|
| Status |
Public on Aug 13, 2016 |
| Title |
U87_3T3_scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Brain and embyro
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell line: U87
cell line: 3T3
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNA molecues were captured using bead-bound oligo dT(30).
Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
U87 cells and 3T3 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplimented with 10% (v/v) Fetal Bovine Serum (FBS).
|
| Data processing |
Read 1 and read 2 fastq files were generated on basespace.
Raw reads from Read 1 were demultiplexed to obtain cell barcode and unique molecular identifier for each read.
Read 2 were pre-processed using faxtx_clipper to remove all poly(A) tails from the 3'-ends of each read. Any resulting fragment shorter than 25 nucleotides were discarded.
Pre-processed reads were then mapped to a concatenated human-murine transcriptome (hg19, UCSC known genes and mm10, UCSC known genes) using bwa-mem. We kept all reads with the correct strandedness that map uniquely to a specific gene with an alignment score that is greater than or equal 85% of the length of the fragment.
Cell barcodes were collapsed to account for PCR duplications. Unique molecular identifiers were collapsed to account for PCR duplications and errors that are associated with unique molecular identifier synthesis, PCR, and sequencing.
All fastq files were generated using Illumina's default pipeline on basespace. Read 1 is 26 bases long which contains cell barcode sequences (12 base long), unique molecular identifier sequences (8 base long) and 6-base long oligo(dT) sequences.Both cell barcode and unique molecular identifier are random sequences. Read 2 is 66 bases long which contains mRNA sequences.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression counts of each individual cell.
|
| |
|
| Submission date |
Aug 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Sims |
| Organization name |
Columbia University
|
| Street address |
3960 Broadway, 2nd Floor, Room 203AC
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL19415 |
| Series (1) |
| GSE85575 |
An automatec microwell platform for large-scale single cell RNA-seq. |
|
| Relations |
| BioSample |
SAMN05571437 |
| SRA |
SRX2019092 |
