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| Status |
Public on Mar 22, 2016 |
| Title |
Spermatid_rep2 Sample 22 |
| Sample type |
SRA |
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| Source name |
Purified spermatids
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| Organism |
Xenopus laevis |
| Characteristics |
cell type: Spermatid purified cells
starting material: 1 M cells
developmental stage/condition/extract protocol: Spermatid
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| Growth protocol |
no growth protocol
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| Extracted molecule |
total RNA |
| Extraction protocol |
none provided by submitter
Illumina TruSeq RNA sample prep kit for RNA-seq,
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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)
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| Submission date |
Nov 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles Bradshaw |
| Organization name |
University of Cambridge
|
| Department |
Gurdon Institute
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| Street address |
Tennis Court Road
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| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
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| Platform ID |
GPL18936 |
| Series (1) |
| GSE75164 |
Sperm is epigenetically programmed to regulate gene transcription in embryo |
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| Relations |
| BioSample |
SAMN04277026 |
| SRA |
SRX1437969 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1944415_SLX-7595.C3C35ACXX.s_4.r_1.Index6.genes.htseq.txt.gz |
269.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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