title: MDA-MB-231

first: Ferhat

last: Ay

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
Raw reads were checked for 2 to 5 bp expected barcodes (TC or AGT for HMEC, CAGT for MCF7, GTCCT for MDA-MB-231) followed by a 24 bp primer (AGGACTCAGTGGCTCTCACCCTAT) and 6 bp HindIII (AAGCTT) cleavage site.
Qualifying sequences were trimmed for their tags and primers and the remaining portions were mapped to whole human genome (hg19) using BWA v0.5.9 with default parameters allowing an edit distance of at most 3, quality score of at least 30. Sequences that mapped to multiple locations in the genome are discarded.
Successfully mapped reads were assigned to the fragment starting with the nearest HindIII cleavage site. After this assignment, restriction fragments interacting (those flanking the cleavage sites with a read count of at least one) with the bait region were identified. ±50 kb region around the bait was discarded from further analysis.
Interacting fragments were segregated into 4 groups according to their genomic distances to the bait region: (i) Bait region interactions: Intrachromosomal interactions below 50kb distance to the bait and are excluded from our analysis. (ii) Proximal intrachromosomal interactions: Intrachromosomal interactions between 50kb to 2Mb distance from the bait.  (iii) Long-range intrachromosomal interactions: Intrachromosomal interactions above 2Mb distance from the bait.  (iv) Interchromosomal interactions: Interactions that are on chromosomes other than the bait chromosome (chr 7).
Depending on the interaction type multiple consecutive restriction fragments were combined into larger windows that are appropriate for statistical analysis. Window size of 20,  for group (ii); 100 for group (iii); 200 for group (iv) were used. For each group of interactions, the number of interacting fragments within a window were counted. Then, a background distribution was generated for each group and z-values were assigned as described in  Splinter et al. Windows that significantly interact with the 4C bait were determined at a false discovery rate (FDR) of 0.01 for each cell line.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files contain the interactions at the resolution of specified window sizes for each of the three cell lines. The header line describes the columns as follows: (GenomicWindow) Genomic coordinates of the start sites for the first and last fragments within the listed genomic window. (X-count) Number of times the bait region interacts with the genomic window for cell line X. (X-count) Z-score of the interaction for the genomic window for cell line X.

source_name: mammary gland/breast; derived from metastatic site: pleural effusion

extract_protocol:
4C was performed as in Gheldof et al. with minor modifications. HMEC, MCF7 and MDA-MB-231 cells (2 x 107) were fixed in 2% formaldehyde in fresh medium for 10 min at room temperature, followed by quenching with 0.125 M glycine. Fixed cells were scraped from culture plates, spun, (750 x g for 10 min), and the frozen pellets were stored at -80°C until lysis. Cells were resuspended in ice-cold lysis buffer (0.2% IGEPAL CA-630, 10 mM NaCl, 10 mM Tris HCl) with SigmaFast complete protease inhibitor tablet (Sigma-Aldrich, St. Louis, MO) and lysed for 30 min on ice. After recovery of nuclei by centrifugation (2000 x g for 5 minutes), nuclei were washed twice in cold 1.2X NEB buffer 2 and resuspended in the same buffer. Nuclei were incubated in the presence of 0.3% SDS for 1h at 37°C with shaking at 950 rpm, followed by the addition of Triton X-100 to 1.8% for 1h at 37°C with shaking at 950 rpm. Nuclei were digested with 1500 U of HindIII (New England Biolabs Ipswich, MA) overnight at 37°C with shaking at 950 rpm. 200 μl of digested nuclei were removed for assessing digestion efficiency by qPCR. The restriction enzyme was inactivated by the addition of 1.6% SDS and was incubated at 65°C for 20 min. The digested nuclei were diluted in 7ml of 1.1X T4 DNA ligase buffer in the presence of 1% Triton X-100 and incubated for 1h at 37°C. Ligation was performed by adding 800 U of T4 DNA Ligase (2,000,000 U/ml; New England Biolabs) to the diluted mixture of digested nuclei and incubating in a 16°C H2O bath for 4 hours followed by a 30 min incubation at room temperature. To reverse cross-links, proteinase K was added to a final concentration of 100 μg/ml and incubated overnight at 65°C. Samples were incubated with 0.5 μg/ml of RNase A at 37°C for 1h and purified by phenol-chloroform extraction followed by ethanol precipitation. DNA concentration was measured using a Qubit® 2.0 Fluorometer (Life Technologies).
A total of 16 inverse PCR reactions with 200 ng input per 4C template were performed for each library with primers that included Illumina adapter sequences and custom barcodes. All PCR reactions were performed with Expand Long Template PCR system (Roche, Indianapolis, IN). Excess primers were removed by gel extraction. HMEC, MCF7 and MDA-MB-231 4C libraries were analyzed on a MultiNA microchip electrophoresis system (Shimadzu Columbia, MD) and mixed in equimolar amounts. Multiplex sequencing was performed on an Illumina genome analyzer IIx (Illumina, San Diego, CA) using variable length barcodes (TC and AGT for HMEC, CAGT for MCF7, GTCCT for MDA-MB-231).

value: Epithelial Cells (Mammary)

tag: type

value: tumor

tag: tumor subtype

value: Triple Negative


title: HSF2_non-treated mitotic K562

status: Public on Aug 04 2013

type: SRA

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH Royal Institute of Technology

library_source: genomic

data_processing:
36nt of each fragment was sequenced with Illumina GAIIx
The sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, and  mapped to human genome (hg19) with Bowtie program
The peaks were called with MACS 1.4 program
Genome_build: hg19
Supplementary_files_format_and_content: fastq files contain the raw reads with quality scores
Supplementary_files_format_and_content: peak files contain coordinates of binding sites and the fold enrichment of each site as analyzed against input
Supplementary_files_format_and_content: wig files contain the sequenced reads in format compatible with genome viewers

molecule: genomic DNA

organism: Homo sapiens

source_name: K562 cells

growth_protocol: Human K562 erythroleukemia cells were maintained at 37°C in a humidified 5% CO2 atmosphere and cultured in RPMI medium (Sigma) containing 10% fetal calf serum, 2 mM L glutamate and streptomycin/penicillin.

extract_protocol:
The cells were cross-linked with a final concentration of 1% formaldehyde followed by quenching with a final concentration of 125 mm glycine. Chromatin was fragmented by sonication (Bioruptor, Diagenode) to 100 - 500 bp. Immunoprecipitation was performed after preclearing with 50% slurry of protein G-coated Sepharose beads containing bovine serum albumin (100 μg/ml, Amersham Biosciences) at 4 °C overnight. Washing of immunocomplexes was performed three times in wash buffer 1 (0.1% SDS, 1% Triton X-100, 2 mm EDTA, pH 8.0, 150 mm NaCl, 20 mm Tris-HCl, pH 8.0), twice in wash buffer 2 (0.1% SDS, 1% Triton X-100, 2 mm EDTA, pH 8.0, 500 mm NaCl, 20 mm Tris-HCl, pH 8.0), and three times in wash buffer 3 (20 mm Tris-HCl, pH 8.0, 1 mm EDTA, pH 8.0, 10% glycerol). Cross-links were reversed by incubating the samples overnight at 65 °C. DNA was purified with phenol:chloroform, and EtOH precipitated. Ten PCR-verified ChIP-replicates per each sample were pooled and purified with Qiaquick columns.
Sequencing libraries were generated using New England BioLabs NEBNext sample preparation kits according to the manufacturer´s protocols. Used adapters, PCR and Index primers were from Bioo Scientific AIR DNA Barcodes kit. Template amplification and cluster generation were performed using cBot and Truseq SR Cluster kit for cBot v.

tag: cell line

value: K562 cells

tag: cell cycle phase

value: arrested to mitosis

tag: treatment

value: no treatment

tag: chip antibody


title: MCF7

status: Public on Aug 03 2013

city: La Jolla

state: CA

country: USA

tag: tissue

value: ER positive


title: HSF1_non-treated mitotic K562


title: HMEC

source_name: mammary gland/breast

value: normal breast


title: heat shock_maltose minimal media

status: Public on Aug 02 2013

first: Haythem

last: Latif

state: California

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive

institute: University of California San Diego

library_source: transcriptomic

data_processing:
Illumina reads were aligned to the T. maritima genome using Bowtie with up to 2 mismatches per read alignment.
Genome_build: CP004077; pending release of the manuscript
Supplementary_files_format_and_content: FPKM values were calculated using Cufflinks v2.0.2. Functional RNA transcripts were excluded from the FPKM calculations.

molecule: total RNA

organism: Thermotoga maritima MSB8

source_name: T. maritima_WT_heat shock

growth_protocol:
T. maritima MSB8 (ATCC: 43589) was grown in an 500 mL serum bottles containing 200 mL of anoxic minimal media [Rinker and Kelly, 1996, Appl Environ Microbiol, 62, 4478-85] with 10 mM maltose as the sole carbon source at 80C.
Heat shock was performed on midlog cultures for a duration of 10 min at 90°C. Temperature shift from 80 °C to 90 °C was achieved in less than 1 min.

extract_protocol: Total RNA was isolated using the TRIzol (Invitrogen) extraction procedure followed by DNase treatment and purification using Fisher SurePrep TrueTotal RNA columns. Paired-end, strand-specific RNAseq was performed using the dUTP method [Levin JZ et al. 2010, Nat Methods 7,709] with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming.

tag: atcc number

tag: genotype/variation

value: Wild type

tag: growth condition

value: heat shock

tag: growth medium

value: maltose minimal media

tag: strain


title: late exponential (carbon limiting)_maltose minimal media

source_name: T. maritima_WT_late exponential phase

growth_protocol: T. maritima MSB8 (ATCC: 43589) was grown in an 1 L bioreactors with pH control set to 6.5 +/- .1 and with continuous removal of evolved hydrogen using 80% Nitrogen and 20% Carbon Dioxide. Cells were cultivated in anoxic minimal media [Rinker and Kelly, 1996, Appl Environ Microbiol, 62, 4478-85] with 5 mM maltose as the sole carbon source at 80C. RNA samples were collected upon the complete utilization of maltose.

value: late exponential


title: hydrogen inhibited_maltose minimal media

source_name: T. maritima_WT_hydrogen inhibited

growth_protocol:
T. maritima MSB8 (ATCC: 43589) was grown in an 500 mL serum bottles containing 200 mL of anoxic minimal media [Rinker and Kelly, 1996, Appl Environ Microbiol, 62, 4478-85] with 10 mM maltose as the sole carbon source at 80C.
Cultures were grown in closed, anaerobic bottles with excess carbon source (maltose). Fermentation of the carbon source results in production of molecular hydrogen which, at increased levels, is inhibitory to growth. Hydrogen inhibition was achieved by allowing for accumulation of molecular hydrogen generated during growth and is marked by a plateau in optical density reads. Samples were harvested during entry into hydrogen inhibition.

value: hydrogen inhibited


title: logphase_maltose minimal media

source_name: T. maritima_WT_log phase

growth_protocol: T. maritima MSB8 (ATCC: 43589) was grown in an 500 mL serum bottles containing 200 mL of anoxic minimal media [Rinker and Kelly, 1996, Appl Environ Microbiol, 62, 4478-85] with 10 mM maltose as the sole carbon source at 80C.

