|
| Status |
Public on Sep 04, 2021 |
| Title |
post-pharyngeal fragments, u22_0h_3 |
| Sample type |
SRA |
| |
|
| Source name |
anterior facing wound fragment
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
strain: CIW4
time: 0 hpa
RNAi: unc-22
RNAi feedings: 4 feedings
|
| Treatment protocol |
Animals fed liver mixed with dsRNA 2 times twice per week. Cut 7 days after 4th feeding
|
| Growth protocol |
Standard planarian culture conditions
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA extracted from anterior facing wound fragments with 750 uL of TriZOL reagent with 5 wounds per replicate. Quantified by Qubit and Agilent Bioanalyser.
KapaHyper mRNA-Seq Kit Illumina Platform (KapaBiosystems)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
bmp_reads_collapsed_v6_reorder.txt
bmp_DEseq_Table.xlsx
|
| Data processing |
Basecalling was performed by Illumina CASAVA 1.9
Sequenced reads from both lanes were concatenated and quality trimmed using cutadapt v1.8 with parameteres -m 20 -q 30,30 and mapped to the ddv4 transcriptome using Bowtie v1.2 with parameter --best.
Raw read counts were generated with Samtools v1.6 idxstats and transcripts from different isoforms were summed (sum of counts for dd_v4_Smed_XXX_Y_Z for all Z)
Differential expression was determined with DESeq
Genome_build: Dresden S. mediterranea Transcriptome Assembly (ddv6, Rozanski et al, Nucleic Acids Research 2019)
Supplementary_files_format_and_content: Tab-separated text and Excel spreadsheet files
|
| |
|
| Submission date |
Jul 01, 2021 |
| Last update date |
Sep 04, 2021 |
| Contact name |
Peter W Reddien |
| Organization name |
Whitehead Institute for Biomedical Research
|
| Department |
MIT Biology
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL15553 |
| Series (2) |
| GSE179291 |
bmp4 RNAi gene expression profiling |
| GSE179295 |
equinox is a planarian wound epidermis gene required for the initiation of regeneration |
|
| Relations |
| BioSample |
SAMN19992349 |
| SRA |
SRX11328001 |
