|
| Status |
Public on May 15, 2020 |
| Title |
Co2 |
| Sample type |
SRA |
| |
|
| Source name |
marginal zone (mesoderm) explant
|
| Organism |
Xenopus laevis |
| Characteristics |
developmental stage: st 10.5, gastrula
treated or not: control untreated
|
| Treatment protocol |
RNA overexpression or MO oligos depletion
|
| Growth protocol |
ectoderm explants and frog embryo culture
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAeasy column (Qiagen)
mRNA was enriched using oligo(dT) beads; mRNA was then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. Then a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment was performed.
Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/μl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM). Libraries were then fed into HiSeq2000 machines according to activity and expected data volume.
quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
no treatment
|
| Data processing |
The original raw data from Illumina HiSeqTM were transformed to Sequenced Reads by base calling. Raw data were recorded in FASTQ files.
Base Quality and Phred score relationship were evaluated with the Illumina CASAVA v1.8 software
Raw reads were filtered to remove reads containing adapters or reads of low quality.
The sequences wer mapped to the Xenopus genome using hisat2
The files were sorted using the Samtools.The sequences were counted using HTSeq.
Genome_build: Xenopus XL-9.1_v1.8.3.2
Supplementary_files_format_and_content: Excel, contains the counts;
|
| |
|
| Submission date |
Jan 16, 2020 |
| Last update date |
May 15, 2020 |
| Contact name |
Olga Ossipova |
| E-mail(s) |
Olga.Ossipova@mssm.edu
|
| Phone |
2122417984
|
| Organization name |
Mount Sinai Hospital
|
| Lab |
Olga Ossipova
|
| Street address |
1 Gustave L Levy Place Anbg 25-90 PO Box 1020
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL17682 |
| Series (1) |
| GSE143795 |
Specification of embryonic mesoderm by Pinhead signaling |
|
| Relations |
| BioSample |
SAMN13872681 |
| SRA |
SRX7571188 |
