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| Status |
Public on Mar 15, 2023 |
| Title |
Identification of dysregulated transcripts in egr-2(RNAi) planarians |
| Organism |
Schmidtea mediterranea |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
egr-2 is an injury-responsive gene that is upregulated in the anterior of planarian tail fragments and required for intestinal remodeling. The goal of this study was to identify differentially expressed transcripts in the anterior region of egr-2(RNAi) tail fragments relative to egfp(RNAi) control fragments.
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| Overall design |
Total RNA was isolated from the anterior region of 0 hr, 2 day, and 4 day planarian tail fragments after egfp RNAi (control) or egr-2 RNAi (fed 6 times, 4 biological replicates per condition, tissue from 10 tail fragments per replicate). Library generation (NEB NEXT ULTRA) and RNA sequencing (2x150bp paired-end, Illumina HiSeq 4000) were conducted by Genewiz. Bioinformatic analysis was conducted using BBDuk, Bowtie2, and edgeR.
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| Contributor(s) |
Morkotinis V, Forsthoefel DJ |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Mar 11, 2023 |
| Last update date |
Mar 15, 2023 |
| Contact name |
David J Forsthoefel |
| E-mail(s) |
david-forsthoefel@omrf.org
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| Phone |
405-271-4047
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| Organization name |
Oklahoma Medical Research Foundation
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| Department |
Genes and Human Disease Research Program
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| Lab |
S-314
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| Street address |
825 NE 13th St
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| City |
Oklahoma |
| State/province |
OK |
| ZIP/Postal code |
73104 |
| Country |
USA |
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| Platforms (1) |
| GPL30113 |
Illumina HiSeq 4000 (Schmidtea mediterranea) |
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| Samples (24)
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| GSM7092553 |
C0_4, control_RNAi, 0_hr, biol_rep_4 |
| GSM7092554 |
E0_1, egr-2_RNAi, 0_hr, biol_rep_1 |
| GSM7092555 |
E0_2, egr-2_RNAi, 0_hr, biol_rep_2 |
| GSM7092556 |
E0_3, egr-2_RNAi, 0_hr, biol_rep_3 |
| GSM7092557 |
E0_4, egr-2_RNAi, 0_hr, biol_rep_4 |
| GSM7092558 |
C2_1, control_RNAi, 2_dpa, biol_rep_1 |
| GSM7092559 |
C2_2, control_RNAi, 2_dpa, biol_rep_2 |
| GSM7092560 |
C2_3, control_RNAi, 2_dpa, biol_rep_3 |
| GSM7092561 |
C2_4, control_RNAi, 2_dpa, biol_rep_4 |
| GSM7092562 |
E2_1, egr-2_RNAi, 2_dpa, biol_rep_1 |
| GSM7092563 |
E2_2, egr-2_RNAi, 2_dpa, biol_rep_2 |
| GSM7092564 |
E2_3, egr-2_RNAi, 2_dpa, biol_rep_3 |
| GSM7092565 |
E2_4, egr-2_RNAi, 2_dpa, biol_rep_4 |
| GSM7092566 |
C4_1, control_RNAi, 4_dpa, biol_rep_1 |
| GSM7092567 |
C4_2, control_RNAi, 4_dpa, biol_rep_2 |
| GSM7092568 |
C4_3, control_RNAi, 4_dpa, biol_rep_3 |
| GSM7092569 |
C4_4, control_RNAi, 4_dpa, biol_rep_4 |
| GSM7092570 |
E4_1, egr-2_RNAi, 4_dpa, biol_rep_1 |
| GSM7092571 |
E4_2, egr-2_RNAi, 4_dpa, biol_rep_2 |
| GSM7092572 |
E4_3, egr-2_RNAi, 4_dpa, biol_rep_3 |
| GSM7092573 |
E4_4, egr-2_RNAi, 4_dpa, biol_rep_4 |
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| Relations |
| BioProject |
PRJNA943428 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE227155_egr2_data_counts.txt.gz |
1022.9 Kb |
(ftp)(http) |
TXT |
| GSE227155_egr2_data_processed.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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