification for 12 cycles. Final libraries were size-selected on PAGE/TBE gels to 60-110 bp insert size. A detailed protocol is available on request.

tag: cell type

value: biotinylated RevErba expressing RAW macrophages

tag: antibody

value: Streptavidin T1 dynabeads (Invitrogen)

tag: genetic background


title: BirA, biotin ChIPseq

value: control RAW macrophages


title: BLRP-RevErbbeta, biotin ChIPseq

value: biotinylated RevErb-beta expressing RAW macrophages


title: 6128-ORSI-22Apr2011

value: CAGATC


title: 3650-WACS-25Mar2011

value: GCCAAT


title: 3713-WACS-25Mar2011

value: ACAGTG


title: 5497-WACA-25Mar2011


title: total scnRNAs from TWI1 KO cells

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

data_processing:
Sequence reads were filtered as described (Schoeberl et al. 2012).
To study the base composition and thermodynamic stability of small RNAs, reads containing any bases other than A, C, G or T were excluded and the remaining reads were collapsed to non-redundant datasets. To study thermodynamic stability, 29 nt RNA sequences were mapped to the LMR genomic region (corresponding to bases 64,932-165,807 of the supercontig 231 in the 2nd assembly of the Tetrahymena thermophila micronuclear genome, obtained from Broad Institute Web site: http://www.broadinstitute.org/annotation/genome/Tetrahymena.1/MultiHome.html) without allowing any mismatches. Then, the passenger strand scnRNA sequences were estimated. The local thermodynamic stabilities (kcal/mol) of 4 base pairs at the ends of the guide and passenger duplexes were calculated using the free energy parameters at 37ºC in 1 M NaCl (Freier et al. 1986) without including the initiation value. To study potential trimming and tailing reactions on small RNAs, 24-32 nt RNA sequences were mapped to the LMR genomic region by allowing two mismatches, and the mismatched positions in the scnRNAs were analyzed.
Genome_build: LMR genomic region (corresponding to bases 64,932-165,807 of the supercontig 231 in the 2nd assembly of the Tetrahymena thermophila micronuclear genome, obtained from Broad Institute Web site: http://www.broadinstitute.org/annotation/genome/Tetrahymena.1/MultiHome.html)
Supplementary_files_format_and_content: The .txt files represent abundance counts of the scnRNAs.

organism: Tetrahymena thermophila

source_name: total scnRNAs from TWI1 KO cells

extract_protocol:
Wild-type Tetrahymena thermophila strains B2086 and CU428 and the complete TWI1 KO strains (Mochizuki and Gorovsky 2004) were used for total RNA preparation. Twi1p was immunoprecipitated (Noto et al. 2010) from either wild-type cells using an anti-Twi1p antibody (Noto et al. 2010) or from the strains expressing HA-Twi1p and HA-Twi1p-hAGO2Lmut (Mochizuki and Kurth in press) using an anti-HA antibody (16B12, Covance). The cDNA libraries were constructed as described (Schoeberl et al. 2012). For multiplex sequencing, oligonucleotides listed below were used. Single-read 36- or 50-base sequences were generated using the Illumina GAII or HiSeq2000, respectively. Sequence reads were filtered as described (Schoeberl et al. 2012).
The 3' adapter for multiplex sequencing: 5’-App-NNN NAG ATC GGA AGA GCA CAC GTC T-3ddC; The 5' adapter for multiplex sequencing: 5'-ACA CUC UUU CCC UAC ACG ACG CUC UUC CGA UCU NNN-3'; The reverse-transcription primer for multiplex sequencing: 5’-CAA GCA GAA GAC GGC ATA CGA GAT BBB BBB GTG ACT GGA GTT CAGACG TGT GCT CTT CCG ATC T-3’ (“BBB BBB" = 6 base barcodes for maltiplex sequencing: 5'-CGT GAT-3', 5'-ACT TCG-3', 5'-GCC TAA-3', 5'- TGG TCA-3', 5'- CAC TGT-3', 5'-ATT GGC-3', 5'- GAT CTG-3', 5'- TCA AGT-3', 5'-CTG ATC -3', or 5'-AAG CTA-3'); The PCR amplification primer for multiplex sequencing: 5’-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GAT CT-3’
The RNA was gel-fractionated, and a small RNA population, including scnRNAs (26–32 nt), was used to construct the cDNA library for deep sequencing.

tag: strain

value: TWI1KO-20-1 x TTWI1KO-20-4

tag: genotype

tag: ip antibody


title: 6138-ORSI-25Mar2011


title: 8362-WACS-25Mar2011


title: 522-WACA-25Mar2011


title: 3653-WACS-25Mar2011


title: 1395-ORSI-25Mar2011


title: 6128-ORSI-25Mar2011


title: 3653-WACS-22Apr2011


title: 3650-WACS-17Jun2011

value: Expression


title: Control: Seed from ColA9 X Col-0 rep2 single

description: Control: Seed from ColA9 X Col-0

value: whole seeds

value: 3 days after pollination


title: 5497-WACA-17Jun2011

value: post-budbreak


title: 3713-WACS-17Jun2011


title: 6138-ORSI-17Jun2011

value: CTTGTA


title: 1383-ORSI-17Jun2011


title: scnRNAs co-immunoprecipitated with Twi1p

value: wild-type

value: anti-Twi1p antibody (Noto et al. 2010)


title: 388-WACA-17Jun2011

value: TGACCA


title: 395-WACA-25Mar2011

value: pre-budbreak

value: CGATGT

value: Reference


title: 3653-WACS-17Jun2011


title: 6128-ORSI-17Jun2011


title: 3713-WACS-06May2011


title: 3650-WACS-06May2011


title: 522-WACA-17Jun2011


title: 388-WACA-25Mar2011


title: 1395-ORSI-17Jun2011


title: 388-WACA-06May2011


title: Hybrid: A. thaliana eco. C24 X A. arenosa rep2

organism: Arabidopsis thaliana x Arabidopsis arenosa

value: C24 X A. arenosa


title: 1383-ORSI-25Mar2011


title: 5497-WACA-06May2011


title: 6138-ORSI-06May2011


title: Hybrid: A. thaliana eco. C24 X A. arenosa rep1


title: Hybrid: A. thaliana eco. Col-0 X A. arenosa rep1

value: Col-0 X A. arenosa


title: Hybrid: A. thaliana eco. Col-0 X A. arenosa rep2


title: 1383-ORSI-06May2011

value: CAGATC


title: 8362-WACS-06May2011

value: GCCAAT


title: Control: Seed from C24A9 X C24 rep2

description: Control: Seed from C24A9 X C24


title: 8362-WACS-17Jun2011


title: 522-WACA-06May2011


title: Control: Seed from ColA9 X Col-0 rep2

description: Control: Seed from ColA9 X Col-0

value: ColA9 X Col-0


title: Control: Seed from C24A9 X C24 rep1

description: Control: Seed from C24A9 X C24


title: 3653-WACS-06May2011

value: ACAGTG


title: Control: Seed from ColA9 X Col-0 rep1

description: Control: Seed from ColA9 X Col-0


title: Brg1

status: Public on Jun 04 2013

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

data_processing:
Sequenced reads were aligned to mouse genome (mm9) and filtered for low quality data using Helicos HeliSphere software suite with default parameters for basic pipeline.
Positions in genome with the numbers of mapped tags above the significance threshold defined by a Z-score of 7 were identified as anomalous and the tags mapped to those positions were discarded.
The tag frequency at each genome position was calculated separately for DNA positive and negative strands.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files list the 5'-end coordinates of sequenced reads retained for the corresponding sample after data filtering for possible library preparation artifacts. These are tab delimited text files.

source_name: embryonic fibroblast

growth_protocol: Primary MEFs were harvested from E13.5 embryos. Cre was introduced into cells via retroviral infection two times at 4-h intervals. Cells were stably selected in medium containing puromycin (2.5 µg/ml) 48 h after infection.

extract_protocol: DNA fragments were RNAse treated, precipitated, gel-extracted and prepared for sequencing following Helicos guidelines.

treatment_protocol: Cells were harvested and nuclei isolated through sucrose gradient.  Nuclei were exposed to micrococcal nuclease to release mononucleosome fragments.

value: Fibroblast cells; embryonic


title: WT

value: wild type


title: Brg1 ChIP

description: Sample 1

data_processing:
Sequenced reads were aligned to the mouse genome (mm9) using Bowtie short sequence aligner with default parameters for paired-end reads, reporting only the reads uniquely mapped to the reference genome.
Positions in genome with the numbers of mapped tags above the significance threshold defined by a Z-score of 7 were identified as anomalous and the tags mapped to those positions were discarded.
The tag frequency at each genome position was calculated separately for DNA positive and negative strands.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files list the 5'-end coordinates of sequenced reads retained for the corresponding sample after data filtering for possible artifacts. These are tab delimited text files.

growth_protocol: Primary MEFs were harvested from E13.5 embryos.

extract_protocol:
Nuclei were isolated and subjected to micrococcal nuclease digestion followed by brief sonication to release nucleosomal fragments. Brg1 ChIP was performed on the lysate and immunoprecipiated DNA was purified.
DNA fragments were RNAse treated, precipitated, gel-extracted and prepared for sequencing following Helicos guidelines.

tag: strain background

value: C57BL/6 and 129 mixed

tag: genotype/variation

tag: developmental age

value: Primary mouse embryonic fibroblasts (MEFs)

tag: chip antibody

value: Rabbit polyclonal Anti-SNF2β/BRG1 Antibody

tag: chip antibody vendor

value: Upstate

tag: chip antibody cat. #

tag: chip antibody lot #


title: Input

description: Sample 2


title: Snf5


title: H3K4me1_ChIPSeq_E2

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18

organism: Homo sapiens

growth_protocol: MCF7 obtained from ATCC were cultured in α-MEM media supplemented with 10% FBS in a 5% CO2 humidified incubator.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The extracted ChIP DNA was ligated to specific adaptors of Truseq system from Illumina, according to the manufacturer’s instructions.

treatment_protocol: Before experiment, the cells were changed to deficient MEM plus 5% charcoal treated phenol red free medium to culture for 3 days, followed by treatemnt of either 100nM 17-β-estrodial or ethanol for 1hr.

tag: cell line

tag: chip vendor/catalog

value: Abcam, ab8899

tag: treatment

value: 1hr treatment with 100nM E2


title: MelJuSo etoposide FAIRE-seq

city: Palo Alto

first: Baoxu

last: Pang

state: CALIFORNIA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description: FAIRE-enriched DNA

data_processing:
Reads were aligned to hg19 using BWA, duplicates and reads with mapping quality less than 60 were removed.
Peaks: Peak regions were called by using F-seq package.

