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| Status |
Public on Dec 01, 2017 |
| Title |
WT RNA-Seq rep2 |
| Sample type |
SRA |
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| Source name |
HUES8 human embryonic stem cells (hESCs)
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HUES8 hESCs
genotype: Wild type sequence
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| Treatment protocol |
No treatments were applied prior to RNA extraction
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| Growth protocol |
HUES8 (NIHhESC-09-0021) hESCs were cultured on irradiated mouse embryonic fibroblasts (iMEFs) feeder layers in DMEM/F12 medium (Life Technologies, 12500-062) supplemented with 20% KnockOut Serum Replacement (Life Technologies, 10828028), 1X MEM Non-Essential Amino Acids (Life Technologies, 11140050), 1X GlutaMAX (Life Technologies, 35050079), 100U/ml Penicillin and 100 μg/ml Streptomycin (Gemini, 15070063), 0.055 mM 2-mercaptoethanol (Life Technologies, 21985023) and 10 ng/ml recombinant human bFGF (EMD Millipore, GF003AF). Cells were incubated at 37 °C with 5% (vol/vol) CO2, and media was changed daily. Cultures were passaged at a 1:6 - 1:12 split ratio every 4 - 6 days using TrypLE (Life Technologies, 12563-029). 5 µM Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Selleck Chemicals, S1049) was added into the culture medium when passaging or thawing cells. Cells are regularly confirmed to be mycoplasma-free by the MSKCC Antibody & Bioresource Core Facility.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the RNeasy Mini Kit (Qiagen, 74136). DNA was removed from RNA samples using genomic DNA eliminator spin columns.
Illumina Truseq kit PolyA method non stranded
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
RNA-seq data was aligned to the hg19 reference genome using Bowtie.
Read counts were derived from HTSeq.scripts.count module in HTSeq-0.6.0 with default parameters. in a non-directional model
Differentially expressed genes were generated by DESeq2-1.4.5 in R.
Up regulated genes were decided by logFC > 2 and p-adj < 0.1 (n=153).
Downregulated genes were decided by logFC < -2 and p-adj < 0.1 (n=233).
Genome_build: hg19
Supplementary_files_format_and_content: RNASeq_WT1.counts Counts for WT sample, first replicate.
Supplementary_files_format_and_content: RNASeq_WT2.counts Counts for WT sample, second replicate.
Supplementary_files_format_and_content: RNASeq_TKO1.counts Counts for TKO sample, first replicate.
Supplementary_files_format_and_content: RNASeq_TKO2.counts Counts for TKO sample, second replicate.
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| Submission date |
Nov 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Nipun Verma |
| E-mail(s) |
nipunver@gmail.com
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| Phone |
646-358-2160
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| Organization name |
Memorial Sloan Kettering Cancer Center
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| Department |
Developmental Biology
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| Lab |
Danwei Huangfu lab
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| Street address |
430 East 67th St
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE89726 |
RNA Sequencing of HUES8 WT and HUES8 TET1/2/3 TKO hESCs |
| GSE89728 |
TET1/2/3 |
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| Relations |
| BioSample |
SAMN06008026 |
| SRA |
SRX2340532 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2387329_RNASeq_WT2.counts.txt.gz |
224.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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