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| Status |
Public on Feb 14, 2023 |
| Title |
Glial translatomes in stroke |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Neuroinflammation is a hallmark of ischemic stroke, which is a leading cause of death and longterm disability. Understanding the exact cellular signaling pathways that initiate and propagate neuroinflammation after stroke will be critical for developing immunomodulatory stroke therapies. In particular, the precise mechanisms of inflammatory signaling in the clinically relevant hyperacute period, hours after stroke, have not been elucidated. We used the RiboTag technique to obtain Astrocyte IP and microglia-derived mRNA transcripts in a hyperacute (4 hours) and acute (3 days) period after stroke, as these two cell types are key modulators of acute neuroinflammation. Microglia initiated a rapid response to stroke at 4 hours by adopting an inflammatory profile associated with the recruitment of immune cells. The hyperacute Astrocyte IP profile was marked by stress response genes and transcription factors, such as Fos and Jun, involved in pro-inflammatory pathways such as TNF-α. By 3 days, microglia shift to a proliferative state and Astrocyte IPs strengthen their inflammatory response. The Astrocyte IP pro-inflammatory response at 3 days is partially driven by the upregulation of the transcription factors C/EBPβ, Spi1, and Rel, which comprise 25% of upregulated transcription factor-target interactions. Surprisingly, few sex differences across all groups were observed. Expression and log2 fold data for all sequenced genes are available on a user-friendly website for researchers to examine gene changes and generate hypotheses for stroke targets. Taken together our data comprehensively describe the Astrocyte IP and microglia-specific translatome response in the hyperacute and acute period after stroke and identify pathways critical for initiating neuroinflammation.
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| Overall design |
Comparative gene expression profiling analysis of microglia and Astrocyte IP ribotag RNA-seq data 4 hours and 3 days after stroke in adult, male and female mice.
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| Contributor(s) |
Hernandez VG, Lechtenberg KJ, Peterson TC, Zhu L, Lucas TA, Owah JO, Dorsey AI, Gentles AJ, Buckwalter MS |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA922165 |
| |
| Submission date |
Feb 11, 2023 |
| Last update date |
Feb 16, 2023 |
| Contact name |
Marion Buckwalter |
| E-mail(s) |
marion.buckwalter@stanford.edu
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| Organization name |
Stanford University
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| Department |
Neurology & Neurological Sciences
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| Lab |
Marion Buckwalter
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| Street address |
1201 Welch Rd
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (132)
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| GSM7039487 |
Astrocyte IP, female, sham, 3 days (110_IP) |
| GSM7039488 |
Astrocyte IP, female, stroke, 3 days (111_IP) |
| GSM7039489 |
Astrocyte IP, female, stroke, 3 days (114_IP) |
| GSM7039490 |
Astrocyte IP, male, stroke, 3 days (133_IP) |
| GSM7039491 |
Astrocyte whole brain input, female, stroke, 3 days (157_Input) |
| GSM7039492 |
Astrocyte IP, female, stroke, 3 days (157_IP) |
| GSM7039493 |
Astrocyte IP, female, stroke, 3 days (159_IP) |
| GSM7039494 |
Astrocyte IP, male, sham, 3 days (161_IP) |
| GSM7039495 |
Astrocyte whole brain input, male, sham, 3 days (182_Input) |
| GSM7039496 |
Astrocyte IP, male, sham, 3 days (182_IP) |
| GSM7039497 |
Astrocyte IP, male, sham, 3 days (183_IP) |
| GSM7039498 |
Astrocyte IP, male, sham, 3 days (184_IP) |
| GSM7039499 |
Astrocyte IP, male, stroke, 3 days (191_IP) |
| GSM7039500 |
Astrocyte IP, male, sham, 3 days (193_IP) |