source_name: MelJuSo cells

growth_protocol: Tissue culture cells were grown in 15cm dishes around 80% confluency.

extract_protocol: After fixation, lysates were cleared from sonicated nuclei and histone-free DNA were isolated by phenol-chloroform extraction. Libraries were prepared according to the provider’s kits and protocols for ChIP samples.

treatment_protocol: Tissue culture cells were treated with indicated drugs for 4 hours then fixed and collected for processing. Mice were injected iv with a single dose of  the indicated drugs and 4 hours later, tissues were fixed and collected for processing.

value: Human skin melanoma cell line

value: MelJuSo

value: Etoposide 60uM

tag: time point

value: 4 hours post treatment


title: ERa_ChIPSeq_repeat1

value: ERa

value: Santa Cruz Biotech, SC-543


title: Brg1 moderate digestion

description: Sample 6

data_processing:
Sequenced reads were aligned to the mouse genome (mm9) using Bowtie short sequence aligner with default parameters for paired-end reads, reporting only the reads uniquely mapped to the reference genome.
Positions in genome with the numbers of mapped tags above the significance threshold defined by a Z-score of 7 were identified as anomalous and the tags mapped to those positions were discarded.
The fragment frequency at each genome position was calculated for the centers of the paired-end fragments.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files list coordinates of the starts and ends of the DNA fragments retained for the corresponding sample after data filtering. These are plain text files.

extract_protocol:
Cells were harvested and nuclei isolated through sucrose gradient.  Nuclei were exposed to micrococcal nuclease to release mononucleosome fragments.
The mono-nucleosomal DNA was then isolated, end-repaired, and treated with Taq polymerase to generate a protruding A base for adaptor ligation. After ligation of a pair of Illumina adaptors, the DNA was size selected and amplified by PCR using the adaptor primers. The amplified DNA was then purified and used for cluster generation and sequencing at Illumina instument.

tag: cell type

tag: digetion degree

value: moderate (4U of Mnase)


title: MelJuSo doxorubicin H3K4me3 ChIP-seq

description: Chromatin IP against H3K4me3

data_processing:
Reads were aligned to hg19 using BWA, duplicates and reads with mapping quality less than 60 were removed.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm with default parameter.

growth_protocol: Cells were grown in 15cm dishes around 80% confluency.

extract_protocol: After fixation, lysates were cleared from sonicated nuclei and antibodies against H3K4me3 were used to IP the histone-DNA complexes. Libraries were prepared according to the provider’s kits and protocols for ChIP samples.

treatment_protocol: Cells were treated with indicated drugs for 2 hours and followed by extensive washing . Cells were further cultured for another 24 hours before cells were fixed and subjected for ChIP procedures.

value: Doxorubicin 9uM 2 hours

value: 24 hours post drug removal

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #


title: MelJuSo etoposide H3K4me3 ChIP-seq

description: Chromatin IP against H3K4me3

value: Etoposide 60uM 2 hours


title: MelJuSo doxorubicin FAIRE-seq

description: FAIRE-enriched DNA

value: Doxorubicin 9uM


title: Snf5 moderate digestion

description: Sample 5

value: C57BL/6 and 129 mixed

value: Primary mouse embryonic fibroblasts (MEFs)


title: WT moderate digestion

description: Sample 4

value: wild type


title: ERa_ChIPSeq_repeat2


title: H3K27ac_ChIPSeq_EtOH

tag: cell antibody

value: Abcam, ab4729

value: 1hr treatment with ethanol


title: H3K27ac_ChIPSeq_E2

value: 1hr treatment with 100nM E2


title: Brg light digestion

description: Sample 3

value: light (0.2U of Mnase)


title: MelJuSo un-treated H3K4me3 ChIP-seq

description: Chromatin IP against H3K4me3

value: Human skin melanoma cell line

value: Un-treated

value: control

value: MelJuSo


title: MelJuSo un-treated FAIRE-seq

description: FAIRE-enriched DNA


title: MelJuSo aclarubicin FAIRE-seq

description: FAIRE-enriched DNA

value: Aclarubicin 20uM

value: 4 hours post treatment


title: Snf5 light digestion

description: Sample 2


title: Mouse heart doxorubicin FAIRE-seq

description: FAIRE-enriched DNA

data_processing:
Reads were aligned to mm9 using BWA, duplicates and reads with mapping quality less than 37 were removed.
Peaks: Peak regions were called by using F-seq package.
Genome_build: mm9
Supplementary_files_format_and_content: bed files indicate the peak regions.

source_name: mouse heart

value: mouse heart cells

value: 10 mg/kg doxorubicin

tag: strain

value: FVB nude

tag: age

value: 10 weeks


title: Mouse heart etoposide FAIRE-seq

description: FAIRE-enriched DNA

value: 35 mg/kg etoposide


title: Mouse heart un-treated FAIRE-seq

description: FAIRE-enriched DNA


title: WT light digestion

description: Sample 1

tag: strain background

value: C57BL/6 and 129 mixed

tag: genotype/variation

value: Primary mouse embryonic fibroblasts (MEFs)


title: R_11282-MethylC-Seq

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Data were mapped to the Glycine max 1.0 reference genome
MethylC-Seq analysis were performed as described in Schmtiz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013).
RNA-Seq RPKM data were generated using Bowtie version 0.12.7 and Tophat version 1.3.3 (flags = -g 1, –F 0). Gene expression values were calculated using Cufflinks version 1.1.0 (flags = -F 0, -b, -N)
Genome_build: Gm1.0

organism: Glycine max

source_name: Trifoliolate leaves from three-week-old plants

growth_protocol: Seeds were surface sterilized [30% bleach, rinsed several times with sterile, double-distillated H2O (ddiH2O)], planted in soil-less medium (SogeMix “SM-2”-general purpose growing medium), and germinated in growth chambers (190 mmol PAR m-2s-1, 230C, 60% R.H., and 16 h photoperiod)

extract_protocol: Genomic DNA (gDNA) was purified from 0.5 g of leaves by using DNeasy Plant MiniKit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. MethylC-Seq libraries were constructed according to Schmitz, R.J. et al. Transgenerational epigenetic instability is a source of novel methylation variants. Science 334, 369-73 (2011).

tag: ecotype

tag: tissue

value: Trifoliolate leaves

value: 3 weeks

tag: genotype

value: 190 mmol PAR m-2s-1, 23C, 60% R.H., and 16 h photoperiod


title: R_11283-MethylC-Seq


title: R_11281-MethylC-Seq


title: R_11278-MethylC-Seq


title: R_11280-MethylC-Seq


title: R_11277-MethylC-Seq


title: R_11279-MethylC-Seq


title: R_11273-MethylC-Seq


title: R_11267-MethylC-Seq


title: R_11263-MethylC-Seq


title: R_11275-MethylC-Seq


title: R_11274-MethylC-Seq


title: R_11258-MethylC-Seq


title: R_11271-MethylC-Seq


title: R_11269-MethylC-Seq


title: R_11264-MethylC-Seq


title: R_11265-MethylC-Seq


title: R_11260-MethylC-Seq


title: R_11266-MethylC-Seq


title: R_11270-MethylC-Seq


title: R_11262-MethylC-Seq


title: R_11261-MethylC-Seq


title: R_11256-MethylC-Seq


title: R_11259-MethylC-Seq


title: 395-WACA-17Jun2011

tag: collection date

tag: dormancy state

value: post-budbreak

tag: source longitude_latitude_elev(m)

tag: flowcell

tag: index

value: CGATGT

tag: purpose

value: Expression


title: R_11250-MethylC-Seq

tag: treatment


title: R_11257-MethylC-Seq


title: R_11251-MethylC-Seq


title: R_11255-MethylC-Seq


title: R_11249-MethylC-Seq


title: R_11276-MethylC-Seq


title: R_11247-MethylC-Seq


title: R_11253-MethylC-Seq


title: R_11245-MethylC-Seq


title: R_11244-MethylC-Seq


title: R_11243-MethylC-Seq


title: R_11240-MethylC-Seq


title: R_11241-MethylC-Seq


title: R_11242-MethylC-Seq


title: R_11238-MethylC-Seq


title: R_11237-MethylC-Seq


title: R_11234-MethylC-Seq


title: R_11239-MethylC-Seq


title: R_11252-MethylC-Seq


title: R_11223-MethylC-Seq


title: R_11220-MethylC-Seq


title: R_11233-MethylC-Seq


title: R_11225-MethylC-Seq


title: R_11230-MethylC-Seq


title: R_11219-MethylC-Seq


title: R_11248-MethylC-Seq


title: R_11221-MethylC-Seq


title: R_11217-MethylC-Seq


title: R_11224-MethylC-Seq


title: R_11218-MethylC-Seq


title: R_11214-MethylC-Seq


title: R_11215-MethylC-Seq


title: R_11216-MethylC-Seq


title: R_11228-MethylC-Seq


title: R_11246-MethylC-Seq


title: R_11212-MethylC-Seq


title: R_11236-MethylC-Seq


title: R_11209-MethylC-Seq


title: R_11231-MethylC-Seq


title: R_11206-MethylC-Seq


title: R_11232-MethylC-Seq


title: R_11208-MethylC-Seq


title: R_11210-MethylC-Seq


title: R_11200-MethylC-Seq


title: R_11205-MethylC-Seq


title: R_11195-MethylC-Seq


title: R_11189-MethylC-Seq


title: R_11202-MethylC-Seq


title: R_11185-MethylC-Seq


title: R_11194-MethylC-Seq


title: R_11196-MethylC-Seq


title: R_11197-MethylC-Seq


title: AML daunorubicin FAIRE-Seq

description: FAIRE-enriched DNA

data_processing:
Reads were aligned to hg19 using BWA, duplicates and reads with mapping quality less than 37 were removed.
Peaks: Peak regions were called by using F-seq package.
Genome_build: hg19
Supplementary_files_format_and_content: bed files indicate the peak regions.

source_name: AML blasts, 90 mg of daunorubicin

extract_protocol:
After fixation, lysates were cleared from sonicated nuclei and histone-free DNA were isolated by phenol-chloroform extraction. Libraries were prepared according to the provider’s kits and protocols for ChIP samples.
Libraries were prepared according to the provider’s kits and protocols for ChIP samples.

