title: Usp_W3L_ChIP_Rep2

extract_protocol:
1. y; bw cn sp flies are cultivated in standard fly food covered with yeast powder.2. Flies are removed from the bottles after 24 hours and eggs are allowed to grow at 25 C for several days until they reach the desired growth stage.3. Wandering third instal larvae are collected from the side of the bottles using a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.4. Chromatin collection is performed as described in The ChIP-chip protocol from the White lab.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.


title: Usp_W3L_Input_Rep2

status: Public on Aug 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: input DNA

library_source: genomic

data_processing: Solexa_Alignment protocol. Raw image files were processed following the following Illumina-compatible pipeline:1.  The Raw images were first processed with the Casava 1.7.0.2.  Base-called sequences with confidence metrics were obtained using OLB-1.9.0.  All multiplexed samples were demultiplexed using Casava 1.7.0.3. Finally the BWA program was used to align the sequence reads to the Drosophila melanogaster (v5.32) genome, allowing up to 2 edit distance in the seed region and 3 in the full read length. Tags that aligned to more than one  location were excluded from our analysis for both ChIP sample and the corresponding control sample (input chromatin). Only properly aligned reads with mapping quality more than 30 were kept. MACS_Peak-calling protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software, version 2 (MACS2). MACS2 was supplied with the following parameters:tagSize = 50mfold = 2genomeSize = 120000000bandwidth = 100pvalue = 1e-5  Processed data are obtained using following parameters: genome version is flybase BDGPv5

molecule: genomic DNA

organism: Drosophila melanogaster

tag: strain

value: USP-GFP

tag: developmental stage

tag: genotype

tag: Sex

value: Unknown

tag: transgene

value: USP genomic coding region


title: TCF_16-24-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: anti-dTCF;target name: pangolin;host: Rabbit;antigen: Raised against N-terminus TCF/Pangolin;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Ken Cadigan Lab;short description: This is a gift from Eric Lai to Matthew Slattery for the modENCODE project.

extract_protocol:
1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.   2. For a 16-24 hours egg laying, new plates are added after a 2 hours pre-egglaying at 12 a.m. and flies are allowed to lay eggs for 8 hours.   3. Embryos are collected at 7.45 a.m. using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 8 a.m. in 1.8% formaldehyde at room temperature for 15 min.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

value: Y cn bw sp

value: Embryo 16-24h


title: Usp_W3L_Input_Rep1

description: input DNA


title: TCF_16-24-seq_ChIP_Rep1


title: TCF_16-24-seq_Input_Rep1

description: input DNA


title: TCF_16-24-seq_Input_Rep2

description: input DNA


title: Su(Hw)_WPP-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: Su(Hw)-PG;target name: Su(Hw);host: Rabbit;antigen: MSASKEGKEKKGKLLGVENISPPKDKRPATRMKLLNDVGAGEDSEASTTT TTSRTPSNKQEKRGSVAGSRIKILNEEILGTPKTEKRGATKSTAPAASTV KILNEKKTPSATVTAVETTKIKTSPSKRKKMEHYVLQAVKSENTKADTTV TVVTEEDDTIDFILADDEEVVPGRIENNNGQEIVVTEDDEDLGEDGDEDG EDSSGKGNSSQTKIKEIVEHVCGKCYKTFRRVQSLKKHLEFCRYDSGYHL RKADMLKNLEKIEKDAVVMEKKDICFCCSESYDTFHLGHINCPDCPKSFK TQTSYERHIFITHSEFSDFPCSICNANLRSEALLALHEEQHKSRGKPYAC KICGKDFTRSYHLKRHQKYSSCSSNETDTMSCKVCDRVFYRLDNLRSHLK QHLGTQVVKKPEYMCHTCKNCFYSLSTLNIHIRTHTGEKPFDCDLCDKKF SALVALKKHRRYHTGEKPYSCTVCNQAFAVKEVLNRHMKRHTGERPHKCD ECGKSFIQATQLRTHSKTHIRPFPCEQCDEKFKTEKQLERHVKTHSRTKR PVFSCAECKRNFRTPALLKEHMDEGKHSPKQQRSSMRSAVKIMERTDCAI CDKNFDSSDTLRRHIRTVHECDPDDIFGVEPHPSKRAKKDIESEEVVPVA LNTSAGSLISSQTDGNGVVVREFLVDEGDGAAQTITLENETYTILPLDGA IEGEQLTDEAGVKPEAKKEEAQVSPVVKKEQRKSLAASLAAAIADNLEES CSEDDFSGEILTEEDIKLKENVGKLIDMLVDPPILKKYGWPNAPEETVLC KVIENCGHDLTKGGENYAELDYGSRMREYCKLLFTVVIHNDSIKSLLNNF PIDDVIEYVLGDEDQDEGGLDKDNESHSGDEEAVSVTGETKTNEIREKPE KKEVSAKSEKKEIVGKAVDKDNSEEVVRENKKKPVGEQEKA;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Pam Geyer's Lab;reference: Parnell T.J. Kuhn E.J. Gilmore B.L. Helou C. Wold M.S. and Geyer P.K. 2006. Identification of genomic sites that bind the Drosophila suppressor of Hairy-wing insulator protein. Mol Cell Biol 26: 5983-5993.;short description: This is gift from Pam Geyer to Nicolas Negre for the modENCODE project.

extract_protocol:
Collection of White pre-pupae for chromatin extraction
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

value: White Prepupae (WPP)


title: USP-GFP_WPP+12-seq_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: GFP ab290;target name: Green Fluorescent Protein;host: Rabbit;antigen: entire GFP sequence;clonal: Polyclonal;purified: Crude;company: Abcam;catalog: ab290;reference: abcam website Jungreis et al. Genome Res. 2011 Dec;21(12):2096-113.;short description: This antibody is reactive against all variants of Aequorea victoria GFP such as S65T-GFP RS-GFP YFP and EGFP.

extract_protocol:
1. y; bw cn sp flies are cultivated in standard fly food covered with yeast powder.2. Flies are removed from the bottles after 24 hours and eggs are allowed to grow at 25 C for several days until they reach the desired growth stage.3. Pupae are collected from the side of the bottles using a brush 12 hours after the puparium formatin. 4. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.chromatin collection is performed as described in The ChIP-chip protocol from the White lab.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.


title: Usp_W3L_ChIP_Rep1


title: Su(Hw)_WPP-seq_Input_Rep2

description: input DNA


title: Su(Hw)_WPP-seq_ChIP_Rep1


title: Su(Hw)_WPP-seq_Input_Rep1

description: input DNA


title: Su(Hw)_16-24-seq_ChIP_Rep2


title: Su(Hw)_16-24-seq_ChIP_Rep1


title: Su(Hw)_16-24-seq_Input_Rep1

description: input DNA


title: Stat92E_WPP-seq_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: Rabbit anti-Stat92E (s1189-1);target name: Stat92E;host: Rabbit;antigen: CGMADFDTITNFENF;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Erika Bach LAb;short description: This is a gift from Erika Bach to Nicolas Negre for the modENCODE project.


