|
| Status |
Public on May 25, 2019 |
| Title |
D16-3162 [unc22_2w3] |
| Sample type |
SRA |
| |
|
| Source name |
control_2_Planarian head
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
strain: asexual CIW4
ploidy: 2N (non-dividing)
control or nr4a rnai: control
weeks of control or nr4a rnai: 2
tissue: Planarian head
|
| Treatment protocol |
Heads were amputated just posterior to the eyes; transverse tail amputation lines were 1/4 of the distance between the tail tip and the posterior aspect of pharynx.
|
| Growth protocol |
Asexual Schmidtea mediterranea strain (CIW4) animals starved 7 days before transection of heads and tails for RNA sequencing
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Resected tissues were homogenized using Qiagen TissueLyser III, and RNA was extracted using TRIzol
cDNA and sequencing libraries were constructed using TruSeq RNA Library Prep Kit V2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
160406RedB_D16-3162
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt
|
| Data processing |
Basecalls performed using CASAVA version 1.7.0.
Reads were trimmed using Trimmomatic-0.32 to remove SmartSeq2 adaptor sequences and low quality 3′ base pairs, and only transcripts with 30bp or more were used for subsequent analysis.
Reads were mapped to dd_Smed_v4 planarian transcriptome assembly using bowtie 1 with --best to generate rawreadcounts file.
Reads for isotigs of contigs (all contig ids that vary only by the final number) were summed.
Reads for mitochondrial and ribosomal RNA (dd_Smed_v4_7_0, and dd_Smed_v4_4_1, mtRNA, rRNA_5s) were discarded.
Differential gene expression analysis was performed between nr4A RNAi and control RNAi heads and tails within each time point (2, 3, 4, and 5 weeks of RNAi) using DESeq.
Transcripts with base meanA average <100 were excluded from analysis
Genome_build: dd_Smed_v4
Supplementary_files_format_and_content: Rawreadcounts: Tab-delineated text file includes unnormalized read counts of contigs. DESeq analyses: tab-delineated text file generated using DESeq differential gene analysis program comparing raw read counts of each transcript in nr4A RNAi vs. control RNAi heads and tails in each of the RNAi time points.
|
| |
|
| Submission date |
Oct 10, 2018 |
| Last update date |
May 25, 2019 |
| Contact name |
Peter W Reddien |
| Organization name |
Whitehead Institute for Biomedical Research
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL15553 |
| Series (2) |
| GSE121046 |
RNA sequencing of the head and tail of planarian Schmidtea mediterranea during nr4A inhibition |
| GSE121048 |
RNA sequencing studies in planarian Schmidtea mediterranea |
|
| Relations |
| BioSample |
SAMN10227381 |
| SRA |
SRX4823218 |
