 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 10, 2014 |
| Title |
16cell_4-6 |
| Sample type |
SRA |
| |
|
| Source name |
16-cell stage blastomere
|
| Organism |
Mus musculus |
| Characteristics |
strain: CAST/EiJ(mother) x C57BL/6J(father)
cross: first generation cross
developmental stage: 16-cell stage blastomere
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
We used lysis buffer of the kit 'SMARTer Ultra Low Input RNA for Illumina Sequencing' from Clontech
We used the kit 'SMARTer Ultra Low Input RNA for Illumina Sequencing' from Clontech
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
16-cell stage embryo 4 cell 6
|
| Data processing |
For expression values, we aligned reads using bowtie 0.12.7, option --best, against the genome and transcriptome (Ensembl, version 16 May 2011) with the genotype of both strains, in mm9 coordinates
Non-uniquely mapped reads were removed
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE.
For allelic ratios, we aligned using gsnap version 2012-07-20, with tolerance for known SNP positions
We used samtools mpileup to extract allelic counts
Genome_build: mm9
Supplementary_files_format_and_content: gene expression values (tab-delimited text)
|
| |
|
| Submission date |
Apr 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Ramsköld |
| E-mail(s) |
daniel.ramskold@ki.se
|
| Organization name |
Karolinska Institutet
|
| Lab |
Rickard Sandberg's group (rickard.sandberg@ki.se) (2008-2014, 2018-); Rheumatology unit (2014-2018)
|
| Street address |
Nobels väg 3
|
| City |
Stockholm |
| ZIP/Postal code |
17177 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE45719 |
Single-cell RNA-Seq reveals dynamic, random monoallelic gene expression in mammalian cells |
|
| Relations |
| SRA |
SRX259126 |
| BioSample |
SAMN01997303 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1112511_16cell_4-6_expression.txt.gz |
310.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