value: log phase


title: Long days LL, ZT14, rep 1

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir. IIBBA- CONICET

data_processing:
RNA-seq reads were estimated using Firecrest and Bustard modules from Illumina Pipeline
R package easyRNAseq was used to generate read count tables at the gene level
genome build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files including gene read counts

organism: Arabidopsis thaliana

source_name: Long days LL, ZT14, rep 1

growth_protocol: Seeds were sown onto MS and grown at 22ºC in continuous light or long day conditions, depending on the experiment.

extract_protocol:
Total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN) following the manufacturer’s protocols. To estimate the concentration and quality of samples, NanoDrop 2000c (Thermo Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies) with Agilent RNA 6000 NanoKit were employed, respectively.
Libraries were prepared following the TruSeq™ RNA Sample Preparation Guide (Illumina).
3 µg of total RNA were polyA-purified, fragmented and first-strand cDNA synthesized by reverse transcriptase (SuperScript II-Invitrogen) and random hexamers. This was followed by RNA degradation and second strand cDNA synthesis. End repair process and adittion of a single ‘A’ nucleotide to the 3’ ends allowed ligation of multiple indexing adapters. Then, an enrichment step of 12 cycles of PCR was performed. Library validation included quality control and quantification.

treatment_protocol: Plants were either grown under continuous light and havested after 9 days under that condition, or grown under long day cycles (16 h light/ 8 h dark) and harvested every 4 hours starting 2 hours after lights on on the 9th day in that condition.

tag: ecotype

tag: genotype

value: link1link2 double mutants

tag: age

value: Nine-day-old seedlings

tag: time point (hrs)


title: Long days LL, ZT22, rep 3

source_name: Long days LL, ZT 22, rep 3


title: Long days LL, ZT6, rep 3

source_name: Long days LL, ZT6, rep 3


title: Long days LL, ZT18, rep 3

source_name: Long days LL, ZT 18, rep 3


title: logphase_maltose minimal media_replicate 2

data_processing:
Illumina reads were aligned to the T. maritima genome using the Mosaik Aligner (http://bioinformatics.bc.edu/marthlab/Mosaik), hash size = 15, mismatch=0.
Genome_build: Pending
Supplementary_files_format_and_content: The 5' end of unique aligned reads were counted and considered as potential transcription start sites. Only 5' sites with read count >5 considered.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and DNA was removed by DNase digestion. RNA quality and concentration was determined by analysis with a Thermo NanoDrop 1000. RNA with 5’-monophosphate end was removed with 5’-phosphate-dependent exonuclease. The 5’-triphosphate end of primary RNA was then converted to 5’-monophosphate end with RNA 5’ polyphosphatase. 5’ sRNA adapter was ligated to the 5’ end of mRNA. cDNAs were then synthesized from the adapter-ligated mRNA using 3’-adapter. Fraction of the cDNA between 100 bp and 300 bp was then gel purified and PCR amplified.

tag: growth stage


title: Long days LL, ZT22, rep 1

source_name: Long days LL, ZT 22, rep 1


title: Long days LL, ZT14, rep 2

source_name: Long days LL, ZT14, rep 2


title: Long days LL, ZT2, rep 2

source_name: Long days LL, ZT2 rep 2


title: Long days LL, ZT6, rep 2

source_name: Long days LL, ZT6, rep 2


title: Long days LL, ZT10, rep 1

source_name: Long days LL, ZT10, rep 1


title: Long days LL, ZT2, rep 1

source_name: Long days LL, ZT2, rep 1


title: Long days WT, ZT22, rep 3

source_name: Long days WT, ZT22, rep 3


title: Long days LL, ZT2, rep 3

source_name: Long days LL, ZT2, rep 3


title: Long days LL, ZT22, rep 2

source_name: Long days LL, ZT 22, rep 2


title: Long days WT, ZT22, rep 2

source_name: Long days WT, ZT22, rep 2


title: Long days LL, ZT10, rep 3

source_name: Long days LL, ZT10, rep 3


title: Long days LL, ZT6, rep 1

source_name: Long days LL, ZT6, rep 1


title: Long days WT, ZT18, rep 3

source_name: Long days WT, ZT18, rep 3


title: Long days WT, ZT22, rep 1

source_name: Long days WT, ZT22, rep 1


title: RPLII_ab5408.Clone_8.Solexa ChIP Rep2

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: ChIP DNA; Antibody information listed below: official name: RPLII ab5408;target name: RNA polymerase II CTD repeat YSPTSPS;host: Mouse;clonal: Monoclonal;purified: Affinity;company: Abcam;catalog: ab5408;reference: Larschan E et al. MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism. Mol Cell 28:121-33 (2007). ChIP; Fruit fly (Drosophila melanogaster);   Krejc? & Bray S Notch activation stimulates transient and selective binding of Su(H)/CSL to target enhancers. Genes Dev 21:1322-7 (2007). ChIP; Fruit fly (Drosophila melanogaster). PubMed: 17545467;short description: Mouse monoclonal [4H8] to RNA polymerase II CTD repeat YSPTSPS - ChIP Grade

data_processing: Bowtie alignment protocol. Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes.Reads that passed default parameters of the Illumina quality filter were mapped with Bowtie 0.12.7. The reference sequence used to built an index for mapping was the Flybase reference r5.22. The reference index was created using the bowtie-build function with default parameters. Reads were mapped using  -n 2 -l 28 -e 70 -k 1 -m 10 --best in Bowtie (-n 2, -l 28, -e 70 default). Parameters-n INT number of allowed mismatch-l INT seed length-e INT maximum permitted total of quality values at all mismatched read positions-m INT suppress all alignments for a particular read or pair if more than INT reportable alignments-k INT report up to INT valid alignments--best report alignments in best-to worst orderReads were converted to SAM formant using the bowtie2sam.pl script provided by the DCC. SPP Peak calling protocol. The aligned reads were called using SPP R package (ver.1.10, Kharchenko et al., Nat.Biotech 2008). The binding characteristics and tag shift were estimated using SPP get.binding.characteristics() function. The reads showing abnormality were removed using SPP remove.local.tag.anomalies() function. The regions of enrichment were identified as continuous blocks of positions that exhibit significant enrichment of IP over input reads. The significance of enrichment was assessed within a 1Kb window around each point using a Poisson model. A position was considered significantly enriched if the number of IP read counts was significantly higher (Z-score > 3) than the number of input read counts, after adjusting for the total number of reads sequenced in IP and input measurements. For each replicate set, if replicates were consistent (>80% agreement for top 40% of peaks/enrichment clusters), reads in each replicates were combined and enrichment regions were called as described above.  Processed data are obtained using following parameters: genome version is FlyBase r5

organism: Drosophila melanogaster

source_name: RPLII_ab5408.Clone_8 ChIP expt.2460

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).
Protocol for making libraries for ChIP-seq with Illumina platform, using the TruSeq DNA Sample Prep Kit.http://www.illumina.com/products/truseq_dna_sample_prep_kit.ilmn

value: dorsal mesothoracic disc

tag: developmental stage

value: third instar larval stage

tag: Sex

value: Male


title: Long days LL, ZT18, rep 2

source_name: Long days LL, ZT 18, rep 2


title: Long days LL, ZT14, rep 3

source_name: Long days LL, ZT14, rep 3


title: Long days LL, ZT18, rep 1

source_name: Long days LL, ZT 18, rep 1


title: Long days WT, ZT18, rep 2

source_name: Long days WT, ZT18, rep 2


title: Long days LL, ZT10, rep 2

source_name: Long days LL, ZT10, rep 2


title: logphase_maltose minimal media_replicate 1

source_name: T. maritima_WT_log phase


title: Long days WT, ZT14, rep 3

source_name: Long days WT, ZT14, rep 3


title: Long days WT, ZT18, rep 1

source_name: Long days WT, ZT18, rep 1


title: Long days WT, ZT14, rep 1

source_name: Long days WT, ZT14, rep 1


title: Long days WT, ZT10, rep 3

source_name: Long days WT, ZT10, rep 3


title: Long days WT, ZT14, rep 2

source_name: Long days WT, ZT14, rep 2


title: Long days WT, ZT10, rep 1

source_name: Long days WT, ZT10, rep 1


title: RPLII_ab5408.Clone_8.Solexa ChIP Rep1

source_name: RPLII_ab5408.Clone_8 ChIP expt.2459

tag: cell line


title: Long days WT, ZT6, rep 2

source_name: Long days WT, ZT6, rep 2


title: RPLII_ab5408.Clone_8.Solexa Input Rep2

description: input DNA

source_name: RPLII_ab5408.Clone_8 Input expt.2434


title: Long days WT, ZT6, rep 3

source_name: Long days WT, ZT6, rep 3


title: Long days WT, ZT6, rep 1

source_name: Long days WT, ZT6, rep 1


title: Long days WT, ZT2, rep 3

source_name: Long days WT, ZT2, rep 3


title: RLPII_phospho5_ab5131.Clone_8.Solexa ChIP Rep2

description: ChIP DNA; Antibody information listed below: official name: RLPII phospho5 ab5131;target name: RNA polymerase II CTD repeat YSPTSPS (phospho S5);host: Rabbit;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab5131;reference: Rahl PB et al. c-Myc regulates transcriptional pause release. Cell 141:432-45 (2010). WB ChIP; Mouse. PubMed: 20434984;short description: Rabbit polyclonal to RNA polymerase II CTD repeat YSPTSPS (phospho S5) - ChIP Grade


title: RLPII_phospho5_ab5131.Clone_8.Solexa ChIP Rep1


title: Long days WT, ZT2, rep 2

source_name: Long days WT, ZT2, rep 2


title: Long days WT, ZT2, rep 1

source_name: Long days WT, ZT2, rep 1


title: LL, rep 3

source_name: LL, rep 3


title: LL, rep 2

source_name: LL, rep 2


title: LL, rep 1

source_name: LL, rep 1


title: LL, WT rep 3

source_name: LL, WT rep 3


title: RLPII_phospho5_ab5131.Kc.Solexa ChIP Rep2

source_name: RLPII_phospho5_ab5131.Kc ChIP expt.2466

value: embryo-derived cell-line

value: late embryonic stage

value: se/e

value: Female


title: LL, WT rep 2

source_name: LL, WT rep 2


title: LL, WT rep 1

source_name: LL, WT rep 1


title: RLPII_phospho5_ab5131.Kc.Solexa ChIP Rep1

source_name: RLPII_phospho5_ab5131.Kc ChIP expt.2465


title: RLPII_phospho5_ab5131.Kc.Solexa Input Rep2

description: input DNA


title: RLPII_phospho5_ab5131.Kc.Solexa Input Rep1

description: input DNA


title: RPLII_ab5408.Clone_8.Solexa Input Rep1

description: input DNA

source_name: RPLII_ab5408.Clone_8 Input expt.2433


title: Long days WT, ZT10, rep 2

source_name: Long days WT, ZT10, rep 2


title: RLPII_phospho2_ab5095.Kc.Solexa ChIP Rep2

description: ChIP DNA; Antibody information listed below: official name: RLPII phospho2 ab5095;target name: RNA polymerase II CTD repeat YSPTSPS (phospho S2);host: Rabbit;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab5095;reference: Antibody was used and validated for ChIP-on ChIP by: Muse GW Gilchrist DA Nechaev S Shah R Parker JS Grissom SF Zeitlinger J Adelman K.  Nat Genet. 2007 Dec;39(12):1507-11. Epub 2007 Nov 11.;short description: Rabbit polyclonal to RNA polymerase II CTD repeat YSPTSPS (phospho S2) - ChIP Grade

