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| Status |
Public on Nov 22, 2016 |
| Title |
wt repeat two |
| Sample type |
SRA |
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| Source name |
WT_hippocampus
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| Organism |
Mus musculus |
| Characteristics |
strain: C57/Bl
genotype/variation: wild type
tissue: hippocampus
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| Treatment protocol |
N/A
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| Growth protocol |
N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
mRNAeasy qiagen RNA extraction kit
Truseq illumina library kit
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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 |
Reads were demultiplexed
Adapters were trimmed from sequences using cutadapt tool
Reads that mapped to rRNA were removed
The rest of the reads were aligned to the mm10 genome built using Tophat (v2.0.10)
Read counting to Refseq genes was done with HTseq-count (version 0.6.1p1)
Differential expression analysis was performed with DESeq2 (1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes the raw counts, normalized counts, fold change, p-value and FDR
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| Submission date |
Jul 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gilgi Friedlander |
| Organization name |
Weizmann Institute of Science
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| Street address |
Hertzel st
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| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE84175 |
RNA-seq of hippocampus from wild type and CTCF cko animals |
| GSE84176 |
CTCF ChIP-seq of WT and RNA-seq of WT and CTCF cko mouse |
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| Relations |
| BioSample |
SAMN05366646 |
| SRA |
SRX1906236 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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