treatment_protocol: AML blasts were isolated from patients’ blood with a BD Vacutainer CPT Cell Preparation Tube according to the manufacturer’s protocol. Mononuclear blasts cells were washed once with cold PBS and counted. Then cells were fixed and processed according to the FAIRE-seq protocol used for cell lines. 1x108 blast cells before and 2 hrs post Daun administration were used for FAIRE experiments.

tag: cell type

value: acute myeloid leukemia

value: 90 mg of daunorubicin

tag: time point

value: 2 hours post infusion


title: R_11186-MethylC-Seq


title: AML un-treated FAIRE-Seq

description: FAIRE-enriched DNA

source_name: AML blasts, untreated

value: Un-treated

value: Before treatment


title: R-11272-RNA-Seq-rep1

data_processing:
Data were mapped to the Glycine max 1.0 reference genome
MethylC-Seq analysis were performed as described in Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-36 (2008), PMID: 18423832.
RNA-Seq RPKM data were generated using Bowtie version 0.12.7 and Tophat version 1.3.3 (flags = -g 1, –F 0). Gene expression values were calculated using Cufflinks version 1.1.0 (flags = -F 0, -b, -N).
Genome_build: Gm1.0
Supplementary_files_format_and_content: mc*.txt file represents MethylC-Seq data.
Supplementary_files_format_and_content: RPKM file represents RNA-Seq data.

extract_protocol: Total RNA was purified from 0.5 g of leaves by using Trizol Reagent (Invitrogen, Carlsbad, CA), according to the manufacturer’s instructions, and subsequently purified using chloroform extraction. RNA-Seq libraries were constructed using the Illumina TruSeq Kit v2 (Illumina, San Diego, CA) according to the manufacturer’s guidelines.


title: R-11268-RNA-Seq-rep3


title: R-11272-RNA-Seq-rep2


title: R_11188-MethylC-Seq


title: GROSeq_siSMC3_E2

description: Nascent RNA sequencing

data_processing:
Basecalls performed using CASAVA version 1.4
Gro-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18

extract_protocol:
MCF7 cells were subjected to nuclear run-on for 5minutes at 30 degree with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing.
We followed a previous published protocol (Ingolia et al., 2009 Science; Wang et al., 2011 Nature). Briefly, the run-on RNA were first added with a polyA tracts by RNA polyA polymerase. This polyA tail enables the run-on RNA to be reverse transcribed into single strand cDNA by Reverse Transcriptase. The cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1, subsequently subjected to PCR amplification and deep sequencing.

tag: cell line

value: 1hr treatment with 100nM E2


title: R-11268-RNA-Seq-rep2


title: R_11211-MethylC-Seq


title: GROSeq_siSMC3_EtOH

description: Nascent RNA sequencing

value: 1hr treatment with ethanol


title: GROSeq_EtOH_repeat2

description: Nascent RNA sequencing


title: R-11268-RNA-Seq-rep1


title: R_11199-MethylC-Seq


title: GROSeq_EtOH_repeat1

description: Nascent RNA sequencing


title: LDX-RNA-Seq-rep2

value: LDX

value: Parental LDX


title: GROSeq_E2_repeat2

description: Nascent RNA sequencing


title: GROSeq_E2_repeat1

description: Nascent RNA sequencing


title: LDX-RNA-Seq-rep3


title: R_11187-MethylC-Seq


title: R-11272-RNA-Seq-rep3


title: SW620 etoposide FAIRE-seq

description: FAIRE-seq

source_name: SW620 cells

value: Human  colon adenocarcinoma

value: Etoposide 60uM

value: 4 hours post treatment


title: LDX-RNA-Seq-rep1

value: Trifoliolate leaves

value: 3 weeks


title: LD-RNA-Seq-rep1

value: LD

value: Parental LD

value: 190 mmol PAR m-2s-1, 23C, 60% R.H., and 16 h photoperiod


title: SW620 doxorubicin FAIRE-seq

description: FAIRE-seq

value: Doxorubicin 20uM


title: SW620 aclarubicin FAIRE-seq

description: FAIRE-seq

value: Aclarubicin 20uM


title: LD-RNA-Seq-rep2


title: SW620 un-treated FAIRE-seq

description: FAIRE-seq

value: control


title: LD-RNA-Seq-rep3


title: LDX-MethylC-Seq


title: R-11272-MethylC-Seq


title: R-11268-MethylC-Seq


title: LD-MethylC-Seq


title: RIL351_DNA_rep1

status: Public on Jun 03 2013

city: Cold Spring Harbor

first: Zhenyuan

last: Lu

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

data_processing:
Base call and quality scores were generated using the standard Illumina Pipeline.
BS-seq reads were trimmed for adaptor sequence and low quality base call, then aligned to ZmB73 4a.53 genome assembly using rmap V2.03  with parameters -Q -v -m 4
Then the C/T counts from aligned BS-seq reads for each cytosine in reference genome were saved in CT count file
RNA-seq reads were aligned to ZmB73 4a.53 and calculated FPKM using Tophat v1.3.2/Cufflinks v1.1.0
smRNA-seq reads were aligned to ZmB73 4a.53 genome aeembly using rmap V2.03 with parameters  -Q -v -m 2, then the mapped 21/22/24 nt smRNA-seq reads were counted in each 1M bin in whole genome
Genome_build: ZmB73 4a.53
Please note that the bed files for B73 DNA rep 1,2,3 and M017 DNA rep 1,2,3,4 Samples are on the Series record.
Supplementary_files_format_and_content: The CT count files have the first 6 columns the same as bed file, the 7th col is count of C, the 8th col is count of T, the 9th col is the 3 nt in reference genome, the 10th col is the context of cytosine
Supplementary_files_format_and_content: The FPKM tracking file format is described in http://cufflinks.cbcb.umd.edu/manual.html
Supplementary_files_format_and_content: The BED from smRNA-seq data contains the count of mapped smRNA-seq reads in each 1M bin in the whole genome

organism: Zea mays

source_name: 5-day-old coleoptyle

growth_protocol: Seeds were grown in the incubator at 25°C in darkness on wet paper towels set in glass Pyrex dish. After 5 days coleoptiles were excised and stored at -80°C.

extract_protocol: For DNA extraction, coleoptiles were ground with mortar and pestle in LN2, and nuclei were washed and separated from organelles by centrifuging through 30% OptiPrep (Axis-Shield PoC, Oslo, Norway, cat #1114542) solution. For each library, 1-5 μg of genomic DNA was sheared using Covaris S220 Adaptive Focused Acoustics ultra sonicator. Libraries were constructed following standard protocol using the NEBNext DNA Sample Prep Master Mix Set 1 (NEB E6040) and Illumina-compatible paired-end adaptors in which all cytosines were methylated. Each library (50 ng) was treated with sodium bisulfite using the EZ DNA Methylation-GoldTM Kit (Zymo Research D5005) according to the manufacturer’s protocol. The purified library (5-10 ng) was amplified using Expand High Fidelity PLUS PCR system (Roche 03300242001), which is capable of efficiently amplifying uracil-containing templates. PCR reactions (50 μl final volume) containing 200 μM each dNTP, 1 μM each primer, 2.5 mM MgCl2 , and 2.5 U Expand HiFi enzyme were performed according to the manufacturer’s instructions for 18 cycles. Amplified libraries were run on 2% MetaPhor® agarose (Lonza 50108) gel. Fragments of 220-350 bp were excised from gel and purified using the QIAquick PCR Purification kit (Qiagen 28104).DNA concentrations were quantified on a Bioanalyzer (Agilent), diluted to 10 nM and loaded on flow cells to generate clusters. Libraries were sequenced on Illumina GAII or HiSeq2000 machines using the paired-end 50 cycle protocol.

tag: strain

value: Recombinant Inbred Line #351


title: RIL327_DNA_rep1

value: Recombinant Inbred Line #327


title: Mo17_smRNA_rep1

extract_protocol: Small RNA fractions (up to 40 nucleotides in length) were isolated by running 20 μg of total RNA (prepared as described above) using FlashPAGE kit (Ambion AM10010 and AM9015) followed by ethanol precipitation. RNA was resuspended in 8 μl of water and processed using the ScriptMinerTM kit (Epicentre SMMP101212). The library was amplified using 15 cycles of PCR. DNA concentrations were quantified on a Bioanalyzer (Agilent), diluted to 10 nM and loaded on flow cells to generate clusters. Libraries were sequenced on Illumina GAII or HiSeq2000 machines using the single-end 36 cycle protocol.


title: Mo17_smRNA_rep2


title: B73_smRNA_rep2


title: B73_smRNA_rep3


title: B73_smRNA_rep1


title: RIL271_DNA_rep1

value: Recombinant Inbred Line #271


title: RIL182_DNA_rep1

value: Recombinant Inbred Line #182


title: RIL126_DNA_rep1

value: Recombinant Inbred Line #126


title: RIL14-2_DNA_rep1

value: Recombinant Inbred Line #14


title: RIL22_DNA_rep1

value: Recombinant Inbred Line #22


title: RIL14-3_DNA_rep1


title: RIL323_DNA_rep1

value: Recombinant Inbred Line #323


title: RIL87_DNA_rep1

value: Recombinant Inbred Line #87


title: RIL14-1_DNA_rep1


title: Mo17_DNA_rep4


title: RIL14_DNA_rep1


title: Mo17_smRNA_rep3


title: Mo17_DNA_rep2


title: Mo17_DNA_rep2_paired


title: Mo17_DNA_rep3_paired


title: B73_DNA_rep2


title: Mo17_DNA_rep1


title: B73_DNA_rep1_paired


title: B73_DNA_rep3


title: B73_RNA_rep3

extract_protocol: Total RNA was prepared by grinding tissue in TRIzol reagent (Invitrogen 15596-026) on dry ice and processed following the protocol provided by manufacturer. To remove DNA, an aliquot of total RNA was treated with RQ1 DNase (Promega M6101), followed by phenol/chloroform/ iso-amyl alcohol extraction, chloroform/iso-amyl alcohol extraction and ethanol precipitation. Total RNA (20 μg) was used for poly(A)+ selection using oligo(dT) magnetic beads (Invitrogen 610-02), eluted in water and used for RNA-seq library construction with ScriptSeqTM kit (Epicentre SS10906) or mRNA-seq Sample Prep kit (Illumina RS-100-0801) according to the manufacturer’s protocol. DNA concentrations were quantified on a Bioanalyzer (Agilent), diluted to 10 nM and loaded on flow cells to generate clusters. Libraries were sequenced on Illumina GAII or HiSeq2000 machines using the paired-end 50 cycle protocol.