source_name: RLPII_phospho2_ab5095.Kc ChIP expt.2462


title: RLPII_phospho2_ab5095.Kc.Solexa ChIP Rep1

source_name: RLPII_phospho2_ab5095.Kc ChIP expt.2461


title: RLPII_phospho5_ab5131.Clone_8.Solexa Input Rep2

description: input DNA


title: RLPII_phospho5_ab5131.Clone_8.Solexa Input Rep1

description: input DNA


title: H4K16ac(M).L3.Solexa Input Rep1

description: input DNA

source_name: H4K16ac(M).L3 Input expt.2402

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Growth conditions and collection protocol to harvest third instar larvae from bottles.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).
Protocol for making libraries for ChIP-seq with Illumina platform, using the TruSeq DNA Sample Prep Kit.http://www.illumina.com/products/truseq_dna_sample_prep_kit.ilmn

value: Oregon-R(official name :Oregon-R-modENCODE genotype :wild type )

value: 3rd Instar Larvae

value: wild type


title: RLPII_phospho2_ab5095.Kc.Solexa Input Rep2

description: input DNA


title: RLPII_phospho2_ab5095.Kc.Solexa Input Rep1

description: input DNA


title: Su(var)3-9-Q2598.L3.Solexa ChIP Rep1

description: ChIP DNA; Antibody information listed below: official name: Su(var)3-9-Q2598;target name: Su(var)3-9;host: Rabbit;antigen: AA's 320-419;clonal: Unknown;purified: Affinity;company: SDI;catalog: Q2598;short description: Affinity purified antibodies from 80mL rabbit antisera


title: H4K8ac.L3.Solexa Input Rep1

description: input DNA

source_name: H4K8ac.L3 Input expt.2402


title: H4K8ac.L3.Solexa ChIP Rep2

description: ChIP DNA; Antibody information listed below: official name: H4K8ac;target name: H4K8ac;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H4 acetylated at K8.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab15823;reference: http://www.abcam.com/Histone-H4-acetyl-K8-antibody-ChIP-Grade-ab15823.html;short description: Rabbit polyclonal to Histone H4 (acetyl K8) - ChIP Grade

source_name: H4K8ac.L3 ChIP expt.2517


title: H4K8ac.L3.Solexa ChIP Rep1

source_name: H4K8ac.L3 ChIP expt.2516


title: H4K16ac(M).L3.Solexa ChIP Rep2

description: ChIP DNA; Antibody information listed below: official name: H4K16ac(M);target name: H4K16ac;host: Rabbit;antigen: Recognizes acetyl-histone H4 (Lys16) Mr ~10 kDa;clonal: Polyclonal;purified: Affinity;company: Upstate;catalog: 07-329;short description: Rabbit polyclonal to Histone H4K16ac

source_name: H4K16ac(M).L3 ChIP expt.2515


title: Su(var)3-9-Q2598.L3.Solexa Input Rep2

description: input DNA


title: Su(var)3-9-Q2598.L3.Solexa Input Rep1

description: input DNA


title: HP1c_(MO_462).L3.Solexa ChIP Rep2

description: ChIP DNA; Antibody information listed below: official name: HP1c (MO 462);target name: HP1c;host: Rabbit;antigen: aa135-237;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: MO 462;short description: E.coli produced protein fragment was used to inocculate rabbit.


title: HP1c_(MO_462).L3.Solexa ChIP Rep1


title: HP1c_(MO_462).L3.Solexa Input Rep2

description: input DNA

source_name: HP1c_(MO_462).L3 Input expt.2224


title: HP1c_(MO_462).L3.Solexa Input Rep1

description: input DNA

source_name: HP1c_(MO_462).L3 Input expt.2222


title: H3K79me3_(Abcam_ab2621_lot_1).L3.Solexa ChIP Rep2

description: ChIP DNA; Antibody information listed below: official name: H3K79me3 (Abcam ab2621 lot 1);target name: H3K79me3;host: Rabbit;antigen: synthetic peptide containing the tri-methylated K79 residue of Histone H3.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2621;reference: http://www.abcam.com/Histone-H3-tri-methyl-K79-antibody-ChIP-Grade-ab2621.html;short description: Rabbit polyclonal antibody raised against a synthetic peptide containing the tri-methylated K79 residue of Histone H3.


title: H3K79me3_(Abcam_ab2621_lot_1).L3.Solexa Input Rep2

description: input DNA


title: H3K79me3_(Abcam_ab2621_lot_1).L3.Solexa ChIP Rep1


title: H3K79me3_(Abcam_ab2621_lot_1).L3.Solexa Input Rep1

description: input DNA


title: H3K79me2_(Abcam_ab3594_lot_1).L3.Solexa ChIP Rep2

description: ChIP DNA; Antibody information listed below: official name: H3K79me2 (Abcam ab3594 lot 1);target name: H3K79me2;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 di methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: AB3594;reference: http://www.abcam.com/Histone-H3-di-methyl-K79-antibody-ChIP-Grade-ab3594.html;short description: Antibody raised against H3 peptide containing K79 Di-methylated residue.


title: H3K79me2_(Abcam_ab3594_lot_1).L3.Solexa ChIP Rep1


title: H4K8ac.L3.Solexa Input Rep2

description: input DNA

source_name: H4K8ac.L3 Input expt.2404


title: H3K79me2_(Abcam_ab3594_lot_1).L3.Solexa Input Rep2

description: input DNA


title: H3K79me2_(Abcam_ab3594_lot_1).L3.Solexa Input Rep1

description: input DNA


title: Su(var)3-9-Q2598.L3.Solexa ChIP Rep2


title: H4K16ac(M).L3.Solexa ChIP Rep1

source_name: H4K16ac(M).L3 ChIP expt.2514


title: H3K79me1_(Abcam_lot_1).L3.Solexa ChIP Rep2

description: ChIP DNA; Antibody information listed below: official name: H3K79me1 (Abcam lot 1);target name: H3K79me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 mono methylated at K79.;clonal: Unknown;purified: Affinity;company: Abcam;catalog: ab2886-100;reference: http://www.abcam.com/Histone-H3-di-methyl-K79-antibody-ChIP-Grade-ab3594.html;short description: Rabbit antisera raised against H3 peptide mono-methylated at K79.


title: H4K16ac(M).L3.Solexa Input Rep2

description: input DNA

source_name: H4K16ac(M).L3 Input expt.2404


title: H3K79me1_(Abcam_lot_1).L3.Solexa Input Rep2

description: input DNA


title: H3K79me1_(Abcam_lot_1).L3.Solexa Input Rep1

description: input DNA


title: H3K79me1_(Abcam_lot_1).L3.Solexa ChIP Rep1


title: H3K4me3_(ab8580_lot_2).L3.Solexa ChIP Rep2

description: ChIP DNA; Antibody information listed below: official name: H3K4me3 (ab8580 lot 2);target name: H3K4me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 tri methylated at K4.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: 8580;short description: Histone H3 (tri methyl K4).


title: H3K4me3_(ab8580_lot_2).L3.Solexa Input Rep2

description: input DNA


title: H3K27me3_(Abcam_lot3).L3.Solexa ChIP Rep1

description: ChIP DNA; Antibody information listed below: official name: H3K27me3 (Abcam lot3);target name: H3K27me3;host: Mouse;antigen: Synthetic peptide derived from residues 1 - 100 of Human Histone H3 tri methylated at K27;clonal: Monoclonal;purified: Affinity;company: Abcam;catalog: ab6002;reference: http://www.abcam.com/Histone-H3-tri-methyl-K27-antibody-mAbcam-6002-ChIP-Grade-ab6002.html;short description: Monoclonal antibody raised against synthetic peptide tri-methylated at K27.

source_name: H3K27me3_(Abcam_lot3).L3 ChIP expt.2342


title: H3K27me3_(Abcam_lot3).L3.Solexa Input Rep2

description: input DNA


title: H3K27me3_(Abcam_lot3).L3.Solexa ChIP Rep2

source_name: H3K27me3_(Abcam_lot3).L3 ChIP expt.2343


title: H3K4me3_(ab8580_lot_2).L3.Solexa Input Rep1

description: input DNA


title: H3K27me1_(Millipore).L3.Solexa ChIP Rep1

description: ChIP DNA; Antibody information listed below: official name: H3K27me1 (Millipore);target name: H3K27me1;host: Rabbit;antigen: KLH-conjugated synthetic 2X-branched peptide containing the sequence ?ARmeKSA? in which meK corresponds to monomethyl-lysine at residue 27 of human histone H3.;clonal: Polyclonal;purified: Affinity;company: Millipore;catalog: 07-448;reference: http://www.millipore.com/catalogue/item/07-448;short description: Anti-monomethyl-Histone H3 (Lys27).Recognizes monomethylated histone H3 (Lys27) Mr 17 kDa.

source_name: H3K27me1_(Millipore).L3 ChIP expt.2338


title: H3K27me1_(Millipore).L3.Solexa Input Rep1

description: input DNA

source_name: H3K27me1_(Millipore).L3 Input expt.2330


title: H3K27me1_(Millipore).L3.Solexa Input Rep2

description: input DNA

source_name: H3K27me1_(Millipore).L3 Input expt.2331


title: H3K27ac_(Active_Motif).L3.Solexa ChIP Rep2

description: ChIP DNA; Antibody information listed below: official name: H3K27ac (Active Motif);target name: H3K27ac;host: Rabbit;antigen: Peptide including acetyl-lysine 27 of H3;clonal: Polyclonal;purified: Crude;company: Active Motif;catalog: 39135;reference: http://www.activemotif.com/catalog/details/39135/histone-h3-acetyl-lys27-antibody-pab-1;short description: abbit antibody recognizing Acetylated K27 of H3.


title: H3K27ac_(Active_Motif).L3.Solexa ChIP Rep1


title: H3K27ac_(Active_Motif).L3.Solexa Input Rep2

description: input DNA


title: H3K27ac_(Active_Motif).L3.Solexa Input Rep1

description: input DNA


title: si-RMST SOX2 ChIP

status: Public on Aug 01 2013

city: Cambridge

first: Shi Yan

last: Ng

state: MA

address: 7 Divinity Ave

institute: Harvard University

description: SOX2 ChIP-DNA

data_processing:
ChIP-seq reads were aligned to the hg18 genome assembly
peaks were called using MACS1.4.2, with default settings.
Redundant reads were removed, and peak enrichment was calculated relative to genome background. A p-value of 10-5 was used to call significant peaks.
High confidence peaks were chosen based on having a peak height greater thab randomly occurring peaks.
Genome_build: hg18
Supplementary_files_format_and_content: bed files were generated

source_name: differentiating neural culture

growth_protocol: N2B27 media

extract_protocol:
Lysates were clarified from sonicated nuclei and SOX2-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.