title: Stat92E_WPP-seq_Input_Rep2

description: input DNA


title: Sin3A_Kc-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: Sin3A-RC;target name: Sin3A;host: Rabbit;antigen: MMKRTRVDEVQFGTRPVPQTSGGVGVGVVGVTGGGPTSGGGGTATVGVNT TGVTIGTVVPSAHNATISGIGSIHHRILTPQHGGAQTIAYLPSTTPTATN LKTTTSIVDSTTAGGPVGAGAQVAVGVGSAAGGGGVVVSTGSTGTQTLQY TTSYSVASIQAGGTLKANTADGANTVQIHVTGGGAANNPASAQTVSSSSQ TGTIRQRTISGTQTVATAVGNLATISQQQPVQQSPLGKAQTPPSSVVANS IPVGGTTPPQGQSGNATPRLKVEDALSYLDQVKYQYADQPQIYNNFLDIM KEFKSHCIDTPGVIERVSTLFKGHTELIYGFNMFLPPGYKIEIHSDALGC SVPVVSMPSPPGAPTSTGTVHMLTGNSSMSGAGHIAIKTTNAATLTPAAG AGAAAAAAAVAQIQSAGAVNLMTHGGASLTQTTIHALQQATPPQSQSPGG GHVHVSVTNSTAANAVVPGQPGISVSAHNVPQNYSRDRERATITPTGQVA GAAANVNASASIVVGGPPTPNSLSELSPHGGAGGGPGAGAAQHNLHHIQQ AHQSILLGETGQQNQPVEFNHAITYVNKIKNRFQNQPAKYKKFLEILHDY QREQKVMKEGSLNQGKMLTEQEVYTQVAKLFGQDEDLLREFGQFLPDATN HQSGQYMSKSASVHNDHGKRPTATLSGGAHITMSSASPAPSGSPLHLGAT TLPQIDKSAHAAAIGNLSAVNTSVSIKTYNNNQQQQNHVIGSGLNATRND ILFEKDYHAGLQQQAHQRGAGVGGHHHLAGTAAGANIGRPGVGASVMVSY DKEHRNNHHVQKYVGHAPNQNLTHGHNAKKSPSYGIPSVIGSMPHISDNS LDRSSPGISYATPPLPSGPHGQHNSGSATRRPGDDSLVGHYASGAPPAKR PKPYCRDVSFSEASSKCTISDAAFFDKVRKALRSPEVYDNFLRCLTLFNQ EIVSKTELLGLVSPFLMKFPDLLRWFTDFLGPPSGQPAGGLIDGMPLAAT QRQGGGSSNSSHDRGTSHQSAAEYVQDVDLSSCKRLGASYCALPQSTVPK KCSGRTALCREVLNDKWVSFPTWASEDSTFVTSRKTQFEETIYRTEDERF ELDLVIEVNSATIRVLENLQKKMSRMSTEELSKFHLDDHLGGTSQTIHQR AIHRIYGDKSGEIITGMKKNPFVAVPIVLKRLKVKEEEWREAQKTFNKQW REQNEKYYLKSLDHQAINFKPNDMKALRSKSLFNEIETLYDERHDQEDDA MEPFGPHLVLPYKDKTILDDAANLLIHHVKRQTGIQKQEKQKIKQIIRQF VPDLFFAPRQPLSDDERDDAFPFLVDDNTKMDVDSPLGRTESSTRNAKST PSESASPARSNASTSSVTPAGIKKETDDSKATTGSFAPASSATASSATPV DDATPSTSSAAAAASAASSSTVSGTEGKPKDDPLSSHKEEGAGSTSSGVA TSPRQAQDTAGAGVDVEIKLEHPADFSNPKLLPPHAHGQREDESYTLFFA NNNWYLFLRLHAILCDRLHVMYERARLLAIEEERCRVNRRESTATALRLK PKPEIQVEDYYPTFLDMLKNVLDGNMDSNTFEDTMREMFGIYAYISFTLD KVVSNAVRQLQYCVTERAALDCVELFATEQRRGCTGGFCRDAHKTFDREM SYQRKAESILNEENCFKVYIYKIDCRVTIELLDSEPEEVDKPAALKAQKF SKYVERLANPALGGGGNTGRSDSALGNDSVVDGSDIKTEADEDTAELRYR EGGIGGAGKARFLVRNKRRSKLLEEQVRQLFEHRRNRIEQHGTAASLEPI SVDSAISSNSTTGGGGSGTNNNNNNNNNNNSWGGKRLERLGAPQVGLAEQ YAFNDRDEISTNISNGRCFVTSKNLKLLKYDAVRRAKKSHCRVTQAKYAH FQTYVNKWLQQHVSEQQQQNCVDWLLGKTADQINASGWGSASKTKTVQQK DTSKTPYRIYNRYRVVQSAVSGGLMSATAPTPDGSVPAVNSAPSGSVSTV NNVQGSAAVSSTSHSMCNSSILSADSTTNTNASAQQQQHCNSAAAATTPN AEALQQVRPMES;clonal: Polyclonal;purified: Crude;company: Other;catalog: Ross Cagan Laboratory produced by Proteintech;short description: This is a gift from Ross Cagan and Tirtha Das to Nicolas Negre for the generation of Sin3A ChIP data in Drosophila.

extract_protocol:
Cell lines (S2, Kc167...) are grown as described by the DGRC and the Cherbas Lab. After expanding the cell line, cells are transfered in a plate. Once confluent, 1.8% formaldehyde is added to the cell culture. Cells are harvested in presence of the formaldehyde with the help of a cell scrapper. After 15 minutes of incubation at room temperature, the cross-linking reaction is quenched with glycine for 5 minutes. Cells pellet are then washed 3 times with lysis buffer. Regular chromatin extraction before sonication is then performed.
Formaldehyde Cross-linking of Chromatin from any Drosophila tissue (Embryos, Larvae, Pupae, Adult flies).1. Homogenize the material (about 150-200 mg of embryos, pupae, adµlts, larvae, sufficient for four-five independent immuno-precipitations) in 5 ml of buffer A1 + 1.8% formaldehyde (290 µl of 37% solution) at room temperature using first a Potter homogenizer and then a Douncer with type A pestle (3 strokes). Wait 15? (total time starting from beginning of homogenization). Add glycin solution to 225 mM (540 µl of 2.5 M solution for 6 ml of cross-linked mixture), mix and incubate 5?. Put on ice. Keep on ice unless specified.2. Transfer the homogenate to a 15 ml tube. Centrifuge 5 min, at 4000 g at 4°C. Discard supernatant. Add 3 ml of buffer A1, resuspend pellet and spin down the same way. Repeat washing step 3 times.3. Wash once in 3 ml of lysis buffer without SDS. Spin down, 5 min at 4000g.4. Resuspend cross-linked material in 0.5 ml of lysis buffer and add SDS to 0.1% (2.5 µl) and N-lauroylsarcosine to 0.5% (12.5 µl). Incubate 10 min at 4°C in a rotating wheel.5. Sonicate in Polypropylene 15ml Falcon tubes according to .Diagenode instructions. The settings are: High power, 15 minutes, 30 seconds off, 30 seconds on. The water bath shoµld be kept cold either in a cold room or by a cold water pump.6. Rotate 10'. Transfer to eppendorf tubes and centrifuge 5', room temperature at maximum speed. Transfer supernatant to the new tube. Add another 0.5 ml of lysis buffer to the pellet, rotate for 10 min. Repeat centrifugation and combine supernatants. Centrifuge the combined supernatant 2x10 min at max speed. The supernatant from this stage will be referred as chromatin extract. Chromatin can be stored at ?80°C for several months at this stage. Add sodium azide to 0.02% for storage.7. [Optional : Purification of chromatin. Put chromatin extract in Centricon YM-100 column (4212), centrifuge 3x40' (or more) at 1000 g while adding lysis buffer. At least 3 vol. of lysis buffer should pass through column. Bring the final volume of chromatin extract to 1 ml by lysis buffer + protease inhibitors.]
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

tag: cell line

tag: tissue

value: embryo-derived cell-line

value: late embryonic stage

value: se/e

value: Female


title: Sin3A_Kc-seq_ChIP_Rep1


title: Stat92E_WPP-seq_Input_Rep1

description: input DNA


title: Sin3A_Kc-seq_Input_Rep2

description: input DNA


title: Stat92E_WPP-seq_ChIP_Rep2


title: Su(Hw)_16-24-seq_Input_Rep2

description: input DNA


title: sc_0-12-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: scute guineapig Crews;target name: scute;host: Guinea Pig;antigen: unknown;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Stephen Crews (http://www.unc.edu/~crews/SteveC.html);short description: Gift from Stephen Crews

extract_protocol:
1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.   2. For a 0-12 hours egg laying, new plates are added after a 2hours pre-egglaying at 9pm and flies are allowed to lay eggs for 12 hours.   3. Embryos are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9am in 1.8% formaldehyde at room temperature for 15 min.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

value: Embryo 0-12h


title: sc_0-12-seq_ChIP_Rep1


title: sc_0-12-seq_Input_Rep2

description: input DNA


title: psq_WPP-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: KW3-psq-D2;target name: psq;host: Rabbit;antigen: GVHGQHGGHVTHADIGGATVMEIDPSQIKHEPGMIITPEIVNMMSSGHMDMYNSDTSEDSMMIANGSPHDQKEPHYTNLDQQHGLGGSV;clonal: Polyclonal;purified: Protein A/G;company: Other;catalog: Aviva-KW3-psq-D2;short description: Antisera raised against a peptide from the psq protein.  Produced commercially for the modENCODE Project by K. White's group.


title: psq_WPP-seq_ChIP_Rep1


title: psq_WPP-seq_Input_Rep2

description: input DNA


title: sc_0-12-seq_Input_Rep1

description: input DNA


title: Prd-RF13_0-12-seq_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: anti-Prd RF13;target name: prd;host: Rabbit;antigen: Raised against an epitope which spans the last 258 residues of Prd with the paired repeat domain deleted (residues 355-552 - deletion - 572-613).;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Claude Desplan Lab;reference: 8787742;short description: This is a gift from Claude Desplan to Nicolas Negre for the modENCODE project.


