|
Status |
Public on Oct 29, 2016 |
Title |
foxn4_crispr_RNAseq_9h_rep_2 |
Sample type |
SRA |
|
|
Source name |
animal cap (dissected ectoderm)
|
Organism |
Xenopus laevis |
Characteristics |
tissue: animal cap (dissected ectoderm) harvest time/stage: 9h @ 22 deg after mid-11 (st 18) injection: Multicilin mRNA + (cas9 protein + foxn4 gRNA)
|
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 |
total 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
|
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 |
BioSample |
SAMN05950864 |
SRA |
SRX2279688 |