title: H3K9me2 antibody2 S2-DRSC D.melanogaster ChIP Rep2

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 -m 1 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 alignmentsReads 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. 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 statistically significant enrichment (or depletion) are defined as regions in which enrichment remains above (below) a threshold T. The region has to be longer than a particular size (default 1Kbp), and contain gaps no longer than a particular length. The threshold T is determined to match a given FDR threshold (1e-3 default). For a treshhold T, the FDR is evaluated as (Nr + 1)/(Ns + 1), where Ns is the number of significantly enriched clusters detected using threshold T on the real data, and Nr is the number determined on the randomized data. The randomized data is generated by randomly reshuffling probe intensities relative to the probe positions. If two probe values happen to be present at the same coordinate, their intensity values are shuffled together. A total of 10 (default value) randomly shuffled whole-genome datasets are used for threshold calculation (and FDR is adjusted accordingly).  Processed data are obtained using following parameters: genome version is FlyBase r5

source_name: H3K9me2 antibody2 S2 ChIP expt.742

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

tag: cell line

value: embryo-derived cell-line

value: late embryonic stage

tag: Sex

value: Male


title: H3K9me2 antibody2 S2-DRSC D.melanogaster Input Rep2

status: Public on May 28 2013

type: SRA

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: Served as Input for: enriched.cluster.742.gff3

library_source: genomic

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: H3K9me2 antibody2 S2 Input expt.741

tag: tissue

tag: developmental stage


title: H3K9me2 antibody2 S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: enriched.cluster.568.gff3

source_name: H3K9me2 antibody2 S2 Input expt.567


title: H3K36me2 W 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2396.enrichment.clusters.gff3

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

source_name: H3K36me2 W 14-16 hr OR Emb Input expt.2308

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.
Embryos not older than 16h were collected, bleached in 2.5-3.0% Na-hypochlorite solution, washed two times in cold EWB. Incubated with freshly made 1.8% formaldehyde in X-linking buffer in the presence of of n-heptane.After incubation, embryos were re-suspended in Stop solution Washed at +40C in ChIP wash A solution and then at +40C in ChIP wash B. After sedimentation of the embryos ChIP wash B solution was removed and the embryos were used in an experiment or frozen in liquid N2.
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

tag: strain

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

value: Embryo 14-16hr OR

tag: genotype

value: wild type


title: H3K36me2 W 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K36me2 W 14-16 hr OR Emb ChIP expt.2396


title: H3K36me2 W 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K36me2 W 14-16 hr OR Emb ChIP expt.2397


title: H3K36me2 W OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2394.enrichment.clusters.gff3

source_name: H3K36me2 W OR Head Nuc Input expt.2305

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.
Collection of fly heads from whole adults using sieves of varying sizes.
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: Mixed Adult


title: H3K36me2 W 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2397.enrichment.clusters.gff3

source_name: H3K36me2 W 14-16 hr OR Emb Input expt.2307


title: H3K36me2 W OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2395.enrichment.clusters.gff3

source_name: H3K36me2 W OR Head Nuc Input expt.2306


title: Su var 3-7-Q3448 OR Head Nuclei ChIP Rep2

source_name: Su var 3-7-Q3448 OR Head Nuclei ChIP expt.2220


title: H3K36me2 W OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K36me2 W OR Head Nuc ChIP expt.2394


title: Su var 3-7-Q3448 OR Head Nuclei ChIP Rep1

source_name: Su var 3-7-Q3448 OR Head Nuclei ChIP expt.2219


title: RPD3 Q3451 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2418.enrichment.clusters.gff3

source_name: RPD3 Q3451 OR Head Nuc Input expt.2415


title: RPD3 Q3451 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: RPD3 Q3451 OR Head Nuc ChIP expt.2413


title: POF MO 459 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: POF MO 459 OR Head Nuc ChIP expt.2204


title: POF MO 459 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2204.enrichment.clusters.gff3

source_name: POF MO 459 OR Head Nuc Input expt.2188


title: RPD3 Q3451 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2413.enrichment.clusters.gff3

source_name: RPD3 Q3451 OR Head Nuc Input expt.2183


title: POF MO 459 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: POF MO 459 OR Head Nuc ChIP expt.2203


title: POF MO 459 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2203.enrichment.clusters.gff3

source_name: POF MO 459 OR Head Nuc Input expt.2187


title: LSD1 Q3430 L3 Nuclei D.melanogaster ChIP Rep1

source_name: LSD1 Q3430 L3 Nuc ChIP expt.2499

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: 3rd Instar Larvae


title: LSD1 Q3430 L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2499.enrichment.clusters.gff3

source_name: LSD1 Q3430 L3 Nuc Input expt.2493


title: LSD1 Q3430 L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2500.enrichment.clusters.gff3

source_name: LSD1 Q3430 L3 Nuc Input expt.2494


title: H3K36me2 W OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K36me2 W OR Head Nuc ChIP expt.2395


title: JMJD2A-KDM4A Q2541 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: JMJD2A-KDM4A Q2541 OR Head Nuc ChIP expt.2315


title: JMJD2A-KDM4A Q2541 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: JMJD2A-KDM4A Q2541 OR Head Nuc ChIP expt.2314


title: H3K9me2 antibody2 S2-DRSC D.melanogaster ChIP Rep1

source_name: H3K9me2 antibody2 S2 ChIP expt.568


title: JMJD2A-KDM4A Q2541 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2315.enrichment.clusters.gff3

source_name: JMJD2A-KDM4A Q2541 OR Head Nuc Input expt.2271


title: JMJD2A-KDM4A Q2541 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2314.enrichment.clusters.gff3

source_name: JMJD2A-KDM4A Q2541 OR Head Nuc Input expt.2270


title: Su var 3-7-Q3448 OR Head Nuclei Input Rep2

description: Served as Input for: 2220.enrichment.clusters.gff3

source_name: Su var 3-7-Q3448 OR Head Nuclei Input expt.2188


title: HP2 Ab2-90 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: HP2 Ab2-90 OR Head Nuc ChIP expt.2193


title: HP2 Ab2-90 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2194.enrichment.clusters.gff3

source_name: HP2 Ab2-90 OR Head Nuc Input expt.2188


title: HP1c MO 462 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: HP1c MO 462 OR Head Nuclei D.melanogaster ChIP expt.2198


title: HP1 wa191 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2217.enrichment.clusters.gff3

source_name: HP1 wa191 OR Head Nuc Input expt.2211


title: HP1c MO 462 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: HP1c MO 462 OR Head Nuclei D.melanogaster ChIP expt.2197


title: HP2 Ab2-90 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2193.enrichment.clusters.gff3

source_name: HP2 Ab2-90 OR Head Nuc Input expt.2187


title: HP1b Q4114 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2196.enrichment.clusters.gff3

source_name: HP1b Q4114 OR Head Nuc Input expt.2188


title: HP1c MO 462 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2198.enrichment.clusters.gff3

source_name: HP1c MO 462 OR Head Nuclei D.melanogaster Input expt.2188


title: H3K79me3 Abcam ab2621 lot 1 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K79me3 Abcam ab2621 lot 1 14-16 hr OR Emb ChIP expt.2547


title: HP1c MO 462 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2197.enrichment.clusters.gff3

source_name: HP1c MO 462 OR Head Nuclei D.melanogaster Input expt.2187


title: LSD1 Q3430 L3 Nuclei D.melanogaster ChIP Rep2

source_name: LSD1 Q3430 L3 Nuc ChIP expt.2500


title: HP1b Q4114 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: HP1b Q4114 OR Head Nuc ChIP expt.2195


title: H3K79me3 Abcam ab2621 lot 1 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2547.enrichment.clusters.gff3

source_name: H3K79me3 Abcam ab2621 lot 1 14-16 hr OR Emb Input expt.2470


title: H3K79me3 Abcam ab2621 lot 1 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K79me3 Abcam ab2621 lot 1 14-16 hr OR Emb ChIP expt.2548


title: H3K9acS10P new lot OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K9acS10P new lot OR Head Nuc ChIP expt.2202


title: H3K9acS10P new lot OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K9acS10P new lot OR Head Nuc ChIP expt.2201


title: HP1 wa191 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2218.enrichment.clusters.gff3

source_name: HP1 wa191 OR Head Nuc Input expt.2212


title: HP1 wa191 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: HP1 wa191 OR Head Nuc ChIP expt.2217


title: H3K9acS10P new lot OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2202.enrichment.clusters.gff3

source_name: H3K9acS10P new lot OR Head Nuc Input expt.2188


title: HP1c MO 462 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: HP1c MO 462 14-16 hr OR Emb ChIP expt.2541


title: HP1c MO 462 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2541.enrichment.clusters.gff3

source_name: HP1c MO 462 14-16 hr OR Emb Input expt.2471


title: HP1c MO 462 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: HP1c MO 462 14-16 hr OR Emb ChIP expt.2032


title: H3K79me3 Abcam ab2621 lot 1 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2548.enrichment.clusters.gff3

source_name: H3K79me3 Abcam ab2621 lot 1 14-16 hr OR Emb Input expt.2471


title: HP1 wa191 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: HP1 wa191 OR Head Nuc ChIP expt.2218


title: H3K79me3 Abcam ab2621 lot 1 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K79me3 Abcam ab2621 lot 1 OR Head Nuc ChIP expt.2373


title: HP1b Q4114 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: HP1b Q4114 OR Head Nuc ChIP expt.2196


title: HP1b Q4114 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2195.enrichment.clusters.gff3

source_name: HP1b Q4114 OR Head Nuc Input expt.2187


title: H3K79me3 Abcam ab2621 lot 1 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K79me3 Abcam ab2621 lot 1 OR Head Nuc ChIP expt.2372