treatment_protocol: non-targeting siRNA or RMST siRNA

value: ReN-VM

value: RMST siRNA

value: Santa Cruz SOX2 (sc-17320)


title: H2B-ubiq_(NRO3).L3.Solexa ChIP Rep2

description: ChIP DNA; Antibody information listed below: official name: H2B-ubiq (NRO3);target name: H2Bubi;host: Mouse;antigen: This antibody was raised against a branched peptide corresponding to the conjugation site of ubiquitin on human histone H2B.;clonal: Monoclonal;purified: Affinity;company: Medimabs;catalog: #MM-0029;short description: Ubiquitinated Histone H2B Mouse Monoclonal Antibody:Isotype: IgG2a

source_name: H2B-ubiq_(NRO3).L3 ChIP expt.2519


title: input

description: input gDNA

value: input - no treatment


title: H2B-ubiq_(NRO3).L3.Solexa ChIP Rep1

source_name: H2B-ubiq_(NRO3).L3 ChIP expt.2518


title: H2B-ubiq_(NRO3).L3.Solexa Input Rep2

description: input DNA

source_name: H2B-ubiq_(NRO3).L3 Input expt.2404


title: H3K4me3_(ab8580_lot_2).L3.Solexa ChIP Rep1


title: si-NT SOX2 ChIP

description: SOX2 ChIP-DNA

value: non-targeting siRNA


title: Δncs2 RNA-seq repeat

city: Baltimore

first: Boris

last: Zinshteyn

state: Maryland

address: 725 N Wolfe St, PCTB 714

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: Small RNA sequencing by polyadenylation and circularization. RNA fragments were dephosphorylated, purified by filtration then gel to isolate ~28nt fragments. Fragments were poly(A) tailed and reverse transcribed with an anchored oligo-dT primer, followed by cDNA circularization and PCR

data_processing:
align first 21nt of reads to rRNA, with up to 3 mismathces allowed, discarding any reads that map
align first 21nt of remaining reads to entire yeast genome, allowing up to 3 mismatches
align remaining unmapped reads to splice junction sequences, and merge with genome mapping
Reads whose 5' ends map from 12nt 3' of CDS start to 14nt 5' of CDS end are assigned to that gene (first 8 codons are ommitted to avoid artifacts due to the use of cylcoheximide in library preparation)
RPKMs are computed as reads per kilobase of CDS sequence per million reads mapping to all CDSs
Genome_build: Saccharomyces cerevisiae May 26 2010
Supplementary_files_format_and_content: tab-delimited tables of reads and RPKMs for all genes and samples. Technical replicates for RNA-seq are pooled.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were grown to mid-exponential phase (OD~0.7) at 30C in YPD

extract_protocol:
Small RNA sequencing by polyadenylation and circularization. RNA fragments were dephosphorylated, purified by filtration then gel to isolate ~28nt fragments. After subtractive hybridization to remove rRNA, fragments were poly(A) tailed and reverse transcribed with an anchored oligo-dT primer, followed by cDNA circularization and PCR. Frozen cell pellets were thawed in lysis buffer and lysis was performed with glass beads as described in the text. Extracts were clarified by a 20' spin at 11,500 rpm in an SS-34 rotor.
Footprints: 50 OD units of extract were treated with 150U of RNAse1 and subsequently purified from the monosome region of a sucrose gradient. RNA was extracted by hot acid phenol. Total RNA: RNA was extracted from 50 OD of extract by SDS and hot acid phenol, and poly(A) RNA was purified on oligo-dT cellulose or DynaBeads. RNA was fragmented at 95C with zinc chloride

treatment_protocol: Cells were treated with 100ug/ml cycloheximide, then harvested by centrifugation. Cell pellet was frozen in liquid nitrogen.

tag: poly-a selection

value: oligo-dT cellulose

tag: triton addition

value: After lysis


title: H3K27me3_(Abcam_lot3).L3.Solexa Input Rep1

description: input DNA


title: Δuba4 RNA-seq 1 repeat

value: Before lysis


title: H3K27me1_(Millipore).L3.Solexa ChIP Rep2

source_name: H3K27me1_(Millipore).L3 ChIP expt.2339


title: H2B-ubiq_(NRO3).L3.Solexa Input Rep1

description: input DNA

source_name: H2B-ubiq_(NRO3).L3 Input expt.2402


title: Δncs6 RNA-seq 2 repeat


title: WT RNA-seq 2 repeat


title: Δuba4 RNA-seq 2 repeat


title: Δncs6 RNA-seq 1 repeat


title: Δelp3 RNA-seq

value: oligo-dT DynaBeads


title: Δuba4 RNA-seq 2


title: Δncs6 RNA-seq 2


title: Δncs2 RNA-seq


title: IkBa_ChIPSeq

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

description: Chromatin IP against IkBa

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and reads were mapped to the human (March, 2006) genome (NCBI36/hg18) using the BOWTIE aligner program (version 0.11.3) (http://bowtie-bio.sourceforge.net/index.shtml) (Ref: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.) All reads mapping uniquely with two or fewer mismatches were retained.

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

source_name: primary epidermal keratinocytes; normal, human neonatal foreskin (origin: ATCCA® ref. PCS-200-010)

growth_protocol: Primary Epidermal Keratinocytes; Normal, Human, Neonatal Foreskin (ATCCA®, ref. PCS-200-010) were seeded at 80% of confluency. Cells were grown in Dermal Cell Basal Media (ATCCA®, ref. PCS-200-030) supplemented with Keratinocyte Growth Kit components (ATCCA®, ref. PCS-200-040) that contains the following growth supplements: Bovine Pituitary Extract (BPE), rh TGF-alfa, L-glutamine, hydrocortisone hemisuccinate, rh Insulin, epinephrine and apo-transferrin. Moreover, optional media supplements were added: Gentamicin-Amphotericin B solution (ATCCA®, ref. PCS-999-025); Penicillin-Streptomycin-Amphotericin B solution (ATCCA®. ref. PCS-999-002) and Phenol-Red (ATCCA®, ref. PCS-999-001).

extract_protocol:
Two nanograms of chipped DNA were used for library preparation. Following end-repair of DNA by incubation with T4 DNA polymerase and Klenow fragment (NEB), DNA was purified with a QIAquick PCR purification kit (Qiagen). Thereafter, 3'-adenylation was performed by incubation with dATP and 3'-5' exo- Klenow fragment (NEB). DNA was purified using MinElute spin columns (Qiagen) and double-stranded Illumina adapters for single-read sequencing were ligated to the DNA using rapid T4 DNA ligase (NEB). The sample was purified again using a MinElute spin column and run on a 2% agarose gel. Fragments containing inserts in the size range 200-450 bp were excised with a sterile single-use scalpel and recovered from the gel by QIAquick gel extraction. Adapter-ligated fragments were enriched with an 18-cycle PCR reaction using Phusion DNA polymerase (Finnzymes). The library quality was confirmed on the Agilent Technologies 2100 Bioanalyzer, and the library subsequently quantified with the Kapa SyBR FAST Universal qPCR kit (Kapa Biosystems).

DNA was loaded into a lane of a single-read flow cell for cluster generation using a single-read cluster generation kit (Illumina). Sequencing was performed on the Illumina Genome Analyzer IIx, and 36 sequencing cycles were performed.

tag: cell type

value: primary epidermal keratinocyte

tag: cell differentiation protocol

value: normal undifferentiated keratinocytes

tag: chip antibody

value: anti-IkappaBalpha

tag: chip antibody vendor

value: Upstate

tag: chip antibody catalog #


title: WT RNA-seq 2


title: WT RNA-seq 1


title: Δncs2 Ribosome Footprint

description: Small RNA sequencing by polyadenylation and circularization. RNA fragments were dephosphorylated, purified by filtration then gel to isolate ~28nt fragments. After subtractive hybridization to remove rRNA, fragments were poly(A) tailed and reverse transcribed with an anchored oligo-dT primer, followed by cDNA circularization and PCR


title: Δuba4 Ribosome Footprint 2


title: Δncs6 RNA-seq 1


title: Δelp3 Ribosome Footprint


title: Δuba4 Ribosome Footprint 1


title: WT Ribosome Footprint 1


title: WT RNA-seq 1 repeat


title: GAF-KD GAF ChIP-seq

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

description: RNAi treated with GAF dsRNA (10ug/ml) for five days.

data_processing:
alignment with bwa. Parameters: bwa aln -n 4 dm3.fasta GAF_ChIP_combined.txt.gz > GAF_ChIP_combined.sai
alignment with bwa. Parameters: bwa aln -n 4 dm3.fasta GAF_RNAi_GAF_ChIP_combined.txt.gz > GAF_RNAi_GAF_ChIP_rep1.sai
peak calling macs14 version 1.4.0. Parameters: macs14 -t GAF_chip_gafKD_reps.unique.sam -c combined_PREimmune.unique.sam --name=GAF_chip_mockKD_reps --gsize=165000000 --tsize=46 --mfold=10,10000 --bw=150 --wig --pvalue=0.0001 --call-subpeaks
peak calling macs14 version 1.4.0. Parameters: macs14 -t GAF_chip_mock_reps.unique.sam -c combined_PREimmune.unique.sam --name=GAF_chip_mockKD_reps --gsize=165000000 --tsize=46 --mfold=10,10000 --bw=150 --wig --pvalue=0.0001 --call-subpeaks
Genome_build: dm3
Supplementary_files_format_and_content: Processed files are linked to GSE40646 and include the wiggle, bed, peaks, subpeaks, and summit files from peak calling. File GSE40646_readme.txt details derivation of each processed file. Pre-immune ChIP was submitted previously to GEO as GSM470838.

source_name: S2 cells depleted of GAF by RNAi

growth_protocol: S2-DRSC (lot 181A1) cells were grown in Schneider’s media (Sigma) with 10% FBS (lot ASD29137).

extract_protocol: The ChIP protocol has been previously described (PMID: 20844575). In short, S2-DRSC (lot 181A1) cells were grown in Schneider's media with 10% FBS (lot ASD29137) and crosslinked with a final concentration of 2% paraformaldhyde for one minute. Crosslinking was quenched by the addition of glycine to a final concentration of 250 mM and the extract was sonicated as previously described (PMID: 20844575). The Protein-A beads were blocked with BSA (1 mg/ml) and Polyvinylpyrrolidone (1 mg/ml) prior to the IP and freshly thawed antiserum was used for each IP.

value: ModENCODE S2-DRSC (lot 181A1)

tag: antibody

value: anti-GAF


title: Δelp3 RNA-seq repeat

tag: strain


title: Δncs6 Ribosome Footprint 1


title: RNA-Seq_Prox

city: College Station

first: Karen

last: Triff

state: TX

address: 321 Kleberg Center, 5523 TAMU

institute: Texas A&M University

description: Processed data file: RNAseq_gene_exp.txt (sample_1)

data_processing:
Illumina Casava software used for basecalling.
RNA-Seq reads were filtered for adapter sequences and trimmed based on sequence quality (threshold of Q20) using ea-utils toolkit. Spliced alignment was performed against the rat genome (Baylor 3.4/rn4) using tophat2 without allowing any mismatches to reduce the number of false positives and the resultant alignments were further processed using cufflinks2 to perform reference annotation based transcript assembly with bias and multi-read correction. Differential expression analyses were performed using cuffdiff2 and cummeRbund.
Genome_build: RGSC_v3.4
Supplementary_files_format_and_content: RNAseq_gene_exp.txt is a tab-delimited text file that includes FPKM values for each Sample.