title: B73_RNA_rep2


title: Mo17_RNA_rep2


title: Mo17_RNA_rep3


title: Mo17_RNA_rep1


title: B73_RNA_rep1


title: RNASeq_C2C12_Mef2D_Alpha

city: Ottawa

first: Marjorie

last: Brand

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

description: RNA-Sequencing of C2C12 expressing exogenous Mef2Da1

data_processing:
Basecalling was performed with Illumina RTA 1.12.4.2
Sequenced reads were initially mapped to the known mm9 transcripts (GTF file from the UCSC) using Bowtie version 2.0.2 using default values with the exception of the -r parameter to 0. Unmapped reads were then mapped to the mm9 genome.
Splice junctions were determined with TopHat version 2.0.6 using default values.
Transcript assembly and quantification was performed with the CuffLinks version 2.0.2 package with default values
Identification of differentially expressed genes was performed with CuffDiff included in the CuffLinks version 2.0.2 package. Genes are called significant if the q-value < 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files represent the read coverage of the RNA-Seq across the genome. The files were generated using the BEDTools suite (version 2.16.2) and UCSC genome browser standalone tools for Unix from the aligned reads output of TopHat version 2.0.6 using default values.
Supplementary_files_format_and_content: FPKM file contains FPKM for each RNA-Seq condition as determined by Cufflinks (version 2.0.2)

growth_protocol: C2 myoblasts (Yaffe and Saxel, 1977) were maintained in Dulbecco’s modified media (4.5g/L glucose) supplemented with 10% fetal calf serum, 4 mM L-Glutamine, 1.5 g/L sodium bicarbonate while not allowing cell density to achieve greater than 80% confluent. For exogenous expression of C2iFRT-Mef2Dα1, C2iFRT-Mef2Dα2, or control (C2iFRT) cells were grown in prolifertive conditions for 24 h in the presence of Doxycycline. Near confluence, cells were then differentiated for a further 24 hr prior in the presence of doxycycline.

extract_protocol:
Total RNA was harvested 24h after the start of differentiation using the RNeasy mini kit (Qiagen) using the standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To differentiate myoblasts, cells were allowed to achieve 90% confluency prior to a shift in culture media to Dulbecco’s modified media containing 2% horse serum with insulin (10 μg/mL) and transferrin (10 μg/mL). Differentiation media was changed every 24 h for up to 5 day. To express exogenous isoforms of Mef2D, a C2 line containing a single insertion of an FRT recombination element was generated using the Flp-In system (Invitrogen). The C2iFRT cell line was then generated to constitutively express the Tet-repressor by selecting for cells transfected with the pPyCAGIP-TetR plasmid. The cDNAs encoding Mef2Dα1, Mef2Dα2, Mef2Dα2(S189A), Mef2Dα1(S190A), or Mef2Dα1(S119/190A) were cloned into the MCS of a modified pCDNA5/FRT plasmid where the CMV promoter was replaced by a CMV containing a Tet-operator. Plasmids were transfected separately into C2iFRT cells and selected for hygromycin expression as outlined in the Flp-In system protocol. To induce exogenous expression of the Mef2D isoforms doxycycline at a concentration of 0.5 µM was added to the growth or differentiation medium.

tag: expression

value: exogenous Mef2Da1


title: dtf1_sRNA

city: Shanghai

first: Heng

last: Zhang

state: Shanghai

address: 300 Fenglin Rd, Room 705

country: China

institute: Shanghai Center for Plant Stress Biology

description: small RNA profiling

data_processing:
For BS-seq, adapter,and low-quality sequences (q < 20) were trimmed and clean reads were mapped to Arabidopsis thaliana TAIR 10 genome using BSMAP allowing two mismatches. Only cytosines with a depth of at least four in all libraries were retained for further analysis.
For sRNA-seq, after adapter sequences were trimmed, clean reads of size 18 nt–30 nt were mapped to the TAIR 10 genome and annotated structural RNAs (rRNAs, tRNAs, snRNAs, and snoRNAs) using Bowtie. Only sRNAs that had at least one perfect match to the genome and did not match structural RNAs were used for downstream analysis.  Read counts were normalized to Reads Per Ten Million (RPTM) according to total number of clean reads (excluding structural sRNAs) in the library and number of hits to the genome. Normalized expression levels of 24-nt sRNAs were summarized in non-overlapping 500-nt windows over the nuclear genome and were compared between each mutant and the wild type. To remove lowly expressed regions, only 500-nt regions that had at least 200 RPTM combined expression in the mutant and the wild type were considered. 500-nt regions that showed 5-fold lower expression in the mutant were selected as sRNA-depleted regions.
Genome_build: TAIR10
Supplementary_files_format_and_content: BS-seq WIG files represent methylation level (from 0 to 1) of each cytosine that are covered ≥4 times in all 4 samples.
Supplementary_files_format_and_content: sRNA WIG files represent normalized RPTM (reads per ten million) counts of 24-nt RNAs that are uniquely mapped to the TAIR10 genome.

source_name: Whole seedling

growth_protocol: Seedlings were grown on 1/2 MS plates supplemented with 0.65% agarose and 1% sucrose for 12 days before harvested

extract_protocol: Small RNA was extracted using the Trizol/PEG method as published (He et al 2009 Genes Dev; doi:10.1101/gad.1765209). Libraries were prepared for sequencing according to the manufacturer's (Illumina, Inc) instructions.

tag: age

value: whole seedling


title: nrpd1_DNA

description: whole-genome DNA methylation profiling

extract_protocol: Genomic DNA was extracted at BGI (Beijing Genomics Institute), Inc.  Libraries were prepared for sequencing according to the manufacturer's (Illumina, Inc) instructions.

tag: genotype/variation


title: RIL8_DNA_rep1

value: Recombinant Inbred Line #8


title: Mo17_DNA_rep3


title: RNASeq_C2C12_Control

description: RNA-Sequencing of C2C12 expressing the control vector


title: nrpe1_sRNA

description: small RNA profiling


title: 3' RNASeq of BMDCs 4hrs post LPS stimulation

status: Public on Jun 01 2013

city: Cambridge

first: Sabah

last: Kadri

state: Massachusetts

address: 7 Cambridge Center

department: Computational Biology

institute: Broad institute

data_processing:
Reads mapping to rRNA were filtered out and tophat v1.4.1 was used for alignment with segment length 20 and maximum multi-hits 15.
Gene expression matrices and peak files for end RNASeq were generated using the software package, ESAT (http://garberlab.umassmed.edu/software/esat/)
Genome_build: Mouse: mm9

source_name: bone marrow

growth_protocol: Mouse BMDC samples: 6-8 week old female C57BL/6J mice were obtained from the Jackson Laboratories. Bone marrow dendritic cells (BMDCs) were collected from femora and tibiae and plated on non-tissue culture  treated plastic dishes in RPMI medium (Gibco, Carlsbad, CA, Invitrogen, Carlsbad, CA), supplemented with 10% FBS, L-glutamine, penicillin/streptomycin, MEM non-essential amino  acids, HEPES, sodium pyruvate, !- mercaptoethanol, and GM-CSF (15 ng/mL; Peprotech, Rocky Hill, NJ).

extract_protocol:
50ng-1ug of total RNA is polyA selected using Oligo-dT beads (Invitrogen) and then fragmented using Ambion Fragmentation buffer using incubation time of 1 min 50sec at 70C. Extractions for ExoCAGE and 3' RNASeq are carried out as described in the paper.
50ng-1ug of total RNA is polyA selected using Oligo-dT beads (Invitrogen) and then fragmented using Ambion Fragmentation buffer using incubation time of 1 min 50sec at 70C.   ExoCAGE: Fragmented RNA is cleaned-up using 2.5X volume on SPRI beads (Agencourt), and incubated with Terminator Exonuclease (Epicentre) for 90 minutes. Reaction mixture is then cleaned up with 2.5X of SPRI beads and then processed the same way as above starting with dephosphorylation and lygation steps. 3' RNA-Seq: Fragmented RNA is cleaned-up using 2.5X volume on SPRI beads (Agencourt) and then subjected to second polyA enrichment step. Specifically, we used cDNA synthesis with custom oligo-dT priming (CCTACACGACGCTCTTCCGATCT-T15) for mouse dendritic cells. Reaction mixture is then processed in the same way as in Full-Length protocol starting with hybrid degradation and so on.

value: bone marrow-derived dendritic cells

tag: timepoint/developmental stage


title: dtf1_DNA

description: whole-genome DNA methylation profiling

tag: tissue


title: nrpe1_DNA

description: whole-genome DNA methylation profiling


title: ExoCAGE of thymoycytes

source_name: thymus

value: thymocytes

value: RAG

value: double negative stage


title: 3' RNASeq of BMDCs 2hrs post LPS stimulation


title: nrpd1_sRNA

description: small RNA profiling


title: 3' RNASeq of BMDCs 0hrs post LPS stimulation


title: B73_DNA_rep1


title: ExoCAGE of BMDCs 0hrs post LPS stimulation


title: IgH_FB_V_reg_22552_BL6_distalV

city: Utrecht

first: sjoerd

last: holwerda

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: 4C PCR product

data_processing:
The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank HindIII or DpnII sites (fragment ends), using custom perl scripts. Due to their ambiguous nature in reporting contacts, repetitive fragment ends were excluded from subsequent analysis. Read pairs are used to identify the 4C capture (raw files with .fq extension) and identify the allele by reading the SNP (raw files with .txt extension). The reduced genome was based on mouse mm9.
Genome_build: mm9
Supplementary_files_format_and_content: The processed files are wiggle tracks (variable step), containing the chromosomal location of the fragment-ends present in a HindIII-DpnII digested genome. The first column contains the location per chromosome, the second column contains the number of reads per fragment-end.

source_name: Fetal brain from 14.5 day post fertilization embryos

growth_protocol: Resting mature B and T cells are isolated from the spleen from 6-8 weeks mice and immediately processed (Day 0). To obtain activated mature B and T cells, resting splenic B and T cells are isolated and subsequently in vitro activated for 4 days after which they are processed (Day 4). Fetal brain cells are isolated at embryonic stage e14.5.

