|
| Status |
Public on Jan 31, 2024 |
| Title |
LP_ICM9_1 |
| Sample type |
SRA |
| |
|
| Source name |
human blastocyst
|
| Organism |
Homo sapiens |
| Characteristics |
phenotype: LP (Low-Potential)
tissue: Inner Cell Mass (ICM)
|
| Treatment protocol |
No treatment
|
| Growth protocol |
blastocysts were derived from ICSI-fertilized oocytes and cultured under standard conditions in the IVF Clinic (7%CO2/5%O2 in G1 media (from Day 0 to 3) and in G2 media (from Day 3 to 5-6) (Vitrolife) covered in mineral oil). Trophectoderm biopsies (3-5 cells) were collected for preimplantation genetic screening (PGS) before freezing by vitrification on day 5 or 6. PGS analysis was performed via either array comparative genomic hybridization (array CGH) or via next generation sequencing (NGS) by outside commercial laboratories. Prior to analysis, embryos were thawed according to standard protocols and cultured in G-PGD media (Vitrolife) for approximately 12 additional hours, at which time a final stage and morphological grade were assigned before laser dissection and freezing for analysis. Vitrification and thawing were conducted using the Cryotop method (Kitazato). An experienced embryologist used laser dissection to separate the mural TE (mTE) from the ICM compartment. The mTE and ICM samples were individually washed in TE Wash Buffer (1mg/ml bovine serum albumin in 1XPBS), transferred to individual 0.2ml PCR tubes, and frozen immediately in liquid nitrogen.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA isolation and cDNA synthesis were carried out using the SMARTer® Ultra® Low Input RNA Kit for Sequencing – v4 (Clontech, Cat.no. 634888).
Libraries were generated from the resulting cDNA (0.2ng/ul per sample) using the Nextera XT DNA library preparation kit (Illumina, Cat.no. FC-131-1024)
Indexed sequence libraries were pooled for multiplexing, normalized by MiSeq read number, and paired-end sequencing was performed on a HiSeq 4000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
P_M9_1
|
| Data processing |
Adapter sequences were trimmed via cutadapt (v1.10)
Mapping to the genome was conducted via STAR (2.5.2a) and annotated using the Ensembl GRCh38 genome.
Samtools was used to process sam files, and to sort and remove PRC duplicates of bam files
Counts for each gene were quantified using the Subread package FeatureCounts using the gene level quantification in paired-end mode (release 1.5.2)
Count data was normalized to TPM using the Bioconductor package edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited txt file includes raw counts and normalized TPM reads for each sample
|
| |
|
| Submission date |
Aug 21, 2019 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Heidi Cook-Andersen |
| E-mail(s) |
hcookandersen@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Department |
Department of Reproductive Medicine
|
| Street address |
2880 Torrey Pines Scenic Drive, Rm 4811
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE136106 |
RNA sequencing of embryonic and abembryonic compartments of euploid human blastocysts of good and poor morphology. |
|
| Relations |
| BioSample |
SAMN12614786 |
| SRA |
SRX6747926 |
