|
| Status |
Public on Jan 17, 2018 |
| Title |
ESC_D01_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cell NMT-seq
|
| Organism |
Mus musculus |
| Characteristics |
cell line: El16 embyonic stem cell
strain: 129xCast/129
|
| Growth protocol |
ESCs were cultured in serum/LIF conditions as described previously (Ficz et al., Cell Stem Cell 13, 351–359)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
DNA and mRNA were seperately purified from single cells using the G&T-seq protocol described previously (Macaulay et al., Nature Protocols, 2016)
Libraries were prepared using the G&T-seq protocol described previously (Macaulay et al., Nature Protocols 2016)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Single-cell RNA-seq
ESC_RNA_counts.txt.gz
|
| Data processing |
Libraries were sequenced on the Illumina HiSeq or NextSeq platform using the default RTA analysis software.
Raw sequences were trimmed with Trim Galore (v0.4.3; Cutadapt v1.9.1) and aligned to the GRCm38 genome with HISAT2 (v2.0.5; options --dta --sp 1000,1000 to disallow soft-clipping). Gene expression counts were quantified from the mapped reads using featureCounts within the R package Rsubread. Gene annotations were obtained from Ensembl version 87. Only protein-coding genes matching canonical chromosomes were considered.
genome build: GRCm38
Supplementary_files_format_and_content: RNA-Seq reports contain raw counts per gene, with one row per gene (Ensembl Gene ID) and one column for each sample.
|
| |
|
| Submission date |
Jan 16, 2018 |
| Last update date |
Jan 24, 2018 |
| Contact name |
Felix Krueger |
| E-mail(s) |
[email protected]
|
| Organization name |
Altos Labs
|
| Department |
Bioinformatics
|
| Street address |
Granta Park
|
| City |
Cambridge |
| ZIP/Postal code |
CB21 6GP |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE109262 |
Joint profiling of chromatin accessibility, DNA methylation and transcription in single cells |
|
| Relations |
| BioSample |
SAMN08368258 |
| SRA |
SRX3585553 |
