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Sample GSM2041879 Query DataSets for GSM2041879
Status Public on Jan 19, 2016
Title CRISPRn, -dox, RepB
Sample type SRA
 
Source name Coriell GM25256
Organism Homo sapiens
Characteristics cell line: WTC-CRISPRn
sgrna: None
doxycycline treatment: -
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM25256
Extracted molecule polyA RNA
Extraction protocol RNA was extracted from approximately 10^5 cells with TRIzol reagent
Strand-specific mRNAseq libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Demultiplexing using Illumina Bcl2Fastq
Reads were aligned to the hg19 genome assembly using the Ensembl 75 reference transcriptome customized to include the GCaMP6f constructs using TopHat2 (v2.1.0) using the following parameters: --library-type fr-firststrand --transcriptome-index --prefilter-multihits
Unaligned reads for CRISPRi and CRIPSRn cell lines were aligned to the appropriate CRISPRi/n transgene sequence and annotation using TopHat2 (v2.1.0) using the following parameters: --library-type fr-firststrand --transcriptome-index --prefilter-multihits
Transcript alignments were counted using SubRead v1.4.6 with the -s 2 flag and otherwise default parameters
For display purposes, alignment counts were incremented with a pseudocount of 0.075 and normalized to reads per million using custom python scripts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample
 
Submission date Jan 19, 2016
Last update date May 15, 2019
Contact name Max A Horlbeck
Organization name UCSF
Department Cellular and Molecular Pharmacology
Lab Weissman Lab
Street address 1700 4th Street
City San Francsico
State/province CA
ZIP/Postal code 94158
Country USA
 
Platform ID GPL20301
Series (1)
GSE76980 iPSC RNA-seq upon CRISPRn or CRISPRi manipulation
Relations
BioSample SAMN04377556
SRA SRX1508862

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

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