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| Status |
Public on Aug 12, 2021 |
| Title |
Astrocyte Nec-1s rep1 |
| Sample type |
SRA |
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| Source name |
Human Astrocytes
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Astrocytes
treatment: Nec-1s
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| Treatment protocol |
Astrocytes were treated with (1) DMSO, (2) Nec-1s, (3) TNF/Smac/zVAD or (4) TNF/Smac/zVAD/Nec-1s for 4 hours prior to lysis and RNA extraction.
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| Growth protocol |
Fetal-derived human astrocytes from Gibco (K1884) were plated in Matrigel-coated plates 6-well plates 2x10^5 cells/well and rested for 48 hours prior to treatment in DMEM-GlutaMAX media with 10% FBS and N2 supplement.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in 350uL RLT Plus Lysis Buffer and RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's instructions.
Astrocytes (BGI): we captured mRNA with oligo dT and constructed mRNA-seq library by strand-specific protocol. Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA were fragmented into small pieces (200-350bp) with fragment buffer at appropriate temperature. Then First-strand cDNA is generated in First Strand reaction system by random hexamer-primed reverse transcription, and the second-strand cDNA was generated with dNTP (dTTP replaced by dUTP). Adapters were added by incubating to end repair. After degradation of the second-strand cDNA, the first Strand were amplified by PCR. Products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on DNBseq platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
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| Description |
16A
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| Data processing |
The raw RNA-seq data were uploaded, processed and analyzed with the RNA-seq process pipeline in OmicSoft Array Studio software (version 10.1.1.3), including data quality control, alignment, quantification, normalization and log2 transformation to obtain the expression values (log2 FPKM) for each sample.
Genome_build: Human B38
Supplementary_files_format_and_content: HumanAstrocyteQuantLog2.txt: Tab-delimited text file includes FPKM values for each Sample.
Supplementary_files_format_and_content: HumanAstrocyteQuantLog2_Annotation.txt: Tab-delimited text file includes gene annotation.
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| Submission date |
Apr 23, 2021 |
| Last update date |
Aug 12, 2021 |
| Contact name |
Dimitry Ofengeim |
| Organization name |
Sanofi
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| Street address |
49 New York Avenue
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| City |
Framingham |
| ZIP/Postal code |
01701 |
| Country |
USA |
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| Platform ID |
GPL28038 |
| Series (1) |
| GSE172027 |
RIPK1 kinase-dependent gene expression in human astrocytes in vitro |
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| Relations |
| BioSample |
SAMN18857435 |
| SRA |
SRX10671628 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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