|
| Status |
Public on Oct 29, 2016 |
| Title |
MCIDAS_9h_RNAseq_rep_3 [re-used] |
| Sample type |
SRA |
| |
|
| Source name |
animal cap (ectoderm)
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: animal cap (ectoderm)
harvest time/stage: 9h @ 22 deg after mid-11 (st 18)
injected mrna: MCIDAS-HGR
|
| Treatment protocol |
Animal caps containing inducible constructs (human glucocorticoid receptor fusion proteins) were induced with 20 micromolar dexamethasone at mid-stage 11.
|
| Growth protocol |
Animal caps (ectoderm) dissected from embryos at stage 10 and cultured in 0.5x MMR. 20 animal caps per condition were used for RNAseq.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNAs were obtained with proteinase K digestion, phenol chloroform extraction and precipitated with ethanol, treated with DNAse, extracted with phenol chloforom, and precipitated with lithium and again with ethanol. See our manuscript (PMID: 24934224) for a more detailed protocol. RNAseq libraries were constructed with Illumina Truseq v2 non-stranded mRNA kits.
Chromatin was obtained as in Ma et al. 2014 (PMID: 24934224)
Illumina Truseq v2, poly-a+
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Poly-A mrNA
RNAseq (non-stranded)
|
| Data processing |
RNAseq reads aligned to transcriptome with RNA-STAR (PMID: 23104886)
RNAseq aligned reads counted with eXpress (PMID: 23160280)
RNAseq counts normalized and differential expression tested with DESeq (PMID: 23975260)
RNAseq and ChIPseq reads aligned to genome with bowtie2 (PMID: 22388286)
Peaks called with HOMER (PMID: 20513432) using input as background (input reads from NCBI GEO: GSE78176, It was pooled reads from GSM2068810 through GSM2068815 (i.e., 6 accessions total)).
BigWigs made with HOMER (PMID: 20513432)
Genome_build: Genome: v7.1, http://www.xenbase.org/
Genome_build: Transcriptome: Mayball interim models, http://daudin.icmb.utexas.edu/
Supplementary_files_format_and_content: RNAseq files are output from eXpress
Supplementary_files_format_and_content: ChIPseq files are bed files from HOMER
|
| |
|
| Submission date |
Oct 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ian K Quigley |
| E-mail(s) |
iquigley@salk.edu
|
| Phone |
858-453-4100
|
| Organization name |
Salk Institute
|
| Department |
Molecular Neurobiology Lab
|
| Lab |
Kintner
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL18936 |
| Series (1) |
| GSE89271 |
RNAseq and ChIPseq profiling of Foxn4 and Foxj1 in multiciliated cells |
|
| Relations |
| Alternative to |
GSM1434785 |
| BioSample |
SAMN05951882 |
| SRA |
SRX2281885 |
