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| Status |
Public on May 21, 2021 |
| Title |
Sample 2_AB10015 |
| Sample type |
SRA |
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| Source name |
LLN PIC MCDD doublet 1
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| Organism |
Mus musculus |
| Characteristics |
strain: c57bl
tissue: liver lymph nodes
cell type: PIC (T + cDC)
selection marker: CD45+Lin-MHC-II+CD11c+TCRb+
infection: NA
time point: 2 weeks
treatment(1): MCDD
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}
single cell RNA-seq for gene expression quantitation
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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. (read2 used to read cell and molecule barcodes only)
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
Supplementary_files_format_and_content: *_metadata_s.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts
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| Submission date |
Mar 23, 2021 |
| Last update date |
May 21, 2021 |
| Contact name |
Ido Amit |
| E-mail(s) |
ido.amit@weizmann.ac.il
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| Phone |
972-8-9343338
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| Organization name |
Weizmann Institute of Science
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| Department |
Immunology
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| Street address |
234 Herzl st.
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| City |
Rehovot |
| ZIP/Postal code |
760001 |
| Country |
Israel |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE169445 |
XCR1+ type 1 conventional dendritic cells drive liver pathology in Non-Alcoholic Steatohepatitis [scRNA-seq] |
| GSE169447 |
XCR1+ type 1 conventional dendritic cells drive liver pathology in Non-Alcoholic Steatohepatitis. |
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| Relations |
| BioSample |
SAMN18440134 |
| SRA |
SRX10421449 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5203166_AB10015.txt.gz |
794.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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