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Sample GSM5333648 Query DataSets for GSM5333648
Status Public on May 24, 2024
Title MBT PolII ChIP-seq rep1
Sample type SRA
 
Source name MBT zebrafish embryo
Organism Danio rerio
Characteristics strain: Tubingen
tissue: embryo
developmental stages: sphere stage
chip antibody: Covance MMS-126R
Treatment protocol 4 datasets were generated from flavopiridol treated emrbyos. Embryos were dechorinated immediately after fertilization, and closely monitored for the development stages. Flavopiridol (Sigma-Aldrich F3055) were added to the embryo water to a final concentration of 10uM to inhibit transcription elongation at 3.75hpf, and the embryos then were collected at sphere stage.
Growth protocol Zebrafish embryos (strain Tübingen) were incubated at 28C
Extracted molecule genomic DNA
Extraction protocol Nuclei from formaldehyde crosslinked (1%; 10min at room temperature) embryos were isolated and chromatin was fragmented using sonicator (Branson). Lysates were cleared and protein-DNA complexes were isolated using target specific antibodies and Dynabeads. DNA fragments were purified and libraries were prepared by NEBnext DNA Library Prep Kit (NEB, E7370L). Adapter ligated DNA was purified using AMPure XP beads (Beckman Coulter, A63881) and sequenced by illumina HiSeq 2500.
NEBnext DNA Library Prep Kit
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description MBT_PolII_peaks.txt
MBT_PolII.bw
Data processing Raw reads were aligned to zv10 using Novoalign ( v2.8 novocraft) with the options [-r None -k -Q 13 -o SAM]
Sam files were converted to bam files using samtools.
Sorted bam files of replicates were then merged using MergeSamFiles.jar from Picard tools (v 1.100)
Peaking calling, relative to paired input, was performed using MACS2 (v2.1.0.20140616), using the following parameters: -f BAM -g 1.4e9 -B --fix-bimodal --extsize 250 -q 0.01
treat_pileup.bdg files from macs2 were then converted to bigWig files using bedGraphtoBigWig
Genome_build: zv10
Supplementary_files_format_and_content: text files are peak profiles generated from MACS2, and bigWig files represent the genome-wide protein occupancy
 
Submission date May 24, 2021
Last update date May 24, 2024
Contact name Bradley R Cairns
E-mail(s) candice.wike@hci.utah.edu
Organization name Huntsman Cancer institute/HHMI
Department oncological Sciences
Street address 2000 Cir of Hope Dr
City Salt Lake City
State/province UT
ZIP/Postal code 84112
Country USA
 
Platform ID GPL18413
Series (2)
GSE175444 Distinctive roles for the chromatin remodeling ATPases Brg1 and Brm in early zebrafish embryos [ChIP-seq]
GSE175447 Distinctive roles for the chromatin remodeling ATPases Brg1 and Brm in early zebrafish embryos
Relations
BioSample SAMN19317916
SRA SRX10973763

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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