|
| Status |
Public on Jan 19, 2016 |
| Title |
CRISPRn, -dox, RepA |
| 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 |
SRX1508861 |
