|
| Status |
Public on Jul 14, 2014 |
| Title |
GATA2_ETV2 d2 |
| Sample type |
SRA |
| |
|
| Source name |
overexpression of GATA2 and ETV2 in Embryonic stem cells; cells collected 2 days after transduction
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: ES-derived cells
cell line: H1
passage: 30-38
|
| Growth protocol |
H1 cells were maintained on matrigel-coated plates in a regular TeSR1 media, supplemented with 4ng of human FGF2. For lenti-viral transductions, cells were washed with PBS, dissociated to a single cell suspension by incubating with Accutase (Invitorgen cat.#A1110501) for 5-7 minutes, collected, pelleted and resuspended in 1-2ml of mTeSR1 media. For one well of 6-well plate 0.68 x10^6 cells were mixed with concentrated viral media (MOI 1-5) in 1ml in the presence of polybrene (6ug/ml), plated on matrigel-coated plates and placed in the cell culture incubator for 12hr. After 12hr, attached cells were maintained in a basal TeSR1 media with hFGF-20ng, SCF-100ng and TPO-50ng. Submitted RNA samples are from cells collected as indicated in “title” for the sample. Non-transduced hESCs grown in the same culture conditions were used as a control.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation procedure was performed according to QIAGEN protocol for RNAeasy micro kit Cat# 74004
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 "
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.
Supplementary_files_format_and_content: 54samples.tpm.tab: normalized expression estimates
Supplementary_files_format_and_content: 54samples.ec.tab: non-normalized abundance estimates
|
| |
|
| Submission date |
May 07, 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) |
| GSE57395 |
Direct Induction of Hematoendothelial Program in Human Pluripotent Stem Cells by Transcriptional Regulators |
|
| Relations |
| BioSample |
SAMN02767230 |
| SRA |
SRX535149 |
