|
| Status |
Public on May 25, 2019 |
| Title |
D14-1371 [NAr1] |
| Sample type |
SRA |
| |
|
| Source name |
regenerating_Non-pole-containing anterior blastema flanking region
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
strain: asexual CIW4
ploidy: 2N (non-dividing)
uninjured or regenerating animal: regenerating animal 72-hours-post transverse amputation
tissue: Non-pole-containing anterior blastema flanking region
|
| Treatment protocol |
Head tip regions from uinjured animals were resected after starvation period, as above. Animals were transversely amputated (just posterior to the eyes), and allowed to regenerate for 72 hours before surgical resection of anterior blastema regions to obtain tissue from 72-hour regenerating animals.
|
| Growth protocol |
Asexual Schmidtea mediterranea strain (CIW4) animals starved 7-14 days before surgical resections.
|
| 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 |
140228Red_D14-1371
processed data file; raw read counts:
rPole_rawreadcounts_complete_Ar_NAr_forGEO.txt
processed data file; differential expression analysis:
ArvsNAr_complete.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.
Differential gene expression analysis was performed between pole-containing and non-pole-containing samples using DESeq
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 pole-containing vs. non-pole containing pieces
|
| |
|
| 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) |
| GSE121045 |
RNA sequencing of pole-containing anterior tip regions in planarian Schmidtea mediterranea |
| GSE121048 |
RNA sequencing studies in planarian Schmidtea mediterranea |
|
| Relations |
| BioSample |
SAMN10227288 |
| SRA |
SRX4823213 |
