GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3543620 Query DataSets for GSM3543620
Status Public on Jan 07, 2019
Title CROP-seq_iPSC_sgRNA_enrichment_for_lane1
Sample type SRA
Source name Human iPSC
Organism Homo sapiens
Characteristics cell type: iPSC
Growth protocol Essential 8 Medium
Extracted molecule polyA RNA
Extraction protocol Single cells were lysed in droplets using the 10X Chromium instrument.
Libraries were prepared according to the Chromium Single Cell 3' Reagent Kits User Guide (v2 Chemistry) from 10X Genomics.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description CROP-seq_sgRNA_enrichment
Data processing For the Quant-seq data, raw reads were trimmed with Bbduk, aligned with STAR Aligner, and counted with HTSeq-count to yield gene counts. For the CROP-seq data, Cell Ranger (version 2.2.0) was used to align reads and generate digital expression matrices from single-cell sequencing data. To map sgRNA transcripts together with other mRNA transcripts to individual cells, a custom reference was generated by extending the human genome assembly (Ensembl GRCh38 release) with ‘pseudo-genes’ representing sgRNA-containing transcripts (one sgRNA sequence per pseudo-gene with 250bp upstream and 230bp downstream sequences).
Genome_build: hg38
Supplementary_files_format_and_content: For the Quant-seq data, files containing gene Ensembl IDs and counts are provided in Tab-delimited text (.txt) format. For the CROP-seq data, expression matrices output by cellranger are provided in Matrix Market (.mtx) format and the associcated gene ID and cell barcode files are provided as Tab Separated Values (.tsv) files. For the sgRNA enrichment data, cell barcodes and their mapped sgRNAs with UMI counts are provided as txt files.
Submission date Jan 06, 2019
Last update date Jan 07, 2019
Contact name Ruilin Tian
Organization name University of California, San Francisco
Department Institute for Neurodegenerative Diseases
Lab Martin Kampmann
Street address 675 Nelson Rising Lane, 3rd Floor
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platform ID GPL24676
Series (1)
GSE124703 CRISPR-based multimodal genetic screens in human iPSC-derived neurons
BioSample SAMN10697309
SRA SRX5210073

Supplementary file Size Download File type/resource
GSM3543620_iPSC_1_sgRNA_mapping.txt.gz 14.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap