|
| Status |
Public on Jan 29, 2019 |
| Title |
SLX_13255.i701_i506 |
| Sample type |
SRA |
| |
|
| Source name |
Pig embryo
|
| Organism |
Sus scrofa |
| Characteristics |
embryo: Generic pig
cell type: EB TE
cell id: AB4
|
| Growth protocol |
embryos were obtained from artificially inseminated pigs
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cells were collected manually into lysis buffer following the SMARTSEQ. 2 protocol published by Picelli et al., 2014 (Nat. Protocols 9, 171-181)
Libraries were constructed using Nextera XT DNA Library Preparation Kit (Illumina), as used Picelli et al., 2014..
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Pig_RawCounts.txt
Pig_TPMs.txt
|
| Data processing |
Basecalls by Illumine Software Suite
Raw PE reads were trimmed against adaptor sequences by scythe (v0.981), and quality-trimmed by sickle (v1.33) using default settings.
Trimmed reads then were directionally aligned to Sus scrofa v10.2 by hisat2 (v2.1.0) with --know-splicestie-infile. Uniquely and correctly mapped reads were extracted for the downstream analysis.
htseq-count was used to count the number of reads aligned to each gene (Sus scrofa v10.2 ensembl annotation build 87). Gene expression level was calculated and normalised by Transcripts Per Kilobase Million (TPM).
Genome_build: sus scrofa v10.2
Supplementary_files_format_and_content: tab-delimited text files for raw read counts and tpms of each gene, as well as rpms
|
| |
|
| Submission date |
Mar 27, 2018 |
| Last update date |
Jan 29, 2019 |
| Contact name |
Fei Sang |
| E-mail(s) |
mbzfs1@exmail.nottingham.ac.uk
|
| Organization name |
University of Nottingham
|
| Department |
School of Life Sciences
|
| Lab |
DeepSeq
|
| Street address |
QMC
|
| City |
Nottingham |
| ZIP/Postal code |
NG72UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19176 |
| Series (1) |
| GSE112380 |
Regulation of lineage segregation, pluripotency and X chromosome inactivation in the pig revealed by scRNA-Seq |
|
| Relations |
| BioSample |
SAMN08801108 |
| SRA |
SRX3852990 |
