|
| Status |
Public on Dec 15, 2022 |
| Title |
68_S1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse hippocampus containing hiPSC-derived glia
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue: Mouse hippocampus containing hiPSC-derived glia
hipsc source: skin fibroblasts
group status: PSEN1 ΔE9, AD3
patient age_(years): 47
patient gender: female
mouse strain: B6.129S7-Rag1tm1Mom/J
mouse age_(months): 18
mouse sex: male
|
| Treatment protocol |
The transplanted mice underwent a panel of behavioral tests at the ages of 8, 12 and 16 months. At the age of 18 months, the mice were terminally anesthetized with Avertin and transcardially perfused with heparinizedd saline. The right hippocampi were quickly dissected out, frozen in the liquid nitrogen and stored at -80 C before the RNA extraction.
|
| Growth protocol |
The generation of PSEN1 ΔE9 mutant and isogenic CTRL iPSC lines and the astrosphere differentiation protocol were described previously (Stem Cell Reports. 2017;9:1885-1897). Glial progenitors were grown in astrocyte differentiation medium in suspension for 6.5-7.5 months before the transplantation. For transplantation, astrospheres were dissociated with Accutase and the cells were resuspended at the concentration of 100,000 cells/µL in phosphate-buffered saline (PBS). A total of 200,000 cells were injected intracerebroventricularly into cryoanestethized newborn pups (P0-P1) at 4 different injection sites (M/L ± 0.8 mm; A/P 1.0 mm, 2.0 mm; D/V −1.5 mm from lambda point; 0.5 μL each) using a 33 G needle cut at 30° angle (Hamilton) at rate 3 μL/min. Further, 100,000 cells in 1 μL PBS were injected into the middle of the cerebellum by freehand. After the injections, the pups were placed in a +37 °C chamber for 5 min to recover from cold anesthesia before being returned to the dams.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIZOL reagent (Sigma). Trace amounts of the leftover DNA were removed by DNAse I treatment (molecular biology grade, Thermo Fisher Scientific) for 30 min at 37 °C. RNA was further purified using RNeasy Mini Kit (Qiagen). The RNA quality was analyzed on the Agilent 2100 Bioanalyzer™ using an RNA6000 assay.
Sequencing libraries were prepared with Illumina NextSeq and SureSelect Strand Specific RNA Seq kits.
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| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
PSEN1 ΔE9 female human glia
counts_AD-astro_hsa.txt.gz
counts_AD-astro_mmu.txt.gz
|
| Data processing |
Each sample was run mixed in all runs and lanes. RNA-sequencing reads for each sample were merged from three Illumina NextSeq 500 runs totalling 12 lanes. Reads were aligned to human genome hg38 and mouse genome mm10 using STAR aligner (Dobin et al. 2013) and annotated to genes using HTSeq (Anders et al. 2015).
Assembly: hg38; mm10
Supplementary files format and content: Tab delimeted text files (2) containing unnormalized (raw) read counts per feature, separately for unique human and mouse alignments.
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| |
|
| Submission date |
Dec 15, 2022 |
| Last update date |
Dec 15, 2022 |
| Contact name |
Iiris Hovatta |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Helsinki
|
| Department |
Department of Psychology and Logopedics
|
| Lab |
Neurogenomics
|
| Street address |
Haartmaninkatu 3
|
| City |
Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
| |
|
| Platform ID |
GPL19415 |
| Series (1) |
| GSE221027 |
Human PSEN1 Mutant Glia Improve Spatial Learning and Memory in Aged Mice |
|
| Relations |
| BioSample |
SAMN32244270 |
| SRA |
SRX18707722 |