title: H3K79me3 Abcam ab2621 lot 1 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2373.enrichment.clusters.gff3

source_name: H3K79me3 Abcam ab2621 lot 1 OR Head Nuc Input expt.2353


title: H3K79me2 Abcam ab3594 lot 1 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K79me2 Abcam ab3594 lot 1 OR Head Nuc ChIP expt.2371


title: H3K79me2 Abcam ab3594 lot 1 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K79me2 Abcam ab3594 lot 1 OR Head Nuc ChIP expt.2370


title: H3K79me1 Abcam lot 1 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K79me1 Abcam lot 1 OR Head Nuc ChIP expt.2369


title: H3K79me2 Abcam ab3594 lot 1 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2370.enrichment.clusters.gff3

source_name: H3K79me2 Abcam ab3594 lot 1 OR Head Nuc Input expt.2352


title: H3K79me1 Abcam lot 1 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K79me1 Abcam lot 1 OR Head Nuc ChIP expt.2368


title: H3K9acS10P new lot OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2201.enrichment.clusters.gff3

source_name: H3K9acS10P new lot OR Head Nuc Input expt.2187


title: HP1c MO 462 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2032.enrichment.clusters.gff3

source_name: HP1c MO 462 14-16 hr OR Emb Input expt.2024


title: H3K27me3 Abcam lot3 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2365.enrichment.clusters.gff3

source_name: H3K27me3 Abcam lot3 OR Head Nuc Input expt.2353


title: H3K27me3 Abcam lot3 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2364.enrichment.clusters.gff3

source_name: H3K27me3 Abcam lot3 OR Head Nuc Input expt.2352


title: H3K27me3 Abcam lot3 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K27me3 Abcam lot3 OR Head Nuc ChIP expt.2365


title: H4K8ac OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H4K8ac OR Head Nuc ChIP expt.2299


title: H4K8ac OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H4K8ac OR Head Nuc ChIP expt.2300


title: H3K27me2 Ab24684 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2362.enrichment.clusters.gff3

source_name: H3K27me2 Ab24684 OR Head Nuc Input expt.2352


title: H3K27me2 Ab24684 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K27me2 Ab24684 OR Head Nuc ChIP expt.2362


title: H3K27me2 Ab24684 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2363.enrichment.clusters.gff3

source_name: H3K27me2 Ab24684 OR Head Nuc Input expt.2353


title: H4K8ac OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2299.enrichment.clusters.gff3

source_name: H4K8ac OR Head Nuc Input expt.2305


title: H3K27me2 Ab24684 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K27me2 Ab24684 OR Head Nuc ChIP expt.2363


title: H3K79me1 Abcam lot 1 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2368.enrichment.clusters.gff3

source_name: H3K79me1 Abcam lot 1 OR Head Nuc Input expt.2352


title: H4K8ac OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2300.enrichment.clusters.gff3

source_name: H4K8ac OR Head Nuc Input expt.2306


title: H3K27me3 Abcam lot3 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K27me3 Abcam lot3 OR Head Nuc ChIP expt.2364


title: H3K79me3 Abcam ab2621 lot 1 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2372.enrichment.clusters.gff3

source_name: H3K79me3 Abcam ab2621 lot 1 OR Head Nuc Input expt.2352


title: H3K27ac Active Motif OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K27ac Active Motif OR Head Nuc ChIP expt.2367


title: H3K27ac Active Motif OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2366.enrichment.clusters.gff3

source_name: H3K27ac Active Motif OR Head Nuc Input expt.2352


title: H3K79me2 Abcam ab3594 lot 1 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2371.enrichment.clusters.gff3

source_name: H3K79me2 Abcam ab3594 lot 1 OR Head Nuc Input expt.2353


title: H3K27ac Active Motif OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K27ac Active Motif OR Head Nuc ChIP expt.2366


title: dSFMBT Q2642 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: dSFMBT Q2642 OR Head Nuc ChIP expt.2428


title: H3K79me1 Abcam lot 1 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2369.enrichment.clusters.gff3

source_name: H3K79me1 Abcam lot 1 OR Head Nuc Input expt.2353


title: dSFMBT Q2642 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: dSFMBT Q2642 OR Head Nuc ChIP expt.2427


title: dSFMBT Q2642 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2427.enrichment.clusters.gff3

source_name: dSFMBT Q2642 OR Head Nuc Input expt.2352


title: JHDM1 Q2634 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: JHDM1 Q2634 OR Head Nuc ChIP expt.2407


title: dSFMBT Q2642 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2428.enrichment.clusters.gff3

source_name: dSFMBT Q2642 OR Head Nuc Input expt.2353


title: JHDM1 Q2634 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: JHDM1 Q2634 OR Head Nuc ChIP expt.2406


title: JHDM1 Q2634 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2407.enrichment.clusters.gff3

source_name: JHDM1 Q2634 OR Head Nuc Input expt.2271


title: LSD1 Q3430 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: LSD1 Q3430 OR Head Nuc ChIP expt.2422


title: LSD1 Q3430 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: LSD1 Q3430 OR Head Nuc ChIP expt.2421


title: HP2 Ab2-90 14-16 hr OR Embryo D.melanogaster ChIP Rep3

source_name: HP2 Ab2-90 14-16 hr OR Emb ChIP expt.2029


title: LSD1 Q3430 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2421.enrichment.clusters.gff3

source_name: LSD1 Q3430 OR Head Nuc Input expt.2270


title: HP2 Ab2-90 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: HP2 Ab2-90 14-16 hr OR Emb ChIP expt.2028


title: LSD1 Q3430 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2422.enrichment.clusters.gff3

source_name: LSD1 Q3430 OR Head Nuc Input expt.2271


title: H3K27ac Active Motif OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2367.enrichment.clusters.gff3

source_name: H3K27ac Active Motif OR Head Nuc Input expt.2353


title: HP2 Ab2-90 14-16 hr OR Embryo D.melanogaster Input Rep3

description: Served as Input for: 2029.enrichment.clusters.gff3

source_name: HP2 Ab2-90 14-16 hr OR Emb Input expt.2025


title: HP2 Ab2-90 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: HP2 Ab2-90 14-16 hr OR Emb ChIP expt.1736


title: H1 14-16 hr OR Embryo D.melanogaster Input Rep4

description: Served as Input for: 2292.enrichment.clusters.gff3

source_name: H1 14-16 hr OR Emb Input expt.2308


title: HP2 Ab2-90 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1736.enrichment.clusters.gff3

source_name: HP2 Ab2-90 14-16 hr OR Emb Input expt.1733


title: H3K9me2 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2200.enrichment.clusters.gff3

source_name: H3K9me2 OR Head Nuc Input expt.2188


title: HP2 Ab2-90 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2028.enrichment.clusters.gff3

source_name: HP2 Ab2-90 14-16 hr OR Emb Input expt.2024


title: H2AV 9751 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H2AV 9751 OR Head Nuc ChIP expt.2272


title: H3K9me2 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2380.enrichment.clusters.gff3

source_name: H3K9me2 OR Head Nuc Input expt.2416


title: H2AV 9751 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2273.enrichment.clusters.gff3

source_name: H2AV 9751 OR Head Nuc Input expt.2271


title: H2AV 9751 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H2AV 9751 OR Head Nuc ChIP expt.2273


title: H3K9me2 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K9me2 OR Head Nuc ChIP expt.2380


title: H1 14-16 hr OR Embryo D.melanogaster Input Rep3

description: Served as Input for: 2291.enrichment.clusters.gff3

source_name: H1 14-16 hr OR Emb Input expt.2307


title: JHDM1 Q2634 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2406.enrichment.clusters.gff3

source_name: JHDM1 Q2634 OR Head Nuc Input expt.2270


title: H1 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H1 14-16 hr OR Emb ChIP expt.1715


title: H1 14-16 hr OR Embryo D.melanogaster ChIP Rep3

source_name: H1 14-16 hr OR Emb ChIP expt.2291


title: H2AV 9751 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2272.enrichment.clusters.gff3

source_name: H2AV 9751 OR Head Nuc Input expt.2270


title: H3K9me2 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K9me2 OR Head Nuc ChIP expt.2200


title: H1 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1715.enrichment.clusters.gff3

source_name: H1 14-16 hr OR Emb Input expt.1729


title: H1 14-16 hr OR Embryo D.melanogaster ChIP Rep4

source_name: H1 14-16 hr OR Emb ChIP expt.2292


title: RPD3 Q3451 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: RPD3 Q3451 OR Head Nuc ChIP expt.2418


title: H1 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1725.enrichment.clusters.gff3

source_name: H1 14-16 hr OR Emb Input expt.1730


title: H1 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H1 14-16 hr OR Emb ChIP expt.1725


title: ZW5 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1827.enrichment.clusters.gff3

source_name: ZW5 14-16 hr OR Emb Input expt.1823


title: ZW5 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1966.enrichment.clusters.gff3

source_name: ZW5 14-16 hr OR Emb Input expt.1962


title: Su var 3-7 Q3448 L3 Nuclei D.melanogaster ChIP Rep2

source_name: Su var 3-7 Q3448 L3 Nuc ChIP expt.2236


title: Su var 3-7 Q3448 L3 Nuclei D.melanogaster ChIP Rep1

source_name: Su var 3-7 Q3448 L3 Nuc ChIP expt.2235


title: ZW5 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: ZW5 14-16 hr OR Emb ChIP expt.1827


title: Su var 3-7 Q3448 L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2235.enrichment.clusters.gff3

