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| Status |
Public on Nov 12, 2024 |
| Title |
Human brain prefrontal cortex BA10, AD sample3 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain
tissue type: AD
cell type: Human brain cells
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The BA10 area from 12 postmortem human brains were harvested and immediately flash frozen, embedded with OCT medium in liquid nitrogen, and then stored at -80°C until ready for the Stereo-seq pipeline. the tissue section on the Stereo-seq chip (10 mm x 10 mm) was incubated at 37°C for 5 mins, and subsequently fixed in pre-cooled methanol (Cat # 34860, Sigma) at -20°C for 30 mins. Once the fixation was completed, the chip was placed under a ventilation hood to allow residual methanol to air dry. The tissue section on the chip was then stained with nucleic acid reagent (Cat # Q10212, 0.5% v/v, Invitrogen) for 5 mins and subsequently washed with 0.1X SSC buffer (Cat # AM9770, 0.05 U/mL RNase inhibitor, Ambion). Stereo-seq transcriptomics chip-captured RNAs from the permeated tissue were then reverse transcribed for 3 hours at 42°C.
The tissue was removed and the cDNAs were released from the chip using the transcriptomics reagent kit (Cat # 111KT114, STOmics America Ltd). After the cDNA obtained was size-selected, amplified, and purified, the concentration was quantified by Qubit dsDNA HS assay kit (Cat # Q32854, Invitrogen). Next, 20 ng of cDNA from each sample were used for library construction using the library preparation kit (Cat # 111KL114, STOmics America Ltd) and subsequently for DNB generation.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
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| Data processing |
The fastq files from Stereo-seq were processed following the standard pipeline (https://github.com/STOmics/SAW)
Assembly: hg38
Supplementary files format and content: The .tissue.gef data is the tissue bin resolution and the .cellbin.gef data is the cellbin resolution
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| Submission date |
Jun 14, 2024 |
| Last update date |
Nov 12, 2024 |
| Contact name |
Yun Gong |
| E-mail(s) |
[email protected]
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| Organization name |
Tulane University
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| Street address |
3720 Clio St
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| City |
New Orleans |
| ZIP/Postal code |
70125 |
| Country |
USA |
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| Platform ID |
GPL29480 |
| Series (1) |
| GSE269906 |
Stereo-seq on human prefrontal cortex from six AD and six normal samples |
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| Relations |
| BioSample |
SAMN41723019 |
| SRA |
SRX24866224 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8330062_C02248B5.cellbin.gef |
124.4 Mb |
(ftp)(http) |
GEF |
| GSM8330062_C02248B5.tissue.gef |
425.4 Mb |
(ftp)(http) |
GEF |
SRA Run Selector |
| Raw data are available in SRA |
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