|
Status |
Public on Sep 04, 2021 |
Title |
post-pharyngeal fragments, u22_24h_1 |
Sample type |
SRA |
|
|
Source name |
anterior facing wound fragment
|
Organism |
Schmidtea mediterranea |
Characteristics |
strain: CIW4 time: 24 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 |
SAMN19992385 |
SRA |
SRX11328019 |