|
| Status |
Public on Oct 03, 2019 |
| Title |
3k3-dox-d14-smart: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone A |
| Sample type |
SRA |
| |
|
| Source name |
healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone A
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: healthy control iPSC cell line 2242-1
treatment: Day 14 NPCs (d14)
|
| Growth protocol |
mTESR1 Complete media with Anti-anti, differentiated under Douvaras 2015 protocol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA purification with RNEasy Kit
Modified Smart-seq2 protocol with oligodT30 VN, ISPCR cDNA amplification, and Nextera XT library preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
iPSC differentiation + doxycycline RNA-seq
TRE-H3.3K27M Clone A Dox
3k3-dox
|
| Data processing |
RNA-seq reads were trimmed of adaptors with cutadapt
Aligned to hg19 with tophat2 v2.1.1
Reads counted in hg19 RefSeq genes using featureCounts
Transcript per million (TPM) for each gene was determined as 1,000,000 * (reads per kilobase of transcript)/(total sum of reads per kilobase of all transcripts)
genome build: hg19
processed data files format and content: TPM spreadsheet
|
| |
|
| Submission date |
Jun 16, 2019 |
| Last update date |
Oct 03, 2019 |
| Contact name |
Michelle Monje |
| E-mail(s) |
mmonje@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
265 Campus Drive, SIM1 G3035
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE126319 |
Variant and cell-context specific H3K27M reprogramming results in distinct enhancer architecture and oncogenic states |
|
| Relations |
| BioSample |
SAMN12070338 |
| SRA |
SRX6075188 |
