|
| Status |
Public on Jun 30, 2022 |
| Title |
mTE-4 |
| Sample type |
SRA |
| |
|
| Source name |
trophectoderm
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: trophectoderm
|
| Treatment protocol |
Single cells were washed with 1x PBS containing 0.1% BSA before placing in lysis buffer.
|
| Growth protocol |
Mouse zygotes were collected after timed mating and cultured in the Optimum medium to the blastocyst stages
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated from single cells and amplified using the SMRT-seq2 protocol
Library construction was performed following Illumina manufacturer suggestions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw reads from the Illumina HiSeq2000 were mapped to the mm10 genome using default parameters in BWA
Mapped transcripts reads were transformed using the reads per kilobase per million (RPKM) metric
Genes with low expression were filtered out, followed by quantile normalization.
Genome_build: mm9
Supplementary_files_format_and_content: mouse_ReadCounts.txt; raw read counts
Supplementary_files_format_and_content: mouse_processed_RPKM.txt; normalized RPKM
|
| |
|
| Submission date |
Dec 07, 2015 |
| Last update date |
Jun 30, 2022 |
| Contact name |
Kevin Huang |
| Phone |
310-267-0438
|
| Organization name |
UCLA
|
| Department |
Human Genetics
|
| Lab |
Guoping Fan
|
| Street address |
Gonda BLDG Rm. 6554, P.O.Box 957088
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7088 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE75764 |
Single-cell analysis of gene networks in trophoectoderm and inner cell mass during human, monkey and mouse preimplantation development |
|
| Relations |
| BioSample |
SAMN04323352 |
| SRA |
SRX1469252 |
