 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 22, 2021 |
| Title |
DPY27_set4xv_L3_AKM60_input_AKM63 |
| Sample type |
SRA |
| |
|
| Source name |
whole worms
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: NM02
developmental stage: L3
genotype: set-4 (n4600) II; X;V (ypT47)
antibody target: DPY-27
chip antibody: JL001
antibody antigen: 1-409 aa
matching input: input_AKM63
|
| Treatment protocol |
Embryos were treated with 2% formaldehyde for 30 minutes, washed with M9, and collected by centifugation and freezing at -80C until extract preparation.
|
| Growth protocol |
Embryos were isolated by bleaching gravid adults grown on plates at 20C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of embryo extract and 3-5 ug of antibody was used per ChIP. Half of the ChIP DNA were ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls were performed using CASAVA version 1.8.
We aligned 50-75bp single-end ChIP-seq reads to C. elegans genome version WS220 using bowtie2 2.3.2 with default parameters (Langmead & Salzberg, 2012). Bam files were then sorted and indexed using samtools version 2.1.1 (Ramirez-Gonzalez, Bonnal, Caccamo, & Maclean, 2012). ChIP enrichment was normalized by either subtracting or dividing it by the input using DeepTools bamCompare using the following parameters: CPM, bin-size of 10bp, ignore duplicates, extend reads to 200bp, exclude chrM and remove blacklisted regions (Ho et al., 2014).For analyzing ChIP-seq data across the X chromosomal repeat block, --very sensitive option was used in bowtie2 and --minMappingQuality was removed for bamCompare.
MACS2 version 2.1.1 was used for fragment size prediction and for peak calling. For single replicate peak calling a minimum false discovery rate of .05 was used and for merged replicates a minimum false discovery rate of .01 was used to call significant peaks. Bedtools intersect was used to determine overlapping peaks between replicates and only those present in the majority of the replicates were chosen as final peaks.
Genome_build: WS220
Supplementary_files_format_and_content: ChIP to input CPM normalized ratio bigwig files for each replicate
Supplementary_files_format_and_content: ChIP to input CPM normalized ratio bigwig files averages
Supplementary_files_format_and_content: ChIP subtracted by input CPM normalized bigwig files for each replicate
Supplementary_files_format_and_content: ChIP subtracted by input CPM normalized bigwig files averages
Supplementary_files_format_and_content: Bed files containing ChIP-seq peaks called by MACS2
|
| |
|
| Submission date |
Mar 24, 2021 |
| Last update date |
Sep 22, 2021 |
| Contact name |
Jun Kim |
| E-mail(s) |
kimj50@nyu.edu
|
| Phone |
7183094777
|
| Organization name |
NYU
|
| Department |
Biology
|
| Lab |
Ercan
|
| Street address |
100 Washington Square East 1009 Silver Center
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
| |
|
| Platform ID |
GPL18245 |
| Series (2) |
| GSE169458 |
Mobility of condensin DC is key to its function in repressing transcription |
| GSE169524 |
Mobility of condensin DC is key to its function in repressing transcription [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN18473314 |
| SRA |
SRX10435526 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5208692_DPY27_set4xv_L3_ext15_AKM60_input_AKM63_inputsubt.bw |
67.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