source_name: Su var 3-7 Q3448 L3 Nuc Input expt.2221


title: Su var 3-7-Q3448 OR Head Nuclei Input Rep1

description: Served as Input for: 2219.enrichment.clusters.gff3

source_name: Su var 3-7-Q3448 OR Head Nuclei Input expt.2187


title: RPD3-Q3451 L3 Nuclei D.melanogaster ChIP Rep1

source_name: RPD3-Q3451 L3 Nuc ChIP expt.2231


title: RPD3-Q3451 L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2231.enrichment.clusters.gff3

source_name: RPD3-Q3451 L3 Nuc Input expt.2221


title: RNA Pol II abcam OR Head Nuclei D.melanogaster ChIP Rep2

source_name: RNA Pol II abcam OR Head Nuc ChIP expt.2419


title: RPD3-Q3451 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: RPD3-Q3451 14-16 hr OR Emb ChIP expt.2484


title: RPD3-Q3451 L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2232.enrichment.clusters.gff3

source_name: RPD3-Q3451 L3 Nuc Input expt.2223


title: Su var 3-7 Q3448 L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2236.enrichment.clusters.gff3

source_name: Su var 3-7 Q3448 L3 Nuc Input expt.2223


title: RPD3-Q3451 L3 Nuclei D.melanogaster ChIP Rep2

source_name: RPD3-Q3451 L3 Nuc ChIP expt.2232


title: RPD3-Q3451 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: RPD3-Q3451 14-16 hr OR Emb ChIP expt.2485


title: RPD3-Q3451 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2484.enrichment.clusters.gff3

source_name: RPD3-Q3451 14-16 hr OR Emb Input expt.1733


title: RPD3-Q3451 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2485.enrichment.clusters.gff3

source_name: RPD3-Q3451 14-16 hr OR Emb Input expt.1734


title: RNA Pol II abcam OR Head Nuclei D.melanogaster ChIP Rep1

source_name: RNA Pol II abcam OR Head Nuc ChIP expt.2414


title: ZW5 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: ZW5 14-16 hr OR Emb ChIP expt.1966


title: RNA Pol II abcam OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2419.enrichment.clusters.gff3

source_name: RNA Pol II abcam OR Head Nuc Input expt.2415


title: RNA Pol II abcam OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2414.enrichment.clusters.gff3

source_name: RNA Pol II abcam OR Head Nuc Input expt.2183


title: RNA Pol II abcam L3 Nuclei D.melanogaster ChIP Rep2

source_name: RNA Pol II abcam L3 Nuc ChIP expt.2412


title: RNA Pol II abcam L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2256.enrichment.clusters.gff3

source_name: RNA Pol II abcam L3 Nuc Input expt.2226


title: RNA Pol II abcam 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: RNA Pol II abcam 14-16 hr OR Emb ChIP expt.2481


title: RNA Pol II abcam 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2481.enrichment.clusters.gff3

source_name: RNA Pol II abcam 14-16 hr OR Emb Input expt.1656


title: RNA Pol II abcam 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: RNA Pol II abcam 14-16 hr OR Emb ChIP expt.2480


title: RNA Pol II abcam 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2480.enrichment.clusters.gff3

source_name: RNA Pol II abcam 14-16 hr OR Emb Input expt.1655


title: POF MO 459 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: POF MO 459 14-16 hr OR Emb ChIP expt.1654


title: POF MO 459 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1654.enrichment.clusters.gff3

source_name: POF MO 459 14-16 hr OR Emb Input expt.1656


title: POF MO 459 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: POF MO 459 14-16 hr OR Emb ChIP expt.1653


title: MEF_rep1_rep2

city: Beijing

first: Hongkui

last: Deng

address: 5th Yiheyuan Road

country: China

institute: Peking University

description:
This Sample represents 2 replicates.
RPKM values and differential expression in the processed data file.
Processed data file: GSE47442_MEF_SKM.GeneDiffExp.txt

library_source: transcriptomic

data_processing:
Reads mapping: We used Tophat 1.3.0. to align the clean reads to the mm9 RefSeq.
Expression level analysis: The gene expression level was calculated by using the RPKM method.
Normalized differentially expressed (DE) genes were detected. The provided P value (Poisson distribution) corresponds to the differential gene expression test. Because the DE gene analysis generated a large multiplicity problem, in which thousands of hypotheses were tested simultaneously, correction for false positive (type I) and false negative (type II) errors was performed using the FDR method. An FDR < 0.01 and an absolute value of the log2 ratio > 1 were used as the threshold to declare gene expression differences as significant.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited text file. RPKM values for two replicates and differential expression.

molecule: total RNA

organism: Mus musculus

source_name: MEFs infected with empty vector

growth_protocol: Culture in Dulbecco's Modified Eagle Medium (DMEM, Hyclone), containing 10% Fetal bovine serum (Hyclone), 2x penicillin/streptomycin (Invitrogen). 37℃. The dox-inducible lentiviral system used has been previously described (Maherali et al., 2008).

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Sigma). Genomic DNA were removed with DNase (Ambion).
Amplified single cell cDNAs were further amplied for another ten cycles of PCR. Then it was sonicated into 200~500bp fragments, then the standard TruSeq DNA library preparation kit was used following the suggested protocol in the manual.

treatment_protocol: In brief, the limbs and tails of  mice were cut off, and the skin was carefully peeled. The isolated mouse skin was then incubated in Collagenase type IV (2mg/ml, Gibco) for 2hrs at 37C. After incubation, the epiderm was carefully removed from the surface of the skin. The remaining tissues were dissociated and minced into 1mm pieces, which were then resuspended by Dulbecco's Modified Eagle Medium (DMEM, Hyclone), containing 10% Fetal bovine serum (Hyclone), 2x penicillin/streptomycin (Invitrogen). The isolated  skin fibroblasts were collected by flowing through cell strainers.

value: OGXICR

tag: age

value: skin

tag: cell type

value: mouse embryonic fibroblasts

tag: infection

value: empty vector


title: SKM_rep1_rep2

description:
This Sample represents 2 replicates.
RPKM values and differential expression in the processed data file.
Processed data file: GSE47442_MEF_SKM.GeneDiffExp.txt
Processed data file: GSE47442_OSKM_SKM.GeneDiffExp.txt
Processed data file: GSE47442_G3SKM_SKM.GeneDiffExp.txt

source_name: MEFs infected with SOX2, KLF4, c-MYC

value: SKM


title: G3SKM_rep1_rep2

description:
This Sample represents 2 replicates.
RPKM values and differential expression in the processed data file.
Processed data file: GSE47442_G3SKM_SKM.GeneDiffExp.txt

source_name: MEFs infected with GATA3, SOX2, KLF4, c-MYC


title: OSKM_rep1_rep2

description:
This Sample represents 2 replicates.
RPKM values and differential expression in the processed data file.
Processed data file: GSE47442_OSKM_SKM.GeneDiffExp.txt

source_name: MEFs infected with OCT4, SOX2, KLF4, c-MYC

value: OSKM


title: RNA Pol II abcam L3 Nuclei D.melanogaster ChIP Rep1

source_name: RNA Pol II abcam L3 Nuc ChIP expt.2256


title: POF MO 459 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1653.enrichment.clusters.gff3

source_name: POF MO 459 14-16 hr OR Emb Input expt.1655


title: RNA Pol II abcam L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2412.enrichment.clusters.gff3

source_name: RNA Pol II abcam L3 Nuc Input expt.2225


title: MBD-R2 Q4167 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2443.enrichment.clusters.gff3

source_name: MBD-R2 Q4167 14-16 hr OR Emb Input expt.2307


title: NURF301 Q2602 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2455.enrichment.clusters.gff3

source_name: NURF301 Q2602 14-16 hr OR Emb Input expt.2307


title: NURF301 Q2602 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: NURF301 Q2602 14-16 hr OR Emb ChIP expt.2456


title: MBD-R2 Q4167 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2444.enrichment.clusters.gff3

source_name: MBD-R2 Q4167 14-16 hr OR Emb Input expt.2308


title: MOF Q4145 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1723.enrichment.clusters.gff3

source_name: MOF Q4145 14-16 hr OR Emb Input expt.1730


title: MOF Q4145 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: MOF Q4145 14-16 hr OR Emb ChIP expt.1723


title: MBD-R2 Q4167 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: MBD-R2 Q4167 14-16 hr OR Emb ChIP expt.2443


title: LSD1 Q3430 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: LSD1 Q3430 14-16 hr OR Emb ChIP expt.1749


title: LSD1 Q3430 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: LSD1 Q3430 14-16 hr OR Emb ChIP expt.1748


title: NURF301 Q2602 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2456.enrichment.clusters.gff3

source_name: NURF301 Q2602 14-16 hr OR Emb Input expt.2308


title: MBD-R2 Q4167 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: MBD-R2 Q4167 14-16 hr OR Emb ChIP expt.2444


title: MOF Q4145 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1713.enrichment.clusters.gff3

source_name: MOF Q4145 14-16 hr OR Emb Input expt.1729


title: NURF301 Q2602 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: NURF301 Q2602 14-16 hr OR Emb ChIP expt.2455


title: LSD1 Q3430 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1749.enrichment.clusters.gff3

source_name: LSD1 Q3430 14-16 hr OR Emb Input expt.1658


title: JHDM1 Q2634 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: JHDM1 Q2634 14-16 hr OR Emb ChIP expt.1664


title: BTV

city: Hangzhou

first: Xiaowei

last: Wang

address: 866 Yuhangtang Road

department: Insect Sciences

institute: Zhejiang University

description: obtain virus on infected tobacco plants

data_processing: The adapter-ligated tags are fixed on the Solexa Sequencing Chip to form single-molecule cluster, and then sequencing by synthesis is performed to generate millions of raw data with sequencing length of 35bp. Raw sequences were transformed into clean tags through removing adaptor sequence, low quality sequences. For annotation, all tags were mapped to the reference sequences and only allowed no more than 1 nucleotide mismatch. For gene expression analysis, the number of unambiguous clean tags for each gene was calculated and then normalized to TPM.

