|
| Status |
Public on Sep 06, 2019 |
| Title |
RNA-seq_D3_2 |
| Sample type |
SRA |
| |
|
| Source name |
DAY3
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 x 129
genotype: OKSM Col1a1/M2rtTA ROSA26
Stage: DAY3
medium: ESC medium with 1ug/ml doxycycline and 50ug/ml ascorbic acid
marker: unsorted
batch: DF5154_2017_08_25
|
| Growth protocol |
Mouse ES V6.5 were cultured on irradiated feeder cells in KO-DMEM media (Invitrogen) supplemented with 15% heat-inactivated fetal bovine serum, GlutaMAX, penicillin-streptomycin, non-essential amino acids, β-mercaptoethanol and 1000 U/ml LIF (ESC medium). All V6.5 samples for HiCHIP and two replicates of ChIPseq were cultured in the presence of 2i (1uM MEKinhibitor (Stemgent 04-0006) and 3uM GSK3 inhibitor (Stemgent 04-0004)). Mouse embryonic fibroblasts (MEFs) were isolated from a "reprogrammable" mouse harboring a polycystronic OKSM cassette in the Col1a1 locus and M2rtTA in the Rosa26 locus. Cells were reprogrammed in the presence of 1ug/ml doxycycline and 50ug/ml ascorbic acid and cultured in ES medium as described above.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared with TRIZOL (Life technologies #15596018) following manufacturer’s instructions.
Libraries were generated by the Weill Cornell Genomics core facility using the Illumina TruSeq stranded mRNA library preparation kit (#20020594) and sequenced on an Illumina HiSeq4000 platform on SE50 mode.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Expression of genes was quantified in transcripts per kilobase million (TPM) using quasi mapping (Salmon, version 0.8.2) to GENCODE (version M6, mm10) reference gene annotation. Salmon provides alignment-free transcript quantification information in a single step.
Genome_build: mm10
Supplementary_files_format_and_content: Plain tab-delimited text files with estimated TPM and read counts.
|
| |
|
| Submission date |
Apr 20, 2018 |
| Last update date |
Oct 10, 2023 |
| Contact name |
Effie Apostolou |
| E-mail(s) |
efa2001@med.cornell.edu
|
| Organization name |
Weill Cornell Medicine
|
| Street address |
1161 York Avenue, Apt 8A
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE113430 |
KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency [RNA-seq] |
| GSE113431 |
KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency |
|
| Relations |
| BioSample |
SAMN08962359 |
| SRA |
SRX3979835 |
