|
| Status |
Public on Apr 07, 2015 |
| Title |
SA1 knock out embrionary brain rep 1_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
SA1 knock out embrionary brain
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: SA1 knock out
age: E17.5 embryo
tissue: whole brain
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA samples (two independent replicates for condition, with material from four animals in each case) from different tissues were extracted using the guanidine thyocianate buffer, followed by acid phenol chloroform and treated with DNaseI.
2 µg of total RNA samples was used as provided by the user. RNA Integrity Numbers were in the range 6.9 to 7.6 (average 7.1) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ RNA fraction was extracted and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq RNA Sample Preparation Guide" (Part # 15008136 Rev. A). Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Isolation of poly A+ RNA from total RNA
|
| Data processing |
Read files were quality-checked with FastQC.
Reads were aligned with the mouse genome (GRCm37/mm9) with TopHat-2.0.0 (using Bowtie 0.12.7 and Samtools 0.1.16), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 1.3.0
Transcripts annotations used were Mus musculus GRCm37.v65 from Ensembl
Genome_build: GRCm37/mm9
Supplementary_files_format_and_content: Cufflinks FPKM tracking files were generated with Cufflinks 1.3.0 and contain transcripts abundance measured in FPKM values
|
| |
|
| Submission date |
Jul 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ana Losada |
| E-mail(s) |
alosada@cnio.es
|
| Phone |
+34 - 917 328 000
|
| Organization name |
Centro Nacional de Investigaciones Oncológicas (CNIO)
|
| Department |
Molecular Oncology Programme
|
| Lab |
Chromosome Dynamics Group
|
| Street address |
C/ Melchor Fernández Almagro, 3.
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE59119 |
The contribution of cohesin-SA1 to chromatin architecture and gene expression in two murine tissues |
|
| Relations |
| BioSample |
SAMN02903966 |
| SRA |
SRX647281 |