organism: Bemisia tabaci

source_name: Viruliferous whitefly on tobacco

growth_protocol: Culture of B biotype whitefly was maintained on cotton plants.

extract_protocol: 1. mRNA is captured using the magnetic oligo(dT) beads from the extracted total RNA and first- and second-strand cDNA is synthesized. 2. Bead-bound cDNA is subsequently digested with restriction enzyme NlaIII (recognition sequence CATG). 3. The fragments apart from the 3âcDNA fragments connected to oligo(dT) beads are washed away and a special adapter containing a restriction site for MmeI is ligated to the sticky 5âend of the digested bead-bound cDNA fragments. 4. The MmeI cuts 17 bp downstream from the recognition site, then product the 21 bp tag starting with the recognition site of restriction enzyme NlaIII (CATG). 5. A second adapter is ligated at the site of MmeI cleavage. After enriched by polymerase chain reaction (PCR) amplification, the adapter-ligated tags are purified by 6% tris borate (TBE) buffer, polyacrylamide gel electrophoresis (PAGE).

treatment_protocol: One thousand of newly emerged adults of whitefly on cotton were released onto the leaves of healthy and viruliferous tobacco plants. After 72 h of oviposition, all the adult whiteflies were discarded, and the progeny allowed to develop to adults. The cultures of MEAM1 on tobacco plants were maintained in climate chambers at 27 Â± 1Â°C, a photoperiod of 14 h light/10 h darkness and 70 Â± 10% relative humidity. Approximately 1,000 female adult whiteflies newly emerged from mock-inoculated tobacco plants and 1,000 female adult whiteflies newly emerged from virus-infected tobacco plants were collected and stored at -80Â°C The RNA was extracted and sequenced using Illunima Analyzer II.

tag: biotype

value: B biotype (MEAM1)

tag: growth condition

value: harvested from tobacco infected with TYLCCNV


title: BT

description: on healthy tobacco plants as an control

source_name: Non-viruliferous whitefly on tobacco

value: harvested from healthy tobacco


title: JHDM1 Q2634 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2098.enrichment.clusters.gff3

source_name: JHDM1 Q2634 14-16 hr OR Emb Input expt.1657


title: HP2 Ab2-90 L3 Nuclei D.melanogaster ChIP Rep1

source_name: HP2 Ab2-90 L3 Nuc ChIP expt.2247


title: HP2 Ab2-90 L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2247.enrichment.clusters.gff3

source_name: HP2 Ab2-90 L3 Nuc Input expt.2222


title: HP2 Ab2-90 L3 Nuclei D.melanogaster ChIP Rep2

source_name: HP2 Ab2-90 L3 Nuc ChIP expt.2248


title: HP2 Ab2-90 L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2248.enrichment.clusters.gff3

source_name: HP2 Ab2-90 L3 Nuc Input expt.2224


title: MOF Q4145 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: MOF Q4145 14-16 hr OR Emb ChIP expt.1713


title: HP2 Ab2-90 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: HP2 Ab2-90 OR Head Nuc ChIP expt.2194


title: HP1b Q4114 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2031.enrichment.clusters.gff3

source_name: HP1b Q4114 14-16 hr OR Emb Input expt.2025


title: HP1b Q4114 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: HP1b Q4114 14-16 hr OR Emb ChIP expt.2031


title: HP1b Q4114 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2030.enrichment.clusters.gff3

source_name: HP1b Q4114 14-16 hr OR Emb Input expt.2024


title: H4K16ac M OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H4K16ac M OR Head Nuc ChIP expt.2303


title: H4K20me1 4th lot 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2496.enrichment.clusters.gff3

source_name: H4K20me1 4th lot 14-16 hr OR Emb Input expt.2471


title: LSD1 Q3430 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1748.enrichment.clusters.gff3

source_name: LSD1 Q3430 14-16 hr OR Emb Input expt.1657


title: H4K20me1 4th lot 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2495.enrichment.clusters.gff3

source_name: H4K20me1 4th lot 14-16 hr OR Emb Input expt.2470


title: H4K20me1 4th lot 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H4K20me1 4th lot 14-16 hr OR Emb ChIP expt.2495


title: H4K20me1 4th lot 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H4K20me1 4th lot 14-16 hr OR Emb ChIP expt.2496


title: H4K16ac M OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H4K16ac M OR Head Nuc ChIP expt.2304


title: H4 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2475.enrichment.clusters.gff3

source_name: H4 14-16 hr OR Emb Input expt.2471


title: H4K16ac M OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2304.enrichment.clusters.gff3

source_name: H4K16ac M OR Head Nuc Input expt.2306


title: H4K16ac M OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2303.enrichment.clusters.gff3

source_name: H4K16ac M OR Head Nuc Input expt.2305


title: H4 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H4 14-16 hr OR Emb ChIP expt.2474


title: H4 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H4 14-16 hr OR Emb ChIP expt.2475


title: H3K9me1 new lot 2 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K9me1 new lot 2 OR Head Nuc ChIP expt.2378


title: JHDM1 Q2634 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1664.enrichment.clusters.gff3

source_name: JHDM1 Q2634 14-16 hr OR Emb Input expt.1658


title: JHDM1 Q2634 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: JHDM1 Q2634 14-16 hr OR Emb ChIP expt.2098


title: H3K9me1 new lot 2 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K9me1 new lot 2 OR Head Nuc ChIP expt.2379


title: H4 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2474.enrichment.clusters.gff3

source_name: H4 14-16 hr OR Emb Input expt.2470


title: H3K9me1 new lot 2 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2378.enrichment.clusters.gff3

source_name: H3K9me1 new lot 2 OR Head Nuc Input expt.2416


title: H3K9me1 new lot 2 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2379.enrichment.clusters.gff3

source_name: H3K9me1 new lot 2 OR Head Nuc Input expt.2417


title: H3K9me1 new lot 2 L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2383.enrichment.clusters.gff3

source_name: H3K9me1 new lot 2 L3 Nuc Input expt.2420


title: H3K9me1 new lot 2 L3 Nuclei D.melanogaster ChIP Rep1

source_name: H3K9me1 new lot 2 L3 Nuc ChIP expt.2382


title: HP1b Q4114 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: HP1b Q4114 14-16 hr OR Emb ChIP expt.2030


title: H3K9acS10P new abcam lot L3 Nuclei D.melanogaster ChIP Rep2

source_name: H3K9acS10P new abcam lot L3 Nuc ChIP expt.2246


title: H3K9acS10P new abcam lot L3 Nuclei D.melanogaster ChIP Rep1

source_name: H3K9acS10P new abcam lot L3 Nuc ChIP expt.2245


title: H3K9acS10P new abcam lot L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2246.enrichment.clusters.gff3

source_name: H3K9acS10P new abcam lot L3 Nuc Input expt.2224


title: H3K9acS10P new abcam lot L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2245.enrichment.clusters.gff3

source_name: H3K9acS10P new abcam lot L3 Nuc Input expt.2222


title: H3K9acS10P Ab12181 lot838296 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K9acS10P Ab12181 lot838296 14-16 hr OR Emb ChIP expt.2023


title: H3K9acS10P Ab12181 lot838296 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K9acS10P Ab12181 lot838296 14-16 hr OR Emb ChIP expt.2022


title: H3K4me3 ab8580 lot 2 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K4me3 ab8580 lot 2 OR Head Nuc ChIP expt.2359


title: H3K4me3 ab8580 lot 2 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K4me3 ab8580 lot 2 OR Head Nuc ChIP expt.2358


title: H3K9acS10P Ab12181 lot838296 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2022.enrichment.clusters.gff3

source_name: H3K9acS10P Ab12181 lot838296 14-16 hr OR Emb Input expt.1655


title: H3K4me3 ab8580 lot 2 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2359.enrichment.clusters.gff3

source_name: H3K4me3 ab8580 lot 2 OR Head Nuc Input expt.2353


title: H3K9acS10P Ab12181 lot838296 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2023.enrichment.clusters.gff3

source_name: H3K9acS10P Ab12181 lot838296 14-16 hr OR Emb Input expt.1656


title: H3K4me3 ab8580 lot 2 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2358.enrichment.clusters.gff3

source_name: H3K4me3 ab8580 lot 2 OR Head Nuc Input expt.2352


title: H3K4me3 ab8580 lot 2 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K4me3 ab8580 lot 2 14-16 hr OR Emb ChIP expt.1960


title: H3K9me1 new lot 2 L3 Nuclei D.melanogaster ChIP Rep2

source_name: H3K9me1 new lot 2 L3 Nuc ChIP expt.2383


title: H3K4me2-Active motif OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K4me2-Active motif OR Head Nuc ChIP expt.2357


title: H3K9me1 new lot 2 L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2382.enrichment.clusters.gff3

source_name: H3K9me1 new lot 2 L3 Nuc Input expt.2227


title: H3K4me3 ab8580 lot 2 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K4me3 ab8580 lot 2 14-16 hr OR Emb ChIP expt.1977


title: H3K4me3 ab8580 lot 2 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1977.enrichment.clusters.gff3

source_name: H3K4me3 ab8580 lot 2 14-16 hr OR Emb Input expt.1815


title: H3K4me2-Active motif OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K4me2-Active motif OR Head Nuc ChIP expt.2356


