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Sample GSM4041219 Query DataSets for GSM4041219
Status Public on Jan 31, 2024
Title LP_ICM4_2
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_M4_2
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 SAMN12614787
SRA SRX6747925

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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