title: psq_WPP-seq_Input_Rep1

description: input DNA


title: Prd-RF13_0-12-seq_Input_Rep2

description: input DNA


title: Prd-RF13_0-12-seq_ChIP_Rep2


title: Prd-RF12_0-12-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: anti-Prd RF12;target name: prd;host: Rabbit;antigen: Raised against an epitope which spans the last 258 residues of Prd with the paired repeat domain deleted (residues 355-552 - deletion - 572-613).;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Claude Desplan Lab;reference: 8787742;short description: This is a gift from Claude Desplan to Nicolas Negre for the modENCODE project.


title: Prd-RF13_0-12-seq_Input_Rep1

description: input DNA


title: Prd-RF12_0-12-seq_ChIP_Rep1


title: Prd-RF12_0-12-seq_Input_Rep2

description: input DNA


title: mod(mdg4)_W3L-seq_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: KW4-mod(mdg4)-D2;target name: mod(mdg4);host: Rabbit;antigen: MPRASARYKIETVDDGLGDEKQSTTQIVIQTTAAPQATIVQQQQPQQAAQQIQSQQLQTGTTTTATLVSTNKRSAQRSSLTPASSSAGVKRSKTSTSANVMDPLDSTTETGC;clonal: Polyclonal;purified: Protein A/G;company: Other;catalog: Aviva-KW4-mod(mdg4)-D2;short description: Antisera raised against a peptide from the MOD(MDG4) protein. Produced commercially for the modENCODE Project by K. White's group.

extract_protocol:
1. y; bw cn sp flies are cultivated in standard fly food covered with yeast powder.2. Flies are removed from the bottles after 24 hours and eggs are allowed to grow at 25 C for several days until they reach the desired growth stage.3. Wandering third instal larvae are collected from the side of the bottles using a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.


title: mod(mdg4)_W3L-seq_ChIP_Rep2


title: mod(mdg4)_W3L-seq_Input_Rep1

description: input DNA


title: Prd-RF12_0-12-seq_Input_Rep1

description: input DNA


title: mod(mdg4)_W3L-seq_Input_Rep2

description: input DNA


title: Fru_0-8-seq_Input_Rep2

description: input DNA

extract_protocol:
1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.   2. For a 8-16 hours egg laying, new plates are added after a 2 hours pre-egglaying at 12 pm and flies are allowed to lay eggs for 8 hours.   3. Embryos are collected at 7.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 8am in 1.8% formaldehyde at room temperature for 15 min.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

value: Embryo 0-8


title: Sin3A_Kc-seq_Input_Rep1

description: input DNA


title: Fru_0-8-seq_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: anti-Fru;target name: fru;host: Rabbit;antigen: YSQYLGWNYGAWRPDDPNPKQQQQQPHRKAQPFNFYARDYYYQQHQQQQQQQQSPISSMSNGNMRQQQQQQQQHRRQQQLPPAQTIIIDESDNELEEEQQMRLSFERYMEQLKQLAPYDPQETLCNSNTNNISNSNRNNNSNSNRSGEPTNANQMEATTTTTNSNNNNNNSYANHSTRNYNKRQQE;clonal: Polyclonal;purified: Protein A/G;company: Other;catalog: Pacific Immunology;short description: This is a custom made polyclonal antibody against Fru generated by the White Lab for the modENCODE project.


title: Fru_0-8-seq_ChIP_Rep2


title: CNC_AdultFemale-seq_Input_Rep1

description: input DNA

extract_protocol:
Collection of Drosophila adult females 2-3 days old for further ChIP experiments or RNA extraction.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

value: Adult Female


title: CNC_AdultFemale-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: KW0-CNC;target name: cap'n collar;host: Rabbit;antigen: LEEEHLTRDEKRARSLNIPISVPDIINLPMDEFNERLSKYDLSENQLSLIRDIRRRGKNKVAAQNCRKRKLDQILTLEDEVNAVVKRKTQLNQD;clonal: Polyclonal;purified: Protein A/G;company: Other;catalog: KW0-CNC;short description: KW0-CNC


title: CNC_AdultFemale-seq_Input_Rep2

description: input DNA


title: CNC_16-24-seq_ChIP_Rep2


title: CNC_16-24-seq_Input_Rep1

description: input DNA


title: CNC_AdultFemale-seq_ChIP_Rep1


title: CNC_16-24-seq_ChIP_Rep1


title: CG8478_WPP_ChIP-seq_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: KW3-CG8478-D1;target name: CG8478;host: Rabbit;antigen: MKAQLPKIGGTSGINHPMTMPQKPQQRISTIPKLAPSQGTQSMAPPSVKKIPKNVAHAGVYRTPTKTVPCHICKQSFRSILEFTNHSLTVHGNNQLKKMTGREDAQSAHDC;clonal: Polyclonal;purified: Protein A/G;company: Other;catalog: Aviva Systems Biology;short description: This is a custom made polyclonal antibody against CG8478 generated by the White Lab for the modENCODE project.


title: CG8478_WPP_ChIP-seq_Input_Rep2

description: input DNA


title: CG8478_WPP_ChIP-seq_Input_Rep1

description: input DNA


title: CG16778_0-8h_embryo_ChIP-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: anti-CG16778;target name: CG16778;host: Rabbit;antigen: NLWRDWAAGAANANPMYFPAFELDQEMNPTPPSLPSRPALHQLACRELSFKPDLFMARRKLKRFRDKRQLQAQIETPTAAVPAPCPVSNALPPLRT;clonal: Polyclonal;purified: Protein A/G;company: Other;catalog: Pacific Immunology;short description: This is a custom made polyclonal antibody against CG16778 generated by the White Lab for the modENCODE project.


title: CG16778_0-8h_embryo_ChIP-seq_ChIP_Rep1


title: CG16778_0-8h_embryo_ChIP-seq_Input_Rep2

description: input DNA


title: broad_0-8h_embryo_ChIP-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: br-core;target name: broad;host: Rabbit;clonal: Polyclonal;company: Lab;catalog: Lepesant;short description: rabbit antibody against common core region of broad (Broad-Complex).


title: broad_0-8h_embryo_ChIP-seq_ChIP_Rep1


title: CG16778_0-8h_embryo_ChIP-seq_Input_Rep1

description: input DNA


title: broad_0-8h_embryo_ChIP-seq_Input_Rep2

description: input DNA


title: broad_0-8h_embryo_ChIP-seq_Input_Rep1

description: input DNA


title: Dfd-GFP_0-8h_embryo_ChIP-seq_Input_Rep2

description: input DNA

extract_protocol:
1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.2. For a 8-16 hours egg laying, new plates are added after a 2 hours pre-egglaying at 12 pm and flies are allowed to lay eggs for 8 hours.3. Embryos are collected at 7.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 8am in 1.8% formaldehyde at room temperature for 15 min.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

value: Dfd-GFP-Pacman

value: Dfd genomic coding region with stop codon replaced with GFP


title: Fru_0-8-seq_Input_Rep1

description: input DNA


title: CNC_16-24-seq_Input_Rep2

description: input DNA


title: TCF_0-8h_embryo_ChIP-seq_ChIP_Rep2


title: Dfd-GFP_0-8h_embryo_ChIP-seq_ChIP_Rep1


title: CG8478_WPP_ChIP-seq_ChIP_Rep2


title: Dfd-GFP_0-8h_embryo_ChIP-seq_ChIP_Rep2


title: Mouse Embryonic Fibroblast 2

city: Stanford

first: Jennifer

last: Brady

state: CA

address: 269 Campus Drive

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence to 50bp and mapped to mm10 after removal of mouse rRNA sequences.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated after alignment to mm10 using SeqMap.
Genome_build: mm10
Supplementary_files_format_and_content: gene name and RPKM values for each Sample.

molecule: polyA RNA

organism: Mus musculus

source_name: embryonic fibroblast

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Micro Kit. Poly A enrichment was performed with Oligo dT bead selection. The resulting poly-A+ RNA was fragmented and cDNA was synthesized using Superscript II and random primers. 500ng of total RNA was used for each library.
Libraries were prepared according to standard Illumina protocol, using the Illumina TruSeq mRNA Sample Prep Kit v2.

