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Sample GSM5945920

Query DataSets for GSM5945920

Status

Public on Mar 27, 2023

Title

st9_hdac1_we_ut_rep2

Sample type

SRA

Source name

whole embryos

Organism

Xenopus tropicalis

Characteristics

strain: wildtype
chip antibody: HDAC1 (Cell Signaling, 34589S)
treatment: untreated

Treatment protocol

For a-Amanitin injection, 1-cell staged embryos were injected at 6pg/embryo. For TSA treatment, 4-cell staged embryos were immersed in 100nM TSA in 1/9 MMR or equavalent volume of DMSO

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.

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.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina NovaSeq 6000

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

Submission date

Mar 10, 2022

Last update date

Mar 27, 2023

Contact name

Ken Cho

E-mail(s)

kwcho@uci.edu

Organization name

University of California, Irvine

Street address

University of California, Irvine