|
| Status |
Public on Jul 01, 2016 |
| Title |
Lung_C57B6_P04_r1 |
| Sample type |
RNA |
| |
|
| Source name |
Lung, C57B6, P04
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
strain: C57BL/6J
stock: #000664
age: P04
stage1 (canonical stages of lung development): 5-ALV
stage2 (molecular divisions of lung development): 6-ALV2
|
| Treatment protocol |
Immediately following dissection, whole lung tissues (or whole embryos for time point e9.5) were placed in RNAlater and stored at -80C.
|
| Growth protocol |
Mice were fed regular lab chow diet ad libitum until time of tissue harvest.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using mirVana isolation kits (Ambion) following manufacturer's instructions. An additional DNAse I (Promega) step was added before organic extraction. RNA quality was assessed using RNA 6000 LabChip assays and 2100 Bioanalyzer (Agilent Technologies). OD 260/280 and OD 260/230 ratios were also measured using nanodrop spectrophotometer (Thermo Fisher Scientific).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol for the Mouse 1.0ST arrays from 250-300ng total RNA.
|
| |
|
| Hybridization protocol |
As per standard Affymetrix protocol for the Mouse 1.0ST arrays.
|
| Scan protocol |
GeneChips were scanned by the GeneChip® Scanner 3000 7G (Affymetrix) using the AGCC Scan Control software program.
|
| Description |
Sample name: B6_P04_512_m512_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]
|
| Data processing |
First data was processed using DeSNPer, a tool developed at the Center for Genome Dynamics (Jackson Laboratory) which removes probes with single nucleotide polymorphisms within the three strains of interest to reduce hybridization bias.​ Then a custom probe annotation pipeline was used to align probe sequences with the Ensembl Release 70 Mus musculus transcriptome. Next, data was log2-transformed, then probe-level hybridization intensities were quantile normalized and median polished to generate summarized expression values. Finally, transcriptome-alignment locations from the remaining probe sequences were converted to genomic locations for gene-level annotation.
RMA log2 expression values.
See supplementary files linked to the Series record.
|
| |
|
| Submission date |
Oct 21, 2015 |
| Last update date |
Jul 01, 2016 |
| Contact name |
Carol Bult |
| E-mail(s) |
carol.bult@jax.org
|
| Phone |
207-288-6324
|
| Organization name |
The Jackson Laboratory
|
| Street address |
600 Main Street
|
| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
| |
|
| Platform ID |
GPL20894 |
| Series (1) |
| GSE74243 |
Genome wide gene expression during lung development in three inbred mouse strains |
|