extract_protocol:
The initial steps of the 4C procedure, as published before (Simonis et al., 2006, Nature Genetics), remain unchanged. Cells are cross linked using 2% formaldehyde for 10min at room temperature in PBS 10%FCS, nuclei are isolated, after which chromatin is digested with HindIII and subsequently ligated under diluted conditions. After reversal of the cross links the DNA is purified and treated with the second restriction enzyme, DpnII. After a second re-ligation step the sample is purified and a 4C PCR is applied. FACS analysis is used to separate the cells on the basis of the allotypic origin of the productive IgH allele. The FVB allele codes for the B cell receptor from the IgMa isotype, whereas the c57Bl/6 allele encodes for the B cell receptor from the IgMb isotype. Allele specific analysis is enabled applying paired end sequencingon the sorted IgMa and IgMb cell populations. One read (P1) reads the 4C capture, whereas the other read (P2) identifies the genotype of the mouse and thus the productive or non-productive allele.
Illumina adaptor attachment is done by extending the 4C PCR primers with the paired-end Illumina adaptors. These extended 4C PCR primers are used in the 4C PCR protocol

treatment_protocol: cells are cross linked using 2% formaldehyde for 10minutes at room temperature in 10%FCS/PBS

value: embryonic stage e14.5

value: Fetal brain

value: Fetal brain cells

tag: sequencing

value: Paired-end


title: Col_sRNA

description: small RNA profiling

value: Col


title: IgH_T_D4_V_reg_22552_FVB_distalV

description: 4C PCR product

source_name: Resting, mature T cells

value: FVB

value: 6-8 wks

value: spleen

value: resting splenic T cells


title: IgH_FB_C_reg_145501_BL6_Cy3

description: 4C PCR product


title: ExoCAGE of BMDCs 4hrs post LPS stimulation


title: RNASeq_C2C12_Mef2D_Prime

description: RNA-Sequencing of C2C12 expressing exogenous Mef2Da2

value: exogenous Mef2Da2


title: IgH_T_D4_C_reg_145501_FVB_Cy3

description: 4C PCR product


title: IgH_T_D4_C_reg_46015_FVB_3RR

description: 4C PCR product


title: IgH_T_D0_V_reg_22552_FVB_distalV

description: 4C PCR product

source_name: Activated, mature T cells

value: in vitro activated, Splenic T cells


title: Col_DNA

description: whole-genome DNA methylation profiling

value: whole seedling


title: IgH_T_D0_C_reg_145501_FVB_Cy3

description: 4C PCR product


title: IgH_T_D0_C_reg_46015_FVB_3RR

description: 4C PCR product


title: ExoCAGE of BMDCs 2hrs post LPS stimulation


title: IgH_T_D4_C_reg_145501_BL6_Cy3

description: 4C PCR product


title: IgH_T_D0_V_reg_22552_BL6_distalV

description: 4C PCR product


title: IgH_T_D4_C_reg_46015_BL6_3RR

description: 4C PCR product


title: IgH_FB_C_reg_46015_BL6_3RR

description: 4C PCR product


title: IgH_IgMb_D4_C_reg_145501_FVB_Cy3

description: 4C PCR product

source_name: Activated, mature B cells

value: in vitro activated, Splenic B cells


title: IgH_T_D0_C_reg_145501_BL6_Cy3

description: 4C PCR product


title: IgH_IgMb_D4_V_reg_22552_FVB_distalV

description: 4C PCR product


title: IgH_T_D0_C_reg_46015_BL6_3RR

description: 4C PCR product


title: IgH_IgMb_D4_C_reg_46015_FVB_3RR

description: 4C PCR product


title: IgH_IgMb_D4_C_reg_46015_BL6_3RR

description: 4C PCR product


title: IgH_IgMa_D4_V_reg_22552_BL6_distalV

description: 4C PCR product


title: IgH_IgMa_D4_C_reg_46015_FVB_3RR

description: 4C PCR product


title: IgH_IgMa_D4_V_reg_22552_FVB_distalV

description: 4C PCR product


title: IgH_IgMa_D4_C_reg_145501_FVB_Cy3

description: 4C PCR product


title: IgH_IgMa_D4_C_reg_145501_BL6_Cy3

description: 4C PCR product


title: IgH_IgMa_D4_C_reg_46015_BL6_3RR

description: 4C PCR product


title: IgH_IgMb_D0_V_reg_22552_FVB_distalV

description: 4C PCR product

source_name: Resting, mature B cells

value: resting splenic B cells


title: IgH_IgMb_D0_C_reg_145501_FVB_Cy3

description: 4C PCR product


title: IgH_IgMb_D0_C_reg_46015_FVB_3RR

description: 4C PCR product


title: IgH_IgMb_D0_V_reg_22552_BL6_distalV

description: 4C PCR product


title: IgH_IgMb_D0_C_reg_145501_BL6_Cy3

description: 4C PCR product


title: IgH_T_D4_V_reg_22552_BL6_distalV

description: 4C PCR product


title: IgH_IgMb_D0_C_reg_46015_Bl6_3RR

description: 4C PCR product


title: IgH_IgMa_D0_V_reg_22552_FVB_distalV

description: 4C PCR product


title: IgH_IgMa_D0_C_reg_46015_FVB_3RR

description: 4C PCR product


title: IgH_IgMa_D0_V_reg_22552_BL6_distalV

description: 4C PCR product


title: IgH_IgMa_D0_C_reg_145501_FVB_Cy3

description: 4C PCR product


title: IgH_IgMb_D4_C_reg_145501_BL6_Cy3

description: 4C PCR product


title: IgH_IgMb_D4_V_reg_22552_BL6_distalV

description: 4C PCR product


title: IgH_IgMa_D0_C_reg_145501_BL6_Cy3

description: 4C PCR product


title: IgH_IgMa_D0_C_reg_46015_BL6_3RR

description: 4C PCR product


title: Mef2Da1-BLOCK

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

description: ChIP-Seq of Mef2Da1 antibody control (antibody blocked with peptide)

data_processing:
Sequence reads were obtained using the Illumina Genome Analyzer II.
Reads were aligned to human genome mm9 using BWA (0.5.9)
Peaks were called using in-house peak calling algorithm
Genome_build: mm9

growth_protocol: C2 myoblasts (Yaffe and Saxel, 1977) were maintained in Dulbecco’s modified media (4.5g/L glucose) supplemented with 10% fetal calf serum, 4 mM L-Glutamine, 1.5 g/L sodium bicarbonate while not allowing cell density to achieve greater than 80% confluent.

extract_protocol:
C2 myoblasts (7 x 107 cells) were differentiated for 5 days. Proteins were cross-linked to DNA for 30 minutes using 1% formaldehyde in DMEM at 22°C. After 30 minutes the formaldehyde containing media was removed, and cells were washed with 125 mM Glycine in PBS for 10 minutes at 22°C. Recovered cells were resuspended in a hypotonic lysis buffer (25 mM Hepes pH7.9, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 0.5 mM DTT, and 0.3 mM PMSF). After 45minutes on ice, myotubes were lysed using a 2 mL dounce homogenizer (B-pestle).Fragmentation of the DNA was stopped by the addition of 1/10th volume of MNase Stop buffer (11 mM EDTA, and 11 mM EGTA). The chromatin was then pelleted at 4000 rpm for 10 min at 4°C. The pellet was then resuspended in shearing buffer (50mM Tris HCl pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5% SDS and add 1% TritonX100), and sonicate using a Bioruptor for 80 cycles of 30 s on and 60 s off to further fragment the chromatin to obtain fragments of 150-300 bp.  Pellets recovered from homogenate were resuspended in nuclease buffer (50 mM Tris HCl  pH 7.5, 140 mM NaCl, 5mM MgCl2 and 1mM CaCl2. MNase (Sigma) was added to the  chromatin at a concentration of 0.12 Units per 100 μg of ribonucleic acids (measured as in (Brand et al., 2008)) and incubated at 37°C for 5 min.
Libraries were generated from immunoprecipitated DNA as outlined in the  Illumina DNA Library Construction Kit protocol except that 21 rounds of PCR were performed for amplification, and DNA fragments ranging from 200-350 bp were isolated during size selection on agarose gel.

treatment_protocol: To differentiate myoblasts, cells were allowed to achieve 90% confluency prior to a shift in culture media to Dulbecco’s modified media containing 2% horse serum with insulin (10 μg/mL) and transferrin (10 μg/mL). Differentiation media was changes every 24 h for up to 5 day.

tag: chip antibody

tag: chip antibody manufacturer

value: Genscript

tag: peptide

value: keyhole limpet hemocyanin coupled peptides - CELDGLFRRYGST


title: Mef2Da2-BLOCK

description: ChIP-Seq of Mef2Da2 antibody control (antibody blocked with peptide)

value: keyhole limpet hemocyanin coupled peptides - CPQTEEKYKKIDEEF


title: Mef2Da2

description: ChIP-Seq of endogenous Mef2Da2 isoform


title: Mef2Da1

description: ChIP-Seq of endogenous Mef2Da1 isoform


title: rde1_non_inf_1

first: Eric

middle: A.

last: Miska

address: Tennis Court Rd

department: Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry We

country: United Kingdom

institute: University of Cambridge

description: smallRNA-seq

data_processing:
Custom Perl scripts were used for processing and run with Perl v5.10.1.  Fastq entries with missing bases or barcodes not matching any of the expected sequences were excluded. Reads were trimmed by removing 5' barcodes (if applicable) and any 3'As. Inserts with length outside the relevant size range (18-30 nucleotides) were excluded.
Supplementary_files_format_and_content: collapsed fasta files showing unique sequences.

organism: Caenorhabditis elegans

source_name: C.elegans whole animal, mixed stage

growth_protocol: C. elegans were grown under standard conditions at 20C The food source used was E. coli strain HB101 (Caenorhabditis Genetics Center, University of Minnesota, Twin Cities, MN, USA). We used bleaching followed by starvation-induced L1 arrest to generate synchronized cultures. The wild-type strain was Bristol N2.

extract_protocol: cDNA libraries were prepared by Vertis Biotechnologie AG (Martinsried). Briefly total RNA was extracted using the mirVana miRNA isolation kit (Ambion). Small RNAs were size selected to ~18-30 nucleotides by denaturing polyacrylamide gel fractionation. cDNA libraries that did not depend on 5'-monophosphates were constructed by tobacco acid pyrophosphatase treatment using adapters recommended for Illumina sequencing as described previously (Das et al. 2008). Each sample was labelled with a unique four base pair barcode. cDNA was purified using the NucleoSpin Extract II kit (Macherey & Nagel).

treatment_protocol: Virus was added to plates 24 hrs after seeding L4s on the plates and RNA was collected 4 days later.