tag: cell type

value: mouse embryonic fibroblast

tag: genetic background

value: BALB/c


title: Mouse ES 1

source_name: embryonic stem cell

value: mouse ES D3 GFP cells


title: Mouse ES 2


title: Mouse 4F iPS clone 1

source_name: induced pluripotent stem cell

value: mouse iPS


title: TCF_0-8h_embryo_ChIP-seq_ChIP_Rep1

value: Unknown


title: Dfd-GFP_0-8h_embryo_ChIP-seq_Input_Rep1

description: input DNA


title: Mouse 4F iPS clone 2


title: Mouse Embryonic Fibroblast 1


title: scute_0-8h_embryo_ChIP-seq_ChIP_Rep2

value: Y cn bw sp


title: scute_0-8h_embryo_ChIP-seq_ChIP_Rep1


title: Mouse 3F + IL6 iPS clone 1

tag: treatment

value: treated with 10ng/mL IL6


title: TCF_0-8h_embryo_ChIP-seq_Input_Rep1

description: input DNA


title: CITH068_Exo_RNA

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

description: Sample name: FGC0181_s_7

data_processing:
Sequence reads and quality scores were extracted using Illumina CASAVA Pipeline v1.7
ChIP-seq reads were aligned to the human genome using ELAND, RNA-seq reads were aligned to the human genome/transcriptome using RUM
H3K4me3 ChIP-seq peak calling was performed with GLITR. H3K27me3 ChIP-seq peak calling was performed with STAR.
RNA-seq transcript quantification was performed with RUM.
Genome_build: hg18
Supplementary_files_format_and_content: Peak calls (ChIP-seq) and transcript quantification (RNA-seq), all in BED format.

molecule: total RNA

organism: Homo sapiens

source_name: FACS-sorted pancreatic islet

extract_protocol:
We performed FACS sorting on dispersed human islets using cell surface antibodies (1:20) and secondary antibodies (1:200; 115-116-075, 115-135-164, Jackson ImmunoResearch) as described before (Dorrell C, et al. Stem Cell Res 2008) to obtain cell populations highly enriched for alpha, beta, and exocrine (duct and acinar) cells. Total RNA was isolated from whole islets, and sorted alpha, beta, and exocrine cells using the Ambion mirVana miRNA Isolation Kit (AM1560) reverse transcribed to cDNA using SuperScript II reverse transcriptase (Invitrogen). ChIP and preparation of ChIP-Seq libraries was performed on individual cell sorts for each cell type and donor (H3K4me3: 8580, Abcam; H3K27me3: 07-449. Upstate).
DNA from ChIP or reverse transcription was treated by blunt end repair and ligation of sequencing adapters. Adapter-ligated fragments were size select to roughly 200bp and amplified by PCR. Final libraries were verified on an Agilent Technologies 2100 BioAnalyzer to check size, purity, and concentration of the library prior to sequencing.

value: pancreatic islets

value: Exocrine

tag: donor id


title: TCF_0-8h_embryo_ChIP-seq_Input_Rep2

description: input DNA


title: CITH053_Exo_RNA

description: Sample name: FGC0181_s_8


title: Mouse 3F + IL6 iPS clone 2


title: CITH070_Beta_RNA-Seq

description: Sample name: FGC0176_s_8

value: Beta


title: CITH068_Beta_RNA-Seq

description: Sample name: FGC0176_s_6


title: homothorax_0-8h_embryo_ChIP-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: anti-Hth;target name: fly genes:hth;host: Guinea Pig;antigen: Raised against full length protein (His-tagged);clonal: Polyclonal;purified: Crude;company: Lab;catalog: Richard Mann Lab;short description: This is a gift from Richard Mann to Matthew Slattery for the modENCODE project.


title: homothorax_0-8h_embryo_ChIP-seq_ChIP_Rep1


title: CITH070_Alpha_RNA-Seq

description: Sample name: FGC0176_s_7

value: Alpha


title: CITH068_Alpha_RNA-Seq

description: Sample name: FGC0176_s_5


title: homothorax_0-8h_embryo_ChIP-seq_Input_Rep2

description: input DNA


title: BSO37_NuGEN

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

data_processing:
Basecalls made by standard Illumina pipleline (Bustard)
The pair end reads were aligned to the human genome build 37.1 using TopHat (1.4.0) and Bowtie (0.12.7). HTSeq (0.5.3p3) was used to perform gene counting while BEDTools (2.7.1) was used to count the reads mapping to individual exons according to RefSeq gene annotations (Feb 2009, GRCh37/hg19) with 23,113 genes.
Genome_build: hg19
Supplementary_files_format_and_content: text; gene level expression count

source_name: human mammary epithelial cell

growth_protocol: All cell lines were grown under conditions recommended by ATCC and RNA was extracted from mid log phase cultures at low passage

extract_protocol:
RNA was extracted from mid log phase cultures at low passage (P1 or P2) using Triazol kit (Invitrogen)
For Illumina libraries, 5ug total RNA were processed according to the mRNA Seq Sample Preparation Kit protocol (part number 1004898 Rev A), with the 300bp gel fragment eluted and purified for sequencing. For NuGEN libraries, 500-800pg total RNA were amplified and converted to cDNA using NuGEN’s Ovation RNA-Seq kit. Following amplification, 4.6-5.0ug cDNA was fragmented to ~200bps using Covaris S2 and the fragmentation parameters described in the NuGEN  ENCORE NGS library preparation protocol. The remainder of the library preparation followed manufacturer’s protocol as described in NGS Library System I and Multiplex System, Part no. 300.

tag: involution

value: Yes

value: human mammary epithelial cell

tag: rna preparation

value: NuGEN Ovation


title: homothorax_0-8h_embryo_ChIP-seq_Input_Rep1

description: input DNA

value: Embryo 0-8


title: CITH053_Beta_RNA-Seq

description: Sample name: FGC0168_s_5


title: BSO36_NuGEN

value: No


title: BSO32N_NuGEN


title: CITH053_Alpha_RNA-Seq

description: Sample name: FGC0168_s_4


title: scute_0-8h_embryo_ChIP-seq_Input_Rep2

description: input DNA


title: Su(H)_8-16h_embryo_ChIP-seq_Input_Rep2

description: input DNA

value: Embryo 8-16h


title: BSO28_NuGEN


title: BSO29_NuGEN


title: BSO30_NuGEN


title: scute_0-8h_embryo_ChIP-seq_Input_Rep1

description: input DNA


title: DHF168_NuGEN


title: Unfused fibroblast rep1

description:
Homo sapiens
Fib1 BC12

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence to 50bp and mapped to hg19 and mm10 after removal of mouse and human rRNA sequences.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using SeqMap. Reads mapping to both organisms were removed. To account for removal of the homologous reads, a mathematical correction was introduced to calculate the effective transcript length (exon length) in which the "effective transcript length" is equal to the "original transcript length - 50bp - 1bp for every unique 50bp sequence read which matched perfectly between mouse and human" for that particular transcript.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: .txt files include mouse and human RPKM values for each Sample. Transcripts with RPKM values of zero have been removed.

source_name: Unfused Human Fib

extract_protocol:
At least 30,000 heterokaryons were FACS sorted and total RNA was extracted using the Qiagen RNeasy Micro Kit.  Poly A enrichment was performed with Oligo dT bead selection. The resulting poly-A+ RNA was fragmented and cDNA was synthesized using Superscript II and random primers.
Libraries were prepared according to standard Illumina protocol, using the NEB Next modules for library construction.

tag: sample type

value: Unfused Human Fib

tag: cell line(s)

value: human fibroblast


title: Su(H)_8-16h_embryo_ChIP-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: Su(H);target name: fly genes:Su(H);host: Rabbit;antigen: Epitope corresponding to amino acids 259-594;clonal: Polyclonal;purified: Protein A/G;company: Santa Cruz Biotechnology Inc.;catalog: sc-25761;reference: http://www.scbt.com/datasheet-25761-suppressor-of-hairless-d-300-antibody.html;short description: Santa Cruz antibody agains Suppressor of Hairless


title: BSO19B_NuGEN


title: Unfused fibroblast rep3

description:
Homo sapiens
Fib3 BC11


title: Su(H)_8-16h_embryo_ChIP-seq_Input_Rep1

description: input DNA


title: mK4_Input

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: LA

address: 1430 Tulane Ave

department: Pediatrics

institute: Tulane University School of Medicine

description: E11.5 Metanephric Immortalized Cell Line

data_processing:
35-nt tags identified using Illumina G2A and mapped using ELAND
Tags extend in silico at their 3' 110-200 bp per Genpathway Software
Density determined using a 32-nt bin size and counting the number of tags therein
Intervals were "called" if 5 consecutive bins with fragment densities greaten than the threshold (10-5)
ELAND files were converted to SAM/BAM and processed using SAMMate version 2.4.1 to generate bedgraph files and calculate RPKM values
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated using SAMMate version 2.4.1; tab-delimited text files include RPKM values for each gene

source_name: mK4 Cells

extract_protocol: Performed by GenPathway™ Using Illumina Pipeline

tag: antibody

value: Input Genomic DNA


title: Su(H)_8-16h_embryo_ChIP-seq_ChIP_Rep1


title: mK3_Input

source_name: mK3 Cells


title: Homokaryon Sample

description:
Homo sapiens
Homok BC6

source_name: Human Fib X Human Fib Homokaryons

value: Human Fib X Human Fib Homokaryons


title: Unfused fibroblast rep2

description:
Homo sapiens
Fib2 BC10


title: mK4_H3K4

tag: chip antibody

tag: antibody vendor/catalog#


title: mK3_H3K4

tag: strain


title: mK3_H3K27

value: Active Motif-39535


title: Co-culture rep2

description:
Mus musculus and Homo sapiens
Co-cult BC9
The co-cultured sample consists of RNA derived from individual mouse and human cells which are cultured together (but not fused - so their membranes remain distinct). The two cell types were pooled together before a single RNA harvest. Thus, this sample is a mixture of D3 mouse ES cells and MRC5 human fibroblasts.