title: wt 2hrs Rep2

city: Manchester

first: Abbie

last: Saunders

address: D.1401 Michael Smith Building, Oxford Road

department: Faculty of Life Sciences

country: United Kingdom

institute: University of Manchester

description:
nascent RNA
Nuclear Run-On

data_processing:
5'-barcode (4 bases) were used to split raw files and the barcodes were also removed.
GRO-seq libraries were sequenced on the Illumina Genome Analyzer II, using standard protocol at the Cornell bioresources center (http//www.BRC.cornell.edu). Bowtie (Langmead, Trapnell, et al, 2009) was used to map 26mers, with up to two mismatches to the DM3 version on the Drosophila genome.  Reads were also mapped to a representative of repetitive genes transcribed specifically by Pol I (rRNA gene; GenBank accession #: M21017.1), and Pol III (tRNAs; parsed from flybase gene set described below).  The rRNA included the extragenic spacers, and tRNAs, were extended +/- 100 bases to account for nascent transcripts that are processed and not part of the annotated tRNA.
Genome_build: dm3
Supplementary_files_format_and_content: bedgraph

source_name: wt 2hrs

extract_protocol:
Staged embryos were collected from yellow white flies, rinsed thoroughly, flash frozen, and stored at -80°C. Embryos were resuspended in cold buffer 1 [250mM sucrose, 10mM Tris pH7.5, 5mM MgCl2, 0.1% triton x-100, 1mM EGTA, 5mM DTT, 1X protease inhibitor cocktail (Roche), 1:5000 superasin (Ambion)] plus 3mM CaCl2, loose dounced 20X, then poured over mesh to remove large debris, and tight dounced a further 10X, at 4°C. Nuclei were pelleted at 700g for 10min at 4°C, washed twice in buffer 1, then once in freezing buffer [50mM Tris pH8.0, 25% glycerol, 5mM MgAc2, 0.1mM EDTA, 5mM DTT, 1X protease inhibitor cocktail (Roche), 1:2500 superasin (Ambion)]. Nuclei were then resuspended in freezing buffer, flash frozen, and stored at -80°C. 7-30X107 nuclei were used in each run-on reaction.
The run-on RNA library was prepared as in Core et al. (2008, Science 322: 1845), with 25min base hydrolysis, and sequenced on the Illumina Genome Analyzer in the Core Laboratories Center at Cornell University, USA.

tag: time

value: embryo

value: yw


title: wt 3hrs Rep2

description:
nascent RNA
Nuclear Run-On

source_name: wt 3hrs


title: wt 3hrs Rep1

description:
nascent RNA
Nuclear Run-On


title: H3K4me2-Active motif OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2357.enrichment.clusters.gff3

source_name: H3K4me2-Active motif OR Head Nuc Input expt.2353


title: H3K4me2-Active motif OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2356.enrichment.clusters.gff3

source_name: H3K4me2-Active motif OR Head Nuc Input expt.2352


title: wt 2hrs Rep1

description:
nascent RNA
Nuclear Run-On


title: H3K4me1 ab8895 new lot 2 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2354.enrichment.clusters.gff3

source_name: H3K4me1 ab8895 new lot 2 OR Head Nuc Input expt.2352


title: H3K4me1 ab8895 new lot 2 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2355.enrichment.clusters.gff3

source_name: H3K4me1 ab8895 new lot 2 OR Head Nuc Input expt.2353


title: H3K4me1 ab8895 new lot 2 L3 Nuclei D.melanogaster ChIP Rep1

source_name: H3K4me1 ab8895 new lot 2 L3 Nuc ChIP expt.2332


title: H3K4me1 ab8895 new lot 2 L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2333.enrichment.clusters.gff3

source_name: H3K4me1 ab8895 new lot 2 L3 Nuc Input expt.2331


title: H3K4me1 ab8895 new lot 2 L3 Nuclei D.melanogaster ChIP Rep2

source_name: H3K4me1 ab8895 new lot 2 L3 Nuc ChIP expt.2333


title: H3K4me1 ab8895 new lot 2 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K4me1 ab8895 new lot 2 OR Head Nuc ChIP expt.2354


title: H3K4me1 ab8895 new lot 2 L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2332.enrichment.clusters.gff3

source_name: H3K4me1 ab8895 new lot 2 L3 Nuc Input expt.2330


title: H3K4me1 ab8895 new lot 2 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1958.enrichment.clusters.gff3

source_name: H3K4me1 ab8895 new lot 2 14-16 hr OR Emb Input expt.1962


title: H3K4me1 ab8895 new lot 2 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K4me1 ab8895 new lot 2 14-16 hr OR Emb ChIP expt.1958


title: H3K4me1 ab8895 new lot 2 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1975.enrichment.clusters.gff3

source_name: H3K4me1 ab8895 new lot 2 14-16 hr OR Emb Input expt.1815


title: H3K36me3 abcam OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K36me3 abcam OR Head Nuc ChIP expt.2302


title: H3K4me1 ab8895 new lot 2 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K4me1 ab8895 new lot 2 14-16 hr OR Emb ChIP expt.1975


title: H3K4me3 ab8580 lot 2 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1960.enrichment.clusters.gff3

source_name: H3K4me3 ab8580 lot 2 14-16 hr OR Emb Input expt.1962


title: H3K36me3 abcam OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2302.enrichment.clusters.gff3

source_name: H3K36me3 abcam OR Head Nuc Input expt.2306


title: H3K4me1 ab8895 new lot 2 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K4me1 ab8895 new lot 2 OR Head Nuc ChIP expt.2355


title: H3K36me3 abcam OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K36me3 abcam OR Head Nuc ChIP expt.2301


title: H3K36me1 OR Head Nuclei D.melanogaster ChIP Rep2

source_name: H3K36me1 OR Head Nuc ChIP expt.2290


title: H3K36me1 OR Head Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2290.enrichment.clusters.gff3

source_name: H3K36me1 OR Head Nuc Input expt.2306


title: H3K36me1 OR Head Nuclei D.melanogaster ChIP Rep1

source_name: H3K36me1 OR Head Nuc ChIP expt.2289


title: H3K36me1 OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2289.enrichment.clusters.gff3

source_name: H3K36me1 OR Head Nuc Input expt.2305


title: H3K27me2 Ab24684 L3 Nuclei D.melanogaster Input Rep2

description: Served as Input for: 2341.enrichment.clusters.gff3

source_name: H3K27me2 Ab24684 L3 Nuc Input expt.2331


title: H3K27me2 Ab24684 L3 Nuclei D.melanogaster ChIP Rep1

source_name: H3K27me2 Ab24684 L3 Nuc ChIP expt.2340


title: H3K27me2 Ab24684 L3 Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2340.enrichment.clusters.gff3

source_name: H3K27me2 Ab24684 L3 Nuc Input expt.2330


title: H3K27me2 Ab24684 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K27me2 Ab24684 14-16 hr OR Emb ChIP expt.1974


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh A6 isolate at 24hpi, replicate 3

status: Public on May 27 2013

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

country: Germany

institute: Max Planck Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to the Bgh DH14 BluGen genome assembly version 3.0 using tophat v1.3.2 with parameters -p 12 -a 10 -g 5 --library-type fr-unstranded -G blugen_dh14_genes.gff
Read counts per gene per sample were obtained using the bedTools suite  v2.13.2 (function coverageBed)
Genome_build: Blumeria graminis fsp. hordeii (Bgh) DH14, BluGen (http://www.blugen.org/) genome assembly version 3.0
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample (Read count matrix)

molecule: polyA RNA

organism: Blumeria hordei

source_name: Bgh-infected leaves

growth_protocol: Growth of plants and pathogens was performed as described in V. Lipka, et al., Science 310, 1180 (2005).

extract_protocol: RNA-seq libraries were prepared from an input of 4 ug total RNA according to recommendations of the supplier (TruSeq RNA sample preparation v2 guide, Illumina). Libraries were quantified by fluorometry, immobilized and processed onto a flow cell with a cBot (Illumina) followed by sequencing-by-synthesis with TruSeq v3 chemistry on a HiSeq2000. Library construction and sequencing were performed by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de).

treatment_protocol: Inoculation of the pathogens was perfomed as described in V. Lipka, et al., Science 310, 1180 (2005).

tag: plant genotype

value: Columbia-0 pen2-1 pad4-1 sag101-2 mutant

tag: fungal pathogen isolate

value: Blumeria graminis f. sp. hordei isolate A6

tag: virulence

value: Virulent

tag: virulence_time (as used for model)

value: leaves


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh A6 isolate at 24hpi, replicate 2


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh A6 isolate at 24hpi, replicate 1


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh K1 isolate at 24hpi, replicate 2

value: Blumeria graminis f. sp. hordei isolate K1


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh K1 isolate at 18hpi, replicate 2


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh K1 isolate at 18hpi, replicate 1


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh K1 isolate at 24hpi, replicate 3


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh K1 isolate at 18hpi, replicate 3


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh K1 isolate at 24hpi, replicate 1


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh A6 isolate at 18hpi, replicate 1


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh A6 isolate at 18hpi, replicate 2


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh A6 isolate at 18hpi, replicate 3


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh A6 isolate at 12hpi, replicate 2


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh K1 isolate at 12hpi, replicate 3


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh A6 isolate at 12hpi, replicate 1


title: H3K36me3 abcam OR Head Nuclei D.melanogaster Input Rep1

description: Served as Input for: 2301.enrichment.clusters.gff3

source_name: H3K36me3 abcam OR Head Nuc Input expt.2305

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

value: Mixed Adult

value: wild type


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh K1 isolate at 12hpi, replicate 2


title: H3K27me2 Ab24684 L3 Nuclei D.melanogaster ChIP Rep2

source_name: H3K27me2 Ab24684 L3 Nuc ChIP expt.2341

value: 3rd Instar Larvae


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh K1 isolate at 12hpi, replicate 1


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh A6 isolate at 6hpi, replicate 3