tag: infection status


title: rde1_inf

description: smallRNA-seq

value: Orsay virus infection


title: N2_non_inf_1

description: smallRNA-seq

value: N2 Bristol


title: N2_non_inf_2

description: smallRNA-seq


title: H3K4me3-NativeChip

city: Sydney

first: Tim

middle: R.

last: Mercer

state: New South Wales

address: 384 Victoria Street Darlinghurst NSW 2010

country: Australia

institute: Garvan

description: Native ChIP-Seq

data_processing:
Base calling was performed using Illumina software pipeline (Genome Analyzer)
ChIP-seq reads were uniquely aligned to the hg19 genome with no mismatch using Bowtie2 (Langmead et al., 2012)
Alignment files (.bam) were converted to raw tag density file (.wig) using BedTools (Quinlan and Hall, 2010)
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq affinity was directly measured through the raw tag density (.bed files).

growth_protocol: K562 cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell).

extract_protocol:
Cells were rinsed with PBS and treated at 37C with MNase for 5 min, before quenching with MNase stop buffer and the chromatin was sheared to 200-500 bp fragments using a Fisher Dismembrator. Chromatin fragments were immunoprecipitated with specific antibodies at 4 °C with gentle rotation. Antibody-chromatin complexes were washed and eluted and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. A quantity of 20-50 ng of ChIP DNA was end-repaired, followed by the addition of adenine, ligation to Illumina adapters, and creation of a Solexa library for sequencing.
20-50 ng of ChIP DNA was processed for library generation using the ChIP-seq Sample Preparation Kit (Illumina) following the manufacturer’s protocol.

tag: chip-antibody

value: H3K4me3 - Millipore (07-449)


title: H3K27me3-NativeChip

description: Native ChIP-Seq

value: H3K27me3 - Cell Signaling (9751B)


title: mESC_Scr_Gapmer_2

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

description: RNA-Seq of polyA-selected RNA from mouse embryonic stem cells transfected with an RNA/DNA Gapmer with a scrambled sequence replicate 2

data_processing:
Basecalls were performed using CASAVA 1.8
Reads were aligned using Tophat2 with default options
Expression quantification and differential analysis was done using Cuffdiff2 using UCSC reference transcriptome .gtf files (mouse or human) and Tophat2 aligned reads as input and default options.
Cuffdiff output files were processed using cummeRbund for indexing, exploration, and visualization of results.
Genome_build: mm9

molecule: polyA RNA

source_name: Mouse Embryonic Stem Cells

growth_protocol: HeLa cells were grown in DMEM + 10% FBS + 1% Pen-strep + 1% L-glutamine at 37ºC at 5% CO2; Mouse ES cells were grown in previously gelatinized (0.2%) dishes with media containing 125 mL DMEM/F12 (Invitrogen), 83.5 μL BSA fraction V (50 μg/ml relative to DMEM) (Invitrogen, 15260-037, 75mg/ml), 125 mL Neurobasal medium (Invitrogen, 21103-049), 625 μL of the Ndiff Neuro2 (200X, relative to Neurobasal medium) (Millipore, SCM012), 2.5 mL B27 minus vitamin A (50X, relative to Neurobasal medium) (Invitrogen, 12587-010), 2 μL beta-mercaptoethanol (for 250 mL medium), 1 μM PD0325901 (Stemgent, 04-0006), 3 μM CHIR99021 (Stemgent 04-0004), 25 μL LIF ESGRO (stock is 107 units LIF/mL from Chemicon, ESG1106), 1% pen-strep (Invitrogen, 15140-163), 1% Non-Essential Amino Acids (Invitrogen, 11140-076), 1% L-glutamine (Invitrogen, 25030-164). The plating density of mES cells was chosen to be 30,000-50,000/cm2.

extract_protocol:
1ml of Trizol and 200μl of chloroform were added and the mix was centrifuged at 4°C at 13,000 rpm for 15 minutes. The aqueous layer was cleaned and DNase treated on RNeasy Mini columns.
Illumina TruSeq RNA

treatment_protocol: siRNAs were transfected using Lipofectamine RNAiMax (5 μl/well) at a final oligo concentration of 75nM; Gapmer oligos were designed with 2-O methyoxyethyl and transfected with Lipofectamine 2000 at a final concentration of 75nM.

tag: knockdown chemistry

value: Gapmer

tag: knockdown target

value: Scramble

value: Embryonic Stem Cells


title: mESC_R2D2_Gapmer_1

description: RNA-Seq of polyA-selected RNA from mouse embryonic stem cells transfected with an RNA/DNA Gapmer targeting the R2D2 repeat region of linc-FIRRE replicate 1

value: R2D2 repeat element of linc-FIRRE

tag: cell type


title: mESC_Scr_Gapmer_3

description: RNA-Seq of polyA-selected RNA from mouse embryonic stem cells transfected with an RNA/DNA Gapmer with a scrambled sequence replicate 3


title: mESC_R2D2_Gapmer_3

description: RNA-Seq of polyA-selected RNA from mouse embryonic stem cells transfected with an RNA/DNA Gapmer targeting the R2D2 repeat region of linc-FIRRE replicate 3


title: N2_inf

description: smallRNA-seq


title: Input-NativeChip

description: Native ChIP-Seq


title: mESC_Scr_Gapmer_1

description: RNA-Seq of polyA-selected RNA from mouse embryonic stem cells transfected with an RNA/DNA Gapmer with a scrambled sequence replicate 1


title: N2

description: smallRNA-seq

treatment_protocol: Synchronized worms were collected as young adults by washes in M9 and worm pellets were snap-frozen in liquid Nitrogen.

value: Bristol N2

value: whole animal

tag: developmental stage

value: young adult


title: PRG-1 F4

description: smallRNA-seq

source_name: PRG-1 F4


title: mESC_R2D2_Gapmer_2

description: RNA-Seq of polyA-selected RNA from mouse embryonic stem cells transfected with an RNA/DNA Gapmer targeting the R2D2 repeat region of linc-FIRRE replicate 2


title: PRG-1 F12

description: smallRNA-seq

source_name: PRG-1 F12


title: RSD-6 F8

source_name: C.elegans whole animal, young adult

tag: strain/line

tag: generation


title: N2 F2

value: wild type


title: N2 F0


title: PRG-1 F8

description: smallRNA-seq

source_name: PRG-1 F8

tag: strain


title: RSD-6 F2


title: RSD-2 F10


title: RSD-2 F2


title: rde1_non_inf_2

description: smallRNA-seq


title: RSD-2 F0


title: RSD-6 F0


title: body_w_ip_rep2

city: Illkirch

first: Anais

middle: Flore

last: Bardet

address: 1 rue Laurent Fries

institute: IGBMC

description: Adult flies collected at ZT13

data_processing:
Base-calling was performed using RTA version 1.8.70.0
We mapped the reads to the Drosophila melanogaster genome reference dm3 (not chrU, chrUextra) obtained from UCSC using bowtie version 0.12.7, allowing only for uniquely mapping reads with up to 3 mismatches (parameters -m 1 -v 3 --best --strata).
We identified peak regions in ChIP samples compared to the corresponding input samples using peakzilla (http://www.starklab.org/data/peakzilla/). Confident peaks are selected with a score ≥ 10 and a fold enrichment of ChIP over input ≥ 2 and enriched regions with a score ≥ 2 and a fold enrichment of ChIP over input ≥ 2.
Genome_build: dm3
Supplementary_files_format_and_content: The peak files contain all enriched regions and are tab-delimited (1: chromosome, 2: start, 3: end, 4: summit, 5: score (IP-Input)*distribution score from peakzilla, 6: fold enrichment IP/Input; score and fold enrichment are normalized to 1 million reads per library)

organism: Drosophila melanogaster

growth_protocol: Drosophila flies were raised on standard food at 25 °C and under 12 hour light: 12 hour dark (LD) cycles.

extract_protocol: Briefly, 5- to 10-days-old flies were collected 1h after lights-off (ZT13), frozen in liquid nitrogen, sieved to separate heads from bodies and kept in -80C until processed. 2 ml of fly heads or bodies were grinded in liquid nitrogen with a mortar pestle to a fine powder. Tissue powder was collected in a chilled 15 ml glass Dounce homogenizer (Wheaton) and immediately homogenized 30 times with a loose pestle in 50ml of NE Buffer (15mM HEPES pH 7.6, 10mM KCl, 0.1mM EDTA, 0.5mM EGTA, 350 mM sucrose, 0.1% Tween, 5mM MgCl2, 1mM DTT, 1mM PMSF plus Protease inhibitor cocktail (Roche)) with 1% formaldehyde (Sigma). Homogenization and fixation were done simultaneously to have a more precise snapshot of CLK and CYC binding. After the 30 strokes with the loose pestle, the fixing homogenate was poured to a 50ml Falcon tube and rotated for a total time of 10 min (starting from the addition of the NE Buffer). Fixation was quenched for 5 min at RT  by the addition of 2.5 ml glycine (2.5M). Homogenate was filtered through a 60 um Streriflip filter (Millipore) and the nuclei were collected by centrifugation at 800g/5 min/40C. Nuclei pellet was washed twice in 10 ml cold NE Buffer (without formaldehyde) and twice more with cold RIPA Buffer (25 mM Tris-HCl 7.6, 150 mM NaCl, 0.5% sodium deoxycholate, 0.1% SDS, 1% NP-40, 0.5mM DTT plus Protease inhibitor cocktail (Roche)). Nuclei were ressuspended in 2 ml cold RIPA Buffer and transferred to a 15ml falcon tube for sonication. Nuclei were sonicated on ice using an Omni Sonic Ruptor 250 Watts sonicator six times (heads) or four times (bodies) for 1min (Duty cycle: 30%, Output: 20%) each time, with 2 min intervals between the sonication steps. Sonicated chromatin was transferred to 1.5 ml eppendorfs and centrifuged at 10000g/10 min/40C. 15 ul of the supernatant were removed for the input sample while 1.5 ml of the supernatant were immediately incubated with 50 ul of blocked V5-agarose beads (Sigma) overnight at 4°C in a rotating wheel. After overnight incubation, beads were washed once with 1.4 ml Low Salt Buffer (20 mM Tris 8.1, 150 mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100), twice with 1.4 ml High Salt Buffer (20 mM Tris 8.1, 500 mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100), twice with 1.4 ml LiCl Buffer (10 mM Tris 8.1, 250 mM LiCl, 1mM EDTA, 1% sodium deoxycholate, 1% NP-40) and twice with 1.4 ml TE. Co-immunoprecipitated DNA fragments were eluted from the beads in 50 ul of V5 Elution Buffer (10mM HEPES, 1.5mM MgCl2, 0.25mM EDTA, 20% glycerol, 250mM KCl, 0.3% NP-40, 0.5mg/ml V5 peptide) three times consecutively, 30 min each, and the three elutes were combined (150 ul). The volumes of the V5 eluted chromatin and input were brought up to 500ul with IP Elution Buffer (10 mM Tris 7.5, 1 mM EDTA, 1% SDS, 100 mM NaHCO3, 200 mM NaCl) plus 15 ul of 10mg/ml RNase A, and incubated for 30 min 370C. RNA-digested chromatin was incubated overnight at 65C with Proteinase K, and in the following day the DNA was purified using standard Phenol:Chloroform extraction. Preparations of DNA libraries for single-end sequencing were done according to the illumina instructions with 36 cycles of extension. Up to 5ng ChIP or input DNA was used in each preparation.