organism: Rattus norvegicus

source_name: proximal colon crypts

growth_protocol: Samples from 7 rats, 14 weeks old, were pooled together for each sequencing run.

extract_protocol:
Colonic crypts were isolated from distal and proximal regions of the colon. RNA was extracted from colonic crypt cells.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: Sprague Dawley

value: 14 weeks

tag: tissue

value: proximal colon crypts


title: RPOLII_ChIPSeq_Prox

data_processing:
Illumina Casava software used for basecalling.
ChIP-Seq reads were aligned to the Baylor 3.4/rn4 genome assembly. Sequence read numbers were summed into 200 bp non-overlapping windows with read position shifted 75 bp to represent the DNA fragment center. Genomic regions with histone modification marks were identified using SICER. The nearest gene to each island, i.e., within 2 kb of the island, was identified using closestBed from the BEDTools software suite and the refGene table downloaded from the UCSC Genome Browser for the Baylor 3.4/rn4 assembly.
Genome_build: RGSC_v3.4
Supplementary_files_format_and_content: ChIP-Seq wig files were generated using SICER, scores represent peak intensity.

source_name: proximal colon crypts, RNA polymerase II ChIP

extract_protocol:
Colonic crypts were isolated from distal and proximal regions of the colon. Lysate from nuclei of colonic crypt cells were ChIPed for histone modifications and RNA Polymerase II.
ChIP libraries were prepared for sequencing using standard Illumina protocols.

tag: age

value: RNA Polymerase II (Abcam, ab5408)


title: Δncs6 Ribosome Footprint 2


title: ChIP-Seq Klf4 in NMuMG cells Biological replicate 2

city: Basel

first: Neha

last: Tiwari

address: Mattenstrasse 28

country: Switzerland

institute: University of Basel

data_processing:
2007 M. musculus genome assembly (mm9) was used as a basis for all analyses.
Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads).
Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100,  tracking up to 100 best alignment positions per query and allowing at most two mismatches.
All quantifications were based on alignments weighted by the inverse of the number of query hits, ensuring that the total weight of a read did not exceed one.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using custom Perl scripts; Scores represent weights in 100bp windows

organism: Mus musculus

source_name: Normal murine mammary epithelial (NMuMG) cells

growth_protocol: NMuMG cells were cultured in DMEM/10% FBS.

extract_protocol:
DNA was extracted as described in Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, et al. (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genetics 39: 457–466.
The ChIP libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102–1001) according to Illumina’s instructions. DNA libraries were sequenced on an Illumina Genome Analyzer 2 following the manufacturer’s protocols.

treatment_protocol: ChIP experiments were performed starting with 70 mg of chromatin and 5 mg of anti-Klf4 (SC-20691, Santa Cruz).

value: Klf4 (SC-20691, Santa Cruz)

value: immortalized yet non-transformed murine mammary epithelial cells


title: H3K9me3_ChIPSeq_Prox

source_name: proximal colon crypts, H3K9me3 ChIP

value: H3K9me3 (Abcam, ab8898)


title: H3K4me3_ChIPSeq_Prox

source_name: proximal colon crypts, H3K4me3 ChIP

value: H3K4me3 (Abcam, ab1012)


title: H3K9me3_ChIPSeq_Dist

source_name: distal colon crypts, H3K9me3 ChIP

value: distal colon crypts


title: ChIP-Seq Klf4 in NMuMG cells Biological replicate 1


title: WT Ribosome Footprint 2

value: After lysis


title: Δuba4 RNA-seq 1

value: oligo-dT DynaBeads

value: Before lysis


title: RNA-Seq_Dist

description: Processed data file: RNAseq_gene_exp.txt (sample_2)

source_name: distal colon crypts


title: GAF ChIP-seq

source_name: untreated S2 cells


title: WM2664

city: Glasgow

first: Peter

middle: D.

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

description: RNA-Seq of WM2664 human melanoma

data_processing:
Basecalls performed using CASAVA 1.8 and filtered to only sequences passing the Illumina QC filter
Sequenced reads were mapped to hg18 whole genome using tophat 1.2.0 with parameters –solexa1.3-quals, -p 7, -r 160, -G Homo_sapiens.NCBI36.54.gtf
Aligned reads normalised by library size (number of fragments) converted to bigWig format
Genome_build: hg18
Supplementary_files_format_and_content: bigWig files represent pileups of the reads at each base.  bigWig files were normalised by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig

molecule: polyA RNA

source_name: WM2664 human melanoma

growth_protocol: Cells were grown using standard conditions and RNA harvested when plates were 80% confluent

extract_protocol:
RNA was extracted using RNA easy mini kit.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment


title: H3K4me3_ChIPSeq_Dist

source_name: distal colon crypts, H3K4me3 ChIP


title: SKMEL5

description: RNA-Seq of SKMEL5 human melanoma

source_name: SKMEL5 human melanoma


title: C32

description: RNA-Seq of C32 human melanoma

source_name: C32 human melanoma


title: A2058

description: RNA-Seq of A2058 human melanoma

source_name: A2058 human melanoma


title: BRAF

description: RNA-Seq of BRAF600V infected primary human melanocytes

data_processing:
Basecalls performed using CASAVA 1.6
Sequenced reads were mapped to hg18 whole genome using tophat 1.2.0 with parameters –solexa1.3-quals, -p 7, -r 160, -G Homo_sapiens.NCBI36.54.gtf
Aligned reads normalised by library size (number of fragments) converted to bigWig format
Genome_build: hg18
Supplementary_files_format_and_content: bigWig files represent pileups of the reads at each base.  bigWig files were normalised by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig

source_name: BRAF

growth_protocol: Cells were infected with respective lentiviruses and RNA was isolated 2 weeks post infection when cells were confirmed fully senescent

treatment_protocol: No treatment other then lentiviral infection

value: Primary human epidermal melanocytes (neonatal)


title: Uninfected

description: RNA-Seq of Uninfected primary human melanocytes

source_name: Uninfected


title: input DNA (reps 1-2)

city: Valbonne

first: Enzo

last: LALLI

address: 660 route des Lucioles

department: CNRS UMR 7275

country: France

institute: IPMC

description:
Replicates:
GKO-1
GKO-4

data_processing:
Basecalls performed using CASAVA version 1.6
ChIP-seq reads were aligned to the hg19 genome assembly using ELAND version 2.0
Pëaks were called from triplicate experiments from each condition (basal and overexpressed SF-1) and each antibody (Millipore or Perseus), compared to input DNA replicates, using the the CisGenome v2 SeqPeak algorithm using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using the cod to bed CisGenome utility

source_name: H295R/TR SF-1 cells

growth_protocol: H295R/TR SF-1 cells were cultured in DMEM-F12 (Invitrogen) supplemented with 2% NuSerum (BD), 1% ITS+ (BD) and penicillin-streptomycin (Invitrogen).

extract_protocol:
Lysates were clarified from sonicated nuclei and SF-1 - DNA complexes were isolated with antibody, as described in Lee TI, Johnstone SE, Young RA (2006) Chromatin immunoprecipitation and microarray-based analysis of protein location. Nature Protoc 1(2):729-748.
Libraries construction was contracted out to Fasteris SA. At Fasteris SA, barcoded libraries were prepared such that four samples could be run per lane. The quality of starting DNA was assessed prior to library construction at Fasteris SA using an Agilent Bioanalyzer (Agilent, Santa Clara, CA, USA).

treatment_protocol: To induce SF-1 overexpression, doxycycline (1 mg/mL) was addred in some samples to the culture medium for 3 days before formaldehyde fixation and harvesting of the cells.

value: H295R adrenocortical tumor cell line

value: None (input control)


title: ChIP-seq_Millipore Ab_overexpressed SF-1  (reps 1-3)

description:
Replicates:
GKO-6
GKO-10
GKO-12

tag: sf-1 dosage

value: overexpressed SF-1

value: SF-1 (Millipore, catalog# 07-618, lot# JBC1355794)


title: ChIP-seq_Millipore Ab_basal SF-1 (reps 1-3)

description:
Replicates:
GKO-3
GKO-8
GKO-11

value: basal SF-1


title: Hoxa9,10,11-/- vas deferens, pooled from n=3

city: Cincinnati

first: Steve

last: Potter

state: OH

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description: VasAKO

data_processing:
Tophat version April 2012 was used for basecalling and Bam files were generated
Avadis NGS version 1.3.1 was used to analyze Bam files and generate nRPKM values for each sample
Avadis NGS NewGene finding option was used
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include nRPKM values for each sample

source_name: Hoxa9,10,11-/- vas deferens

extract_protocol:
Total RNA was extracted from fresh tissue using the Qiagen RNeasy Mini kit
RNA libraries were prepared for sequencing using Illumina TruSeq reagents and protocols

tag: strain background

tag: genotype/variation

value: vas deferens


title: Hoxa9,10,11+/-d9,10,11-/- uterus, pooled from n=3

description: UtAHDK

value: uterus


title: WT epididymis, pooled from n=3

description: EpiWT

source_name: WT epididymis

value: WT

value: caudal epididymis


title: SKMEL28

description: RNA-Seq of SKMEL28 human melanoma

source_name: SKMEL28 human melanoma


title: WT vas deferens, pooled from n=3

description: VasWT

source_name: WT vas deferens


title: WT oviduct, pooled from n=3

description: OviWT

source_name: WT oviduct

value: oviduct


title: Hoxa9,10,11+/-d9,10,11-/- vas deferens, pooled from n=3

description: VasAHDK


title: inoculated with diazothrophic bacteria

city: Rio de Janeiro

first: Paulo

last: Ferreira

address: Rua Rodolpho Paulo Rocco s/nº, CCS, Bl.L, Cidade Universitária

country: Brazil

institute: Universidade Federal do Rio de Janeiro

data_processing:
Quality of the sequences was evaluated by measuring the quality of the reads according to the percentage of bases having a base quality greater or equal than 30 (Q30)
3’ Illumina adapters (CTGTAGGCACCATCAAT) and “N” bases were trimmed
Using the UEA sRNA toolkit-Plant version filter pipeline (http://srna-tools.cmp.uea.ac.uk/) and  three different databases -  all plant t/rRNAs from Rfam, all Arabidopsis tRNAs from The Genomic tRNA Database and all plant t/rRNA sequences from EMBL release - reads with low-complexity (less than 3 different bases) and both sense and antisense matches with t/rRNAs were removed
Detection of conserved miRNAs with UEA sRNA toolkit-Plant version miRProf pipeline was done allowing one mismatch with mature miRNAs from miRBase (v19.0). Only reads with match to Zea mays were included in the analysis.
Detection of new miRNAs with UEA sRNA toolkit-Plant version miRCat pipeline was done allowing one mismatch with Zea mays genome.
The output of the miRProf and miRCat contains information about unique sequences counts. Counts were normalized in reads per 1 million (RPM) and total reads counts after the final trimming and filtering steps were used for normalization.
Genome_build: Zea mays v.2
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

organism: Zea mays

source_name: whole plant

growth_protocol: Herbaspirillum seropedicae provided by EMBRAPA Agrobiology were grown in NFb and JNFb media, respectively, at 30°C. Maize seeds of the variety UENF 506-8 [13] were surface-sterilized for 15 min with a 10% (v/v) solution of a commercial bleach containing 5.25% (w/v) of NaCl and then washed several times with distilled water [14]. Seeds were then soaked overnight in distilled water and germinated at 25°C in wet paper. Seven days after germination the seedlings were moved to 0.5x Hoagland’s solution in a growth chamber at 24°C on 10-h days and left for two weeks. The Hoagland’s solution was renewed every 3 or 4 days. After this period the seedlings were moved to pots with sand and vermiculite (2:1) and left for a week.