organism:
Homo sapiens
Mus musculus

source_name: Co-cultured Mouse ES and Human Fib

value: Co-cultured Mouse ES and Human Fib

value: mouse ES cells and human fibroblast


title: Het Day3 rep2

description:
Mus musculus and Homo sapiens
Het Day3 BC7
The heterokaryon sample is a fused cell product (a transient, multinucleate mixed species entity generated by the cytoplasmic membrane fusion of mouse embroynic stem cells and human fibroblasts).  The cell lines used to make the fusion product were D3 mouse ES cells and human fibroblast MRC5 cells. It is important to note that the sample is a transient heterokaryon, and not a hybrid (in hybrids, the nuclei have fused and the cells re-enter the cell cycle. Heterokaryons have separate nuclei and are not propogated as stable mono-nuclear cell lines.)

source_name: Mouse ES X Human Fib Heterokaryons

value: Mouse ES X Human Fib Heterokaryons

tag: time


title: Het Day2 rep2

description:
Mus musculus and Homo sapiens
Het Day2 BC4
The heterokaryon sample is a fused cell product (a transient, multinucleate mixed species entity generated by the cytoplasmic membrane fusion of mouse embroynic stem cells and human fibroblasts).  The cell lines used to make the fusion product were D3 mouse ES cells and human fibroblast MRC5 cells. It is important to note that the sample is a transient heterokaryon, and not a hybrid (in hybrids, the nuclei have fused and the cells re-enter the cell cycle. Heterokaryons have separate nuclei and are not propogated as stable mono-nuclear cell lines.)


title: Co-culture rep1

description:
Mus musculus and Homo sapiens
Co-cult BC8
The co-cultured sample consists of RNA derived from individual mouse and human cells which are cultured together (but not fused - so their membranes remain distinct). The two cell types were pooled together before a single RNA harvest. Thus, this sample is a mixture of D3 mouse ES cells and MRC5 human fibroblasts.


title: Het Day3 rep1

description:
Mus musculus and Homo sapiens
Het Day3 BC5
The heterokaryon sample is a fused cell product (a transient, multinucleate mixed species entity generated by the cytoplasmic membrane fusion of mouse embroynic stem cells and human fibroblasts).  The cell lines used to make the fusion product were D3 mouse ES cells and human fibroblast MRC5 cells. It is important to note that the sample is a transient heterokaryon, and not a hybrid (in hybrids, the nuclei have fused and the cells re-enter the cell cycle. Heterokaryons have separate nuclei and are not propogated as stable mono-nuclear cell lines.)


title: Wild Louisiana N. crassa isolate 2489 Tip

city: Berkeley

first: Charles

middle: Robert

last: Hall

address: 341 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to FGSC 2489 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods. 2008.  The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the transcript and by the size of the library.
Genome_build: V10
Supplementary_files_format_and_content: tab-delimited text file including gene specific RPKM values for each Sample

organism: Neurospora crassa

source_name: Mycelia, Tip (1 hour growth)

extract_protocol:
mycelia were harvested, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: source

value: mycelia

tag: age

value: 1 hour


title: Het Day2 rep1

description:
Mus musculus and Homo sapiens
Het Day2 BC3
The heterokaryon sample is a fused cell product (a transient, multinucleate mixed species entity generated by the cytoplasmic membrane fusion of mouse embroynic stem cells and human fibroblasts).  The cell lines used to make the fusion product were D3 mouse ES cells and human fibroblast MRC5 cells. It is important to note that the sample is a transient heterokaryon, and not a hybrid (in hybrids, the nuclei have fused and the cells re-enter the cell cycle. Heterokaryons have separate nuclei and are not propogated as stable mono-nuclear cell lines.)


title: Het Day1 rep2

description:
Mus musculus and Homo sapiens
Het Day1 BC2
The heterokaryon sample is a fused cell product (a transient, multinucleate mixed species entity generated by the cytoplasmic membrane fusion of mouse embroynic stem cells and human fibroblasts).  The cell lines used to make the fusion product were D3 mouse ES cells and human fibroblast MRC5 cells. It is important to note that the sample is a transient heterokaryon, and not a hybrid (in hybrids, the nuclei have fused and the cells re-enter the cell cycle. Heterokaryons have separate nuclei and are not propogated as stable mono-nuclear cell lines.)


title: Het Day1 rep1

description:
Mus musculus and Homo sapiens
Het Day1 BC1
The heterokaryon sample is a fused cell product (a transient, multinucleate mixed species entity generated by the cytoplasmic membrane fusion of mouse embroynic stem cells and human fibroblasts).  The cell lines used to make the fusion product were D3 mouse ES cells and human fibroblast MRC5 cells. It is important to note that the sample is a transient heterokaryon, and not a hybrid (in hybrids, the nuclei have fused and the cells re-enter the cell cycle. Heterokaryons have separate nuclei and are not propogated as stable mono-nuclear cell lines.)


title: Mock-NELFA_ChIPSeq

city: Evanston

first: Jonathan

middle: E

last: Freaney

state: Illinois

address: 2200 Campus Drive

institute: Northwestern University

data_processing:
All sequence data were with aligned the human hg19 assembly using BioScope v1.3.1.
The reference genome was converted to colorspace for appropriate alignment with colorspace reads, initially locating perfect, full-length 50 bp matches for each read.  If a perfect match could not be found, then 25 bases were aligned with 2 colorspace mismatches allowed, starting at position 0 (i.e. the first sequenced base).  The alignment was then extended base-by-base toward the 3' end.  If the alignment failed within the first 25 bp of the read, then 25 bases of the read were aligned, with 2 allowed colorspace mismatches, starting at position 15 of the read (i.e. the 16th sequenced base), and extended toward the 5' end, and forward toward the 3' end until the best alignment is obtained.
Operating under the default parameters and using the sequenced input DNA as the control, MACS software was used to identify binding sites (or peaks) in each sample.
Subsequently, we further filtered peaks that are contained in signal artifact regions, as specified by the set of blacklists used for Grch37/hg19 (ftp://encodeftp.cse.ucsc.edu/users/akundaje/rawdata/blacklists/hg19/).
Data analysis was performed using HOMER, a software suite for ChIP-Seq analysis.  Each ChIP-Seq experiment was normalized to a total of 107 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.  This normalization was used for all downstream analysis.
Genome_build: Grch37
Supplementary_files_format_and_content: bigWig and BED files. Both file types we made using the software suite HOMER.  (For details see http://biowhat.ucsd.edu/homer/)

growth_protocol: Human immortalized Namalwa B cell line (ATCC CRL-1432) were cultured in RPMI 1640 medium (Life Technologies) containing 10% cosmic calf serum (Hyclone), glutamine, 1 mM sodium pyruvate (Cellgro), and 1% penicillin/streptomycin (Life Technologies).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Purified immunoprecipitated DNA was prepared for sequencing according to the 5500 Series SOLiD Systems Fragment Library Preparation protocol.  Fragmented DNA was prepared by blunt-ending the DNA, size selecting DNA between 100-250 bp using Agencourt AMPure XP Reagent beads, and adding a dA-tail to allow for directional ligation.  Following the addition of a single adenine nucleotide overhang, a 1:20 dilution of the appropriate adaptor pair was used in the ligation step.  After ligation, the DNA library was size selected to a narrow range of fragment sizes by using Agenoncourt AMPure XP Reagent (~200-300 bp, which represents shear fragments between 100 and 200 nt in length and ~100 bp of primer sequence).  A subsequent PCR with limited (14-17) amplification was conducted and a final size selection was carried out prior to e-PCR and paired-end sequencing on the ABI SOLiD series 5500 DNA sequencing platform.

