|
| Status |
Public on Jul 23, 2018 |
| Title |
AB593 |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Thymus
selection marker: CD45-
treatment: untreated
mouse age: 4-6 weeks
|
| Treatment protocol |
Mice were sacrified by CO2
|
| Growth protocol |
All mice were maintained under specific pathogen-free conditions
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Thymus: Murine thymi were treated with enzymes cocktail (Collagenase, Dispase and Dnase) at 37C. Cells were separated by Percoll gradient density centrifugation, filtered and stained with Flow cytometry antibodies.
Intestine: Murine small intestines were flushed with PBS, treated with EDTA, Dispase and Dnase, filtered and stained with Flow cytometry antibodies.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
thymus_stroma_WT_mouse1
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.
|
| Data processing |
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each sample. Meta data file associating each single cell with its amplification batch and index sorting readouts is available on the series record in the file "metadata.txt".
|
| |
|
| Submission date |
Sep 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ido Amit |
| E-mail(s) |
ido.amit@weizmann.ac.il
|
| Phone |
972-8-9343338
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Immunology
|
| Street address |
234 Herzl st.
|
| City |
Rehovot |
| ZIP/Postal code |
760001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE103967 |
Large-scale single cell mapping of the thymic stroma identifies a new thymic epithelial cell lineage [single-cell RNA-seq] |
| GSE103970 |
Large-scale single cell mapping of the thymic stroma identifies a new thymic epithelial cell lineage |
|
| Relations |
| BioSample |
SAMN07664441 |
| SRA |
SRX3195940 |
