|
| Status |
Public on Apr 03, 2018 |
| Title |
Blank - Negative Control 3 |
| Sample type |
SRA |
| |
|
| Source name |
water
|
| Organism |
other sequences |
| Characteristics |
tissue: blank
sample type: water
treatment: negative control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ERCC spike-in standards and either water or dilute whole brain total RNA (Agilent Technologies, catalog #540005) were converted to cDNA using Smartseq2 protocol.
Libraries were prepared using Fludigm’s recommendations for Illumina NexteraXT at ¼ volume with minor modifcations.
Single cell RNA-sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Smartseq2 on wells containing only water and ERCC spike-in molecules
raw_counts.tsv
brainandblanks_adjustedcpm_counts.tsv
|
| Data processing |
Libraries were mapped to hg19 using STAR v2.5.2a with the GENCODE (release 25) annotation.
Aligned reads were filtered to remove exact position duplicates.
Transcriptome features were counted using HTseq with the intersection-strict parameter.
Genes were removed with zero observations across all samples to produce the raw_counts.tsv file.
An adjusted cpm normalization was applied as described by Hicks et al. using edgeR v3.12.1. The normalization was applied across all 93 samples to yield the file brainandblanks_adjustedcpm_counts.tsv and across only brain total RNA samples to yield the processed file brainonly_adjustedcpm_counts.tsv.
Genome_build: hg19
Supplementary_files_format_and_content: The raw_counts.tsv contains the feature counts without normalization for all 93 samples. The brainandblanks_adjustedcpm_counts.tsv file contains the adjusted cpm normalized counts for all 93 samples, and the brain_only_adjustedcpm_counts.tsv contains the adjusted cpm normalized counts restricted to the samples obtained from dilute total brain RNA. In all three tab-delimited count matrix files, the columns are samples and the rows are ENSEMBL gene id tags.
|
| |
|
| Submission date |
Feb 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin Schuster-Böckler |
| E-mail(s) |
benjamin.schuster-boeckler@ludwig.ox.ac.uk
|
| Phone |
+44 1865 617481
|
| Organization name |
University of Oxford
|
| Department |
Ludwig Institute for Cancer Research
|
| Lab |
Schuster-Böckler Lab
|
| Street address |
Old Road Research Campus Building, Roosevelt Drive
|
| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 7DQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24839 |
| Series (1) |
| GSE95155 |
BEARscc: robustness of single-cell clusters determined using simulated technical replicates |
|
| Relations |
| SRA |
SRX2581167 |
| BioSample |
SAMN06364988 |
