|
| Status |
Public on Jan 27, 2021 |
| Title |
ESR2_Day0_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Induced pluripotent stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: esr2 knockdown
age: Day 0 of neuronal differentiation
passage: 13-14
strain: Induced pluripotent stem cell line GM25256
|
| Biomaterial provider |
Coriell Cell Repositories https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25256
|
| Treatment protocol |
N/A
|
| Growth protocol |
DMEM/F12 medium supplemented with 1x N2, 1x B27 -Vitamin A, 1x GlutaMAX, 1x MEM-NEAA, 0.5 mM dibutyryl cAMP, 0.2 mM ascorbic acid, 1 μM PD0325901, 5 μM SU5402, 10 μM DAPT, 20 ng/mL BDNF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Mini kit
Ion AmpliSeq kit
Ion Torrent NGS, Ion GeneStudio S5 System
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent S5 |
| |
|
| Description |
ESR2_iPSC_rawcounts.csv
ESR2_iPSC_filtered_cpm.csv
|
| Data processing |
Raw data was processed with the Ion Torrent Suite Server v5.8.0 (ThermoFisher)
Reads were aligned reads to the hg19 AmpliSeq Transcriptome reference (v1.1) with the coverageAnalysis plugin v5.8.0.8 which runs the command `tmap mapall -q 50000 -f hg19_AmpliSeq_Transcriptome_v1.1.fasta -r Sample_1.fastq -s Sample_TMAP.aln.sam stage1 map4`
Reads were quantified using the ampliSeqRNA plugin v5.8.0.3 with default settings.
Genes with greater than 1 count per million in three samples were retained for clustering and DEX analysis; this is represented in the filtered_cpm processed file.
Genome_build: hg19_AmpliSeq_Transcriptome_v1.1.fasta
Supplementary_files_format_and_content: rawcounts.csv, filtered_cpm.csv
|
| |
|
| Submission date |
Aug 03, 2020 |
| Last update date |
Jan 27, 2021 |
| Contact name |
Arthur Jeremy Willsey |
| E-mail(s) |
jeremy.willsey@ucsf.edu
|
| Phone |
4158023105
|
| Organization name |
UCSF
|
| Department |
Psychiatry
|
| Lab |
Willsey Lab
|
| Street address |
675 Nelson Rising Lane, Mail Code 0518
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL23934 |
| Series (2) |
| GSE155552 |
Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience [human] |
| GSE155554 |
Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience |
|
| Relations |
| BioSample |
SAMN15702253 |
| SRA |
SRX8867422 |
