|
| Status |
Public on Feb 18, 2019 |
| Title |
dKO rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
dKO_telencephalons
|
| Organism |
Mus musculus |
| Characteristics |
strain background: mixed lineage
genotype/variation: Lats1/2 dko
developmental stage: E12.5
tissue: Telencephalons
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Telencephalons from E12.5 embryos were dissected, dissociated with StemPro Accutase, and passed through a 40-μm cell strainer to obtain single-cell suspensions. Cells were counted and 1.0 x 106 cells were pelleted by centrifugation. Diluted ERCC spike-in mix (1:20, Thermo Fisher Scientific 4456740) was added to cell pellets and Trizol prior to RNA extraction at a ratio of 1 μl of diluted ERCC spike-in mix per million cells. RNA was purified using a Direct-zol RNA kit (Zymo Research R2052) and eluted in 25 μl of elution buffer.
Library preparation and sequencing were performed by the Genome Sequencing Facility at St. Jude Children’s Research Hospital. RNA quality was checked by a 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) before library generation. Libraries were prepared from 350 ng of total RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina 20020597), then quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies). Samples were sequenced on Illumina HiSeq4000, obtaining 100 million 100-bp paired-end reads. RNAs from 5 control and 4 dKO embryos were sequenced.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
SJMMNORM054776_G1-X90Mutant_S23
|
| Data processing |
Sequences were mapped to the mm9 genome with additional ERCC sequences using the STAR aligner (Dobin et al., 2013).
Transcript level data was counted using HTSEQ (Anders et al., 2015). Raw counts were divided into transcript counts and ERCC counts. For quality control purposes, the linearity of the ERCC spike-in controls were considered and two spike-ins that consistently across all samples did not conform to the expected order (which is likely to be a manufacturer’s error) were excluded from the ERCC raw counts.
Genome_build: mm9
Supplementary_files_format_and_content: raw count text files for each sample which include ERCC counts
|
| |
|
| Submission date |
Sep 16, 2018 |
| Last update date |
Feb 19, 2019 |
| Contact name |
David Finkelstein |
| E-mail(s) |
david.finkelstein@stjude.org
|
| Phone |
9014953931
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Computational Biology
|
| Street address |
332 N. Lauderdale St.
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE120015 |
The Hippo Pathway Prevents YAP/TAZ–Driven Hypertranscription and Controls Neural Progenitor Number [RNA-seq] |
| GSE120016 |
The Hippo Pathway Prevents YAP/TAZ–Driven Hypertranscription and Controls Neural Progenitor Number |
|
| Relations |
| BioSample |
SAMN10076258 |
| SRA |
SRX4701637 |
