|
| Status |
Public on Mar 20, 2023 |
| Title |
Apex, PTEN WT/I135L, Passage5, rep1 [Apex_5_1] |
| Sample type |
SRA |
| |
|
| Source name |
Apex
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Apex
cell type: neural progenitor cells
genotype: PTEN WT/I135L
passage: 5
|
| Growth protocol |
Neural progenitor cells were maintained in Neural Expansion Medium (Neurbasal (catalog: 21103049) /Advanced DMEM/F12(catalog: 12634028) 50:50, 1X neural induction supplement (catalog: A1647801)) with 5% CO2 at 37C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using Direct-zol RNA Miniprep Plus Kit (Zymo Research). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNextUltra™II RNA Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
log2.cpm.filtered.norm.df_PTEN_P5.tsv
|
| Data processing |
Paired-end RNA sequencing reads were pseudoaligned to the human reference transriptome GRCh38.p13 release 103 using Kallisto version 0.46.2 for transcript abundance quantification.
Tximport R package was used to summarize transcript quantification data to genes followed by the R package edgeR TMM method for normalization
Genes with <1 CPM among 3 sample replicates, were filtered out.
Assembly: GRCh38.p13 release 103
Supplementary files format and content: tsv files for log2 normalized cpm value for each sample in passage 3
Supplementary files format and content: tsv files for log2 normalized cpm value for each sample in passage 4
Supplementary files format and content: tsv files for log2 normalized cpm value for each sample in passage 5
|
| |
|
| Submission date |
Sep 27, 2022 |
| Last update date |
Mar 20, 2023 |
| Contact name |
Shuai Fu |
| E-mail(s) |
[email protected]
|
| Organization name |
Case Western Reserve University
|
| Department |
Department of Genetics and Genome Sciences
|
| Lab |
Anthony Wynshaw-Boris
|
| Street address |
10900 Euclid Avenue
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE214323 |
Bulk RNA-seq on isogenic PTEN panel iPSC-derived neural progenitor cells to study the effect of ASD specific PTEN mutation and the effects of autism genetic background |
|
| Relations |
| BioSample |
SAMN31046568 |
| SRA |
SRX17726431 |
