|
| Status |
Public on May 31, 2018 |
| Title |
glp-1_rep1_H3K4me3ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
glp-1_whole_worm
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain background: N2
genotype/variation: glp-1
developmental stage: L4
chip antibody: H3K4me3 (Millipore, Billerica, MA 17-614, lot:2756917)
|
| Growth protocol |
L4 worms were cultured and harvested on NGM plates
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA-seq: RNA was extracted using Trizol reagent.
ChIP-seq: Crosslinked protein-DNA complex were isolated with antibody.
RNA libraries were prepared for sequencing using Ovation Human FFPE RNA-Seq Library Systems (NuGEN) kit
ChIP-seq libraries were prepared for sequencing using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file: glp1_k4_H3_pooled.bedgraph
|
| Data processing |
RNA-seq:
Rawdata was filtered by fastq_quality_filter, adaptor was cut by cutadapt and rRNA was removed by bowtie2;
tophat2 was used to align reads to WS250 genome
cufflink was used to generate raw count for each gene
EdgeR was used to calculate the significant changed gene
ChIP-seq:
Two replicate ChIP-Seq raw data were pooled. Raw data were first filtered by fastx_trimmer and fastq_quality_filter
bowtie2 was used to align reads to WS250 genome
PCR duplicate was removed by samtools and the data were converted to bam files
bamCoverage was used to generate bedgraph files
Genome_build: Genome build: WS250
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bedgraph containing z-score in 50bp window; excel containing raw counts
|
| |
|
| Submission date |
Jan 08, 2018 |
| Last update date |
May 31, 2018 |
| Contact name |
Siu Sylvia Lee |
| E-mail(s) |
[email protected]
|
| Organization name |
Cornell University
|
| Street address |
520 Campus road
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platform ID |
GPL19757 |
| Series (1) |
| GSE108848 |
SET-9 and SET-26 are H3K4me3 readers and play critical roles in germline development and longevity |
|
| Relations |
| BioSample |
SAMN08325487 |
| SRA |
SRX3583340 |
