|
| Status |
Public on May 25, 2011 |
| Title |
Input control 3 |
| Sample type |
SRA |
| |
|
| Source name |
L3 embyros
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
developmental stage: L3
chip antibody: none
|
| Treatment protocol |
Worm_L3_extraction_vPK1. 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 Bioruptor. Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
|
| Growth protocol |
Worm_L3_growth_and_harvest_vPK1. About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to Illumina's instructions for "Preparing Samples for ChIP Sequencing of DNA", with some variation. DNA was end-repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 DNA polymerase. A's were then added to the 3' ends of the fragments using Kelow fragment (3' 5' exo minus). Paired-end adapters were then ligated onto the ends of the fragments. DNA library was size selected by gel purification, fragments of 250-500 bp were band isolated from an agarose gel. DNA was PCR amplified for 18 cycles. The Bioanalyzer was used to verify fragment purification and quantify DNA.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
input DNA
|
| Data processing |
Alignment: Sequence reads were mapped to the WS190 reference sequence using BWA
Summary WIG files: Mapped sequence reads were extended to 200 bp, which was the estimated mean insert size targeted in the size selection step when preparing the libraries. A genomic profile of signal levels was then generated by counting the number of extended sequence reads (i.e. read count) overlapping sampling points spaced at regular 50-bp across the genome.
|
| |
|
| Submission date |
May 20, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas A Down |
| E-mail(s) |
thomas.down@gurdon.cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
WT/CRUK Gurdon Institute
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9269 |
| Series (1) |
| GSE29427 |
Systematic bias in high-throughput sequencing data and its correction by BEADS |
|
| Relations |
| SRA |
SRX063961 |
| BioSample |
SAMN00619192 |
