|
| Status |
Public on Aug 31, 2014 |
| Title |
CML17 iCD34+ Control |
| Sample type |
SRA |
| |
|
| Source name |
induced pluripotent stem cell-derived hematopoietic cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lin-CD34+CD45+
cell origin: CML17
treatment: DMSO
|
| Treatment protocol |
DMSO or 5 μM for 16 hours in expansion medium supplemented with 200 ng/ml GM-CSF
|
| Growth protocol |
Differentiated cells derived from Day 9th induced pluripotent stem cell/OP9 coculture were cultured in 10%FBS in αMEM supplemented with 200 ng/ml GM-CSF (expansion medium) for 2 days before FACs sorting for lin-CD34+CD45+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PureLink RNA micro kit (Life Technology) with on-column DNaseI digestion
Samples were then prepared for sequencing using the Illumina TruSeq RNA Sample Preparation Kit v2 (RS-122-2001), according to the manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 "
Differential expression likelihoods obtained using EBSeq 1.1.6
GO analysis performed using DAVID on genes with 1.000 Posterior Probability of differential expression, and estimated TPM > 10 in at least one sample
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing non-normalized "Expected Counts" and normalized "Transcripts Per Million" expression estimates calculated by RSEM.
|
| |
|
| Submission date |
Aug 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Scott Swanson |
| E-mail(s) |
SSWANSON@MORGRIDGEINSTITUTE.ORG
|
| Organization name |
Morgridge Institute for Research
|
| Lab |
Thomson
|
| Street address |
330 N. Orchard St
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53715 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE60065 |
Chronic Myeloid Leukemia (CML), induced pluripotent stem cell (iPSC)-derived lin-CD34+CD45+ (iCD34) cell population |
|
| Relations |
| BioSample |
SAMN02951505 |
| SRA |
SRX669199 |