extract_protocol:
Total RNA was isolated from whole plants using Trizol (Invitrogen, CA, USA) as described by the manufacturer.
TruSeq Small RNA Sample Prep Kit

treatment_protocol: Fresh overnight Herbaspirillum seropedicae cultures were resuspended in 5 mM MES at pH 5.5 to 1 x 108 cells/mL and 100uL were injected in the stems of plants with a sterile 1 ml hypodermic syringe. Control plants were mock inoculated. Four plants of every variety were inoculated with bacteria suspensions. After seven days of inoculation the plants were analyzed phenotypically and quickly frozen in liquid nitrogen. Colonization was confirmed by plate counting in the same media for all the bacteria.

tag: treatment

value: inoculated with Herbaspirillum seropedicae

tag: time

value: seven days cultivation


title: control

value: control


title: WT uterus, pooled from n=3

description: UtWT

source_name: WT uterus


title: Hoxd9,10,11-/- vas deferens, pooled from n=3

description: VasDKO

source_name: Hoxd9,10,11-/- vas deferens


title: Hoxa9,10,11-/-d9,10,11+/- vas deferens, pooled from n=3

description: VasAKDH


title: Hoxd9,10,11-/- uterus, pooled from n=3

description: UtDKO

source_name: Hoxd9,10,11-/- uterus


title: Hoxa9,10,11-/-d9,10,11+/- uterus, pooled from n=3

description: UtAKDH


title: MalMe3M

description: RNA-Seq of MalMe3M human melanoma

source_name: MalMe3M human melanoma

tag: cell line


title: wild-type (FGSC4200)

city: Dallas

first: Yunkun

last: Dang

address: 5323 Harry Hines Blvd

department: Physiology

institute: University of Texas Southwestern Medical Center

data_processing:
Raw sequences are processed using a customized PERL script: sequences were identified using the first 6nt of the 3' linker.
The alignment tool Bowtie (ver 0.12.7) was used to map the small RNAs  on to the N. crassa genome. Parameter: v 2 -a -m5 --best --strata
Alignment results were processed into gff file with a customized PERL scrit. One read  matching serval loci of the genome were normalized based on the number of matches. Please request the script by emailing yunkun.dang@utsouthwestern.edu

organism: Neurospora crassa

source_name: wild-type (FGSC4200)

growth_protocol: constant light, 1x Vogel's 2% sucrose, 25 C

extract_protocol:
total RNAs of each sample were extracted and small RNAs were enriched with 5% polyethylene glycol (MW8000) and 500 mM NaCl
illumina standard TruSeq small RNA preparation. For each sample, small RNAs of 18-30 nt were purified from PAGE gel. The 3' and 5' RNA adaptors were then ligated and RT-PCR were performed to amplify the library (18 cycles). Libraries were analysed with Illumina HiSeq 2000. Please see instruction of illumina Truseq small RNA preparation guide and BGI website for detailed information

value: wild-type


title: A375

description: RNA-Seq of A375 human melanoma

source_name: A375 human melanoma


title: 35S:SlHsfA3-6

city: Harbin

first: jingfu

last: li

address: Mucai street

country: China

institute: Northeast Agricultural University

data_processing:
Illumina Casava version 1.7 software was used for basecalling
Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using a protocol from Mortazavi et al., Nature, 2008
MARS (MA-plot-based method with Random Sampling model) from DEGseq package was used for identifying differentially expressed genes (Wang et al., 2010)
Pathways and Gene Ontology (GO) analysis were performed using Molecule Annotation System (MAS)
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample and Pathway and Gene Ontology analysis of differentially expressed genes

source_name: Aerial part

growth_protocol: Seedlings of 35S:SlHsfA3 and Col-0 (WT) plants were grown in a chamber at 22 ℃ in a photoperiod of 16 h light and 8 h darkness

extract_protocol: Total RNA was isolated with Trizol reagent (Invitrogen, USA) from the aerial part of our material and purified with Micropoly(A) PuristTM mRNA purification kit (Ambion, USA, Cat. No:1919). cDNA first- and second-strand synthesis was performed using Superscript II reverse transcriptase (Invitrogen,USA) and Ex Taq polymerase (TaKaRa, Japan), respectively.The newly synthesized double-strand cDNA was fractured into 300-500bp fragments using an ultrasonic instrument (Fisher) and then purified with AMPure beads (Agencourt, USA). The sequencing library was prepared and PCR amplified using TruSeqTM DNA Sample Prep Kit-Set A (Illumina, USA) and TruSeq PE Cluster Kit (Illumina, USA), respectively. Sequencing was performed on the Illumina HiSeq 2000 sequencing platform.

tag: developmental stage

value: 4-week-old seedlings

tag: number of plants

value: 20 seedlings

tag: genotype

value: SlHsfA3-overexpressing line

tag: cultivar


title: 35S:SlHsfA3-3


title: white collar 2 knockout mutant

source_name: white collar 2 knockout mutant

value: wc-2 KO


title: Col-0


title: error-proof in vitro 2 (GreAB/Mn2+)

city: Frederick

first: Masahiko

last: Imashimizu

state: MD

department: NCI/CCR

institute: NCI

description: mRNA synthesized in vitro transcription

data_processing:
CASAVA version 1.4
A single large fastq  format file of high quality reads (Q ≥ 30) was split into about 10 smaller files by using a shell script splitReads.sh
The obtained reads were aligned  and mapped to the pPR9 plasmid DNA sequences using   Bowtie 0.12.7.
The numbers of 4 bases A, T, G, C, and N were counted in each position of the mapped reads by using the program  SAMtools 0.1.18 with supplemental use of a Perl script.
Each type of error rates per position was determined as  the number of sequence reads with a particular type of base-substitution  divided by the number of the reads with the reference base in each DNA  position.
Genome_build: pPR9 plasmid (ref is Kashlec et al., 1989, PMID: 2547695)
Supplementary_files_format_and_content: tab-delimited text file of transition error rate per position. The position is corresponding to the position of "Sequenced region of pPR9 plasmid" (one of the attached txt file).

organism: Escherichia coli

source_name: error-proof in vitro MnCl2 +GreAB

growth_protocol: Cells were cultured in LB medium containing ampicillin at 28˚C. The overnight cell culture was inoculated into the fresh  medium at 1/70 (v/v) and was incubated for  2 hr at 28˚C (OD600 reached  0.35) and then for 2 hr at 42˚C (OD600 reached 2.3) to induce the PR promoter.

extract_protocol:
In vitro RNA preparation: The 5.7 kb RNA was purified from the digested DNA, NTPs, abortive oligo-RNA products, and proteins by Acidic phenol extraction, G50 spin column, followed by EtOH precipitation.
In vivo RNA preparation: The cells in 200 ml culture were harvested and resuspended with a solution containing 0.5% SDS, 20 mM sodium acetate (pH 5.5), and 10 mM EDTA. The suspended cells were mixed with an equal volume of pre-warmed saturated phenol (20 mM sodium acetate, 10 mM EDTA pH 5.5) and incubated for 5 min at 60  C. The mixture was centrifuged, and RNA and DNA were precipitated with ethanol from the supernatant. The pellet was dissolved in DNase I buffer with 10U of DNaseI and incubated for 30 min. RNA was separated from the digested DNA by acidic phenol extraction followed by G-50 Micro column (GE Healthcare) purification, and then precipitated with ethanol. The pellet was dissolved in diethylpyrocarbonate-treated water and used for cDNA synthesis.
The cells culture were harvested and resuspended with a  solution containing 0.5% SDS, 20 mM sodium acetate (pH 5.5), and 10 mM  EDTA. The suspended cells were mixed with an equal volume of pre-warmed  saturated phenol (20 mM sodium acetate, 10 mM EDTA pH 5.5) and incubated  for 5 min at 60˚C.
We established a method for preparing five different cDNA  libraries each with its own barcode for Illumina sequencing. Each 6-nt barcode allows multiplexing all five in vitro and  in vivo preparations in a single sequencing analysis. our method introduces internal control sequences to the library  that are subjected to the artifact errors, but are not for RNAP  errors. The 5’ fragment of the 5.7 kb RNA  transcripts was reverse transcribed to make the cDNA.  The cDNA was subjected to PCR reactions that generated  six  200 bp segments. The primers contained a specific barcode  for each of the five starting preparations and the inner Illuminasequencing  adapters. The 2nd-step of PCR generated  the final cDNA libraries for the Illumina sequencing by using  the 1st-step PCR product as a template and primers containing  the outer sequencing adapters in the 5’ tails.
mRNA-seq with barcode (Illumina  TruSeq Index 1-5)

tag: mrna synthesis

value: in vitro MnCl2 +GreAB


title: in vivo

description: mRNA purified from E. coli cells

source_name: E.coli strain MG1655

value: in vivo


title: IL-33 1hr

first: Mark

last: Rochman

address: 3333 Burnett Ave

department: Allergy and Immunology

institute: CCHMC

data_processing:
tophat 1.4.1 was used to produce aligned files. Tophat was run as tophat --num-threads 12 --segment-length 20 --no-novel-juncs -G mm9_ucsc_annotation.gtf --segment-mismatches 3 --max-deletion-length 20 -T
then cuffdiff 1.2.1 was run with the same annotation as tophat for each pair of control vs. treatment files to produce FPKMs.
then four cuffdiff output files were joined by gene name and only  genes with significant changes for at least one isoform and FPKM >2 in at least one condition were kept.
The processed data file contains significance calls and log2 fold changes over control. For log fold calculations all values below 1 were considered to be equal to 1.
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff output tab delimited files.GSE43660_significantly_regulated_genes.txt includes log2 ratio values and significance status.

source_name: Low density bone marrow derived eosinophils at day 14

growth_protocol: Total bone marrow cells were isolated, and erythrocytes were lysed by red blood cell lysis buffer. After a density gradient of Histopaque 1083, the low-density bone marrow (LDBM) cells were collected and plated at 1x106 cells/ml in IMDM supplemented with 10% FBS, penicillin-streptomycin, L-glutamine 200 mM , and β-mercaptoethanol 55 μM. During the first 4 days, the medium also contained stem cell factor (SCF) and Fms-like tyrosine kinase 3 (FLT3)-ligand  at 100 ng/ml each. From day 4 to day 14, the cells were cultured in medium containing 10 ng/ml IL-5. The medium was changed every 2 days until day 14.

