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Sample GSM3842208 Query DataSets for GSM3842208
Status Public on Nov 18, 2019
Title Intermediate-activity sgRNA perturb-seq experiment (gemgroup2)
Sample type SRA
 
Source name K562 cells
Organism Homo sapiens
Characteristics cell line: K562 chronic myelogenous leukemia cell line
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.
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)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description Single-cell RNA-seq data, gemgroup 2
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.
 
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 SAMN11936308
SRA SRX5952708

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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