| GSM7039501 |
Astrocyte whole brain input, female, sham, 3 days (196_Input) |
| GSM7039502 |
Astrocyte IP, female, sham, 3 days (196_IP) |
| GSM7039503 |
Astrocyte IP, female, stroke, 3 days (198_IP) |
| GSM7039504 |
Astrocyte IP, female, sham, 3 days (202_IP) |
| GSM7039505 |
Astrocyte IP, female, stroke, 3 days (203_IP) |
| GSM7039506 |
Astrocyte whole brain input, female, sham, 4 hours (222_Input) |
| GSM7039507 |
Astrocyte IP, female, sham, 4 hours (222_IP) |
| GSM7039508 |
Astrocyte whole brain input, female, stroke, 4 hours (223_Input) |
| GSM7039509 |
Astrocyte IP, female, stroke, 4 hours (223_IP) |
| GSM7039510 |
Astrocyte IP, male, sham, 4 hours (228_IP) |
| GSM7039511 |
Astrocyte IP, male, sham, 4 hours (230_IP) |
| GSM7039512 |
Astrocyte IP, female, stroke, 4 hours (277_IP) |
| GSM7039513 |
Astrocyte IP, male, stroke, 4 hours (287_IP) |
| GSM7039514 |
Astrocyte IP, male, stroke, 4 hours (288_IP) |
| GSM7039515 |
Astrocyte IP, male, stroke, 4 hours (289_IP) |
| GSM7039516 |
Astrocyte IP, female, sham, 3 days (300_IP) |
| GSM7039517 |
Astrocyte whole brain input, male, stroke, 3 days (305_Input) |
| GSM7039518 |
Astrocyte IP, male, stroke, 3 days (305_IP) |
| GSM7039519 |
Astrocyte IP, male, stroke, 3 days (306_IP) |
| GSM7039520 |
Astrocyte IP, female, sham, 3 days (311_IP) |
| GSM7039521 |
Astrocyte IP, female, sham, 3 days (317_IP) |
| GSM7039522 |
Astrocyte IP, male, sham, 4 hours (326_IP) |
| GSM7039523 |
Astrocyte whole brain input, male, stroke, 4 hours (331_Input) |
| GSM7039524 |
Astrocyte IP, male, stroke, 4 hours (331_IP) |
| GSM7039525 |
Astrocyte IP, female, stroke, 4 hours (338_IP) |
| GSM7039526 |
Astrocyte IP, male, stroke, 4 hours (350_IP) |
| GSM7039527 |
Astrocyte IP, female, stroke, 4 hours (355_IP) |
| GSM7039528 |
Astrocyte IP, female, stroke, 4 hours (357_IP) |
| GSM7039529 |
Astrocyte whole brain input, male, sham, 4 hours (363_Input) |
| GSM7039530 |
Astrocyte IP, male, sham, 4 hours (363_IP) |
| GSM7039531 |
Astrocyte IP, female, stroke, 4 hours (364_IP) |
| GSM7039532 |
Astrocyte IP, male, sham, 3 days (368_IP) |
| GSM7039533 |
Astrocyte IP, male, stroke, 3 days (371_IP) |
| GSM7039534 |
Astrocyte IP, male, stroke, 3 days (373_IP) |
| GSM7039535 |
Astrocyte IP, male, stroke, 4 hours (378_IP) |
| GSM7039536 |
Astrocyte IP, female, sham, 4 hours (478_IP) |
| GSM7039537 |
Astrocyte IP, male, sham, 4 hours (480_IP) |
| GSM7039538 |
Astrocyte IP, male, stroke, 4 hours (481_IP) |
| GSM7039539 |
Astrocyte IP, male, stroke, 4 hours (483_IP) |
| GSM7039540 |
Astrocyte IP, female, stroke, 4 hours (484_IP) |
| GSM7039541 |
Astrocyte IP, female, stroke, 4 hours (490_IP) |
| GSM7039542 |
Astrocyte IP, female, sham, 4 hours (491_IP) |
| GSM7039543 |
Astrocyte IP, male, stroke, 4 hours (495_IP) |
| GSM7039544 |
Astrocyte IP, male, sham, 4 hours (497_IP) |
| GSM7039545 |
Astrocyte IP, female, sham, 4 hours (499_IP) |
| GSM7039546 |
Astrocyte IP, female, stroke, 4 hours (502_IP) |
| GSM7039547 |
Astrocyte IP, male, sham, 4 hours (506_IP) |
| GSM7039548 |
Astrocyte IP, female, sham, 3 days (523_IP) |
| GSM7039549 |
Astrocyte IP, female, stroke, 3 days (526_IP) |
| GSM7039550 |
Astrocyte whole brain input, male, stroke, 3 days (527_Input) |
| GSM7039551 |
Astrocyte IP, male, stroke, 3 days (527_IP) |
| GSM7039552 |
Astrocyte IP, female, stroke, 3 days (529_IP) |
| GSM7039553 |
Astrocyte IP, female, sham, 3 days (530_IP) |
| GSM7039554 |
Astrocyte whole brain input, male, sham, 3 days (531_Input) |
| GSM7039555 |
Astrocyte IP, male, sham, 3 days (531_IP) |
| GSM7039556 |
Astrocyte IP, male, sham, 3 days (534_IP) |
| GSM7039557 |
Astrocyte IP, male, stroke, 3 days (535_IP) |
| GSM7039558 |
Astrocyte whole brain input, male, stroke, 4 hours (536_Input) |
| GSM7039559 |
Astrocyte IP, male, stroke, 4 hours (536_IP) |
| GSM7039560 |
Astrocyte IP, female, stroke, 4 hours (541_IP) |
| GSM7039561 |
Astrocyte whole brain input, male, sham, 4 hours (542_Input) |
| GSM7039562 |