extract_protocol:
RNA was harvested using Trizol reagent and isolated by RNeasy kit with on-column DNaseI treatment
RNA libraries for single read sequencing were prepared using standard Illumina protocols

treatment_protocol: At day 14 in culture 4X10X6 eosinophils were treated with either IL-4 or IL-33 at 10ng/ml for 1hr or 4hr.

value: BALB/c

value: 4-8 weeks

tag: cell type


title: Control 4hr

value: Low density bone marrow derived eosinophils


title: IL-33 4hr


title: error-prone in vitro (Mn2+)

description: mRNA synthesized in vitro transcription

source_name: error-prone in vitro MnCl2

value: in vitro MnCl2


title: IL-4 4hr


title: Hoxa9,10,11-/- uterus, pooled from n=3

description: UtAKO

source_name: Hoxa9,10,11-/- uterus

value: uterus


title: IL-4 1hr


title: Control 1hr


title: Sheep 7 51-53 hours

city: Clayton

first: Melissa

last: Burke

state: VIC

address: Wellington Road

country: Australia

institute: Monash University

data_processing:
As limited annotation data is available for ovine genes, the reads were aligned to mRNA sequences from the Bos taurus genome (NCBI build 5, version 2) as validated previously (Jager, 2011 BMC Genomics (PMID 21435219)). Reads were aligned to the bovine genome using the SHRiMP read aligner.
Read alignment counts per gene were analysed using edgeR (Robinson et al., 2010). Genes with less than 10 alignments in total were discarded. EdgeR uses a Generalized Linear Model with a log link function and a negative binomial noise distribution. The dispersion was estimated using EdgeR's trend mode, that is, dispersion was taken to be a smoothly varying function of the total count for each gene. A likelihood ratio test was performed to identify genes whose expression changed significantly over time.
Genome_build: Bos taurus NCBI build 5, version 2.
Supplementary_files_format_and_content: Data from all samples is combined into a single text file, which is linked to the Series record as a supplementary file. Expression is displayed as log2 average fold-change relative to matched pre-vaccination controls. Feature = Entrez Gene ID; log2 concentration = Log2 of the proportion of alignments; log2 timeXXX = Log2 fold-change between PRE and the specified time; p = p-value from likelihood ratio test; FDR = False Discovery Rate (adjusted p-value); Gene ID= Feature; Gene= Gene symbol; Product= Gene name or description; Note= Additional gene information; [Sample ID] = Raw count of alignments to gene per sample; RPKM [Sample ID] = Reads Per Kilobase of exonic sequence per Million mapped reads; Ambiguous alignment = Number of times there was a read that aligned equally well to other genes.

organism: Ovis aries

source_name: Afferent lymph myeloid cells, 51-53 hours

growth_protocol: This study employed an ovine model of pseudoafferent lymphatic cannulation (see de Veer et al. 2010, Vaccine) to characterise the innate immune response within the afferent lymph to vaccination with liposomes+poly (I:C)+ diptheria toxoid. The sheep used in this study had both their pre-femoral lymph nodes removed at 1 year of age. Approximately 1 year after the lymph node removal, a second surgery was performed to insert a 0.96_0.58mm heparin-coated polyvinyl chloride cannula into the pseudoafferent (previous efferent) lymphatic duct of both sides. At least seven days were allowed for healing to occur after surgery before vaccinations were administered and experimental lymph samples were collected. Handling of animals and experimental procedures were all approved by the Monash University Animal Ethics Committee in accordance with the relevant licensing agreement. Vaccinations were injected subcutaneously in the area drained by the prefemoral lymph node. Afferent lymphatic samples were collected prior to vaccination as a control (PRE) and at 4-6, 26-28, 51-53 and 76-78 hours post vaccination with liposomes+poly (I:C)+ diptheria toxoid.

extract_protocol: Total RNA was extracted from cells preserved in buffer RLT using a Qiagen RNeasy Mini Kit. Only two samples yielded sufficient RNA for sequencing at the 4-6 and 26-28hrs time points. Three samples were used for all other time points. mRNA sequencing libraries were then prepared using an Illumina mRNA-seq-8 sample preparation kit. Briefly, poly-A mRNA was purified from total RNA using poly-T-oligo attached magnetic beads. The RNA was then fragmented into small pieces using divalent cations under elevated temperature. First strand cDNA synthesis was then performed using reverse transcriptase and random primers and was followed by second strand synthesis with DNA polymerase I and RNase H. End repair processing, polyadenylation and ligation of adaptors was then performed. The product was then purified and enriched by PCR.

treatment_protocol: Lymphatic collections were obtained prior to vaccination and at 4-6 hours, 26-28 hours, 51-53 hours and 76-78 hours post vaccination. Experimental lymph samples were collected in sterile 50-ml tubes containing 0.05 IU of heparin (Pfizer, Parkville, VIC, Australia) and 20 ml of 100x cell culture penicillin-streptomycin (Invitrogen, Carlsbad, CA, USA). Only cannulation sites with continuous lymph flow over the observation period were used for data analysis. Lymphocytes were depleted using antibody coupled magnetic depletion. Lymph cells were collected for 2 hours, red cell lysis was performed and the pellet was resuspended in 1 ml of depletion mix (anti-CD45R clone 20.96 (neat hybridoma supernatant), anti-CD4 clone 44.38 (1/100 hybridoma supernatant) and anti γδ TCR clone 86D (1/25 hybridoma supernatant). The mix was incubated on ice for 15 min, and then 9ml of FACS wash was added and the cells centrifuged. The pellet was washed twice with 10 ml of FACS wash and then resuspended in FACS wash at 2x10^7 cells/ml. The magnetic beads coupled with anti-mouse Ig (BioMag, Polysciences Inc., Warrington, PA) were washed 3 times with 5 ml of FACS wash and added to the cells for depletion at 5 beads per cell. The mixture of beads and cells were gently rotated for 20 minutes at 4 oC before the tubes were placed beside a neodynium magnet until the solution cleared. The process was repeated on the supernatant to ensure all beads were removed. The main cell pellet was resuspended in 350 ul of RLT (Qiagen) and total RNA was extracted using an RNeasy Micro Plus Kit (Qiagen, Valencia, USA) according to the manufacturer's instructions. RNA quantity was measured using a Nanodrop (Nanodrop Technologies, Wilmington, USA) and RNA quality was assessed using an Agilent Bioanalyzer (Agilent Technologies, Foster City, USA).

tag: time post-vaccination

value: 51-53 hours

value: afferent lymph myeloid cells

tag: sample id


title: Sheep 1 76-78 hours

source_name: Afferent lymph myeloid cells, 76-78 hours

value: vaccination with liposomes+poly (I:C)+ diptheria toxoid

value: 76-78 hours


title: Sheep 3 76-78 hours


title: Sheep 3 4-6 hours

source_name: Afferent lymph myeloid cells, 4-6 hours

value: 4-6 hours


title: Sheep 7 Pre

source_name: Afferent lymph myeloid cells, pre-challenge

value: pre-challenge


title: Sheep 7 76-78 hours


title: Sheep 3 Pre


title: Sheep 3 26-28 hours

source_name: Afferent lymph myeloid cells, 26-28 hours

value: 26-28 hours


title: ChIP-seq_NRSF/REST_basal SF-1

data_processing:
Basecalls performed using CASAVA version 1.6
ChIP-seq reads were aligned to the hg19 genome assembly using ELAND version 2.0
Pëaks were called using the the CisGenome v2 SeqPeak algorithm using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using the cod to bed CisGenome utility

source_name: ChIP-seq_NRSF/REST_basal SF-1

tag: chip antibody

value: NRSF/REST Millipore #07-579

value: adrenocortical tumor

value: H295R/TR SF-1 cells


title: Sheep 1 26-28 hours


title: Sheep 1 51-53 hours


title: input DNA (replicate 1)

source_name: input DNA


title: Sheep 1 Pre


title: standard in vitro (Mg2+)

description: mRNA synthesized in vitro transcription

source_name: standard in vitro MgCl2

tag: strain

value: in vitro MgCl2


title: error-proof in vitro 1 (GreAB/Mg2+)

description: mRNA synthesized in vitro transcription

source_name: error-proof in vitro MgCl2 +GreAB

value: in vitro MgCl2 +GreAB


title: PC3-EMT14-OVOL2_2

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

description: Sample 19

data_processing:
Base Calling: Illumina HiSeq
Quality Control: FastQC
Alignment: Tophat2.0.3  --b2-very-sensitive
Abundance Measurement: CuffLinks/CuffDiff2.0.2, UCSC hg19.gtf transcriptome, with -u, -N, --compatible-hits-norm, and -b (relative to the UCSC hg19.fa)
Format Output: Format cufflinks output using a locally derived Perl script
Genome_build: HG19
Supplementary_files_format_and_content: Processed data files are output text files (.diff.txt files) from CuffDiff.  The file names have been edited to be specific to the relevant CuffDiff run.

extract_protocol:
Rneasy (Qiagen)
TruSeq SBS Kit v3
TruSeq PE Cluster Kit v3 - cBot - HS
TruSeq Multiplex Sequencing Primer Box

value: prostate cancer cells

value: Mesenchymal with OVOL2 overexpression


title: HeLa_U6atac_AMO

city: philadelphia

first: Ihab

last: Younis

state: PA

address: 415 Curie Blvd

department: Biochemistry and Biophysics

institute: University of Pennsylvania

description: Sample 2

data_processing:
RNA-seq reads were aligned to the reference genome (UCSC, hg19) using Tophat by default parameters
FPKMs were generated using BEDTools
The analysis of differential gene expression was performed using Cufflinks
Significant genes were detected based on FDR level at 0.05 using Benjamini-Hochberg correction for multiple-testing
alternative spliced genes were identified by MISO
Genome_build: hg19
Supplementary_files_format_and_content: xlsx files containing RPKMs

source_name: HeLa_U6atac knockdown

growth_protocol: Cells grown in DMEM supplemented with 10% FBS and 1% antibiotics

extract_protocol:
Total RNA extractde using trizol, polyA mRNA extracted using Rneasy Kit, nascent RNA linked to Biotin and etracted on magnetic streptavidin beads
Libraries were prepared according to instructions accompanying the Nugen kits. Briefly, RNA was converted to cDNA using the Ovation RNA-seq System and starting with 100ng RNA. cDNA was amplified using SPIA protocol recommended by Nugen Kit. Libraries for RNA-seq were prepared from the amplified cDNA using Encore NGS Library System I.

