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Sample GSM1944410 Query DataSets for GSM1944410
Status Public on Mar 22, 2016
Title Spermatid_PE1_rep6 Sample 13
Sample type SRA
 
Source name ICSI on UV radiated Eggs
Organism Xenopus laevis
Characteristics pairing of samples: Group6
cell type: Spermatid-derived embryos
starting material: pool of 5 embryos
developmental stage/condition/extract protocol: Haploid Embryo 10.5-11.5
Growth protocol no growth protocol
Extracted molecule total RNA
Extraction protocol none provided by submitter
Illumina TruSeq RNA sample prep kit for RNA-seq,
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Group_1_Counts_All.tsv
Data processing fastq file processed by filering out low quality reads (<Q20) and llow quality bases (<Q20) with sickle. Adaptors were removed with cutadapt 1.0.
RNA-seq data have been aligned to X. Laevis genome 6.1 using TopHat 2.0.6
ChIP-seq data have been aligned to X. Laevis genome 6.1 using BWA 0.6.2 with default options. Duplicate reads were then removed
Peaks were called using MACS2 2.0.9 with --broad options and q-value<0.01.
The list of confirmed peaks across replicates consisted of peaks with pvalue <0.01 detected in at least 2 out of 3 replicates.
MNase-seq data have been aligned to X. Laevis genome 6.1 with BWA with default options and duplicates reads were removed. Nucleosomes positions have been estimated on cell-specific merged bam files with NucHunter (-fLen = 150, -wrad 146)
MBD-seq data have been processed as ChIP-seq
Counts from RNA-seq data were extracted using HT-seq count
Differential analysis was conducted using EdgeR package
Supplementary_files_format_and_content: counts files contain counts generated using htseq-count
Supplementary_files_format_and_content: .cov files contain counts per million coverage normalized to total number of reads 1kb around TSS
Supplementary_files_format_and_content: bw files contain coverage across genome binned in 200bp windows
Supplementary_files_format_and_content: bw files contain coverage across genome binned in 50bp windows
Supplementary_files_format_and_content: bed files contains coordinate of features (i.e. for Nucleosome, putative locations of stable nucleosomes)
 
Submission date Nov 18, 2015
Last update date May 15, 2019
Contact name Charles Bradshaw
Organization name University of Cambridge
Department Gurdon Institute
Street address Tennis Court Road
City Cambridge
ZIP/Postal code CB2 1QN
Country United Kingdom
 
Platform ID GPL17682
Series (1)
GSE75164 Sperm is epigenetically programmed to regulate gene transcription in embryo
Relations
BioSample SAMN04277021
SRA SRX1437964

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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