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh A6 isolate at 12hpi, replicate 3


title: H3K27me2 Ab24684 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K27me2 Ab24684 14-16 hr OR Emb ChIP expt.1956

value: Embryo 14-16hr OR


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh K1 isolate at 6hpi, replicate 3


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh A6 isolate at 6hpi, replicate 2


title: Log RM1221 R2 plus TEX

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Removal of polyA-tails from Fasta sequences
Size filtering: discarding reads shorter than 12 nt
Read mapping using segemehl version 0.1.2
Genome_build: Campylobacter jejuni  81116: NC_009839.1
Genome_build: Campylobacter jejuni 81-176: NC_008770.1, NC_008787.1, NC_008790.1
Genome_build: Campylobacter jejuni  NCTC11168: NC_002163.1
Genome_build: Campylobacter jejuni  RM1221: NC_003912.7
Supplementary_files_format_and_content: Unnormalized read coverages in wiggle format (*_plus.wig = plus strand; *_minus_= _minus_strand.wig)

organism: Campylobacter jejuni RM1221

growth_protocol: Bacteria were grown on Brucella broth agar plates supplemented with 10µg/ml vancomycin at 37°C under microaerobic conditions (10% CO2, 5% O2). For liquid cultures, bacteria grown on plates were harvested and a starter culture was inoculated to a final OD600 of 0.04 in a flask containing 20 ml of Brucella broth (BB) medium including 10µg/ml Vancomycin. The starter culture was grown by incubating the flasks overnight at 37°C under microaerobic atmosphere and agitation at 140 rpm. The next day, the starter culture was used to inoculate a flask containing 50 ml Brucella broth (BB) including 10µg/ml vancomycin to a final OD600 of 0.04. The culture was grown under the above described conditions and harvested for RNA extraction at different phases.

extract_protocol: Construction of cDNA libraries for dRNA-seq and Illumina sequencing. Total RNA was freed of residual genomic DNA by DNase I treatment. For depletion of processed transcripts, equal amounts of Campylobacter RNA were incubated with TerminatorTM 5'-phosphate-dependent exonuclease (TEX) (Epicentre #TER51020) as previously described 23.  Libraries for Solexa sequencing (HiSeq) of cDNA were constructed by vertis Biotechnology AG, Germany (http://www.vertis-biotech.com/), as described previously for eukaryotic microRNA (Berezikov et al., 2006) but omitting the RNA size-fractionation step prior to cDNA synthesis.

treatment_protocol: The harvested cell samples were immediately mixed with stop mix (95% EtOH and 5% Phenol by volume), frozen in liquid N2 and stored at -80°C until RNA extraction. Frozen were thawed on ice, and resuspended in lysis solution containing 800 µl of 0.5 mg/ml lysozyme in TE buffer (pH 8.0) and 80 µl 10% SDS. Bacterial cells were lysed by placing the samples for 1–2 minutes at 65°C in a water bath. Afterwards, total RNA was extracted from the lysates using the hot-phenol method described in (Blomberg et al., 1990). Further DNase I treatment wa also perfromed on the RNA.


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh A6 isolate at 6hpi, replicate 1


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh K1 isolate at 6hpi, replicate 2


title: Log RM1221 R2 minus TEX


title: Triple mutant (pen2 pad4 sag101) plants challenged with Bgh K1 isolate at 6hpi, replicate 1


title: MLA1 expressing plants challenged with Bgh K1 isolate at 24hpi, replicate 2

value: Columbia-0 pen2-1 pad4-1 sag101-2 mutant expressing MLA1-HA

value: Avirulent


title: MLA1 expressing plants challenged with Bgh K1 isolate at 12hpi, replicate 1


title: MLA1 expressing plants challenged with Bgh K1 isolate at 12hpi, replicate 2


title: MLA1 expressing plants challenged with Bgh A6 isolate at 24hpi, replicate 3


title: MLA1 expressing plants challenged with Bgh K1 isolate at 24hpi, replicate 1


title: MLA1 expressing plants challenged with Bgh K1 isolate at 12hpi, replicate 3


title: MLA1 expressing plants challenged with Bgh A6 isolate at 12hpi, replicate 3


title: Log RM1221 R1 minus TEX


title: MLA1 expressing plants challenged with Bgh A6 isolate at 24hpi, replicate 1


title: MLA1 expressing plants challenged with Bgh A6 isolate at 12hpi, replicate 1


title: MLA1 expressing plants challenged with Bgh K1 isolate at 18hpi, replicate 2


title: MLA1 expressing plants challenged with Bgh A6 isolate at 12hpi, replicate 2


title: MLA1 expressing plants challenged with Bgh A6 isolate at 24hpi, replicate 2


title: Log RM1221 R1 plus TEX


title: MLA1 expressing plants challenged with Bgh K1 isolate at 18hpi, replicate 1


title: MLA1 expressing plants challenged with Bgh K1 isolate at 18hpi, replicate 3


title: MLA1 expressing plants challenged with Bgh A6 isolate at 18hpi, replicate 2


title: MLA1 expressing plants challenged with Bgh A6 isolate at 18hpi, replicate 3


title: Log 81-176 R2 plus TEX

organism: Campylobacter jejuni subsp. jejuni 81-176


title: Ze2

city: Montpellier

first: Sophie

last: Gaudriault

address: case courrier 54, Place Eugène Bataillon

country: France

institute: Université Montpellier 2 - Institut National de la Recherche Agronomique

description: Isogenic mutant omegaFliZ, logarithmic phase, replicate 2

data_processing:
Sequenced reads were mapped to Xenorhabdus nematophila str. F1 genome (accession numbers: CAVM010000001-CAVM010000351) using ssaha2 version 2.5.1 with parameters -solexa -s (read length)/2.
samtools (version 0.1.12a (r862)) were used to discard reads corresponding to multiple matches and convert ssaha2 SAM output file to generic BAM file.
Transcripts coverage (Read Count Analysis) were performed using the Genomic_Features R package (version 1.4.3) running on R (version 2.13.1).
Differential Expression Analyses were performed using the DESeq R package (version 1.4.1) running on R (version 2.13.1).
Genome_build: CAVM010000001-CAVM010000351
Supplementary_files_format_and_content: Tab-delimited text files with two columns: the first contains a gene identifier, the second the count data. *CountRaw.txt include raw counts, and *CountNorm include normalized counts. The normalized abundance measurements were calculated using the DESeq statistical package.

organism: Xenorhabdus nematophila

source_name: entomopathogenic bacteria from the Enterobacteriaceae family, fliZ mutant

growth_protocol: Logarithmic culture phase in mot broth at 28°C.

extract_protocol:
RNeasy QIAGEN kit.
RNA libraries were prepared for sequencing using standard Illumina protocols using the kit « TrueSeq RNA sample preparation Kit ».

treatment_protocol: RNAprotect Bacteria reagent 5 min.

tag: strain/background

value: fliZ mutant

value: mot broth


title: Ze

description: Isogenic mutant omegaFliZ, logarithmic phase, replicate 1


title: Log 81-176 R2 minus TEX


title: Fe2

description: Wild type strain, logarithmic phase, replicate 2

source_name: entomopathogenic bacteria from the Enterobacteriaceae family, WT

value: WT


title: MLA1 expressing plants challenged with Bgh A6 isolate at 18hpi, replicate 1


title: MLA1 expressing plants challenged with Bgh K1 isolate at 24hpi, replicate 3


title: Fe

description: Wild type strain, logarithmic phase, replicate 1


title: Log 81-176 R1 minus TEX


title: Log 81-176 R1 plus TEX


title: MLA1 expressing plants challenged with Bgh K1 isolate at 6hpi, replicate 2


title: MLA1 expressing plants challenged with Bgh K1 isolate at 6hpi, replicate 3


title: Log NCTC11168 R2 minus TEX

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819


title: Log NCTC11168 R2 plus TEX


title: MLA1 expressing plants challenged with Bgh K1 isolate at 6hpi, replicate 1


title: Log NCTC11168 R1 plus TEX


title: MLA1 expressing plants challenged with Bgh A6 isolate at 6hpi, replicate 3


title: MLA1 expressing plants challenged with Bgh A6 isolate at 6hpi, replicate 1


title: Log NCTC11168 R1 minus TEX


title: MLA1 expressing plants challenged with Bgh A6 isolate at 6hpi, replicate 2


title: Log 81116 R2 plus TEX

organism: Campylobacter jejuni subsp. jejuni 81116


title: Log 81116 R2 minus TEX


title: IgG_ChIPseq

city: Hamburg

first: Neele

middle: Margarete

last: Kriebitzsch

address: Martinistraße 52

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

data_processing:
Illumina Casava 1.8.2 software was used for base calling.
Sequence tags were aligned to the mm9 assembly (NCBI Build 37) with Bowtie (v. 0.12.8) reporting only top scoring unique mapping tags.
The MACS algorithm was used to identify bound regions by comparing the enrichment of the Runx1-IP sample against a control IgG-IP for background correction. MACS version 1.4.01 was run with all parameters at their default settings, except m-fold, which was set at 8,30, to identify Runx1-bound regions.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file identifies Runx1-bound regions

source_name: BMiFLT3 (15-3) cells

growth_protocol: Cells were routinely grown in α-MEM with 10% FCS, glutamine and sodium pyruvate.

extract_protocol:
ChIP experiments using anti-Runx1 or anti-IgG antibodies were performed using the EZ-ChIP Kit (Upstate/Millipore) according to the manufacturer’s protocol.
Purified DNA from chromatin immunoprecipitations (10-50 ng) was adapter-ligated using the Illumina-compatible NEXTflexTM ChIP Seq-Kit (Bioo Scientific) for DNA inserts ≥70 bps.DNA fragments between 350-550 bp were isolated using PippinPrep (Sage Science) and quantified and sized on a microfluidics-based Bioanalyzer 1200 using a High Sensitivity DNA Kit (Agilent).

