|
| Status |
Public on Jan 07, 2019 |
| Title |
Quant-seq_Day 14_neuron_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Human iPSC-derived neuron
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Day 14 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 |
SAMN10697316 |
| SRA |
SRX5210066 |
