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Sample GSM3861105 Query DataSets for GSM3861105
Status Public on Jun 07, 2019
Title Input DNA control for SOM-H3K27ac ChIP rep2
Sample type SRA
 
Source name 2% formaldehyde pre-fixed glp-1(q224) young adult animals
Organism Caenorhabditis elegans
Characteristics developmental stage: young adult (YA)
tissue: Soma
chipped factor: none - input
antibody: none - input
strain: JK1107
Extracted molecule genomic DNA
Extraction protocol Growth: glp-1(q224) animals were cultured to starvation on NGM plates at 15°C. L1 worms were floated and plated on one 15-cm NGM plate. Worms were cultured at 15°C for four days until gravid. Adult worms were bleached and embryos were incubated with shaking at 15°C for 36-42 hours. L1s were plated to three peptone enriched plates with 50K L1s per plate and cultured at 25°C for 46-48 hours until adult stage. Adult glp-1(q224) animals were harvested by 3X washes with M9. Extraction: Worms were crosslinked in 50 mL 2% formaldehyde for 30 minutes in a 50 mL conical tube at room temperature. Formaldehyde was quenched by 1 M Tris (pH 7.5) wash. Worms were then washed 2 more times with M9. Worms were transferred to a 15 mL conical tube and washed with 15 mL prechilled FA buffer. Worm pellets were frozen in liquid nitrogen and stored at -80°C. Worm pellets were thawed on ice and 750 µl of FA buffer was added to each sample. Samples were transferred to a 2 mL Kontes Dounce. Samples were Dounced 15 times with the small “A” pestle for two cycles and 15 times with the large “B” pestle for four cycles. Samples were sonicated with a SFX250 sonifier in an ice bath at 22% amplitude with 10 sec on/1 min off pulses for 34 cycles. 100-650 bp DNA fragments were enriched after sonication. 4.4 mg protein was used for each ChIP sample. 5% of lysate was removed for input sample and stocked at -20°C overnight. Library construction: The Yale Center for Genome Analysis (YCGA) prepared the library and performed sequencing. The KAPA Hyper Library Preparation kit was used for ChIP sequencing library prep. DNA fragment ends were repaired with T4 DNA Polymerase, and Polynucleotide Kinase and “A” base added using Klenow fragment in a single reaction followed by ligation of custom adapters (IDT) using T4 ligase. Adaptor-ligated DNA fragments were purified and size selected with Agencourt AMPure XP magnetic beads. Adaptor-ligated DNA fragments were amplified by LM-PCR using custom-made primers (IDT). During LM-PCR, unique 10 base indices were inserted at each DNA fragment and amplified products were purified.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description a fraction of the input total chromatin that was used for glp-1(q224) soma control H3K27ac ChIP
SOM-H3K27ac_ChIP-input.wig
Data processing ChIP-seq: The raw paired-end ChIP and corresponding input sequencing fastq reads were mapped to ce10 genome by mapping with Bowtie2 (v2.3.2) with default parameters.
ChIP-seq: Wig files were generated by a custom script (https://github.com/guifengwei/glib/blob/master/bam2wig.py),
ChIP-seq: Peaks were called by MACS2 (v2.1.1) with the key parameter (-q 0.001 --nomodel --extsize 150).
RNA-seq: The raw paired-end RNA-seq fastq reads were first mapped to rRNA build by bowtie2 (v2.1.0)
RNA-seq: The remaining unmapped reads were further aligned to ce10 genome by HISAT2 (v2.0.4) with the mode suppressing the unpaired reads
RNA-seq: The gene annotation was downloaded from UCSC Genome Browser, filtered to remove transcripts <50 nt, then was employed to estimate gene expression and call differential gene expression by Cuffdiff program [20] (v2.2.1) under the default parameters between VC2010 and glp-1(q224) strains.
Genome_build: ce10
Supplementary_files_format_and_content: wig or BigWig files were generated as an output
 
Submission date Jun 07, 2019
Last update date Jun 09, 2019
Contact name Valerie Reinke
E-mail(s) valerie.reinke@yale.edu
Phone 203-785-5228
Organization name Yale University School of Medicine
Department Genetics
Lab Reinke lab
Street address 333 Cedar St
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platform ID GPL9269
Series (1)
GSE117061 Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression
Relations
BioSample SAMN11975698
SRA SRX5985671

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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