|
| Status |
Public on Feb 09, 2015 |
| Title |
Neural Plate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Flk1+ mesoderm
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1(ICR)
age: E7.5 embryo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Timed matings were set up and embryos were staged according to morphologic criteria. Suspensions of embryo cells were prepared as described previously (Tanaka et al 2012 PNAS) and single cell suspensions were stained with Flk-1-APC (AVAS12; BD Bioscience). Cells were sorted into 2 μl of lysis buffer (0.2 % (v/v) Triton X-100 and 2 U/μl RNase inhibitor (Clontech)) and stored at -80 °C.
RNAseq was carried out using the Smart-seq2 protocol according to Picelli et al 2014 Nature Protocols and sequenced on an Illumina HiSeq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
NP2
|
| Data processing |
RNA-seq reads aligned to mm10 using STAR (version 2.3.0) with parameters --outFilterMultimapScoreRange 1 --outSAMstrandField intronMotif --genomeLoad NoSharedMemory --outStd SAM.
SAM files converted to BAM format and then sorted using samtools (version 0.1.18).
Read counts for features were calculated using HTSeq (version 0.6.1).
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts/spreadsheet.
|
| |
|
| Submission date |
Sep 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Evangelia Diamanti |
| E-mail(s) |
ed347@cam.ac.uk
|
| Phone |
01223 62317
|
| Organization name |
University of Cambridge
|
| Department |
Haematology
|
| Lab |
Gottgens
|
| Street address |
Wellcome Trust / MRC Building, Hills Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0XY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE61470 |
Decoding the regulatory network of early blood development from single-cell gene expression measurements. |
|
| Relations |
| BioSample |
SAMN03069724 |
| SRA |
SRX701742 |
