|
| Status |
Public on Nov 09, 2014 |
| Title |
seq-NA_N2_LTemb_Lemb4C |
| Sample type |
SRA |
| |
|
| Source name |
whole body
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
Stage: L3
|
| Treatment 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 Diagenode Bioruptor (40 pulses of 30 seconds with 1 minute rests in between at full power). Extracts are then spun down and the soluble fraction is stored for quality tests and future ChIP. http://wiki.modencode.org/project/index.php/Worm_popcorn_chromatin_extract_protocol_vSS1:JL:1
|
| 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. http://wiki.modencode.org/project/index.php/Worm_embryo_growth_and_harvest:JL:SS7
|
| 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 |
BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse. Genome build: ce6
|
| |
|
| Submission date |
Nov 09, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Tristan De Buysscher |
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Biology
|
| Lab |
Lieb
|
| Street address |
CB# 3280, Coker Hall
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-3280 |
| Country |
USA |
| |
|
| Platform ID |
GPL9269 |
| Series (1) |
| GSE33594 |
C elegans N2 Late embryo input control |
|
| Relations |
| SRA |
SRX105313 |
| BioSample |
SAMN00752539 |
