|
| Status |
Public on Feb 14, 2018 |
| Title |
aPS_RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
Anterior pre-streak epiblast
|
| Organism |
Gallus gallus |
| Characteristics |
tissue type: Anterior pre-streak epiblast
developmental stage: Pre-streak EGKXII/XIII
|
| Treatment protocol |
Tissue: Neural plate, anterior and posterior pre-placodal region, non-neural/ non-placodal head ectoderm were dissected from HH6/7 embryos. Anterior prestreak and central epiblast from pre-streak EGKXII/XIII embryos. Hensen's node was grafted into the area opaca of HH4 chick embryos and the epiblast in contact with the node was collected after 5 hours (5hrs induced); the contralateral area opaca from the same embryos was collected a the same time (uninduced area opaca).
|
| Growth protocol |
Chicken embryos were grown to stage EGKXII/XIII, HH4-/4, or HH6/7
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted by using the RNAqueous-Micro Kit (Ambion AM1931)
RNASeq library was prepared using the TrueSeq RNA sample preparation V2 kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Data from Claudio Stern's laboratory
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Alignment was performed with Tophat2 with following parameters: -N 4 --read-edit-dist 6 -m 1 --max-insertion-length 5 --max-deletion-length 5 --no-discordant --no-mixed --microexon-search --library-type fr-unstranded
Normalized FPKM for each gene was generated with cuffdiff2 with following parameters: -u -N --library-type fr-unstranded --library-norm-method geometric --dispersion-method blind
easyRNAseq(R package) was used to get the raw count.
Genome_build: Gallus_gallus-4.0 (galGal4.71)
|
| |
|
| Submission date |
Oct 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrea Streit |
| E-mail(s) |
andrea.streit@kcl.ac.uk
|
| Organization name |
Kings College London
|
| Department |
Centre for Craniofacial & Regenerative Biology
|
| Lab |
Streit
|
| Street address |
Centre for Craniofacial & Regenerative Biology, King's College London
|
| City |
London |
| ZIP/Postal code |
SE1 9RT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16133 |
| Series (1) |
| GSE106346 |
Neural induction by the node and placode induction by head mesoderm share an initial state resembling neural plate border |
|
| Relations |
| BioSample |
SAMN07949714 |
| SRA |
SRX3343620 |