treatment_protocol: 24 hours before DNA extraction, cells were either treated with 0.2 µM Tamoxifen to ensure Runx1-ERt2 translocation into the nucleus or treated with the appropriate amount of ethanol as a control.

tag: cell line

value: proB cells from a murine BCP-ALL

tag: genetic modification

value: cells transduced with Runx1-ERt2

tag: chip-seq antibody

value: rabbit anti-IgG [Abcam,catalog #37415, lot #905012]


title: Runx1_ChIPseq

value: rabbit anti-Runx1 [generated against a C-terminal peptide (kindly provided by Y. Groner and D. Levanon (Weizmann Institute, Rehovot))]


title: Log 81116 R1 plus TEX


title: HP1a-/- ESC RNA-Seq

status: Public on May 25 2013

city: Vancouver

first: Patrick

last: Plettner

state: BC

address: 100-570 West 7th Avenue

institute: BC Cancer Agency GSC

data_processing:
Sequence reads were aligned to the mouse reference genome (mm9) using BWA v0.5.9 (Li et al., 2008) with Smith-Waterman alignment disabled and annotated exon-exon junctions compiled from Ensembl, RefSeq and UCSC (downloaded from http://genome.ucsc.edu on 08/17/11).
Sequence reads that could be uniquely assigned a position in the transcript resource (exon-exon junctions) were computationally repositioned to the genomic mm9 coordinates and a single merged bam file (Li et al., 2009) generated for downstream analyses.
Wigs (RNA-seq):The Samtools pileup utility (Li et al., 2009) and FindPeaks 3.1 (Fejes et al., 2008) was used to generate strand-specific (positive and negative) data tracks for visualization (wig and bigWig (Kent et al., 2010)) in the UCSC browser. Repbase (Jurka et al., 2005), a comprehensive database of repetitive elements, was used for alignment of reads to repetitive elements.
Genome_build: mm9

source_name: embryonic stem cells

growth_protocol: Embryonic stem cells were grown on gelatinized plates in standard ES FBS Medium

extract_protocol:
Cells harvested and flash frozen using liquid nitrogen.  RNA was then extracted using Sigma GenElute Mammalian Total RNA Extraction Kit
RNA-seq libraries were prepared from mRNA as described in Morin et al from 10ug of DnaseI treated total RNA (Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T, McDonald H, Varhol R, Jones S, Marra M: Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques 2008, 45:81-94.)

value: embryonic stem cells

tag: genetic background


title: HP1b-/- ESC RNA-Seq


title: HM1 ESC RNA-Seq


title: LCLBACWT

city: Aurora

first: Neelanjan

last: Mukherjee

state: CO

department: BMG/RBI

country: USA

institute: University of Colorado School of Medicine

data_processing:
PAR-CLIP: Libraries were stripped of the 3’ adapter sequence and 5' barcode using the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).  Reads that were less than 13 nt in length or contained an ambiguous nucleotide were discarded.  The small RNA files are in a tab-delimited form: SEQUENCE READCOUNT.  The Ago2 PARCLIP reads were aligned to the human genome (hg19), with up to 2 mismatches allowed, by the Bowtie algorithm (Langmead et al., 2009).  Mapped locations were only reported for those with the minimum number of observed mismatches for each read.  All T to C mismatches between the RNA fragment and the genome were subtracted from the mismatch count for each mapped location.  After subtraction only reads that mapped to a single genomic location at the minimum number of mismatches were used for further analysis.  The location that a read mapped, relative to a known transcript, was determined based on the ENSEMBL v57 database 1 (Hubbard et al., 2007).  If a read mapped to a location representing multiple categories, it was reported to belong to the category based on the following order of preference: 3’UTR, coding sequence, 5’UTR, intron, non-coding RNA, intergenic. Defining microRNA interaction sites by PARalyzer: Overlapping reads were grouped together for further analysis. A group must have contained ≥5 reads with conversions at two or more locations. Separate kernel density estimates were calculated across all positions based on read counts both with and without T to C conversions, as long as there was a minimum read depth of 5 at a position to ensure a robust density estimate. Clusters (*.bed files) were defined as regions for which the conversion density was greater than the non-conversion density for at least 5 consecutive nucleotides, and extended until the group read depth fell below 5. Following filtering (see supplemental methods), clusters were scored by a cross-linking index (CLI) = log2(1+T to C conversion events for all reads within a cluster). PARalyzer is available at http://www.genome.duke.edu/labs/ohler/research/PARalyzer
RNA-seq: RNA-seq data was aligned and quantified using RSEM with reference genome and transcript annotation [B. Li and C. Dewey (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323]. All necessary transcript annotation, genomic sequence, and alignment indices were downloaded from the Illumina iGenomes collection for Ensembl build GRCh37. Differential analysis was performed using EBseq within RSEM [Leng, N., J.A. Dawson, J.A. Thomson, V. Ruotti, A.I. Rissman, B.M.G. Smits, J.D. Haag, M.N. Gould, R.M. Stewart, and C. Kendziorski. EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments, UW-Madison Department of Biostatistics and Medical Informatics Paper, Bioinformatics 2012].
Genome_build: hg19
Supplementary_files_format_and_content: bed and expression

organism: Homo sapiens

source_name: LCL cell line established using EBV B95-8 BACmid

growth_protocol: The established lymphoblastoid cell line (LCL-BAC-D2) is infected with an EBV B95-8 BACmid (BAC) and was analyzed four months post-infection.  LCL-BAC-D2 was maintained in RPMI 1640 medium supplemented with 15% FBS and 10 μg/mL gentamicin (GIBCO).  LCL-BAC-D2 (mutationally inactivated for miR-BHRF1-2 expression) is infected with an EBV miRNA-mutant virus described in (Feederle, et. al., J. Vir., 2011), and were generated from the same donor as LCL-BAC, LCL-BAC-D1, and LCL-BAC-D3 (Skalsky, et. al., PloS Path., 2012; GEO GSE41437).

extract_protocol: Total RNA was extracted with TRIzol (Life Technologies) and paired-end RNA seq libraries were generated using Ribozero and Scriptseq v2 kits (Epicentre).

value: LCL-BAC


title: LCLBACD3

source_name: LCL cell line established using EBV B95-8 BACmid lacking ebv-mir-BHRF1-3 (D3)


title: Ago2 PAR-CLIP

description: Ago2 ribonucleoprotein complexes

data_processing:
Library strategy: PAR-CLIP
PAR-CLIP: Libraries were stripped of the 3’ adapter sequence and 5' barcode using the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).  Reads that were less than 13 nt in length or contained an ambiguous nucleotide were discarded.  The small RNA files are in a tab-delimited form: SEQUENCE READCOUNT.  The Ago2 PARCLIP reads were aligned to the human genome (hg19), with up to 2 mismatches allowed, by the Bowtie algorithm (Langmead et al., 2009).  Mapped locations were only reported for those with the minimum number of observed mismatches for each read.  All T to C mismatches between the RNA fragment and the genome were subtracted from the mismatch count for each mapped location.  After subtraction only reads that mapped to a single genomic location at the minimum number of mismatches were used for further analysis.  The location that a read mapped, relative to a known transcript, was determined based on the ENSEMBL v57 database 1 (Hubbard et al., 2007).  If a read mapped to a location representing multiple categories, it was reported to belong to the category based on the following order of preference: 3’UTR, coding sequence, 5’UTR, intron, non-coding RNA, intergenic. Defining microRNA interaction sites by PARalyzer: Overlapping reads were grouped together for further analysis. A group must have contained ≥5 reads with conversions at two or more locations. Separate kernel density estimates were calculated across all positions based on read counts both with and without T to C conversions, as long as there was a minimum read depth of 5 at a position to ensure a robust density estimate. Clusters (*.bed files) were defined as regions for which the conversion density was greater than the non-conversion density for at least 5 consecutive nucleotides, and extended until the group read depth fell below 5. Following filtering (see supplemental methods), clusters were scored by a cross-linking index (CLI) = log2(1+T to C conversion events for all reads within a cluster). PARalyzer is available at http://www.genome.duke.edu/labs/ohler/research/PARalyzer
RNA-seq: RNA-seq data was aligned and quantified using RSEM with reference genome and transcript annotation [B. Li and C. Dewey (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323]. All necessary transcript annotation, genomic sequence, and alignment indices were downloaded from the Illumina iGenomes collection for Ensembl build GRCh37. Differential analysis was performed using EBseq within RSEM [Leng, N., J.A. Dawson, J.A. Thomson, V. Ruotti, A.I. Rissman, B.M.G. Smits, J.D. Haag, M.N. Gould, R.M. Stewart, and C. Kendziorski. EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments, UW-Madison Department of Biostatistics and Medical Informatics Paper, Bioinformatics 2012].
Genome_build: hg19
Supplementary_files_format_and_content: bed and expression

source_name: LCL cell line established using EBV B95-8 BACmid lacking ebv-mir-BHRF1-2 (D2)

extract_protocol:
For UV crosslinking, ~4 L of cells were cultured in R-15 containing 100 microMolar 4-thiouridine overnight and collected by centrifugation.  Cells were washed once with ice-cold PBS and irradiated on ice at UV 365 nm in a Stratalinker 2400 (Stratagene). Cross-linked cells were collected by centrifugation at 500×g for 5 min.
The pellets of cells crosslinked with UV 365 nm were resuspended in NP40 lysis buffer and incubated on ice for 10 min. The cell lysate was cleared by centrifugation at 13,000g. RNase T1 (Fermentas) was added to the cleared cell lysates and the reaction mixture was incubated at 22ºC for 15 min and subsequently cooled for 5 min on ice before addition of antibody-conjugated magnetic beads. The recovered RNA was carried through a cDNA library preparation protocol originally described for cloning of small regulatory RNAs (Hafner et al., 2008). The first step, 3' adapter ligation, was carried out as described on a 20 ul scale using 10.5 ul of the recovered RNA. UV 365 nm crosslinked sample RNAs were ligated to Illumina sequencing adapter sets and reversed transcribed to cDNA.  Following PCR amplification of the cDNA, products were gel-extracted and sequenced on the Illumina GAIIX sequence analyzer.

