|
| Status |
Public on Mar 02, 2015 |
| Title |
Mmu bRG replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
bRG
|
| Organism |
Mus musculus |
| Characteristics |
age: E14.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNAeasy Mini kit (Qiagen) according to the manufacturer's instructions.
Complete cDNA was synthesized from half of the isolated mRNA with SmartScribe reverse transcriptase (Clontech) using a universally tailed poly-dT primer and template switching oligos. This was followed by amplification of the purified cDNA with the Advantage 2 DNA Polymerase (12 cylces). After ultrasonic shearing of the amplified cDNA (Covaris S2), samples were subjected to standard Illumina fragment library preparation using the NEBnext chemistries (New England Biolabs), in brief: fragments were end repaired, A-tailed and ligated to indexed Illumina Truseq adapters. Subsequently, the NGS libraries were finalized by a universally primed PCR amplification (15 cycles). Libraries were purified using XP beads (Beckman Coulter), quantified by qPCR (KAPA Biosysytems) and subjected to Illumina 75-bp single end sequencing on the Illumina HiSeq 2000 platform providing on average 35 Mio reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Mmu_bRG_2
mmu_fpkm_matrix.txt
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Reads were trimmed with cutadapt (-m 20 -q 25)
Trimmed Reads were mapped using tophat v2.0.11 (-G $gtfFile -g1)
Abundance estimation was performed using cuffdiff (v2.2.1)
Genome_build: mm10, hg19
Supplementary_files_format_and_content: FPKM normalized expressoin score tables as provided by cummerbund::countMatrix
|
| |
|
| Submission date |
Jan 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mareike Albert |
| Organization name |
TUD Dresden University of Technology
|
| Department |
Center for Regenerative Therapies TU Dresden
|
| Street address |
Fetscherstr. 105
|
| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE65000 |
Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion |
|
| Relations |
| BioSample |
SAMN03284932 |
| SRA |
SRX844293 |
