|
| Status |
Public on Aug 01, 2012 |
| Title |
H4K20me1 ChIP-seq of set-4 mutant, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
L3 larvae, set-4 mutant, H4K20me1 ChIP
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype: set-4(n4600)
tissue: whole body
developmental stage: L3 larvae
chip antibody: anti-H4K20me1
chip antibody vendor: Abcam
antibody catalog#: ab9051
antibody lot#: 602259
|
| Treatment protocol |
Worms are frozen, ground and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue is washed, resuspended in FA buffer and sonicated to an average size of 200bp using a Bioruptor. Extracts are then spun down and the soluble fraction is used for ChIP.
|
| Growth protocol |
About 2-7 million 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. The 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 made using the TruSeq DNA Sample Prep kit (Illumina). 1-10ng of ChIP or 10ng of input are blunted (T4 polymerase), an A-overhang is added (Klenow), DNA is ligated to adaptors, amplified by PCR, and the library is size-selected to a 250-400 bp range using Agencourt AMPure XP beads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
AA015
|
| Data processing |
ChIP-seq reads were aligned to the WS190 assembly of the C. elegans genome using BWA (Li and Durbin, 2010 (PMID 20080505)) with default settings.
Data were normalized using BEADS (Cheung et al., 2011 (PMID 21646344)). BEADS scores were converted to log2, and then the datasets were z-scored.
Signals were averaged in 50bp windows and wig files were generated.
Genome_build: WS190
Supplementary_files_format_and_content: Wig files were generated using the BEADS pipeline in R. Scores represent log2-transformed BEADS scores (single experiments). The wig file for the mean of AA015 and AA016 was generated by z-scoring the average of the single log2 scores.
|
| |
|
| Submission date |
Jul 31, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Przemyslaw Aleksander Stempor |
| Organization name |
University of Cambridge
|
| Department |
The Gurdon Institute
|
| Lab |
Ahringer Lab
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| State/province |
United Kingdom |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE39789 |
H4K20me1 contributes to downregulation of X-linked genes for Caenorhabditis elegans dosage compensation |
|
| Relations |
| SRA |
SRX172526 |
| BioSample |
SAMN01096297 |
| Named Annotation |
GSM979033_H4K20me1_ab9051_AC1_F_set4_L3_NORM_log2_25bp_AA015_F0f00539.wig.gz |
| Named Annotation |
GSM979033_Mean_AA015+AA016_H4K20me1_ab9051_AC1+AC2__F_set4_L3_norm_log2zsc_50bp.wig.gz |