tag: antibody

value: Anti-Ago2 (clone 9E8, Millipore cat#04-642)


title: LCLBACD1_1

source_name: LCL cell line established using EBV B95-8 BACmid lacking ebv-mir-BHRF1-1 (D1), RNA-seq biological replicate #1


title: Log 81116 R1 minus TEX

tag: strain


title: LCLBACD2


title: ES_Rep1_5C_library

status: Public on May 24 2013

city: Worcester

first: Jennifer

middle: Elizabeth

last: Phillips-Cremins

state: MA

address: 364 Plantation Street

department: Program in Systems Biology and Department of Biology

institute: University of Massachusetts Medical School and Emory University

description: 3C and 5C

data_processing:
Reads were aligned to a pseudo-genome consisting of all 5C primers using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) (Langmead, 2010).  To account for poor quality reads, sequences were required to have only one unique alignment and 5 and 3 bases were trimmed from the 5’ and 3’ ends of the read, respectively.  Interactions were counted when both paired end reads could be uniquely mapped to the 5C primer pseudo-genome. Only interactions between forward-reverse primer pairs were tallied as a true count, as forward-forward or reverse-reverse primer pairs represent an artifact in the 5C procedure.
To account for bias intrinsic to all 3C-based methods, as well as to 5C specifically, we developed a probabilistic model that simultaneously captures the non-biological contribution of specific primers and the distance-dependent background level of non-specific chromatin interactions (Imakaev et al., 2012; Yaffe and Tanay, 2011).  For each region, model parameters describing the expected value and signal-dependent variance of each interaction under a normal-lognormal distribution were learned using stochastic gradient descent. Using the learned parameters, empirical p-values were computed under this distribution via Monte Carlo simulation for each observed interaction count.  Interaction scores were derived using the inverse cumulative density function for a standard normal distribution.  The resulting p-values and derived interactions scores are directly comparable within and between experiments and allow for robust detection of fragment-to-fragment looping interactions that are significant above the expected background signal.
The processed data file contains the following information for each forward-reverse primer combination possible in cis:  “Region” (5C Region), “Fprimer” (Forward primer ID), “Rprimer” (Reverse primer ID), “Distance” (mid-to-mid distance between fragments represented by forward and reverse primers), “Raw” (raw number of reads for a particular forward-reverse primer combination), “_.Predicted” (expected number of reads modeled from learned parameters for a particular forward-reverse primer combination), “_.PE” (primer-corrected counts for a particular forward-reverse primer combination), “_.DD”  (primer-corrected and distance-corrected counts for a particular forward-reverse primer combination), “_.Pvalue” (pvalue assigning significance to the counts for a particular forward-reverse primer combination after comparison to the expected distribution of counts at that distance scale), and “_.InteractionScore” (for each forward-reverse primer combination, interaction scores were derived from pvalues using the inverse cumulative density function for a standard normal distribution).  Processed data file includes information for 2 replicates of ES cells and 2 replicates of ES-derived NPCs (ES_Rep1, ES_Rep2, NPC_Rep1, and NPC_Rep2).

source_name: V6.5 ES cells

growth_protocol: Murine V6.5 ES cells were expanded on Mitomycin-C-inactivated MEF feeder layers in pluripotent media supplemented with LIF.  After initial expansion, ES cells were passaged 2-3 times on 0.1% gelatin to remove contaminating feeder cells.  ES cells were ~70% confluent the time of fixation with 1% formaldehyde before downstream assay.

extract_protocol: 3C templates were generated using HindIII as previously described (Dekker et al., 2002; van Berkum and Dekker, 2009). 5C libraries were generated from 3C templates using an alternating primer design across 1-2 Mb regions around Oct4, Nanog, Sox2, Nestin, Olig1-Olig2, Klf4, and a gene desert negative control  (described previously Dostie and Dekker, 2007; Dostie et al., 2006; van Berkum and Dekker, 2009).

value: V6.5 ES cells

value: 129SvJae x C57BL/6

tag: gender

value: male

tag: chip antibody


title: horse3879_day33_CG_RNAseq

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

institute: Cornell University

description: Illumina mRNA-seq

data_processing: Alignment: The reads were truncated to 40 bp and aligned to the horse reference genome (UCSC version equCab2) using Burrows-Wheeler Alignment (BWA) with a maximum of four mismatches. On average, 67.1% of the reads were mapped to the horse reference genome.

organism: Equus caballus

source_name: horse embryonic day 33 chorionic girdle sample

extract_protocol: The mRNA-seq libraries were made with 2.5 ug of starting total RNA samples using the mRNA-Seq 8-Sample Prep Kit (Illumina Inc., CA), following the Illumina protocol for mRNA sequencing sample preparation.

tag: tissue

value: chorionic girdle

tag: developmental stage

value: embryonic day 33


title: ES_Rep2_5C_library

description: 3C and 5C

tag: cell type


title: LCLBACD1_2

source_name: LCL cell line established using EBV B95-8 BACmid lacking ebv-mir-BHRF1-1 (D1), RNA-seq biological replicate #2


title: donkey3689_day33_CG_RNAseq

description: Illumina mRNA-seq

organism: Equus asinus

source_name: donkey embryonic day 33 chorionic girdle sample


title: hinny3702_day33_CG_RNAseq

description:
Hinny: Offspring of male horse and female donkey.
Illumina mRNA-seq

organism: Equus caballus x Equus asinus

source_name: hinny embryonic day 33 chorionic girdle sample


title: Smc1_NPC_ChIPSeq

description: ChIP-seq

data_processing: Sequences were aligned to NCBI Build 37 (UCSC mm9) using default parameters (-v1 -m1) in Bowtie.  Only sequences that mapped uniquely to the genome were used for further analysis.  Model-based Analysis for ChIP-Sequencing (MACS) was used for peak calling (http://liulab.dfci.harvard.edu/MACS/00README.html) (Zhang et al., 2008). Default parameters were used with a p-value cutoff of P<1E-8. A background whole cell extract input control was used to assess significance.

source_name: Neural progenitor cells

growth_protocol: Murine V6.5 ES cells were expanded on Mitomycin-C-inactivated MEF feeder layers in pluripotent media supplemented with LIF.  After initial expansion, ES cells were passaged 2-3 times on 0.1% gelatin to remove contaminating feeder cells.

extract_protocol: Chromatin immunoprecipitation (ChIP) was performed as previously described with minor modifications (Kagey et al., 2010).  Briefly, 50x106 NPCs were lysed and chromatin was sonicated with a Branson Sonifier 250 for 30 x 12 sec pulses. Chromatin was pre-cleared with Protein A Sepharose beads and then immunoprecipitated with approximately 10 μg of the appropriate antibody coupled to Protein A sepharose beads.  For Smc1a ChIP using Bethyl Laboratories (A300-055A) affinity purified rabbit polyclonal antibody, beads were washed 1X with LB3, 1X with 20mM Tris-HCl pH8, 500mM NaCl, 2mM EDTA, 0.1% SDS, 1%Triton X-100, 1X with 10mM Tris-HCl pH8, 250nM LiCl, 2mM EDTA, 1% NP40 and 1X with TE containing 50 mM NaCl.  For CTCF ChIP using an Upstate 07-729 rabbit polyclonal antibody, beads were washed 7 times with RIPA buffer and 1X with TE containing 50 mM NaCl.  Bound complexes were eluted from the beads by heating at 65°C for 15 min with occasional vortexing.  Cross-links were reversed by overnight incubation at 65°C. Whole cell extract DNA reserved from the sonication step was also treated for crosslink reversal. ChIP-seq libraries were prepared for sequencing as recommended by Illumina/Solexa.

treatment_protocol: V6.5 ES cells were differentiated into neural progenitor cells (NPCs) using established techniques (Meissner et al., 2008; Mikkelsen et al., 2007; Okabe et al., 1996).  Briefly, after expansion, ES cells were trypsinized and cultured in bacterial dishes for 4 days in the absence of LIF to promote embryoid body formation.  Embryoid bodies were then plated on tissue-culture plastic dishes and cultured in serum-free, defined media (ITSFn).  After 5-7 days selection in ITSFn, adherent cells were trypsinized, triturated to a single cell suspension, and re-plated on tissue culture dishes coated with 15 ug/ml poly-L-ornithine (Sigma) and 1 ug/ml human plasma fibronectin (Gibco).  NPCs were further propagated for 2-4 days in DMEM/F12 supplemented with 25 ug/ml insulin, 50 ug/ml human APO transferrin, 30 nM sodium selenite, 20 nM progesterone (Sigma), 100 nM putrescine (Sigma), 1 ug/ml laminin (Sigma), 10 ng/ml Fgf2 (R&D Systems), and 1x penicillin/streptomycin. NPCs were ~60-75% confluent at the time of fixation with 1% formaldehyde before downstream assay.

value: ES-derived neural progenitor cells

value: Smc1 (Bethyl; A300-055A)

tag: catalog/lot#


title: NPC_Rep1_5C_library

description: 3C and 5C