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| Status |
Public on Aug 13, 2020 |
| Title |
EFL1.lin15B.rep2 |
| Sample type |
SRA |
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| Source name |
EFL1.lin15B.whole worm
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: lin-15B (n744)
developmental stage: starved L1
growth temperature: 25°C
tissue: whole worm
chip antibody: EFL1
sample id: CG142
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| Growth protocol |
Starved L1 animals were collected by bleaching synchronized adults grown in liquid culture using standard S-basal medium with HB101 E. coli at 20°C. Following bleaching, eggs were hatched at 25°C in M9 and starved L1s were sucrose floated and collected 20-22 hours following hatching by flash freezing in liquid nitrogen.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen starved L1 worms were ground to a powder, which was incubated in 1.5 mM EGS (Pierce 21565) in PBS for 8 minutes, followed by the addition of formaldehyde to a final concentration of 1%, and incubated for a further 8 minutes. The fixation was quenched for 5 minutes by the addition of 0.125 M glycine. Fixed tissue was washed 2X with PBS with protease inhibitors (Roche EDTA-free protease inhibitor cocktail tablets 05056489001) and once in FA buffer (50 mM Hepes pH7.5, 1 mM EDTA, 1% TritonX-100, 0.1% sodium deoxycholate, and 150 mM NaCl) with protease inhibitors (FA+), then resuspended in 1 ml FA+ buffer per 1 ml of ground worm powder. The extract was sonicated to an average size of ~250 base pairs using a Bioruptor Pico (Diagenode), and 10-20 ug of DNA was used per ChIP reaction.
ChIP DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads. Illumina TruSeq adaptors and barcodes were used.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
EFL1.lin15B.rep2.CG142
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| Data processing |
ChIP-seq reads were aligned to a concatenated ce11+cb3 assembly of the C. elegans and C. briggsae genomes using BWA v. 0.7.7 with default settings (BWA-backtrack algorithm) (Li and Durbin, 2010).
The SAMtools v. 0.1.19 ‘view’ utility (Li et al., 2009) was used to convert the alignments to BAM format. Normalized mapq10 ChIP-seq coverage tracks were generated using the BEADS algorithm (Cheung et al., 2011).
Genome_build: ce11 + cb3 (concatenated)
Supplementary_files_format_and_content: BEADS-normalized genome-wide linear read coverage (from reads with MAPQ value >= 10)
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| Submission date |
Jul 27, 2020 |
| Last update date |
Aug 13, 2020 |
| Contact name |
Francesco Nicola Carelli |
| E-mail(s) |
fr.carelli@gmail.com
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| Organization name |
University of Cambridge
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| Lab |
Julie Ahringer
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| Street address |
Henry Wellcome Building of Cancer and Developmental Biology, Tennis Court Road
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| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
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| Platform ID |
GPL18730 |
| Series (2) |
| GSE155189 |
DREAM represses distinct targets by cooperating with different THAP domain proteins [CHIP-seq] |
| GSE155191 |
DREAM represses distinct targets by cooperating with different THAP domain proteins |
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| Relations |
| BioSample |
SAMN15651185 |
| SRA |
SRX8832096 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4697083_EFL1.lin15B.rep2.CG142.BEADSQ10NU_linear.bw |
163.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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