treatment_protocol: Infection of cells with Sendai virus, Cantell strain was performed at 5 plaque-forming units per cell (pfu/cell) in serum-free media.  After 1 hr, cells were lightly centrifuged, washed, and re-suspended in growth media supplemented with 2% CCS.  For mock-infection, cells were subjected to all manipulations with PBS substituted for virus inoculum.

tag: cell line

tag: infection

value: mock

tag: chip-antibody

value: NELFA (Santa Cruz (A-20), sc-23599)


title: Sendai_Virus-Pol_II_(S2P)_ChIPSeq

value: immortalized Namalwa B cell line (ATCC CRL-1432)

value: Sendai virus (Cantell strain)

value: Ser2P Pol II (Abcam, ab5095)


title: Mock-Pol_II_(S2P)_ChIPSeq


title: Sendai_Virus-NELFA_ChIPSeq


title: Mock-MED1_ChIPSeq

value: MED1 (Bethyl Labs, A300-793A)


title: Mock-Pol_II_(8WG16)_ChIPSeq

value: Pol II [8WG16] (Abcam, ab817)


title: mK4_H3K27


title: Sendai_Virus-p65_ChIPSeq

value: NFκB p65 (Abcam, ab7970)


title: Mock-p65_ChIPSeq


title: Sendai_Virus-Pol_II_(8WG16)_ChIPSeq


title: Sendai_Virus-IRF3_ChIPSeq

value: IRF3 (Abcam, ab76367)


title: Input_DNA


title: Sendai_Virus-MED1_ChIPSeq


title: Mock-IRF3_ChIPSeq


title: Nasonia_vitripennis_24h_adult_female_Bisulfite-Seq_GAllx

status: Public on Aug 27 2013

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

institute: Cornell University

description: Illumina WGBS-seq

data_processing:
Illumina CASAVA 1.7 software was used for HiSeq2000 basecalling and Illumina pipeline v1.3 was used for GAIIx basecalling.
Adapter sequences were removed from the raw reads by custom scripts (0.7% in GAIIx lane and 0.9% in HiSeq lane). The sequence reads were trimmed to 75 bp to include only high quality bases in the analysis.
We built C->T converted reference genomes for both the Watson (+) and Crick (-) strand for Nasonia vitripennis reference genome, with all Cs in CpGs context remains Cs (meth_genome) and all CpG Cs converted to Ts (unmeth_genome).
Illumina sequencing reads were aligned to the converted genomes using BWA with a maximum of four mismatches, and summarized in a single BAM file. 80% of the reads could be mapped to the converted naosnia reference genome. To get accurate methylation estimation, we only used uniquely mapped reads without any indel (60% of total reads) for the methylation quantification.
Base counts were summarized at all 14 million CpG positions in the genome. CpG methylation percentages were estimated from the proportion of remaining Cs in CpG context.
Genome_build: Nvit_1.0
Supplementary_files_format_and_content: tab-delimited text file includes the C and T counts at every signle CpG position in nasonia vitripennis genome.

organism: Nasonia vitripennis

source_name: 24h adult Nasonia vitripennis female whole body

extract_protocol:
Genomic DNA samples were extracted from a pool of 50 24h adult females from the standard N. vitripennis strain AsymCX using Qiagen DNeasy Blood & Tissue Kit.
20 ug of female Nasonia genomic DNA and 5ug unmethylated control lambda DNA (catalog #: D1521, Promega, WI) were sheared by Covaris S2 system (Covaris, MA) for 480 second with 10% duty cycle, level 5 intensity and 200 cycles per burst. The DNA fragments were purified with Zymo DNA Clean & Concentrator-5 columns (Zymo Research, CA), size-selected for 130-180bp with E-Gel system (Life technologies, CA) and QIAquick Gel Extraction Kit (Qiagen, CA), end-repaired with NEBnext end repair module and NEBnext dA tailing module (New England Biolabs Inc., MA), ligated with Illumina methylated PE adapter oligo (part #1005560, Illumina, CA) and then purified with Agencourt AMPure XP beads (Beckman Coulter, CA). We performed bisulfite conversion on purified nasonia adult DNA and lambda control DNA using Qiagen EpiTect Bisulfite kit with 2x bisulfite conversion cycles to improve the conversion efficiency and then purified the elute by AMPure XP beads. The purified converted DNA was amplified with PfuTurbo Cx Hotstart DNA Polymerase (Agilent Technologies, CA) using 15 cycles. The final libraries were purified again using AMPure XP beads and the library concentration was measured by Qubit (Life technologies, CA). The library size distribution was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, CA).

tag: developmental stage

value: 24-hour adult

tag: tissue

value: whole body

tag: Sex

value: female


title: Nasonia_vitripennis_24h_adult_female_RNA-Seq

description: Illumina WGBS-seq

data_processing:
Illumina CASAVA 1.8.2 software was used for basecalling.
Adapter sequences were removed from the raw reads by custom scripts.
Illumina short reads were mapped to the nasonia reference genome v1.0 using TopHat program with a maximum of 3 mismatches. The expression level was quantified for nasonia OGS2 (official gene set 2) genes using cufflinks software with '-u' parameter.
Genome_build: Nvit_1.0
Supplementary_files_format_and_content: tab-delimited text file includes the FPKM value for expressed nasonia OGS2 (official gene set 2) genes.

extract_protocol:
Total RNA samples were extracted from adult females ~24 hours following eclosion from pupation, using RNeasy Plus mini kit (Qiagen, CA) following the manufacturer’s protocol. The RNA concentration and the A260nm/A280nm absorption ratios were measured by NanoDrop ND-1000 Spectrophotometer (Thermo Scientific, DE) to make sure they have good quality. RNA integrity was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies, CA). All of the samples had a RIN (RNA integrity number) in the range 9.8-10.0 (RINmax = 10.0).
The mRNA-Seq library was made from 3.5ug total RNA samples from 24 hour adult females, using TruSeq RNA Sample Preparation Kits v2 (Illumina Inc., CA).


title: Input, replicate 1

city: Houston

first: Ashlee

middle: Renae

last: Lain

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
DNA libraries were sequenced on an Illumina Genome Analyzer II.
Sequences (36-nt reads) were aligned to the mouse genome (mm9) using the Burrows-Wheeler Aligner algorithm.
Aligns were extended in silico at their 3'-ends to a length of 150bp and assigned to 21-nt bins along the genome.
The resulting histograms were stored as Binary Analysis Results (BAR) files.
Peak locations were determined using the Model-based Analysis of ChIP-seq Algorithm (MACS).
Signal maps and peak locations were used as input data to the Genpathway proprietary analysis program, which provided detailed information on sample comparison, peak metrics, peak locations, and gene annotations.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: WIG files containing peaks were generated using MACS.

source_name: Mammary glands of 10-week-old wildtype mice treated with E+EP6h, input

growth_protocol: 10-week-old ovariectomized mice.

extract_protocol:
Mammary glands were treated with a TissueTearer followed by dounce-homogenization in lysis buffer. Lysates were sonicated and PR-DNA complexes were isolated using a PR antibody.
ChIP and input DNA were amplified using the Illumina ChIP-Seq DNA Sample Prep Kit.

treatment_protocol: Treated subcutaneously with 17β-Estradiol (100ng) for 24 hours and then 17β-Estradiol (100ng) plus Progesterone (2.5ug) for 6 hours.

tag: strain/background

value: BALB/c

tag: genotype

value: wildtype

tag: gender

value: mammary gland

value: 10 weeks

tag: treatment

value: 17β-estradiol for 24 hours and then 17β-estradiol plus progesterone for 6 hrs


title: Input, replicate 2


title: PR ChIP-seq, replicate 2

source_name: Mammary glands of 10-week-old wildtype mice treated with E+EP6h, PR ChIP

value: anti-PR (Santa Cruz, sc-7208)


title: PR ChIP-seq, replicate 1


title: am28

city: Baltimore

first: Allan

middle: C

last: Spradling

state: MD

address: 3520 San Martin Dr.

department: Embryology

institute: Carnegie Institution/HHMI

data_processing:
basecalling:  CASAVA v1.8.2
reads aligned to genome using Bowtie2 v 2.0.6
identified reads hitting transcripts using TopHat v 2.0.7 with -G  --no novel juncs and Refseq dm3-iGenomes.gtf
calculated transcript fpkm values and gene fpkm values using Cufflinks version 2.02 -G with dm3-iGenomes.gtf
Genome_build: Refseq annotation file:dm3 and dm3-iGenomes.gtf
Supplementary_files_format_and_content: Cufflinks output file: genes.fpkm_tracking:

source_name: posterior midgut

growth_protocol: Fertilized adult females 4-14 days of age were employed to avoid the final steps of gut maturation that take place in young adults, as well as age-induced decline.  Flies were kept at a controlled density in fresh vials, at 25°C and provided with a uniform level of nutrition before and during the study period.  Under these conditions, the cellular structure of the midgut was stable and reproducible as assessed by cell counts along its length.

