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| Status |
Public on Jul 26, 2013 |
| Title |
seq-SDQ3166_LIN37_N2_LTemb_ChIP_Rep2 |
| Sample type |
SRA |
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| Source name |
seq-SDQ3166_LIN37_N2_LTemb_ChIP_Rep2
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
developmental stage: Late Embryos
genotype: wild type
Sex: Hermaphrodite
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| Growth protocol |
Worm_embryo_growth_and_harvest_vSS7. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Embryos were incubated for 3.5 hours in M9 then frozen in liquid nitrogen.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later,washed pellets are resuspended in FA buffer and subjected to sonication in a DiagenodeBioruptor (40 pulses of 30 seconds with 1 minute rests in between at full power). Extractsare then spun down and the soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit. For a detailed protocol see http://www.modencode.org/.
Short description for UNC NimbleGen Database:Both ChIP and input DNA samples have their ends blunted and phosphorylated with KlenowDNAP, T4 DNAP, and T4 PNK. 3?-dA overhangs are then added with Klenow Fragment (3? to 5?exo minus), and Illumina adapters are subsequently ligated to the ends. Next, PCRamplification is performed using Illumina 1.1 and 2.1 primers, for a total of 18 cycles. AmplifiedDNA libraries are size-selected on a 2% agarose gel so that fragments sized between 250-350bp are obtained; gel extraction is carried out at room temperature.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
ChIP DNA; Antibody information listed below: official name: BH00003 LIN37;target name: LIN-37;host: Rabbit;antigen: Full length;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Bob Horvitz;input DNA
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| Data processing |
to be updated
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| Submission date |
Jul 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
DCC modENCODE |
| E-mail(s) |
[email protected]
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| Phone |
416-673-8579
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| Organization name |
Ontario Institute for Cancer Research
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| Lab |
modENCODE DCC
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| Street address |
MaRS Centre, South Tower, 101 College Street, Suite 800
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| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
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| Platform ID |
GPL9309 |
| Series (1) |
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| Relations |
| Reanalyzed by |
GSE95071 |
| BioSample |
SAMN02264731 |
| SRA |
SRX529221 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1195398_seq-SDQ3166_LIN37_N2_LTemb_2_peaks.gff.gz |
28.1 Kb |
(ftp)(http) |
GFF |
| GSM1195398_seq-SDQ3166_LIN37_N2_LTemb_2_treat_afterfiting_all.wig.gz |
29.7 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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