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| Status |
Public on Mar 27, 2023 |
| Title |
st10.5_hdac1_DMSO_we |
| Sample type |
SRA |
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| Source name |
whole embryo
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| Organism |
Xenopus tropicalis |
| Characteristics |
tissue: whole embryo
antibody: HDAC1 (Cell Signaling, 34589S)
genotype: wildtype
treatment: DMSO solvent control
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| Treatment protocol |
For a-Amanitin injection, 1-cell staged embryos were injected at 6pg/embryo. For TSA/ VPA treatment, 4-cell staged embryos were immersed in 100nM TSA/ 10 mM VPA in 1/9 MMR or equavalent volume of DMSO/ H2O
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| Growth protocol |
Xenopus tropicalis embryos were obtained by in vitro fertilization according to Ogino et al. (2006) and staged according to Nieuwkoop and Faber (1994). All embryos were cultured in 1/9X Marc’s modified Ringers (MMR) at 25C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For embryo dissection, animal caps or vegetal mass explants were dissected from late blastula embryos in 1X MMR, TSA treatment to embryos were maintained during dissection
For ChIP-seq, NEBNext Ultra II DNA library prep (E7645S) protocol was followed. For RNA-seq, NEBNext Ultra II RNA library prep (E7770S) protocol was followed.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The multiplexed libraries were sequenced on the Novaseq 6000. The version of Novaseq control software was NVCS ver 1.7.0 with real time analysis software, RTA 3.4.4.
For ChIP-seq, reads were aligned to Xenopus tropicalis v10.0 genome (Xenbase) using Bowtie2 v2.4.4. For RNA-seq, reads were aligned to Xenopus tropicalis v10.0 genome (Xenbase) using STAR v2.7.3a
For ChIP-seq, PCR duplicates were removed from aligned bam files using Samtools v1.10. For RNA-seq, RSEM v1.3.3 was used to calculate raw counts and expression values in transcripts per million (TPM)
For non-histone ChIP-seq, peaks were called using Macs2 v2.7.1 followed by IDR analysis using idr v2.0.4.2 in anaconda v4.11.0. For histone ChIP-seq, peaks were called using Macs2 v2.7.1 followed by reproduciable peak analysis using overlap method in Bedtools v2.29.2. For RNA-seq, differential expression analysis was performed using edgeR v3.36.0 in R v4.1.2
For ChIP-seq, bigwig files were generated from PCR deduplicated bam using Deeptools v3.5.0
Assembly: Xenopus tropicalis v10.0 (Xenbase)
Supplementary files format and content: For ChIP-seq, IDR peak bed files were included. For RNA-seq, raw count files were included
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| Submission date |
Nov 06, 2022 |
| Last update date |
Mar 31, 2023 |
| Contact name |
Ken Cho |
| E-mail(s) |
kwcho@uci.edu
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| Organization name |
University of California, Irvine
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| Street address |
University of California, Irvine
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| City |
Irvine |
| ZIP/Postal code |
92617 |
| Country |
USA |
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| Platform ID |
GPL30018 |
| Series (1) |
| GSE198378 |
Histone deacetylase 1 maintains lineage integrity through histone acetylome refinement during early embryogenesis |
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| Relations |
| BioSample |
SAMN31627034 |
| SRA |
SRX18185045 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6716692_pcrFree.st105_hdac1_DMSO_chip_peak_peaks.narrowPeak.gz |
1.4 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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