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| Status |
Public on Aug 27, 2015 |
| Title |
ES control rep2 |
| Sample type |
SRA |
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| Source name |
HS181
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| Organism |
Homo sapiens |
| Characteristics |
cell line (background): HS181
cell type: human embryonic stem cells (HESCs)
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| Growth protocol |
The HESC line HS181 (Hovatta et al., 2003) was cultured as described previously (Imreh et al., 2004). In brief: cells were kept at 37°C, 6.8% CO2, high humidity, in HESC medium (=80% KO DMEM + 20% SR + 2 mM L-glutamine + 1% non-essential amino acids + 0.1 mM β-mercapoethanol + 4 ng/ml bFGF). For feeder cells, human foreskin fibroblasts (hFS) (CRL-2429) were cultured in Iscove's Medium + 10% FCS, irradiated with 35 Gy and seeded at a concentration of 2.1 × 104 cells/cm2. The HS181 cells were dissociated using Dispase enzyme (10 mg/ml) and mild mechanical splitting. Embryoid bodies (EBs) were produced using Dispase and kept in HESC medium without bFGF for 12 days in Petri dishes.
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| Extracted molecule |
total RNA |
| Extraction protocol |
HESCs and HEBs were harvested using Trizol reagent. Illumina TruSeq Stranded Total RNA Sample Prep Kit (Cat#RS-122-2201) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the TruSeq Stranded Total RNA protocol.
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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 |
Libraries were clustered using cBot and sequenced on HiSeq2500 (HiSeq Control Software 2.0.12.0/RTA 1.17.21.3) with a 2x101 setup in RapidRun mode. Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite. The quality scale is Sanger / phred33 / Illumina 1.8+. Sequenced reads were mapped using Tophat v2.0.10 with parameter --library-type=fr-firststrand to Ensembl’s GRCh37 whole genome and specifying the corresponding GTF transcript annotation files, both provided by Illumina's iGenomes project (versions as of May, 2014). Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated with Cufflinks v.2.2.0 (with parameter --library-type fr-firststrand) using the same GTF transcript annotation file, and masking the annotated ribosomal RNA and mitochondrial transcripts. The raw FPKM values were filtered for protein coding genes, and the normalized FPKM values (zFPKM) were calculated as described in (Hart et al., 2013).
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: tab-delimited text files include FPKM, log2FPKM, and zFPKM values for each Sample
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| Submission date |
Jul 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Anita Göndör |
| Organization name |
Karolinska Institutet
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| Department |
MTC
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| Lab |
Anita Göndör group
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| Street address |
Nobels väg 16, KI Solna Campus, Karolinska Institutet, Box 280
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| City |
Stockholm |
| ZIP/Postal code |
171 77 |
| Country |
Sweden |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE26880 |
PARP1- and CTCF-mediated interactions between active and repressed chromatin at the lamina promote oscillating transcription |
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| Relations |
| BioSample |
SAMN02911817 |
| SRA |
SRX652618 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1436352_EScontrol2.txt.gz |
380.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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