|
| Status |
Public on May 05, 2021 |
| Title |
AB3122 269 UT m_2 CD45 |
| Sample type |
SRA |
| |
|
| Source name |
269 UT m_2 CD45
|
| Organism |
Mus musculus |
| Characteristics |
strain: c57bl/6
organ: MCA205 tumor
cell type: Immune cells
selection marker: CD45
age: 8 weeks
Sex: female
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cells were sorted into 384-well plates and single cell RNA-seq libraries were generated using a modified version of the single cell MARS-seq protocol [Jaitin et al., Science 2014; Keren-Shaul et al., Nature Protocols 2019]. In brief, mRNA from cells sorted into cell capture plates were barcoded, converted into cDNA and pooled using an automated pipeline. The pooled cDNA are then amplified and Illumina libraries are being generated.
single cell RNA-seq for gene expression quantitation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
AB3122
|
| 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: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
|
| |
|
| Submission date |
May 03, 2021 |
| Last update date |
May 06, 2021 |
| 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 |
GPL24247 |
| Series (2) |
| GSE173773 |
Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation (scMARS-Seq) |
| GSE173778 |
Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation |
|
| Relations |
| BioSample |
SAMN18988700 |
| SRA |
SRX10760593 |