value: w-

value: V5 (Sigma)


title: body_w_input_rep2

description: Adult flies collected at ZT13


title: N2 F8


title: body_cyc_ip_rep2

description: Adult flies collected at ZT13

value: cyc


title: body_w_input_rep1

description: Adult flies collected at ZT13


title: body_clk_input_rep1

description: Adult flies collected at ZT13

value: Clk


title: head_w_input_rep2

description: Adult flies collected at ZT13


title: body_clk_input_rep2

description: Adult flies collected at ZT13


title: body_clk_ip_rep2

description: Adult flies collected at ZT13


title: body_cyc_ip_rep1

description: Adult flies collected at ZT13


title: body_cyc_input_rep1

description: Adult flies collected at ZT13


title: head_w_ip_rep2

description: Adult flies collected at ZT13


title: body_clk_ip_rep1

description: Adult flies collected at ZT13


title: head_w_ip_rep1

description: Adult flies collected at ZT13


title: head_cyc_input_rep2

description: Adult flies collected at ZT13


title: head_cyc_ip_rep2

description: Adult flies collected at ZT13


title: head_clk_input_rep2

description: Adult flies collected at ZT13


title: head_clk_ip_rep2

description: Adult flies collected at ZT13


title: head_cyc_ip_rep1

description: Adult flies collected at ZT13


title: head_cyc_input_rep1

description: Adult flies collected at ZT13


title: head_clk_input_rep1

description: Adult flies collected at ZT13


title: head_clk_ip_rep1

description: Adult flies collected at ZT13


title: body_cyc_input_rep2

description: Adult flies collected at ZT13


title: body_w_ip_rep1

description: Adult flies collected at ZT13


title: Nutlin.2h.rp

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description: ribosome-protected fragments

data_processing:
Reads were aligned to a reference set of human transcripts using Bowtie
Number of reads mapping to each transcript was counted and normalized to FPKMs
Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads

source_name: Immortalized primary fibroblasts

growth_protocol: Immortalized human BJ primary fibroblast cells (by hTERT expression) were cultured in DMEM supplemented with 10% heat-inactivated fetal calf serum (FCS) in 5% CO2 at 37 °C.

extract_protocol:
Cells were treated with cycloheximide (100 μg/ml) for 8-10 minutes, washed with ice-cold PBS (cycloheximide, 100 μg/ml), pelleted, and lysed in buffer A (20 mM Tris-HCl, pH7.8, 100mM KCl, 10mM MgCl2, 1% Triton X-100, 2mM DTT, 100 μg/ml cycloheximide, 1x complete protease inhibitor). Lysates were centrifuged at 5000 rpm and the supernatant was treated with 2U/μl of RNase I (Ambion) for 40 minutes at room temperature. Lysates were fractionated on a linear sucrose gradient (7%-47%) using the SW-41Ti rotor at 36,000 rpm for 2hrs. Fractions enriched in monosomes were polled and treated wih proteinase K (Roche) in 1%SDS. Released RNA fragments were purified using trizol and precipitated in the presence of glycogen.
RNA from the pooled monosomes was gel-purified on a denaturing 10% polyacrylamide urea (7M) gel. A section corresponding to 30-33 nucleotides, the region where most of the ribosome-protected fragments are comprised, was excised, eluted, and ethanol precipitated. The resulting fragments were 3′-dephosphorylated using T4 PNK (NEB) for 6 h at 37 °C in MES buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3′ adaptor was added with T4 RNA ligase 1 (NEB) for 2.5h at 37°C. Ligation products were 5′-phosphorylated with T4 PNK for 30 min at 37°C. 5′ adaptor was added with T4 RNA ligase 1 for 18h at 22°C.

tag: cell line

value: BJ cells

tag: condition

value: Nutlin-3a, 2h


title: Nutlin.4h.rp

description: ribosome-protected fragments

value: Nutlin-3a, 4h


title: Nutlin.6h.rp

description: ribosome-protected fragments

value: Nutlin-3a, 6h


title: C.rp

description: ribosome-protected fragments

value: Control sample


title: Nutlin.19h.rna

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen), following the  manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen)
Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the  manufacturer's instructions.

value: Nutlin-3a, 19h


title: head_w_input_rep1

description: Adult flies collected at ZT13


title: Nutlin.4h.rna


title: HeLa_hnRNPU_siRNA_2

description: RNA-Seq of polyA-selected RNA from HeLa cells transfected with a siRNA targeting the hnRNPU RNA replicate 2

data_processing:
Basecalls were performed using CASAVA 1.8
Reads were aligned using Tophat2 with default options
Expression quantification and differential analysis was done using Cuffdiff2 using UCSC reference transcriptome .gtf files (mouse or human) and Tophat2 aligned reads as input and default options.
Cuffdiff output files were processed using cummeRbund for indexing, exploration, and visualization of results.
Genome_build: hg19

source_name: HeLa Cells

value: siRNA

value: hnRNPU

value: HeLa


title: Nutlin.2h.rna


title: Nutlin.6h.rna


title: HeLa_hnRNPU_siRNA_1

description: RNA-Seq of polyA-selected RNA from HeLa cells transfected with a siRNA targeting the hnRNPU RNA replicate 1


title: HeLa_Scramble_siRNA_1

description: RNA-Seq of polyA-selected RNA from HeLa cells transfected with a scrambled siRNA control replicate 1

value: Scramble


title: HeLa_Scramble_siRNA_2

description: RNA-Seq of polyA-selected RNA from HeLa cells transfected with a scrambled siRNA control replicate 2


title: HeLa_FIRRE_Gapmer_4

description: RNA-Seq of polyA-selected RNA from HeLa cells transfected with an RNA/DNA Gapmer targeting the linc-FIRRE RNA sequence replicate 4

value: Gapmer

value: linc-FIRRE


title: Nutlin.19h.rp

description: ribosome-protected fragments


title: HeLa_Control_Gapmer_2

description: RNA-Seq of polyA-selected RNA from HeLa cells transfected with an RNA/DNA Gapmer with a scrambled sequence replicate 2


title: C.rna


title: HeLa_FIRRE_Gapmer_3

description: RNA-Seq of polyA-selected RNA from HeLa cells transfected with an RNA/DNA Gapmer targeting the linc-FIRRE RNA sequence replicate 3


title: HeLa_Control_Gapmer_1

description: RNA-Seq of polyA-selected RNA from HeLa cells transfected with an RNA/DNA Gapmer with a scrambled sequence replicate 1


title: C2C12-diff-60h-MyoD-10480

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

institute: STANFORD UNIVERSITY

data_processing:
base calling:Casava1.4
read alignment: Bowtie 0.12.7
bedgraph track generation: custom-written python script
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph of read coverage, normalized to RPM (Read Per Million)

growth_protocol: C2C12 cells were differentiated in DMEM media upon serum withdrawal (2% Equine Serum and 0.1% insulin)

extract_protocol:
Cells were fixed in 1% forlamdehyde for 15 minutes except for the EGS input which was generated from cells fixed with 1%FA for 10 minutes followed by additional 15 minutes in the presence of 1.5 mM EGS. Cell lysis was performed using standard chromatin immunoprecipitation protocols, and sheared by sonication.
Libraries were generated following Illumina's DNA Sample Prep Kit protocol

tag: ChIP

value: MyoD

value: Santa Cruz; sc-32758


title: C2C12-diff-60h-1pFA-Input-11610


title: C2C12-diff-60h-myogenin-12152

value: myogenin

value: Santa Cruz; sc-12732


title: C2C12-diff-60h-1pFA+EGS-Input-60h-11132


title: C2C12-diff-60h-myogenin-10598


title: HeLa_FIRRE_Gapmer_1

description: RNA-Seq of polyA-selected RNA from HeLa cells transfected with an RNA/DNA Gapmer targeting the linc-FIRRE RNA sequence replicate 1


title: drh-2

data_processing:
Adaptors were removed with Cutadapt ver 1.0
Fastq files were converted to fasta files using a custom perl script run in Perl version 5.8.12
Fasta files were collapsed using FastX toolkit
Collapsed fasta files were trimmed so that only reads with length of 15 nucleotides or above were included, using a custom perl script run in Perl version 5.8.12
Supplementary_files_format_and_content: collapsed fasta files with adaptors removed with the header sequence number-read count_sequence

source_name: C.elegans whole animal, Orsay virus infected, mixed stage

growth_protocol: C. elegans were grown under standard conditions at 20C The food source used was E. coli strain HB101 (Caenorhabditis Genetics Center, University of Minnesota, Twin Cities, MN, USA). Uninfected animals were picked as L4s and virus laid onto the plates after 24hrs.

extract_protocol: cDNA libraries were prepared from total RNA using the Illumina Truseq protocol according to the manufacturer's instructions.

treatment_protocol: RNA was extracted from worms 4 days after infection with the Orsay virus using Trizol.

