|
| Status |
Public on Apr 25, 2020 |
| Title |
GT_16_5_RNAseq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
genital tubercule
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wildtype
developmental stage: E16.5
strain: CBA / C57BL/6 mix
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Micro-dissected GT from different embryonic stages were stored individually at -80°C in RNAlater stabilization reagent (Ambion) before further sample processing. Total RNA was extracted from tissues using QIAGEN RNeasy Plus Micro Kit after disruption and homogenization. RNA quality was assessed using an Agilent 2100 Bioanalyser. Sequencing libraries were prepared according to TruSeq Stranded mRNA Illumina protocol, with polyA selection.
RNA-seq libraries were prepared with the Illumina TruSeq Stranded mRNA protocol and sequenced on an Illumina HiSeq 2500 sequencer. Single-end, 100bp reads were produced.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw RNA-seq reads were aligned on the mouse mm10 genome assembly using TopHat 2.0.9 (Yates et al., 2016). Gene expression computations were performed using uniquely mapping reads extracted from TopHat alignments and genomic annotations from filtered gtf from Ensembl release 82 (Kim et al., 2013) as described in (Amândio et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph
|
| |
|
| Submission date |
Oct 07, 2019 |
| Last update date |
Apr 26, 2020 |
| Contact name |
Ana Rita Amandio Lhopitallier |
| E-mail(s) |
rita.lhopitallier@epfl.ch
|
| Organization name |
EPFL
|
| Department |
SV-ISREC-EPFL
|
| Lab |
Laboratory of Developmental Genomics
|
| Street address |
SV2842, Station 19
|
| City |
Lausanne |
| ZIP/Postal code |
CH-1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE138511 |
A complex regulatory landscape involved in the development of external genitals [RNA-Seq] |
| GSE138514 |
A complex regulatory landscape involved in the development of external genitals |
|
| Relations |
| BioSample |
SAMN12982910 |
| SRA |
SRX6958332 |
