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| Status |
Public on Jan 20, 2016 |
| Title |
L1-Starved-DpnII |
| Sample type |
SRA |
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| Source name |
L1-Starved-DpnII
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
tissue: whole organism
genotype: wild-type
developmental stage: L1
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Animals were harvested by chilling on ice, centrifugation at 950g for two minutes and washing several times with cold M9. Pellets consisting each of approximately 100µl of closely packed worms were flash frozen in liquid nitrogen and stored in -80°C. The flash frozen worm pellets were ground to fine powder in liquid nitrogen. The grinding was performed either using mortar and pestle or using an electric drill with “Cellcrusher” drill-bit and “Cellcrusher” base held at liquid nitrogen temperatures. The grinding was done for several minutes, until reaching a fine powder. The powder was stored at -80°C. To get the DNA used for libraries construction, freeze-ground tissue was processed using procedures from (Kalhor, et al, 2012) with some modifications.
Libraries were prepared according to Illumina's instructions in Nextera DNA Sample Preparation Guide (Part# 15027987Rev. B) with some modifications. Briefly, DNA was tagmented using Tagmentase (TDE1), then cleaned-up using Zymo DNA Clean & Concentrator™-5 kit. The biotinylated purified DNA was selected using MyOne Streptavidin C1 magnetic beads (Invitrogen), fragments ion the beads were PCR amplified with Illumina primers for 12 cycles and library fragments of ~500 bp (insert plus adaptor and PCR primer sequences) were band isolated from 1% agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
Raw data files for this sample were generated from Illumina MiSeq and Illumina HiSeq 2000 instruments.
animals starved for 24 hours after bleaching
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| Data processing |
Library strategy: Tethered Chromosome Conformation Capture
Basecalls performed using Illumina Casava software
Read pairs obtained by massive parallel sequencing were aligned to the C. elegans reference genome (ce10) using an iterative mapping approach utilizing ICE software, utilizing Bowtie2 v2.2.5
Uniquely mapped pairs were filtered from duplicates and pairs that map concordantly (distance<500 and correct orientation)
Exact locations of contact junctions were calculated using specific alignments to the reference genome (ce10)
Genome_build: ce10
Supplementary_files_format_and_content: TSV files containing detected contact of chromatin architecture, the files contain the following fields: readname, mapped chr read1, mapped position read1, boolean of sense strand of read1, aligned sequence of read1, mapped chr read2, mapped position read2, boolean of sense strand of read2, aligned sequence of read2, reference sequenced read1 was aligned to, reference sequence read2 was aligned to, read1 sequence, read2 sequence, contact read1 chr, contact read1 pos, contact read2 chr, contact read2 pos. In case of single ended sequencing run, alignment is performed using two sides of a single read.
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| Submission date |
Jan 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Idan Gabdank |
| E-mail(s) |
gabdank@stanford.edu
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| Organization name |
Stanford
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| Department |
Genetics
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| Street address |
3165 Porter Drive
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94304 |
| Country |
USA |
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| Platform ID |
GPL15716 |
| Series (1) |
| GSE76930 |
A Streamlined Tethered Chromosome Conformation Capture Protocol |
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| Relations |
| BioSample |
SAMN04420243 |
| SRA |
SRX1533864 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2041034_n2_l1_starved_dpn.TSV.gz |
1.7 Gb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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