Astrocyte IP, male, sham, 4 hours (542_IP) |
| GSM7039563 |
Microglia whole brain input, male, sham, 4 hours (input_109) |
| GSM7039564 |
Microglia whole brain input, female, stroke, 4 hours (input_143) |
| GSM7039565 |
Microglia whole brain input, male, stroke, 4 hours (input_166) |
| GSM7039566 |
Microglia whole brain input, male, stroke, 4 hours (input_185) |
| GSM7039567 |
Microglia whole brain input, female, stroke, 4 hours (input_217) |
| GSM7039568 |
Microglia whole brain input, female, sham, 4 hours (input_239) |
| GSM7039569 |
Microglia whole brain input, female, sham, 4 hours (input_240) |
| GSM7039570 |
Microglia whole brain input, female, sham, 3 days (input_88) |
| GSM7039571 |
Microglia whole brain input, male, stroke, 3 days (input_89) |
| GSM7039572 |
Microglia whole brain input, male, sham, 3 days (input_91) |
| GSM7039573 |
Microglia whole brain input, female, sham, 3 days (input_92) |
| GSM7039574 |
Microglia whole brain input, female, stroke, 3 days (input_93) |
| GSM7039575 |
Microglia whole brain input, male, sham, 3 days (input_97) |
| GSM7039576 |
Microglia whole brain input, male, stroke, 3 days (input_98) |
| GSM7039577 |
Microglia IP, female, sham, 3 days (IP_100) |
| GSM7039578 |
Microglia IP, female, stroke, 4 hours (IP_101) |
| GSM7039579 |
Microglia IP, male, sham, 3 days (IP_104) |
| GSM7039580 |
Microglia IP, male, stroke, 4 hours (IP_105) |
| GSM7039581 |
Microglia IP, male, stroke, 3 days (IP_107) |
| GSM7039582 |
Microglia IP, male, sham, 4 hours (IP_108) |
| GSM7039583 |
Microglia IP, male, sham, 4 hours (IP_109) |
| GSM7039584 |
Microglia IP, female, stroke, 3 days (IP_110) |
| GSM7039585 |
Microglia IP, female, stroke, 4 hours (IP_143) |
| GSM7039586 |
Microglia IP, male, stroke, 3 days (IP_149) |
| GSM7039587 |
Microglia IP, female, stroke, 3 days (IP_151) |
| GSM7039588 |
Microglia IP, male, sham, 4 hours (IP_153) |
| GSM7039589 |
Microglia IP, male, stroke, 4 hours (IP_166) |
| GSM7039590 |
Microglia IP, female, stroke, 4 hours (IP_181) |
| GSM7039591 |
Microglia IP, female, stroke, 3 days (IP_182) |
| GSM7039592 |
Microglia IP, male, stroke, 4 hours (IP_185) |
| GSM7039593 |
Microglia IP, male, stroke, 4 hours (IP_188) |
| GSM7039594 |
Microglia IP, female, stroke, 4 hours (IP_192) |
| GSM7039595 |
Microglia IP, male, stroke, 3 days (IP_196) |
| GSM7039596 |
Microglia IP, male, sham, 4 hours (IP_200) |
| GSM7039597 |
Microglia IP, female, stroke, 3 days (IP_210) |
| GSM7039598 |
Microglia IP, female, stroke, 4 hours (IP_215) |
| GSM7039599 |
Microglia IP, female, sham, 4 hours (IP_216) |
| GSM7039600 |
Microglia IP, female, stroke, 4 hours (IP_217) |
| GSM7039601 |
Microglia IP, female, sham, 3 days (IP_218) |
| GSM7039602 |
Microglia IP, female, sham, 3 days (IP_219) |
| GSM7039603 |
Microglia IP, male, stroke, 3 days (IP_221) |
| GSM7039604 |
Microglia IP, male, sham, 3 days (IP_223) |
| GSM7039605 |
Microglia IP, female, sham, 4 hours (IP_239) |
| GSM7039606 |
Microglia IP, female, sham, 4 hours (IP_240) |
| GSM7039607 |
Microglia IP, female, stroke, 3 days (IP_241) |
| GSM7039608 |
Microglia IP, female, sham, 3 days (IP_243) |
| GSM7039609 |
Microglia IP, male, sham, 4 hours (IP_248) |
| GSM7039610 |
Microglia IP, male, stroke, 4 hours (IP_251) |
| GSM7039611 |
Microglia IP, male, stroke, 3 days (IP_252) |
| GSM7039612 |
Microglia IP, male, sham, 3 days (IP_253) |
| GSM7039613 |
Microglia IP, female, sham, 4 hours (IP_257) |
| GSM7039614 |
Microglia IP, female, sham, 3 days (IP_88) |
| GSM7039615 |
Microglia IP, male, sham, 3 days (IP_91) |
| GSM7039616 |
Microglia IP, female, stroke, 3 days (IP_93) |
| GSM7039617 |
Microglia IP, male, sham, 3 days (IP_97) |
| GSM7039618 |
Microglia IP, male, stroke, 3 days (IP_98) |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE225110_RAW.tar |
226.0 Mb |
(http)(custom) |
TAR (of RESULTS) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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