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| Status |
Public on Jun 07, 2019 |
| Title |
Biosample_8018_4132_46901_HFYYWBGX2_S2_InSituHiC_HS_1_CGATGT |
| Sample type |
SRA |
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| Source name |
S2
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: S2
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| Treatment protocol |
Growing S2 cells were transferred to a shaking water bath maintained at room temperature (NHS) or at 36.5°C (HS). Simultaneously, an equal volume of medium (without FBS), kept at room temperature or at 48°C was added into the NHS or HS cells respectively. Cells were incubated for 20 min.
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| Growth protocol |
Drosophila S2 cells were grown in M3+BPYE medium with 10% FBS at 25°C incubator.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde for 10 min, quenched and permeabilized. Nuclei were digested with MboI and ends were biotinylated with biotin-14-dATP followed by in-situ ligation. Crosslinks were reversed and DNA was purified, sonicated and pulled down by streptavidin beads.
DNA was end repaired with T4 DNA polymerase, DNA polymerase I large (Klenow) polymerase and T4 polynucleotide kinase. DNA ends were adenylated by dATP and Klenow (3'-5' exo-) polymerase. Illumina Truseq adapters were ligated to the DNA ends and PCR amplified for 8 cycles. Library was purified with Qiaquick PCR purfication kit and sequenced on Illumina Nextseq 500.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Fastq files were processed using the Aiden Lab's Juicer pipeline. The reference genome used was dm3, and the restriction enzyme was MboI
The resulting contact matices (.hic files) were produced at resolutions of 20 Mb, 10 Mb, 5 Mb, 2.5 Mb, 1 Mb, 500 Kb, 250 Kb, 100 Kb, 50 Kb, 25 Kb, 10 Kb, 5 Kb, and 1 Kb, using only high quality reads (MAPQ score >= 30)
Genome_build: dm3
Supplementary_files_format_and_content: hic files - highly compressed binary files that store contact matrices at multiple resolutions
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| Submission date |
May 06, 2019 |
| Last update date |
Jun 09, 2019 |
| Contact name |
Charles Danko |
| E-mail(s) |
dankoc@gmail.com
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| Organization name |
Cornell University
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| Department |
Computational Biology
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| Lab |
Danko Lab
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| Street address |
235 Hungerford Drive
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
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| Platform ID |
GPL19132 |
| Series (2) |
| GSE130776 |
Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock [S2] |
| GSE130778 |
Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock |
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| Relations |
| BioSample |
SAMN11582891 |
| SRA |
SRX5797720 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3753419_S2_InSitu_HS_1_inter_30.hic |
466.4 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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