|
| Status |
Public on May 16, 2016 |
| Title |
NT Kdm4d 2-cell 1 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
NT Kdm4d 2-cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6D2F1 (C57BL/6 X DBA/2)
development stage: 2-cell
genotype/variation: Kdm4d overexpression
tissue: nuclear transfer embryo
|
| Treatment protocol |
We separated the blastomeres of lived 2- or 4-cell stage embryos. One blastomere was harvested for single-cell sequencing, and the rest were further cultured in an aggregation plate to record the final development fate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Harvested cells were washed three times in 0.5% BSA-PBS solution and transferred into the lysis buffer. cDNA were synthesized using primers with 24-nt poly(dT),then a universal tail was added to the second strand cDNAs. After 18-20 cyclesof PCR, the PCR product is purified by QIAquick PCR purification kit(28104).
The prepared cDNA are sheared using Covaris S220. Fragment ends are repaired using NEBNext End Repair Module(E6050), then a NEBNext dA-Tailing Module(E6053) was used to yield a protruding 3- 'A' base for ligation of Illumina's adapters.After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles. library fragments of 200-500bp were band isolated from an agarose gel.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v1.3.3 with default parameters.
Gene expression for each sample was quantified to RPKM using Cufflinks(v 1.2.0).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each transcript.
|
| |
|
| Submission date |
Jul 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Shaorong Gao |
| Organization name |
Tongji University
|
| Department |
School of life science and technology
|
| Lab |
Gaolab
|
| Street address |
1239 Siping Road, Yangpu District
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE70605 |
Single Cell Sequencing Identifies Key Epigenetic Regulators in Nuclear Transfer Mediated Reprogramming [RNA-seq] |
| GSE70608 |
Single Cell Sequencing Identifies Key Epigenetic Regulators in Nuclear Transfer Mediated Reprogramming. |
|
| Relations |
| BioSample |
SAMN03842842 |
| SRA |
SRX1084809 |
