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| Status |
Public on May 14, 2024 |
| Title |
embryo2_cell4 |
| Sample type |
SRA |
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| Source name |
Blastocyst
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Blastocyst
cell type: ICM
genotype: WT
developmental stage: E6
Sex: Male
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were collected directly into 2.5 μl methyltransferase reaction mixture which was comprised of 1 × M.CviPI Reaction buffer, 2 U M.CviPI, 160 μM S-adenosylmethionine, 1 U μl−1 RNAsein, 0.1% IGEPAL then incubated for 15 min at 37 °C. The reaction was stopped and the RNA preserved with the addition of 5 μl RLT plus.
Single-cell RNA sequencing libraries were prepared according to the RNA half of the scNMT-seq protocol (https://doi.org/10.1038/s41467-018-03149-4). Briefly, biotinylated oligo-dT was bound to magnetic beads which were added to single-cell lysates in 96w plates. The captured mRNA was then reverse transcribed and PCR amplified on beads accordingto the Smartseq2 protocol (https://doi.org/10.1038/nprot.2016.138,https://doi.org/10.1038/nprot.2014.006). Indexed Illumina libraries were prepared from the amplified cDNA using Nextera XT reagents and then pooled and sequenced on a HiSeq 2000 instrument using 75bp paired-end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
lane6372_TCCTGAGC_CCTAGAGT_PlateC_C04
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| Data processing |
Raw reads were processed as previously (https://doi.org/10.1038/s41467-018-03149-4), aligning to the GRCh38 reference genome using Hisat2 (https://doi.org/10.1038/s41587-019-0201-4).
Gene expression counts were computed from the mapped data using the featureCounts function within RSubread (https://doi.org/10.1093/nar/gkz114).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file with raw counts for each sample
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| Submission date |
Oct 05, 2023 |
| Last update date |
May 14, 2024 |
| Contact name |
Lawrence E Bates |
| E-mail(s) |
lbates@ed.ac.uk
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| Organization name |
University of Edinburgh
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| Department |
Human Genetics Unit
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| Lab |
Nichols Lab
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| Street address |
Crewe Road
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| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE244721 |
Mechanisms to prepare human polar trophectoderm for blastocyst implantation |
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| Relations |
| BioSample |
SAMN37700512 |
| SRA |
SRX22006495 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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