|
| Status |
Public on May 02, 2019 |
| Title |
Sample 21_AB329 |
| Sample type |
SRA |
| |
|
| Source name |
ES
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell line: ES
tissue/cell type: Cell line
treatment/sample info.: low volume
protocol optimization parameter: Evaluation of protocol performance, using low volume RT
|
| Growth protocol |
6 to 8 weeks-old mice housed at the Weizmann Institute animal facility; Cell lines were grown in tissue culture
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For samples 1-16: Each mouse was euthanized and bone marrow harvested by crushing of the femur, tibia and ilia. Cell suspensions were stained with FACS antibodies and single cells sorted into capture plates
For samples 17-34: Cells were trypsinzed to form a single cell suspension and FACS sorted into capture plates
3' end mRNA libraries were prepared for sequencing using MARS-seq2.0 - improvements to MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation; Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| 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 or hg19
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
|
| |
|
| Submission date |
Dec 06, 2018 |
| Last update date |
May 02, 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 (1) |
| GSE123392 |
MARS-seq2.0 an experimental and analytical pipeline for indexed sorting combined with Single-cell RNA sequencing |
|
| Relations |
| BioSample |
SAMN10525966 |
| SRA |
SRX5099370 |
