|
Status |
Public on Jul 14, 2014 |
Title |
GATA3 |
Sample type |
SRA |
|
|
Source name |
overexpression of GATA3 in Embryonic stem cells; cells collected 5 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
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|
|
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 |
SAMN02767218 |
SRA |
SRX535137 |