|
Status |
Public on Aug 31, 2014 |
Title |
CML15 iCD34+ Imatinib |
Sample type |
SRA |
|
|
Source name |
induced pluripotent stem cell-derived hematopoietic cells
|
Organism |
Homo sapiens |
Characteristics |
cell type: lin-CD34+CD45+ cell origin: CML15 treatment: 5 uM imatinib
|
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 |
SAMN02951508 |
SRA |
SRX669202 |