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| Status |
Public on Dec 15, 2016 |
| Title |
Epistasis experiment guide barcodes (gemgroup 1) |
| Sample type |
SRA |
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| Source name |
K562 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cells were lysed in droplets using the 10X Chromium instrument
Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev A
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Guide barcode reads
read length: Read 1: 98, Index read 1 (i7): 14, Index read 2 (i5): 8, Read 2: 10
Custom paired end, all 4 reads informative
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| Data processing |
BAM files were generated directly from raw Illumina BCL files using 10X Genomics Cellranger version 1.1 with default paramaters (cellranger demux)
Gene-barcode matrices were determined using 10X Genomics Cellranger version 1.1 with default parameters (cellranger run)
Guide barcode identities were determined as described in the paper.
Genome_build: hg19
Supplementary_files_format_and_content: BAM files were generated by cellranger and contain raw reads for single-cell RNAseq, including cell identity, UMI information, and gemgroup id (referred to in guide barcode filenames). Gene-barcode matrices are the UMI-collapsed counts of these reads, representing counts of molecules per cell as determined and filtered by cellranger. These are provided in the format outputted by cellranger: the matrix itself is in matrix market exchange format, with the rows (cell barcodes) and columns (gene identities) labels given in TSV format as described in the cellranger documentation. Guide barcodes were specifically amplified from the RNAseq libraries and sequenced to higher coverage, and then identities were called as discussed in the paper.
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| Submission date |
Nov 25, 2016 |
| Last update date |
Apr 16, 2019 |
| Contact name |
Thomas Norman |
| Organization name |
UCSF
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| Lab |
Weissman
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| Street address |
1700 4th St
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE90546 |
A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response |
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| Relations |
| BioSample |
SAMN06055345 |
| SRA |
SRX2400168 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data not provided for this record |
| Raw data are available in SRA |
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