extract_protocol:
We identified GAL4 lines with regional expression, then dissected and sectioned gut regions based on the presence or absence of GFP under a fluorescent dissecting microscope.   Gut regions were isolated, no more than 5 at a time, and moved to iced tripure (Roche/Boehringer Mannheim cat: 11667157001) to avoid RNA degradation (which occurred unless guts were processed within 30 min of isolation (or 10-15 minutes in the case of the copper region samples).  After 25 or 50 gut regions were collected in 200μl tripure, they were homogenized.  600μl of fresh tripure was added, mixed, and allowed to stand at room temperature for 5-10 min.  After adding 180μl chloroform, samples were vortexed 2 x 45 secs, and incubated at room temperature for 10 minutes.  Samples were then centrifuged for 15 min at 12,000 rpm at 4°C, and the aqueous layer was moved to a fresh tube.  RNA was precipitated by adding 400μl of isopropanol, vortexing for 15 seconds, and incubating at room temperature for 15 min, and centrifuging at 12,000 rpm for 15 min at 4°C.  After washing the pellet with 75% EtOH, the RNA was dried in air dry for 5 minutes, resuspended in 50μl nuclease free H2O, and stored at -80°C.
cDNA libraries were constructed from poly(A)-selected RNA using Illumina TruSeq RNA Library Prep Kit v2

value: Oregon R

tag: Stage

value: 6-14 day old adult female

tag: subregion

tag: replicate


title: am29

tag: strain


title: am30


title: am27


title: am26


title: am25


title: am24

source_name: middle midgut

value: Fe


title: am23


title: Nasonia_vitripennis_24h_adult_female_Bisulfite-Seq_HiSeq2000

description: Illumina WGBS-seq


title: am22


title: am20

value: LFCFe


title: Mammary tumor RNA from AKXD RI Strain 27

city: Rockville

first: Ying

last: Hu

email: yhu@mail.nih.gov, hunterk@mail.nih.gov

address: 9609 Medical Center Dr.

department: NCI/CCR

institute: NIH

data_processing:
Trim adaptor sequences and trailing Ns: in-house perl script
Merge to unique reads: in-house perl script
Build sequence database: formatdb
Query with miRBase known miRNA sequence: blastall
Parse matched sequence and extract read counts: in-house perl script
Map to mm9 reference genome: bwa
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: RPM matrix in text tab-delimited file

extract_protocol:
Tumors were snap-frozen upon harvesting and stored at −80°C. All tumors were homogenized on dry ice in an RNase-free environment. The RNA was isolated using the mirVana miRNA Isolation Kit (Ambion).
Library construction was constructed by the NCI Sequencing Core.

value: Mammary tumor

value: [AKXD RI x FVB/N-TgN(MMTV-PyVT)634Mul]F1 sublines


title: am21


title: am18

value: Cu


title: Ehf ChIP

city: Irvine

first: Bogi

last: Andersen

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

description:
Ehf chip sample
Single end 50bp sequencing

data_processing:
Base-calls were made using RTA  version 1.12.4.2
Reads were aligned to mouse genome mm9 using Bowtie version 0.12.7, only uniquely aligning reads were retained (-m 1)
Bam file were converted to BED using Bedtools (bamToBed v2.11.2)
Peaks were called using macs14, with input aligned sequences as the control file
Galaxy was used for further data analysis (performing intersection/subtraction analysis, extracting features)
Genome_build: mm9
Supplementary_files_format_and_content: interval file from galaxy, containing chromosome and coordinates of peak locations

source_name: mouse corneal epithelium

growth_protocol: CB6 mice, ages 2-3 months, were used.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. 24 ug of sonicated chromatin was used for the Ehf IP.
Sequencing libraries were generated for the Ehf and Input samples using Illumina Tru-Seq ChIP-Seq kit, multiplexed to be sequenced in a single lane, according to the Illumina protocol for ChIP-Seq library preparation, with some modification. After adaptor ligation, PCR amplification was performed prior to size selection of the library [Schmidt D, Methods, 2009]. Clustering and 50-cycle single end sequencing were performed on the Illumina Hi-Seq 2000 Genome Analyzer.

treatment_protocol: Whole eye globes were washed 3x5min in PBS+ Pen/Strep.  Corneal epithelium was isolated by digestion in 50% EMEM/dispase II with 50 mM sorbitol for two hours at 37°C.  Samples from 15 mice were pooled and then fixed for ChIP.

tag: genotype/variation

value: wild type

value: corneal epithelium

tag: chip antibody

value: ESE-3A (E-15) antibody [Santa Cruz Biotechnology, Catalog# sc-15450, Lot# I1704]


title: Mammary tumor RNA from AKXD RI Strain 25


title: Mammary tumor RNA from AKXD RI Strain 28


title: Mammary tumor RNA from AKXD RI Strain 24


title: am17


title: am15

source_name: anterior midgut


title: Input control

description:
input control sample
Single end 50bp sequencing


title: Mammary tumor RNA from AKXD RI Strain 23


title: am16


title: Mammary tumor RNA from AKXD RI Strain 21


title: Mammary tumor RNA from AKXD RI Strain 18


title: Mammary tumor RNA from AKXD RI Strain 16


title: am12


title: am11


title: Mammary tumor RNA from AKXD RI Strain 13


title: am9


title: am8


title: am13


title: am10


title: am19


title: Mammary tumor RNA from AKXD RI Strain 14


title: Mammary tumor RNA from AKXD RI Strain 10


title: Mammary tumor RNA from AKXD RI Strain 9

source_name: Mammary tumor RNA from AKXD RI Strain 9


title: am7


title: am5

value: CuLFCFe


title: am4


title: Mammary tumor RNA from AKXD RI Strain 3

source_name: Mammary tumor RNA from AKXD RI Strain 3


title: am2


title: am1


title: Sample_LincRNA_P3C4-5h

status: Public on Aug 26 2013

city: Worcester

first: Daniel

last: Aiello

state: ma

address: 364 plantation Street

department: Division of Infectious Diseases and Immunology, Department of Medicine

institute: UMASS Medical School

description: mRNA-seq

data_processing:
Basecalls performed using CASAVA version 1.8
Short reads were aligned to the Mus musculus genome using tophat
Gene level read counts based on resulting alignments were calculated with HTSeq
Genome_build: NCBIM37 (ie, MGSCv37)
Supplementary_files_format_and_content: Gene count files were generated with the HTSeq program.

source_name: Bone marrow cells from wild-type mice

growth_protocol: Bone marrow cells from wild-type mice were cultured in DMEM with 10% fetal bovine serum and 20% L929 supernatants.

extract_protocol:
RNA was extracted with RNeasy kit (QIAGEN, CA), 1g of total or nuclear RNA was used for cDNA synthesis.
10ug of total RNA was used and libraries were generated using an illumina mRNA sample preparation kit (#RS-930-1001). Once samples were sized, quantified, and proofed they were read on a High-Seq System (Illumina) as 50bp reads.

treatment_protocol: Cells were stimulated with Pam3Cys4 (100nM) and treated with shRNA specifically targetting lncRNA-COX2.

tag: stimulant

tag: shRNA treatment

tag: cell type

value: Bone marrow cells


title: am14


title: Mammary tumor RNA from AKXD RI Strain 22


title: am3


title: Mammary tumor RNA from AKXD RI Strain 20


title: Mammary tumor RNA from AKXD RI Strain 2

source_name: Mammary tumor RNA from AKXD RI Strain 2


title: Sample_LincRNA_CTL

description: mRNA-seq

value: No stimulation

value: shRNA specifically targetting lncRNA-COX2


title: Mammary tumor RNA from AKXD RI Strain 11


title: Sample_EV_CTL_P3C4-5h

description: mRNA-seq

value: No shRNA


title: Sample_EV_CTL

description: mRNA-seq


title: H3K27me3_ChIPSeq

city: Dublin

first: Adrian

middle: P.

