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Sample GSM3543616 Query DataSets for GSM3543616
Status Public on Jan 07, 2019
Title Quant-seq_Day 28_neuron_rep1
Sample type SRA
 
Source name Human iPSC-derived neuron
Organism Homo sapiens
Characteristics cell type: Day 28 neuron
Growth protocol Classic Neuronal Medium
Extracted molecule polyA RNA
Extraction protocol RNA was extracted using the Quick-RNA Miniprep Kit (Zymo; Cat. No. R1054), and RNA concentrations were determined with the Qubit RNA HS Assay Kit (Invitrogen; Cat. No. Q32855) on a Qubit 2.0 Fluorometer (Invitrogen; Cat. No. Q32866)
Libraries were prepared according to protocol accompanying the Lexogen‘s QuantSeqTM 3‘ mRNA-Seq Kit (Cat. No. 015)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description Quant-seq
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
E-mail(s) Ruilin.Tian@ucsf.edu
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 GPL20301
Series (1)
GSE124703 CRISPR-based multimodal genetic screens in human iPSC-derived neurons
Relations
BioSample SAMN10697313
SRA SRX5210069

Supplementary file Size Download File type/resource
GSM3543616_D28_C1_read_counts.txt.gz 183.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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