|
Status |
Public on Jan 13, 2017 |
Title |
DON2531A130 |
Sample type |
SRA |
|
|
Source name |
HUES2 Embryonic stem cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line: HUES2 cell type: embryonic stem cell derived macrophage macrophage batch: WTB macrophage samhd1: wildtype macrophage culture time in hours: 8 macrophage culture media: standard media
|
Growth protocol |
Macrophages grown on fibronectin coated polaris chip in XVIVO 15 + MCSF + FCS + PS LPS 100ng/ml in either XVIVO 15 + FCS + MCSF or from previously cultured Macrophages exposed to same batch of LPS
|
Extracted molecule |
total RNA |
Extraction protocol |
FluidigmC1 RNAseq protocol: cDNA was generated using SMARTer Ultra Low RNA Kit (Clontech) Nextera XT DNA Library Preparation Kit (Illumina); Illumina RNAseq HiSeq4000 75bp PE
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
Adapter trimming: RNA-seq reads were trimmed for Nextera and Illumina adapter sequences using skewer-v0.1.125 Alignment: Reads in gzipped fastq format were aligned using Hisat2 version-2.0.0-beta with default parameters to a modified reference genome comprising the human genome, Homo sapiens GRCh37 - human_g1k_v37, and fasta sequences for ERCC spike-ins Mark Duplicates: Duplicate reads were marked using MarkDuplicates.jar implemented in Picard tools v1.92 Read counts: Reads mapping uniquely to genes annotated in ENSEMBL release 75 were counted using featureCounts implemented in subread-v1.5.0 Genome_build: GRCh37 Supplementary_files_format_and_content: Count_table.txt: raw read counts for all 63677 ENSEMBL annotated genes Supplementary_files_format_and_content: additional_file_2.xlsx: Contains multiple excel sheets with Sheet1= tpm table (subset for 13873 expressed genes); Supplementary_files_format_and_content: additional_file_2.xlsx: Sheet2= cell metadata with information regarding chip, sequencing batch, imaging, and QC metrics; Supplementary_files_format_and_content: additional_file_2.xlsx: Sheet3= wildtype differential expression; Supplementary_files_format_and_content: additional_file_2.xlsx: Sheet4= knockout differential expression
|
|
|
Submission date |
Oct 17, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Eshita Sharma |
Organization name |
Wellcome Trust Centre for Human Genetics
|
Department |
Bioinformatics
|
Street address |
Roosevelt Drive, Headington
|
City |
Oxford |
State/province |
Oxfordshire |
ZIP/Postal code |
OX3 7BN |
Country |
United Kingdom |
|
|
Platform ID |
GPL20301 |
Series (1) |
GSE87849 |
The Nature and Nurture of Cell Heterogeneity: Accounting for Macrophage Gene-environment Interactions with Single-cell RNA-Seq |
|
Relations |
BioSample |
SAMN05914337 |
SRA |
SRX2249752 |