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Status |
Public on Nov 18, 2019 |
Title |
Intermediate-activity sgRNA perturb-seq experiment (gemgroup1) |
Sample type |
SRA |
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Source name |
K562 cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: K562 chronic myelogenous leukemia cell line
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Growth protocol |
K562 cells expressing dCas9-KRAB were transduced with lentivirus carrying the sgRNA expression cassettes and a BFP marker. Transduced cells were isolated by FACS 3 days after transduction and grown for 2 additional days. Growth was performed in RPMI media supplemented with FBS and Pen/Strep/Gln.
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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 (v2 chemistry)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Description |
Single-cell RNA-seq data, gemgroup 1 10X_barcodes.tsv 10X_genes.tsv 10X_matrix.mtx cell_identities.csv
|
Data processing |
Fastq.gz files were generated from raw Illumina BCL files using bcl2fastq BAM files were generated from the fastq.gz files using 10X Genomics Cellranger version 2.1.1 with default paramaters (cellranger count). Read 1: 26, Index read 1 (i7): 8, Read 2: 98 Custom paired end, all 3 reads informative Reads from multiple channels (gemgroups) of the 10X run were combined using 10X Genomics Cellranger version 2.1.1 (cellranger aggr) Gene-barcode matrices were determined using 10X Genomics Cellranger version 2.1.1 with default parameters Guide barcode identities were determined as described in the paper. Genome_build: hg38 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 RNA-seq libraries and sequenced to higher coverage, and then identities were called as discussed in the paper.
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Submission date |
Jun 03, 2019 |
Last update date |
Nov 18, 2019 |
Contact name |
Marco Jost |
E-mail(s) |
marco_jost@hms.harvard.edu
|
Organization name |
Harvard Medical School
|
Street address |
77 Ave Louis Pasteur, NRB848
|
City |
Boston |
State/province |
MA |
ZIP/Postal code |
02115 |
Country |
USA |
|
|
Platform ID |
GPL20301 |
Series (1) |
GSE132080 |
Titrating gene expression with allelic series of CRISPR guide RNAs |
|
Relations |
BioSample |
SAMN11936309 |
SRA |
SRX5952707 |