last: Bracken

address: 1 Lincoln Place

department: Department of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
Alignment; 50bp short reads were mapped onto the Human genome (hg19, Feb 2009) using the burrows-wheeler alignment tool, allowing for up to two mismatches in each read.
Peak detection was performed using MACS (Zhang et al. 2008) where the FBio-Ctrl or Input_DNA datasets served as a normalization controls for the FBio-CHD5 and H3K27me3 datasets, respectively.
Tag density files for each dataset were generated using the IGV toolkit.
Genome_build: hg19, Feb 2009
Supplementary_files_format_and_content: tag density files

source_name: FBio-CHD5 expressing SH-SY5Y cells

growth_protocol: SH-SY5Y cells were grown in DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol:
Differentiated SH-SY5Y cells cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin from FBio-CHD5 and Fbio-Ctrl expressing SH-SY5Y cells was precipitated with magnetic streptavidin beads (Invitrogen) or the H3K27me3 antibody and recovered DNA and an Input DNA control were used for high throughput sequencing.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 14 cycles and library fragments of 150-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was sent to BGI genomics for sequencing on an Illumina Hi-Seq 2000 platform.

treatment_protocol: SH-SY5Y cells were treated for 8 days in the presence of 10uM Retinoic Acid (Media was changed on Days  2, 4, 6)

value: neuroblastoma cell line

tag: cell line

tag: expression

value: Retinoic Acid treatmeant (8 Days)

value: H3K27me3 (Millipore, 07-449)


title: Input_DNA


title: Mid-maturation-stage embryonic axis

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Whole embryonic axis devoid of the plumule was collected from mid-maturation stage embryos.  Seeds containing mid-maturation embryos are 1.1 - 1.3 cm in length and have a fresh weight between 200 - 250 mg.

data_processing:
Basecalls performed using RTA version 1.12.4.2
Original data file from the Illumina sequencing pipeline.  Each lane of sequencing is attached as an individual compressed file.  The sequence data are in the QSEQ format
We aligned the raw reads to a pre-processed reference genome using BS Seeker [Chen et al. BMC Bioinformatics (2010)] allowing for two mismatches.  The pre-processed reference genome consisted of sequences from the soybean genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net), soybean chloroplast genome (GenBank: DQ317523), lambda reference genome (GenBank: J02459), and Phi-X174 reference genome (GenBank: J02482).
Reads containing three consecutive methylation in the non-CG sites were removed, possibly representing non-converted cytosines (Cokus et al. Nature 2008). Clonal reads possibly arising during the PCR amplification step were collapsed into one read.
Methylation level of sampled cytosine was calculated as (methylated calls / (methylated calls + unmethylated calls)).
Genome_build: Glyma version 1.01
Supplementary_files_format_and_content: tab-delimited text file including methylation level of each sampled cytosine

organism: Glycine max

source_name: Soybean mid-maturation-stage embryonic axis part

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010).  The mid-maturation (MM) stage seeds are 1.1 - 1.3 cm in length and have a fresh weight between 200 - 250 mg. The tip of the embryonic axis is yellow while the rest of the embryonic axis is green. The embryo was dissected out of the seed coat and the axis was manually separated from the cotyledons of the MM-stage embryo.

extract_protocol: Collected tissues were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Genomic DNA  was isolated from the powder using the DNEASY Plant Mini kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.Approximately one microgram of genomic DNA was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications. We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion. Two libraries were constructed from genomic DNA isolated from seed coat. One library was spiked in ~ three nanogram of unmethylated lambda DNA as all other libraries; the other library was spiked in ~ three nanogram of methylated lambda DNA to serve as a control for over conversion (i.e. conversion of methylated cytosine to uracil) during the bisulfite conversion step. The methylated lambda DNA was generated by treating unmethylated lambda DNA with CpG Methyltransferase (New England BioLabs). Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA).  BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase.  PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: cultivar

value: Williams 82

tag: developmental stage

value: mid-maturation

tag: tissue

value: embryonic axis


title: ldl1 ldl2

city: Dallas

first: Hume

last: Stroud

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
mRNA-Seq reads were first trimmed to 50mers and mapped with Bowtie (Langmead, et al. 2009 Genome Biol.) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads.
Genome_build: TAIR8
Supplementary_files_format_and_content: Processed files indicate the coordinates of uniquely mapped reads. Column 1 is chromosome. Column 2 is the genomic strand (+/-). Column 3 is the genomic coordinate.

organism: Arabidopsis thaliana

source_name: ldl1 ldl2

growth_protocol: All plants were grown under long day conditions.

extract_protocol: Leaves from wild type Col-0, suvr5-1, ldl1-2 ldl2 and suvr5-1 ldl1-2 ldl2 3 week-old plants were used for RNA extraction using Trizol (Invitrogen) following the manufacturer instructions. 10 mg of total RNA was treated with DNaseI (Roche), and cleaned up with RNeasy columns (Qiagen). Poly(A) was purified using the Dynabeads mRNA Purification Kit (Invitrogen) and used to generate the mRNA-seq libraries following the manufacturer’s instructions (Illumina).

tag: ecotype

tag: genetic variant

value: ldl1 ldl2

value: leaves


title: Mid-maturation-stage seed coat

description: Seed coat was collected from mid-maturation stage embryos.  Seeds containing mid-maturation embryos are 1.1 - 1.3 cm in length and have a fresh weight between 200 - 250 mg.

source_name: Soybean mid-maturation-stage seed coat

value: seed coat


title: Col0

value: wild type


title: Mid-maturation-stage embryonic cotyledons

description: Whole embryonic cotyledons were collected from mid-maturation stage embryos.  Seeds containing mid-maturation embryos are 1.1 - 1.3 cm in length and have a fresh weight between 200 - 250 mg.

source_name: Soybean mid- maturation-stage embryonic cotyledons

value: embyronic cotyledon


title: am6

value: Oregon R

value: 6-14 day old adult female


title: Fbio-Ctrl_ChIPSeq

source_name: Fbio-Ctrl expressing SH-SY5Y cells

value: FBio-Ctrl

tag: treatment

value: Streptavidin (Dynabeads, M-280)


title: FBio-CHD5_ChIPSeq


title: Mammary tumor RNA from AKXD RI Strain 7

source_name: Mammary tumor RNA from AKXD RI Strain 7

value: Mammary tumor

value: [AKXD RI x FVB/N-TgN(MMTV-PyVT)634Mul]F1 sublines


title: H3K4me1_ChIPSeq_mt

status: Public on Aug 24 2013

city: Uppsala

first: Lin

last: Jiang

address: Husargatan 3, Box 582

department: Department Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala University

data_processing:
Alignment: ChIP-sequencing reads were aligned to the Mouse genome July 2007 (NCBI37/mm9) assembly by using Mosaik (version 1.0.1384) (http://bioinformatics.bc.edu/marthlab/Mosaik) with default parameters.
Peaks: The uniquely aligned reads were submitted for calling peaks by using Model-based analysis of ChIP-sequencing (MACS)

source_name: C2C12 myotube

growth_protocol: Near-confluent myoblasts growing with 10% serum and myotubes with~5 days post-differentiation (serum withdrawal). The myotubes were separated from unfused residual cells by light trypsination.

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

value: C2C12 myotube

tag: passages


title: 1027

city: Toronto

first: Viviane

last: Labrie

address: 250 College st.

institute: Centre for Addiction and Mental Health

description: Brain genomic DNA analyzed with mTAG-seq. Unmodified CpG sites were labelled with M.SssI (25% labelling efficiency).

data_processing:
Paired end sequencing was completed on an Illumina HiSeq platform generating ~100 million paired-end reads with a read length of 90 bp.
These reads were mapped to human genome assembly hg19 using BWA with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: Brain

extract_protocol:
The sample was sheared at an average length of 300 bp and labelled using the mTAG approach as described in the high-throughput mTAG-click protocol.
Library preparation involving adenylation of 3’-ends, adaptor ligation and PCR amplification with unique index primers was performed as described in the Illumina Multiplexing Sample Preparation Oligonucleotide kit. The only changes in this library preparation protocol were that the samples were treated with 10 mM 2-mercaptoethanol for 10 min at room temperature prior to PCR amplification, and only 14 cycles of PCR were performed.

tag: enrichment protocol

value: mTAG

tag: gender

value: male

tag: age

tag: pmi

tag: sample source

value: Harvard Brain Tissue Resource Centre


title: H3K27ac_ChIPSeq_mt

tag: strain

tag: chip antibody


title: H3K27me3_ChIPSeq_mt

tag: cell type


title: H3K36me3_ChIPSeq_mt


title: H3K36me3_ChIPSeq_mb

source_name: C2C12 myoblast

value: C2C12 myoblast


title: H3K4me2_ChIPSeq_mt


title: H3K27ac_ChIPSeq_mb


title: H3K27me3_ChIPSeq_mb


title: H3K4me1_ChIPSeq_mb


title: H3K4me2_ChIPSeq_mb


title: suvr5 ldl1 ldl2

source_name: suvr5 ldl1 ldl2

value: suvr5 ldl1 ldl2


title: H3K4me3_ChIPSeq_mb


title: suvr5-1