treatment_protocol: Cells transfected with antisense morpholino to control or U6atac using Neon system for 8 hours

value: HeLa PV

value: Human Carcinoma Cells

tag: transfected with

value: antisense morpholino to U6atac

tag: molecule subtype

value: nascent polyA mRNA


title: PC3-EMT14-OVOL2_1

description: Sample 17


title: PC3-EMT14-OVOL1_2

description: Sample 13

value: Mesenchymal with OVOL1 overexpression


title: Sheep 7 4-6 hours

value: vaccination with liposomes+poly (I:C)+ diptheria toxoid

value: afferent lymph myeloid cells


title: HeLa_Control_AMO

description: Sample 1

value: antisense morpholino to control


title: PC3-EMT14-OVOL1_3

description: Sample 15


title: PC3-EMT14-OVOL1_1

description: Sample 11


title: ChIP-seq_NRSF/REST_overexpressed SF-1

source_name: ChIP-seq_NRSF/REST_overexpressed SF-1


title: PC3-EMT14_3

description: Sample 9

value: Transformed to Mesenchymal Phenotype


title: PC3-EMT14_2

description: Sample 7


title: PC3-EMT14_1

description: Sample 5


title: PC3-Epi_2

description: Sample 3

value: Control (Epithelial)


title: ChIP-seq_Perseus Ab_overexpressed SF-1 (reps 1-3)

description:
Replicates:
GKO-29
GKO-44
GKO-46

source_name: H295R/TR SF-1 cells

value: H295R adrenocortical tumor cell line

tag: sf-1 dosage

value: overexpressed SF-1

value: SF-1 (Perseus Proteomics, catalog# PP-N1665-00, lot# A-2)


title: ChIP-seq_Perseus Ab_basal SF-1 (reps 1-3)

description:
Replicates:
GKO-27
GKO-43
GKO-45

value: basal SF-1


title: FAIRE-seq SF-1 overexpression

description: library_strategy: FAIRE-seq

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the hg19 genome assembly using ELAND version 2.0
Pëaks were called from each FAIRE-seq sample compared to input DNA in SF-1 basal and overexpression conditions, using the the CisGenome v2 SeqPeak algorithm using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using the cod to bed CisGenome utility

extract_protocol:
FAIRE-seq was performed according to the method described in Giresi PG, Lieb JD (2009) Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods 48: 233-239.
Libraries construction was contracted out to Fasteris SA. At Fasteris SA, barcoded libraries were prepared such that four samples could be run per lane. The quality of starting DNA was assessed prior to library construction at Fasteris SA using an Agilent Bioanalyzer (Agilent, Santa Clara, CA, USA).

tag: sample type

value: enriched for soluble chromatin by FAIRE


title: FAIRE-seq basal SF-1 expression

description: library_strategy: FAIRE-seq


title: PC3-Epi_1

description: Sample 1

value: prostate cancer cells

tag: treatment


title: input DNA (replicate 2)

value: adrenocortical tumor

value: H295R/TR SF-1 cells


title: input DNA basal SF-1 expression

value: input DNA


title: Input, 3T3-L1 Day7 1h Rosi

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Quality of all libraries were assessed using FastQC (Babraham Bioinformatics). Reads were trimmed and/or filtered using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Sequenced reads were aligned to the genome (mm9) using bowtie (Langmead B, et al. 2009. Genome Biol. 10:R25) with the options: -m 1 --best --strata
Reads from paired Rosi and DMSO libraries were combined into one library and peaks were called using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576–589) with the default settings, and using sonicated input samples as control.
Binding intensity was scored using HOMER for each factor and each condition by counting tags aligning within detected peaks, and normalizing to a total read depth of 10^7 aligned reads.
Expression was scored by counting RNAPII ChIP-seq reads mapping within RefSeq gene bodies longer than 1 kb (omitting the initial 250 bp) using HOMER. Differential expression was called using edgeR (Robinson MD, et al. 2010. Bioinformatics 26:139-140)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files created using HOMER for visualization of binding profiles in the UCSC genome browser. HOMER peak files with tag counts were generated using the HOMER annotatePeaks.pl script using the -d option. The files contain read counts of PPARγ, C/EBPα, MED1, and CBP ChIP-seq libraries (from both conditions). The read counts were normalized to a total read depth of 10^7 aligned reads.

source_name: 3T3-L1 adipocytes (Day 7)

growth_protocol: 3T3-L1 cells were maintained in DMEM supplemented with calf serum. Two days post confluency (day 0), the cells were induced to differentiate into adipocytes using a cocktail of adipogenic inducers (1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxantine, 1 μg/mL insulin, 10% FCS). Two days post induction, medium was changed to DMEM supplemented with FCS and insulin, and four days post induction the medium was changed to DMEM supplemented with FCS. The medium was changed a final time at day 6 post induction and all experiments were performed on day 7.

extract_protocol:
Chromatin was prepared from 149 mm culture dishes first by crosslinking in 1% formaldehyde in PBS (10 minutes, RT). Cross-linking was stopped by adding glycine to a final concentration of 1 M (10 minutes, RT). The cells were washed twice in ice-cold PBS, and harvested in ice-cold lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0,5% NP-40). Nuclei were subsequently released using a Dounce homogenizer, and crude nuclei were resuspended at 10^7 nuclei / mL in RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) and sonicated at high setting in a Bioruptor-Twin (Diagenode) at a volume of 300 μL in 1.5-mL tubes for 40 cycles of 30 seconds on and 30 seconds off. The chromatin IPs were performed as described in (Siersbæk MS, et al. 2012. Mol Cell Biol. 32:3452-3463).
ChIP-seq libraries were constructed according to the manufacturer's instructions (Illumina).

treatment_protocol: Day 7 3T3-L1 adipocytes were treated directly in incubators, by supplementing the culture media with either 1 μM rosiglitazone or 0.1% DMSO (vehicle). Chromatin was harvested after 1 hour of treatment.

value: 3T3-L1 adipocytes

value: 1 μM rosiglitazone / 0.1% DMSO for 1 hour


title: Input, 3T3-L1 Day7 1h DMSO

value: 0.1% DMSO (Vehicle) for 1 hour


title: input DNA SF-1 overexpression


title: zebrafish 5 days old larvae yolk infection with Mycobacterium marinum total RNA

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

description: Wildtype zebrafish injected with Mycobacterium at 2 hpf

data_processing:
Base calling was done by the Illumina HCS version 1.15.1
Sequence reads were quality trimmed using the quality_trim module in the CLCbio Assembly Cell v4.0.6. Filtered reads were mapped to Ensembl transcripts (Zv9_63) using the ref_assemle_short module in the CLCbio Assembly Cell v4.0.6.
Accumulation of transcripts to Ensembl genes was done by first converting the mapping files to a table with the assembly_table module in the CLCbio Assembly Cell v4.0.6. Secondly, a custom script was used that sums all reads belonging to the same gene. Non-uniquely mapped reads were divided between genes according to their ratio of uniquely mapped reads. Finally, read counts of transcripts belonging to the same gene were summed to obtain count data at Ensembl gene level.
Fold-change and differential expression significance values were calculated from gene level read counts using the DESeq package (version 1.8.3) available in Bioconductor (version 2.10).
Genome_build: Zv9 (toplevel)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample mapped to ENSDARG genes

organism: Danio rerio

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol:
Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Zebrafish embryos were either untreated or micro-injected into the yolk (2hpf) with 12 CFU (+/- 7) of Mycobacterium strain E11 mCherry bacteria suspended in PVP (Polyvinylpyrrolidone),  At 5 days post fertilization embryos were snap frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

value: 5 days post fertilisation embryos

tag: agent

value: Mycobacterium marinum


title: CBP ChIP-seq, 3T3-L1 Day7 1h DMSO

value: anti-CBP (sc-369; Santa Cruz)


title: zebrafish 5 days old larvae total RNA

description: Wildtype zebrafish embryos untreated

source_name: zebrafish 5 days old larvae total RNA

value: none (control)


title: zebrafish 5 days old larvae injected with PVP as a control

description: Wildtype zebrafish injected with PVP control 2 hpf

source_name: zebrafish 5 days old larvae injected with PVP total RNA

value: PVP (control)


title: CBP ChIP-seq, 3T3-L1 Day7 1h Rosi


title: Sheep 3 51-53 hours

value: vaccination with liposomes+poly (I:C)+ diptheria toxoid

value: 51-53 hours

value: afferent lymph myeloid cells


title: C/EBPα ChIP-seq, 3T3-L1 Day7 1h Rosi

value: anti-C/EBPα (sc-61; Santa Cruz)


title: RNAPII ChIP-seq, 3T3-L1 Day7 1h DMSO rep2

value: anti-RNAPII (AC-055-100; Diagenode)


title: RNAPII ChIP-seq, 3T3-L1 Day7 1h DMSO rep1


title: RNAPs_ChIP_seq_1

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
The number of sequence reads per base pair was normalized to the total number of reads and expressed as a log2 value.
ChIP-seq reads were alligned to the M. smegmatis Mc2155 genome. Sequences that alligned more than once were discarded except for those corresponding to the ribosomal RNA operons. In this case the reads for the ribosomal RNA were split between operons.
Genome_build: NC_008596.1
Supplementary_files_format_and_content: wig files were generated and the scores represent number of sequence reads per base pair was normalized to the total number of reads and expressed as a log2 value.

organism: Mycolicibacterium smegmatis

growth_protocol: All M. smegmatis strains were isogenic to mc2155 and were grown at 37 oC in LB supplemented with 0.5% dextrose, 0.5% glycerol, and 0.05% Tween 80 to late log phase (OD600 of 1.0) before crosslinking the protein-nucleic acid complexes.

extract_protocol:
1. Monoclonal antibodies specific for HA from Sigma Aldrich and the catalog number is 89658
2. Monoclonal antibodies specific for RNAP beta subunit from Neoclone, Madison, WI. The antibody clone was 8RB13 and the catalog number is WP023
3. Monoclonal antibodies specific for RNAP sigma subunit from Neoclone, Madison, WI. The antibody clone was 2G10 and the catalog number is W0004
The cell pellet was resuspended in TE with protease inhibitors. Cells were lysed and DNA was sheered to 100bp fragments in the Covaris focused ultrasonicator.
Cell lysates (in 50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 1% Triton X-100) containing protein-nucleic acid complexes were incubated with immobilized HA specific antibodies to immunoprecipitate CarD containing complexes from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain and unfused HA from the Mc2155 attB::pmsg431. RNAPb and RNAPs containing complexes were immunoprecipitated  from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain using specific monoclonal antibodies immobilized on Gammabind sepharose. Co-precipitated  complexes were washed 4 times in 10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA with increasing salt. Co-precipitated complexes were eluted in 50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% sodium dodecyl sulfate at 65 oC. Eluate crosslinks were reversed by incubating overnight at 65 oC. The samples were treated with 100 ug/ml of proteinase K to each sample and incubate at 37 oC for 2 hours. DNA was extracted by phenol:chloroform:IAA (25:24:1) extraction, precipitated with ethanol, and resuspended in water.

treatment_protocol: 2% Formaldehyde was added to each culture, which was then incubated shaking at RT for 30 minutes to crosslink DNA and proteins. Glycine was then added to quench the crosslinking and the cells were spun down cells at 4 oC for 10 minutes at 3700 rpm

value: Mc2155 delta-carD attB::tetcarD-HA

tag: growth phase

value: Log


title: RNAPII ChIP-seq, 3T3-L1 Day7 1h Rosi rep2


title: C/EBPα ChIP-seq, 3T3-L1 Day7 1h DMSO


title: RNAPII ChIP-seq, 3T3-L1 Day7 1h Rosi rep1