tag: 5' end dependence

value: 5' Independent (RNA treated with 5' RNA polyphosphatase (Epicentre) for 30 minutes at 37C)

tag: genotype

value: drh-2 ok951

tag: tissue

value: whole animal


title: drh-3_5D

value: 5' Dependent

value: drh-3 ne301


title: drh-1_drh-3_5D


title: rde-1_5D

value: rde-1 ne219


title: drh-1_5D


title: JU1580_5D


title: N2_5D

value: N2 (Bristol)


title: drh-1_rde-4


title: rde-4

value: rde-4 ne301


title: HeLa_FIRRE_Gapmer_2

description: RNA-Seq of polyA-selected RNA from HeLa cells transfected with an RNA/DNA Gapmer targeting the linc-FIRRE RNA sequence replicate 2


title: drh-3


title: drh-1_drh-3


title: JU1580_Rescue

value: JU1580 with DRH-1 from N2


title: drh-1_1


title: drh-1_2


title: drh-1_rde-1


title: rrf-1


title: drh-1_3


title: rde-1_2


title: C2C12-diff-60h-myogenin-10158


title: MAGO_12


title: JU1580


title: N2_3


title: N2_1


title: T_cell_Day4_Up_IgH

description: 4C PCR product

tag: age

value: 6-8 wks

value: spleen

value: in vitro activated, Splenic T cells

tag: sequencing

value: Single-end


title: T_cell_Day0_Up_IgH

description: 4C PCR product

value: resting splenic T cells


title: B_cell_IgMb_Day4_Up_IgH

description: 4C PCR product

value: in vitro activated, Splenic B cells


title: B_cell_IgMa_Day0_Up_IgH

description: 4C PCR product

value: resting splenic B cells


title: B_cell_IgMb_Day0_Up_IgH

description: 4C PCR product


title: H3K27me3_Phc2_mutant_ChIPSeq

city: Yokohama

first: Takaho

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7 with default parameters.
Tag concentration in blocks and around TSS (-4kb to +2kb) were counted using in-house C++ programs.
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle-formatted files are prepared using in-house C++ program.

source_name: embryonic fibroblasts

growth_protocol: MEFs were cultured in Dulbecco’s minimal essential medium containing 10% fetal calf serum and 1% (w/v) penicillin/streptomycin on gelatin-coated dishes at 37˚C and 5% CO2.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: embryonic day 12.5

tag: antibody

tag: vendor

value: Upstate/Millipore

tag: lot#


title: B_cell_IgMa_Day4_Up_IgH

description: 4C PCR product


title: H3K27me3_WT_ChIPSeq

tag: passage no.

value: wild type


title: FACS-sorted eGFP+ CPCs input

first: Serge

last: Gregoire

address: 185 Cambridge ST

institute: Massachusetts General Hospital

data_processing:
Counts: Sequence reads were obtained and mapped to the mouse mm9 genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.

Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).

source_name: Cardiac progenitor cells, input

growth_protocol: Embryonic stem (ES) cells were cultured on a monolayer of mitomycin-inactivated mouse embryonic fibroblasts and maintained in media containing DMEM with high glucose, 15% FCS, 5000 i.u./mL penicillin/streptomycin, 2 mM L-glutamine, 0.1 mM non-essential amino acid solution, 0.1 mM beta-mercaptoethanol, and 103u/mL leukemia inhibitory factor.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with the YY1 antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation, DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of ~250-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Mouse ES cells harboring the transgene Nkx2.5 driving the GFP reporter were in vitro differentiated using the embryoid body (EB) method for 6 days. Then, the eGFP+ CPCs were FACS purified.

tag: cell type

value: ES-derived cardiac progenitor cells (CPCs)

tag: differentiation time

value: day 6 of EB differentiation

tag: chip antibody


title: FACS-sorted eGFP+ CPCs, rep1

data_processing:
Counts: Sequence reads were obtained and mapped to the mouse mm9 genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.

Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).

Genome Build:
egfp_positive_cells_sample1_aligned.bed: mm9
egfp_positive_cells_sample_1_peaks.bigwig: mm9

source_name: Cardiac progenitor cells, YYI ChIP

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog #

tag: antibody lot


title: FACS-sorted eGFP+ CPCs, rep2

data_processing:
Counts: Sequence reads were obtained and mapped to the mouse mm9 genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.

Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).

Genome Build:
egfp_positive_cells_sample2_aligned.bed: mm9
egfp_positive_cells_sample_2_peaks.bigwig: mm9

tag: strain


title: GEA-7

city: Hamilton

first: Turlough

middle: M

last: Finan

address: 1280 Main Street West

department: Biology

institute: McMaster University

data_processing:
Two independent cDNA runs from each of the two RNA samples (P0 and P2) were pooled to give RNA sequence reads that were aligned by matching the 34 nucleotide sequence of the read to the S. meliloti genome.
34 nucleotide reads were aligned against a file of all 34-mers (+ and - strands) from the S. meliloti genome using a hash table and a program writted in C.
The DNA sequences for the 34-mer table were taken from NCBI genbank files: AL591985, AL591688, AE006469
The first pass found perfect matches (PM), a second found single mismatched reads (MM1) and a third pass matched the remaing reads to the S. meliloti genome by Blast (BM). The file SmP_summary contains summary information about the reads matched and unmatched.
Read counts were multiplicity corrected by dividing by the number of times the 34-mer appeared in the S. meliloti genome.
Pooled PM read counts for P0 and P2 were normalized: P0 (multiplied by 1.026) and P2 (1.057) so that the total number of normalized, perfectly matched read counts for each experiment would be 10,000,000.
Supplementary_files_format_and_content: Three files (chromosome, pSymA, pSymB) contained the multiplicity corrected, normalized nymber of directionally matched PM reads by genome position (see processed_data_readme.txt).

organism: Sinorhizobium meliloti

source_name: Cell culture

growth_protocol: S. meliloti RmP110 strain cultures were grown in LB medium containing 2.5mM MgSO4 and 2.5mM CaCl2 (LBmc). Subcultured in phosphate-free MOPS-buffered minimal medium (MOPS-P0 (17)), contained 40 mM MOPS pH 7.4 with KOH, 20 mM NH4Cl, 100 mM NaCl, 1.2 mM CaCl2, 2 mM MgSO4, with 0.3 µg ml -1 biotin, 10 ng ml-1 CoCl2, 15 mM glucose as carbon source and trace minerals (22). Phosphate rich medium, MOPS-P2 was MOPS-P0 with K2HPO4 at a final concentration of 2 mM.

extract_protocol: A directional mRNA-sequence library was prepared following Illumina's protocol. Briefly, RNA samples were prepared as described above and Zn-treated for fragmentation. Specific primers were added, first to the 3' end and then to the 5’ end of RNA fragments by single-stranded ligation. cDNA was then synthesized using a primer complementing the 3' adapter and the final library was obtained by PCR using two primers that complement the flanking adapter sequences. The library preparation and Illumina sequence reads of 34 nucleotides was performed by FASTERIS SA (Geneva, Switzerland).

treatment_protocol: RNA was prepared from S. meliloti grown in MOPS minimal media containing 20 µM (MOPS-P0) or 2 mM (MOPS-P2) inorganic phosphate respectively.   Total RNA was isolated using the hot-phenol method; DNase I treated and cleaned using Qiagen RNeasy mini columns. rRNA was removed via two purifications using the Ambion MicrobExpress Bacterial mRNA Enrichment kit.

tag: culture conditions

value: P0:MOPS + 20 µM Pi

tag: growth phase

value: Exponential phase


title: HEA-8

value: P2:MOPS + 2 mM Pi


title: GEA-8


title: Condylura_DRG3

status: Public on May 31 2013

city: Berkeley

first: Maurizio

last: Pellegrino

address: 355 LSA

institute: University of California - Berkeley

description:
readcounts_cc.txt
DRG_Cc.txt
DRG_overlap.txt

data_processing:
Alignments were performed with Stampy v1.0.11 (substitution rate = 0.03). For Condylura sequences, the total read count was the sum of all reads aligning to the homologs of that gene in Homo sapiens, Canis familiaris, or Mus musculus (Entrez Gene database, ncbi.nlm.nih.gov, Jan 2011). Homology was based on the HomoloGene database (build 64) and manual annotation. For Mus sequences, only the Mus musculus transcriptome database was used.
Differential expression was assessed using the DESeq package for R, with a padj < 0.05
Genome_build: Homo sapiens transcriptome downloaded Nov 25th 2010 (genome.ucsc.edu). Canis lupus familiaris and Mus musculus transcriptomes downloaded Nov28th 2010, (ncbi.nlm.nih.gov)
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values and variance for each sample based on the analysis performed using DESeq
Supplementary_files_format_and_content: readcounts_cc.txt: Read counts for genes in Condylura cristata trigeminal and dorsal root ganglia
Supplementary_files_format_and_content: readcounts_mm.txt: Read counts for genes in Mus musculus trigeminal and dorsal root ganglia
Supplementary_files_format_and_content: TG_Cc.txt: Genes overexpressed in Condylura cristata trigeminal versus dorsal root ganglia
Supplementary_files_format_and_content: DRG_Cc.txt: Genes overexpressed in Condylura cristata dorsal root versus trigeminal ganglia
Supplementary_files_format_and_content: TG_overlap.txt: Set of genes overxpressed in both mouse and mole trigeminal versus dorsal root ganglia
Supplementary_files_format_and_content: DRG_overlap.txt: Set of genes overxpressed in both mouse and mole dorsal root versus trigeminal ganglia

organism: Condylura cristata

source_name: dorsal root ganglia

extract_protocol:
Tissues were removed and homogenized in Trizol (Invitrogen) as per the manufacturer’s instructions.
Illumina TruSeq RNA Sample Prep Kit was used with about 1 ug of total RNA for the construction of sequencing libraries. After poly-A mRNA selection, the first Condylura trigeminal and dorsal root ganglia samples (Condylura_TG1 and Condylura_DRG1) were retrotranscribed and the Illumina Genomic Sample Prep Kit was used to generate libraries. These were sequenced on a Genome Analyzer II (76 bp). The remaining Condylura and Mus samples were processed using the Illumina TruSeq kit, and libraries were sequenced on a HighSeq 2000 (36 bp or 50bp). WHICH ONES ON WHICH The Condylura samples are single reads, the Mus samples are paired-end.

value: dorsal root ganglia

value: adult

tag: Sex

value: male

value: wild


title: human GBM1 GSCs+BMI1 knockdown+BMP7+Arvanil+doxycycline

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

country: Germany

institute: Max Delbrüch Center

data_processing:
FPKM from tag density files and genomeCoverageBed
Genome_build: Ensembl and RefSeq genes
Supplementary_files_format_and_content: FPKM

extract_protocol: PCR amplification

tag: treatment

value: BMI1 knockdown+BMP7+Arvanil+doxycycline

value: human GBM-derived "stem-like" cells

tag: genotype

value: BMI1 dox-inducible


title: human GBM1 GSCs

source_name: human GBM1 GSCs


title: human GBM1 GSCs+BMI1 knockdown+BMP7+Arvanil+doxycycline rep