|
| Status |
Public on Nov 25, 2020 |
| Title |
4CBS_downstream_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: F123 ESC
strain: F1 hybrid (castaneus X 129/SvJae)
genotype: 4CBS-downstream-insertion
|
| Growth protocol |
Cells were cultured on feeder-free, serum free 2i condition (Serum free mouse ES medium supplemented with 1uM PD03259010, 3uM CHIR99021, 2mM glutamine, 0.15uM Monothioglycerol, 1000U/ml LIF). The growth medium was changed every day. Cells were dissociated by Accutase (AT104) and passaged to onto 0.2% gelatin-coated plates every 2-3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cells was extracted using the TRIzol Plus RNA purification kit (Thermo Fisher Scientific, Catlog: 12183555).
RNA-Seq libraries were prepared from 4 µg total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit Set A (RS-122-2101; Illumina) or Set B (RS-122-2102; Illumina). RNA-seq libraries were sequenced on illumine Next-seq 550 and Hi-seq4000 platforms (75-bp paired ends).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The RNA-Seq alignment and quantification pipeline is available at https://github.com/ren-lab/rnaseq-pipeline. Briefly, reads were aligned to mm10 (GRCm38) and GENCODE GTF version M25 with rnaSTAR77.
PCR duplicates were removed using Picard. Raw reads for each gene were quantified using featureCounts. RPKM values were calculated for each gene
Particularly, we created two extra chromosomes for the two tagged Sox2 alleles. Reads uniquely mapped to egfp and mCherry sequences were counted using samtools. Expression level of Sox2 gene from CAST and 129 allele was calculated by RPKM values of the egfp and mCherry gene, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
Nov 24, 2020 |
| Last update date |
Nov 25, 2020 |
| Contact name |
Bing Ren |
| Organization name |
University of California, San Diego School of Medicine
|
| Street address |
9500 Gilman Dr., CMM-East, Admin Area/Rm 2071
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE153403 |
CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains |
| GSE162101 |
CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains [RNA-seq] |
|
| Relations |
| BioSample |
SAMN16883412 |
| SRA |
SRX9569055 |
